Answer: It sounds as if you are doing everything right with your tomatoes. Yellow leaves can be caused by many things including lack of nitrogen, insufficient light, water-logged soil (plant roots need oxygen to thrive), dry soil, or iron deficiency. If the older bottom leaves are yellow, but new growth is green, it's usually a lack of nitrogen. If new leaves are yellow, with green veins, it's usually a lack of iron. Lack of nitrogen is a more common problem than lack of iron and that sounds like it could be a possibility in your case. However, the lack of sunlight could be a factor, as tomatoes need full sun to thrive. And, if the soil is overly wet from rain, roots could be suffering as they also need oxygen to live. Soil should be kept moderately moist (but not wet) while plants establish. Finally, transplant shock can contribute to yellowing. Since you did fertilize, and new growth shows up as green, that might be the problem. One more thing: are the roots packed within the newspaper pot? Or did you cut the bottom off so they could grow outward? Sometimes it takes longer than expected for newspaper and peat pots to disintegrate and the roots become rootbound. I hope this info helps.
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