Multiple sequence alignment - TraesCS4A01G029900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G029900 chr4A 100.000 3415 0 0 1 3415 22077784 22074370 0.000000e+00 6307
1 TraesCS4A01G029900 chr4A 98.524 271 4 0 3145 3415 22061964 22061694 2.380000e-131 479
2 TraesCS4A01G029900 chr4A 98.519 270 4 0 3145 3414 355691444 355691713 8.570000e-131 477
3 TraesCS4A01G029900 chr4A 98.155 271 5 0 3145 3415 22965494 22965224 1.110000e-129 473
4 TraesCS4A01G029900 chr4A 80.061 652 90 29 3 634 22077188 22077819 6.720000e-122 448
5 TraesCS4A01G029900 chr4D 92.457 2625 146 16 1 2586 444875234 444872623 0.000000e+00 3703
6 TraesCS4A01G029900 chr4D 91.776 535 36 7 2613 3144 444872635 444872106 0.000000e+00 737
7 TraesCS4A01G029900 chr4D 80.650 646 91 22 3 634 444874644 444875269 1.430000e-128 470
8 TraesCS4A01G029900 chr4B 93.707 2018 107 9 1 2014 555219386 555221387 0.000000e+00 3005
9 TraesCS4A01G029900 chr4B 92.035 1155 66 14 2008 3143 555547331 555548478 0.000000e+00 1600
10 TraesCS4A01G029900 chr4B 92.182 857 47 8 2008 2847 555225031 555225884 0.000000e+00 1194
11 TraesCS4A01G029900 chr4B 88.449 303 28 3 2843 3144 555297507 555297803 3.240000e-95 359
12 TraesCS4A01G029900 chr3A 98.535 273 4 0 3143 3415 447724401 447724129 1.840000e-132 483
13 TraesCS4A01G029900 chr2A 98.524 271 4 0 3145 3415 163556992 163557262 2.380000e-131 479
14 TraesCS4A01G029900 chr2A 83.854 192 20 7 2920 3107 506626304 506626488 4.530000e-39 172
15 TraesCS4A01G029900 chr6A 98.519 270 4 0 3145 3414 54814548 54814817 8.570000e-131 477
16 TraesCS4A01G029900 chr6A 98.519 270 4 0 3145 3414 383861302 383861571 8.570000e-131 477
17 TraesCS4A01G029900 chr6A 98.155 271 5 0 3144 3414 54802247 54802517 1.110000e-129 473
18 TraesCS4A01G029900 chr1A 98.162 272 5 0 3144 3415 561184714 561184985 3.080000e-130 475
19 TraesCS4A01G029900 chr1A 81.043 211 25 12 2915 3121 273449889 273449690 1.640000e-33 154
20 TraesCS4A01G029900 chr2D 87.946 224 23 4 2920 3143 457852849 457852630 9.400000e-66 261
21 TraesCS4A01G029900 chr5D 84.956 226 30 2 2919 3144 362428012 362428233 3.430000e-55 226
22 TraesCS4A01G029900 chr6B 80.374 214 29 11 2917 3125 450229104 450229309 2.120000e-32 150
23 TraesCS4A01G029900 chr1B 80.383 209 30 8 2920 3125 376114420 376114620 7.640000e-32 148


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G029900 chr4A 22074370 22077784 3414 True 6307.0 6307 100.0000 1 3415 1 chr4A.!!$R2 3414
1 TraesCS4A01G029900 chr4A 22077188 22077819 631 False 448.0 448 80.0610 3 634 1 chr4A.!!$F1 631
2 TraesCS4A01G029900 chr4D 444872106 444875234 3128 True 2220.0 3703 92.1165 1 3144 2 chr4D.!!$R1 3143
3 TraesCS4A01G029900 chr4D 444874644 444875269 625 False 470.0 470 80.6500 3 634 1 chr4D.!!$F1 631
4 TraesCS4A01G029900 chr4B 555219386 555225884 6498 False 2099.5 3005 92.9445 1 2847 2 chr4B.!!$F3 2846
5 TraesCS4A01G029900 chr4B 555547331 555548478 1147 False 1600.0 1600 92.0350 2008 3143 1 chr4B.!!$F2 1135

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
579 622 0.804364 GTGGCGTTCTGATCATTGCA 59.196 50.0 0.0 0.0 0.0 4.08 F
1677 1749 0.039256 CCCGTTCCATGTTGTTGCTG 60.039 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 5746 1.005394 GAGAACTGGTCCCGCGAAA 60.005 57.895 8.23 0.0 0.00 3.46 R
3247 6988 0.031585 TGTCTTGAACCCGTCGAGTG 59.968 55.000 0.00 0.0 38.72 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 24 5.530519 TTCAGTTACGATTAGCTTTGCAG 57.469 39.130 0.00 0.00 0.00 4.41
76 78 2.087009 CGTCCGTGGCTCGTCTTTC 61.087 63.158 8.25 0.00 37.94 2.62
78 80 2.049433 CCGTGGCTCGTCTTTCGT 60.049 61.111 8.25 0.00 40.80 3.85
251 257 3.564225 GGACAAAACTCGTTGGAATCAGT 59.436 43.478 0.00 0.00 32.50 3.41
256 262 1.066858 ACTCGTTGGAATCAGTCGCAT 60.067 47.619 0.00 0.00 0.00 4.73
258 264 1.067213 TCGTTGGAATCAGTCGCATGA 60.067 47.619 0.00 0.00 0.00 3.07
370 406 3.377172 CCTCGTTCCAACAAGTTTTGTCT 59.623 43.478 0.00 0.00 44.59 3.41
403 439 3.958147 ACCTACCACTCCAAACCAAAAAG 59.042 43.478 0.00 0.00 0.00 2.27
532 575 1.675641 CGGTAGCAAAAGGCCAGCT 60.676 57.895 5.01 11.46 46.50 4.24
534 577 1.747206 CGGTAGCAAAAGGCCAGCTAT 60.747 52.381 18.11 0.94 46.50 2.97
579 622 0.804364 GTGGCGTTCTGATCATTGCA 59.196 50.000 0.00 0.00 0.00 4.08
767 835 1.007618 GATCCGCTACCCACTACGC 60.008 63.158 0.00 0.00 0.00 4.42
899 968 3.652057 ATGGTTCTACCCCTTGTGATG 57.348 47.619 0.00 0.00 37.50 3.07
900 969 2.344592 TGGTTCTACCCCTTGTGATGT 58.655 47.619 0.00 0.00 37.50 3.06
1057 1126 4.316823 TGGCCACGTCCTCCTCCT 62.317 66.667 0.00 0.00 0.00 3.69
1074 1143 3.440522 CCTCCTTTCGTCATTTCTTTCCC 59.559 47.826 0.00 0.00 0.00 3.97
1079 1148 1.066430 TCGTCATTTCTTTCCCCTCGG 60.066 52.381 0.00 0.00 0.00 4.63
1081 1150 0.695924 TCATTTCTTTCCCCTCGGCA 59.304 50.000 0.00 0.00 0.00 5.69
1122 1191 2.702302 CCTCCCCTCTACCCGTCCT 61.702 68.421 0.00 0.00 0.00 3.85
1171 1240 7.781324 ATTACCCACTTCATCAATTTCAAGT 57.219 32.000 0.00 0.00 0.00 3.16
1198 1267 1.440353 GCCGCAAACAACTACGCTG 60.440 57.895 0.00 0.00 0.00 5.18
1228 1297 2.349627 CGGAAGTTCTACGCTATCCTCG 60.350 54.545 2.25 0.00 0.00 4.63
1344 1413 3.002348 GGTTCTATGCTACCATTTGCGAC 59.998 47.826 0.00 0.00 34.48 5.19
1560 1632 3.895232 AGTGAACCAGTTAGCGATGAT 57.105 42.857 0.00 0.00 0.00 2.45
1565 1637 5.049828 TGAACCAGTTAGCGATGATATGTG 58.950 41.667 0.00 0.00 0.00 3.21
1666 1738 0.254747 CTTTATCCAGGCCCGTTCCA 59.745 55.000 0.00 0.00 0.00 3.53
1677 1749 0.039256 CCCGTTCCATGTTGTTGCTG 60.039 55.000 0.00 0.00 0.00 4.41
1698 1770 6.153170 TGCTGGAAGAAATCAATCTTAATGCA 59.847 34.615 0.00 0.00 39.70 3.96
1699 1771 7.147794 TGCTGGAAGAAATCAATCTTAATGCAT 60.148 33.333 0.00 0.00 39.70 3.96
1768 1840 2.608368 CCAACTCCACCCCCGGTA 60.608 66.667 0.00 0.00 32.11 4.02
1931 2003 3.567579 CTCAGCGGGCCCCTCAAAA 62.568 63.158 18.66 0.00 0.00 2.44
1990 2062 1.751351 CTCAGGGATACTCGTTGCTCA 59.249 52.381 0.00 0.00 0.00 4.26
2024 5746 0.753262 ATCTTTATGCCGTCGCCTCT 59.247 50.000 0.00 0.00 0.00 3.69
2025 5747 0.535335 TCTTTATGCCGTCGCCTCTT 59.465 50.000 0.00 0.00 0.00 2.85
2054 5776 1.468224 CCAGTTCTCCGTGATCGACAG 60.468 57.143 0.00 0.00 39.71 3.51
2201 5924 6.578691 GCTTGTCGTAGTTTAGTTGTTAGTG 58.421 40.000 0.00 0.00 0.00 2.74
2379 6103 9.775854 TTTGATCCATATGTTTGTTTTGTGAAT 57.224 25.926 1.24 0.00 0.00 2.57
2444 6168 9.961265 TTCGAAAGATCTATATTCGCTTTTCTA 57.039 29.630 18.82 2.42 44.04 2.10
2524 6257 0.613260 AGCTTCGTTAGTGGCCATGA 59.387 50.000 9.72 0.00 0.00 3.07
2562 6295 3.444742 CCTTCTTGTGATAAGCCAATGCA 59.555 43.478 0.00 0.00 41.13 3.96
2667 6404 7.116662 CCAAAATACATTGTGATTTGTGGACTG 59.883 37.037 19.21 8.59 31.68 3.51
2687 6424 6.599638 GGACTGTGCCAATTTATAGTTTCTCT 59.400 38.462 0.00 0.00 0.00 3.10
2692 6429 7.094377 TGTGCCAATTTATAGTTTCTCTGGTTC 60.094 37.037 0.00 0.00 0.00 3.62
2706 6443 1.831736 CTGGTTCCCAGTACTACCCTG 59.168 57.143 9.57 0.62 45.82 4.45
2806 6545 6.780706 ACGTTTTCTATAACTGACAAGTGG 57.219 37.500 0.00 0.00 36.51 4.00
2819 6558 0.112412 CAAGTGGGCCCTGGTTAGTT 59.888 55.000 25.70 8.47 0.00 2.24
2828 6567 1.353022 CCCTGGTTAGTTGGTTAGCCA 59.647 52.381 0.00 0.00 44.38 4.75
2873 6613 3.023832 GTTTAACCATCATGGGTCCCAG 58.976 50.000 17.70 8.78 43.37 4.45
2879 6620 1.561769 ATCATGGGTCCCAGCGTCAA 61.562 55.000 17.70 0.00 36.75 3.18
2918 6659 0.817654 GCTTTGATTGCCCCCACTAC 59.182 55.000 0.00 0.00 0.00 2.73
2944 6685 6.917477 CACTACAAACTTTGCTCTATTTTGCA 59.083 34.615 1.14 0.00 37.42 4.08
2973 6714 5.242434 TCACTTGTGTCATGTATAACCCAC 58.758 41.667 0.46 0.00 0.00 4.61
2991 6732 6.780457 ACCCACTTTCATCATGGAAAATAG 57.220 37.500 0.00 0.00 36.42 1.73
2994 6735 8.281531 ACCCACTTTCATCATGGAAAATAGATA 58.718 33.333 0.00 0.00 36.42 1.98
2995 6736 8.571336 CCCACTTTCATCATGGAAAATAGATAC 58.429 37.037 0.00 0.00 36.42 2.24
2996 6737 9.347240 CCACTTTCATCATGGAAAATAGATACT 57.653 33.333 0.00 0.00 36.42 2.12
3004 6745 7.594714 TCATGGAAAATAGATACTCTAGCGAC 58.405 38.462 0.00 0.00 31.67 5.19
3005 6746 6.954487 TGGAAAATAGATACTCTAGCGACA 57.046 37.500 0.00 0.00 31.67 4.35
3016 6757 3.250744 CTCTAGCGACATTTTTCGGTCA 58.749 45.455 0.00 0.00 46.33 4.02
3017 6758 2.991190 TCTAGCGACATTTTTCGGTCAC 59.009 45.455 0.00 0.00 46.33 3.67
3033 6774 2.607750 ACCGCTCCCACCATCACT 60.608 61.111 0.00 0.00 0.00 3.41
3110 6851 4.770795 AGTTGGCATATTAGGTGACAGAC 58.229 43.478 0.00 0.00 35.70 3.51
3111 6852 4.225042 AGTTGGCATATTAGGTGACAGACA 59.775 41.667 0.00 0.00 35.70 3.41
3138 6879 2.687370 TGTCACCAGTGATCATGTTCG 58.313 47.619 3.41 0.00 42.18 3.95
3144 6885 2.354103 CCAGTGATCATGTTCGGTGACT 60.354 50.000 0.00 0.00 0.00 3.41
3145 6886 2.669924 CAGTGATCATGTTCGGTGACTG 59.330 50.000 0.00 7.29 0.00 3.51
3146 6887 2.562738 AGTGATCATGTTCGGTGACTGA 59.437 45.455 0.00 0.00 0.00 3.41
3147 6888 3.196469 AGTGATCATGTTCGGTGACTGAT 59.804 43.478 0.00 0.00 0.00 2.90
3148 6889 3.308053 GTGATCATGTTCGGTGACTGATG 59.692 47.826 0.00 0.00 0.00 3.07
3149 6890 3.195396 TGATCATGTTCGGTGACTGATGA 59.805 43.478 0.00 0.00 0.00 2.92
3150 6891 3.676291 TCATGTTCGGTGACTGATGAA 57.324 42.857 0.00 0.00 0.00 2.57
3151 6892 3.588955 TCATGTTCGGTGACTGATGAAG 58.411 45.455 0.00 0.00 0.00 3.02
3152 6893 3.258123 TCATGTTCGGTGACTGATGAAGA 59.742 43.478 0.00 0.00 0.00 2.87
3153 6894 3.026630 TGTTCGGTGACTGATGAAGAC 57.973 47.619 0.00 0.00 0.00 3.01
3154 6895 2.364002 TGTTCGGTGACTGATGAAGACA 59.636 45.455 0.00 0.00 0.00 3.41
3155 6896 2.724977 TCGGTGACTGATGAAGACAC 57.275 50.000 0.00 0.00 46.75 3.67
3160 6901 3.243336 GTGACTGATGAAGACACGTACC 58.757 50.000 0.00 0.00 40.77 3.34
3161 6902 3.057456 GTGACTGATGAAGACACGTACCT 60.057 47.826 0.00 0.00 40.77 3.08
3162 6903 4.155462 GTGACTGATGAAGACACGTACCTA 59.845 45.833 0.00 0.00 40.77 3.08
3163 6904 4.395231 TGACTGATGAAGACACGTACCTAG 59.605 45.833 0.00 0.00 0.00 3.02
3164 6905 3.695060 ACTGATGAAGACACGTACCTAGG 59.305 47.826 7.41 7.41 0.00 3.02
3165 6906 3.021695 TGATGAAGACACGTACCTAGGG 58.978 50.000 14.81 0.00 0.00 3.53
3166 6907 2.592102 TGAAGACACGTACCTAGGGT 57.408 50.000 14.81 0.00 40.16 4.34
3167 6908 3.719268 TGAAGACACGTACCTAGGGTA 57.281 47.619 14.81 0.12 37.09 3.69
3168 6909 3.614092 TGAAGACACGTACCTAGGGTAG 58.386 50.000 14.81 5.91 39.02 3.18
3178 6919 1.777941 CCTAGGGTAGGGACACAGAC 58.222 60.000 0.00 0.00 42.42 3.51
3179 6920 1.688627 CCTAGGGTAGGGACACAGACC 60.689 61.905 0.00 0.00 42.42 3.85
3180 6921 1.288335 CTAGGGTAGGGACACAGACCT 59.712 57.143 0.00 0.00 40.89 3.85
3181 6922 0.252284 AGGGTAGGGACACAGACCTG 60.252 60.000 0.00 0.00 37.72 4.00
3182 6923 0.252103 GGGTAGGGACACAGACCTGA 60.252 60.000 3.76 0.00 37.72 3.86
3183 6924 1.622725 GGGTAGGGACACAGACCTGAT 60.623 57.143 3.76 0.00 37.72 2.90
3184 6925 1.757699 GGTAGGGACACAGACCTGATC 59.242 57.143 3.76 1.40 37.72 2.92
3185 6926 2.457598 GTAGGGACACAGACCTGATCA 58.542 52.381 3.76 0.00 37.72 2.92
3186 6927 2.030027 AGGGACACAGACCTGATCAA 57.970 50.000 3.76 0.00 35.30 2.57
3187 6928 2.338809 AGGGACACAGACCTGATCAAA 58.661 47.619 3.76 0.00 35.30 2.69
3188 6929 2.304180 AGGGACACAGACCTGATCAAAG 59.696 50.000 3.76 0.00 35.30 2.77
3189 6930 2.303022 GGGACACAGACCTGATCAAAGA 59.697 50.000 3.76 0.00 0.00 2.52
3190 6931 3.594134 GGACACAGACCTGATCAAAGAG 58.406 50.000 3.76 0.00 0.00 2.85
3191 6932 3.007398 GGACACAGACCTGATCAAAGAGT 59.993 47.826 3.76 0.00 0.00 3.24
3192 6933 4.241681 GACACAGACCTGATCAAAGAGTC 58.758 47.826 3.76 1.98 0.00 3.36
3193 6934 3.007398 ACACAGACCTGATCAAAGAGTCC 59.993 47.826 3.76 0.00 0.00 3.85
3194 6935 3.260380 CACAGACCTGATCAAAGAGTCCT 59.740 47.826 3.76 0.00 0.00 3.85
3195 6936 4.464244 CACAGACCTGATCAAAGAGTCCTA 59.536 45.833 3.76 0.00 0.00 2.94
3196 6937 4.464597 ACAGACCTGATCAAAGAGTCCTAC 59.535 45.833 3.76 0.00 0.00 3.18
3197 6938 4.027437 AGACCTGATCAAAGAGTCCTACC 58.973 47.826 0.00 0.00 0.00 3.18
3198 6939 3.108376 ACCTGATCAAAGAGTCCTACCC 58.892 50.000 0.00 0.00 0.00 3.69
3199 6940 3.246167 ACCTGATCAAAGAGTCCTACCCT 60.246 47.826 0.00 0.00 0.00 4.34
3200 6941 4.016479 ACCTGATCAAAGAGTCCTACCCTA 60.016 45.833 0.00 0.00 0.00 3.53
3201 6942 4.586841 CCTGATCAAAGAGTCCTACCCTAG 59.413 50.000 0.00 0.00 0.00 3.02
3219 6960 1.094269 AGGACACCCCTAGGAGAAGT 58.906 55.000 11.48 1.10 45.48 3.01
3220 6961 1.007359 AGGACACCCCTAGGAGAAGTC 59.993 57.143 11.48 10.90 45.48 3.01
3221 6962 1.273098 GGACACCCCTAGGAGAAGTCA 60.273 57.143 11.48 0.00 36.73 3.41
3222 6963 1.826096 GACACCCCTAGGAGAAGTCAC 59.174 57.143 11.48 0.00 36.73 3.67
3223 6964 1.196012 CACCCCTAGGAGAAGTCACC 58.804 60.000 11.48 0.00 36.73 4.02
3224 6965 1.094269 ACCCCTAGGAGAAGTCACCT 58.906 55.000 11.48 2.74 40.15 4.00
3225 6966 1.437547 ACCCCTAGGAGAAGTCACCTT 59.562 52.381 11.48 0.00 38.01 3.50
3226 6967 2.157989 ACCCCTAGGAGAAGTCACCTTT 60.158 50.000 11.48 0.00 38.01 3.11
3227 6968 2.502130 CCCCTAGGAGAAGTCACCTTTC 59.498 54.545 11.48 0.00 38.01 2.62
3228 6969 3.173965 CCCTAGGAGAAGTCACCTTTCA 58.826 50.000 11.48 0.00 38.01 2.69
3229 6970 3.583086 CCCTAGGAGAAGTCACCTTTCAA 59.417 47.826 11.48 0.00 38.01 2.69
3230 6971 4.226168 CCCTAGGAGAAGTCACCTTTCAAT 59.774 45.833 11.48 0.00 38.01 2.57
3231 6972 5.423886 CCTAGGAGAAGTCACCTTTCAATC 58.576 45.833 1.05 0.00 38.01 2.67
3232 6973 3.931578 AGGAGAAGTCACCTTTCAATCG 58.068 45.455 0.00 0.00 32.93 3.34
3233 6974 3.578716 AGGAGAAGTCACCTTTCAATCGA 59.421 43.478 0.00 0.00 32.93 3.59
3234 6975 3.680458 GGAGAAGTCACCTTTCAATCGAC 59.320 47.826 0.00 0.00 0.00 4.20
3235 6976 4.561105 GAGAAGTCACCTTTCAATCGACT 58.439 43.478 0.00 0.00 38.55 4.18
3236 6977 4.962155 AGAAGTCACCTTTCAATCGACTT 58.038 39.130 2.93 2.93 46.66 3.01
3237 6978 4.752101 AGAAGTCACCTTTCAATCGACTTG 59.248 41.667 7.75 0.00 44.66 3.16
3238 6979 4.336889 AGTCACCTTTCAATCGACTTGA 57.663 40.909 6.28 6.28 42.15 3.02
3247 6988 4.402056 TCAATCGACTTGAAGGTATCCC 57.598 45.455 0.00 0.00 40.92 3.85
3248 6989 3.772572 TCAATCGACTTGAAGGTATCCCA 59.227 43.478 0.00 0.00 40.92 4.37
3249 6990 3.821421 ATCGACTTGAAGGTATCCCAC 57.179 47.619 0.00 0.00 0.00 4.61
3250 6991 2.816411 TCGACTTGAAGGTATCCCACT 58.184 47.619 0.00 0.00 0.00 4.00
3251 6992 2.758979 TCGACTTGAAGGTATCCCACTC 59.241 50.000 0.00 0.00 0.00 3.51
3252 6993 2.479730 CGACTTGAAGGTATCCCACTCG 60.480 54.545 0.00 0.00 0.00 4.18
3253 6994 2.758979 GACTTGAAGGTATCCCACTCGA 59.241 50.000 0.00 0.00 0.00 4.04
3254 6995 2.496470 ACTTGAAGGTATCCCACTCGAC 59.504 50.000 0.00 0.00 0.00 4.20
3255 6996 1.100510 TGAAGGTATCCCACTCGACG 58.899 55.000 0.00 0.00 0.00 5.12
3256 6997 0.384669 GAAGGTATCCCACTCGACGG 59.615 60.000 0.00 0.00 0.00 4.79
3257 6998 1.041447 AAGGTATCCCACTCGACGGG 61.041 60.000 8.65 8.65 46.03 5.28
3258 6999 1.755783 GGTATCCCACTCGACGGGT 60.756 63.158 13.67 0.00 44.81 5.28
3259 7000 1.325476 GGTATCCCACTCGACGGGTT 61.325 60.000 13.67 8.96 44.81 4.11
3260 7001 0.101939 GTATCCCACTCGACGGGTTC 59.898 60.000 13.67 4.02 44.81 3.62
3261 7002 0.323633 TATCCCACTCGACGGGTTCA 60.324 55.000 13.67 0.00 44.81 3.18
3262 7003 1.189524 ATCCCACTCGACGGGTTCAA 61.190 55.000 13.67 0.00 44.81 2.69
3263 7004 1.374252 CCCACTCGACGGGTTCAAG 60.374 63.158 0.00 0.00 39.05 3.02
3264 7005 1.663739 CCACTCGACGGGTTCAAGA 59.336 57.895 0.00 0.00 0.00 3.02
3265 7006 0.666577 CCACTCGACGGGTTCAAGAC 60.667 60.000 0.00 0.00 0.00 3.01
3266 7007 0.031585 CACTCGACGGGTTCAAGACA 59.968 55.000 0.00 0.00 0.00 3.41
3267 7008 0.031721 ACTCGACGGGTTCAAGACAC 59.968 55.000 0.00 0.00 0.00 3.67
3268 7009 0.314302 CTCGACGGGTTCAAGACACT 59.686 55.000 0.00 0.00 0.00 3.55
3269 7010 0.313043 TCGACGGGTTCAAGACACTC 59.687 55.000 0.00 0.00 0.00 3.51
3270 7011 1.002250 CGACGGGTTCAAGACACTCG 61.002 60.000 0.00 0.00 0.00 4.18
3271 7012 0.313043 GACGGGTTCAAGACACTCGA 59.687 55.000 0.00 0.00 0.00 4.04
3272 7013 0.031721 ACGGGTTCAAGACACTCGAC 59.968 55.000 0.00 0.00 0.00 4.20
3273 7014 0.666577 CGGGTTCAAGACACTCGACC 60.667 60.000 0.00 0.00 0.00 4.79
3274 7015 0.391597 GGGTTCAAGACACTCGACCA 59.608 55.000 0.00 0.00 0.00 4.02
3275 7016 1.202604 GGGTTCAAGACACTCGACCAA 60.203 52.381 0.00 0.00 0.00 3.67
3276 7017 2.135933 GGTTCAAGACACTCGACCAAG 58.864 52.381 0.00 0.00 0.00 3.61
3277 7018 2.223971 GGTTCAAGACACTCGACCAAGA 60.224 50.000 0.00 0.00 0.00 3.02
3278 7019 3.454375 GTTCAAGACACTCGACCAAGAA 58.546 45.455 0.00 0.00 0.00 2.52
3279 7020 3.371102 TCAAGACACTCGACCAAGAAG 57.629 47.619 0.00 0.00 0.00 2.85
3280 7021 1.795286 CAAGACACTCGACCAAGAAGC 59.205 52.381 0.00 0.00 0.00 3.86
3281 7022 1.333177 AGACACTCGACCAAGAAGCT 58.667 50.000 0.00 0.00 0.00 3.74
3282 7023 2.515854 AGACACTCGACCAAGAAGCTA 58.484 47.619 0.00 0.00 0.00 3.32
3283 7024 3.093057 AGACACTCGACCAAGAAGCTAT 58.907 45.455 0.00 0.00 0.00 2.97
3284 7025 3.129638 AGACACTCGACCAAGAAGCTATC 59.870 47.826 0.00 0.00 0.00 2.08
3285 7026 2.826128 ACACTCGACCAAGAAGCTATCA 59.174 45.455 0.00 0.00 0.00 2.15
3286 7027 3.182967 CACTCGACCAAGAAGCTATCAC 58.817 50.000 0.00 0.00 0.00 3.06
3287 7028 3.093057 ACTCGACCAAGAAGCTATCACT 58.907 45.455 0.00 0.00 0.00 3.41
3288 7029 3.129638 ACTCGACCAAGAAGCTATCACTC 59.870 47.826 0.00 0.00 0.00 3.51
3289 7030 2.097629 TCGACCAAGAAGCTATCACTCG 59.902 50.000 0.00 0.00 0.00 4.18
3290 7031 2.097629 CGACCAAGAAGCTATCACTCGA 59.902 50.000 0.00 0.00 0.00 4.04
3291 7032 3.440228 GACCAAGAAGCTATCACTCGAC 58.560 50.000 0.00 0.00 0.00 4.20
3292 7033 2.166664 ACCAAGAAGCTATCACTCGACC 59.833 50.000 0.00 0.00 0.00 4.79
3293 7034 2.166459 CCAAGAAGCTATCACTCGACCA 59.834 50.000 0.00 0.00 0.00 4.02
3294 7035 3.181471 CCAAGAAGCTATCACTCGACCAT 60.181 47.826 0.00 0.00 0.00 3.55
3295 7036 3.724508 AGAAGCTATCACTCGACCATG 57.275 47.619 0.00 0.00 0.00 3.66
3296 7037 3.291584 AGAAGCTATCACTCGACCATGA 58.708 45.455 0.00 0.00 0.00 3.07
3297 7038 3.701542 AGAAGCTATCACTCGACCATGAA 59.298 43.478 0.00 0.00 0.00 2.57
3298 7039 3.724508 AGCTATCACTCGACCATGAAG 57.275 47.619 0.00 0.00 0.00 3.02
3299 7040 2.131183 GCTATCACTCGACCATGAAGC 58.869 52.381 0.00 0.00 0.00 3.86
3300 7041 2.748605 CTATCACTCGACCATGAAGCC 58.251 52.381 0.00 0.00 0.00 4.35
3301 7042 0.904649 ATCACTCGACCATGAAGCCA 59.095 50.000 0.00 0.00 0.00 4.75
3302 7043 0.684535 TCACTCGACCATGAAGCCAA 59.315 50.000 0.00 0.00 0.00 4.52
3303 7044 0.798776 CACTCGACCATGAAGCCAAC 59.201 55.000 0.00 0.00 0.00 3.77
3304 7045 0.321653 ACTCGACCATGAAGCCAACC 60.322 55.000 0.00 0.00 0.00 3.77
3305 7046 0.321564 CTCGACCATGAAGCCAACCA 60.322 55.000 0.00 0.00 0.00 3.67
3306 7047 0.605319 TCGACCATGAAGCCAACCAC 60.605 55.000 0.00 0.00 0.00 4.16
3307 7048 0.606401 CGACCATGAAGCCAACCACT 60.606 55.000 0.00 0.00 0.00 4.00
3308 7049 1.168714 GACCATGAAGCCAACCACTC 58.831 55.000 0.00 0.00 0.00 3.51
3309 7050 0.606401 ACCATGAAGCCAACCACTCG 60.606 55.000 0.00 0.00 0.00 4.18
3310 7051 0.321564 CCATGAAGCCAACCACTCGA 60.322 55.000 0.00 0.00 0.00 4.04
3311 7052 0.798776 CATGAAGCCAACCACTCGAC 59.201 55.000 0.00 0.00 0.00 4.20
3312 7053 0.687354 ATGAAGCCAACCACTCGACT 59.313 50.000 0.00 0.00 0.00 4.18
3313 7054 0.249868 TGAAGCCAACCACTCGACTG 60.250 55.000 0.00 0.00 0.00 3.51
3314 7055 0.033504 GAAGCCAACCACTCGACTGA 59.966 55.000 0.00 0.00 0.00 3.41
3315 7056 0.249911 AAGCCAACCACTCGACTGAC 60.250 55.000 0.00 0.00 0.00 3.51
3316 7057 1.069090 GCCAACCACTCGACTGACA 59.931 57.895 0.00 0.00 0.00 3.58
3317 7058 0.946221 GCCAACCACTCGACTGACAG 60.946 60.000 0.00 0.00 0.00 3.51
3318 7059 0.319900 CCAACCACTCGACTGACAGG 60.320 60.000 7.51 0.00 0.00 4.00
3319 7060 0.673985 CAACCACTCGACTGACAGGA 59.326 55.000 7.51 0.00 0.00 3.86
3320 7061 0.962489 AACCACTCGACTGACAGGAG 59.038 55.000 7.51 7.25 0.00 3.69
3321 7062 0.110678 ACCACTCGACTGACAGGAGA 59.889 55.000 13.71 8.39 0.00 3.71
3322 7063 0.523966 CCACTCGACTGACAGGAGAC 59.476 60.000 13.71 0.00 0.00 3.36
3323 7064 0.523966 CACTCGACTGACAGGAGACC 59.476 60.000 13.71 0.00 0.00 3.85
3324 7065 0.402504 ACTCGACTGACAGGAGACCT 59.597 55.000 13.71 0.00 0.00 3.85
3325 7066 1.629353 ACTCGACTGACAGGAGACCTA 59.371 52.381 13.71 0.00 29.64 3.08
3326 7067 2.040012 ACTCGACTGACAGGAGACCTAA 59.960 50.000 13.71 0.00 29.64 2.69
3327 7068 3.082548 CTCGACTGACAGGAGACCTAAA 58.917 50.000 7.51 0.00 29.64 1.85
3328 7069 3.082548 TCGACTGACAGGAGACCTAAAG 58.917 50.000 7.51 0.00 29.64 1.85
3329 7070 2.820787 CGACTGACAGGAGACCTAAAGT 59.179 50.000 7.51 0.00 29.64 2.66
3330 7071 3.119779 CGACTGACAGGAGACCTAAAGTC 60.120 52.174 7.51 12.56 46.71 3.01
3339 7080 1.997669 GACCTAAAGTCACTCCGCAG 58.002 55.000 0.00 0.00 45.55 5.18
3355 7096 4.250305 AGGCAAACGGTCGGCTGT 62.250 61.111 0.00 0.00 36.55 4.40
3356 7097 3.284449 GGCAAACGGTCGGCTGTT 61.284 61.111 8.80 8.80 45.42 3.16
3357 7098 1.962306 GGCAAACGGTCGGCTGTTA 60.962 57.895 15.82 0.00 42.91 2.41
3358 7099 1.508808 GGCAAACGGTCGGCTGTTAA 61.509 55.000 15.82 0.00 42.91 2.01
3359 7100 0.110373 GCAAACGGTCGGCTGTTAAG 60.110 55.000 15.82 11.88 42.91 1.85
3360 7101 1.223187 CAAACGGTCGGCTGTTAAGT 58.777 50.000 15.82 0.00 42.91 2.24
3361 7102 2.406130 CAAACGGTCGGCTGTTAAGTA 58.594 47.619 15.82 0.00 42.91 2.24
3362 7103 2.358939 AACGGTCGGCTGTTAAGTAG 57.641 50.000 13.66 0.00 42.00 2.57
3363 7104 1.251251 ACGGTCGGCTGTTAAGTAGT 58.749 50.000 0.00 0.00 0.00 2.73
3364 7105 1.200948 ACGGTCGGCTGTTAAGTAGTC 59.799 52.381 0.00 0.00 0.00 2.59
3365 7106 1.471684 CGGTCGGCTGTTAAGTAGTCT 59.528 52.381 0.00 0.00 0.00 3.24
3366 7107 2.094854 CGGTCGGCTGTTAAGTAGTCTT 60.095 50.000 0.00 0.00 37.65 3.01
3367 7108 3.613432 CGGTCGGCTGTTAAGTAGTCTTT 60.613 47.826 0.00 0.00 35.36 2.52
3368 7109 4.379813 CGGTCGGCTGTTAAGTAGTCTTTA 60.380 45.833 0.00 0.00 35.36 1.85
3369 7110 5.658468 GGTCGGCTGTTAAGTAGTCTTTAT 58.342 41.667 0.00 0.00 35.36 1.40
3370 7111 5.519206 GGTCGGCTGTTAAGTAGTCTTTATG 59.481 44.000 0.00 0.00 35.36 1.90
3371 7112 6.327934 GTCGGCTGTTAAGTAGTCTTTATGA 58.672 40.000 0.00 0.00 35.36 2.15
3372 7113 6.979238 GTCGGCTGTTAAGTAGTCTTTATGAT 59.021 38.462 0.00 0.00 35.36 2.45
3373 7114 7.167801 GTCGGCTGTTAAGTAGTCTTTATGATC 59.832 40.741 0.00 0.00 35.36 2.92
3374 7115 6.978659 CGGCTGTTAAGTAGTCTTTATGATCA 59.021 38.462 0.00 0.00 35.36 2.92
3375 7116 7.653713 CGGCTGTTAAGTAGTCTTTATGATCAT 59.346 37.037 13.81 13.81 35.36 2.45
3376 7117 9.331282 GGCTGTTAAGTAGTCTTTATGATCATT 57.669 33.333 14.65 0.00 35.36 2.57
3395 7136 9.944376 TGATCATTATAGCACTTTATTAGGGAC 57.056 33.333 0.00 0.00 0.00 4.46
3396 7137 9.088512 GATCATTATAGCACTTTATTAGGGACG 57.911 37.037 0.00 0.00 0.00 4.79
3397 7138 7.959175 TCATTATAGCACTTTATTAGGGACGT 58.041 34.615 0.00 0.00 0.00 4.34
3398 7139 8.426489 TCATTATAGCACTTTATTAGGGACGTT 58.574 33.333 0.00 0.00 0.00 3.99
3399 7140 9.701098 CATTATAGCACTTTATTAGGGACGTTA 57.299 33.333 0.00 0.00 0.00 3.18
3400 7141 9.702494 ATTATAGCACTTTATTAGGGACGTTAC 57.298 33.333 0.00 0.00 0.00 2.50
3401 7142 4.763073 AGCACTTTATTAGGGACGTTACC 58.237 43.478 2.26 2.26 0.00 2.85
3402 7143 4.223477 AGCACTTTATTAGGGACGTTACCA 59.777 41.667 12.07 0.00 0.00 3.25
3403 7144 4.569564 GCACTTTATTAGGGACGTTACCAG 59.430 45.833 12.07 3.09 0.00 4.00
3404 7145 5.625197 GCACTTTATTAGGGACGTTACCAGA 60.625 44.000 12.07 1.53 0.00 3.86
3405 7146 6.400568 CACTTTATTAGGGACGTTACCAGAA 58.599 40.000 12.07 6.54 0.00 3.02
3406 7147 6.875195 CACTTTATTAGGGACGTTACCAGAAA 59.125 38.462 12.07 4.64 0.00 2.52
3407 7148 6.875726 ACTTTATTAGGGACGTTACCAGAAAC 59.124 38.462 12.07 0.00 0.00 2.78
3412 7153 4.364817 CGTTACCAGAAACGCCCA 57.635 55.556 0.00 0.00 44.83 5.36
3413 7154 2.619362 CGTTACCAGAAACGCCCAA 58.381 52.632 0.00 0.00 44.83 4.12
3414 7155 0.236449 CGTTACCAGAAACGCCCAAC 59.764 55.000 0.00 0.00 44.83 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 24 1.202973 CGACGTGGCGATCTGATCAC 61.203 60.000 17.19 7.74 0.00 3.06
78 80 2.666862 CAAGGCACGCACCGGTAA 60.667 61.111 6.87 0.00 33.69 2.85
121 127 0.941542 CAAACTGTTCCGCCGAAAGA 59.058 50.000 0.00 0.00 0.00 2.52
251 257 3.261580 CCGATATTAGCCATTCATGCGA 58.738 45.455 0.00 0.00 0.00 5.10
256 262 3.495983 CCACCACCGATATTAGCCATTCA 60.496 47.826 0.00 0.00 0.00 2.57
258 264 2.224769 CCCACCACCGATATTAGCCATT 60.225 50.000 0.00 0.00 0.00 3.16
403 439 1.226018 GTGCACGCGATGGCTAAAC 60.226 57.895 15.93 4.30 36.88 2.01
487 524 1.126079 CGTGTACACTTGTGACCGAC 58.874 55.000 23.01 1.37 0.00 4.79
488 525 0.031043 CCGTGTACACTTGTGACCGA 59.969 55.000 23.01 0.00 0.00 4.69
489 526 1.554042 GCCGTGTACACTTGTGACCG 61.554 60.000 23.01 7.77 0.00 4.79
490 527 0.531090 TGCCGTGTACACTTGTGACC 60.531 55.000 23.01 4.81 0.00 4.02
579 622 6.640518 TCATCTCCAGTTACGATTAGCTTTT 58.359 36.000 0.00 0.00 0.00 2.27
899 968 3.724374 TCGCTGCCCTGTTTATATACAC 58.276 45.455 0.00 0.00 0.00 2.90
900 969 3.386726 ACTCGCTGCCCTGTTTATATACA 59.613 43.478 0.00 0.00 0.00 2.29
1057 1126 3.071479 CGAGGGGAAAGAAATGACGAAA 58.929 45.455 0.00 0.00 0.00 3.46
1074 1143 2.032528 TTCTTGGTGCTGCCGAGG 59.967 61.111 13.00 0.00 46.73 4.63
1079 1148 2.151049 CTTGGCCTTCTTGGTGCTGC 62.151 60.000 3.32 0.00 38.35 5.25
1081 1150 1.905354 GCTTGGCCTTCTTGGTGCT 60.905 57.895 3.32 0.00 38.35 4.40
1122 1191 3.094062 GCGGTGCATAGGAGGCTCA 62.094 63.158 17.69 0.00 0.00 4.26
1171 1240 1.730064 GTTGTTTGCGGCGAGATCTAA 59.270 47.619 12.98 0.00 0.00 2.10
1198 1267 0.524862 TAGAACTTCCGCGTCCACTC 59.475 55.000 4.92 0.00 0.00 3.51
1228 1297 2.403586 GGCGCAGTCGTATTTGGC 59.596 61.111 10.83 0.00 38.14 4.52
1344 1413 2.223688 CCTCACCACTTGATAGAGCTCG 60.224 54.545 8.37 0.00 32.17 5.03
1527 1596 3.158537 TTCACTTGCGTCGAGGGCA 62.159 57.895 7.31 7.13 38.93 5.36
1540 1612 3.895232 ATCATCGCTAACTGGTTCACT 57.105 42.857 0.00 0.00 0.00 3.41
1551 1623 3.996363 GCAATGTCCACATATCATCGCTA 59.004 43.478 0.00 0.00 35.10 4.26
1560 1632 4.036616 CGGATCATTTGCAATGTCCACATA 59.963 41.667 0.00 0.00 35.10 2.29
1565 1637 2.033801 CCTCGGATCATTTGCAATGTCC 59.966 50.000 0.00 4.99 0.00 4.02
1666 1738 5.534207 TTGATTTCTTCCAGCAACAACAT 57.466 34.783 0.00 0.00 0.00 2.71
1677 1749 8.192774 TCACATGCATTAAGATTGATTTCTTCC 58.807 33.333 0.00 0.00 37.20 3.46
1698 1770 1.217057 ATCCCTTGGCCCTGTCACAT 61.217 55.000 0.00 0.00 0.00 3.21
1699 1771 1.852157 ATCCCTTGGCCCTGTCACA 60.852 57.895 0.00 0.00 0.00 3.58
1768 1840 3.512724 CCTTGATTCCCATTGTTGCTTCT 59.487 43.478 0.00 0.00 0.00 2.85
1839 1911 1.586154 CCATCCAGGGTCGTTGTTGC 61.586 60.000 0.00 0.00 0.00 4.17
1990 2062 3.393426 AAAGATGGATGCCATGGAGTT 57.607 42.857 18.40 0.00 45.26 3.01
2024 5746 1.005394 GAGAACTGGTCCCGCGAAA 60.005 57.895 8.23 0.00 0.00 3.46
2025 5747 2.654877 GAGAACTGGTCCCGCGAA 59.345 61.111 8.23 0.00 0.00 4.70
2223 5946 7.743749 ACCGAGATGAGTATAACTAGTAGGAA 58.256 38.462 0.00 0.00 0.00 3.36
2379 6103 1.965414 TTCCCTTGGTGGCTAGATCA 58.035 50.000 0.00 0.00 0.00 2.92
2420 6144 9.181805 TGTAGAAAAGCGAATATAGATCTTTCG 57.818 33.333 19.16 19.16 43.72 3.46
2667 6404 6.759497 ACCAGAGAAACTATAAATTGGCAC 57.241 37.500 0.00 0.00 0.00 5.01
2692 6429 4.569719 AAAATGACAGGGTAGTACTGGG 57.430 45.455 5.39 0.00 40.23 4.45
2740 6479 8.950007 ACCAGATTTGTTTCTAAGGGAAAATA 57.050 30.769 0.00 0.00 44.34 1.40
2806 6545 1.953785 GCTAACCAACTAACCAGGGCC 60.954 57.143 0.00 0.00 0.00 5.80
2819 6558 4.947388 CCTAATTAAACAGCTGGCTAACCA 59.053 41.667 19.93 5.66 46.51 3.67
2828 6567 7.631007 ACTTAGCCTTACCTAATTAAACAGCT 58.369 34.615 0.00 0.00 0.00 4.24
2879 6620 2.594592 GCGTGGGCAGGTCAAACT 60.595 61.111 0.00 0.00 39.62 2.66
2918 6659 6.363357 GCAAAATAGAGCAAAGTTTGTAGTGG 59.637 38.462 16.70 0.29 32.89 4.00
2944 6685 2.288666 ACATGACACAAGTGAAGCGTT 58.711 42.857 7.28 0.00 0.00 4.84
2991 6732 5.041940 ACCGAAAAATGTCGCTAGAGTATC 58.958 41.667 0.00 0.00 39.74 2.24
2994 6735 3.251571 GACCGAAAAATGTCGCTAGAGT 58.748 45.455 0.00 0.00 39.74 3.24
2995 6736 3.060895 GTGACCGAAAAATGTCGCTAGAG 59.939 47.826 0.00 0.00 39.74 2.43
2996 6737 2.991190 GTGACCGAAAAATGTCGCTAGA 59.009 45.455 0.00 0.00 39.74 2.43
2997 6738 2.093783 GGTGACCGAAAAATGTCGCTAG 59.906 50.000 0.00 0.00 40.82 3.42
3016 6757 2.607750 AGTGATGGTGGGAGCGGT 60.608 61.111 0.00 0.00 0.00 5.68
3017 6758 2.124983 CAGTGATGGTGGGAGCGG 60.125 66.667 0.00 0.00 0.00 5.52
3021 6762 1.296392 CGCTTCAGTGATGGTGGGA 59.704 57.895 8.02 0.00 0.00 4.37
3033 6774 2.087501 TTTTCTATGACGGCGCTTCA 57.912 45.000 6.90 11.25 0.00 3.02
3132 6873 3.006859 TGTCTTCATCAGTCACCGAACAT 59.993 43.478 0.00 0.00 0.00 2.71
3138 6879 2.440539 ACGTGTCTTCATCAGTCACC 57.559 50.000 0.00 0.00 38.06 4.02
3144 6885 3.021695 CCCTAGGTACGTGTCTTCATCA 58.978 50.000 8.29 0.00 0.00 3.07
3145 6886 3.022406 ACCCTAGGTACGTGTCTTCATC 58.978 50.000 8.29 0.00 32.11 2.92
3146 6887 3.097342 ACCCTAGGTACGTGTCTTCAT 57.903 47.619 8.29 0.00 32.11 2.57
3147 6888 2.592102 ACCCTAGGTACGTGTCTTCA 57.408 50.000 8.29 0.00 32.11 3.02
3148 6889 2.948315 CCTACCCTAGGTACGTGTCTTC 59.052 54.545 8.29 0.00 41.18 2.87
3149 6890 2.357569 CCCTACCCTAGGTACGTGTCTT 60.358 54.545 8.29 0.00 44.73 3.01
3150 6891 1.213926 CCCTACCCTAGGTACGTGTCT 59.786 57.143 8.29 0.00 44.73 3.41
3151 6892 1.212935 TCCCTACCCTAGGTACGTGTC 59.787 57.143 8.29 0.00 44.73 3.67
3152 6893 1.064389 GTCCCTACCCTAGGTACGTGT 60.064 57.143 8.29 0.03 44.73 4.49
3153 6894 1.064463 TGTCCCTACCCTAGGTACGTG 60.064 57.143 8.29 0.00 44.73 4.49
3154 6895 1.064389 GTGTCCCTACCCTAGGTACGT 60.064 57.143 8.29 0.84 44.73 3.57
3155 6896 1.064463 TGTGTCCCTACCCTAGGTACG 60.064 57.143 8.29 0.00 44.73 3.67
3156 6897 2.243221 TCTGTGTCCCTACCCTAGGTAC 59.757 54.545 8.29 0.00 44.73 3.34
3157 6898 2.243221 GTCTGTGTCCCTACCCTAGGTA 59.757 54.545 8.29 0.00 44.73 3.08
3158 6899 1.006878 GTCTGTGTCCCTACCCTAGGT 59.993 57.143 8.29 0.00 44.73 3.08
3159 6900 1.688627 GGTCTGTGTCCCTACCCTAGG 60.689 61.905 0.06 0.06 45.81 3.02
3160 6901 1.288335 AGGTCTGTGTCCCTACCCTAG 59.712 57.143 0.00 0.00 32.10 3.02
3161 6902 1.006758 CAGGTCTGTGTCCCTACCCTA 59.993 57.143 0.00 0.00 32.10 3.53
3162 6903 0.252284 CAGGTCTGTGTCCCTACCCT 60.252 60.000 0.00 0.00 32.10 4.34
3163 6904 0.252103 TCAGGTCTGTGTCCCTACCC 60.252 60.000 0.00 0.00 32.10 3.69
3164 6905 1.757699 GATCAGGTCTGTGTCCCTACC 59.242 57.143 0.00 0.00 0.00 3.18
3165 6906 2.457598 TGATCAGGTCTGTGTCCCTAC 58.542 52.381 0.00 0.00 0.00 3.18
3166 6907 2.919772 TGATCAGGTCTGTGTCCCTA 57.080 50.000 0.00 0.00 0.00 3.53
3167 6908 2.030027 TTGATCAGGTCTGTGTCCCT 57.970 50.000 0.00 0.00 0.00 4.20
3168 6909 2.303022 TCTTTGATCAGGTCTGTGTCCC 59.697 50.000 0.00 0.00 0.00 4.46
3169 6910 3.007398 ACTCTTTGATCAGGTCTGTGTCC 59.993 47.826 0.00 0.00 0.00 4.02
3170 6911 4.241681 GACTCTTTGATCAGGTCTGTGTC 58.758 47.826 0.00 0.00 0.00 3.67
3171 6912 3.007398 GGACTCTTTGATCAGGTCTGTGT 59.993 47.826 14.88 5.57 0.00 3.72
3172 6913 3.260380 AGGACTCTTTGATCAGGTCTGTG 59.740 47.826 14.88 3.29 0.00 3.66
3173 6914 3.515562 AGGACTCTTTGATCAGGTCTGT 58.484 45.455 14.88 5.58 0.00 3.41
3174 6915 4.142049 GGTAGGACTCTTTGATCAGGTCTG 60.142 50.000 14.88 0.00 0.00 3.51
3175 6916 4.027437 GGTAGGACTCTTTGATCAGGTCT 58.973 47.826 14.88 7.86 0.00 3.85
3176 6917 3.133183 GGGTAGGACTCTTTGATCAGGTC 59.867 52.174 0.00 3.89 0.00 3.85
3177 6918 3.108376 GGGTAGGACTCTTTGATCAGGT 58.892 50.000 0.00 0.00 0.00 4.00
3178 6919 3.379452 AGGGTAGGACTCTTTGATCAGG 58.621 50.000 0.00 0.00 0.00 3.86
3179 6920 5.782893 CTAGGGTAGGACTCTTTGATCAG 57.217 47.826 0.00 0.00 27.79 2.90
3192 6933 1.238615 TAGGGGTGTCCTAGGGTAGG 58.761 60.000 9.46 0.00 45.98 3.18
3199 6940 2.244252 GACTTCTCCTAGGGGTGTCCTA 59.756 54.545 19.82 0.00 45.98 2.94
3201 6942 1.273098 TGACTTCTCCTAGGGGTGTCC 60.273 57.143 24.34 13.34 0.00 4.02
3202 6943 1.826096 GTGACTTCTCCTAGGGGTGTC 59.174 57.143 22.15 22.15 0.00 3.67
3203 6944 1.552719 GGTGACTTCTCCTAGGGGTGT 60.553 57.143 8.98 9.15 0.00 4.16
3204 6945 1.196012 GGTGACTTCTCCTAGGGGTG 58.804 60.000 8.98 5.71 0.00 4.61
3205 6946 1.094269 AGGTGACTTCTCCTAGGGGT 58.906 55.000 8.98 2.98 37.44 4.95
3213 6954 7.230711 TCAAGTCGATTGAAAGGTGACTTCTC 61.231 42.308 3.15 0.00 44.92 2.87
3214 6955 5.453339 TCAAGTCGATTGAAAGGTGACTTCT 60.453 40.000 3.15 0.00 44.92 2.85
3215 6956 4.750098 TCAAGTCGATTGAAAGGTGACTTC 59.250 41.667 3.15 0.00 44.92 3.01
3217 6958 4.336889 TCAAGTCGATTGAAAGGTGACT 57.663 40.909 7.53 0.00 45.00 3.41
3246 6987 0.666577 GTCTTGAACCCGTCGAGTGG 60.667 60.000 0.00 0.00 38.72 4.00
3247 6988 0.031585 TGTCTTGAACCCGTCGAGTG 59.968 55.000 0.00 0.00 38.72 3.51
3248 6989 0.031721 GTGTCTTGAACCCGTCGAGT 59.968 55.000 0.00 0.00 38.72 4.18
3249 6990 0.314302 AGTGTCTTGAACCCGTCGAG 59.686 55.000 0.00 0.00 38.95 4.04
3250 6991 0.313043 GAGTGTCTTGAACCCGTCGA 59.687 55.000 0.00 0.00 0.00 4.20
3251 6992 1.002250 CGAGTGTCTTGAACCCGTCG 61.002 60.000 0.00 0.00 0.00 5.12
3252 6993 0.313043 TCGAGTGTCTTGAACCCGTC 59.687 55.000 0.00 0.00 0.00 4.79
3253 6994 0.031721 GTCGAGTGTCTTGAACCCGT 59.968 55.000 0.00 0.00 0.00 5.28
3254 6995 0.666577 GGTCGAGTGTCTTGAACCCG 60.667 60.000 0.00 0.00 0.00 5.28
3255 6996 0.391597 TGGTCGAGTGTCTTGAACCC 59.608 55.000 0.00 0.00 30.88 4.11
3256 6997 2.135933 CTTGGTCGAGTGTCTTGAACC 58.864 52.381 0.00 0.00 30.88 3.62
3257 6998 3.093717 TCTTGGTCGAGTGTCTTGAAC 57.906 47.619 0.00 0.00 32.49 3.18
3258 6999 3.717707 CTTCTTGGTCGAGTGTCTTGAA 58.282 45.455 0.00 0.00 0.00 2.69
3259 7000 2.545952 GCTTCTTGGTCGAGTGTCTTGA 60.546 50.000 0.00 0.00 0.00 3.02
3260 7001 1.795286 GCTTCTTGGTCGAGTGTCTTG 59.205 52.381 0.00 0.00 0.00 3.02
3261 7002 1.689273 AGCTTCTTGGTCGAGTGTCTT 59.311 47.619 0.00 0.00 0.00 3.01
3262 7003 1.333177 AGCTTCTTGGTCGAGTGTCT 58.667 50.000 0.00 0.00 0.00 3.41
3263 7004 3.119459 TGATAGCTTCTTGGTCGAGTGTC 60.119 47.826 0.00 0.00 0.00 3.67
3264 7005 2.826128 TGATAGCTTCTTGGTCGAGTGT 59.174 45.455 0.00 0.00 0.00 3.55
3265 7006 3.119316 AGTGATAGCTTCTTGGTCGAGTG 60.119 47.826 0.00 0.00 0.00 3.51
3266 7007 3.093057 AGTGATAGCTTCTTGGTCGAGT 58.907 45.455 0.00 0.00 0.00 4.18
3267 7008 3.701241 GAGTGATAGCTTCTTGGTCGAG 58.299 50.000 0.00 0.00 0.00 4.04
3268 7009 2.097629 CGAGTGATAGCTTCTTGGTCGA 59.902 50.000 0.00 0.00 0.00 4.20
3269 7010 2.097629 TCGAGTGATAGCTTCTTGGTCG 59.902 50.000 0.00 0.00 0.00 4.79
3270 7011 3.440228 GTCGAGTGATAGCTTCTTGGTC 58.560 50.000 0.00 0.00 0.00 4.02
3271 7012 2.166664 GGTCGAGTGATAGCTTCTTGGT 59.833 50.000 0.00 0.00 0.00 3.67
3272 7013 2.166459 TGGTCGAGTGATAGCTTCTTGG 59.834 50.000 0.00 0.00 0.00 3.61
3273 7014 3.510388 TGGTCGAGTGATAGCTTCTTG 57.490 47.619 0.00 0.00 0.00 3.02
3274 7015 3.701542 TCATGGTCGAGTGATAGCTTCTT 59.298 43.478 0.00 0.00 0.00 2.52
3275 7016 3.291584 TCATGGTCGAGTGATAGCTTCT 58.708 45.455 0.00 0.00 0.00 2.85
3276 7017 3.717400 TCATGGTCGAGTGATAGCTTC 57.283 47.619 0.00 0.00 0.00 3.86
3277 7018 3.739519 GCTTCATGGTCGAGTGATAGCTT 60.740 47.826 0.00 0.00 31.68 3.74
3278 7019 2.223923 GCTTCATGGTCGAGTGATAGCT 60.224 50.000 14.77 0.00 31.68 3.32
3279 7020 2.131183 GCTTCATGGTCGAGTGATAGC 58.869 52.381 0.00 0.35 0.00 2.97
3280 7021 2.101415 TGGCTTCATGGTCGAGTGATAG 59.899 50.000 0.00 0.00 0.00 2.08
3281 7022 2.107366 TGGCTTCATGGTCGAGTGATA 58.893 47.619 0.00 0.00 0.00 2.15
3282 7023 0.904649 TGGCTTCATGGTCGAGTGAT 59.095 50.000 0.00 0.00 0.00 3.06
3283 7024 0.684535 TTGGCTTCATGGTCGAGTGA 59.315 50.000 0.00 0.00 0.00 3.41
3284 7025 0.798776 GTTGGCTTCATGGTCGAGTG 59.201 55.000 0.00 0.00 0.00 3.51
3285 7026 0.321653 GGTTGGCTTCATGGTCGAGT 60.322 55.000 0.00 0.00 0.00 4.18
3286 7027 0.321564 TGGTTGGCTTCATGGTCGAG 60.322 55.000 0.00 0.00 0.00 4.04
3287 7028 0.605319 GTGGTTGGCTTCATGGTCGA 60.605 55.000 0.00 0.00 0.00 4.20
3288 7029 0.606401 AGTGGTTGGCTTCATGGTCG 60.606 55.000 0.00 0.00 0.00 4.79
3289 7030 1.168714 GAGTGGTTGGCTTCATGGTC 58.831 55.000 0.00 0.00 0.00 4.02
3290 7031 0.606401 CGAGTGGTTGGCTTCATGGT 60.606 55.000 0.00 0.00 0.00 3.55
3291 7032 0.321564 TCGAGTGGTTGGCTTCATGG 60.322 55.000 0.00 0.00 0.00 3.66
3292 7033 0.798776 GTCGAGTGGTTGGCTTCATG 59.201 55.000 0.00 0.00 0.00 3.07
3293 7034 0.687354 AGTCGAGTGGTTGGCTTCAT 59.313 50.000 0.00 0.00 0.00 2.57
3294 7035 0.249868 CAGTCGAGTGGTTGGCTTCA 60.250 55.000 12.66 0.00 0.00 3.02
3295 7036 0.033504 TCAGTCGAGTGGTTGGCTTC 59.966 55.000 19.86 0.00 0.00 3.86
3296 7037 0.249911 GTCAGTCGAGTGGTTGGCTT 60.250 55.000 19.86 0.00 0.00 4.35
3297 7038 1.367840 GTCAGTCGAGTGGTTGGCT 59.632 57.895 19.86 0.00 0.00 4.75
3298 7039 0.946221 CTGTCAGTCGAGTGGTTGGC 60.946 60.000 19.86 6.58 0.00 4.52
3299 7040 0.319900 CCTGTCAGTCGAGTGGTTGG 60.320 60.000 19.86 14.34 0.00 3.77
3300 7041 0.673985 TCCTGTCAGTCGAGTGGTTG 59.326 55.000 19.86 9.73 0.00 3.77
3301 7042 0.962489 CTCCTGTCAGTCGAGTGGTT 59.038 55.000 19.86 0.00 0.00 3.67
3302 7043 0.110678 TCTCCTGTCAGTCGAGTGGT 59.889 55.000 19.86 0.00 0.00 4.16
3303 7044 0.523966 GTCTCCTGTCAGTCGAGTGG 59.476 60.000 19.86 4.21 0.00 4.00
3304 7045 0.523966 GGTCTCCTGTCAGTCGAGTG 59.476 60.000 14.33 14.33 0.00 3.51
3305 7046 0.402504 AGGTCTCCTGTCAGTCGAGT 59.597 55.000 0.00 0.00 29.57 4.18
3306 7047 2.404923 TAGGTCTCCTGTCAGTCGAG 57.595 55.000 0.00 0.00 34.61 4.04
3307 7048 2.873094 TTAGGTCTCCTGTCAGTCGA 57.127 50.000 0.00 0.00 34.61 4.20
3308 7049 2.820787 ACTTTAGGTCTCCTGTCAGTCG 59.179 50.000 0.00 0.00 34.61 4.18
3309 7050 3.827302 TGACTTTAGGTCTCCTGTCAGTC 59.173 47.826 0.00 12.70 44.74 3.51
3310 7051 3.574826 GTGACTTTAGGTCTCCTGTCAGT 59.425 47.826 7.41 3.09 44.74 3.41
3311 7052 3.829601 AGTGACTTTAGGTCTCCTGTCAG 59.170 47.826 7.41 0.00 44.74 3.51
3312 7053 3.827302 GAGTGACTTTAGGTCTCCTGTCA 59.173 47.826 0.00 1.60 44.74 3.58
3313 7054 3.193903 GGAGTGACTTTAGGTCTCCTGTC 59.806 52.174 0.00 0.00 44.74 3.51
3314 7055 3.166679 GGAGTGACTTTAGGTCTCCTGT 58.833 50.000 0.00 0.00 44.74 4.00
3315 7056 2.164624 CGGAGTGACTTTAGGTCTCCTG 59.835 54.545 0.00 0.00 44.74 3.86
3316 7057 2.448453 CGGAGTGACTTTAGGTCTCCT 58.552 52.381 0.00 0.00 44.74 3.69
3317 7058 1.135053 GCGGAGTGACTTTAGGTCTCC 60.135 57.143 0.00 0.00 44.74 3.71
3318 7059 1.544691 TGCGGAGTGACTTTAGGTCTC 59.455 52.381 0.00 0.00 44.74 3.36
3319 7060 1.546476 CTGCGGAGTGACTTTAGGTCT 59.454 52.381 0.00 0.00 44.74 3.85
3320 7061 1.404315 CCTGCGGAGTGACTTTAGGTC 60.404 57.143 2.36 0.00 44.70 3.85
3321 7062 0.608640 CCTGCGGAGTGACTTTAGGT 59.391 55.000 2.36 0.00 0.00 3.08
3322 7063 0.741221 GCCTGCGGAGTGACTTTAGG 60.741 60.000 2.36 0.00 0.00 2.69
3323 7064 0.037326 TGCCTGCGGAGTGACTTTAG 60.037 55.000 2.36 0.00 0.00 1.85
3324 7065 0.394938 TTGCCTGCGGAGTGACTTTA 59.605 50.000 2.36 0.00 0.00 1.85
3325 7066 0.465460 TTTGCCTGCGGAGTGACTTT 60.465 50.000 2.36 0.00 0.00 2.66
3326 7067 1.148273 TTTGCCTGCGGAGTGACTT 59.852 52.632 2.36 0.00 0.00 3.01
3327 7068 1.598130 GTTTGCCTGCGGAGTGACT 60.598 57.895 2.36 0.00 0.00 3.41
3328 7069 2.946762 GTTTGCCTGCGGAGTGAC 59.053 61.111 2.36 0.00 0.00 3.67
3329 7070 2.664851 CGTTTGCCTGCGGAGTGA 60.665 61.111 2.36 0.00 0.00 3.41
3337 7078 3.726517 CAGCCGACCGTTTGCCTG 61.727 66.667 0.00 0.00 0.00 4.85
3338 7079 2.386064 TAACAGCCGACCGTTTGCCT 62.386 55.000 0.00 0.00 0.00 4.75
3339 7080 1.508808 TTAACAGCCGACCGTTTGCC 61.509 55.000 0.00 0.00 0.00 4.52
3340 7081 0.110373 CTTAACAGCCGACCGTTTGC 60.110 55.000 0.00 0.00 0.00 3.68
3341 7082 1.223187 ACTTAACAGCCGACCGTTTG 58.777 50.000 0.00 0.00 0.00 2.93
3342 7083 2.036346 ACTACTTAACAGCCGACCGTTT 59.964 45.455 0.00 0.00 0.00 3.60
3343 7084 1.615392 ACTACTTAACAGCCGACCGTT 59.385 47.619 0.00 0.00 0.00 4.44
3344 7085 1.200948 GACTACTTAACAGCCGACCGT 59.799 52.381 0.00 0.00 0.00 4.83
3345 7086 1.471684 AGACTACTTAACAGCCGACCG 59.528 52.381 0.00 0.00 0.00 4.79
3346 7087 3.589495 AAGACTACTTAACAGCCGACC 57.411 47.619 0.00 0.00 34.28 4.79
3347 7088 6.327934 TCATAAAGACTACTTAACAGCCGAC 58.672 40.000 0.00 0.00 35.05 4.79
3348 7089 6.519679 TCATAAAGACTACTTAACAGCCGA 57.480 37.500 0.00 0.00 35.05 5.54
3349 7090 6.978659 TGATCATAAAGACTACTTAACAGCCG 59.021 38.462 0.00 0.00 35.05 5.52
3350 7091 8.894768 ATGATCATAAAGACTACTTAACAGCC 57.105 34.615 6.36 0.00 35.05 4.85
3369 7110 9.944376 GTCCCTAATAAAGTGCTATAATGATCA 57.056 33.333 0.00 0.00 0.00 2.92
3370 7111 9.088512 CGTCCCTAATAAAGTGCTATAATGATC 57.911 37.037 0.00 0.00 0.00 2.92
3371 7112 8.594550 ACGTCCCTAATAAAGTGCTATAATGAT 58.405 33.333 0.00 0.00 0.00 2.45
3372 7113 7.959175 ACGTCCCTAATAAAGTGCTATAATGA 58.041 34.615 0.00 0.00 0.00 2.57
3373 7114 8.603242 AACGTCCCTAATAAAGTGCTATAATG 57.397 34.615 0.00 0.00 0.00 1.90
3374 7115 9.702494 GTAACGTCCCTAATAAAGTGCTATAAT 57.298 33.333 0.00 0.00 0.00 1.28
3375 7116 8.143835 GGTAACGTCCCTAATAAAGTGCTATAA 58.856 37.037 0.00 0.00 0.00 0.98
3376 7117 7.287466 TGGTAACGTCCCTAATAAAGTGCTATA 59.713 37.037 5.88 0.00 42.51 1.31
3377 7118 6.098695 TGGTAACGTCCCTAATAAAGTGCTAT 59.901 38.462 5.88 0.00 42.51 2.97
3378 7119 5.421693 TGGTAACGTCCCTAATAAAGTGCTA 59.578 40.000 5.88 0.00 42.51 3.49
3379 7120 4.223477 TGGTAACGTCCCTAATAAAGTGCT 59.777 41.667 5.88 0.00 42.51 4.40
3380 7121 4.506758 TGGTAACGTCCCTAATAAAGTGC 58.493 43.478 5.88 0.00 42.51 4.40
3381 7122 5.969423 TCTGGTAACGTCCCTAATAAAGTG 58.031 41.667 5.88 0.00 42.51 3.16
3382 7123 6.610075 TTCTGGTAACGTCCCTAATAAAGT 57.390 37.500 5.88 0.00 42.51 2.66
3383 7124 6.035327 CGTTTCTGGTAACGTCCCTAATAAAG 59.965 42.308 5.88 0.00 44.28 1.85
3384 7125 5.868801 CGTTTCTGGTAACGTCCCTAATAAA 59.131 40.000 5.88 0.04 44.28 1.40
3385 7126 5.410067 CGTTTCTGGTAACGTCCCTAATAA 58.590 41.667 5.88 0.00 44.28 1.40
3386 7127 4.997565 CGTTTCTGGTAACGTCCCTAATA 58.002 43.478 5.88 0.00 44.28 0.98
3387 7128 3.853475 CGTTTCTGGTAACGTCCCTAAT 58.147 45.455 5.88 0.00 44.28 1.73
3388 7129 3.302365 CGTTTCTGGTAACGTCCCTAA 57.698 47.619 5.88 0.00 44.28 2.69
3390 7131 3.900446 CGTTTCTGGTAACGTCCCT 57.100 52.632 5.88 0.00 44.28 4.20


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.