Multiple sequence alignment - TraesCS6A01G163600

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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 TraesCS6A01G163600 chr6A 100.000 4674 0 0 1 4674 158944175 158939502 0.000000e+00 8632.0
1 TraesCS6A01G163600 chr6B 91.040 1875 113 32 768 2613 212417858 212419706 0.000000e+00 2481.0
2 TraesCS6A01G163600 chr6B 96.073 1146 39 4 2647 3789 212419704 212420846 0.000000e+00 1862.0
3 TraesCS6A01G163600 chr6B 88.499 713 36 22 1 677 212417042 212417744 0.000000e+00 821.0
4 TraesCS6A01G163600 chr6B 100.000 38 0 0 714 751 212417820 212417857 2.330000e-08 71.3
5 TraesCS6A01G163600 chr6D 89.065 1829 136 36 801 2611 120670548 120668766 0.000000e+00 2211.0
6 TraesCS6A01G163600 chr6D 95.771 1135 42 4 2671 3803 120668740 120667610 0.000000e+00 1825.0
7 TraesCS6A01G163600 chr6D 88.283 734 39 21 106 804 120671298 120670577 0.000000e+00 835.0
8 TraesCS6A01G163600 chr6D 98.361 61 1 0 1 61 120671368 120671308 1.780000e-19 108.0
9 TraesCS6A01G163600 chr2B 91.100 809 70 2 3861 4667 385529460 385530268 0.000000e+00 1094.0
10 TraesCS6A01G163600 chr2B 91.032 814 68 5 3864 4674 733143343 733142532 0.000000e+00 1094.0
11 TraesCS6A01G163600 chr1D 91.089 808 70 2 3869 4674 38370020 38370827 0.000000e+00 1092.0
12 TraesCS6A01G163600 chr1D 90.786 814 73 2 3863 4674 14476647 14475834 0.000000e+00 1086.0
13 TraesCS6A01G163600 chr1A 90.418 814 73 5 3858 4668 241958858 241959669 0.000000e+00 1066.0
14 TraesCS6A01G163600 chr3D 90.406 813 73 5 3864 4674 113467977 113467168 0.000000e+00 1064.0
15 TraesCS6A01G163600 chr3D 90.000 820 79 3 3858 4674 541407533 541406714 0.000000e+00 1057.0
16 TraesCS6A01G163600 chr3D 90.074 816 78 3 3861 4674 547517301 547516487 0.000000e+00 1055.0
17 TraesCS6A01G163600 chr7B 90.172 814 77 3 3863 4674 362546481 362545669 0.000000e+00 1057.0


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 TraesCS6A01G163600 chr6A 158939502 158944175 4673 True 8632.000 8632 100.000 1 4674 1 chr6A.!!$R1 4673
1 TraesCS6A01G163600 chr6B 212417042 212420846 3804 False 1308.825 2481 93.903 1 3789 4 chr6B.!!$F1 3788
2 TraesCS6A01G163600 chr6D 120667610 120671368 3758 True 1244.750 2211 92.870 1 3803 4 chr6D.!!$R1 3802
3 TraesCS6A01G163600 chr2B 385529460 385530268 808 False 1094.000 1094 91.100 3861 4667 1 chr2B.!!$F1 806
4 TraesCS6A01G163600 chr2B 733142532 733143343 811 True 1094.000 1094 91.032 3864 4674 1 chr2B.!!$R1 810
5 TraesCS6A01G163600 chr1D 38370020 38370827 807 False 1092.000 1092 91.089 3869 4674 1 chr1D.!!$F1 805
6 TraesCS6A01G163600 chr1D 14475834 14476647 813 True 1086.000 1086 90.786 3863 4674 1 chr1D.!!$R1 811
7 TraesCS6A01G163600 chr1A 241958858 241959669 811 False 1066.000 1066 90.418 3858 4668 1 chr1A.!!$F1 810
8 TraesCS6A01G163600 chr3D 113467168 113467977 809 True 1064.000 1064 90.406 3864 4674 1 chr3D.!!$R1 810
9 TraesCS6A01G163600 chr3D 541406714 541407533 819 True 1057.000 1057 90.000 3858 4674 1 chr3D.!!$R2 816
10 TraesCS6A01G163600 chr3D 547516487 547517301 814 True 1055.000 1055 90.074 3861 4674 1 chr3D.!!$R3 813
11 TraesCS6A01G163600 chr7B 362545669 362546481 812 True 1057.000 1057 90.172 3863 4674 1 chr7B.!!$R1 811

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
695 733 0.109458 ACACATGAGCTGCAAATGCG 60.109 50.0 12.70 7.5 45.83 4.73 F
1079 1211 0.110486 GTCCCTTGGGAGAACTGCAA 59.890 55.0 8.93 0.0 0.00 4.08 F
1693 1829 0.324091 AAAGGAGGGGCATCTGCTTG 60.324 55.0 12.81 0.0 43.11 4.01 F
2374 2527 0.325933 TCAGGTCAGGACAATGCAGG 59.674 55.0 1.41 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1768 0.106419 AACCAAGCAAAACGAGGGGA 60.106 50.000 0.00 0.0 0.00 4.81 R
3067 3228 0.108233 CCATCAAAAACCCCATGGCG 60.108 55.000 6.09 0.0 33.59 5.69 R
3075 3236 1.200020 CCTCTGCGTCCATCAAAAACC 59.800 52.381 0.00 0.0 0.00 3.27 R
4125 4292 0.106268 TTGGTGTGCCAGGTGTGATT 60.106 50.000 0.00 0.0 46.91 2.57 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
97 98 8.474025 TGTGTTGTTTCTTGGAGAAATTGTATT 58.526 29.630 6.42 0.00 44.94 1.89
192 195 7.700022 AGAAGAAAGGAATTGATTTCTCCAG 57.300 36.000 12.55 0.00 43.25 3.86
199 202 4.158579 GGAATTGATTTCTCCAGGTGGTTC 59.841 45.833 0.00 0.00 34.56 3.62
275 303 0.390340 TCTCTGTCAAGCGACCATGC 60.390 55.000 0.00 0.00 41.85 4.06
349 377 4.937201 AAAGCCAAACTTTACTGAAGGG 57.063 40.909 0.00 0.00 46.95 3.95
388 416 3.157087 TCCTCACTGGATTCCTTTTTGC 58.843 45.455 3.95 0.00 40.56 3.68
391 419 4.039609 CCTCACTGGATTCCTTTTTGCTTT 59.960 41.667 3.95 0.00 38.35 3.51
392 420 4.947645 TCACTGGATTCCTTTTTGCTTTG 58.052 39.130 3.95 0.00 0.00 2.77
393 421 4.648762 TCACTGGATTCCTTTTTGCTTTGA 59.351 37.500 3.95 0.00 0.00 2.69
441 478 4.119862 AGTGTTGTATCGTATGCATGGTC 58.880 43.478 10.16 0.00 0.00 4.02
448 485 1.217585 CGTATGCATGGTCTCTGCCG 61.218 60.000 10.16 0.00 38.89 5.69
464 501 0.879090 GCCGGTTGTACTTGGGAAAG 59.121 55.000 1.90 0.00 0.00 2.62
473 510 7.551617 CGGTTGTACTTGGGAAAGATATAACTT 59.448 37.037 0.00 0.00 0.00 2.66
526 563 4.380867 GGCTTCCAACAAGACATACAATGG 60.381 45.833 0.00 0.00 33.60 3.16
568 605 4.475944 CTTTTGCCGTTTCTCCATGTAAG 58.524 43.478 0.00 0.00 0.00 2.34
570 607 0.733150 GCCGTTTCTCCATGTAAGCC 59.267 55.000 0.00 0.00 0.00 4.35
606 644 5.248640 AGAAATGTGATGTCATCGTCCTTT 58.751 37.500 8.29 8.85 0.00 3.11
608 646 3.961480 TGTGATGTCATCGTCCTTTCT 57.039 42.857 8.29 0.00 0.00 2.52
643 681 2.561419 CACGACTGGTTTCTTCCTCCTA 59.439 50.000 0.00 0.00 0.00 2.94
645 683 3.447944 ACGACTGGTTTCTTCCTCCTATC 59.552 47.826 0.00 0.00 0.00 2.08
646 684 3.181474 CGACTGGTTTCTTCCTCCTATCC 60.181 52.174 0.00 0.00 0.00 2.59
679 717 2.853235 AACTAAGCTGGTGGGTACAC 57.147 50.000 0.00 0.00 46.97 2.90
695 733 0.109458 ACACATGAGCTGCAAATGCG 60.109 50.000 12.70 7.50 45.83 4.73
789 866 2.288666 TCAGAAACGCAGCAGAAAAGT 58.711 42.857 0.00 0.00 0.00 2.66
794 871 4.844267 GAAACGCAGCAGAAAAGTTTCTA 58.156 39.130 5.99 0.00 45.23 2.10
815 924 3.555966 ACAGATATTTGGTTAGCCCAGC 58.444 45.455 0.00 0.00 46.31 4.85
830 939 2.667536 AGCAACAGAGCACTGCCG 60.668 61.111 11.37 3.64 46.95 5.69
887 996 7.630242 TTTATTTGCCTTCTGGATAAGACAG 57.370 36.000 0.00 0.00 33.46 3.51
921 1031 6.183810 TGATAGATCATGTGAGGCTCAAAT 57.816 37.500 20.62 17.43 0.00 2.32
973 1088 6.350445 CCAAAGGGAAATATCTTGTGTTCCAG 60.350 42.308 3.87 0.00 41.17 3.86
974 1089 4.273318 AGGGAAATATCTTGTGTTCCAGC 58.727 43.478 3.87 0.00 41.17 4.85
975 1090 4.016444 GGGAAATATCTTGTGTTCCAGCA 58.984 43.478 3.87 0.00 41.17 4.41
976 1091 4.646492 GGGAAATATCTTGTGTTCCAGCAT 59.354 41.667 3.87 0.00 41.17 3.79
977 1092 5.127682 GGGAAATATCTTGTGTTCCAGCATT 59.872 40.000 3.87 0.00 41.17 3.56
978 1093 6.351286 GGGAAATATCTTGTGTTCCAGCATTT 60.351 38.462 3.87 0.00 41.17 2.32
981 1096 8.538409 AAATATCTTGTGTTCCAGCATTTTTC 57.462 30.769 0.00 0.00 0.00 2.29
982 1097 4.320608 TCTTGTGTTCCAGCATTTTTCC 57.679 40.909 0.00 0.00 0.00 3.13
984 1099 4.037923 TCTTGTGTTCCAGCATTTTTCCTC 59.962 41.667 0.00 0.00 0.00 3.71
985 1100 3.565307 TGTGTTCCAGCATTTTTCCTCT 58.435 40.909 0.00 0.00 0.00 3.69
986 1101 3.960102 TGTGTTCCAGCATTTTTCCTCTT 59.040 39.130 0.00 0.00 0.00 2.85
987 1102 4.202141 TGTGTTCCAGCATTTTTCCTCTTG 60.202 41.667 0.00 0.00 0.00 3.02
988 1103 3.243839 TGTTCCAGCATTTTTCCTCTTGC 60.244 43.478 0.00 0.00 35.34 4.01
989 1104 1.541147 TCCAGCATTTTTCCTCTTGCG 59.459 47.619 0.00 0.00 40.00 4.85
990 1105 1.541147 CCAGCATTTTTCCTCTTGCGA 59.459 47.619 0.00 0.00 40.00 5.10
991 1106 2.415090 CCAGCATTTTTCCTCTTGCGAG 60.415 50.000 0.00 0.00 40.00 5.03
992 1107 2.227388 CAGCATTTTTCCTCTTGCGAGT 59.773 45.455 0.00 0.00 40.00 4.18
993 1108 2.227388 AGCATTTTTCCTCTTGCGAGTG 59.773 45.455 0.00 0.00 40.00 3.51
994 1109 2.589014 CATTTTTCCTCTTGCGAGTGC 58.411 47.619 0.00 0.00 43.20 4.40
1013 1145 2.514824 GCCCATGCTCCTCGTTCC 60.515 66.667 0.00 0.00 33.53 3.62
1028 1160 3.427573 TCGTTCCTCCACAACTATCAGA 58.572 45.455 0.00 0.00 0.00 3.27
1030 1162 4.282449 TCGTTCCTCCACAACTATCAGAAA 59.718 41.667 0.00 0.00 0.00 2.52
1074 1206 3.243907 CGATATCTGTCCCTTGGGAGAAC 60.244 52.174 8.93 0.00 0.00 3.01
1079 1211 0.110486 GTCCCTTGGGAGAACTGCAA 59.890 55.000 8.93 0.00 0.00 4.08
1106 1238 1.974236 CTCTGAAGACCTTCACCCTGT 59.026 52.381 8.27 0.00 43.90 4.00
1112 1244 0.326264 GACCTTCACCCTGTGCTCAT 59.674 55.000 0.00 0.00 32.98 2.90
1122 1254 3.201290 CCCTGTGCTCATCATGTAAGTC 58.799 50.000 0.00 0.00 0.00 3.01
1138 1270 5.850614 TGTAAGTCACACTTTCTACCTTCC 58.149 41.667 0.00 0.00 39.51 3.46
1140 1272 6.779049 TGTAAGTCACACTTTCTACCTTCCTA 59.221 38.462 0.00 0.00 39.51 2.94
1149 1281 8.661345 ACACTTTCTACCTTCCTAAATTCTTCT 58.339 33.333 0.00 0.00 0.00 2.85
1150 1282 8.940952 CACTTTCTACCTTCCTAAATTCTTCTG 58.059 37.037 0.00 0.00 0.00 3.02
1152 1284 9.157104 CTTTCTACCTTCCTAAATTCTTCTGAC 57.843 37.037 0.00 0.00 0.00 3.51
1153 1285 7.184067 TCTACCTTCCTAAATTCTTCTGACC 57.816 40.000 0.00 0.00 0.00 4.02
1168 1300 5.418840 TCTTCTGACCTTTTTATTCCCATGC 59.581 40.000 0.00 0.00 0.00 4.06
1173 1305 3.769300 ACCTTTTTATTCCCATGCTCACC 59.231 43.478 0.00 0.00 0.00 4.02
1302 1437 7.305474 CAAAACTTCTCAAACAACACACTAGT 58.695 34.615 0.00 0.00 0.00 2.57
1305 1440 6.170506 ACTTCTCAAACAACACACTAGTTCA 58.829 36.000 0.00 0.00 0.00 3.18
1314 1449 4.408182 ACACACTAGTTCACTCTGCTTT 57.592 40.909 0.00 0.00 0.00 3.51
1317 1452 4.051922 ACACTAGTTCACTCTGCTTTTCG 58.948 43.478 0.00 0.00 0.00 3.46
1341 1476 2.094286 TGTGAACTTGGTTTGCAGTTGG 60.094 45.455 0.00 0.00 33.22 3.77
1342 1477 2.165437 GTGAACTTGGTTTGCAGTTGGA 59.835 45.455 0.00 0.00 33.22 3.53
1357 1492 4.278975 AGTTGGAACTGACATCTCTTCC 57.721 45.455 0.00 0.00 37.98 3.46
1358 1493 3.008485 AGTTGGAACTGACATCTCTTCCC 59.992 47.826 0.00 0.00 37.98 3.97
1359 1494 2.907892 TGGAACTGACATCTCTTCCCT 58.092 47.619 0.00 0.00 32.56 4.20
1385 1520 5.423704 TCCACCGTATGAATTTCAGGTTA 57.576 39.130 5.21 0.00 0.00 2.85
1523 1658 3.304794 CCTCTAGATACGGCGAAAGGAAG 60.305 52.174 16.62 3.66 0.00 3.46
1524 1659 2.621998 TCTAGATACGGCGAAAGGAAGG 59.378 50.000 16.62 0.00 0.00 3.46
1525 1660 0.464452 AGATACGGCGAAAGGAAGGG 59.536 55.000 16.62 0.00 0.00 3.95
1632 1768 3.801307 AAAATCCTACCTTCACCGGTT 57.199 42.857 2.97 0.00 38.49 4.44
1658 1794 3.018149 TCGTTTTGCTTGGTTTACACCT 58.982 40.909 0.00 0.00 44.61 4.00
1664 1800 2.158740 TGCTTGGTTTACACCTGCACTA 60.159 45.455 12.85 0.00 43.48 2.74
1668 1804 4.159244 TGGTTTACACCTGCACTAAAGT 57.841 40.909 0.00 0.00 44.61 2.66
1676 1812 3.066621 CACCTGCACTAAAGTTCAGCAAA 59.933 43.478 4.47 0.00 37.85 3.68
1683 1819 2.001076 AAAGTTCAGCAAAGGAGGGG 57.999 50.000 0.00 0.00 0.00 4.79
1685 1821 1.228552 GTTCAGCAAAGGAGGGGCA 60.229 57.895 0.00 0.00 0.00 5.36
1693 1829 0.324091 AAAGGAGGGGCATCTGCTTG 60.324 55.000 12.81 0.00 43.11 4.01
1701 1837 2.789917 CATCTGCTTGGCGAGTGC 59.210 61.111 3.19 0.00 41.71 4.40
1714 1855 1.796796 GAGTGCCATCGTTTCCTGC 59.203 57.895 0.00 0.00 0.00 4.85
1759 1900 3.224324 CTCATGCATGCAGGGGGC 61.224 66.667 30.00 0.00 45.13 5.80
1855 1996 1.142748 GGACATCCTGGAGCTCGTG 59.857 63.158 7.83 2.49 0.00 4.35
1864 2005 2.659610 GAGCTCGTGCAGAAGGGT 59.340 61.111 12.58 0.00 42.74 4.34
1867 2008 1.185618 AGCTCGTGCAGAAGGGTACA 61.186 55.000 12.58 0.00 42.74 2.90
1899 2040 4.463879 CTGGGAGGCGCTGGACAG 62.464 72.222 7.64 7.83 0.00 3.51
2374 2527 0.325933 TCAGGTCAGGACAATGCAGG 59.674 55.000 1.41 0.00 0.00 4.85
2391 2544 1.664965 GGCACTCACACCGACAGAC 60.665 63.158 0.00 0.00 0.00 3.51
2397 2550 2.029828 ACTCACACCGACAGACAGATTC 60.030 50.000 0.00 0.00 0.00 2.52
2418 2571 1.003233 GGTGGTGTTCTCTCCAGGC 60.003 63.158 0.00 0.00 37.81 4.85
2445 2598 3.611433 GTACAACGCGTACCTCGAT 57.389 52.632 14.46 0.00 44.11 3.59
2467 2620 3.602513 CTGCTCAAGGCGAGGTGCT 62.603 63.158 0.00 0.00 45.43 4.40
2491 2644 2.830704 GAAGGCGGTGGAGGTGTACG 62.831 65.000 0.00 0.00 0.00 3.67
2550 2703 3.706594 AGACGTACACCCTCATGATCAAT 59.293 43.478 0.00 0.00 0.00 2.57
2559 2712 3.555795 CCCTCATGATCAATGTCTACGGG 60.556 52.174 0.00 0.00 37.56 5.28
2564 2717 2.158957 TGATCAATGTCTACGGGAAGGC 60.159 50.000 0.00 0.00 0.00 4.35
2591 2745 3.569250 GGCAACTTTTTCGCTATGGAA 57.431 42.857 0.00 0.00 0.00 3.53
2593 2747 4.494484 GGCAACTTTTTCGCTATGGAAAT 58.506 39.130 0.00 0.00 35.95 2.17
2596 2750 5.060940 GCAACTTTTTCGCTATGGAAATGTC 59.939 40.000 0.00 0.00 35.95 3.06
2637 2798 7.449934 AAAAAGTGTGTTGTTTTCGATGATC 57.550 32.000 0.00 0.00 0.00 2.92
2638 2799 5.749596 AAGTGTGTTGTTTTCGATGATCA 57.250 34.783 0.00 0.00 0.00 2.92
2639 2800 5.095691 AGTGTGTTGTTTTCGATGATCAC 57.904 39.130 0.00 0.00 0.00 3.06
2640 2801 4.024048 AGTGTGTTGTTTTCGATGATCACC 60.024 41.667 0.00 0.00 0.00 4.02
2641 2802 3.879892 TGTGTTGTTTTCGATGATCACCA 59.120 39.130 0.00 0.00 0.00 4.17
2642 2803 4.518590 TGTGTTGTTTTCGATGATCACCAT 59.481 37.500 0.00 0.00 38.43 3.55
2643 2804 5.009510 TGTGTTGTTTTCGATGATCACCATT 59.990 36.000 0.00 0.00 35.17 3.16
2644 2805 5.569059 GTGTTGTTTTCGATGATCACCATTC 59.431 40.000 0.00 0.00 35.17 2.67
2645 2806 5.473162 TGTTGTTTTCGATGATCACCATTCT 59.527 36.000 0.00 0.00 35.17 2.40
2646 2807 6.016360 TGTTGTTTTCGATGATCACCATTCTT 60.016 34.615 0.00 0.00 35.17 2.52
2647 2808 5.941733 TGTTTTCGATGATCACCATTCTTG 58.058 37.500 0.00 0.00 35.17 3.02
2648 2809 5.704978 TGTTTTCGATGATCACCATTCTTGA 59.295 36.000 0.00 0.00 35.17 3.02
2649 2810 6.128200 TGTTTTCGATGATCACCATTCTTGAG 60.128 38.462 0.00 0.00 35.17 3.02
2650 2811 5.343307 TTCGATGATCACCATTCTTGAGA 57.657 39.130 0.00 0.00 35.17 3.27
2651 2812 5.343307 TCGATGATCACCATTCTTGAGAA 57.657 39.130 0.00 0.00 35.17 2.87
2652 2813 5.111989 TCGATGATCACCATTCTTGAGAAC 58.888 41.667 0.00 0.00 36.80 3.01
2653 2814 5.105187 TCGATGATCACCATTCTTGAGAACT 60.105 40.000 0.00 0.00 36.80 3.01
3022 3183 3.286576 CGAGGTACGTACGTCAATCATC 58.713 50.000 34.60 18.00 40.15 2.92
3023 3184 3.242511 CGAGGTACGTACGTCAATCATCA 60.243 47.826 34.60 0.85 40.15 3.07
3067 3228 4.459089 GAGGTGCCGAGCCTGACC 62.459 72.222 0.00 0.00 36.29 4.02
3075 3236 4.864334 GAGCCTGACCGCCATGGG 62.864 72.222 15.13 3.37 44.64 4.00
3235 3399 3.052082 CAGCTGCACAAGTCGGGG 61.052 66.667 0.00 0.00 0.00 5.73
3679 3843 5.385198 ACCTTGTTCACCATATGACAAAGT 58.615 37.500 3.65 4.07 36.92 2.66
3680 3844 5.241506 ACCTTGTTCACCATATGACAAAGTG 59.758 40.000 3.65 3.52 36.92 3.16
3690 3855 7.920151 CACCATATGACAAAGTGTGAAGAAAAA 59.080 33.333 3.65 0.00 0.00 1.94
3826 3991 7.621832 TTTACAAGTTTGATTCAGCAAATCG 57.378 32.000 0.00 0.00 45.78 3.34
3827 3992 5.186996 ACAAGTTTGATTCAGCAAATCGT 57.813 34.783 0.00 0.00 45.78 3.73
3828 3993 5.215160 ACAAGTTTGATTCAGCAAATCGTC 58.785 37.500 0.00 1.99 45.78 4.20
3829 3994 5.009010 ACAAGTTTGATTCAGCAAATCGTCT 59.991 36.000 0.00 3.71 45.78 4.18
3830 3995 5.039480 AGTTTGATTCAGCAAATCGTCTG 57.961 39.130 7.18 0.00 45.78 3.51
3831 3996 4.516698 AGTTTGATTCAGCAAATCGTCTGT 59.483 37.500 7.18 0.00 45.78 3.41
3832 3997 5.700832 AGTTTGATTCAGCAAATCGTCTGTA 59.299 36.000 7.18 0.00 45.78 2.74
3833 3998 5.530519 TTGATTCAGCAAATCGTCTGTAC 57.469 39.130 7.18 0.00 45.78 2.90
3834 3999 4.565022 TGATTCAGCAAATCGTCTGTACA 58.435 39.130 0.00 0.00 45.78 2.90
3835 4000 4.994217 TGATTCAGCAAATCGTCTGTACAA 59.006 37.500 0.00 0.00 45.78 2.41
3836 4001 4.725556 TTCAGCAAATCGTCTGTACAAC 57.274 40.909 0.00 0.00 0.00 3.32
3837 4002 3.723260 TCAGCAAATCGTCTGTACAACA 58.277 40.909 0.00 0.00 0.00 3.33
3838 4003 4.123506 TCAGCAAATCGTCTGTACAACAA 58.876 39.130 0.00 0.00 0.00 2.83
3839 4004 4.572795 TCAGCAAATCGTCTGTACAACAAA 59.427 37.500 0.00 0.00 0.00 2.83
3840 4005 5.238432 TCAGCAAATCGTCTGTACAACAAAT 59.762 36.000 0.00 0.00 0.00 2.32
3841 4006 5.340403 CAGCAAATCGTCTGTACAACAAATG 59.660 40.000 0.00 0.00 0.00 2.32
3842 4007 5.008613 AGCAAATCGTCTGTACAACAAATGT 59.991 36.000 0.00 0.00 46.36 2.71
3843 4008 5.115472 GCAAATCGTCTGTACAACAAATGTG 59.885 40.000 0.00 2.76 43.77 3.21
3844 4009 3.870723 TCGTCTGTACAACAAATGTGC 57.129 42.857 0.00 0.00 43.77 4.57
3845 4010 3.462982 TCGTCTGTACAACAAATGTGCT 58.537 40.909 0.00 0.00 44.16 4.40
3846 4011 3.247411 TCGTCTGTACAACAAATGTGCTG 59.753 43.478 0.00 0.00 44.16 4.41
3847 4012 3.247411 CGTCTGTACAACAAATGTGCTGA 59.753 43.478 0.00 3.02 45.49 4.26
3849 4014 5.611796 TCTGTACAACAAATGTGCTGATC 57.388 39.130 0.00 0.00 43.83 2.92
3850 4015 4.455533 TCTGTACAACAAATGTGCTGATCC 59.544 41.667 0.00 0.00 43.83 3.36
3851 4016 3.505680 TGTACAACAAATGTGCTGATCCC 59.494 43.478 0.00 0.00 44.16 3.85
3852 4017 2.880443 ACAACAAATGTGCTGATCCCT 58.120 42.857 0.00 0.00 41.93 4.20
3853 4018 2.559668 ACAACAAATGTGCTGATCCCTG 59.440 45.455 0.00 0.00 41.93 4.45
3854 4019 2.559668 CAACAAATGTGCTGATCCCTGT 59.440 45.455 0.00 0.00 0.00 4.00
3855 4020 2.165167 ACAAATGTGCTGATCCCTGTG 58.835 47.619 0.00 0.00 0.00 3.66
3856 4021 2.224843 ACAAATGTGCTGATCCCTGTGA 60.225 45.455 0.00 0.00 0.00 3.58
3857 4022 2.414994 AATGTGCTGATCCCTGTGAG 57.585 50.000 0.00 0.00 0.00 3.51
3858 4023 1.576577 ATGTGCTGATCCCTGTGAGA 58.423 50.000 0.00 0.00 0.00 3.27
3859 4024 1.576577 TGTGCTGATCCCTGTGAGAT 58.423 50.000 0.00 0.00 0.00 2.75
3872 4037 0.521735 GTGAGATTTGGGGCGTGTTC 59.478 55.000 0.00 0.00 0.00 3.18
3922 4087 6.599356 TTGCATACACTTCTCAACCTAGTA 57.401 37.500 0.00 0.00 0.00 1.82
3941 4106 8.107095 ACCTAGTATGGTTGAGCAAAAATAAGA 58.893 33.333 0.00 0.00 36.89 2.10
4027 4192 3.324993 CAAGTGCACTTTGTTTGGTTGT 58.675 40.909 29.23 0.88 33.11 3.32
4031 4196 2.560542 TGCACTTTGTTTGGTTGTCTGT 59.439 40.909 0.00 0.00 0.00 3.41
4044 4209 0.403655 TGTCTGTATTGGCCCAAGCA 59.596 50.000 1.16 2.82 42.56 3.91
4045 4210 1.202989 TGTCTGTATTGGCCCAAGCAA 60.203 47.619 1.16 0.00 42.56 3.91
4065 4230 5.042593 GCAACACATGAACAAGATGTTTGA 58.957 37.500 0.00 0.00 41.28 2.69
4066 4231 5.519566 GCAACACATGAACAAGATGTTTGAA 59.480 36.000 0.00 0.00 41.28 2.69
4086 4251 3.646650 GCATACGGCGTACTTGGTA 57.353 52.632 23.50 0.00 0.00 3.25
4093 4259 1.202325 CGGCGTACTTGGTATGCTACA 60.202 52.381 17.60 0.00 46.54 2.74
4100 4266 6.202188 GCGTACTTGGTATGCTACATTGTATT 59.798 38.462 12.81 0.00 44.68 1.89
4108 4274 8.700973 TGGTATGCTACATTGTATTCTAGTTGA 58.299 33.333 0.00 0.00 0.00 3.18
4125 4292 5.435686 AGTTGATGAGCTTACCCACAATA 57.564 39.130 0.00 0.00 0.00 1.90
4135 4302 4.096382 GCTTACCCACAATAATCACACCTG 59.904 45.833 0.00 0.00 0.00 4.00
4158 4325 1.377987 ACCAACGCCACAACACAGT 60.378 52.632 0.00 0.00 0.00 3.55
4163 4330 1.961793 ACGCCACAACACAGTAATGT 58.038 45.000 0.00 0.00 0.00 2.71
4213 4380 0.538057 TCAGCTTCAGCCCAAACTGG 60.538 55.000 0.00 0.00 43.38 4.00
4244 4411 2.664402 AGCACCTTCCACTTTGACAT 57.336 45.000 0.00 0.00 0.00 3.06
4252 4419 4.392940 CTTCCACTTTGACATCTCCAACT 58.607 43.478 0.00 0.00 0.00 3.16
4255 4422 5.935945 TCCACTTTGACATCTCCAACTTTA 58.064 37.500 0.00 0.00 0.00 1.85
4358 4526 5.105187 CCTCTATGGCTGCTGTTGCTATATA 60.105 44.000 0.00 0.00 40.48 0.86
4488 4657 2.029649 AGCAAATCAATGGAGCACACAC 60.030 45.455 0.00 0.00 0.00 3.82
4526 4695 2.859538 CACACAAACAACAATGGAGCAC 59.140 45.455 0.00 0.00 0.00 4.40
4565 4734 4.628766 GCATGCATGATCATACGACATAGT 59.371 41.667 30.64 0.00 0.00 2.12
4644 4813 0.981183 TCCTACCACCGCAAGTTCAT 59.019 50.000 0.00 0.00 0.00 2.57
4668 4837 2.364324 TCATCGTGAGGGGTTAGTATGC 59.636 50.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 117 7.408756 TCCAAAAGCTGCAATTGAGTAATAT 57.591 32.000 10.34 0.00 0.00 1.28
192 195 1.620822 ATTGTCAGGCTTGAACCACC 58.379 50.000 0.00 0.00 34.49 4.61
199 202 3.941483 CAGTAGGGTAATTGTCAGGCTTG 59.059 47.826 0.00 0.00 0.00 4.01
275 303 8.017373 CCTTGAAATGTATTGTCAGTGTAAGTG 58.983 37.037 0.00 0.00 39.10 3.16
349 377 3.153919 AGGATCTCATTCGAGCTCTACC 58.846 50.000 12.85 0.00 39.30 3.18
386 414 9.617523 TTTCTGATACATTCTATCATCAAAGCA 57.382 29.630 0.00 0.00 33.93 3.91
417 445 4.141937 ACCATGCATACGATACAACACTCT 60.142 41.667 0.00 0.00 0.00 3.24
419 447 4.119862 GACCATGCATACGATACAACACT 58.880 43.478 0.00 0.00 0.00 3.55
441 478 0.673644 CCCAAGTACAACCGGCAGAG 60.674 60.000 0.00 0.00 0.00 3.35
448 485 8.803397 AAGTTATATCTTTCCCAAGTACAACC 57.197 34.615 0.00 0.00 0.00 3.77
504 541 4.218417 ACCATTGTATGTCTTGTTGGAAGC 59.782 41.667 0.00 0.00 0.00 3.86
526 563 0.655733 CACCAAGTTCCACGACACAC 59.344 55.000 0.00 0.00 0.00 3.82
531 568 1.403679 CAAAAGCACCAAGTTCCACGA 59.596 47.619 0.00 0.00 0.00 4.35
570 607 1.288932 ACATTTCTCCCCCAGGATTGG 59.711 52.381 0.00 0.00 42.93 3.16
643 681 9.988815 CAGCTTAGTTTCATACAACTATAGGAT 57.011 33.333 4.43 0.00 38.71 3.24
645 683 8.204836 ACCAGCTTAGTTTCATACAACTATAGG 58.795 37.037 4.43 0.00 38.71 2.57
646 684 9.035607 CACCAGCTTAGTTTCATACAACTATAG 57.964 37.037 0.00 0.00 38.71 1.31
679 717 2.221552 CGCGCATTTGCAGCTCATG 61.222 57.895 8.75 0.00 42.21 3.07
686 724 0.376852 GGTTATCTCGCGCATTTGCA 59.623 50.000 8.75 0.00 42.21 4.08
695 733 2.798847 GGTAAATCCACGGTTATCTCGC 59.201 50.000 0.00 0.00 35.97 5.03
757 834 5.530519 TGCGTTTCTGAATTCTGATACAC 57.469 39.130 24.68 19.20 0.00 2.90
810 919 2.623915 GCAGTGCTCTGTTGCTGGG 61.624 63.158 16.59 0.00 43.05 4.45
815 924 2.667536 AGCGGCAGTGCTCTGTTG 60.668 61.111 16.11 10.52 42.95 3.33
887 996 3.599730 TGATCTATCATCCATCCGTGC 57.400 47.619 0.00 0.00 0.00 5.34
921 1031 5.949952 TGTTCTATCTAGTTCTAGTGTGCCA 59.050 40.000 6.73 0.00 0.00 4.92
966 1081 3.243839 GCAAGAGGAAAAATGCTGGAACA 60.244 43.478 0.00 0.00 35.93 3.18
967 1082 3.320626 GCAAGAGGAAAAATGCTGGAAC 58.679 45.455 0.00 0.00 35.93 3.62
968 1083 2.030007 CGCAAGAGGAAAAATGCTGGAA 60.030 45.455 0.00 0.00 43.02 3.53
969 1084 1.541147 CGCAAGAGGAAAAATGCTGGA 59.459 47.619 0.00 0.00 43.02 3.86
970 1085 1.541147 TCGCAAGAGGAAAAATGCTGG 59.459 47.619 0.00 0.00 45.01 4.85
996 1111 2.514824 GGAACGAGGAGCATGGGC 60.515 66.667 0.00 0.00 41.61 5.36
1000 1132 0.904865 TGTGGAGGAACGAGGAGCAT 60.905 55.000 0.00 0.00 0.00 3.79
1004 1136 2.297698 TAGTTGTGGAGGAACGAGGA 57.702 50.000 0.00 0.00 0.00 3.71
1013 1145 5.121454 GCTTCTGTTTCTGATAGTTGTGGAG 59.879 44.000 0.00 0.00 0.00 3.86
1028 1160 0.663153 GCTTGTGGTCGCTTCTGTTT 59.337 50.000 0.00 0.00 0.00 2.83
1030 1162 0.601311 GAGCTTGTGGTCGCTTCTGT 60.601 55.000 0.00 0.00 36.45 3.41
1079 1211 2.439507 TGAAGGTCTTCAGAGGCAAACT 59.560 45.455 9.13 0.00 43.90 2.66
1106 1238 4.541973 AGTGTGACTTACATGATGAGCA 57.458 40.909 0.00 0.00 42.24 4.26
1112 1244 6.665992 AGGTAGAAAGTGTGACTTACATGA 57.334 37.500 0.00 0.00 42.24 3.07
1122 1254 8.622948 AAGAATTTAGGAAGGTAGAAAGTGTG 57.377 34.615 0.00 0.00 0.00 3.82
1140 1272 8.491045 TGGGAATAAAAAGGTCAGAAGAATTT 57.509 30.769 0.00 0.00 0.00 1.82
1149 1281 4.462483 GTGAGCATGGGAATAAAAAGGTCA 59.538 41.667 0.00 0.00 0.00 4.02
1150 1282 4.142160 GGTGAGCATGGGAATAAAAAGGTC 60.142 45.833 0.00 0.00 0.00 3.85
1152 1284 3.132824 GGGTGAGCATGGGAATAAAAAGG 59.867 47.826 0.00 0.00 0.00 3.11
1153 1285 3.768757 TGGGTGAGCATGGGAATAAAAAG 59.231 43.478 0.00 0.00 0.00 2.27
1161 1293 0.482446 AAAACTGGGTGAGCATGGGA 59.518 50.000 0.00 0.00 0.00 4.37
1168 1300 0.609131 ATCGGGCAAAACTGGGTGAG 60.609 55.000 0.00 0.00 0.00 3.51
1173 1305 0.527565 CCTGAATCGGGCAAAACTGG 59.472 55.000 0.00 0.00 0.00 4.00
1314 1449 2.797792 GCAAACCAAGTTCACATGCGAA 60.798 45.455 0.00 0.00 0.00 4.70
1317 1452 2.129607 CTGCAAACCAAGTTCACATGC 58.870 47.619 0.00 0.00 0.00 4.06
1320 1455 2.094286 CCAACTGCAAACCAAGTTCACA 60.094 45.455 0.00 0.00 0.00 3.58
1341 1476 3.517500 AGGAAGGGAAGAGATGTCAGTTC 59.482 47.826 0.00 0.00 0.00 3.01
1342 1477 3.517500 GAGGAAGGGAAGAGATGTCAGTT 59.482 47.826 0.00 0.00 0.00 3.16
1354 1489 1.200519 CATACGGTGGAGGAAGGGAA 58.799 55.000 0.00 0.00 0.00 3.97
1355 1490 0.337082 TCATACGGTGGAGGAAGGGA 59.663 55.000 0.00 0.00 0.00 4.20
1356 1491 1.200519 TTCATACGGTGGAGGAAGGG 58.799 55.000 0.00 0.00 0.00 3.95
1357 1492 3.560636 AATTCATACGGTGGAGGAAGG 57.439 47.619 0.00 0.00 0.00 3.46
1358 1493 4.513442 TGAAATTCATACGGTGGAGGAAG 58.487 43.478 0.00 0.00 0.00 3.46
1359 1494 4.513442 CTGAAATTCATACGGTGGAGGAA 58.487 43.478 0.00 0.00 0.00 3.36
1385 1520 0.107654 GCAACGGAGCCTGTATCCTT 60.108 55.000 0.00 0.00 34.45 3.36
1523 1658 2.282674 GGGTGTTTCCGGTTCCCC 60.283 66.667 0.00 1.21 37.00 4.81
1524 1659 2.670592 CGGGTGTTTCCGGTTCCC 60.671 66.667 0.00 6.72 45.78 3.97
1632 1768 0.106419 AACCAAGCAAAACGAGGGGA 60.106 50.000 0.00 0.00 0.00 4.81
1658 1794 3.550820 TCCTTTGCTGAACTTTAGTGCA 58.449 40.909 0.00 0.00 31.56 4.57
1664 1800 2.001076 CCCCTCCTTTGCTGAACTTT 57.999 50.000 0.00 0.00 0.00 2.66
1668 1804 0.323725 GATGCCCCTCCTTTGCTGAA 60.324 55.000 0.00 0.00 0.00 3.02
1676 1812 2.687610 CCAAGCAGATGCCCCTCCT 61.688 63.158 0.14 0.00 43.38 3.69
1683 1819 2.789917 CACTCGCCAAGCAGATGC 59.210 61.111 0.00 0.00 42.49 3.91
1701 1837 0.953471 TCAACGGCAGGAAACGATGG 60.953 55.000 0.00 0.00 34.29 3.51
1704 1840 1.265635 CATTTCAACGGCAGGAAACGA 59.734 47.619 0.00 0.00 35.99 3.85
1705 1841 1.665735 CCATTTCAACGGCAGGAAACG 60.666 52.381 0.00 0.00 35.99 3.60
1706 1842 1.339929 ACCATTTCAACGGCAGGAAAC 59.660 47.619 0.00 0.00 35.99 2.78
1714 1855 4.237349 AGCTGTAAAACCATTTCAACGG 57.763 40.909 0.00 0.00 0.00 4.44
1810 1951 4.785453 GGGCTGAGCACCGGGAAG 62.785 72.222 6.82 0.00 0.00 3.46
1855 1996 1.448013 GGCGTCTGTACCCTTCTGC 60.448 63.158 0.00 0.00 0.00 4.26
1864 2005 3.291101 GACCTTGGCGGCGTCTGTA 62.291 63.158 14.51 0.00 35.61 2.74
1867 2008 4.379243 CAGACCTTGGCGGCGTCT 62.379 66.667 14.51 11.36 37.34 4.18
2027 2170 3.668447 GTCCATCAGAGCTTCAACTGAA 58.332 45.455 6.91 0.00 44.47 3.02
2134 2277 0.321671 TGAGCAGGTTGTAGCAGACC 59.678 55.000 0.00 0.00 36.15 3.85
2329 2472 3.702045 AGACTTTCTTACTCGGAGGGATG 59.298 47.826 10.23 0.00 0.00 3.51
2374 2527 0.941463 CTGTCTGTCGGTGTGAGTGC 60.941 60.000 0.00 0.00 0.00 4.40
2391 2544 3.937706 GAGAGAACACCACCATGAATCTG 59.062 47.826 0.00 0.00 0.00 2.90
2397 2550 1.339438 CCTGGAGAGAACACCACCATG 60.339 57.143 0.00 0.00 33.52 3.66
2445 2598 4.399395 CTCGCCTTGAGCAGCCCA 62.399 66.667 0.00 0.00 44.04 5.36
2491 2644 1.068921 GCTCCCGCTTCATCCTCTC 59.931 63.158 0.00 0.00 0.00 3.20
2550 2703 1.870055 GACGTGCCTTCCCGTAGACA 61.870 60.000 0.00 0.00 37.44 3.41
2559 2712 1.166531 AAGTTGCCTGACGTGCCTTC 61.167 55.000 0.00 0.00 0.00 3.46
2564 2717 1.741993 CGAAAAAGTTGCCTGACGTG 58.258 50.000 0.00 0.00 0.00 4.49
2570 2723 2.790433 TCCATAGCGAAAAAGTTGCCT 58.210 42.857 0.00 0.00 0.00 4.75
2591 2745 4.897509 TCAGTCAGGTGATGAAGACATT 57.102 40.909 0.00 0.00 40.43 2.71
2593 2747 4.687901 TTTCAGTCAGGTGATGAAGACA 57.312 40.909 0.00 0.00 40.43 3.41
2619 2780 3.879892 TGGTGATCATCGAAAACAACACA 59.120 39.130 0.00 0.00 0.00 3.72
2620 2781 4.481930 TGGTGATCATCGAAAACAACAC 57.518 40.909 0.00 0.00 0.00 3.32
2621 2782 5.473162 AGAATGGTGATCATCGAAAACAACA 59.527 36.000 0.00 2.42 34.44 3.33
2622 2783 5.942872 AGAATGGTGATCATCGAAAACAAC 58.057 37.500 0.00 0.00 34.44 3.32
2623 2784 6.206438 TCAAGAATGGTGATCATCGAAAACAA 59.794 34.615 0.00 0.00 34.44 2.83
2626 2787 6.172630 TCTCAAGAATGGTGATCATCGAAAA 58.827 36.000 0.00 0.00 34.44 2.29
2627 2788 5.733676 TCTCAAGAATGGTGATCATCGAAA 58.266 37.500 0.00 0.00 34.44 3.46
2629 2790 5.105187 AGTTCTCAAGAATGGTGATCATCGA 60.105 40.000 0.00 0.00 36.33 3.59
2630 2791 5.114780 AGTTCTCAAGAATGGTGATCATCG 58.885 41.667 0.00 0.00 36.33 3.84
2631 2792 6.373774 ACAAGTTCTCAAGAATGGTGATCATC 59.626 38.462 0.00 0.00 36.33 2.92
2632 2793 6.243900 ACAAGTTCTCAAGAATGGTGATCAT 58.756 36.000 0.00 0.00 36.33 2.45
2633 2794 5.624159 ACAAGTTCTCAAGAATGGTGATCA 58.376 37.500 0.00 0.00 36.33 2.92
2634 2795 6.429385 AGAACAAGTTCTCAAGAATGGTGATC 59.571 38.462 9.56 0.00 46.13 2.92
2635 2796 6.302269 AGAACAAGTTCTCAAGAATGGTGAT 58.698 36.000 9.56 0.00 46.13 3.06
2636 2797 5.684704 AGAACAAGTTCTCAAGAATGGTGA 58.315 37.500 9.56 0.00 46.13 4.02
2649 2810 5.101628 TGCAATTGACACAAGAACAAGTTC 58.898 37.500 10.34 4.82 39.78 3.01
2650 2811 5.070770 TGCAATTGACACAAGAACAAGTT 57.929 34.783 10.34 0.00 0.00 2.66
2651 2812 4.158394 ACTGCAATTGACACAAGAACAAGT 59.842 37.500 10.34 0.00 0.00 3.16
2652 2813 4.675510 ACTGCAATTGACACAAGAACAAG 58.324 39.130 10.34 0.00 0.00 3.16
2653 2814 4.671377 GACTGCAATTGACACAAGAACAA 58.329 39.130 10.34 0.00 0.00 2.83
3022 3183 2.809601 CCGGCGTTCGAGGAGTTG 60.810 66.667 6.01 0.00 42.43 3.16
3023 3184 4.736896 GCCGGCGTTCGAGGAGTT 62.737 66.667 12.58 0.00 42.43 3.01
3067 3228 0.108233 CCATCAAAAACCCCATGGCG 60.108 55.000 6.09 0.00 33.59 5.69
3075 3236 1.200020 CCTCTGCGTCCATCAAAAACC 59.800 52.381 0.00 0.00 0.00 3.27
3103 3267 1.618640 GCTTCAGCGACTCGAACACC 61.619 60.000 1.63 0.00 0.00 4.16
3801 3966 7.867403 ACGATTTGCTGAATCAAACTTGTAAAT 59.133 29.630 11.96 0.00 43.59 1.40
3802 3967 7.199766 ACGATTTGCTGAATCAAACTTGTAAA 58.800 30.769 11.96 0.00 43.59 2.01
3804 3969 6.204688 AGACGATTTGCTGAATCAAACTTGTA 59.795 34.615 11.96 0.00 43.59 2.41
3805 3970 5.009010 AGACGATTTGCTGAATCAAACTTGT 59.991 36.000 11.96 3.11 43.59 3.16
3806 3971 5.341462 CAGACGATTTGCTGAATCAAACTTG 59.659 40.000 11.96 0.00 43.59 3.16
3807 3972 5.009010 ACAGACGATTTGCTGAATCAAACTT 59.991 36.000 11.96 0.00 43.59 2.66
3808 3973 4.516698 ACAGACGATTTGCTGAATCAAACT 59.483 37.500 11.96 6.33 43.59 2.66
3809 3974 4.787598 ACAGACGATTTGCTGAATCAAAC 58.212 39.130 11.96 4.74 43.59 2.93
3810 3975 5.468409 TGTACAGACGATTTGCTGAATCAAA 59.532 36.000 11.96 0.00 43.59 2.69
3811 3976 4.994217 TGTACAGACGATTTGCTGAATCAA 59.006 37.500 11.96 0.00 43.59 2.57
3812 3977 4.565022 TGTACAGACGATTTGCTGAATCA 58.435 39.130 11.96 0.00 43.59 2.57
3813 3978 5.107104 TGTTGTACAGACGATTTGCTGAATC 60.107 40.000 0.00 4.03 40.65 2.52
3814 3979 4.754618 TGTTGTACAGACGATTTGCTGAAT 59.245 37.500 0.00 0.00 36.07 2.57
3815 3980 4.123506 TGTTGTACAGACGATTTGCTGAA 58.876 39.130 0.00 0.00 36.07 3.02
3816 3981 3.723260 TGTTGTACAGACGATTTGCTGA 58.277 40.909 0.00 0.00 36.07 4.26
3817 3982 4.466567 TTGTTGTACAGACGATTTGCTG 57.533 40.909 0.00 0.00 38.10 4.41
3818 3983 5.008613 ACATTTGTTGTACAGACGATTTGCT 59.991 36.000 0.00 0.00 36.57 3.91
3819 3984 5.115472 CACATTTGTTGTACAGACGATTTGC 59.885 40.000 0.00 0.00 36.57 3.68
3820 3985 5.115472 GCACATTTGTTGTACAGACGATTTG 59.885 40.000 0.00 2.66 36.57 2.32
3821 3986 5.008613 AGCACATTTGTTGTACAGACGATTT 59.991 36.000 0.00 0.00 36.57 2.17
3822 3987 4.515191 AGCACATTTGTTGTACAGACGATT 59.485 37.500 0.00 0.00 36.57 3.34
3823 3988 4.065088 AGCACATTTGTTGTACAGACGAT 58.935 39.130 0.00 0.00 36.57 3.73
3824 3989 3.247411 CAGCACATTTGTTGTACAGACGA 59.753 43.478 0.00 0.00 36.57 4.20
3825 3990 3.247411 TCAGCACATTTGTTGTACAGACG 59.753 43.478 0.00 0.00 36.57 4.18
3826 3991 4.811555 TCAGCACATTTGTTGTACAGAC 57.188 40.909 0.00 0.00 36.57 3.51
3827 3992 4.455533 GGATCAGCACATTTGTTGTACAGA 59.544 41.667 0.00 0.00 36.57 3.41
3828 3993 4.379813 GGGATCAGCACATTTGTTGTACAG 60.380 45.833 0.00 0.00 36.57 2.74
3829 3994 3.505680 GGGATCAGCACATTTGTTGTACA 59.494 43.478 0.00 0.00 36.57 2.90
3830 3995 3.758554 AGGGATCAGCACATTTGTTGTAC 59.241 43.478 0.00 0.00 36.57 2.90
3831 3996 3.758023 CAGGGATCAGCACATTTGTTGTA 59.242 43.478 0.00 0.00 36.57 2.41
3832 3997 2.559668 CAGGGATCAGCACATTTGTTGT 59.440 45.455 0.00 0.00 39.91 3.32
3833 3998 2.559668 ACAGGGATCAGCACATTTGTTG 59.440 45.455 0.00 0.00 35.34 3.33
3834 3999 2.559668 CACAGGGATCAGCACATTTGTT 59.440 45.455 0.00 0.00 0.00 2.83
3835 4000 2.165167 CACAGGGATCAGCACATTTGT 58.835 47.619 0.00 0.00 0.00 2.83
3836 4001 2.422479 CTCACAGGGATCAGCACATTTG 59.578 50.000 0.00 0.00 0.00 2.32
3837 4002 2.306805 TCTCACAGGGATCAGCACATTT 59.693 45.455 0.00 0.00 0.00 2.32
3838 4003 1.911357 TCTCACAGGGATCAGCACATT 59.089 47.619 0.00 0.00 0.00 2.71
3839 4004 1.576577 TCTCACAGGGATCAGCACAT 58.423 50.000 0.00 0.00 0.00 3.21
3840 4005 1.576577 ATCTCACAGGGATCAGCACA 58.423 50.000 0.00 0.00 0.00 4.57
3841 4006 2.681848 CAAATCTCACAGGGATCAGCAC 59.318 50.000 0.00 0.00 0.00 4.40
3842 4007 2.356432 CCAAATCTCACAGGGATCAGCA 60.356 50.000 0.00 0.00 0.00 4.41
3843 4008 2.295885 CCAAATCTCACAGGGATCAGC 58.704 52.381 0.00 0.00 0.00 4.26
3844 4009 2.422519 CCCCAAATCTCACAGGGATCAG 60.423 54.545 0.00 0.00 44.30 2.90
3845 4010 1.565759 CCCCAAATCTCACAGGGATCA 59.434 52.381 0.00 0.00 44.30 2.92
3846 4011 1.752084 GCCCCAAATCTCACAGGGATC 60.752 57.143 0.00 0.00 44.30 3.36
3847 4012 0.259938 GCCCCAAATCTCACAGGGAT 59.740 55.000 0.00 0.00 44.30 3.85
3848 4013 1.691219 GCCCCAAATCTCACAGGGA 59.309 57.895 0.00 0.00 44.30 4.20
3849 4014 1.750399 CGCCCCAAATCTCACAGGG 60.750 63.158 0.00 0.00 41.02 4.45
3850 4015 1.002134 ACGCCCCAAATCTCACAGG 60.002 57.895 0.00 0.00 0.00 4.00
3851 4016 0.606401 ACACGCCCCAAATCTCACAG 60.606 55.000 0.00 0.00 0.00 3.66
3852 4017 0.179004 AACACGCCCCAAATCTCACA 60.179 50.000 0.00 0.00 0.00 3.58
3853 4018 0.521735 GAACACGCCCCAAATCTCAC 59.478 55.000 0.00 0.00 0.00 3.51
3854 4019 0.953471 CGAACACGCCCCAAATCTCA 60.953 55.000 0.00 0.00 0.00 3.27
3855 4020 1.644786 CCGAACACGCCCCAAATCTC 61.645 60.000 0.00 0.00 0.00 2.75
3856 4021 1.674322 CCGAACACGCCCCAAATCT 60.674 57.895 0.00 0.00 0.00 2.40
3857 4022 1.520600 AACCGAACACGCCCCAAATC 61.521 55.000 0.00 0.00 0.00 2.17
3858 4023 1.520600 GAACCGAACACGCCCCAAAT 61.521 55.000 0.00 0.00 0.00 2.32
3859 4024 2.124236 AACCGAACACGCCCCAAA 60.124 55.556 0.00 0.00 0.00 3.28
3893 4058 3.941573 TGAGAAGTGTATGCAATGCAGA 58.058 40.909 14.98 6.18 40.43 4.26
3922 4087 7.775053 TTAGGTCTTATTTTTGCTCAACCAT 57.225 32.000 0.00 0.00 0.00 3.55
3941 4106 2.170607 ACTTGTAGATGGCGCATTAGGT 59.829 45.455 10.83 0.00 0.00 3.08
3988 4153 4.570772 CACTTGCGTATTACCTAATGCAGT 59.429 41.667 0.00 0.00 29.88 4.40
4027 4192 1.202989 TGTTGCTTGGGCCAATACAGA 60.203 47.619 21.25 8.92 37.74 3.41
4031 4196 1.549620 CATGTGTTGCTTGGGCCAATA 59.450 47.619 21.25 9.43 37.74 1.90
4044 4209 6.201425 GCATTCAAACATCTTGTTCATGTGTT 59.799 34.615 0.00 0.00 40.14 3.32
4045 4210 5.693104 GCATTCAAACATCTTGTTCATGTGT 59.307 36.000 0.00 0.00 40.14 3.72
4065 4230 1.295792 CCAAGTACGCCGTATGCATT 58.704 50.000 3.54 0.00 41.33 3.56
4066 4231 0.177141 ACCAAGTACGCCGTATGCAT 59.823 50.000 3.79 3.79 41.33 3.96
4081 4246 9.325198 CAACTAGAATACAATGTAGCATACCAA 57.675 33.333 0.00 0.00 42.12 3.67
4086 4251 9.486497 CTCATCAACTAGAATACAATGTAGCAT 57.514 33.333 0.00 0.00 0.00 3.79
4093 4259 7.934120 GGGTAAGCTCATCAACTAGAATACAAT 59.066 37.037 0.00 0.00 0.00 2.71
4100 4266 4.093743 TGTGGGTAAGCTCATCAACTAGA 58.906 43.478 0.00 0.00 0.00 2.43
4108 4274 5.590259 GTGTGATTATTGTGGGTAAGCTCAT 59.410 40.000 0.00 0.00 0.00 2.90
4125 4292 0.106268 TTGGTGTGCCAGGTGTGATT 60.106 50.000 0.00 0.00 46.91 2.57
4158 4325 3.342377 TTGCCCAGTTCATCGACATTA 57.658 42.857 0.00 0.00 0.00 1.90
4163 4330 0.400213 ACCTTTGCCCAGTTCATCGA 59.600 50.000 0.00 0.00 0.00 3.59
4213 4380 0.107654 AAGGTGCTAAGGTGGATCGC 60.108 55.000 0.00 0.00 0.00 4.58
4244 4411 4.080807 TGTTGACAGTGGTAAAGTTGGAGA 60.081 41.667 0.00 0.00 0.00 3.71
4488 4657 1.798223 TGTGCTACTTTGCTTGCTACG 59.202 47.619 0.00 0.00 0.00 3.51
4526 4695 5.618056 TGCATGCTTTACTTCTTCTCTTG 57.382 39.130 20.33 0.00 0.00 3.02
4565 4734 5.597182 CCATGGTAGTGCTAGGTAGAACTTA 59.403 44.000 2.57 0.00 39.16 2.24
4644 4813 2.747177 ACTAACCCCTCACGATGATGA 58.253 47.619 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.