Multiple sequence alignment - TraesCS3A01G366600

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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 TraesCS3A01G366600 chr3A 100.000 3406 0 0 379 3784 615724131 615720726 0.000000e+00 6290
1 TraesCS3A01G366600 chr3A 100.000 1353 0 0 4047 5399 615720463 615719111 0.000000e+00 2499
2 TraesCS3A01G366600 chr3A 81.266 379 60 4 381 754 532313815 532314187 4.090000e-76 296
3 TraesCS3A01G366600 chr3A 100.000 147 0 0 1 147 615724509 615724363 6.890000e-69 272
4 TraesCS3A01G366600 chr3D 94.977 2867 106 22 938 3784 473462829 473459981 0.000000e+00 4462
5 TraesCS3A01G366600 chr3D 92.821 780 27 8 4047 4820 473459942 473459186 0.000000e+00 1103
6 TraesCS3A01G366600 chr3D 90.476 378 34 2 379 755 473465683 473465307 1.040000e-136 497
7 TraesCS3A01G366600 chr3D 83.684 380 33 13 4976 5341 473459026 473458662 1.120000e-86 331
8 TraesCS3A01G366600 chr3D 79.404 369 69 3 387 754 418868189 418867827 2.500000e-63 254
9 TraesCS3A01G366600 chr3D 93.103 145 10 0 1 145 473465899 473465755 4.240000e-51 213
10 TraesCS3A01G366600 chr3D 96.000 125 5 0 4822 4946 473459150 473459026 2.550000e-48 204
11 TraesCS3A01G366600 chr3D 86.905 168 6 6 757 919 473462969 473462813 2.000000e-39 174
12 TraesCS3A01G366600 chr3B 96.323 1958 46 14 1844 3784 628478761 628476813 0.000000e+00 3193
13 TraesCS3A01G366600 chr3B 91.009 912 56 12 938 1841 628479766 628478873 0.000000e+00 1206
14 TraesCS3A01G366600 chr3B 90.098 919 39 11 4047 4932 628476772 628475873 0.000000e+00 1146
15 TraesCS3A01G366600 chr3B 84.881 377 56 1 379 755 628482053 628481678 3.950000e-101 379
16 TraesCS3A01G366600 chr3B 83.469 369 36 9 4983 5341 628475868 628475515 2.430000e-83 320
17 TraesCS3A01G366600 chr3B 81.522 368 54 7 389 754 545207994 545207639 1.900000e-74 291
18 TraesCS3A01G366600 chr3B 87.195 164 8 5 757 919 628479901 628479750 2.000000e-39 174


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 TraesCS3A01G366600 chr3A 615719111 615724509 5398 True 3020.333333 6290 100.000000 1 5399 3 chr3A.!!$R1 5398
1 TraesCS3A01G366600 chr3D 473458662 473465899 7237 True 997.714286 4462 91.138000 1 5341 7 chr3D.!!$R2 5340
2 TraesCS3A01G366600 chr3B 628475515 628482053 6538 True 1069.666667 3193 88.829167 379 5341 6 chr3B.!!$R2 4962

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
927 3568 0.251608 TCATCCACCCAGTGTCTCGA 60.252 55.000 0.00 0.0 0.00 4.04 F
928 3569 0.608130 CATCCACCCAGTGTCTCGAA 59.392 55.000 0.00 0.0 0.00 3.71 F
1450 4093 0.666913 CTGCTTCTGTTTGCTGCTGT 59.333 50.000 0.00 0.0 0.00 4.40 F
1481 4125 0.673644 GCACACACCGCTATTCCACT 60.674 55.000 0.00 0.0 0.00 4.00 F
1557 4201 1.060698 GATTAAGGTTCAGCGACGTGC 59.939 52.381 0.00 0.0 46.98 5.34 F
2316 5070 1.680522 CTAGTGCTGTGGGGATCGCT 61.681 60.000 9.90 0.0 0.00 4.93 F
3768 6540 0.029834 CAGTGTGCAAAGCAGTCACC 59.970 55.000 8.53 0.0 40.08 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 4417 0.608640 ACAGACATCCGGACTTCCAC 59.391 55.000 6.12 0.00 35.14 4.02 R
2781 5535 1.033746 AACATGCAGCGGAATCAGGG 61.034 55.000 0.00 0.00 0.00 4.45 R
2955 5710 3.066291 TGTGCCATTTCGGATAAGTGT 57.934 42.857 0.00 0.00 36.56 3.55 R
3453 6219 5.065859 GGTAGCACAAAAACTTGGCATTTTT 59.934 36.000 5.87 5.87 39.30 1.94 R
3522 6288 4.084287 CCCAGCAGCATATATCCACATTT 58.916 43.478 0.00 0.00 0.00 2.32 R
4228 7007 0.611618 ATGGCAGCAAATGTTCCGGA 60.612 50.000 0.00 0.00 0.00 5.14 R
5201 8025 0.251165 TTTGACACCCTAAGCCCTGC 60.251 55.000 0.00 0.00 0.00 4.85 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
28 29 0.542333 TATTTGGCGATCCCGGTTGA 59.458 50.000 0.00 0.00 35.87 3.18
38 39 3.047877 CCGGTTGACAGGTTCGGC 61.048 66.667 0.00 0.00 34.17 5.54
71 72 2.165998 GAACATGCTCTTTCCTTGCCT 58.834 47.619 0.00 0.00 0.00 4.75
73 74 1.202976 ACATGCTCTTTCCTTGCCTGT 60.203 47.619 0.00 0.00 32.39 4.00
75 76 1.321474 TGCTCTTTCCTTGCCTGTTG 58.679 50.000 0.00 0.00 0.00 3.33
91 92 4.083271 GCCTGTTGGACAACTGAGTTTATC 60.083 45.833 19.45 0.00 41.07 1.75
110 111 1.146774 TCCCCAAGTCTGAATGCCAAA 59.853 47.619 0.00 0.00 0.00 3.28
117 118 4.574599 AGTCTGAATGCCAAACAAGTTC 57.425 40.909 0.00 0.00 0.00 3.01
145 146 1.281867 TGGGAGCTGGTATCTTTGGTG 59.718 52.381 0.00 0.00 0.00 4.17
433 434 6.433847 TGGGTCTCTTTTGAGTCTGATTTA 57.566 37.500 0.00 0.00 46.30 1.40
520 521 0.604780 AGTAGGCACAACTGCTGCTG 60.605 55.000 4.89 4.89 43.66 4.41
527 528 2.223572 GCACAACTGCTGCTGTTTTACT 60.224 45.455 20.25 0.00 40.63 2.24
534 535 4.256920 CTGCTGCTGTTTTACTAGGTGAT 58.743 43.478 0.00 0.00 0.00 3.06
535 536 4.002982 TGCTGCTGTTTTACTAGGTGATG 58.997 43.478 0.00 0.00 0.00 3.07
540 541 4.081087 GCTGTTTTACTAGGTGATGGAGGA 60.081 45.833 0.00 0.00 0.00 3.71
550 551 5.261040 AGGTGATGGAGGAAATTTCTTGA 57.739 39.130 17.42 0.05 0.00 3.02
587 588 1.014352 ATTTCATAGGTTGCCGACGC 58.986 50.000 0.00 0.00 0.00 5.19
598 599 0.885150 TGCCGACGCAATTACCACAA 60.885 50.000 0.00 0.00 43.74 3.33
625 626 5.279859 GCAATGGATATGAGAGATGGTCTGA 60.280 44.000 0.00 0.00 34.71 3.27
632 633 5.752036 ATGAGAGATGGTCTGAAACTTGA 57.248 39.130 0.00 0.00 34.71 3.02
668 669 2.896685 TCAACCGGATTGAGGCAAAATT 59.103 40.909 9.46 0.00 42.62 1.82
700 701 7.495901 TCTTCAAGTGATTAATTTTTGCACCA 58.504 30.769 0.00 0.00 0.00 4.17
723 724 2.562298 GCAAACAAGATGGTGGGATGAA 59.438 45.455 0.00 0.00 0.00 2.57
733 734 1.293924 GTGGGATGAAGCATCGACAG 58.706 55.000 0.00 0.00 41.35 3.51
759 3396 1.331756 GCAGAGTGCGTGGATAATTGG 59.668 52.381 0.00 0.00 31.71 3.16
787 3424 1.065600 CGGCCCATACAAATTGCGG 59.934 57.895 0.00 0.00 0.00 5.69
840 3478 2.347114 CCAGCATCACGGACCACA 59.653 61.111 0.00 0.00 0.00 4.17
850 3488 0.951558 ACGGACCACATGAACAAAGC 59.048 50.000 0.00 0.00 0.00 3.51
864 3505 1.071814 AAAGCGAGCCCGTAAACCA 59.928 52.632 0.00 0.00 38.24 3.67
865 3506 0.953960 AAAGCGAGCCCGTAAACCAG 60.954 55.000 0.00 0.00 38.24 4.00
866 3507 3.497031 GCGAGCCCGTAAACCAGC 61.497 66.667 0.00 0.00 38.24 4.85
867 3508 3.186047 CGAGCCCGTAAACCAGCG 61.186 66.667 0.00 0.00 0.00 5.18
868 3509 3.497031 GAGCCCGTAAACCAGCGC 61.497 66.667 0.00 0.00 0.00 5.92
871 3512 3.124921 CCCGTAAACCAGCGCCAG 61.125 66.667 2.29 0.00 0.00 4.85
872 3513 2.358247 CCGTAAACCAGCGCCAGT 60.358 61.111 2.29 0.00 0.00 4.00
873 3514 1.079681 CCGTAAACCAGCGCCAGTA 60.080 57.895 2.29 0.00 0.00 2.74
874 3515 1.082117 CCGTAAACCAGCGCCAGTAG 61.082 60.000 2.29 0.00 0.00 2.57
915 3556 2.636830 CACCTCACCTGAATCATCCAC 58.363 52.381 0.00 0.00 0.00 4.02
916 3557 1.561542 ACCTCACCTGAATCATCCACC 59.438 52.381 0.00 0.00 0.00 4.61
917 3558 1.133976 CCTCACCTGAATCATCCACCC 60.134 57.143 0.00 0.00 0.00 4.61
918 3559 1.561076 CTCACCTGAATCATCCACCCA 59.439 52.381 0.00 0.00 0.00 4.51
919 3560 1.561076 TCACCTGAATCATCCACCCAG 59.439 52.381 0.00 0.00 0.00 4.45
920 3561 1.283029 CACCTGAATCATCCACCCAGT 59.717 52.381 0.00 0.00 0.00 4.00
921 3562 1.283029 ACCTGAATCATCCACCCAGTG 59.717 52.381 0.00 0.00 0.00 3.66
922 3563 1.283029 CCTGAATCATCCACCCAGTGT 59.717 52.381 0.00 0.00 0.00 3.55
923 3564 2.636830 CTGAATCATCCACCCAGTGTC 58.363 52.381 0.00 0.00 0.00 3.67
924 3565 2.238144 CTGAATCATCCACCCAGTGTCT 59.762 50.000 0.00 0.00 0.00 3.41
925 3566 2.237143 TGAATCATCCACCCAGTGTCTC 59.763 50.000 0.00 0.00 0.00 3.36
926 3567 0.826715 ATCATCCACCCAGTGTCTCG 59.173 55.000 0.00 0.00 0.00 4.04
927 3568 0.251608 TCATCCACCCAGTGTCTCGA 60.252 55.000 0.00 0.00 0.00 4.04
928 3569 0.608130 CATCCACCCAGTGTCTCGAA 59.392 55.000 0.00 0.00 0.00 3.71
929 3570 1.001974 CATCCACCCAGTGTCTCGAAA 59.998 52.381 0.00 0.00 0.00 3.46
930 3571 1.124780 TCCACCCAGTGTCTCGAAAA 58.875 50.000 0.00 0.00 0.00 2.29
931 3572 1.487142 TCCACCCAGTGTCTCGAAAAA 59.513 47.619 0.00 0.00 0.00 1.94
1386 4029 3.528370 CTCTCCCAGGCGTACGGG 61.528 72.222 18.39 9.71 44.60 5.28
1429 4072 1.073897 GTGCAGGTTCCCAGCTCTT 59.926 57.895 0.00 0.00 36.95 2.85
1447 4090 4.240049 GCTGCTTCTGTTTGCTGC 57.760 55.556 0.00 0.00 44.21 5.25
1450 4093 0.666913 CTGCTTCTGTTTGCTGCTGT 59.333 50.000 0.00 0.00 0.00 4.40
1454 4097 2.466846 CTTCTGTTTGCTGCTGTTTGG 58.533 47.619 0.00 0.00 0.00 3.28
1462 4105 1.007734 CTGCTGTTTGGCTGCACTG 60.008 57.895 0.50 0.00 45.14 3.66
1471 4115 4.318021 GCTGCACTGCACACACCG 62.318 66.667 0.00 0.00 33.79 4.94
1480 4124 0.953471 TGCACACACCGCTATTCCAC 60.953 55.000 0.00 0.00 0.00 4.02
1481 4125 0.673644 GCACACACCGCTATTCCACT 60.674 55.000 0.00 0.00 0.00 4.00
1487 4131 3.031736 ACACCGCTATTCCACTAGTGAT 58.968 45.455 24.68 12.90 32.15 3.06
1488 4132 3.068307 ACACCGCTATTCCACTAGTGATC 59.932 47.826 24.68 5.39 32.15 2.92
1490 4134 2.351835 CCGCTATTCCACTAGTGATCGG 60.352 54.545 24.68 19.56 32.15 4.18
1491 4135 2.678324 GCTATTCCACTAGTGATCGGC 58.322 52.381 24.68 16.03 0.00 5.54
1493 4137 1.794714 ATTCCACTAGTGATCGGCCT 58.205 50.000 24.68 0.00 0.00 5.19
1495 4139 1.101635 TCCACTAGTGATCGGCCTCG 61.102 60.000 24.68 4.10 37.82 4.63
1497 4141 1.828660 ACTAGTGATCGGCCTCGGG 60.829 63.158 0.00 0.00 36.95 5.14
1498 4142 2.520982 TAGTGATCGGCCTCGGGG 60.521 66.667 0.00 0.00 36.95 5.73
1499 4143 2.978298 CTAGTGATCGGCCTCGGGGA 62.978 65.000 4.80 0.00 36.95 4.81
1500 4144 4.222847 GTGATCGGCCTCGGGGAC 62.223 72.222 4.80 0.00 37.25 4.46
1501 4145 4.770362 TGATCGGCCTCGGGGACA 62.770 66.667 8.62 0.00 41.90 4.02
1502 4146 4.222847 GATCGGCCTCGGGGACAC 62.223 72.222 8.62 0.00 41.90 3.67
1505 4149 4.096003 CGGCCTCGGGGACACAAT 62.096 66.667 8.62 0.00 41.90 2.71
1532 4176 6.371548 GTGTTTGGTGATAGAATGCTCAACTA 59.628 38.462 0.00 0.00 30.26 2.24
1547 4191 4.264849 GCTCAACTACGACGATTAAGGTTC 59.735 45.833 0.00 0.00 0.00 3.62
1549 4193 5.396484 TCAACTACGACGATTAAGGTTCAG 58.604 41.667 0.00 0.00 0.00 3.02
1550 4194 3.767278 ACTACGACGATTAAGGTTCAGC 58.233 45.455 0.00 0.00 0.00 4.26
1551 4195 1.625616 ACGACGATTAAGGTTCAGCG 58.374 50.000 0.00 0.00 0.00 5.18
1553 4197 1.582502 CGACGATTAAGGTTCAGCGAC 59.417 52.381 0.00 0.00 0.00 5.19
1557 4201 1.060698 GATTAAGGTTCAGCGACGTGC 59.939 52.381 0.00 0.00 46.98 5.34
1592 4236 9.347934 TCAATTGCAATTACGGTTTAATACTTG 57.652 29.630 23.69 7.99 0.00 3.16
1596 4240 8.903570 TGCAATTACGGTTTAATACTTGAATG 57.096 30.769 0.00 0.00 0.00 2.67
1597 4241 7.971168 TGCAATTACGGTTTAATACTTGAATGG 59.029 33.333 0.00 0.00 0.00 3.16
1598 4242 8.185505 GCAATTACGGTTTAATACTTGAATGGA 58.814 33.333 0.00 0.00 0.00 3.41
1601 4245 8.851541 TTACGGTTTAATACTTGAATGGAAGT 57.148 30.769 0.00 0.00 39.54 3.01
1602 4246 7.141100 ACGGTTTAATACTTGAATGGAAGTG 57.859 36.000 0.00 0.00 36.80 3.16
1841 4486 6.043411 CCACTGCCTATACTGTTCTAGTTTC 58.957 44.000 0.00 0.00 40.89 2.78
1912 4666 6.039159 TGTGTTTTTGATGCTTCATACAGTCA 59.961 34.615 2.75 2.46 0.00 3.41
1993 4747 2.268920 GGGAAGCGAGTCATGGCA 59.731 61.111 0.00 0.00 31.54 4.92
2204 4958 6.757897 TCATGCTTTTACCAGAACCTAATG 57.242 37.500 0.00 0.00 0.00 1.90
2208 4962 6.744112 TGCTTTTACCAGAACCTAATGTTTG 58.256 36.000 0.00 0.00 37.29 2.93
2236 4990 2.676471 GTTGCCCTGCCCGTCAAT 60.676 61.111 0.00 0.00 0.00 2.57
2316 5070 1.680522 CTAGTGCTGTGGGGATCGCT 61.681 60.000 9.90 0.00 0.00 4.93
2558 5312 7.177744 ACCTCAAGTTCAAGGTGAAAAACTAAA 59.822 33.333 5.79 0.00 44.26 1.85
2683 5437 2.205074 GGTTAGATCGTGCCATGTGAG 58.795 52.381 0.00 0.00 0.00 3.51
2781 5535 5.151389 CCAGTGTATTTCAAAACCGTAAGC 58.849 41.667 0.00 0.00 0.00 3.09
2955 5710 2.472695 GGCTGGTGTTGTATCAGACA 57.527 50.000 0.00 0.00 45.53 3.41
3009 5764 1.869767 CTCGGAAGATAATGCAGGTGC 59.130 52.381 0.00 0.00 40.84 5.01
3150 5911 6.544038 TTGTGATATGATGAACTATTGGCG 57.456 37.500 0.00 0.00 0.00 5.69
3238 5999 3.726557 AGGCATGGATGTTCTCAAAGA 57.273 42.857 0.00 0.00 0.00 2.52
3310 6073 7.712205 AGGCATGGATATTTTCAAAGCAATTAC 59.288 33.333 0.00 0.00 0.00 1.89
3453 6219 8.057011 TGGTAAATCACAGTAGATACTCTGGTA 58.943 37.037 0.00 0.00 36.17 3.25
3492 6258 2.089201 GCTACCACCTGCCGTTTATTT 58.911 47.619 0.00 0.00 0.00 1.40
3494 6260 3.690628 GCTACCACCTGCCGTTTATTTAA 59.309 43.478 0.00 0.00 0.00 1.52
3496 6262 5.163591 GCTACCACCTGCCGTTTATTTAATT 60.164 40.000 0.00 0.00 0.00 1.40
3498 6264 6.837471 ACCACCTGCCGTTTATTTAATTAA 57.163 33.333 0.00 0.00 0.00 1.40
3757 6529 7.158697 ACTTGTATACATTAGTTCAGTGTGCA 58.841 34.615 6.36 0.00 0.00 4.57
3768 6540 0.029834 CAGTGTGCAAAGCAGTCACC 59.970 55.000 8.53 0.00 40.08 4.02
4228 7007 3.377172 GCTAACAGGAATGGCAAATACGT 59.623 43.478 0.00 0.00 0.00 3.57
4401 7180 0.530650 TTGATGGCACTAGCTAGCGC 60.531 55.000 22.81 22.81 40.87 5.92
4408 7187 1.281899 CACTAGCTAGCGCCAAAGAC 58.718 55.000 20.91 0.00 36.60 3.01
4409 7188 0.179134 ACTAGCTAGCGCCAAAGACG 60.179 55.000 20.91 0.00 36.60 4.18
4417 7196 4.376109 GCTAGCGCCAAAGACGAAATATAC 60.376 45.833 2.29 0.00 0.00 1.47
4432 7211 9.615779 GACGAAATATACAGTAAACGATTTGAC 57.384 33.333 0.00 0.00 0.00 3.18
4455 7236 2.092968 TCACTGGGAGTATTGTGGCATC 60.093 50.000 0.00 0.00 0.00 3.91
4461 7242 3.755378 GGGAGTATTGTGGCATCATCATC 59.245 47.826 0.00 0.00 0.00 2.92
4480 7261 5.853936 TCATCTGGGATAGTACCGAAAATG 58.146 41.667 0.00 0.00 0.00 2.32
4531 7312 4.168922 TCTGTACTACAACATCGTGTGG 57.831 45.455 0.00 0.00 36.17 4.17
4547 7328 3.562141 CGTGTGGTTCAATGTAGTGGAAA 59.438 43.478 0.00 0.00 0.00 3.13
4626 7407 0.320334 TTTCTGATGCGCAAGTCCGA 60.320 50.000 17.11 7.70 41.68 4.55
4627 7408 0.320334 TTCTGATGCGCAAGTCCGAA 60.320 50.000 17.11 13.92 41.68 4.30
4628 7409 0.320334 TCTGATGCGCAAGTCCGAAA 60.320 50.000 17.11 0.00 41.68 3.46
4629 7410 0.729116 CTGATGCGCAAGTCCGAAAT 59.271 50.000 17.11 0.00 41.68 2.17
4630 7411 0.447406 TGATGCGCAAGTCCGAAATG 59.553 50.000 17.11 0.00 41.68 2.32
4631 7412 0.447801 GATGCGCAAGTCCGAAATGT 59.552 50.000 17.11 0.00 41.68 2.71
4632 7413 0.168788 ATGCGCAAGTCCGAAATGTG 59.831 50.000 17.11 0.00 41.68 3.21
4633 7414 0.882484 TGCGCAAGTCCGAAATGTGA 60.882 50.000 8.16 0.00 41.68 3.58
4634 7415 0.237235 GCGCAAGTCCGAAATGTGAA 59.763 50.000 0.30 0.00 41.68 3.18
4635 7416 1.135689 GCGCAAGTCCGAAATGTGAAT 60.136 47.619 0.30 0.00 41.68 2.57
4636 7417 2.668279 GCGCAAGTCCGAAATGTGAATT 60.668 45.455 0.30 0.00 41.68 2.17
4637 7418 3.564511 CGCAAGTCCGAAATGTGAATTT 58.435 40.909 0.00 0.00 0.00 1.82
4638 7419 3.603770 CGCAAGTCCGAAATGTGAATTTC 59.396 43.478 1.85 1.85 37.23 2.17
4639 7420 4.545610 GCAAGTCCGAAATGTGAATTTCA 58.454 39.130 10.77 0.00 39.76 2.69
4640 7421 5.163513 GCAAGTCCGAAATGTGAATTTCAT 58.836 37.500 1.78 0.00 39.76 2.57
4641 7422 5.287035 GCAAGTCCGAAATGTGAATTTCATC 59.713 40.000 1.78 0.00 39.76 2.92
4642 7423 5.567138 AGTCCGAAATGTGAATTTCATCC 57.433 39.130 1.78 0.00 39.76 3.51
4643 7424 4.094887 AGTCCGAAATGTGAATTTCATCCG 59.905 41.667 1.78 2.92 39.76 4.18
4816 7622 0.107508 TTGGTGAGGCTAGCAGATGC 60.108 55.000 18.24 0.00 42.49 3.91
4909 7723 4.645136 AGACAGCAATATAAGTCGTGGAGA 59.355 41.667 0.00 0.00 36.18 3.71
4910 7724 5.303078 AGACAGCAATATAAGTCGTGGAGAT 59.697 40.000 0.00 0.00 36.18 2.75
4928 7742 7.800380 CGTGGAGATCATTTAAACTCATAATGC 59.200 37.037 0.00 0.00 31.08 3.56
4946 7760 3.438297 TGCGAGGCTACTGTAAAGATC 57.562 47.619 0.00 0.00 0.00 2.75
4947 7761 2.100916 TGCGAGGCTACTGTAAAGATCC 59.899 50.000 0.00 0.00 0.00 3.36
4948 7762 2.100916 GCGAGGCTACTGTAAAGATCCA 59.899 50.000 0.00 0.00 0.00 3.41
4949 7763 3.797184 GCGAGGCTACTGTAAAGATCCAG 60.797 52.174 0.00 0.00 34.82 3.86
4950 7764 3.632604 CGAGGCTACTGTAAAGATCCAGA 59.367 47.826 4.00 0.00 32.93 3.86
4951 7765 4.098044 CGAGGCTACTGTAAAGATCCAGAA 59.902 45.833 4.00 0.00 32.93 3.02
4952 7766 5.221342 CGAGGCTACTGTAAAGATCCAGAAT 60.221 44.000 4.00 0.00 32.93 2.40
4953 7767 6.567602 AGGCTACTGTAAAGATCCAGAATT 57.432 37.500 4.00 0.00 32.93 2.17
4954 7768 6.587273 AGGCTACTGTAAAGATCCAGAATTC 58.413 40.000 0.00 0.00 32.93 2.17
4955 7769 6.385467 AGGCTACTGTAAAGATCCAGAATTCT 59.615 38.462 0.88 0.88 32.93 2.40
4956 7770 6.704050 GGCTACTGTAAAGATCCAGAATTCTC 59.296 42.308 4.57 0.00 32.93 2.87
4957 7771 7.418483 GGCTACTGTAAAGATCCAGAATTCTCT 60.418 40.741 4.57 0.00 32.93 3.10
4959 7773 7.251321 ACTGTAAAGATCCAGAATTCTCTGT 57.749 36.000 4.57 0.00 46.71 3.41
4960 7774 7.327214 ACTGTAAAGATCCAGAATTCTCTGTC 58.673 38.462 4.57 3.86 46.71 3.51
4961 7775 6.333416 TGTAAAGATCCAGAATTCTCTGTCG 58.667 40.000 4.57 0.00 46.71 4.35
4962 7776 4.399004 AAGATCCAGAATTCTCTGTCGG 57.601 45.455 4.57 3.61 46.71 4.79
4963 7777 2.102252 AGATCCAGAATTCTCTGTCGGC 59.898 50.000 4.57 0.00 46.71 5.54
4964 7778 1.561643 TCCAGAATTCTCTGTCGGCT 58.438 50.000 4.57 0.00 46.71 5.52
4965 7779 1.902508 TCCAGAATTCTCTGTCGGCTT 59.097 47.619 4.57 0.00 46.71 4.35
4966 7780 2.093973 TCCAGAATTCTCTGTCGGCTTC 60.094 50.000 4.57 0.00 46.71 3.86
4967 7781 2.354103 CCAGAATTCTCTGTCGGCTTCA 60.354 50.000 4.57 0.00 46.71 3.02
4968 7782 2.670414 CAGAATTCTCTGTCGGCTTCAC 59.330 50.000 4.57 0.00 43.64 3.18
4969 7783 2.300152 AGAATTCTCTGTCGGCTTCACA 59.700 45.455 0.88 0.00 0.00 3.58
4970 7784 2.839486 ATTCTCTGTCGGCTTCACAA 57.161 45.000 0.00 0.00 0.00 3.33
4971 7785 2.839486 TTCTCTGTCGGCTTCACAAT 57.161 45.000 0.00 0.00 0.00 2.71
4972 7786 2.084610 TCTCTGTCGGCTTCACAATG 57.915 50.000 0.00 0.00 0.00 2.82
4973 7787 1.344438 TCTCTGTCGGCTTCACAATGT 59.656 47.619 0.00 0.00 0.00 2.71
4974 7788 2.146342 CTCTGTCGGCTTCACAATGTT 58.854 47.619 0.00 0.00 0.00 2.71
4975 7789 2.549754 CTCTGTCGGCTTCACAATGTTT 59.450 45.455 0.00 0.00 0.00 2.83
4991 7805 6.019640 CACAATGTTTGTTCACTTTAGCTTGG 60.020 38.462 0.00 0.00 43.23 3.61
4993 7807 4.020543 TGTTTGTTCACTTTAGCTTGGGT 58.979 39.130 0.00 0.00 0.00 4.51
4996 7810 2.158871 TGTTCACTTTAGCTTGGGTCGT 60.159 45.455 0.00 0.00 0.00 4.34
4997 7811 2.876550 GTTCACTTTAGCTTGGGTCGTT 59.123 45.455 0.00 0.00 0.00 3.85
5003 7817 1.504359 TAGCTTGGGTCGTTGTTTCG 58.496 50.000 0.00 0.00 0.00 3.46
5007 7821 1.666700 CTTGGGTCGTTGTTTCGTGAA 59.333 47.619 0.00 0.00 0.00 3.18
5009 7823 2.290464 TGGGTCGTTGTTTCGTGAAAT 58.710 42.857 0.00 0.00 32.36 2.17
5010 7824 2.683867 TGGGTCGTTGTTTCGTGAAATT 59.316 40.909 0.00 0.00 32.36 1.82
5046 7862 9.046296 CGAAGGAGAACTATAGTTATTGCAATT 57.954 33.333 18.75 1.86 38.56 2.32
5089 7905 5.105063 TGTTTGATGTGCGAAAAATGTTGA 58.895 33.333 0.00 0.00 0.00 3.18
5112 7934 7.334858 TGAATGGTTGTAACTATCAGCATACA 58.665 34.615 0.00 0.00 29.20 2.29
5113 7935 7.826744 TGAATGGTTGTAACTATCAGCATACAA 59.173 33.333 0.00 0.00 36.27 2.41
5124 7946 2.846206 TCAGCATACAAAGTCCCCTCAT 59.154 45.455 0.00 0.00 0.00 2.90
5128 7950 5.934625 CAGCATACAAAGTCCCCTCATATAC 59.065 44.000 0.00 0.00 0.00 1.47
5162 7986 0.038744 ACAGAGGGGGCATTGAGTTG 59.961 55.000 0.00 0.00 0.00 3.16
5200 8024 2.703798 CCCCGCTGATGCCAAACAG 61.704 63.158 0.00 0.00 37.22 3.16
5201 8025 2.703798 CCCGCTGATGCCAAACAGG 61.704 63.158 0.00 0.00 41.84 4.00
5235 8059 5.170748 GGTGTCAAAATGCCCTGAATAAAG 58.829 41.667 0.00 0.00 0.00 1.85
5283 8108 2.736144 ATGGACGAACGTGTACATGT 57.264 45.000 15.10 15.10 41.87 3.21
5292 8117 4.201551 CGAACGTGTACATGTTGGTCATAC 60.202 45.833 32.63 17.59 40.35 2.39
5296 8121 5.109210 CGTGTACATGTTGGTCATACTGAT 58.891 41.667 2.30 0.00 34.67 2.90
5301 8126 6.748333 ACATGTTGGTCATACTGATTCTTG 57.252 37.500 0.00 0.00 34.67 3.02
5327 8155 5.186797 TGAAAGAACAAACACCAAACCTGAT 59.813 36.000 0.00 0.00 0.00 2.90
5341 8169 3.287867 ACCTGATAATCAACTGCTGGG 57.712 47.619 0.00 0.00 0.00 4.45
5342 8170 2.092212 ACCTGATAATCAACTGCTGGGG 60.092 50.000 0.00 0.00 0.00 4.96
5343 8171 2.092212 CCTGATAATCAACTGCTGGGGT 60.092 50.000 0.00 0.00 0.00 4.95
5344 8172 2.947652 CTGATAATCAACTGCTGGGGTG 59.052 50.000 0.00 0.00 0.00 4.61
5345 8173 2.301346 GATAATCAACTGCTGGGGTGG 58.699 52.381 0.00 0.00 0.00 4.61
5346 8174 0.323360 TAATCAACTGCTGGGGTGGC 60.323 55.000 0.00 0.00 0.00 5.01
5347 8175 3.925630 ATCAACTGCTGGGGTGGCG 62.926 63.158 0.00 0.00 0.00 5.69
5348 8176 4.954970 CAACTGCTGGGGTGGCGT 62.955 66.667 0.00 0.00 0.00 5.68
5349 8177 4.643387 AACTGCTGGGGTGGCGTC 62.643 66.667 0.00 0.00 0.00 5.19
5354 8182 4.263572 CTGGGGTGGCGTCCAACA 62.264 66.667 14.52 7.36 44.30 3.33
5355 8183 3.567579 CTGGGGTGGCGTCCAACAT 62.568 63.158 14.52 0.00 44.30 2.71
5356 8184 2.750237 GGGGTGGCGTCCAACATC 60.750 66.667 14.52 4.15 44.30 3.06
5357 8185 3.124921 GGGTGGCGTCCAACATCG 61.125 66.667 14.52 0.00 44.30 3.84
5358 8186 2.358247 GGTGGCGTCCAACATCGT 60.358 61.111 8.77 0.00 41.64 3.73
5359 8187 2.677003 GGTGGCGTCCAACATCGTG 61.677 63.158 8.77 0.00 41.64 4.35
5360 8188 2.358125 TGGCGTCCAACATCGTGG 60.358 61.111 0.00 0.00 40.33 4.94
5361 8189 3.799755 GGCGTCCAACATCGTGGC 61.800 66.667 0.00 0.00 38.68 5.01
5362 8190 4.147322 GCGTCCAACATCGTGGCG 62.147 66.667 0.00 0.00 38.68 5.69
5363 8191 4.147322 CGTCCAACATCGTGGCGC 62.147 66.667 0.00 0.00 38.68 6.53
5364 8192 3.799755 GTCCAACATCGTGGCGCC 61.800 66.667 22.73 22.73 38.68 6.53
5365 8193 4.321966 TCCAACATCGTGGCGCCA 62.322 61.111 29.03 29.03 38.68 5.69
5366 8194 3.361158 CCAACATCGTGGCGCCAA 61.361 61.111 34.66 18.73 0.00 4.52
5367 8195 2.176546 CAACATCGTGGCGCCAAG 59.823 61.111 34.66 33.80 0.00 3.61
5368 8196 2.281484 AACATCGTGGCGCCAAGT 60.281 55.556 35.82 25.89 0.00 3.16
5369 8197 2.325082 AACATCGTGGCGCCAAGTC 61.325 57.895 35.82 22.06 0.00 3.01
5370 8198 2.741985 CATCGTGGCGCCAAGTCA 60.742 61.111 35.82 22.14 0.00 3.41
5371 8199 2.108514 CATCGTGGCGCCAAGTCAT 61.109 57.895 35.82 23.29 36.54 3.06
5372 8200 1.815421 ATCGTGGCGCCAAGTCATC 60.815 57.895 35.82 20.62 36.54 2.92
5373 8201 3.499737 CGTGGCGCCAAGTCATCC 61.500 66.667 34.66 16.34 36.54 3.51
5374 8202 2.359850 GTGGCGCCAAGTCATCCA 60.360 61.111 34.66 0.58 36.54 3.41
5375 8203 1.750399 GTGGCGCCAAGTCATCCAT 60.750 57.895 34.66 0.00 36.54 3.41
5376 8204 1.451927 TGGCGCCAAGTCATCCATC 60.452 57.895 30.74 0.00 0.00 3.51
5377 8205 1.451927 GGCGCCAAGTCATCCATCA 60.452 57.895 24.80 0.00 0.00 3.07
5378 8206 1.031571 GGCGCCAAGTCATCCATCAA 61.032 55.000 24.80 0.00 0.00 2.57
5379 8207 0.379669 GCGCCAAGTCATCCATCAAG 59.620 55.000 0.00 0.00 0.00 3.02
5380 8208 1.019673 CGCCAAGTCATCCATCAAGG 58.980 55.000 0.00 0.00 39.47 3.61
5381 8209 1.396653 GCCAAGTCATCCATCAAGGG 58.603 55.000 0.00 0.00 38.24 3.95
5382 8210 2.025863 GCCAAGTCATCCATCAAGGGG 61.026 57.143 0.00 0.00 38.24 4.79
5383 8211 1.396653 CAAGTCATCCATCAAGGGGC 58.603 55.000 0.00 0.00 38.24 5.80
5384 8212 1.064166 CAAGTCATCCATCAAGGGGCT 60.064 52.381 0.00 0.00 38.24 5.19
5385 8213 0.549950 AGTCATCCATCAAGGGGCTG 59.450 55.000 0.00 0.00 38.24 4.85
5386 8214 0.548031 GTCATCCATCAAGGGGCTGA 59.452 55.000 0.00 0.00 38.24 4.26
5387 8215 1.064463 GTCATCCATCAAGGGGCTGAA 60.064 52.381 0.00 0.00 38.24 3.02
5388 8216 1.064463 TCATCCATCAAGGGGCTGAAC 60.064 52.381 0.00 0.00 38.24 3.18
5389 8217 0.259938 ATCCATCAAGGGGCTGAACC 59.740 55.000 0.00 0.00 38.24 3.62
5390 8218 1.750399 CCATCAAGGGGCTGAACCG 60.750 63.158 0.00 0.00 40.62 4.44
5391 8219 1.002134 CATCAAGGGGCTGAACCGT 60.002 57.895 0.00 0.00 40.62 4.83
5392 8220 1.026718 CATCAAGGGGCTGAACCGTC 61.027 60.000 0.00 0.00 40.62 4.79
5393 8221 2.198304 ATCAAGGGGCTGAACCGTCC 62.198 60.000 0.00 0.00 40.62 4.79
5394 8222 2.852075 AAGGGGCTGAACCGTCCA 60.852 61.111 0.00 0.00 40.62 4.02
5395 8223 2.895424 AAGGGGCTGAACCGTCCAG 61.895 63.158 0.00 0.00 40.62 3.86
5396 8224 3.319198 GGGGCTGAACCGTCCAGA 61.319 66.667 0.00 0.00 40.62 3.86
5397 8225 2.670148 GGGGCTGAACCGTCCAGAT 61.670 63.158 0.00 0.00 40.62 2.90
5398 8226 1.450312 GGGCTGAACCGTCCAGATG 60.450 63.158 0.00 0.00 40.62 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.511600 CCTGTCAACCGGGATCGC 60.512 66.667 6.32 0.00 42.95 4.58
28 29 0.611714 AATTACCGAGCCGAACCTGT 59.388 50.000 0.00 0.00 0.00 4.00
38 39 5.942872 AGAGCATGTTCAAAAATTACCGAG 58.057 37.500 12.41 0.00 0.00 4.63
71 72 4.394729 GGGATAAACTCAGTTGTCCAACA 58.605 43.478 19.04 0.00 43.47 3.33
73 74 3.396276 TGGGGATAAACTCAGTTGTCCAA 59.604 43.478 19.04 8.06 34.74 3.53
75 76 3.713826 TGGGGATAAACTCAGTTGTCC 57.286 47.619 12.04 12.04 33.33 4.02
91 92 1.273327 GTTTGGCATTCAGACTTGGGG 59.727 52.381 0.00 0.00 0.00 4.96
110 111 2.551071 GCTCCCAACAGCTAGAACTTGT 60.551 50.000 0.00 0.00 36.38 3.16
394 395 5.782845 AGAGACCCAAGAAAGTGTCTTCTAT 59.217 40.000 0.00 0.00 45.25 1.98
396 397 3.970640 AGAGACCCAAGAAAGTGTCTTCT 59.029 43.478 0.00 0.00 45.25 2.85
433 434 5.625197 GCATTGATCAGGCTTACACCATTTT 60.625 40.000 12.65 0.00 0.00 1.82
520 521 7.939784 AATTTCCTCCATCACCTAGTAAAAC 57.060 36.000 0.00 0.00 0.00 2.43
527 528 6.387192 TCAAGAAATTTCCTCCATCACCTA 57.613 37.500 14.61 0.00 0.00 3.08
534 535 5.078949 TGAGCAATCAAGAAATTTCCTCCA 58.921 37.500 14.61 0.00 0.00 3.86
535 536 5.649782 TGAGCAATCAAGAAATTTCCTCC 57.350 39.130 14.61 0.00 0.00 4.30
563 564 4.584394 GTCGGCAACCTATGAAATAAACG 58.416 43.478 0.00 0.00 0.00 3.60
587 588 7.980662 TCATATCCATTGCTTTTGTGGTAATTG 59.019 33.333 0.00 0.00 34.61 2.32
598 599 5.950023 ACCATCTCTCATATCCATTGCTTT 58.050 37.500 0.00 0.00 0.00 3.51
625 626 4.388577 AGCCAAGGGAGTTATCAAGTTT 57.611 40.909 0.00 0.00 0.00 2.66
632 633 2.618045 CGGTTGAAGCCAAGGGAGTTAT 60.618 50.000 0.00 0.00 32.06 1.89
700 701 0.482446 TCCCACCATCTTGTTTGCCT 59.518 50.000 0.00 0.00 0.00 4.75
723 724 1.426816 CTGCGAATGCTGTCGATGCT 61.427 55.000 12.86 0.00 43.86 3.79
777 3414 2.547026 GGTACGACCCGCAATTTGT 58.453 52.632 0.00 0.00 30.04 2.83
807 3445 1.733402 CTGGCGCTGGTTTGTTTGGA 61.733 55.000 7.64 0.00 0.00 3.53
809 3447 1.950630 GCTGGCGCTGGTTTGTTTG 60.951 57.895 7.64 0.00 0.00 2.93
810 3448 1.747325 ATGCTGGCGCTGGTTTGTTT 61.747 50.000 7.64 0.00 36.97 2.83
840 3478 0.036765 TACGGGCTCGCTTTGTTCAT 60.037 50.000 5.51 0.00 40.63 2.57
850 3488 3.186047 CGCTGGTTTACGGGCTCG 61.186 66.667 3.27 3.27 43.02 5.03
864 3505 1.239296 TGACGTGTACTACTGGCGCT 61.239 55.000 7.64 0.00 0.00 5.92
865 3506 1.069378 GTGACGTGTACTACTGGCGC 61.069 60.000 0.00 0.00 0.00 6.53
866 3507 0.520404 AGTGACGTGTACTACTGGCG 59.480 55.000 0.00 0.00 0.00 5.69
867 3508 1.978542 CAGTGACGTGTACTACTGGC 58.021 55.000 0.00 0.00 37.48 4.85
868 3509 1.268625 TGCAGTGACGTGTACTACTGG 59.731 52.381 0.00 0.00 40.55 4.00
869 3510 2.316792 GTGCAGTGACGTGTACTACTG 58.683 52.381 0.00 0.77 42.51 2.74
870 3511 1.268899 GGTGCAGTGACGTGTACTACT 59.731 52.381 0.00 0.00 33.85 2.57
871 3512 1.001048 TGGTGCAGTGACGTGTACTAC 60.001 52.381 0.00 0.00 33.85 2.73
872 3513 1.320507 TGGTGCAGTGACGTGTACTA 58.679 50.000 0.00 0.00 33.85 1.82
873 3514 0.462375 TTGGTGCAGTGACGTGTACT 59.538 50.000 0.00 0.00 33.85 2.73
874 3515 1.459592 GATTGGTGCAGTGACGTGTAC 59.540 52.381 0.00 0.00 32.68 2.90
931 3572 3.173151 GGGTGGATGATTCAGGGTTTTT 58.827 45.455 0.00 0.00 0.00 1.94
932 3573 2.111613 TGGGTGGATGATTCAGGGTTTT 59.888 45.455 0.00 0.00 0.00 2.43
933 3574 1.715931 TGGGTGGATGATTCAGGGTTT 59.284 47.619 0.00 0.00 0.00 3.27
934 3575 1.005924 GTGGGTGGATGATTCAGGGTT 59.994 52.381 0.00 0.00 0.00 4.11
935 3576 0.625849 GTGGGTGGATGATTCAGGGT 59.374 55.000 0.00 0.00 0.00 4.34
936 3577 0.106519 GGTGGGTGGATGATTCAGGG 60.107 60.000 0.00 0.00 0.00 4.45
937 3578 0.625316 TGGTGGGTGGATGATTCAGG 59.375 55.000 0.00 0.00 0.00 3.86
938 3579 1.283029 AGTGGTGGGTGGATGATTCAG 59.717 52.381 0.00 0.00 0.00 3.02
939 3580 1.371467 AGTGGTGGGTGGATGATTCA 58.629 50.000 0.00 0.00 0.00 2.57
940 3581 2.369394 GAAGTGGTGGGTGGATGATTC 58.631 52.381 0.00 0.00 0.00 2.52
941 3582 1.005924 GGAAGTGGTGGGTGGATGATT 59.994 52.381 0.00 0.00 0.00 2.57
942 3583 0.625849 GGAAGTGGTGGGTGGATGAT 59.374 55.000 0.00 0.00 0.00 2.45
943 3584 0.770166 TGGAAGTGGTGGGTGGATGA 60.770 55.000 0.00 0.00 0.00 2.92
944 3585 0.609131 GTGGAAGTGGTGGGTGGATG 60.609 60.000 0.00 0.00 0.00 3.51
945 3586 0.772124 AGTGGAAGTGGTGGGTGGAT 60.772 55.000 0.00 0.00 0.00 3.41
946 3587 1.385347 AGTGGAAGTGGTGGGTGGA 60.385 57.895 0.00 0.00 0.00 4.02
947 3588 1.073199 GAGTGGAAGTGGTGGGTGG 59.927 63.158 0.00 0.00 0.00 4.61
948 3589 1.073199 GGAGTGGAAGTGGTGGGTG 59.927 63.158 0.00 0.00 0.00 4.61
949 3590 2.516888 CGGAGTGGAAGTGGTGGGT 61.517 63.158 0.00 0.00 0.00 4.51
1142 3785 3.314331 CGGGACACAGGAGGCTGT 61.314 66.667 0.00 0.00 38.21 4.40
1429 4072 1.105167 AGCAGCAAACAGAAGCAGCA 61.105 50.000 4.70 0.00 44.45 4.41
1447 4090 1.299620 GTGCAGTGCAGCCAAACAG 60.300 57.895 20.42 0.00 40.08 3.16
1450 4093 2.050934 TGTGTGCAGTGCAGCCAAA 61.051 52.632 20.42 6.24 40.08 3.28
1454 4097 4.318021 CGGTGTGTGCAGTGCAGC 62.318 66.667 20.42 15.06 40.08 5.25
1462 4105 0.673644 AGTGGAATAGCGGTGTGTGC 60.674 55.000 0.00 0.00 0.00 4.57
1471 4115 2.610727 GGCCGATCACTAGTGGAATAGC 60.611 54.545 22.48 17.36 0.00 2.97
1480 4124 2.565645 CCCCGAGGCCGATCACTAG 61.566 68.421 0.00 0.00 38.22 2.57
1481 4125 2.520982 CCCCGAGGCCGATCACTA 60.521 66.667 0.00 0.00 38.22 2.74
1488 4132 3.622060 AATTGTGTCCCCGAGGCCG 62.622 63.158 0.00 0.00 0.00 6.13
1490 4134 1.303317 ACAATTGTGTCCCCGAGGC 60.303 57.895 11.07 0.00 29.49 4.70
1491 4135 2.555123 CACAATTGTGTCCCCGAGG 58.445 57.895 27.08 1.59 40.96 4.63
1501 4145 6.015180 AGCATTCTATCACCAAACACAATTGT 60.015 34.615 4.92 4.92 37.67 2.71
1502 4146 6.392354 AGCATTCTATCACCAAACACAATTG 58.608 36.000 3.24 3.24 0.00 2.32
1505 4149 5.069318 TGAGCATTCTATCACCAAACACAA 58.931 37.500 0.00 0.00 0.00 3.33
1532 4176 1.200716 TCGCTGAACCTTAATCGTCGT 59.799 47.619 0.00 0.00 0.00 4.34
1550 4194 2.807045 GAGCACTGGAGCACGTCG 60.807 66.667 0.00 0.00 36.85 5.12
1551 4195 0.671781 ATTGAGCACTGGAGCACGTC 60.672 55.000 0.00 0.00 36.85 4.34
1553 4197 0.167470 CAATTGAGCACTGGAGCACG 59.833 55.000 0.00 0.00 36.85 5.34
1557 4201 3.587797 AATTGCAATTGAGCACTGGAG 57.412 42.857 23.54 0.00 45.61 3.86
1592 4236 1.971167 TGCCACCGCACTTCCATTC 60.971 57.895 0.00 0.00 41.12 2.67
1614 4258 0.821517 ATACCAGCGTGTCATCCGAA 59.178 50.000 0.00 0.00 0.00 4.30
1666 4311 8.169977 AGAAACTGAAAGAATTAGCATGTGAA 57.830 30.769 0.00 0.00 37.43 3.18
1772 4417 0.608640 ACAGACATCCGGACTTCCAC 59.391 55.000 6.12 0.00 35.14 4.02
1841 4486 3.340814 AGAGGCACAAAGTCATGTAGG 57.659 47.619 0.00 0.00 30.84 3.18
1912 4666 2.785857 CAGATACCCCCAAAGGAAGGAT 59.214 50.000 0.00 0.00 38.24 3.24
1993 4747 3.463329 AGGACCATAAAGCCACACCATAT 59.537 43.478 0.00 0.00 0.00 1.78
2056 4810 3.390135 TCTCGTTGAGATGAACAACCAC 58.610 45.455 0.00 0.00 42.87 4.16
2164 4918 9.635520 AAAAGCATGAAGATTAATCAAGTGAAG 57.364 29.630 17.56 2.79 0.00 3.02
2175 4929 7.175104 AGGTTCTGGTAAAAGCATGAAGATTA 58.825 34.615 0.00 0.00 0.00 1.75
2177 4931 5.574188 AGGTTCTGGTAAAAGCATGAAGAT 58.426 37.500 0.00 0.00 0.00 2.40
2184 4938 6.322712 ACAAACATTAGGTTCTGGTAAAAGCA 59.677 34.615 0.00 0.00 39.29 3.91
2204 4958 5.729176 GCAGGGCAACAAAAACAATACAAAC 60.729 40.000 0.00 0.00 39.74 2.93
2208 4962 2.805671 GGCAGGGCAACAAAAACAATAC 59.194 45.455 0.00 0.00 39.74 1.89
2236 4990 7.760340 GGCCCAATGTAAACGTTTTCATAAATA 59.240 33.333 26.74 5.95 29.66 1.40
2558 5312 5.008331 GGTTTCTAAACGGAGGGATCTTTT 58.992 41.667 0.00 0.00 39.77 2.27
2662 5416 1.552792 TCACATGGCACGATCTAACCA 59.447 47.619 0.00 0.60 36.43 3.67
2671 5425 1.935873 CAGTATTCCTCACATGGCACG 59.064 52.381 0.00 0.00 0.00 5.34
2683 5437 9.057089 CAAGAGATTACCCATAAACAGTATTCC 57.943 37.037 0.00 0.00 0.00 3.01
2781 5535 1.033746 AACATGCAGCGGAATCAGGG 61.034 55.000 0.00 0.00 0.00 4.45
2955 5710 3.066291 TGTGCCATTTCGGATAAGTGT 57.934 42.857 0.00 0.00 36.56 3.55
3150 5911 5.957842 TGATGTATCTTGTGAAACCAACC 57.042 39.130 0.00 0.00 34.36 3.77
3453 6219 5.065859 GGTAGCACAAAAACTTGGCATTTTT 59.934 36.000 5.87 5.87 39.30 1.94
3517 6283 8.959548 CCAGCAGCATATATCCACATTTTAATA 58.040 33.333 0.00 0.00 0.00 0.98
3518 6284 7.093640 CCCAGCAGCATATATCCACATTTTAAT 60.094 37.037 0.00 0.00 0.00 1.40
3521 6287 4.525487 CCCAGCAGCATATATCCACATTTT 59.475 41.667 0.00 0.00 0.00 1.82
3522 6288 4.084287 CCCAGCAGCATATATCCACATTT 58.916 43.478 0.00 0.00 0.00 2.32
4228 7007 0.611618 ATGGCAGCAAATGTTCCGGA 60.612 50.000 0.00 0.00 0.00 5.14
4401 7180 8.176814 TCGTTTACTGTATATTTCGTCTTTGG 57.823 34.615 0.00 0.00 0.00 3.28
4417 7196 5.334105 CCCAGTGAAGTCAAATCGTTTACTG 60.334 44.000 0.00 0.00 34.40 2.74
4432 7211 2.290260 TGCCACAATACTCCCAGTGAAG 60.290 50.000 0.00 0.00 33.99 3.02
4455 7236 5.468540 TTTCGGTACTATCCCAGATGATG 57.531 43.478 0.00 0.00 0.00 3.07
4461 7242 4.141801 TGGACATTTTCGGTACTATCCCAG 60.142 45.833 0.00 0.00 0.00 4.45
4480 7261 2.801342 GCTCATCTCTCGGTTCATGGAC 60.801 54.545 0.00 0.00 0.00 4.02
4531 7312 5.065988 ACCGCATATTTCCACTACATTGAAC 59.934 40.000 0.00 0.00 0.00 3.18
4547 7328 6.238731 CCACAATAAGACAATTCACCGCATAT 60.239 38.462 0.00 0.00 0.00 1.78
4643 7424 6.207417 TCCTTGACTCCTGAAATTCACATTTC 59.793 38.462 0.00 1.42 46.08 2.17
4816 7622 5.181811 TCACCTTTTCACTAATCATGCAGTG 59.818 40.000 12.95 12.95 42.88 3.66
4909 7723 6.488006 AGCCTCGCATTATGAGTTTAAATGAT 59.512 34.615 0.00 0.00 33.38 2.45
4910 7724 5.822519 AGCCTCGCATTATGAGTTTAAATGA 59.177 36.000 0.00 0.00 33.38 2.57
4928 7742 3.632604 TCTGGATCTTTACAGTAGCCTCG 59.367 47.826 0.00 0.00 36.17 4.63
4948 7762 2.300152 TGTGAAGCCGACAGAGAATTCT 59.700 45.455 7.95 7.95 0.00 2.40
4949 7763 2.688507 TGTGAAGCCGACAGAGAATTC 58.311 47.619 0.00 0.00 0.00 2.17
4950 7764 2.839486 TGTGAAGCCGACAGAGAATT 57.161 45.000 0.00 0.00 0.00 2.17
4951 7765 2.839486 TTGTGAAGCCGACAGAGAAT 57.161 45.000 0.00 0.00 0.00 2.40
4952 7766 2.224281 ACATTGTGAAGCCGACAGAGAA 60.224 45.455 0.00 0.00 0.00 2.87
4953 7767 1.344438 ACATTGTGAAGCCGACAGAGA 59.656 47.619 0.00 0.00 0.00 3.10
4954 7768 1.800805 ACATTGTGAAGCCGACAGAG 58.199 50.000 0.00 0.00 0.00 3.35
4955 7769 2.254546 AACATTGTGAAGCCGACAGA 57.745 45.000 0.00 0.00 0.00 3.41
4956 7770 2.033299 ACAAACATTGTGAAGCCGACAG 59.967 45.455 0.00 0.00 43.48 3.51
4957 7771 2.020720 ACAAACATTGTGAAGCCGACA 58.979 42.857 0.00 0.00 43.48 4.35
4958 7772 2.774439 ACAAACATTGTGAAGCCGAC 57.226 45.000 0.00 0.00 43.48 4.79
4959 7773 2.685388 TGAACAAACATTGTGAAGCCGA 59.315 40.909 0.00 0.00 44.59 5.54
4960 7774 2.788786 GTGAACAAACATTGTGAAGCCG 59.211 45.455 0.00 0.00 44.59 5.52
4961 7775 4.045636 AGTGAACAAACATTGTGAAGCC 57.954 40.909 0.00 0.00 44.59 4.35
4962 7776 6.291796 GCTAAAGTGAACAAACATTGTGAAGC 60.292 38.462 0.00 0.00 44.59 3.86
4963 7777 6.974622 AGCTAAAGTGAACAAACATTGTGAAG 59.025 34.615 0.00 0.00 44.59 3.02
4964 7778 6.862209 AGCTAAAGTGAACAAACATTGTGAA 58.138 32.000 0.00 0.00 44.59 3.18
4965 7779 6.449635 AGCTAAAGTGAACAAACATTGTGA 57.550 33.333 0.00 0.00 44.59 3.58
4966 7780 6.019640 CCAAGCTAAAGTGAACAAACATTGTG 60.020 38.462 0.00 0.00 44.59 3.33
4968 7782 5.463061 CCCAAGCTAAAGTGAACAAACATTG 59.537 40.000 0.00 0.00 0.00 2.82
4969 7783 5.128663 ACCCAAGCTAAAGTGAACAAACATT 59.871 36.000 0.00 0.00 0.00 2.71
4970 7784 4.649218 ACCCAAGCTAAAGTGAACAAACAT 59.351 37.500 0.00 0.00 0.00 2.71
4971 7785 4.020543 ACCCAAGCTAAAGTGAACAAACA 58.979 39.130 0.00 0.00 0.00 2.83
4972 7786 4.607955 GACCCAAGCTAAAGTGAACAAAC 58.392 43.478 0.00 0.00 0.00 2.93
4973 7787 3.314080 CGACCCAAGCTAAAGTGAACAAA 59.686 43.478 0.00 0.00 0.00 2.83
4974 7788 2.875933 CGACCCAAGCTAAAGTGAACAA 59.124 45.455 0.00 0.00 0.00 2.83
4975 7789 2.158871 ACGACCCAAGCTAAAGTGAACA 60.159 45.455 0.00 0.00 0.00 3.18
4991 7805 4.099824 ACAAATTTCACGAAACAACGACC 58.900 39.130 0.00 0.00 37.03 4.79
4993 7807 7.164498 GTCAATACAAATTTCACGAAACAACGA 59.836 33.333 0.00 0.00 37.03 3.85
4996 7810 6.415280 CGGTCAATACAAATTTCACGAAACAA 59.585 34.615 0.00 0.00 32.51 2.83
4997 7811 5.910166 CGGTCAATACAAATTTCACGAAACA 59.090 36.000 0.00 0.00 32.51 2.83
5003 7817 6.148811 TCTCCTTCGGTCAATACAAATTTCAC 59.851 38.462 0.00 0.00 0.00 3.18
5007 7821 6.238648 AGTTCTCCTTCGGTCAATACAAATT 58.761 36.000 0.00 0.00 0.00 1.82
5009 7823 5.223449 AGTTCTCCTTCGGTCAATACAAA 57.777 39.130 0.00 0.00 0.00 2.83
5010 7824 4.884668 AGTTCTCCTTCGGTCAATACAA 57.115 40.909 0.00 0.00 0.00 2.41
5062 7878 7.887996 ACATTTTTCGCACATCAAACATTAT 57.112 28.000 0.00 0.00 0.00 1.28
5063 7879 7.436376 TCAACATTTTTCGCACATCAAACATTA 59.564 29.630 0.00 0.00 0.00 1.90
5064 7880 6.257411 TCAACATTTTTCGCACATCAAACATT 59.743 30.769 0.00 0.00 0.00 2.71
5065 7881 5.752472 TCAACATTTTTCGCACATCAAACAT 59.248 32.000 0.00 0.00 0.00 2.71
5066 7882 5.105063 TCAACATTTTTCGCACATCAAACA 58.895 33.333 0.00 0.00 0.00 2.83
5067 7883 5.633996 TCAACATTTTTCGCACATCAAAC 57.366 34.783 0.00 0.00 0.00 2.93
5068 7884 6.292757 CCATTCAACATTTTTCGCACATCAAA 60.293 34.615 0.00 0.00 0.00 2.69
5069 7885 5.177142 CCATTCAACATTTTTCGCACATCAA 59.823 36.000 0.00 0.00 0.00 2.57
5070 7886 4.685165 CCATTCAACATTTTTCGCACATCA 59.315 37.500 0.00 0.00 0.00 3.07
5071 7887 4.685628 ACCATTCAACATTTTTCGCACATC 59.314 37.500 0.00 0.00 0.00 3.06
5085 7901 6.494893 TGCTGATAGTTACAACCATTCAAC 57.505 37.500 0.00 0.00 0.00 3.18
5089 7905 8.574251 TTTGTATGCTGATAGTTACAACCATT 57.426 30.769 0.00 0.00 35.06 3.16
5112 7934 5.455326 GCACATCAGTATATGAGGGGACTTT 60.455 44.000 0.00 0.00 46.22 2.66
5113 7935 4.040952 GCACATCAGTATATGAGGGGACTT 59.959 45.833 0.00 0.00 46.22 3.01
5124 7946 6.036577 TCTGTTTCACAGCACATCAGTATA 57.963 37.500 0.00 0.00 45.54 1.47
5128 7950 2.483106 CCTCTGTTTCACAGCACATCAG 59.517 50.000 0.00 0.00 45.54 2.90
5162 7986 1.197036 GAGCTCCAAGTGGCGTTTTAC 59.803 52.381 0.87 0.00 34.44 2.01
5194 8018 0.967380 CCCTAAGCCCTGCCTGTTTG 60.967 60.000 0.00 0.00 0.00 2.93
5200 8024 2.137177 TTGACACCCTAAGCCCTGCC 62.137 60.000 0.00 0.00 0.00 4.85
5201 8025 0.251165 TTTGACACCCTAAGCCCTGC 60.251 55.000 0.00 0.00 0.00 4.85
5202 8026 2.286365 TTTTGACACCCTAAGCCCTG 57.714 50.000 0.00 0.00 0.00 4.45
5203 8027 2.807676 CATTTTGACACCCTAAGCCCT 58.192 47.619 0.00 0.00 0.00 5.19
5204 8028 1.204704 GCATTTTGACACCCTAAGCCC 59.795 52.381 0.00 0.00 0.00 5.19
5282 8107 7.836486 CTTTCAGCAAGAATCAGTATGACCAAC 60.836 40.741 0.00 0.00 41.29 3.77
5283 8108 6.149973 CTTTCAGCAAGAATCAGTATGACCAA 59.850 38.462 0.00 0.00 41.29 3.67
5301 8126 3.616821 GGTTTGGTGTTTGTTCTTTCAGC 59.383 43.478 0.00 0.00 0.00 4.26
5327 8155 0.323360 GCCACCCCAGCAGTTGATTA 60.323 55.000 0.00 0.00 0.00 1.75
5341 8169 2.358247 ACGATGTTGGACGCCACC 60.358 61.111 0.00 0.00 30.78 4.61
5342 8170 2.677003 CCACGATGTTGGACGCCAC 61.677 63.158 0.00 0.00 39.24 5.01
5343 8171 2.358125 CCACGATGTTGGACGCCA 60.358 61.111 0.00 0.00 39.24 5.69
5344 8172 3.799755 GCCACGATGTTGGACGCC 61.800 66.667 0.00 0.00 39.24 5.68
5345 8173 4.147322 CGCCACGATGTTGGACGC 62.147 66.667 0.00 0.00 39.24 5.19
5346 8174 4.147322 GCGCCACGATGTTGGACG 62.147 66.667 0.00 0.00 39.24 4.79
5347 8175 3.799755 GGCGCCACGATGTTGGAC 61.800 66.667 24.80 0.00 39.24 4.02
5348 8176 3.834013 TTGGCGCCACGATGTTGGA 62.834 57.895 32.95 8.41 39.24 3.53
5349 8177 3.326889 CTTGGCGCCACGATGTTGG 62.327 63.158 32.95 7.98 39.98 3.77
5350 8178 2.176546 CTTGGCGCCACGATGTTG 59.823 61.111 32.95 9.50 0.00 3.33
5351 8179 2.281484 ACTTGGCGCCACGATGTT 60.281 55.556 36.53 13.84 0.00 2.71
5352 8180 2.742372 GACTTGGCGCCACGATGT 60.742 61.111 36.53 27.08 0.00 3.06
5353 8181 2.040213 GATGACTTGGCGCCACGATG 62.040 60.000 36.53 24.30 0.00 3.84
5354 8182 1.815421 GATGACTTGGCGCCACGAT 60.815 57.895 36.53 21.79 0.00 3.73
5355 8183 2.434185 GATGACTTGGCGCCACGA 60.434 61.111 36.53 20.20 0.00 4.35
5356 8184 3.499737 GGATGACTTGGCGCCACG 61.500 66.667 32.95 31.02 0.00 4.94
5357 8185 1.718757 GATGGATGACTTGGCGCCAC 61.719 60.000 32.95 19.47 0.00 5.01
5358 8186 1.451927 GATGGATGACTTGGCGCCA 60.452 57.895 29.03 29.03 0.00 5.69
5359 8187 1.031571 TTGATGGATGACTTGGCGCC 61.032 55.000 22.73 22.73 0.00 6.53
5360 8188 0.379669 CTTGATGGATGACTTGGCGC 59.620 55.000 0.00 0.00 0.00 6.53
5361 8189 1.019673 CCTTGATGGATGACTTGGCG 58.980 55.000 0.00 0.00 38.35 5.69
5362 8190 1.396653 CCCTTGATGGATGACTTGGC 58.603 55.000 0.00 0.00 38.35 4.52
5363 8191 2.025863 GCCCCTTGATGGATGACTTGG 61.026 57.143 0.00 0.00 38.35 3.61
5364 8192 1.064166 AGCCCCTTGATGGATGACTTG 60.064 52.381 0.00 0.00 38.35 3.16
5365 8193 1.064166 CAGCCCCTTGATGGATGACTT 60.064 52.381 0.00 0.00 41.83 3.01
5366 8194 0.549950 CAGCCCCTTGATGGATGACT 59.450 55.000 0.00 0.00 41.83 3.41
5367 8195 0.548031 TCAGCCCCTTGATGGATGAC 59.452 55.000 0.00 0.00 43.00 3.06
5368 8196 1.064463 GTTCAGCCCCTTGATGGATGA 60.064 52.381 0.00 0.00 45.96 2.92
5369 8197 1.396653 GTTCAGCCCCTTGATGGATG 58.603 55.000 0.00 0.00 40.64 3.51
5370 8198 0.259938 GGTTCAGCCCCTTGATGGAT 59.740 55.000 0.00 0.00 38.35 3.41
5371 8199 1.691219 GGTTCAGCCCCTTGATGGA 59.309 57.895 0.00 0.00 38.35 3.41
5372 8200 1.750399 CGGTTCAGCCCCTTGATGG 60.750 63.158 0.00 0.00 0.00 3.51
5373 8201 1.002134 ACGGTTCAGCCCCTTGATG 60.002 57.895 0.00 0.00 0.00 3.07
5374 8202 1.299976 GACGGTTCAGCCCCTTGAT 59.700 57.895 0.00 0.00 0.00 2.57
5375 8203 2.747686 GACGGTTCAGCCCCTTGA 59.252 61.111 0.00 0.00 0.00 3.02
5376 8204 2.359975 GGACGGTTCAGCCCCTTG 60.360 66.667 0.00 0.00 0.00 3.61
5377 8205 2.852075 TGGACGGTTCAGCCCCTT 60.852 61.111 0.00 0.00 0.00 3.95
5378 8206 3.322466 CTGGACGGTTCAGCCCCT 61.322 66.667 2.95 0.00 0.00 4.79
5379 8207 2.670148 ATCTGGACGGTTCAGCCCC 61.670 63.158 11.74 0.00 32.63 5.80
5380 8208 1.450312 CATCTGGACGGTTCAGCCC 60.450 63.158 11.74 0.00 32.63 5.19
5381 8209 4.208632 CATCTGGACGGTTCAGCC 57.791 61.111 11.74 0.00 32.63 4.85


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

AutoCloner maintained by Alex Coulton.