Multiple sequence alignment - TraesCS4A01G401500

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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 TraesCS4A01G401500 chr4A 100.000 3437 0 0 1 3437 675527381 675523945 0.000000e+00 6348.0
1 TraesCS4A01G401500 chr4A 88.927 1454 140 13 1001 2450 742586545 742585109 0.000000e+00 1773.0
2 TraesCS4A01G401500 chr4A 87.543 1469 154 15 1009 2471 697970057 697971502 0.000000e+00 1672.0
3 TraesCS4A01G401500 chr4A 95.046 545 22 4 1 542 672784219 672783677 0.000000e+00 852.0
4 TraesCS4A01G401500 chr4A 95.531 537 17 3 1 534 677784562 677784030 0.000000e+00 852.0
5 TraesCS4A01G401500 chr4A 94.679 545 22 4 1 542 672645300 672644760 0.000000e+00 839.0
6 TraesCS4A01G401500 chr4A 94.495 545 23 4 1 542 672666457 672665917 0.000000e+00 833.0
7 TraesCS4A01G401500 chr4A 75.275 728 132 34 2727 3437 485015599 485016295 1.550000e-78 303.0
8 TraesCS4A01G401500 chr4A 80.526 190 21 6 2139 2328 742387066 742387239 7.740000e-27 132.0
9 TraesCS4A01G401500 chr7A 94.493 1616 47 12 940 2543 63060504 63058919 0.000000e+00 2453.0
10 TraesCS4A01G401500 chr7A 87.038 1489 156 18 1001 2474 1690790 1692256 0.000000e+00 1646.0
11 TraesCS4A01G401500 chr7A 86.869 198 15 7 594 789 63061066 63060878 9.660000e-51 211.0
12 TraesCS4A01G401500 chr7A 93.651 63 4 0 534 596 140983096 140983158 1.020000e-15 95.3
13 TraesCS4A01G401500 chr7A 93.651 63 4 0 534 596 141260266 141260328 1.020000e-15 95.3
14 TraesCS4A01G401500 chr7A 93.651 63 4 0 534 596 142129666 142129728 1.020000e-15 95.3
15 TraesCS4A01G401500 chr7A 90.411 73 5 2 533 604 160111593 160111664 1.020000e-15 95.3
16 TraesCS4A01G401500 chr7D 88.404 1466 144 12 1009 2470 30761251 30759808 0.000000e+00 1742.0
17 TraesCS4A01G401500 chr7D 87.818 1453 136 20 1009 2450 1999992 1998570 0.000000e+00 1664.0
18 TraesCS4A01G401500 chr7D 79.734 1426 235 39 1022 2411 625615354 625616761 0.000000e+00 983.0
19 TraesCS4A01G401500 chr7D 79.530 723 112 18 1695 2403 1996744 1996044 1.850000e-132 483.0
20 TraesCS4A01G401500 chr4B 94.256 766 39 3 2672 3437 89572887 89573647 0.000000e+00 1166.0
21 TraesCS4A01G401500 chr4B 90.445 764 58 8 2672 3434 103324840 103325589 0.000000e+00 992.0
22 TraesCS4A01G401500 chr4B 89.822 786 47 7 2672 3437 381156722 381155950 0.000000e+00 977.0
23 TraesCS4A01G401500 chr4B 95.677 532 17 4 1 531 402981002 402980476 0.000000e+00 850.0
24 TraesCS4A01G401500 chr7B 78.457 1439 247 40 1022 2417 682374163 682372745 0.000000e+00 881.0
25 TraesCS4A01G401500 chr7B 95.865 532 17 2 1 531 43649506 43650033 0.000000e+00 856.0
26 TraesCS4A01G401500 chr7B 96.190 525 13 4 10 531 113076692 113076172 0.000000e+00 852.0
27 TraesCS4A01G401500 chr7B 95.349 129 4 2 2542 2669 616773382 616773509 1.620000e-48 204.0
28 TraesCS4A01G401500 chr7B 90.323 93 6 3 2532 2621 60477560 60477468 6.030000e-23 119.0
29 TraesCS4A01G401500 chr6B 95.370 540 20 2 1 539 703395101 703395636 0.000000e+00 854.0
30 TraesCS4A01G401500 chr2B 95.677 532 15 4 1 531 767958086 767958610 0.000000e+00 848.0
31 TraesCS4A01G401500 chr2B 94.737 76 4 0 2546 2621 749224468 749224393 6.030000e-23 119.0
32 TraesCS4A01G401500 chr2A 83.533 668 82 15 2672 3335 622196432 622195789 1.770000e-167 599.0
33 TraesCS4A01G401500 chr6A 94.737 76 4 0 2546 2621 546476245 546476170 6.030000e-23 119.0
34 TraesCS4A01G401500 chr5B 94.737 76 4 0 2546 2621 350395675 350395600 6.030000e-23 119.0
35 TraesCS4A01G401500 chr1B 93.939 66 4 0 533 598 1210157 1210222 2.180000e-17 100.0
36 TraesCS4A01G401500 chr5D 93.846 65 4 0 533 597 480470500 480470436 7.850000e-17 99.0
37 TraesCS4A01G401500 chr5D 89.041 73 8 0 536 608 138565615 138565543 1.310000e-14 91.6
38 TraesCS4A01G401500 chr2D 90.411 73 7 0 531 603 493075339 493075411 2.820000e-16 97.1
39 TraesCS4A01G401500 chr2D 91.176 68 6 0 533 600 579092403 579092470 3.650000e-15 93.5
40 TraesCS4A01G401500 chr4D 94.595 37 0 2 3263 3298 463702559 463702524 4.790000e-04 56.5


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 TraesCS4A01G401500 chr4A 675523945 675527381 3436 True 6348.0 6348 100.000 1 3437 1 chr4A.!!$R4 3436
1 TraesCS4A01G401500 chr4A 742585109 742586545 1436 True 1773.0 1773 88.927 1001 2450 1 chr4A.!!$R6 1449
2 TraesCS4A01G401500 chr4A 697970057 697971502 1445 False 1672.0 1672 87.543 1009 2471 1 chr4A.!!$F2 1462
3 TraesCS4A01G401500 chr4A 672783677 672784219 542 True 852.0 852 95.046 1 542 1 chr4A.!!$R3 541
4 TraesCS4A01G401500 chr4A 677784030 677784562 532 True 852.0 852 95.531 1 534 1 chr4A.!!$R5 533
5 TraesCS4A01G401500 chr4A 672644760 672645300 540 True 839.0 839 94.679 1 542 1 chr4A.!!$R1 541
6 TraesCS4A01G401500 chr4A 672665917 672666457 540 True 833.0 833 94.495 1 542 1 chr4A.!!$R2 541
7 TraesCS4A01G401500 chr4A 485015599 485016295 696 False 303.0 303 75.275 2727 3437 1 chr4A.!!$F1 710
8 TraesCS4A01G401500 chr7A 1690790 1692256 1466 False 1646.0 1646 87.038 1001 2474 1 chr7A.!!$F1 1473
9 TraesCS4A01G401500 chr7A 63058919 63061066 2147 True 1332.0 2453 90.681 594 2543 2 chr7A.!!$R1 1949
10 TraesCS4A01G401500 chr7D 30759808 30761251 1443 True 1742.0 1742 88.404 1009 2470 1 chr7D.!!$R1 1461
11 TraesCS4A01G401500 chr7D 1996044 1999992 3948 True 1073.5 1664 83.674 1009 2450 2 chr7D.!!$R2 1441
12 TraesCS4A01G401500 chr7D 625615354 625616761 1407 False 983.0 983 79.734 1022 2411 1 chr7D.!!$F1 1389
13 TraesCS4A01G401500 chr4B 89572887 89573647 760 False 1166.0 1166 94.256 2672 3437 1 chr4B.!!$F1 765
14 TraesCS4A01G401500 chr4B 103324840 103325589 749 False 992.0 992 90.445 2672 3434 1 chr4B.!!$F2 762
15 TraesCS4A01G401500 chr4B 381155950 381156722 772 True 977.0 977 89.822 2672 3437 1 chr4B.!!$R1 765
16 TraesCS4A01G401500 chr4B 402980476 402981002 526 True 850.0 850 95.677 1 531 1 chr4B.!!$R2 530
17 TraesCS4A01G401500 chr7B 682372745 682374163 1418 True 881.0 881 78.457 1022 2417 1 chr7B.!!$R3 1395
18 TraesCS4A01G401500 chr7B 43649506 43650033 527 False 856.0 856 95.865 1 531 1 chr7B.!!$F1 530
19 TraesCS4A01G401500 chr7B 113076172 113076692 520 True 852.0 852 96.190 10 531 1 chr7B.!!$R2 521
20 TraesCS4A01G401500 chr6B 703395101 703395636 535 False 854.0 854 95.370 1 539 1 chr6B.!!$F1 538
21 TraesCS4A01G401500 chr2B 767958086 767958610 524 False 848.0 848 95.677 1 531 1 chr2B.!!$F1 530
22 TraesCS4A01G401500 chr2A 622195789 622196432 643 True 599.0 599 83.533 2672 3335 1 chr2A.!!$R1 663

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
591 599 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2442 2790 0.603065 CAGAGTGGTGACATGGACGA 59.397 55.0 0.0 0.0 46.14 4.2 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 23 2.355108 GCCAGCAGAATCAGTAGGTTGA 60.355 50.000 0.00 0.00 0.00 3.18
35 36 2.710902 GGTTGAATGGGAAGGCGGC 61.711 63.158 0.00 0.00 0.00 6.53
37 38 0.393808 GTTGAATGGGAAGGCGGCTA 60.394 55.000 13.71 0.00 0.00 3.93
315 317 3.745975 TCCATATTGTTATGCACTAGCGC 59.254 43.478 0.00 0.00 46.23 5.92
423 429 0.634465 GAGGAAGAGGGAGGGAGAGT 59.366 60.000 0.00 0.00 0.00 3.24
424 430 0.338120 AGGAAGAGGGAGGGAGAGTG 59.662 60.000 0.00 0.00 0.00 3.51
425 431 0.041982 GGAAGAGGGAGGGAGAGTGT 59.958 60.000 0.00 0.00 0.00 3.55
531 539 1.665161 CGCACGGACGTTCTTCTAGTT 60.665 52.381 0.00 0.00 0.00 2.24
535 543 4.614535 GCACGGACGTTCTTCTAGTTTAGA 60.615 45.833 0.00 0.00 0.00 2.10
539 547 6.428159 ACGGACGTTCTTCTAGTTTAGAACTA 59.572 38.462 21.40 1.11 45.05 2.24
540 548 7.041098 ACGGACGTTCTTCTAGTTTAGAACTAA 60.041 37.037 21.40 0.00 45.05 2.24
541 549 7.805071 CGGACGTTCTTCTAGTTTAGAACTAAA 59.195 37.037 21.40 3.31 45.05 1.85
542 550 9.468532 GGACGTTCTTCTAGTTTAGAACTAAAA 57.531 33.333 21.40 0.00 45.05 1.52
585 593 2.373540 TGGACAAGTATTTCCGGACG 57.626 50.000 1.83 0.00 34.24 4.79
586 594 1.066716 TGGACAAGTATTTCCGGACGG 60.067 52.381 1.83 3.96 34.24 4.79
587 595 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
588 596 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
589 597 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
590 598 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
591 599 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
592 600 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
635 643 3.152341 CAGGATGAATCTAATGGTGCCC 58.848 50.000 0.00 0.00 39.69 5.36
743 752 9.503427 CTTTATATTTTGAAACGGAGGATTCAC 57.497 33.333 0.00 0.00 37.23 3.18
744 753 8.801882 TTATATTTTGAAACGGAGGATTCACT 57.198 30.769 0.00 0.00 37.23 3.41
745 754 5.629079 ATTTTGAAACGGAGGATTCACTC 57.371 39.130 0.00 0.00 37.23 3.51
789 798 9.520204 TGATTTGCTAAAATAGAATTGCTAAGC 57.480 29.630 0.00 0.00 36.10 3.09
790 799 9.520204 GATTTGCTAAAATAGAATTGCTAAGCA 57.480 29.630 0.00 0.00 37.41 3.91
813 1088 4.965119 TGCGCGTATCTGTAGATATCAT 57.035 40.909 8.43 0.00 39.03 2.45
817 1092 4.497251 CGCGTATCTGTAGATATCATGTGC 59.503 45.833 5.32 0.00 39.03 4.57
828 1103 9.194972 TGTAGATATCATGTGCCCAAATTAAAA 57.805 29.630 5.32 0.00 0.00 1.52
833 1108 9.902684 ATATCATGTGCCCAAATTAAAAATGAA 57.097 25.926 0.00 0.00 0.00 2.57
836 1111 9.075678 TCATGTGCCCAAATTAAAAATGAAATT 57.924 25.926 0.00 0.00 38.98 1.82
897 1172 3.639094 CCACCAACCAACCAAATCAGTAA 59.361 43.478 0.00 0.00 0.00 2.24
899 1174 5.229423 CACCAACCAACCAAATCAGTAATG 58.771 41.667 0.00 0.00 0.00 1.90
900 1175 4.898861 ACCAACCAACCAAATCAGTAATGT 59.101 37.500 0.00 0.00 0.00 2.71
901 1176 5.365314 ACCAACCAACCAAATCAGTAATGTT 59.635 36.000 0.00 0.00 0.00 2.71
902 1177 6.551601 ACCAACCAACCAAATCAGTAATGTTA 59.448 34.615 0.00 0.00 0.00 2.41
903 1178 7.070074 ACCAACCAACCAAATCAGTAATGTTAA 59.930 33.333 0.00 0.00 0.00 2.01
904 1179 8.093927 CCAACCAACCAAATCAGTAATGTTAAT 58.906 33.333 0.00 0.00 0.00 1.40
905 1180 9.487790 CAACCAACCAAATCAGTAATGTTAATT 57.512 29.630 0.00 0.00 0.00 1.40
908 1183 9.301153 CCAACCAAATCAGTAATGTTAATTAGC 57.699 33.333 0.00 0.00 0.00 3.09
909 1184 9.853555 CAACCAAATCAGTAATGTTAATTAGCA 57.146 29.630 4.36 4.36 0.00 3.49
911 1186 9.855021 ACCAAATCAGTAATGTTAATTAGCAAC 57.145 29.630 6.08 1.47 0.00 4.17
912 1187 9.301153 CCAAATCAGTAATGTTAATTAGCAACC 57.699 33.333 6.08 0.00 0.00 3.77
913 1188 9.301153 CAAATCAGTAATGTTAATTAGCAACCC 57.699 33.333 6.08 0.00 0.00 4.11
914 1189 7.582667 ATCAGTAATGTTAATTAGCAACCCC 57.417 36.000 6.08 0.00 0.00 4.95
915 1190 6.727394 TCAGTAATGTTAATTAGCAACCCCT 58.273 36.000 6.08 0.00 0.00 4.79
916 1191 7.863722 TCAGTAATGTTAATTAGCAACCCCTA 58.136 34.615 6.08 0.00 0.00 3.53
917 1192 7.771826 TCAGTAATGTTAATTAGCAACCCCTAC 59.228 37.037 6.08 4.20 0.00 3.18
918 1193 7.554835 CAGTAATGTTAATTAGCAACCCCTACA 59.445 37.037 6.08 0.00 0.00 2.74
919 1194 8.110908 AGTAATGTTAATTAGCAACCCCTACAA 58.889 33.333 6.08 0.00 0.00 2.41
920 1195 7.784470 AATGTTAATTAGCAACCCCTACAAA 57.216 32.000 6.08 0.00 0.00 2.83
921 1196 7.971368 ATGTTAATTAGCAACCCCTACAAAT 57.029 32.000 6.08 0.00 0.00 2.32
922 1197 7.784470 TGTTAATTAGCAACCCCTACAAATT 57.216 32.000 0.00 0.00 0.00 1.82
923 1198 8.196378 TGTTAATTAGCAACCCCTACAAATTT 57.804 30.769 0.00 0.00 0.00 1.82
924 1199 8.308207 TGTTAATTAGCAACCCCTACAAATTTC 58.692 33.333 0.00 0.00 0.00 2.17
925 1200 8.528643 GTTAATTAGCAACCCCTACAAATTTCT 58.471 33.333 0.00 0.00 0.00 2.52
926 1201 5.975693 TTAGCAACCCCTACAAATTTCTG 57.024 39.130 0.00 0.00 0.00 3.02
927 1202 2.562738 AGCAACCCCTACAAATTTCTGC 59.437 45.455 0.00 0.00 0.00 4.26
928 1203 2.562738 GCAACCCCTACAAATTTCTGCT 59.437 45.455 0.00 0.00 0.00 4.24
929 1204 3.367395 GCAACCCCTACAAATTTCTGCTC 60.367 47.826 0.00 0.00 0.00 4.26
930 1205 3.087370 ACCCCTACAAATTTCTGCTCC 57.913 47.619 0.00 0.00 0.00 4.70
931 1206 2.378547 ACCCCTACAAATTTCTGCTCCA 59.621 45.455 0.00 0.00 0.00 3.86
932 1207 3.181423 ACCCCTACAAATTTCTGCTCCAA 60.181 43.478 0.00 0.00 0.00 3.53
933 1208 4.026052 CCCCTACAAATTTCTGCTCCAAT 58.974 43.478 0.00 0.00 0.00 3.16
934 1209 4.467438 CCCCTACAAATTTCTGCTCCAATT 59.533 41.667 0.00 0.00 0.00 2.32
935 1210 5.046376 CCCCTACAAATTTCTGCTCCAATTT 60.046 40.000 0.00 0.00 33.70 1.82
981 1256 5.629079 GCAACAAACCTGCTACTAATCTT 57.371 39.130 0.00 0.00 36.84 2.40
982 1257 6.013842 GCAACAAACCTGCTACTAATCTTT 57.986 37.500 0.00 0.00 36.84 2.52
983 1258 7.141100 GCAACAAACCTGCTACTAATCTTTA 57.859 36.000 0.00 0.00 36.84 1.85
984 1259 7.762382 GCAACAAACCTGCTACTAATCTTTAT 58.238 34.615 0.00 0.00 36.84 1.40
990 1265 5.670361 ACCTGCTACTAATCTTTATCCCCAA 59.330 40.000 0.00 0.00 0.00 4.12
999 1274 1.543802 CTTTATCCCCAAACAAGCGCA 59.456 47.619 11.47 0.00 0.00 6.09
1038 1316 4.617520 ATGGTGCGCGTGGTGTCA 62.618 61.111 8.43 0.00 0.00 3.58
1164 1466 1.984570 CAGACCCTCTTCCTCGGCA 60.985 63.158 0.00 0.00 0.00 5.69
1165 1467 1.002274 AGACCCTCTTCCTCGGCAT 59.998 57.895 0.00 0.00 0.00 4.40
1166 1468 1.045911 AGACCCTCTTCCTCGGCATC 61.046 60.000 0.00 0.00 0.00 3.91
1167 1469 2.034048 GACCCTCTTCCTCGGCATCC 62.034 65.000 0.00 0.00 0.00 3.51
1179 1481 4.554036 GCATCCGCCCTCTCCACC 62.554 72.222 0.00 0.00 0.00 4.61
1180 1482 4.227134 CATCCGCCCTCTCCACCG 62.227 72.222 0.00 0.00 0.00 4.94
1356 1664 4.409218 GAGGTCGTGCACGCCGTA 62.409 66.667 33.63 14.65 39.38 4.02
2177 2516 2.986306 GCTTCTTCGACCCGACCGA 61.986 63.158 0.00 0.00 34.89 4.69
2182 2521 3.557903 TTCGACCCGACCGAGACCT 62.558 63.158 0.00 0.00 37.35 3.85
2442 2790 4.006319 CGGAGAAGAAGCCTTGAATCTTT 58.994 43.478 0.00 0.00 33.73 2.52
2501 2861 4.569943 TCTCAGAAAAACTTCCGGATCTG 58.430 43.478 19.95 19.95 36.50 2.90
2510 2870 5.629079 AACTTCCGGATCTGTTCATTTTC 57.371 39.130 4.15 0.00 0.00 2.29
2518 2878 7.227314 TCCGGATCTGTTCATTTTCTATTCATG 59.773 37.037 0.00 0.00 0.00 3.07
2522 2882 6.855836 TCTGTTCATTTTCTATTCATGGCAC 58.144 36.000 0.00 0.00 0.00 5.01
2523 2883 6.660521 TCTGTTCATTTTCTATTCATGGCACT 59.339 34.615 0.00 0.00 0.00 4.40
2525 2885 7.988737 TGTTCATTTTCTATTCATGGCACTAG 58.011 34.615 0.00 0.00 0.00 2.57
2526 2886 6.624352 TCATTTTCTATTCATGGCACTAGC 57.376 37.500 0.00 0.00 41.10 3.42
2532 2892 0.677731 TTCATGGCACTAGCACCAGC 60.678 55.000 9.92 0.00 44.61 4.85
2535 2895 0.251297 ATGGCACTAGCACCAGCAAA 60.251 50.000 9.92 0.00 45.49 3.68
2536 2896 0.251297 TGGCACTAGCACCAGCAAAT 60.251 50.000 0.18 0.00 45.49 2.32
2538 2898 2.091541 GGCACTAGCACCAGCAAATAA 58.908 47.619 0.00 0.00 45.49 1.40
2539 2899 2.689983 GGCACTAGCACCAGCAAATAAT 59.310 45.455 0.00 0.00 45.49 1.28
2542 2902 5.163561 GGCACTAGCACCAGCAAATAATAAA 60.164 40.000 0.00 0.00 45.49 1.40
2543 2903 5.973565 GCACTAGCACCAGCAAATAATAAAG 59.026 40.000 0.00 0.00 45.49 1.85
2544 2904 6.183360 GCACTAGCACCAGCAAATAATAAAGA 60.183 38.462 0.00 0.00 45.49 2.52
2545 2905 7.412853 CACTAGCACCAGCAAATAATAAAGAG 58.587 38.462 0.00 0.00 45.49 2.85
2546 2906 7.280876 CACTAGCACCAGCAAATAATAAAGAGA 59.719 37.037 0.00 0.00 45.49 3.10
2547 2907 6.690194 AGCACCAGCAAATAATAAAGAGAG 57.310 37.500 0.00 0.00 45.49 3.20
2548 2908 6.183347 AGCACCAGCAAATAATAAAGAGAGT 58.817 36.000 0.00 0.00 45.49 3.24
2549 2909 6.094603 AGCACCAGCAAATAATAAAGAGAGTG 59.905 38.462 0.00 0.00 45.49 3.51
2550 2910 6.261118 CACCAGCAAATAATAAAGAGAGTGC 58.739 40.000 0.00 0.00 0.00 4.40
2551 2911 5.358160 ACCAGCAAATAATAAAGAGAGTGCC 59.642 40.000 0.00 0.00 0.00 5.01
2552 2912 5.591877 CCAGCAAATAATAAAGAGAGTGCCT 59.408 40.000 0.00 0.00 0.00 4.75
2553 2913 6.767902 CCAGCAAATAATAAAGAGAGTGCCTA 59.232 38.462 0.00 0.00 0.00 3.93
2554 2914 7.041508 CCAGCAAATAATAAAGAGAGTGCCTAG 60.042 40.741 0.00 0.00 0.00 3.02
2555 2915 7.712639 CAGCAAATAATAAAGAGAGTGCCTAGA 59.287 37.037 0.00 0.00 0.00 2.43
2556 2916 8.267894 AGCAAATAATAAAGAGAGTGCCTAGAA 58.732 33.333 0.00 0.00 0.00 2.10
2557 2917 8.338986 GCAAATAATAAAGAGAGTGCCTAGAAC 58.661 37.037 0.00 0.00 0.00 3.01
2558 2918 9.606631 CAAATAATAAAGAGAGTGCCTAGAACT 57.393 33.333 0.00 0.00 0.00 3.01
2559 2919 9.825109 AAATAATAAAGAGAGTGCCTAGAACTC 57.175 33.333 14.46 14.46 43.66 3.01
2560 2920 6.859112 AATAAAGAGAGTGCCTAGAACTCA 57.141 37.500 20.90 6.63 45.38 3.41
2561 2921 7.430760 AATAAAGAGAGTGCCTAGAACTCAT 57.569 36.000 20.90 10.80 45.38 2.90
2562 2922 4.734398 AAGAGAGTGCCTAGAACTCATG 57.266 45.455 20.90 0.00 45.38 3.07
2563 2923 3.707316 AGAGAGTGCCTAGAACTCATGT 58.293 45.455 20.90 6.82 45.38 3.21
2564 2924 4.861196 AGAGAGTGCCTAGAACTCATGTA 58.139 43.478 20.90 0.00 45.38 2.29
2565 2925 4.887071 AGAGAGTGCCTAGAACTCATGTAG 59.113 45.833 20.90 0.00 45.38 2.74
2566 2926 3.383185 AGAGTGCCTAGAACTCATGTAGC 59.617 47.826 20.90 1.84 45.38 3.58
2567 2927 3.370104 AGTGCCTAGAACTCATGTAGCT 58.630 45.455 0.00 0.00 0.00 3.32
2568 2928 3.131933 AGTGCCTAGAACTCATGTAGCTG 59.868 47.826 0.00 0.00 0.00 4.24
2569 2929 3.131223 GTGCCTAGAACTCATGTAGCTGA 59.869 47.826 0.00 0.00 0.00 4.26
2570 2930 3.382865 TGCCTAGAACTCATGTAGCTGAG 59.617 47.826 0.00 0.00 46.59 3.35
2583 2943 9.579768 CTCATGTAGCTGAGTTATAATATGGTC 57.420 37.037 0.00 0.00 38.27 4.02
2584 2944 9.314133 TCATGTAGCTGAGTTATAATATGGTCT 57.686 33.333 0.00 0.00 0.00 3.85
2585 2945 9.579768 CATGTAGCTGAGTTATAATATGGTCTC 57.420 37.037 0.00 0.00 0.00 3.36
2586 2946 8.706322 TGTAGCTGAGTTATAATATGGTCTCA 57.294 34.615 0.00 0.00 0.00 3.27
2587 2947 9.314133 TGTAGCTGAGTTATAATATGGTCTCAT 57.686 33.333 0.00 0.00 37.40 2.90
2590 2950 8.874156 AGCTGAGTTATAATATGGTCTCATTCA 58.126 33.333 2.69 0.00 34.96 2.57
2591 2951 8.930760 GCTGAGTTATAATATGGTCTCATTCAC 58.069 37.037 2.69 0.00 34.96 3.18
2592 2952 9.429359 CTGAGTTATAATATGGTCTCATTCACC 57.571 37.037 2.69 0.00 34.96 4.02
2593 2953 9.159254 TGAGTTATAATATGGTCTCATTCACCT 57.841 33.333 0.00 0.00 34.66 4.00
2594 2954 9.429359 GAGTTATAATATGGTCTCATTCACCTG 57.571 37.037 0.00 0.00 34.66 4.00
2595 2955 9.159254 AGTTATAATATGGTCTCATTCACCTGA 57.841 33.333 0.00 0.00 34.66 3.86
2596 2956 9.950496 GTTATAATATGGTCTCATTCACCTGAT 57.050 33.333 0.00 0.00 34.66 2.90
2597 2957 9.948964 TTATAATATGGTCTCATTCACCTGATG 57.051 33.333 0.00 0.00 34.66 3.07
2598 2958 5.901413 ATATGGTCTCATTCACCTGATGT 57.099 39.130 0.00 0.00 34.66 3.06
2599 2959 7.379059 AATATGGTCTCATTCACCTGATGTA 57.621 36.000 0.00 0.00 34.66 2.29
2600 2960 5.901413 ATGGTCTCATTCACCTGATGTAT 57.099 39.130 0.00 0.00 34.66 2.29
2601 2961 5.027293 TGGTCTCATTCACCTGATGTATG 57.973 43.478 0.00 0.00 37.42 2.39
2602 2962 3.812053 GGTCTCATTCACCTGATGTATGC 59.188 47.826 0.00 0.00 36.34 3.14
2603 2963 4.444022 GGTCTCATTCACCTGATGTATGCT 60.444 45.833 0.00 0.00 36.34 3.79
2604 2964 4.510711 GTCTCATTCACCTGATGTATGCTG 59.489 45.833 0.00 0.00 36.34 4.41
2605 2965 4.406649 TCTCATTCACCTGATGTATGCTGA 59.593 41.667 0.00 0.00 36.34 4.26
2606 2966 5.071384 TCTCATTCACCTGATGTATGCTGAT 59.929 40.000 0.00 0.00 36.34 2.90
2607 2967 5.061179 TCATTCACCTGATGTATGCTGATG 58.939 41.667 0.00 0.00 36.34 3.07
2608 2968 4.492494 TTCACCTGATGTATGCTGATGT 57.508 40.909 0.00 0.00 0.00 3.06
2609 2969 4.063998 TCACCTGATGTATGCTGATGTC 57.936 45.455 0.00 0.00 0.00 3.06
2610 2970 3.451902 TCACCTGATGTATGCTGATGTCA 59.548 43.478 0.00 0.00 0.00 3.58
2611 2971 3.558829 CACCTGATGTATGCTGATGTCAC 59.441 47.826 0.00 0.00 0.00 3.67
2612 2972 3.198417 ACCTGATGTATGCTGATGTCACA 59.802 43.478 0.00 0.00 0.00 3.58
2613 2973 4.141551 ACCTGATGTATGCTGATGTCACAT 60.142 41.667 0.00 0.00 32.70 3.21
2614 2974 4.213482 CCTGATGTATGCTGATGTCACATG 59.787 45.833 0.00 0.00 30.25 3.21
2615 2975 5.026038 TGATGTATGCTGATGTCACATGA 57.974 39.130 0.00 0.00 30.25 3.07
2616 2976 5.617252 TGATGTATGCTGATGTCACATGAT 58.383 37.500 0.00 0.00 30.25 2.45
2617 2977 6.761312 TGATGTATGCTGATGTCACATGATA 58.239 36.000 0.00 0.00 30.25 2.15
2618 2978 6.872020 TGATGTATGCTGATGTCACATGATAG 59.128 38.462 0.00 0.00 30.25 2.08
2619 2979 6.165700 TGTATGCTGATGTCACATGATAGT 57.834 37.500 0.00 0.00 0.00 2.12
2620 2980 6.585416 TGTATGCTGATGTCACATGATAGTT 58.415 36.000 0.00 0.00 0.00 2.24
2621 2981 7.049754 TGTATGCTGATGTCACATGATAGTTT 58.950 34.615 0.00 0.00 0.00 2.66
2622 2982 8.203485 TGTATGCTGATGTCACATGATAGTTTA 58.797 33.333 0.00 0.00 0.00 2.01
2623 2983 9.212641 GTATGCTGATGTCACATGATAGTTTAT 57.787 33.333 0.00 0.00 0.00 1.40
2624 2984 8.687292 ATGCTGATGTCACATGATAGTTTATT 57.313 30.769 0.00 0.00 0.00 1.40
2625 2985 8.510243 TGCTGATGTCACATGATAGTTTATTT 57.490 30.769 0.00 0.00 0.00 1.40
2626 2986 8.959548 TGCTGATGTCACATGATAGTTTATTTT 58.040 29.630 0.00 0.00 0.00 1.82
2627 2987 9.793252 GCTGATGTCACATGATAGTTTATTTTT 57.207 29.630 0.00 0.00 0.00 1.94
2648 3008 4.362932 TTTTTGAGCAAATGTCACGTGA 57.637 36.364 15.76 15.76 0.00 4.35
2649 3009 4.566545 TTTTGAGCAAATGTCACGTGAT 57.433 36.364 23.12 3.16 0.00 3.06
2650 3010 5.681337 TTTTGAGCAAATGTCACGTGATA 57.319 34.783 23.12 20.30 0.00 2.15
2651 3011 4.926860 TTGAGCAAATGTCACGTGATAG 57.073 40.909 23.12 8.57 0.00 2.08
2652 3012 3.925379 TGAGCAAATGTCACGTGATAGT 58.075 40.909 23.12 16.13 0.00 2.12
2653 3013 4.314961 TGAGCAAATGTCACGTGATAGTT 58.685 39.130 23.12 21.43 0.00 2.24
2654 3014 4.152223 TGAGCAAATGTCACGTGATAGTTG 59.848 41.667 35.74 35.74 41.78 3.16
2655 3015 4.065088 AGCAAATGTCACGTGATAGTTGT 58.935 39.130 37.57 27.52 41.23 3.32
2656 3016 4.152402 AGCAAATGTCACGTGATAGTTGTC 59.848 41.667 37.57 31.48 41.23 3.18
2657 3017 4.669197 GCAAATGTCACGTGATAGTTGTCC 60.669 45.833 37.57 26.23 41.23 4.02
2658 3018 2.736144 TGTCACGTGATAGTTGTCCC 57.264 50.000 23.12 5.78 0.00 4.46
2659 3019 1.068125 TGTCACGTGATAGTTGTCCCG 60.068 52.381 23.12 0.00 0.00 5.14
2660 3020 0.528924 TCACGTGATAGTTGTCCCGG 59.471 55.000 15.76 0.00 0.00 5.73
2661 3021 0.245539 CACGTGATAGTTGTCCCGGT 59.754 55.000 10.90 0.00 0.00 5.28
2662 3022 0.529378 ACGTGATAGTTGTCCCGGTC 59.471 55.000 0.00 0.00 0.00 4.79
2663 3023 0.179119 CGTGATAGTTGTCCCGGTCC 60.179 60.000 0.00 0.00 0.00 4.46
2664 3024 1.192428 GTGATAGTTGTCCCGGTCCT 58.808 55.000 0.00 0.00 0.00 3.85
2665 3025 1.553704 GTGATAGTTGTCCCGGTCCTT 59.446 52.381 0.00 0.00 0.00 3.36
2666 3026 2.027469 GTGATAGTTGTCCCGGTCCTTT 60.027 50.000 0.00 0.00 0.00 3.11
2667 3027 2.640826 TGATAGTTGTCCCGGTCCTTTT 59.359 45.455 0.00 0.00 0.00 2.27
2668 3028 2.845363 TAGTTGTCCCGGTCCTTTTC 57.155 50.000 0.00 0.00 0.00 2.29
2669 3029 0.109913 AGTTGTCCCGGTCCTTTTCC 59.890 55.000 0.00 0.00 0.00 3.13
2670 3030 0.109913 GTTGTCCCGGTCCTTTTCCT 59.890 55.000 0.00 0.00 0.00 3.36
2707 3067 1.873165 CGTTATGCGGCAAACTGGT 59.127 52.632 6.82 0.00 36.85 4.00
2716 3076 1.032014 GGCAAACTGGTGAAGCTTCA 58.968 50.000 25.16 25.16 34.20 3.02
2907 3274 5.054477 GCAATCATTTAAGTAGCGGGACTA 58.946 41.667 0.00 0.00 0.00 2.59
3177 4535 8.573035 AGTTGGAAATATTAGAAAAGCGAACAA 58.427 29.630 0.00 0.00 0.00 2.83
3202 4560 8.791327 ATTTGTGGAAGAGTCAAACAATTTTT 57.209 26.923 0.00 0.00 34.00 1.94
3203 4561 7.593875 TTGTGGAAGAGTCAAACAATTTTTG 57.406 32.000 0.00 6.71 30.86 2.44
3204 4562 6.929625 TGTGGAAGAGTCAAACAATTTTTGA 58.070 32.000 10.04 10.04 36.21 2.69
3205 4563 7.555087 TGTGGAAGAGTCAAACAATTTTTGAT 58.445 30.769 14.58 7.68 40.12 2.57
3206 4564 7.706179 TGTGGAAGAGTCAAACAATTTTTGATC 59.294 33.333 14.58 12.95 40.12 2.92
3207 4565 6.917477 TGGAAGAGTCAAACAATTTTTGATCG 59.083 34.615 14.58 0.00 40.12 3.69
3218 4576 9.480053 AAACAATTTTTGATCGATCTTGAACAT 57.520 25.926 25.02 12.82 0.00 2.71
3338 4720 7.346751 ACTCTGAACCAAAATCTAAAAAGCA 57.653 32.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.109323 GCAATAGCCGCCTTCCCATT 61.109 55.000 0.00 0.00 33.58 3.16
35 36 1.005924 ACCAAGGGACAAGGGCAATAG 59.994 52.381 0.00 0.00 0.00 1.73
37 38 0.542702 CACCAAGGGACAAGGGCAAT 60.543 55.000 0.00 0.00 0.00 3.56
72 73 3.341823 CAATGAGCAAGTTAGTGAGGCT 58.658 45.455 0.00 0.00 37.56 4.58
315 317 7.852454 CCATAATTCATCTATTTCACACACACG 59.148 37.037 0.00 0.00 0.00 4.49
423 429 0.610687 TCCTCACACACACACACACA 59.389 50.000 0.00 0.00 0.00 3.72
424 430 1.953559 ATCCTCACACACACACACAC 58.046 50.000 0.00 0.00 0.00 3.82
425 431 2.682352 CAAATCCTCACACACACACACA 59.318 45.455 0.00 0.00 0.00 3.72
459 467 5.758296 AGTTCAATATTACGACATTGGCGAT 59.242 36.000 20.74 5.02 33.77 4.58
561 569 8.946860 CCGTCCGGAAATACTTGTCCAAGTAA 62.947 46.154 20.31 7.58 45.48 2.24
562 570 7.576451 CCGTCCGGAAATACTTGTCCAAGTA 62.576 48.000 19.12 19.12 45.92 2.24
563 571 6.888939 CCGTCCGGAAATACTTGTCCAAGT 62.889 50.000 5.23 16.21 45.02 3.16
564 572 2.671396 CGTCCGGAAATACTTGTCCAAG 59.329 50.000 5.23 5.51 43.79 3.61
565 573 2.613474 CCGTCCGGAAATACTTGTCCAA 60.613 50.000 5.23 0.00 37.50 3.53
566 574 1.066716 CCGTCCGGAAATACTTGTCCA 60.067 52.381 5.23 0.00 37.50 4.02
567 575 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
568 576 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
569 577 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
570 578 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
571 579 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
572 580 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
573 581 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
574 582 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
575 583 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
576 584 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
577 585 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
578 586 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
579 587 1.696063 TTTATACTCCCTCCGTCCGG 58.304 55.000 0.00 0.00 0.00 5.14
580 588 5.458041 TTATTTTATACTCCCTCCGTCCG 57.542 43.478 0.00 0.00 0.00 4.79
668 676 9.503399 AACCTCTCTAAGTTTGACGAAATTTAT 57.497 29.630 0.00 0.00 0.00 1.40
687 695 3.430333 TTTTGAAACGGCAAACCTCTC 57.570 42.857 0.00 0.00 37.48 3.20
718 727 9.238368 AGTGAATCCTCCGTTTCAAAATATAAA 57.762 29.630 0.00 0.00 33.90 1.40
719 728 8.801882 AGTGAATCCTCCGTTTCAAAATATAA 57.198 30.769 0.00 0.00 33.90 0.98
721 730 6.318900 GGAGTGAATCCTCCGTTTCAAAATAT 59.681 38.462 0.00 0.00 45.64 1.28
740 749 2.364002 TCAGATTTCACGTGTGGAGTGA 59.636 45.455 16.51 11.41 45.68 3.41
741 750 2.476619 GTCAGATTTCACGTGTGGAGTG 59.523 50.000 16.51 9.26 40.71 3.51
743 752 2.733552 CAGTCAGATTTCACGTGTGGAG 59.266 50.000 16.51 2.50 0.00 3.86
744 753 2.364002 TCAGTCAGATTTCACGTGTGGA 59.636 45.455 16.51 3.04 0.00 4.02
745 754 2.754472 TCAGTCAGATTTCACGTGTGG 58.246 47.619 16.51 0.31 0.00 4.17
746 755 4.997905 AATCAGTCAGATTTCACGTGTG 57.002 40.909 16.51 6.08 44.48 3.82
789 798 5.095490 TGATATCTACAGATACGCGCATTG 58.905 41.667 5.73 2.03 39.57 2.82
790 799 5.310720 TGATATCTACAGATACGCGCATT 57.689 39.130 5.73 0.00 39.57 3.56
805 1080 9.550406 CATTTTTAATTTGGGCACATGATATCT 57.450 29.630 0.00 0.00 0.00 1.98
813 1088 8.455903 TCAATTTCATTTTTAATTTGGGCACA 57.544 26.923 0.00 0.00 0.00 4.57
828 1103 2.433239 GGCCAGCCAGATCAATTTCATT 59.567 45.455 3.12 0.00 35.81 2.57
833 1108 0.396695 CCAGGCCAGCCAGATCAATT 60.397 55.000 12.03 0.00 38.92 2.32
836 1111 0.913934 TTACCAGGCCAGCCAGATCA 60.914 55.000 12.03 0.00 38.92 2.92
873 1148 0.319469 GATTTGGTTGGTTGGTGGCG 60.319 55.000 0.00 0.00 0.00 5.69
897 1172 7.971368 ATTTGTAGGGGTTGCTAATTAACAT 57.029 32.000 0.00 0.00 0.00 2.71
899 1174 8.528643 AGAAATTTGTAGGGGTTGCTAATTAAC 58.471 33.333 0.00 0.00 29.81 2.01
900 1175 8.527810 CAGAAATTTGTAGGGGTTGCTAATTAA 58.472 33.333 0.00 0.00 29.81 1.40
901 1176 7.363443 GCAGAAATTTGTAGGGGTTGCTAATTA 60.363 37.037 0.00 0.00 29.81 1.40
902 1177 6.574269 GCAGAAATTTGTAGGGGTTGCTAATT 60.574 38.462 0.00 0.00 30.79 1.40
903 1178 5.105351 GCAGAAATTTGTAGGGGTTGCTAAT 60.105 40.000 0.00 0.00 0.00 1.73
904 1179 4.219725 GCAGAAATTTGTAGGGGTTGCTAA 59.780 41.667 0.00 0.00 0.00 3.09
905 1180 3.761752 GCAGAAATTTGTAGGGGTTGCTA 59.238 43.478 0.00 0.00 0.00 3.49
906 1181 2.562738 GCAGAAATTTGTAGGGGTTGCT 59.437 45.455 0.00 0.00 0.00 3.91
907 1182 2.562738 AGCAGAAATTTGTAGGGGTTGC 59.437 45.455 0.00 0.00 0.00 4.17
908 1183 3.193479 GGAGCAGAAATTTGTAGGGGTTG 59.807 47.826 0.00 0.00 0.00 3.77
909 1184 3.181423 TGGAGCAGAAATTTGTAGGGGTT 60.181 43.478 0.00 0.00 0.00 4.11
910 1185 2.378547 TGGAGCAGAAATTTGTAGGGGT 59.621 45.455 0.00 0.00 0.00 4.95
911 1186 3.085952 TGGAGCAGAAATTTGTAGGGG 57.914 47.619 0.00 0.00 0.00 4.79
912 1187 5.665916 AATTGGAGCAGAAATTTGTAGGG 57.334 39.130 0.00 0.00 0.00 3.53
913 1188 6.956299 CAAATTGGAGCAGAAATTTGTAGG 57.044 37.500 16.47 0.00 43.75 3.18
918 1193 6.925165 CAGTGTACAAATTGGAGCAGAAATTT 59.075 34.615 0.00 0.00 36.63 1.82
919 1194 6.040842 ACAGTGTACAAATTGGAGCAGAAATT 59.959 34.615 0.00 0.00 0.00 1.82
920 1195 5.536161 ACAGTGTACAAATTGGAGCAGAAAT 59.464 36.000 0.00 0.00 0.00 2.17
921 1196 4.887071 ACAGTGTACAAATTGGAGCAGAAA 59.113 37.500 0.00 0.00 0.00 2.52
922 1197 4.460263 ACAGTGTACAAATTGGAGCAGAA 58.540 39.130 0.00 0.00 0.00 3.02
923 1198 4.065088 GACAGTGTACAAATTGGAGCAGA 58.935 43.478 0.00 0.00 0.00 4.26
924 1199 3.189287 GGACAGTGTACAAATTGGAGCAG 59.811 47.826 0.00 0.00 0.00 4.24
925 1200 3.146066 GGACAGTGTACAAATTGGAGCA 58.854 45.455 0.00 0.00 0.00 4.26
926 1201 3.146066 TGGACAGTGTACAAATTGGAGC 58.854 45.455 5.46 0.00 0.00 4.70
927 1202 3.189287 GCTGGACAGTGTACAAATTGGAG 59.811 47.826 10.03 0.00 0.00 3.86
928 1203 3.146066 GCTGGACAGTGTACAAATTGGA 58.854 45.455 10.03 0.00 0.00 3.53
929 1204 2.228822 GGCTGGACAGTGTACAAATTGG 59.771 50.000 10.03 0.00 0.00 3.16
930 1205 3.058016 CAGGCTGGACAGTGTACAAATTG 60.058 47.826 10.03 4.18 0.00 2.32
931 1206 3.149196 CAGGCTGGACAGTGTACAAATT 58.851 45.455 10.03 0.00 0.00 1.82
932 1207 2.783135 CAGGCTGGACAGTGTACAAAT 58.217 47.619 10.03 0.00 0.00 2.32
933 1208 1.813862 GCAGGCTGGACAGTGTACAAA 60.814 52.381 17.64 0.00 0.00 2.83
934 1209 0.250295 GCAGGCTGGACAGTGTACAA 60.250 55.000 17.64 0.00 0.00 2.41
935 1210 1.371183 GCAGGCTGGACAGTGTACA 59.629 57.895 17.64 8.21 0.00 2.90
936 1211 0.671781 CTGCAGGCTGGACAGTGTAC 60.672 60.000 17.64 0.00 0.00 2.90
937 1212 1.673477 CTGCAGGCTGGACAGTGTA 59.327 57.895 17.64 0.00 0.00 2.90
938 1213 2.429058 CTGCAGGCTGGACAGTGT 59.571 61.111 17.64 0.00 0.00 3.55
976 1251 3.119137 GCGCTTGTTTGGGGATAAAGATT 60.119 43.478 0.00 0.00 0.00 2.40
977 1252 2.427095 GCGCTTGTTTGGGGATAAAGAT 59.573 45.455 0.00 0.00 0.00 2.40
978 1253 1.816224 GCGCTTGTTTGGGGATAAAGA 59.184 47.619 0.00 0.00 0.00 2.52
979 1254 1.543802 TGCGCTTGTTTGGGGATAAAG 59.456 47.619 9.73 0.00 0.00 1.85
980 1255 1.621992 TGCGCTTGTTTGGGGATAAA 58.378 45.000 9.73 0.00 0.00 1.40
981 1256 1.621992 TTGCGCTTGTTTGGGGATAA 58.378 45.000 9.73 0.00 0.00 1.75
982 1257 1.476085 CATTGCGCTTGTTTGGGGATA 59.524 47.619 9.73 0.00 0.00 2.59
983 1258 0.247185 CATTGCGCTTGTTTGGGGAT 59.753 50.000 9.73 0.00 0.00 3.85
984 1259 1.664873 CATTGCGCTTGTTTGGGGA 59.335 52.632 9.73 0.00 0.00 4.81
990 1265 2.255252 GACGGCATTGCGCTTGTT 59.745 55.556 9.73 0.00 41.91 2.83
1110 1388 0.535335 TCTGGATGTAGTTGGCGGAC 59.465 55.000 0.00 0.00 0.00 4.79
1873 2197 2.747460 GGTGATGCAGCGCCAGAA 60.747 61.111 28.83 0.00 38.32 3.02
1936 2260 2.359354 CCCGCGGTTGTTGATGGA 60.359 61.111 26.12 0.00 0.00 3.41
2177 2516 1.606531 GAGCTGCCCATCAAGGTCT 59.393 57.895 0.00 0.00 34.66 3.85
2205 2544 1.445410 GTCGCAGCCGTACATGTCA 60.445 57.895 0.00 0.00 35.54 3.58
2442 2790 0.603065 CAGAGTGGTGACATGGACGA 59.397 55.000 0.00 0.00 46.14 4.20
2480 2839 4.319177 ACAGATCCGGAAGTTTTTCTGAG 58.681 43.478 28.66 10.68 41.37 3.35
2482 2841 4.515191 TGAACAGATCCGGAAGTTTTTCTG 59.485 41.667 22.94 22.94 39.06 3.02
2483 2842 4.714632 TGAACAGATCCGGAAGTTTTTCT 58.285 39.130 9.01 1.87 33.68 2.52
2484 2843 5.629079 ATGAACAGATCCGGAAGTTTTTC 57.371 39.130 9.01 8.66 0.00 2.29
2485 2844 6.405278 AAATGAACAGATCCGGAAGTTTTT 57.595 33.333 9.01 9.50 0.00 1.94
2486 2845 6.265422 AGAAAATGAACAGATCCGGAAGTTTT 59.735 34.615 9.01 5.29 0.00 2.43
2487 2846 5.770162 AGAAAATGAACAGATCCGGAAGTTT 59.230 36.000 9.01 0.91 0.00 2.66
2490 2849 7.280876 TGAATAGAAAATGAACAGATCCGGAAG 59.719 37.037 9.01 4.00 0.00 3.46
2491 2850 7.109501 TGAATAGAAAATGAACAGATCCGGAA 58.890 34.615 9.01 0.00 0.00 4.30
2492 2851 6.649155 TGAATAGAAAATGAACAGATCCGGA 58.351 36.000 6.61 6.61 0.00 5.14
2494 2853 7.358066 CCATGAATAGAAAATGAACAGATCCG 58.642 38.462 0.00 0.00 0.00 4.18
2495 2854 7.144000 GCCATGAATAGAAAATGAACAGATCC 58.856 38.462 0.00 0.00 0.00 3.36
2501 2861 6.914757 GCTAGTGCCATGAATAGAAAATGAAC 59.085 38.462 0.00 0.00 0.00 3.18
2510 2870 3.136763 CTGGTGCTAGTGCCATGAATAG 58.863 50.000 7.66 0.00 38.71 1.73
2518 2878 1.750193 TATTTGCTGGTGCTAGTGCC 58.250 50.000 0.00 0.00 40.48 5.01
2522 2882 7.497249 ACTCTCTTTATTATTTGCTGGTGCTAG 59.503 37.037 0.00 0.00 40.48 3.42
2523 2883 7.280876 CACTCTCTTTATTATTTGCTGGTGCTA 59.719 37.037 0.00 0.00 40.48 3.49
2525 2885 6.261118 CACTCTCTTTATTATTTGCTGGTGC 58.739 40.000 0.00 0.00 40.20 5.01
2526 2886 6.261118 GCACTCTCTTTATTATTTGCTGGTG 58.739 40.000 0.00 0.00 0.00 4.17
2532 2892 9.606631 AGTTCTAGGCACTCTCTTTATTATTTG 57.393 33.333 0.00 0.00 41.75 2.32
2535 2895 8.540507 TGAGTTCTAGGCACTCTCTTTATTAT 57.459 34.615 18.44 0.00 41.25 1.28
2536 2896 7.956328 TGAGTTCTAGGCACTCTCTTTATTA 57.044 36.000 18.44 0.37 41.25 0.98
2538 2898 6.382570 ACATGAGTTCTAGGCACTCTCTTTAT 59.617 38.462 18.44 6.03 41.25 1.40
2539 2899 5.717178 ACATGAGTTCTAGGCACTCTCTTTA 59.283 40.000 18.44 4.41 41.25 1.85
2542 2902 3.707316 ACATGAGTTCTAGGCACTCTCT 58.293 45.455 18.44 7.98 41.25 3.10
2543 2903 4.499019 GCTACATGAGTTCTAGGCACTCTC 60.499 50.000 18.44 8.29 41.25 3.20
2544 2904 3.383185 GCTACATGAGTTCTAGGCACTCT 59.617 47.826 18.44 6.54 41.25 3.24
2545 2905 3.383185 AGCTACATGAGTTCTAGGCACTC 59.617 47.826 13.40 13.40 41.75 3.51
2546 2906 3.131933 CAGCTACATGAGTTCTAGGCACT 59.868 47.826 0.00 0.00 46.37 4.40
2547 2907 3.131223 TCAGCTACATGAGTTCTAGGCAC 59.869 47.826 0.00 0.00 0.00 5.01
2548 2908 3.365472 TCAGCTACATGAGTTCTAGGCA 58.635 45.455 0.00 0.00 0.00 4.75
2549 2909 3.976169 CTCAGCTACATGAGTTCTAGGC 58.024 50.000 0.00 0.00 41.52 3.93
2558 2918 9.314133 AGACCATATTATAACTCAGCTACATGA 57.686 33.333 0.00 0.00 0.00 3.07
2559 2919 9.579768 GAGACCATATTATAACTCAGCTACATG 57.420 37.037 0.00 0.00 0.00 3.21
2560 2920 9.314133 TGAGACCATATTATAACTCAGCTACAT 57.686 33.333 0.00 0.00 32.04 2.29
2561 2921 8.706322 TGAGACCATATTATAACTCAGCTACA 57.294 34.615 0.00 0.00 32.04 2.74
2564 2924 8.874156 TGAATGAGACCATATTATAACTCAGCT 58.126 33.333 0.00 0.00 37.70 4.24
2565 2925 8.930760 GTGAATGAGACCATATTATAACTCAGC 58.069 37.037 0.00 0.00 37.70 4.26
2566 2926 9.429359 GGTGAATGAGACCATATTATAACTCAG 57.571 37.037 0.00 0.00 37.70 3.35
2567 2927 9.159254 AGGTGAATGAGACCATATTATAACTCA 57.841 33.333 0.00 0.00 38.44 3.41
2568 2928 9.429359 CAGGTGAATGAGACCATATTATAACTC 57.571 37.037 0.00 0.00 35.76 3.01
2569 2929 9.159254 TCAGGTGAATGAGACCATATTATAACT 57.841 33.333 0.00 0.00 35.76 2.24
2570 2930 9.950496 ATCAGGTGAATGAGACCATATTATAAC 57.050 33.333 0.00 0.00 35.76 1.89
2571 2931 9.948964 CATCAGGTGAATGAGACCATATTATAA 57.051 33.333 0.00 0.00 35.76 0.98
2572 2932 9.104713 ACATCAGGTGAATGAGACCATATTATA 57.895 33.333 0.00 0.00 35.76 0.98
2573 2933 7.982252 ACATCAGGTGAATGAGACCATATTAT 58.018 34.615 0.00 0.00 35.76 1.28
2574 2934 7.379059 ACATCAGGTGAATGAGACCATATTA 57.621 36.000 0.00 0.00 35.76 0.98
2575 2935 6.257994 ACATCAGGTGAATGAGACCATATT 57.742 37.500 0.00 0.00 35.76 1.28
2576 2936 5.901413 ACATCAGGTGAATGAGACCATAT 57.099 39.130 0.00 0.00 35.76 1.78
2577 2937 6.742363 GCATACATCAGGTGAATGAGACCATA 60.742 42.308 0.00 0.00 35.76 2.74
2578 2938 5.618236 CATACATCAGGTGAATGAGACCAT 58.382 41.667 0.00 0.00 35.76 3.55
2579 2939 4.684214 GCATACATCAGGTGAATGAGACCA 60.684 45.833 0.00 0.00 35.76 4.02
2580 2940 3.812053 GCATACATCAGGTGAATGAGACC 59.188 47.826 0.00 0.00 31.44 3.85
2581 2941 4.510711 CAGCATACATCAGGTGAATGAGAC 59.489 45.833 0.00 0.00 35.37 3.36
2582 2942 4.406649 TCAGCATACATCAGGTGAATGAGA 59.593 41.667 0.00 0.00 39.09 3.27
2583 2943 4.700700 TCAGCATACATCAGGTGAATGAG 58.299 43.478 0.00 0.00 39.09 2.90
2584 2944 4.758773 TCAGCATACATCAGGTGAATGA 57.241 40.909 0.00 0.00 39.09 2.57
2585 2945 4.820173 ACATCAGCATACATCAGGTGAATG 59.180 41.667 0.00 0.00 44.29 2.67
2586 2946 5.045012 ACATCAGCATACATCAGGTGAAT 57.955 39.130 0.00 0.00 44.29 2.57
2587 2947 4.080975 TGACATCAGCATACATCAGGTGAA 60.081 41.667 0.00 0.00 44.29 3.18
2588 2948 3.451902 TGACATCAGCATACATCAGGTGA 59.548 43.478 0.00 0.00 45.06 4.02
2589 2949 3.558829 GTGACATCAGCATACATCAGGTG 59.441 47.826 0.00 0.00 34.72 4.00
2590 2950 3.198417 TGTGACATCAGCATACATCAGGT 59.802 43.478 0.00 0.00 0.00 4.00
2591 2951 3.800531 TGTGACATCAGCATACATCAGG 58.199 45.455 0.00 0.00 0.00 3.86
2592 2952 5.054477 TCATGTGACATCAGCATACATCAG 58.946 41.667 0.00 0.00 30.15 2.90
2593 2953 5.026038 TCATGTGACATCAGCATACATCA 57.974 39.130 0.00 0.00 30.15 3.07
2594 2954 6.872547 ACTATCATGTGACATCAGCATACATC 59.127 38.462 0.00 0.00 30.15 3.06
2595 2955 6.766429 ACTATCATGTGACATCAGCATACAT 58.234 36.000 0.00 0.00 32.60 2.29
2596 2956 6.165700 ACTATCATGTGACATCAGCATACA 57.834 37.500 0.00 0.00 0.00 2.29
2597 2957 7.488187 AAACTATCATGTGACATCAGCATAC 57.512 36.000 0.00 0.00 0.00 2.39
2598 2958 9.783081 AATAAACTATCATGTGACATCAGCATA 57.217 29.630 0.00 0.00 0.00 3.14
2599 2959 8.687292 AATAAACTATCATGTGACATCAGCAT 57.313 30.769 0.00 0.00 0.00 3.79
2600 2960 8.510243 AAATAAACTATCATGTGACATCAGCA 57.490 30.769 0.00 0.00 0.00 4.41
2601 2961 9.793252 AAAAATAAACTATCATGTGACATCAGC 57.207 29.630 0.00 0.00 0.00 4.26
2627 2987 4.362932 TCACGTGACATTTGCTCAAAAA 57.637 36.364 15.76 0.00 33.56 1.94
2628 2988 4.566545 ATCACGTGACATTTGCTCAAAA 57.433 36.364 22.71 0.00 33.56 2.44
2629 2989 4.754618 ACTATCACGTGACATTTGCTCAAA 59.245 37.500 22.71 0.00 34.46 2.69
2630 2990 4.314961 ACTATCACGTGACATTTGCTCAA 58.685 39.130 22.71 0.00 0.00 3.02
2631 2991 3.925379 ACTATCACGTGACATTTGCTCA 58.075 40.909 22.71 0.00 0.00 4.26
2632 2992 4.152402 ACAACTATCACGTGACATTTGCTC 59.848 41.667 22.27 0.00 0.00 4.26
2633 2993 4.065088 ACAACTATCACGTGACATTTGCT 58.935 39.130 22.27 8.55 0.00 3.91
2634 2994 4.394795 GACAACTATCACGTGACATTTGC 58.605 43.478 22.27 13.57 0.00 3.68
2635 2995 4.142902 GGGACAACTATCACGTGACATTTG 60.143 45.833 22.71 21.78 0.00 2.32
2636 2996 4.000988 GGGACAACTATCACGTGACATTT 58.999 43.478 22.71 7.06 0.00 2.32
2637 2997 3.596214 GGGACAACTATCACGTGACATT 58.404 45.455 22.71 12.49 0.00 2.71
2638 2998 2.416836 CGGGACAACTATCACGTGACAT 60.417 50.000 22.71 8.85 40.72 3.06
2639 2999 1.068125 CGGGACAACTATCACGTGACA 60.068 52.381 22.71 8.81 40.72 3.58
2640 3000 1.625616 CGGGACAACTATCACGTGAC 58.374 55.000 22.71 5.92 40.72 3.67
2641 3001 0.528924 CCGGGACAACTATCACGTGA 59.471 55.000 22.48 22.48 44.24 4.35
2642 3002 0.245539 ACCGGGACAACTATCACGTG 59.754 55.000 9.94 9.94 44.24 4.49
2643 3003 0.529378 GACCGGGACAACTATCACGT 59.471 55.000 6.32 0.00 44.24 4.49
2644 3004 0.179119 GGACCGGGACAACTATCACG 60.179 60.000 6.32 0.00 45.35 4.35
2645 3005 1.192428 AGGACCGGGACAACTATCAC 58.808 55.000 6.32 0.00 0.00 3.06
2646 3006 1.946984 AAGGACCGGGACAACTATCA 58.053 50.000 6.32 0.00 0.00 2.15
2647 3007 3.268330 GAAAAGGACCGGGACAACTATC 58.732 50.000 6.32 0.00 0.00 2.08
2648 3008 2.026542 GGAAAAGGACCGGGACAACTAT 60.027 50.000 6.32 0.00 0.00 2.12
2649 3009 1.348696 GGAAAAGGACCGGGACAACTA 59.651 52.381 6.32 0.00 0.00 2.24
2650 3010 0.109913 GGAAAAGGACCGGGACAACT 59.890 55.000 6.32 0.00 0.00 3.16
2651 3011 0.109913 AGGAAAAGGACCGGGACAAC 59.890 55.000 6.32 0.00 0.00 3.32
2652 3012 0.109723 CAGGAAAAGGACCGGGACAA 59.890 55.000 6.32 0.00 0.00 3.18
2653 3013 1.758592 CAGGAAAAGGACCGGGACA 59.241 57.895 6.32 0.00 0.00 4.02
2654 3014 1.002502 CCAGGAAAAGGACCGGGAC 60.003 63.158 6.32 0.00 43.60 4.46
2655 3015 2.228480 CCCAGGAAAAGGACCGGGA 61.228 63.158 6.32 0.00 43.60 5.14
2656 3016 2.228480 TCCCAGGAAAAGGACCGGG 61.228 63.158 6.32 0.00 41.28 5.73
2657 3017 1.002502 GTCCCAGGAAAAGGACCGG 60.003 63.158 0.00 0.00 45.76 5.28
2658 3018 4.716003 GTCCCAGGAAAAGGACCG 57.284 61.111 0.00 0.00 45.76 4.79
2661 3021 0.196118 AGGAGGTCCCAGGAAAAGGA 59.804 55.000 0.00 0.00 37.41 3.36
2662 3022 1.966845 TAGGAGGTCCCAGGAAAAGG 58.033 55.000 0.00 0.00 37.41 3.11
2663 3023 2.846827 ACATAGGAGGTCCCAGGAAAAG 59.153 50.000 0.00 0.00 37.41 2.27
2664 3024 2.576191 CACATAGGAGGTCCCAGGAAAA 59.424 50.000 0.00 0.00 37.41 2.29
2665 3025 2.196595 CACATAGGAGGTCCCAGGAAA 58.803 52.381 0.00 0.00 37.41 3.13
2666 3026 1.879575 CACATAGGAGGTCCCAGGAA 58.120 55.000 0.00 0.00 37.41 3.36
2667 3027 0.691078 GCACATAGGAGGTCCCAGGA 60.691 60.000 0.00 0.00 37.41 3.86
2668 3028 1.700042 GGCACATAGGAGGTCCCAGG 61.700 65.000 0.00 0.00 37.41 4.45
2669 3029 1.832912 GGCACATAGGAGGTCCCAG 59.167 63.158 0.00 0.00 37.41 4.45
2670 3030 2.063979 CGGCACATAGGAGGTCCCA 61.064 63.158 0.00 0.00 37.41 4.37
2707 3067 0.319900 GACGCCTCTGTGAAGCTTCA 60.320 55.000 25.16 25.16 34.20 3.02
2716 3076 1.300697 GTTGGTTCGACGCCTCTGT 60.301 57.895 6.74 0.00 0.00 3.41
2742 3102 3.006728 CGGGGTTGGCTACCTGGA 61.007 66.667 17.47 0.00 46.86 3.86
2772 3132 4.092968 AGCGCGAATCGTTTTCTCTAAAAT 59.907 37.500 12.10 0.00 41.07 1.82
2776 3136 2.273370 AGCGCGAATCGTTTTCTCTA 57.727 45.000 12.10 0.00 41.07 2.43
2809 3169 0.782384 CGAGTAAGCGTTGCGAGTTT 59.218 50.000 0.00 0.00 0.00 2.66
2907 3274 8.907885 GTCCATCTCTTTTAGGAATTTTATGCT 58.092 33.333 0.00 0.00 0.00 3.79
3177 4535 8.667463 CAAAAATTGTTTGACTCTTCCACAAAT 58.333 29.630 0.00 0.00 36.25 2.32
3278 4640 8.144478 TGTTCCATTTATTCCAAAAATGTTCGA 58.856 29.630 7.53 0.00 40.93 3.71
3279 4641 8.304202 TGTTCCATTTATTCCAAAAATGTTCG 57.696 30.769 7.53 0.00 40.93 3.95


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

AutoCloner maintained by Alex Coulton.