Multiple sequence alignment - TraesCS3B01G555200

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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 TraesCS3B01G555200 chr3B 100.000 3440 0 0 1 3440 789054925 789051486 0.000000e+00 6353.0
1 TraesCS3B01G555200 chr3B 79.708 616 106 17 2542 3145 795055681 795055073 8.820000e-116 427.0
2 TraesCS3B01G555200 chr3B 85.849 212 25 3 839 1049 823869401 823869194 1.610000e-53 220.0
3 TraesCS3B01G555200 chr3B 84.434 212 28 3 839 1049 825527674 825527467 1.620000e-48 204.0
4 TraesCS3B01G555200 chr2A 90.497 1347 117 5 1806 3145 87689910 87688568 0.000000e+00 1768.0
5 TraesCS3B01G555200 chr2A 79.379 1513 235 38 1691 3143 694813111 694814606 0.000000e+00 994.0
6 TraesCS3B01G555200 chr2A 88.866 485 53 1 1285 1769 87698362 87697879 2.290000e-166 595.0
7 TraesCS3B01G555200 chr2A 82.667 675 106 6 1695 2365 19485743 19486410 3.820000e-164 588.0
8 TraesCS3B01G555200 chr2A 89.831 59 5 1 1055 1113 19485276 19485333 1.320000e-09 75.0
9 TraesCS3B01G555200 chr3A 89.848 1251 103 9 1901 3146 25002871 25001640 0.000000e+00 1585.0
10 TraesCS3B01G555200 chr3A 90.752 638 47 6 850 1478 25003812 25003178 0.000000e+00 841.0
11 TraesCS3B01G555200 chr3A 91.077 325 28 1 1492 1816 25003194 25002871 4.080000e-119 438.0
12 TraesCS3B01G555200 chr4A 87.513 969 101 8 2174 3137 658436056 658435103 0.000000e+00 1101.0
13 TraesCS3B01G555200 chr4A 87.644 955 98 9 2176 3126 658488637 658487699 0.000000e+00 1092.0
14 TraesCS3B01G555200 chr4A 79.425 904 155 15 1691 2569 4874521 4873624 8.160000e-171 610.0
15 TraesCS3B01G555200 chr4A 82.545 275 45 2 842 1116 625261519 625261790 4.440000e-59 239.0
16 TraesCS3B01G555200 chr5A 79.477 1491 230 41 1691 3122 558971524 558970051 0.000000e+00 989.0
17 TraesCS3B01G555200 chr5A 77.908 1023 158 34 2177 3146 455539826 455538819 2.980000e-160 575.0
18 TraesCS3B01G555200 chr3D 79.235 1411 219 40 1771 3126 388344215 388345606 0.000000e+00 915.0
19 TraesCS3B01G555200 chr3D 87.393 817 68 17 12 803 590137725 590136919 0.000000e+00 905.0
20 TraesCS3B01G555200 chr3D 95.270 296 12 2 3146 3440 590136899 590136605 5.200000e-128 468.0
21 TraesCS3B01G555200 chr3D 87.346 324 36 4 839 1161 614967725 614967406 1.950000e-97 366.0
22 TraesCS3B01G555200 chr2B 89.160 655 61 7 2497 3146 17705184 17704535 0.000000e+00 808.0
23 TraesCS3B01G555200 chr2B 86.441 236 29 3 2263 2498 17743784 17743552 4.410000e-64 255.0
24 TraesCS3B01G555200 chr6D 87.654 567 64 4 2582 3144 452480477 452479913 0.000000e+00 654.0
25 TraesCS3B01G555200 chr6D 74.650 785 132 43 2385 3145 394728866 394728125 5.620000e-73 285.0
26 TraesCS3B01G555200 chr1B 77.623 1077 175 39 1835 2874 392534915 392533868 8.220000e-166 593.0
27 TraesCS3B01G555200 chr1B 80.988 405 66 6 1889 2289 651432869 651433266 9.270000e-81 311.0
28 TraesCS3B01G555200 chr5D 81.422 619 88 16 2538 3146 354543528 354542927 6.680000e-132 481.0
29 TraesCS3B01G555200 chr5D 78.339 554 93 18 839 1388 541614804 541615334 1.980000e-87 333.0
30 TraesCS3B01G555200 chr5D 83.385 325 47 5 842 1164 243095935 243095616 9.340000e-76 294.0
31 TraesCS3B01G555200 chr6B 80.744 618 101 14 2538 3146 120135092 120135700 1.870000e-127 466.0
32 TraesCS3B01G555200 chr6B 70.929 829 195 32 1766 2558 50462534 50463352 1.650000e-33 154.0
33 TraesCS3B01G555200 chrUn 85.366 205 27 1 839 1043 235916359 235916560 3.480000e-50 209.0
34 TraesCS3B01G555200 chr4B 71.739 828 190 31 1767 2558 139143491 139144310 3.500000e-45 193.0
35 TraesCS3B01G555200 chr4B 85.000 60 5 3 2368 2426 465734721 465734665 1.330000e-04 58.4
36 TraesCS3B01G555200 chr2D 85.185 81 12 0 1255 1335 186828877 186828797 2.200000e-12 84.2
37 TraesCS3B01G555200 chr7D 82.716 81 14 0 1255 1335 414371685 414371605 4.760000e-09 73.1


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 TraesCS3B01G555200 chr3B 789051486 789054925 3439 True 6353.000000 6353 100.0000 1 3440 1 chr3B.!!$R1 3439
1 TraesCS3B01G555200 chr3B 795055073 795055681 608 True 427.000000 427 79.7080 2542 3145 1 chr3B.!!$R2 603
2 TraesCS3B01G555200 chr2A 87688568 87689910 1342 True 1768.000000 1768 90.4970 1806 3145 1 chr2A.!!$R1 1339
3 TraesCS3B01G555200 chr2A 694813111 694814606 1495 False 994.000000 994 79.3790 1691 3143 1 chr2A.!!$F1 1452
4 TraesCS3B01G555200 chr2A 19485276 19486410 1134 False 331.500000 588 86.2490 1055 2365 2 chr2A.!!$F2 1310
5 TraesCS3B01G555200 chr3A 25001640 25003812 2172 True 954.666667 1585 90.5590 850 3146 3 chr3A.!!$R1 2296
6 TraesCS3B01G555200 chr4A 658435103 658436056 953 True 1101.000000 1101 87.5130 2174 3137 1 chr4A.!!$R2 963
7 TraesCS3B01G555200 chr4A 658487699 658488637 938 True 1092.000000 1092 87.6440 2176 3126 1 chr4A.!!$R3 950
8 TraesCS3B01G555200 chr4A 4873624 4874521 897 True 610.000000 610 79.4250 1691 2569 1 chr4A.!!$R1 878
9 TraesCS3B01G555200 chr5A 558970051 558971524 1473 True 989.000000 989 79.4770 1691 3122 1 chr5A.!!$R2 1431
10 TraesCS3B01G555200 chr5A 455538819 455539826 1007 True 575.000000 575 77.9080 2177 3146 1 chr5A.!!$R1 969
11 TraesCS3B01G555200 chr3D 388344215 388345606 1391 False 915.000000 915 79.2350 1771 3126 1 chr3D.!!$F1 1355
12 TraesCS3B01G555200 chr3D 590136605 590137725 1120 True 686.500000 905 91.3315 12 3440 2 chr3D.!!$R2 3428
13 TraesCS3B01G555200 chr2B 17704535 17705184 649 True 808.000000 808 89.1600 2497 3146 1 chr2B.!!$R1 649
14 TraesCS3B01G555200 chr6D 452479913 452480477 564 True 654.000000 654 87.6540 2582 3144 1 chr6D.!!$R2 562
15 TraesCS3B01G555200 chr6D 394728125 394728866 741 True 285.000000 285 74.6500 2385 3145 1 chr6D.!!$R1 760
16 TraesCS3B01G555200 chr1B 392533868 392534915 1047 True 593.000000 593 77.6230 1835 2874 1 chr1B.!!$R1 1039
17 TraesCS3B01G555200 chr5D 354542927 354543528 601 True 481.000000 481 81.4220 2538 3146 1 chr5D.!!$R2 608
18 TraesCS3B01G555200 chr5D 541614804 541615334 530 False 333.000000 333 78.3390 839 1388 1 chr5D.!!$F1 549
19 TraesCS3B01G555200 chr6B 120135092 120135700 608 False 466.000000 466 80.7440 2538 3146 1 chr6B.!!$F2 608

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
833 882 0.034059 AGTTCTGCCGTGACCAAGAG 59.966 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2694 3221 0.038251 TCACGCACAGTCATCACCTC 60.038 55.0 0.0 0.0 0.0 3.85 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
18 19 2.511818 TGAGTGGTGTGAAGACCGT 58.488 52.632 0.00 0.00 39.07 4.83
68 69 4.766404 ATTAGGAAAGACTTTGGTTGCG 57.234 40.909 4.85 0.00 0.00 4.85
99 100 1.214589 GTTTCGTAGCCAGCGGAGA 59.785 57.895 0.00 0.00 0.00 3.71
128 129 1.153168 GGGTCGTGGACATGATGGG 60.153 63.158 0.00 0.00 33.68 4.00
138 139 2.205074 GACATGATGGGTGATGACGAC 58.795 52.381 0.00 0.00 0.00 4.34
151 152 4.210093 ACGACAACACCGACGCCA 62.210 61.111 0.00 0.00 0.00 5.69
162 163 0.385751 CCGACGCCAGTATCTCATGT 59.614 55.000 0.00 0.00 0.00 3.21
163 164 1.600663 CCGACGCCAGTATCTCATGTC 60.601 57.143 0.00 0.00 0.00 3.06
164 165 1.065551 CGACGCCAGTATCTCATGTCA 59.934 52.381 0.00 0.00 0.00 3.58
165 166 2.287849 CGACGCCAGTATCTCATGTCAT 60.288 50.000 0.00 0.00 0.00 3.06
166 167 3.055591 GACGCCAGTATCTCATGTCATG 58.944 50.000 6.47 6.47 0.00 3.07
167 168 2.432146 ACGCCAGTATCTCATGTCATGT 59.568 45.455 12.54 0.00 0.00 3.21
168 169 2.798847 CGCCAGTATCTCATGTCATGTG 59.201 50.000 12.54 10.33 0.00 3.21
183 184 3.118454 GTGGCATCCGTCGGTGTG 61.118 66.667 11.88 12.51 0.00 3.82
201 202 3.627123 GTGTGTACCGGGTTTAAGTTGTT 59.373 43.478 4.31 0.00 0.00 2.83
235 256 1.666553 CGTAAGCCGTTGGTGCTCA 60.667 57.895 0.00 0.00 38.34 4.26
236 257 1.225376 CGTAAGCCGTTGGTGCTCAA 61.225 55.000 0.00 0.00 38.34 3.02
252 273 2.159599 GCTCAAAGACAGATTTGCTCCG 60.160 50.000 0.00 0.00 39.51 4.63
253 274 2.417933 CTCAAAGACAGATTTGCTCCGG 59.582 50.000 0.00 0.00 39.51 5.14
254 275 2.154462 CAAAGACAGATTTGCTCCGGT 58.846 47.619 0.00 0.00 33.71 5.28
257 278 3.695830 AGACAGATTTGCTCCGGTTTA 57.304 42.857 0.00 0.00 0.00 2.01
266 287 1.134521 TGCTCCGGTTTATCGCTCAAT 60.135 47.619 0.00 0.00 0.00 2.57
267 288 1.940613 GCTCCGGTTTATCGCTCAATT 59.059 47.619 0.00 0.00 0.00 2.32
380 410 1.281960 GTCAGCTGCTGCACACTTG 59.718 57.895 24.38 6.88 42.74 3.16
381 411 1.146707 TCAGCTGCTGCACACTTGA 59.853 52.632 24.38 9.19 42.74 3.02
413 443 3.437049 GTGCAGACAGGGTATCAACTTTC 59.563 47.826 0.00 0.00 0.00 2.62
418 448 2.374170 ACAGGGTATCAACTTTCGGGTT 59.626 45.455 0.00 0.00 0.00 4.11
438 468 2.806434 TGGTCACCCATCCTCAAATTG 58.194 47.619 0.00 0.00 35.17 2.32
446 476 2.479049 CCATCCTCAAATTGCTCAAGCG 60.479 50.000 0.00 0.00 45.83 4.68
452 482 3.371168 TCAAATTGCTCAAGCGAAACAC 58.629 40.909 0.00 0.00 45.83 3.32
491 521 1.574134 TGTGAACGACTCCCGAAAAC 58.426 50.000 0.00 0.00 41.76 2.43
495 525 0.810823 AACGACTCCCGAAAACGCAA 60.811 50.000 0.00 0.00 41.76 4.85
518 548 9.807649 GCAAAAATTCCTTGTTGATATGAGTAT 57.192 29.630 3.07 0.00 0.00 2.12
529 559 9.889128 TTGTTGATATGAGTATTCAGTCAATCA 57.111 29.630 16.50 13.98 40.69 2.57
538 568 9.516314 TGAGTATTCAGTCAATCATAGTAAACG 57.484 33.333 0.00 0.00 30.95 3.60
544 574 6.697455 TCAGTCAATCATAGTAAACGAGATGC 59.303 38.462 0.00 0.00 0.00 3.91
549 579 9.841880 TCAATCATAGTAAACGAGATGCTATAC 57.158 33.333 0.00 0.00 0.00 1.47
557 587 7.921745 AGTAAACGAGATGCTATACCTTCTTTC 59.078 37.037 0.00 0.00 0.00 2.62
559 589 4.338682 ACGAGATGCTATACCTTCTTTCGT 59.661 41.667 0.00 0.00 0.00 3.85
564 594 7.085116 AGATGCTATACCTTCTTTCGTTATCG 58.915 38.462 0.00 0.00 38.55 2.92
569 599 8.235905 GCTATACCTTCTTTCGTTATCGAGTAT 58.764 37.037 0.00 3.23 46.81 2.12
574 604 5.571784 TCTTTCGTTATCGAGTATGGTGT 57.428 39.130 0.00 0.00 46.81 4.16
591 624 5.720371 TGGTGTCATTATTTCAACCTTGG 57.280 39.130 0.00 0.00 0.00 3.61
616 649 1.067693 TTGAACTGTAGACATGCGCG 58.932 50.000 0.00 0.00 0.00 6.86
631 664 2.076628 CGCGTGCAACACTGAATGC 61.077 57.895 0.00 5.08 39.50 3.56
647 680 2.029838 ATGCAGTACAGGCTTGCTAC 57.970 50.000 10.02 0.00 0.00 3.58
687 720 1.522258 CGTGCAAGTTGCCAATGAAAC 59.478 47.619 24.59 12.97 44.23 2.78
695 728 0.187117 TGCCAATGAAACTGGTCCCA 59.813 50.000 0.00 0.00 0.00 4.37
731 764 4.471747 TGCACAGGACAACCCATACTAATA 59.528 41.667 0.00 0.00 37.41 0.98
783 816 7.464178 GCATTCCTACTTCATACAACTACAACG 60.464 40.741 0.00 0.00 0.00 4.10
790 823 7.208080 ACTTCATACAACTACAACGACTCTTT 58.792 34.615 0.00 0.00 0.00 2.52
818 867 6.707599 ATTTGCTCTTACGTACAGAAGTTC 57.292 37.500 0.00 0.00 0.00 3.01
819 868 5.449107 TTGCTCTTACGTACAGAAGTTCT 57.551 39.130 0.00 0.00 0.00 3.01
828 877 2.533318 CAGAAGTTCTGCCGTGACC 58.467 57.895 19.55 0.00 37.72 4.02
829 878 0.249868 CAGAAGTTCTGCCGTGACCA 60.250 55.000 19.55 0.00 37.72 4.02
830 879 0.468226 AGAAGTTCTGCCGTGACCAA 59.532 50.000 4.10 0.00 0.00 3.67
831 880 0.868406 GAAGTTCTGCCGTGACCAAG 59.132 55.000 0.00 0.00 0.00 3.61
832 881 0.468226 AAGTTCTGCCGTGACCAAGA 59.532 50.000 0.00 0.00 0.00 3.02
833 882 0.034059 AGTTCTGCCGTGACCAAGAG 59.966 55.000 0.00 0.00 0.00 2.85
834 883 1.301716 TTCTGCCGTGACCAAGAGC 60.302 57.895 0.00 0.00 0.00 4.09
835 884 3.114616 CTGCCGTGACCAAGAGCG 61.115 66.667 0.00 0.00 0.00 5.03
905 954 2.937959 GATCTCCTCCCTCCAGCCGT 62.938 65.000 0.00 0.00 0.00 5.68
910 959 1.048724 CCTCCCTCCAGCCGTCATTA 61.049 60.000 0.00 0.00 0.00 1.90
923 972 2.483876 CGTCATTACATCCGCCAAGAT 58.516 47.619 0.00 0.00 0.00 2.40
1024 1073 0.457443 TCTCGCATCTGCTTCGTCAT 59.543 50.000 0.09 0.00 39.32 3.06
1164 1213 2.456119 CGTTGTCGCTGCATCTCCC 61.456 63.158 0.00 0.00 0.00 4.30
1166 1215 4.819761 TGTCGCTGCATCTCCCGC 62.820 66.667 0.00 0.00 0.00 6.13
1352 1419 1.369091 GCAACGGCGTCCATGATTCT 61.369 55.000 15.17 0.00 0.00 2.40
1389 1464 4.463879 CCCCGGACTGCTGCTGAG 62.464 72.222 13.69 0.00 0.00 3.35
1440 1515 2.505982 CCATCACCCCCTACTGCG 59.494 66.667 0.00 0.00 0.00 5.18
1472 1547 4.415332 GTCCGCGACTCTTGCCGA 62.415 66.667 8.23 0.00 0.00 5.54
1473 1548 3.676605 TCCGCGACTCTTGCCGAA 61.677 61.111 8.23 0.00 0.00 4.30
1474 1549 3.181967 CCGCGACTCTTGCCGAAG 61.182 66.667 8.23 0.00 0.00 3.79
1475 1550 3.843240 CGCGACTCTTGCCGAAGC 61.843 66.667 0.00 0.00 40.48 3.86
1476 1551 3.491652 GCGACTCTTGCCGAAGCC 61.492 66.667 0.00 0.00 38.69 4.35
1477 1552 3.181967 CGACTCTTGCCGAAGCCG 61.182 66.667 0.00 0.00 38.69 5.52
1478 1553 3.491652 GACTCTTGCCGAAGCCGC 61.492 66.667 0.00 0.00 38.69 6.53
1479 1554 3.941657 GACTCTTGCCGAAGCCGCT 62.942 63.158 0.00 0.00 38.69 5.52
1480 1555 2.743928 CTCTTGCCGAAGCCGCTT 60.744 61.111 4.98 4.98 38.69 4.68
1481 1556 2.742372 TCTTGCCGAAGCCGCTTC 60.742 61.111 21.22 21.22 38.69 3.86
1482 1557 3.049674 CTTGCCGAAGCCGCTTCA 61.050 61.111 28.20 10.85 40.17 3.02
1483 1558 2.359850 TTGCCGAAGCCGCTTCAT 60.360 55.556 28.20 0.00 40.17 2.57
1484 1559 2.315038 CTTGCCGAAGCCGCTTCATC 62.315 60.000 28.20 19.83 40.17 2.92
1485 1560 2.819595 GCCGAAGCCGCTTCATCA 60.820 61.111 28.20 0.00 40.17 3.07
1486 1561 2.182842 GCCGAAGCCGCTTCATCAT 61.183 57.895 28.20 0.00 40.17 2.45
1487 1562 1.937391 CCGAAGCCGCTTCATCATC 59.063 57.895 28.20 5.76 40.17 2.92
1488 1563 1.502163 CCGAAGCCGCTTCATCATCC 61.502 60.000 28.20 4.99 40.17 3.51
1489 1564 0.531532 CGAAGCCGCTTCATCATCCT 60.532 55.000 28.20 0.00 40.17 3.24
1490 1565 1.673168 GAAGCCGCTTCATCATCCTT 58.327 50.000 25.19 0.00 39.95 3.36
1496 1571 2.208431 CGCTTCATCATCCTTGACTCC 58.792 52.381 0.00 0.00 33.85 3.85
1582 1657 0.735978 TTCGTGTAGCTCACATGCCG 60.736 55.000 14.09 7.42 46.44 5.69
1583 1658 1.446099 CGTGTAGCTCACATGCCGT 60.446 57.895 14.09 0.00 46.44 5.68
1596 1671 1.126846 CATGCCGTCGAAGAAGTTGAC 59.873 52.381 0.00 0.00 39.69 3.18
1643 1718 1.987807 CTCCCCGTCCTGCCATCATT 61.988 60.000 0.00 0.00 0.00 2.57
1654 1729 3.430790 CCTGCCATCATTCTCGTCAACTA 60.431 47.826 0.00 0.00 0.00 2.24
1752 2145 4.007644 CAGGAGGTGCTGCCACGA 62.008 66.667 0.00 0.00 43.00 4.35
1899 2292 0.248012 TTCGATGCTCCCGCTGTTTA 59.752 50.000 0.00 0.00 36.97 2.01
2036 2439 4.955335 TCCTATGAAGGTCCCTTGAAGTA 58.045 43.478 2.65 0.00 44.09 2.24
2059 2462 2.607750 TTCCCTCTGAGGCGCCTT 60.608 61.111 33.34 15.01 32.73 4.35
2097 2500 2.747989 GTCTGTCGTCTCTGGTATCACA 59.252 50.000 0.00 0.00 0.00 3.58
2105 2508 3.133721 GTCTCTGGTATCACAGGCTCAAT 59.866 47.826 0.00 0.00 38.98 2.57
2107 2510 4.225942 TCTCTGGTATCACAGGCTCAATTT 59.774 41.667 0.00 0.00 38.98 1.82
2169 2575 2.143876 AAGTGTTGCAAGGTCTGGTT 57.856 45.000 0.00 0.00 0.00 3.67
2266 2672 3.082579 GCTCTGATCCCGCGTCCTT 62.083 63.158 4.92 0.00 0.00 3.36
2508 2963 2.159099 GCGAACTCATGTGAGGGACATA 60.159 50.000 14.05 0.00 43.96 2.29
2624 3151 0.179100 CTGATCATTCGACGCCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
2694 3221 3.716006 CGCACGTGGTTGCAGGAG 61.716 66.667 18.88 0.00 43.15 3.69
2724 3251 0.317160 TGTGCGTGAGAAGGTCGATT 59.683 50.000 0.00 0.00 0.00 3.34
2733 3260 5.220873 CGTGAGAAGGTCGATTAGATTCTCA 60.221 44.000 18.54 18.54 45.46 3.27
2822 3350 1.274416 TGTGGAGGAGGCCCTTAGAAT 60.274 52.381 0.00 0.00 44.53 2.40
2824 3352 1.060729 GGAGGAGGCCCTTAGAATCC 58.939 60.000 0.00 0.00 44.53 3.01
2897 3466 0.036010 CTTGGATTCTCGTGGTGCCT 60.036 55.000 0.00 0.00 0.00 4.75
2927 3497 0.106167 ATGGATTCTCTCGTCGGGGA 60.106 55.000 0.00 0.00 0.00 4.81
3053 3657 5.071115 TCCATATGTGATGGGTTTGTATCGA 59.929 40.000 1.24 0.00 39.60 3.59
3127 3732 5.649782 AATCGATGAGGCAAATCTTTTGT 57.350 34.783 0.00 0.00 0.00 2.83
3179 3784 9.802039 AAGTTTGTAGTGGTCCTGATTAAATAA 57.198 29.630 0.00 0.00 0.00 1.40
3243 3848 0.034756 AGCACATACACTTGTCGGCA 59.965 50.000 0.00 0.00 0.00 5.69
3263 3868 5.987953 CGGCAAGATCATAAATCTGAGAAGA 59.012 40.000 0.00 0.00 0.00 2.87
3279 3885 7.521529 TCTGAGAAGAAAATTCGCAATACAAG 58.478 34.615 0.00 0.00 0.00 3.16
3285 3891 7.156876 AGAAAATTCGCAATACAAGAATGGA 57.843 32.000 0.00 0.00 35.11 3.41
3308 3914 5.998454 ATATTTCTTCCATCAGCGTGAAG 57.002 39.130 0.00 0.00 37.44 3.02
3316 3922 3.128764 TCCATCAGCGTGAAGTAGTAGTG 59.871 47.826 0.00 0.00 0.00 2.74
3335 3941 7.170965 AGTAGTGTGTCATTGGAATGAGAAAT 58.829 34.615 2.20 0.00 45.38 2.17
3379 3985 2.060326 TCTTGATCGACCAACACGAC 57.940 50.000 0.00 0.00 42.37 4.34
3408 4014 4.101448 CTCCCTGGCAACTCGGGG 62.101 72.222 9.46 6.08 44.93 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.611977 CTACGGTCTTCACACCACTCA 59.388 52.381 0.00 0.00 36.01 3.41
1 2 1.884579 TCTACGGTCTTCACACCACTC 59.115 52.381 0.00 0.00 36.01 3.51
2 3 1.612463 GTCTACGGTCTTCACACCACT 59.388 52.381 0.00 0.00 36.01 4.00
3 4 1.336609 GGTCTACGGTCTTCACACCAC 60.337 57.143 0.00 0.00 36.01 4.16
4 5 0.963962 GGTCTACGGTCTTCACACCA 59.036 55.000 0.00 0.00 36.01 4.17
5 6 0.963962 TGGTCTACGGTCTTCACACC 59.036 55.000 0.00 0.00 0.00 4.16
7 8 2.224113 GGTTTGGTCTACGGTCTTCACA 60.224 50.000 0.00 0.00 0.00 3.58
8 9 2.036862 AGGTTTGGTCTACGGTCTTCAC 59.963 50.000 0.00 0.00 0.00 3.18
9 10 2.036733 CAGGTTTGGTCTACGGTCTTCA 59.963 50.000 0.00 0.00 0.00 3.02
10 11 2.036862 ACAGGTTTGGTCTACGGTCTTC 59.963 50.000 0.00 0.00 0.00 2.87
11 12 2.044758 ACAGGTTTGGTCTACGGTCTT 58.955 47.619 0.00 0.00 0.00 3.01
12 13 1.713297 ACAGGTTTGGTCTACGGTCT 58.287 50.000 0.00 0.00 0.00 3.85
13 14 3.665745 TTACAGGTTTGGTCTACGGTC 57.334 47.619 0.00 0.00 0.00 4.79
14 15 3.642848 TCTTTACAGGTTTGGTCTACGGT 59.357 43.478 0.00 0.00 0.00 4.83
15 16 3.992427 GTCTTTACAGGTTTGGTCTACGG 59.008 47.826 0.00 0.00 0.00 4.02
16 17 3.992427 GGTCTTTACAGGTTTGGTCTACG 59.008 47.826 0.00 0.00 0.00 3.51
17 18 3.992427 CGGTCTTTACAGGTTTGGTCTAC 59.008 47.826 0.00 0.00 0.00 2.59
18 19 3.896888 TCGGTCTTTACAGGTTTGGTCTA 59.103 43.478 0.00 0.00 0.00 2.59
68 69 1.721133 CGAAACGCAAGACCGCAAC 60.721 57.895 0.00 0.00 43.62 4.17
99 100 0.253044 CCACGACCCTGTGATTCCAT 59.747 55.000 0.00 0.00 42.55 3.41
110 111 1.153168 CCCATCATGTCCACGACCC 60.153 63.158 0.00 0.00 0.00 4.46
114 115 1.134431 TCATCACCCATCATGTCCACG 60.134 52.381 0.00 0.00 0.00 4.94
128 129 0.782384 GTCGGTGTTGTCGTCATCAC 59.218 55.000 13.33 13.33 41.10 3.06
138 139 0.108804 AGATACTGGCGTCGGTGTTG 60.109 55.000 12.83 0.00 33.86 3.33
151 152 4.504514 GGATGCCACATGACATGAGATACT 60.505 45.833 22.19 2.11 0.00 2.12
162 163 2.186644 CCGACGGATGCCACATGA 59.813 61.111 8.64 0.00 0.00 3.07
163 164 2.125147 ACCGACGGATGCCACATG 60.125 61.111 23.38 0.00 0.00 3.21
164 165 2.125147 CACCGACGGATGCCACAT 60.125 61.111 23.38 0.00 0.00 3.21
165 166 3.621805 ACACCGACGGATGCCACA 61.622 61.111 23.38 0.00 0.00 4.17
166 167 2.495366 TACACACCGACGGATGCCAC 62.495 60.000 23.38 0.00 0.00 5.01
167 168 2.276853 TACACACCGACGGATGCCA 61.277 57.895 23.38 7.24 0.00 4.92
168 169 1.808390 GTACACACCGACGGATGCC 60.808 63.158 23.38 8.85 0.00 4.40
183 184 5.889219 TCAAAAACAACTTAAACCCGGTAC 58.111 37.500 0.00 0.00 0.00 3.34
218 239 0.948678 TTTGAGCACCAACGGCTTAC 59.051 50.000 0.00 0.00 42.78 2.34
235 256 2.568623 ACCGGAGCAAATCTGTCTTT 57.431 45.000 9.46 0.00 31.71 2.52
236 257 2.568623 AACCGGAGCAAATCTGTCTT 57.431 45.000 9.46 0.00 31.71 3.01
267 288 9.119418 TCAACTTGTCTCATGAGTTATGAAAAA 57.881 29.630 21.92 2.71 44.84 1.94
315 337 3.299977 TGCCGTGAGTGCTACCGT 61.300 61.111 0.00 0.00 0.00 4.83
426 456 2.421073 TCGCTTGAGCAATTTGAGGATG 59.579 45.455 0.00 0.00 42.21 3.51
429 459 2.982470 GTTTCGCTTGAGCAATTTGAGG 59.018 45.455 0.00 0.00 42.21 3.86
446 476 5.911280 GGAACCTTAAAGTTAAGCGTGTTTC 59.089 40.000 5.45 1.23 38.99 2.78
452 482 5.237779 TCACAAGGAACCTTAAAGTTAAGCG 59.762 40.000 5.75 2.67 38.99 4.68
478 508 0.305313 TTTTGCGTTTTCGGGAGTCG 59.695 50.000 0.00 0.00 44.29 4.18
479 509 2.478547 TTTTTGCGTTTTCGGGAGTC 57.521 45.000 0.00 0.00 44.29 3.36
480 510 3.377439 GAATTTTTGCGTTTTCGGGAGT 58.623 40.909 0.00 0.00 44.29 3.85
481 511 2.729360 GGAATTTTTGCGTTTTCGGGAG 59.271 45.455 0.00 0.00 44.29 4.30
482 512 2.362717 AGGAATTTTTGCGTTTTCGGGA 59.637 40.909 0.00 0.00 44.29 5.14
491 521 6.808212 ACTCATATCAACAAGGAATTTTTGCG 59.192 34.615 4.17 0.00 0.00 4.85
518 548 7.222805 GCATCTCGTTTACTATGATTGACTGAA 59.777 37.037 0.00 0.00 0.00 3.02
522 552 8.749841 ATAGCATCTCGTTTACTATGATTGAC 57.250 34.615 0.00 0.00 0.00 3.18
529 559 8.638629 AGAAGGTATAGCATCTCGTTTACTAT 57.361 34.615 3.91 0.00 0.00 2.12
532 562 7.096558 CGAAAGAAGGTATAGCATCTCGTTTAC 60.097 40.741 9.89 0.00 0.00 2.01
537 567 4.861210 ACGAAAGAAGGTATAGCATCTCG 58.139 43.478 9.89 12.13 0.00 4.04
538 568 7.271653 CGATAACGAAAGAAGGTATAGCATCTC 59.728 40.741 9.89 1.12 42.66 2.75
557 587 7.869016 AATAATGACACCATACTCGATAACG 57.131 36.000 0.00 0.00 35.07 3.18
559 589 9.825109 TTGAAATAATGACACCATACTCGATAA 57.175 29.630 0.00 0.00 31.59 1.75
564 594 7.865706 AGGTTGAAATAATGACACCATACTC 57.134 36.000 0.00 0.00 31.59 2.59
569 599 5.242838 GTCCAAGGTTGAAATAATGACACCA 59.757 40.000 0.00 0.00 0.00 4.17
574 604 5.004361 TGGGTCCAAGGTTGAAATAATGA 57.996 39.130 0.00 0.00 0.00 2.57
591 624 3.375299 GCATGTCTACAGTTCAATGGGTC 59.625 47.826 0.00 0.00 0.00 4.46
631 664 3.257393 CTTGAGTAGCAAGCCTGTACTG 58.743 50.000 0.00 0.00 46.67 2.74
632 665 3.601443 CTTGAGTAGCAAGCCTGTACT 57.399 47.619 0.00 0.00 46.67 2.73
647 680 2.258726 TGCACTGCAGCAGCTTGAG 61.259 57.895 26.04 8.49 40.11 3.02
687 720 0.467384 CCAGTCTAGCATGGGACCAG 59.533 60.000 5.39 0.00 33.39 4.00
695 728 1.140452 CCTGTGCATCCAGTCTAGCAT 59.860 52.381 3.87 0.00 39.43 3.79
754 787 5.109903 AGTTGTATGAAGTAGGAATGCGAC 58.890 41.667 0.00 0.00 0.00 5.19
757 790 7.464178 CGTTGTAGTTGTATGAAGTAGGAATGC 60.464 40.741 0.00 0.00 0.00 3.56
790 823 9.048446 ACTTCTGTACGTAAGAGCAAATTAAAA 57.952 29.630 12.51 0.00 43.62 1.52
793 826 8.086522 AGAACTTCTGTACGTAAGAGCAAATTA 58.913 33.333 12.51 0.00 43.62 1.40
798 847 4.795268 CAGAACTTCTGTACGTAAGAGCA 58.205 43.478 10.27 0.00 39.58 4.26
818 867 3.114616 CGCTCTTGGTCACGGCAG 61.115 66.667 0.00 0.00 0.00 4.85
878 927 1.064824 AGGGAGGAGATCAATGGGGC 61.065 60.000 0.00 0.00 0.00 5.80
881 930 1.698532 CTGGAGGGAGGAGATCAATGG 59.301 57.143 0.00 0.00 0.00 3.16
905 954 3.387699 TCTGATCTTGGCGGATGTAATGA 59.612 43.478 0.00 0.00 0.00 2.57
910 959 1.071385 GGATCTGATCTTGGCGGATGT 59.929 52.381 16.61 0.00 31.74 3.06
923 972 2.042537 AGAGCAGCCCGGATCTGA 60.043 61.111 22.53 0.00 31.19 3.27
1138 1187 4.070552 AGCGACAACGGGCCTCTC 62.071 66.667 0.84 0.00 40.15 3.20
1166 1215 4.034258 GCATGCCCGCATCCATCG 62.034 66.667 6.36 0.00 33.90 3.84
1312 1379 3.801997 AGCAGAAGCCGGGGATGG 61.802 66.667 2.18 0.00 43.56 3.51
1339 1406 0.652592 CCGACAAGAATCATGGACGC 59.347 55.000 0.00 0.00 0.00 5.19
1375 1442 1.447489 CTTCCTCAGCAGCAGTCCG 60.447 63.158 0.00 0.00 0.00 4.79
1421 1496 2.679342 GCAGTAGGGGGTGATGGCA 61.679 63.158 0.00 0.00 0.00 4.92
1461 1536 3.491652 GCGGCTTCGGCAAGAGTC 61.492 66.667 0.00 0.00 43.96 3.36
1462 1537 3.537206 AAGCGGCTTCGGCAAGAGT 62.537 57.895 9.94 0.00 43.96 3.24
1463 1538 2.743928 AAGCGGCTTCGGCAAGAG 60.744 61.111 9.94 0.00 43.96 2.85
1464 1539 2.742372 GAAGCGGCTTCGGCAAGA 60.742 61.111 25.24 0.00 43.96 3.02
1465 1540 2.315038 GATGAAGCGGCTTCGGCAAG 62.315 60.000 30.97 0.00 42.78 4.01
1466 1541 2.359850 ATGAAGCGGCTTCGGCAA 60.360 55.556 30.97 18.11 42.78 4.52
1467 1542 2.819595 GATGAAGCGGCTTCGGCA 60.820 61.111 30.97 18.97 42.78 5.69
1468 1543 2.110734 GATGATGAAGCGGCTTCGGC 62.111 60.000 30.97 25.55 42.78 5.54
1469 1544 1.502163 GGATGATGAAGCGGCTTCGG 61.502 60.000 30.97 0.00 42.78 4.30
1470 1545 0.531532 AGGATGATGAAGCGGCTTCG 60.532 55.000 30.97 0.00 42.78 3.79
1471 1546 1.332997 CAAGGATGATGAAGCGGCTTC 59.667 52.381 30.72 30.72 40.54 3.86
1472 1547 1.065199 TCAAGGATGATGAAGCGGCTT 60.065 47.619 16.36 16.36 0.00 4.35
1473 1548 0.543277 TCAAGGATGATGAAGCGGCT 59.457 50.000 0.00 0.00 0.00 5.52
1474 1549 0.659957 GTCAAGGATGATGAAGCGGC 59.340 55.000 0.00 0.00 38.01 6.53
1475 1550 2.208431 GAGTCAAGGATGATGAAGCGG 58.792 52.381 0.00 0.00 38.01 5.52
1476 1551 2.158986 AGGAGTCAAGGATGATGAAGCG 60.159 50.000 0.00 0.00 38.01 4.68
1477 1552 3.204526 CAGGAGTCAAGGATGATGAAGC 58.795 50.000 0.00 0.00 38.01 3.86
1478 1553 3.118334 AGCAGGAGTCAAGGATGATGAAG 60.118 47.826 0.00 0.00 38.01 3.02
1479 1554 2.842496 AGCAGGAGTCAAGGATGATGAA 59.158 45.455 0.00 0.00 38.01 2.57
1480 1555 2.433604 GAGCAGGAGTCAAGGATGATGA 59.566 50.000 0.00 0.00 38.01 2.92
1481 1556 2.169978 TGAGCAGGAGTCAAGGATGATG 59.830 50.000 0.00 0.00 38.01 3.07
1482 1557 2.475155 TGAGCAGGAGTCAAGGATGAT 58.525 47.619 0.00 0.00 38.01 2.45
1483 1558 1.942776 TGAGCAGGAGTCAAGGATGA 58.057 50.000 0.00 0.00 0.00 2.92
1484 1559 2.630158 CTTGAGCAGGAGTCAAGGATG 58.370 52.381 5.04 0.00 44.87 3.51
1489 1564 1.004560 CGGCTTGAGCAGGAGTCAA 60.005 57.895 5.24 0.00 44.36 3.18
1490 1565 2.210013 ACGGCTTGAGCAGGAGTCA 61.210 57.895 7.97 0.00 44.36 3.41
1496 1571 3.730761 GTGGCACGGCTTGAGCAG 61.731 66.667 0.00 3.34 44.36 4.24
1529 1604 1.066430 TGTCTAATCCCGTTGCAGTCC 60.066 52.381 0.00 0.00 0.00 3.85
1530 1605 2.000447 GTGTCTAATCCCGTTGCAGTC 59.000 52.381 0.00 0.00 0.00 3.51
1534 1609 0.108520 TCCGTGTCTAATCCCGTTGC 60.109 55.000 0.00 0.00 0.00 4.17
1539 1614 1.207329 AGTTGCTCCGTGTCTAATCCC 59.793 52.381 0.00 0.00 0.00 3.85
1582 1657 1.707637 GTCGTCGTCAACTTCTTCGAC 59.292 52.381 6.50 6.50 45.70 4.20
1583 1658 1.658373 CGTCGTCGTCAACTTCTTCGA 60.658 52.381 0.00 0.00 0.00 3.71
1635 1710 3.786635 AGTAGTTGACGAGAATGATGGC 58.213 45.455 0.00 0.00 0.00 4.40
1638 1713 4.440802 GGCTGAGTAGTTGACGAGAATGAT 60.441 45.833 0.00 0.00 0.00 2.45
1643 1718 1.174783 GGGCTGAGTAGTTGACGAGA 58.825 55.000 0.00 0.00 0.00 4.04
1665 1740 2.514824 GGCTGCTCCCGATCCAAC 60.515 66.667 0.00 0.00 0.00 3.77
1683 1758 4.368808 CACACCTCGGCAAACGCG 62.369 66.667 3.53 3.53 43.86 6.01
1689 1764 4.248842 CCCACACACACCTCGGCA 62.249 66.667 0.00 0.00 0.00 5.69
1823 2216 2.357075 CAAGACATCTGCAGCATCTGT 58.643 47.619 9.47 9.65 33.43 3.41
1860 2253 0.254178 ATGGATCTCTGCAAACCGCT 59.746 50.000 0.00 0.00 43.06 5.52
1863 2256 3.009723 TCGAAATGGATCTCTGCAAACC 58.990 45.455 0.00 0.00 0.00 3.27
1927 2320 3.628646 GAGGACGCCATGGGTTGCT 62.629 63.158 15.13 5.40 0.00 3.91
2036 2439 1.606531 GCCTCAGAGGGAAGCACAT 59.393 57.895 18.83 0.00 35.37 3.21
2059 2462 2.264480 CGCCCAAGATCCACGACA 59.736 61.111 0.00 0.00 0.00 4.35
2097 2500 2.039084 ACCAGACGAGAAAATTGAGCCT 59.961 45.455 0.00 0.00 0.00 4.58
2105 2508 1.540363 GCTCCACACCAGACGAGAAAA 60.540 52.381 0.00 0.00 0.00 2.29
2107 2510 0.827925 AGCTCCACACCAGACGAGAA 60.828 55.000 0.00 0.00 0.00 2.87
2169 2575 0.937304 GAAAGCTCTCAACACGTGCA 59.063 50.000 17.22 0.00 0.00 4.57
2211 2617 3.764466 ACGAGGGAGAGCTTGCCG 61.764 66.667 0.00 0.00 43.23 5.69
2266 2672 2.925724 ACCAACATCGAAAACACCAGA 58.074 42.857 0.00 0.00 0.00 3.86
2508 2963 2.550639 GCCCACATGACAAAGGCAAATT 60.551 45.455 0.00 0.00 43.32 1.82
2694 3221 0.038251 TCACGCACAGTCATCACCTC 60.038 55.000 0.00 0.00 0.00 3.85
2724 3251 6.305272 AGCTCAACCTGAAATGAGAATCTA 57.695 37.500 6.95 0.00 44.64 1.98
2733 3260 2.555757 GCTGTGAAGCTCAACCTGAAAT 59.444 45.455 0.00 0.00 0.00 2.17
2822 3350 2.612212 GCGTCACTCTTCTTTGTTTGGA 59.388 45.455 0.00 0.00 0.00 3.53
2824 3352 2.354510 TGGCGTCACTCTTCTTTGTTTG 59.645 45.455 0.00 0.00 0.00 2.93
2897 3466 4.621510 CGAGAGAATCCATTGAAGACCACA 60.622 45.833 0.00 0.00 33.66 4.17
2927 3497 4.322198 CCCACTGCTACATTGCAAAGAAAT 60.322 41.667 8.96 0.00 42.83 2.17
3053 3657 1.324383 ACAGAAAACCGGGCGAAAAT 58.676 45.000 6.32 0.00 0.00 1.82
3146 3751 3.985925 GGACCACTACAAACTTCTGTACG 59.014 47.826 0.00 0.00 0.00 3.67
3147 3752 4.989168 CAGGACCACTACAAACTTCTGTAC 59.011 45.833 0.00 0.00 0.00 2.90
3148 3753 4.897076 TCAGGACCACTACAAACTTCTGTA 59.103 41.667 0.00 0.00 0.00 2.74
3149 3754 3.709653 TCAGGACCACTACAAACTTCTGT 59.290 43.478 0.00 0.00 0.00 3.41
3150 3755 4.336889 TCAGGACCACTACAAACTTCTG 57.663 45.455 0.00 0.00 0.00 3.02
3151 3756 5.568620 AATCAGGACCACTACAAACTTCT 57.431 39.130 0.00 0.00 0.00 2.85
3152 3757 7.739498 TTTAATCAGGACCACTACAAACTTC 57.261 36.000 0.00 0.00 0.00 3.01
3153 3758 9.802039 TTATTTAATCAGGACCACTACAAACTT 57.198 29.630 0.00 0.00 0.00 2.66
3154 3759 9.975218 ATTATTTAATCAGGACCACTACAAACT 57.025 29.630 0.00 0.00 0.00 2.66
3179 3784 3.012518 GACCACTTGCTGCATGACTAAT 58.987 45.455 20.66 3.12 0.00 1.73
3256 3861 7.433708 TCTTGTATTGCGAATTTTCTTCTCA 57.566 32.000 0.00 0.00 0.00 3.27
3285 3891 5.882557 ACTTCACGCTGATGGAAGAAATATT 59.117 36.000 7.54 0.00 40.28 1.28
3303 3909 5.779922 TCCAATGACACACTACTACTTCAC 58.220 41.667 0.00 0.00 0.00 3.18
3308 3914 6.631016 TCTCATTCCAATGACACACTACTAC 58.369 40.000 0.00 0.00 40.32 2.73
3316 3922 7.327761 CACTCAAATTTCTCATTCCAATGACAC 59.672 37.037 0.00 0.00 40.32 3.67
3335 3941 7.686438 AACATATGCAGTATTGTCACTCAAA 57.314 32.000 1.58 0.00 39.62 2.69
3408 4014 3.385111 CACTACATTCCCCACTACTCTCC 59.615 52.174 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.