Multiple sequence alignment - TraesCS7A01G500400

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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 TraesCS7A01G500400 chr7A 100.000 2528 0 0 1 2528 690425159 690427686 0.000000e+00 4669.0
1 TraesCS7A01G500400 chr7A 79.960 1507 230 44 104 1583 690517171 690518632 0.000000e+00 1044.0
2 TraesCS7A01G500400 chr7A 79.209 1568 237 43 1 1536 690195985 690194475 0.000000e+00 1007.0
3 TraesCS7A01G500400 chr7A 84.000 750 108 7 836 1583 690439330 690440069 0.000000e+00 710.0
4 TraesCS7A01G500400 chr7A 78.502 721 112 24 46 755 690438589 690439277 1.390000e-117 433.0
5 TraesCS7A01G500400 chr7A 84.112 107 16 1 1 107 690438497 690438602 4.450000e-18 102.0
6 TraesCS7A01G500400 chr7B 91.863 1659 97 19 1 1651 676452110 676453738 0.000000e+00 2281.0
7 TraesCS7A01G500400 chr7B 80.581 1550 243 35 1 1536 676211235 676209730 0.000000e+00 1142.0
8 TraesCS7A01G500400 chr7B 80.166 1563 240 39 49 1583 676535111 676533591 0.000000e+00 1105.0
9 TraesCS7A01G500400 chr7B 79.846 1295 192 35 318 1583 676993419 676994673 0.000000e+00 881.0
10 TraesCS7A01G500400 chr7B 80.016 1236 192 29 373 1583 676862190 676860985 0.000000e+00 863.0
11 TraesCS7A01G500400 chr7B 77.675 972 187 22 557 1509 676424417 676425377 1.310000e-157 566.0
12 TraesCS7A01G500400 chr7B 80.075 803 122 24 1 799 676217188 676216420 1.700000e-156 562.0
13 TraesCS7A01G500400 chr7B 77.337 353 69 8 2147 2497 318475589 318475932 5.520000e-47 198.0
14 TraesCS7A01G500400 chr7D 94.764 1356 54 5 490 1836 597574914 597573567 0.000000e+00 2095.0
15 TraesCS7A01G500400 chr7D 81.150 1618 228 39 1 1583 597570453 597568878 0.000000e+00 1227.0
16 TraesCS7A01G500400 chr7D 80.547 1609 239 40 1 1583 597619596 597621156 0.000000e+00 1170.0
17 TraesCS7A01G500400 chr7D 80.620 1548 229 41 61 1583 597546573 597545072 0.000000e+00 1131.0
18 TraesCS7A01G500400 chr7D 95.893 487 17 2 1 486 597580538 597580054 0.000000e+00 785.0
19 TraesCS7A01G500400 chr7D 90.141 142 13 1 2361 2501 21952733 21952874 1.540000e-42 183.0
20 TraesCS7A01G500400 chr2D 88.906 667 66 6 1834 2498 118818515 118819175 0.000000e+00 815.0
21 TraesCS7A01G500400 chr2D 88.168 262 28 3 1577 1836 614175241 614175501 2.440000e-80 309.0
22 TraesCS7A01G500400 chr6D 87.324 639 76 4 1834 2468 38519257 38519894 0.000000e+00 726.0
23 TraesCS7A01G500400 chr6B 84.036 664 98 8 1838 2498 155189003 155188345 1.280000e-177 632.0
24 TraesCS7A01G500400 chr5B 82.840 676 104 10 1827 2500 473480241 473479576 1.670000e-166 595.0
25 TraesCS7A01G500400 chr6A 82.222 675 104 12 1838 2504 500077158 500077824 3.650000e-158 568.0
26 TraesCS7A01G500400 chr1A 84.896 192 23 5 2298 2488 444456931 444457117 3.320000e-44 189.0
27 TraesCS7A01G500400 chr1A 100.000 29 0 0 472 500 506366566 506366538 1.000000e-03 54.7
28 TraesCS7A01G500400 chr4A 89.474 114 11 1 2387 2499 711346476 711346589 2.620000e-30 143.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G500400 chr7A 690425159 690427686 2527 False 4669 4669 100.000000 1 2528 1 chr7A.!!$F1 2527
1 TraesCS7A01G500400 chr7A 690517171 690518632 1461 False 1044 1044 79.960000 104 1583 1 chr7A.!!$F2 1479
2 TraesCS7A01G500400 chr7A 690194475 690195985 1510 True 1007 1007 79.209000 1 1536 1 chr7A.!!$R1 1535
3 TraesCS7A01G500400 chr7A 690438497 690440069 1572 False 415 710 82.204667 1 1583 3 chr7A.!!$F3 1582
4 TraesCS7A01G500400 chr7B 676452110 676453738 1628 False 2281 2281 91.863000 1 1651 1 chr7B.!!$F3 1650
5 TraesCS7A01G500400 chr7B 676209730 676211235 1505 True 1142 1142 80.581000 1 1536 1 chr7B.!!$R1 1535
6 TraesCS7A01G500400 chr7B 676533591 676535111 1520 True 1105 1105 80.166000 49 1583 1 chr7B.!!$R3 1534
7 TraesCS7A01G500400 chr7B 676993419 676994673 1254 False 881 881 79.846000 318 1583 1 chr7B.!!$F4 1265
8 TraesCS7A01G500400 chr7B 676860985 676862190 1205 True 863 863 80.016000 373 1583 1 chr7B.!!$R4 1210
9 TraesCS7A01G500400 chr7B 676424417 676425377 960 False 566 566 77.675000 557 1509 1 chr7B.!!$F2 952
10 TraesCS7A01G500400 chr7B 676216420 676217188 768 True 562 562 80.075000 1 799 1 chr7B.!!$R2 798
11 TraesCS7A01G500400 chr7D 597568878 597574914 6036 True 1661 2095 87.957000 1 1836 2 chr7D.!!$R3 1835
12 TraesCS7A01G500400 chr7D 597619596 597621156 1560 False 1170 1170 80.547000 1 1583 1 chr7D.!!$F2 1582
13 TraesCS7A01G500400 chr7D 597545072 597546573 1501 True 1131 1131 80.620000 61 1583 1 chr7D.!!$R1 1522
14 TraesCS7A01G500400 chr2D 118818515 118819175 660 False 815 815 88.906000 1834 2498 1 chr2D.!!$F1 664
15 TraesCS7A01G500400 chr6D 38519257 38519894 637 False 726 726 87.324000 1834 2468 1 chr6D.!!$F1 634
16 TraesCS7A01G500400 chr6B 155188345 155189003 658 True 632 632 84.036000 1838 2498 1 chr6B.!!$R1 660
17 TraesCS7A01G500400 chr5B 473479576 473480241 665 True 595 595 82.840000 1827 2500 1 chr5B.!!$R1 673
18 TraesCS7A01G500400 chr6A 500077158 500077824 666 False 568 568 82.222000 1838 2504 1 chr6A.!!$F1 666

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
567 5089 0.03392 TGATGTTCTGTCAGCGCAGT 59.966 50.0 11.47 0.0 37.7 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 6993 0.040514 CGCGATCAGTAGCAGAGAGG 60.041 60.0 0.0 0.0 0.0 3.69 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
71 4533 6.924612 TGACCGCATAACGCTCTAATATAAAA 59.075 34.615 0.00 0.00 41.76 1.52
72 4534 7.601130 TGACCGCATAACGCTCTAATATAAAAT 59.399 33.333 0.00 0.00 41.76 1.82
74 4536 7.386848 ACCGCATAACGCTCTAATATAAAATGT 59.613 33.333 0.00 0.00 41.76 2.71
76 4538 7.688167 CGCATAACGCTCTAATATAAAATGTGG 59.312 37.037 0.00 0.00 39.08 4.17
77 4539 8.717821 GCATAACGCTCTAATATAAAATGTGGA 58.282 33.333 0.00 0.00 37.77 4.02
79 4541 7.492352 AACGCTCTAATATAAAATGTGGACC 57.508 36.000 0.00 0.00 0.00 4.46
80 4542 5.694910 ACGCTCTAATATAAAATGTGGACCG 59.305 40.000 0.00 0.00 0.00 4.79
129 4638 3.878086 ACGTACATCTGCAACACTTTG 57.122 42.857 0.00 0.00 35.62 2.77
130 4639 3.202906 ACGTACATCTGCAACACTTTGT 58.797 40.909 0.00 0.00 34.90 2.83
203 4712 4.528596 GCCAGATAGCTAAGATGGGAAGTA 59.471 45.833 18.63 0.00 0.00 2.24
342 4851 4.595538 TGACGCCGGCAACTTCGT 62.596 61.111 28.98 15.30 43.16 3.85
352 4861 1.562575 GCAACTTCGTGTACACCGGG 61.563 60.000 20.11 11.88 0.00 5.73
468 4977 1.463693 CGTCGACTTCTACGGTGAGTG 60.464 57.143 14.70 0.00 35.51 3.51
501 5018 8.938906 CATGCATGTATGTATGTATATGTGTGT 58.061 33.333 18.91 0.00 43.18 3.72
502 5019 8.900983 TGCATGTATGTATGTATATGTGTGTT 57.099 30.769 0.00 0.00 0.00 3.32
503 5020 8.987890 TGCATGTATGTATGTATATGTGTGTTC 58.012 33.333 0.00 0.00 0.00 3.18
504 5021 8.443160 GCATGTATGTATGTATATGTGTGTTCC 58.557 37.037 0.00 0.00 0.00 3.62
505 5022 9.487790 CATGTATGTATGTATATGTGTGTTCCA 57.512 33.333 0.00 0.00 0.00 3.53
510 5027 7.569240 TGTATGTATATGTGTGTTCCAATCCA 58.431 34.615 0.00 0.00 0.00 3.41
525 5046 5.750524 TCCAATCCAAATAGTCCGATTTCA 58.249 37.500 0.00 0.00 0.00 2.69
529 5051 7.445402 CCAATCCAAATAGTCCGATTTCATACT 59.555 37.037 0.00 0.00 0.00 2.12
555 5077 3.608073 GCTAAATTTGGTGCGTGATGTTC 59.392 43.478 0.00 0.00 0.00 3.18
566 5088 0.441533 GTGATGTTCTGTCAGCGCAG 59.558 55.000 11.47 0.00 34.88 5.18
567 5089 0.033920 TGATGTTCTGTCAGCGCAGT 59.966 50.000 11.47 0.00 37.70 4.40
698 5223 5.593679 TCTTCAAGAGGTATAACTTCGGG 57.406 43.478 0.00 0.00 0.00 5.14
708 5233 0.683973 TAACTTCGGGGTGCCGTTTA 59.316 50.000 0.00 0.00 34.52 2.01
733 5258 2.775856 GCCTCGACGATCAGCTGGA 61.776 63.158 15.13 0.48 0.00 3.86
778 5303 1.625818 GATTGCTCCGGGAGATGGTAT 59.374 52.381 27.95 11.54 0.00 2.73
794 5319 4.090138 TGGTATGTAACGCATGCAAAAG 57.910 40.909 19.57 3.36 41.19 2.27
1387 5971 1.954733 GCCATACATGCAACCAGACCA 60.955 52.381 0.00 0.00 0.00 4.02
1509 6093 2.356553 GCCGACACACCGTTGCTA 60.357 61.111 0.00 0.00 0.00 3.49
1510 6094 2.380410 GCCGACACACCGTTGCTAG 61.380 63.158 0.00 0.00 0.00 3.42
1511 6095 2.380410 CCGACACACCGTTGCTAGC 61.380 63.158 8.10 8.10 0.00 3.42
1512 6096 2.716828 CGACACACCGTTGCTAGCG 61.717 63.158 10.77 0.00 0.00 4.26
1513 6097 3.011760 GACACACCGTTGCTAGCGC 62.012 63.158 10.77 0.00 0.00 5.92
1514 6098 2.738521 CACACCGTTGCTAGCGCT 60.739 61.111 17.26 17.26 36.97 5.92
1542 6126 5.278266 CGTTTGCTAGGAAAATTCAGTTCCA 60.278 40.000 11.32 0.00 46.01 3.53
1545 6129 4.635765 TGCTAGGAAAATTCAGTTCCATCG 59.364 41.667 9.52 0.23 46.01 3.84
1595 6181 7.301054 GGCTGATGATACTTTGTAACATATGC 58.699 38.462 1.58 11.88 0.00 3.14
1599 6185 8.974408 TGATGATACTTTGTAACATATGCGTAC 58.026 33.333 1.58 6.43 0.00 3.67
1623 6209 2.475818 ACCGCGGGAAAAACAAAAATC 58.524 42.857 31.76 0.00 0.00 2.17
1651 6237 5.972107 AGACATATGCTATTTGCCAATCC 57.028 39.130 1.58 0.00 42.00 3.01
1652 6238 4.456911 AGACATATGCTATTTGCCAATCCG 59.543 41.667 1.58 0.00 42.00 4.18
1653 6239 3.507233 ACATATGCTATTTGCCAATCCGG 59.493 43.478 1.58 0.00 42.00 5.14
1654 6240 2.071778 ATGCTATTTGCCAATCCGGT 57.928 45.000 0.00 0.00 42.00 5.28
1655 6241 1.846007 TGCTATTTGCCAATCCGGTT 58.154 45.000 0.00 0.00 42.00 4.44
1656 6242 2.175202 TGCTATTTGCCAATCCGGTTT 58.825 42.857 0.00 0.00 42.00 3.27
1657 6243 2.564947 TGCTATTTGCCAATCCGGTTTT 59.435 40.909 0.00 0.00 42.00 2.43
1658 6244 3.764434 TGCTATTTGCCAATCCGGTTTTA 59.236 39.130 0.00 0.00 42.00 1.52
1659 6245 4.142271 TGCTATTTGCCAATCCGGTTTTAG 60.142 41.667 0.00 0.00 42.00 1.85
1660 6246 4.097286 GCTATTTGCCAATCCGGTTTTAGA 59.903 41.667 0.00 0.00 36.97 2.10
1661 6247 5.221244 GCTATTTGCCAATCCGGTTTTAGAT 60.221 40.000 0.00 0.00 36.97 1.98
1662 6248 4.448537 TTTGCCAATCCGGTTTTAGATG 57.551 40.909 0.00 0.00 36.97 2.90
1663 6249 3.080300 TGCCAATCCGGTTTTAGATGT 57.920 42.857 0.00 0.00 36.97 3.06
1664 6250 2.752354 TGCCAATCCGGTTTTAGATGTG 59.248 45.455 0.00 0.00 36.97 3.21
1665 6251 2.099098 GCCAATCCGGTTTTAGATGTGG 59.901 50.000 0.00 0.00 36.97 4.17
1666 6252 3.352648 CCAATCCGGTTTTAGATGTGGT 58.647 45.455 0.00 0.00 0.00 4.16
1667 6253 3.377172 CCAATCCGGTTTTAGATGTGGTC 59.623 47.826 0.00 0.00 0.00 4.02
1668 6254 3.992943 ATCCGGTTTTAGATGTGGTCA 57.007 42.857 0.00 0.00 0.00 4.02
1669 6255 3.328382 TCCGGTTTTAGATGTGGTCAG 57.672 47.619 0.00 0.00 0.00 3.51
1670 6256 2.635915 TCCGGTTTTAGATGTGGTCAGT 59.364 45.455 0.00 0.00 0.00 3.41
1671 6257 2.742053 CCGGTTTTAGATGTGGTCAGTG 59.258 50.000 0.00 0.00 0.00 3.66
1672 6258 2.742053 CGGTTTTAGATGTGGTCAGTGG 59.258 50.000 0.00 0.00 0.00 4.00
1673 6259 2.488153 GGTTTTAGATGTGGTCAGTGGC 59.512 50.000 0.00 0.00 0.00 5.01
1674 6260 3.146066 GTTTTAGATGTGGTCAGTGGCA 58.854 45.455 0.00 0.00 0.00 4.92
1675 6261 2.472695 TTAGATGTGGTCAGTGGCAC 57.527 50.000 10.29 10.29 0.00 5.01
1676 6262 1.347062 TAGATGTGGTCAGTGGCACA 58.653 50.000 21.41 0.00 0.00 4.57
1677 6263 0.473755 AGATGTGGTCAGTGGCACAA 59.526 50.000 21.41 4.33 44.16 3.33
1678 6264 1.133823 AGATGTGGTCAGTGGCACAAA 60.134 47.619 21.41 3.91 44.16 2.83
1679 6265 1.680735 GATGTGGTCAGTGGCACAAAA 59.319 47.619 21.41 1.06 44.16 2.44
1680 6266 1.102154 TGTGGTCAGTGGCACAAAAG 58.898 50.000 21.41 6.73 44.16 2.27
1681 6267 1.102978 GTGGTCAGTGGCACAAAAGT 58.897 50.000 21.41 0.00 44.16 2.66
1682 6268 2.294074 GTGGTCAGTGGCACAAAAGTA 58.706 47.619 21.41 0.00 44.16 2.24
1683 6269 2.884639 GTGGTCAGTGGCACAAAAGTAT 59.115 45.455 21.41 0.00 44.16 2.12
1684 6270 3.317993 GTGGTCAGTGGCACAAAAGTATT 59.682 43.478 21.41 0.00 44.16 1.89
1685 6271 4.517453 GTGGTCAGTGGCACAAAAGTATTA 59.483 41.667 21.41 0.00 44.16 0.98
1686 6272 5.183140 GTGGTCAGTGGCACAAAAGTATTAT 59.817 40.000 21.41 0.00 44.16 1.28
1687 6273 5.182950 TGGTCAGTGGCACAAAAGTATTATG 59.817 40.000 21.41 5.12 44.16 1.90
1688 6274 5.183140 GGTCAGTGGCACAAAAGTATTATGT 59.817 40.000 21.41 0.00 44.16 2.29
1689 6275 6.086222 GTCAGTGGCACAAAAGTATTATGTG 58.914 40.000 21.41 4.37 44.16 3.21
1690 6276 5.767665 TCAGTGGCACAAAAGTATTATGTGT 59.232 36.000 21.41 0.00 44.16 3.72
1691 6277 5.858049 CAGTGGCACAAAAGTATTATGTGTG 59.142 40.000 21.41 0.00 44.16 3.82
1692 6278 5.767665 AGTGGCACAAAAGTATTATGTGTGA 59.232 36.000 21.41 0.00 44.16 3.58
1693 6279 5.856455 GTGGCACAAAAGTATTATGTGTGAC 59.144 40.000 13.86 3.70 44.16 3.67
1694 6280 5.767665 TGGCACAAAAGTATTATGTGTGACT 59.232 36.000 9.19 0.00 41.47 3.41
1695 6281 6.264292 TGGCACAAAAGTATTATGTGTGACTT 59.736 34.615 9.19 0.00 41.47 3.01
1696 6282 6.582295 GGCACAAAAGTATTATGTGTGACTTG 59.418 38.462 6.30 0.00 44.79 3.16
1697 6283 7.359595 GCACAAAAGTATTATGTGTGACTTGA 58.640 34.615 6.30 0.00 44.79 3.02
1698 6284 8.023128 GCACAAAAGTATTATGTGTGACTTGAT 58.977 33.333 6.30 0.00 44.79 2.57
1699 6285 9.897744 CACAAAAGTATTATGTGTGACTTGATT 57.102 29.630 0.00 0.00 37.56 2.57
1755 6341 9.853555 AAATAAGATCAAATTAAACACGCATGA 57.146 25.926 0.00 0.00 0.00 3.07
1756 6342 8.841444 ATAAGATCAAATTAAACACGCATGAC 57.159 30.769 0.00 0.00 0.00 3.06
1757 6343 6.252967 AGATCAAATTAAACACGCATGACA 57.747 33.333 0.00 0.00 0.00 3.58
1758 6344 6.086222 AGATCAAATTAAACACGCATGACAC 58.914 36.000 0.00 0.00 0.00 3.67
1759 6345 5.175090 TCAAATTAAACACGCATGACACA 57.825 34.783 0.00 0.00 0.00 3.72
1760 6346 5.767269 TCAAATTAAACACGCATGACACAT 58.233 33.333 0.00 0.00 0.00 3.21
1761 6347 6.903419 TCAAATTAAACACGCATGACACATA 58.097 32.000 0.00 0.00 0.00 2.29
1762 6348 7.020602 TCAAATTAAACACGCATGACACATAG 58.979 34.615 0.00 0.00 0.00 2.23
1763 6349 6.735678 AATTAAACACGCATGACACATAGA 57.264 33.333 0.00 0.00 0.00 1.98
1764 6350 6.735678 ATTAAACACGCATGACACATAGAA 57.264 33.333 0.00 0.00 0.00 2.10
1765 6351 6.546972 TTAAACACGCATGACACATAGAAA 57.453 33.333 0.00 0.00 0.00 2.52
1766 6352 5.627499 AAACACGCATGACACATAGAAAT 57.373 34.783 0.00 0.00 0.00 2.17
1767 6353 6.735678 AAACACGCATGACACATAGAAATA 57.264 33.333 0.00 0.00 0.00 1.40
1768 6354 6.925610 AACACGCATGACACATAGAAATAT 57.074 33.333 0.00 0.00 0.00 1.28
1769 6355 8.432110 AAACACGCATGACACATAGAAATATA 57.568 30.769 0.00 0.00 0.00 0.86
1770 6356 8.607441 AACACGCATGACACATAGAAATATAT 57.393 30.769 0.00 0.00 0.00 0.86
1771 6357 9.705290 AACACGCATGACACATAGAAATATATA 57.295 29.630 0.00 0.00 0.00 0.86
1772 6358 9.140286 ACACGCATGACACATAGAAATATATAC 57.860 33.333 0.00 0.00 0.00 1.47
1773 6359 8.595533 CACGCATGACACATAGAAATATATACC 58.404 37.037 0.00 0.00 0.00 2.73
1774 6360 7.764443 ACGCATGACACATAGAAATATATACCC 59.236 37.037 0.00 0.00 0.00 3.69
1775 6361 7.981789 CGCATGACACATAGAAATATATACCCT 59.018 37.037 0.00 0.00 0.00 4.34
1779 6365 8.963725 TGACACATAGAAATATATACCCTACGG 58.036 37.037 0.00 0.00 0.00 4.02
1793 6379 4.451629 CCCTACGGGCTACATAGTAATG 57.548 50.000 0.00 0.00 35.35 1.90
1794 6380 4.084287 CCCTACGGGCTACATAGTAATGA 58.916 47.826 0.00 0.00 35.35 2.57
1795 6381 4.710375 CCCTACGGGCTACATAGTAATGAT 59.290 45.833 0.00 0.00 35.35 2.45
1796 6382 5.187186 CCCTACGGGCTACATAGTAATGATT 59.813 44.000 0.00 0.00 35.35 2.57
1797 6383 6.379133 CCCTACGGGCTACATAGTAATGATTA 59.621 42.308 0.00 0.00 35.35 1.75
1798 6384 7.069578 CCCTACGGGCTACATAGTAATGATTAT 59.930 40.741 0.00 0.00 35.35 1.28
1799 6385 9.128404 CCTACGGGCTACATAGTAATGATTATA 57.872 37.037 0.00 0.00 36.54 0.98
1930 6516 2.504274 AACGACCGGTTGCAGAGGA 61.504 57.895 22.37 0.00 37.50 3.71
1944 6530 0.553612 AGAGGAGGGGCTGGGAAAAT 60.554 55.000 0.00 0.00 0.00 1.82
2022 6608 2.611800 TGCAGGGTGGCCAGAGAT 60.612 61.111 5.11 0.00 0.00 2.75
2051 6637 0.674581 CAAGCAGCGACATGGAAGGA 60.675 55.000 0.00 0.00 0.00 3.36
2107 6693 1.078759 CAGTTCGACCACGGAGATGC 61.079 60.000 0.00 0.00 40.21 3.91
2110 6696 1.248101 TTCGACCACGGAGATGCTGA 61.248 55.000 0.00 0.00 40.21 4.26
2127 6713 2.415090 GCTGACCATGATCACAAGCAAC 60.415 50.000 0.00 0.00 0.00 4.17
2166 6752 5.087323 AGAAGAGGGATTCTGTCACTAACA 58.913 41.667 0.00 0.00 41.91 2.41
2183 6770 1.289160 ACAGCCCTAATCTCTTGGCA 58.711 50.000 1.86 0.00 46.45 4.92
2203 6790 2.097466 CACATATGGCTGGAACGAAACC 59.903 50.000 7.80 0.00 0.00 3.27
2255 6845 2.587194 AGACATCATCGGCGCTGC 60.587 61.111 12.58 0.00 0.00 5.25
2275 6865 1.876156 CCAGAAGTGACTTGGAGCAAC 59.124 52.381 0.90 0.00 0.00 4.17
2350 6942 8.009974 CGTGAGATAAACGTTTTTCTGATCTTT 58.990 33.333 30.38 11.48 36.31 2.52
2384 6978 0.981277 TCCCCTAGTTGCTAGCCCAC 60.981 60.000 13.29 9.19 33.12 4.61
2385 6979 1.527370 CCCTAGTTGCTAGCCCACC 59.473 63.158 13.29 0.00 33.12 4.61
2397 6993 1.692411 AGCCCACCTTTTGTTCTCAC 58.308 50.000 0.00 0.00 0.00 3.51
2434 7030 1.800655 GCGTTCTCGATCAGTCAGCAT 60.801 52.381 0.00 0.00 39.71 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 4533 0.544357 TGAGTTCCCTCGGTCCACAT 60.544 55.000 0.00 0.00 40.85 3.21
72 4534 0.544357 ATGAGTTCCCTCGGTCCACA 60.544 55.000 0.00 0.00 40.85 4.17
74 4536 0.041238 AGATGAGTTCCCTCGGTCCA 59.959 55.000 0.00 0.00 40.85 4.02
76 4538 0.461961 CCAGATGAGTTCCCTCGGTC 59.538 60.000 0.00 0.00 40.85 4.79
77 4539 0.041238 TCCAGATGAGTTCCCTCGGT 59.959 55.000 0.00 0.00 40.85 4.69
78 4540 1.195115 TTCCAGATGAGTTCCCTCGG 58.805 55.000 0.00 0.00 40.85 4.63
79 4541 2.831333 CATTCCAGATGAGTTCCCTCG 58.169 52.381 0.00 0.00 40.85 4.63
80 4542 2.092753 TGCATTCCAGATGAGTTCCCTC 60.093 50.000 0.00 0.00 38.27 4.30
129 4638 6.869388 GCTACCTAGCTATCTGGTTATGAAAC 59.131 42.308 8.34 0.00 45.62 2.78
130 4639 6.994221 GCTACCTAGCTATCTGGTTATGAAA 58.006 40.000 8.34 0.00 45.62 2.69
155 4664 0.618968 AGGAGAAATCAGGGACGCCT 60.619 55.000 0.00 0.00 0.00 5.52
166 4675 4.504689 GCTATCTGGCTAAGCAGGAGAAAT 60.505 45.833 0.00 0.00 36.26 2.17
203 4712 2.066340 TGGAACAGAGGCGATTGGT 58.934 52.632 0.00 0.00 0.00 3.67
242 4751 1.811359 GAGCAGCAGAACAGCAAAGAT 59.189 47.619 0.00 0.00 36.85 2.40
342 4851 0.321021 ATTGTTACGCCCGGTGTACA 59.679 50.000 10.48 9.28 0.00 2.90
352 4861 4.272748 GGACCTGGATTCTTATTGTTACGC 59.727 45.833 0.00 0.00 0.00 4.42
484 5001 8.217111 TGGATTGGAACACACATATACATACAT 58.783 33.333 0.00 0.00 39.29 2.29
488 5005 7.953005 TTTGGATTGGAACACACATATACAT 57.047 32.000 0.00 0.00 39.29 2.29
492 5009 7.285401 GGACTATTTGGATTGGAACACACATAT 59.715 37.037 0.00 0.00 39.29 1.78
493 5010 6.601613 GGACTATTTGGATTGGAACACACATA 59.398 38.462 0.00 0.00 39.29 2.29
494 5011 5.418840 GGACTATTTGGATTGGAACACACAT 59.581 40.000 0.00 0.00 39.29 3.21
495 5012 4.764823 GGACTATTTGGATTGGAACACACA 59.235 41.667 0.00 0.00 39.29 3.72
496 5013 4.142687 CGGACTATTTGGATTGGAACACAC 60.143 45.833 0.00 0.00 39.29 3.82
498 5015 4.258543 TCGGACTATTTGGATTGGAACAC 58.741 43.478 0.00 0.00 39.29 3.32
499 5016 4.561500 TCGGACTATTTGGATTGGAACA 57.438 40.909 0.00 0.00 0.00 3.18
500 5017 6.094881 TGAAATCGGACTATTTGGATTGGAAC 59.905 38.462 0.00 0.00 0.00 3.62
501 5018 6.184068 TGAAATCGGACTATTTGGATTGGAA 58.816 36.000 0.00 0.00 0.00 3.53
502 5019 5.750524 TGAAATCGGACTATTTGGATTGGA 58.249 37.500 0.00 0.00 0.00 3.53
503 5020 6.639632 ATGAAATCGGACTATTTGGATTGG 57.360 37.500 0.00 0.00 0.00 3.16
504 5021 8.383318 AGTATGAAATCGGACTATTTGGATTG 57.617 34.615 0.00 0.00 0.00 2.67
525 5046 6.317642 TCACGCACCAAATTTAGCATTAGTAT 59.682 34.615 9.27 0.00 0.00 2.12
529 5051 5.105957 ACATCACGCACCAAATTTAGCATTA 60.106 36.000 9.27 0.00 0.00 1.90
555 5077 2.661566 CCAACGACTGCGCTGACAG 61.662 63.158 21.92 13.02 43.59 3.51
698 5223 1.583495 GGCTCCAAGTAAACGGCACC 61.583 60.000 0.00 0.00 0.00 5.01
708 5233 0.965866 TGATCGTCGAGGCTCCAAGT 60.966 55.000 9.32 0.00 0.00 3.16
733 5258 3.062639 CGCGAGCACTTTCTTGAATGTAT 59.937 43.478 0.00 0.00 0.00 2.29
794 5319 4.988540 TGATAAGCTGACCATAACGTATGC 59.011 41.667 0.00 0.00 34.85 3.14
828 5369 2.229792 GACCAAGAAGACATGTTGCCA 58.770 47.619 0.00 0.00 31.11 4.92
830 5372 3.316308 AGTTGACCAAGAAGACATGTTGC 59.684 43.478 0.00 0.00 31.11 4.17
833 5375 6.431234 GGAATAAGTTGACCAAGAAGACATGT 59.569 38.462 0.00 0.00 0.00 3.21
877 5452 1.673665 GACTCTTGGTGGCAGCTGG 60.674 63.158 17.12 10.31 0.00 4.85
1215 5799 0.948141 GCGACTTGAGCTTGCTGACT 60.948 55.000 0.00 0.00 0.00 3.41
1374 5958 0.675633 GCTTTGTGGTCTGGTTGCAT 59.324 50.000 0.00 0.00 0.00 3.96
1387 5971 2.200337 GGTCGGGGCAAAGCTTTGT 61.200 57.895 33.47 2.65 40.24 2.83
1509 6093 1.738099 CTAGCAAACGTGGAGCGCT 60.738 57.895 11.27 11.27 46.11 5.92
1510 6094 2.740714 CCTAGCAAACGTGGAGCGC 61.741 63.158 0.00 0.00 46.11 5.92
1512 6096 1.519408 TTTCCTAGCAAACGTGGAGC 58.481 50.000 0.00 0.00 0.00 4.70
1513 6097 4.215399 TGAATTTTCCTAGCAAACGTGGAG 59.785 41.667 0.00 0.00 0.00 3.86
1514 6098 4.138290 TGAATTTTCCTAGCAAACGTGGA 58.862 39.130 0.00 0.00 0.00 4.02
1545 6129 7.481798 CCGCAGTAATTATTCAAGTCTCAAAAC 59.518 37.037 0.00 0.00 0.00 2.43
1595 6181 1.505477 TTTTCCCGCGGTTTGGTACG 61.505 55.000 26.12 5.84 0.00 3.67
1599 6185 0.179108 TTGTTTTTCCCGCGGTTTGG 60.179 50.000 26.12 8.83 0.00 3.28
1607 6193 8.821894 TGTCTTTATTGATTTTTGTTTTTCCCG 58.178 29.630 0.00 0.00 0.00 5.14
1637 6223 2.959507 AAACCGGATTGGCAAATAGC 57.040 45.000 9.46 0.00 43.94 2.97
1643 6229 2.752354 CACATCTAAAACCGGATTGGCA 59.248 45.455 9.46 0.00 43.94 4.92
1645 6231 3.352648 ACCACATCTAAAACCGGATTGG 58.647 45.455 9.46 4.99 46.41 3.16
1651 6237 2.742053 CCACTGACCACATCTAAAACCG 59.258 50.000 0.00 0.00 0.00 4.44
1652 6238 2.488153 GCCACTGACCACATCTAAAACC 59.512 50.000 0.00 0.00 0.00 3.27
1653 6239 3.058224 GTGCCACTGACCACATCTAAAAC 60.058 47.826 0.00 0.00 32.37 2.43
1654 6240 3.146066 GTGCCACTGACCACATCTAAAA 58.854 45.455 0.00 0.00 32.37 1.52
1655 6241 2.105649 TGTGCCACTGACCACATCTAAA 59.894 45.455 0.00 0.00 37.07 1.85
1656 6242 1.696884 TGTGCCACTGACCACATCTAA 59.303 47.619 0.00 0.00 37.07 2.10
1657 6243 1.347062 TGTGCCACTGACCACATCTA 58.653 50.000 0.00 0.00 37.07 1.98
1658 6244 0.473755 TTGTGCCACTGACCACATCT 59.526 50.000 0.00 0.00 41.16 2.90
1659 6245 1.317613 TTTGTGCCACTGACCACATC 58.682 50.000 0.00 0.00 41.16 3.06
1660 6246 1.682854 CTTTTGTGCCACTGACCACAT 59.317 47.619 0.00 0.00 41.16 3.21
1661 6247 1.102154 CTTTTGTGCCACTGACCACA 58.898 50.000 0.00 0.00 39.95 4.17
1662 6248 1.102978 ACTTTTGTGCCACTGACCAC 58.897 50.000 0.00 0.00 0.00 4.16
1663 6249 2.719531 TACTTTTGTGCCACTGACCA 57.280 45.000 0.00 0.00 0.00 4.02
1664 6250 5.183140 ACATAATACTTTTGTGCCACTGACC 59.817 40.000 0.00 0.00 0.00 4.02
1665 6251 6.086222 CACATAATACTTTTGTGCCACTGAC 58.914 40.000 0.00 0.00 34.89 3.51
1666 6252 5.767665 ACACATAATACTTTTGTGCCACTGA 59.232 36.000 9.42 0.00 43.51 3.41
1667 6253 5.858049 CACACATAATACTTTTGTGCCACTG 59.142 40.000 9.42 0.00 43.51 3.66
1668 6254 5.767665 TCACACATAATACTTTTGTGCCACT 59.232 36.000 9.42 0.00 43.51 4.00
1669 6255 5.856455 GTCACACATAATACTTTTGTGCCAC 59.144 40.000 9.42 0.00 43.51 5.01
1670 6256 5.767665 AGTCACACATAATACTTTTGTGCCA 59.232 36.000 9.42 0.00 43.51 4.92
1671 6257 6.254281 AGTCACACATAATACTTTTGTGCC 57.746 37.500 9.42 0.00 43.51 5.01
1672 6258 7.359595 TCAAGTCACACATAATACTTTTGTGC 58.640 34.615 9.42 0.00 43.51 4.57
1673 6259 9.897744 AATCAAGTCACACATAATACTTTTGTG 57.102 29.630 8.33 8.33 44.85 3.33
1729 6315 9.853555 TCATGCGTGTTTAATTTGATCTTATTT 57.146 25.926 5.68 0.00 0.00 1.40
1730 6316 9.289303 GTCATGCGTGTTTAATTTGATCTTATT 57.711 29.630 5.68 0.00 0.00 1.40
1731 6317 8.458052 TGTCATGCGTGTTTAATTTGATCTTAT 58.542 29.630 5.68 0.00 0.00 1.73
1732 6318 7.748683 GTGTCATGCGTGTTTAATTTGATCTTA 59.251 33.333 5.68 0.00 0.00 2.10
1733 6319 6.582295 GTGTCATGCGTGTTTAATTTGATCTT 59.418 34.615 5.68 0.00 0.00 2.40
1734 6320 6.086222 GTGTCATGCGTGTTTAATTTGATCT 58.914 36.000 5.68 0.00 0.00 2.75
1735 6321 5.855925 TGTGTCATGCGTGTTTAATTTGATC 59.144 36.000 5.68 0.00 0.00 2.92
1736 6322 5.767269 TGTGTCATGCGTGTTTAATTTGAT 58.233 33.333 5.68 0.00 0.00 2.57
1737 6323 5.175090 TGTGTCATGCGTGTTTAATTTGA 57.825 34.783 5.68 0.00 0.00 2.69
1738 6324 7.020602 TCTATGTGTCATGCGTGTTTAATTTG 58.979 34.615 5.68 0.00 0.00 2.32
1739 6325 7.139896 TCTATGTGTCATGCGTGTTTAATTT 57.860 32.000 5.68 0.00 0.00 1.82
1740 6326 6.735678 TCTATGTGTCATGCGTGTTTAATT 57.264 33.333 5.68 0.00 0.00 1.40
1741 6327 6.735678 TTCTATGTGTCATGCGTGTTTAAT 57.264 33.333 5.68 0.00 0.00 1.40
1742 6328 6.546972 TTTCTATGTGTCATGCGTGTTTAA 57.453 33.333 5.68 0.00 0.00 1.52
1743 6329 6.735678 ATTTCTATGTGTCATGCGTGTTTA 57.264 33.333 5.68 0.00 0.00 2.01
1744 6330 5.627499 ATTTCTATGTGTCATGCGTGTTT 57.373 34.783 5.68 0.00 0.00 2.83
1745 6331 6.925610 ATATTTCTATGTGTCATGCGTGTT 57.074 33.333 5.68 0.00 0.00 3.32
1746 6332 9.140286 GTATATATTTCTATGTGTCATGCGTGT 57.860 33.333 5.68 0.00 0.00 4.49
1747 6333 8.595533 GGTATATATTTCTATGTGTCATGCGTG 58.404 37.037 0.00 0.00 0.00 5.34
1748 6334 7.764443 GGGTATATATTTCTATGTGTCATGCGT 59.236 37.037 0.00 0.00 0.00 5.24
1749 6335 7.981789 AGGGTATATATTTCTATGTGTCATGCG 59.018 37.037 0.00 0.00 0.00 4.73
1773 6359 5.916661 ATCATTACTATGTAGCCCGTAGG 57.083 43.478 5.50 0.00 39.31 3.18
1815 6401 9.911788 ATGAGGTTTAGTGAACATTCAATAGAT 57.088 29.630 7.85 0.00 38.72 1.98
1816 6402 9.383519 GATGAGGTTTAGTGAACATTCAATAGA 57.616 33.333 7.85 0.00 38.72 1.98
1817 6403 9.388506 AGATGAGGTTTAGTGAACATTCAATAG 57.611 33.333 7.85 0.00 38.72 1.73
1818 6404 9.166173 CAGATGAGGTTTAGTGAACATTCAATA 57.834 33.333 7.85 0.00 40.13 1.90
1819 6405 7.121759 CCAGATGAGGTTTAGTGAACATTCAAT 59.878 37.037 7.85 0.00 40.13 2.57
1820 6406 6.430925 CCAGATGAGGTTTAGTGAACATTCAA 59.569 38.462 7.85 0.00 40.13 2.69
1821 6407 5.939883 CCAGATGAGGTTTAGTGAACATTCA 59.060 40.000 0.00 3.84 40.13 2.57
1822 6408 6.173339 TCCAGATGAGGTTTAGTGAACATTC 58.827 40.000 0.00 0.00 40.13 2.67
1823 6409 6.126863 TCCAGATGAGGTTTAGTGAACATT 57.873 37.500 0.00 0.00 40.13 2.71
1824 6410 5.762179 TCCAGATGAGGTTTAGTGAACAT 57.238 39.130 0.00 0.00 40.13 2.71
1825 6411 5.306937 TCTTCCAGATGAGGTTTAGTGAACA 59.693 40.000 0.00 0.00 40.13 3.18
1826 6412 5.639931 GTCTTCCAGATGAGGTTTAGTGAAC 59.360 44.000 0.00 0.00 37.53 3.18
1827 6413 5.280011 GGTCTTCCAGATGAGGTTTAGTGAA 60.280 44.000 0.00 0.00 0.00 3.18
1828 6414 4.223032 GGTCTTCCAGATGAGGTTTAGTGA 59.777 45.833 0.00 0.00 0.00 3.41
1829 6415 4.223923 AGGTCTTCCAGATGAGGTTTAGTG 59.776 45.833 0.00 0.00 35.89 2.74
1830 6416 4.223923 CAGGTCTTCCAGATGAGGTTTAGT 59.776 45.833 0.00 0.00 35.89 2.24
1831 6417 4.383552 CCAGGTCTTCCAGATGAGGTTTAG 60.384 50.000 0.00 0.00 35.89 1.85
1832 6418 3.519510 CCAGGTCTTCCAGATGAGGTTTA 59.480 47.826 0.00 0.00 35.89 2.01
1930 6516 0.636101 TATGCATTTTCCCAGCCCCT 59.364 50.000 3.54 0.00 0.00 4.79
1944 6530 3.244181 TGCAGAGTTGACAGAAGTATGCA 60.244 43.478 7.31 7.31 43.10 3.96
2022 6608 1.226916 CGCTGCTTGTTGCCAAACA 60.227 52.632 0.00 0.00 44.59 2.83
2107 6693 2.815503 TGTTGCTTGTGATCATGGTCAG 59.184 45.455 9.47 0.00 0.00 3.51
2110 6696 1.536766 CGTGTTGCTTGTGATCATGGT 59.463 47.619 0.00 0.00 0.00 3.55
2140 6726 5.159273 AGTGACAGAATCCCTCTTCTTTC 57.841 43.478 0.00 0.00 33.18 2.62
2166 6752 1.289160 TGTGCCAAGAGATTAGGGCT 58.711 50.000 0.00 0.00 46.53 5.19
2183 6770 2.365582 GGTTTCGTTCCAGCCATATGT 58.634 47.619 1.24 0.00 0.00 2.29
2203 6790 0.662619 TTGTTCTTGAAGGTGCAGCG 59.337 50.000 10.78 0.00 0.00 5.18
2255 6845 1.876156 GTTGCTCCAAGTCACTTCTGG 59.124 52.381 0.00 0.00 0.00 3.86
2333 6923 8.379457 ACTAGCTTAAAGATCAGAAAAACGTT 57.621 30.769 0.00 0.00 0.00 3.99
2335 6925 9.907576 CATACTAGCTTAAAGATCAGAAAAACG 57.092 33.333 0.00 0.00 0.00 3.60
2342 6934 6.107901 AGCCCATACTAGCTTAAAGATCAG 57.892 41.667 0.00 0.00 35.22 2.90
2350 6942 2.025636 GGGGAGCCCATACTAGCTTA 57.974 55.000 8.02 0.00 44.65 3.09
2384 6978 2.810852 GCAGAGAGGTGAGAACAAAAGG 59.189 50.000 0.00 0.00 0.00 3.11
2385 6979 3.737850 AGCAGAGAGGTGAGAACAAAAG 58.262 45.455 0.00 0.00 0.00 2.27
2397 6993 0.040514 CGCGATCAGTAGCAGAGAGG 60.041 60.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.