Multiple sequence alignment - TraesCS6A01G310500

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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 TraesCS6A01G310500 chr6A 100.000 2854 0 0 1 2854 546602889 546600036 0.000000e+00 5271
1 TraesCS6A01G310500 chr6A 91.824 318 24 2 287 603 305480811 305481127 2.610000e-120 442
2 TraesCS6A01G310500 chr6D 89.474 1368 84 36 1504 2854 400653040 400651716 0.000000e+00 1674
3 TraesCS6A01G310500 chr6D 86.735 882 60 24 614 1482 400653967 400653130 0.000000e+00 928
4 TraesCS6A01G310500 chr6D 87.037 594 65 9 17 603 114804313 114803725 0.000000e+00 660
5 TraesCS6A01G310500 chr6D 87.328 363 32 8 1931 2285 400566577 400566221 1.230000e-108 403
6 TraesCS6A01G310500 chr6B 88.565 1408 101 37 1389 2776 599695812 599694445 0.000000e+00 1653
7 TraesCS6A01G310500 chr6B 83.569 779 72 30 605 1371 599696799 599696065 0.000000e+00 678
8 TraesCS6A01G310500 chr6B 78.095 945 123 46 998 1887 267748889 267749804 3.260000e-144 521
9 TraesCS6A01G310500 chr6B 90.606 330 25 6 276 603 658979397 658979722 1.570000e-117 433
10 TraesCS6A01G310500 chr6B 92.063 126 6 2 1948 2073 267749815 267749936 1.050000e-39 174
11 TraesCS6A01G310500 chr6B 96.875 64 2 0 2790 2853 599694354 599694291 1.080000e-19 108
12 TraesCS6A01G310500 chr1A 91.438 619 36 7 1 604 110064144 110063528 0.000000e+00 833
13 TraesCS6A01G310500 chr1A 91.558 616 35 7 1 603 487615694 487616305 0.000000e+00 833
14 TraesCS6A01G310500 chr1A 87.597 387 33 9 1505 1887 63974569 63974194 4.370000e-118 435
15 TraesCS6A01G310500 chr1A 93.966 116 3 2 1951 2066 63974180 63974069 3.780000e-39 172
16 TraesCS6A01G310500 chr2B 92.724 536 33 3 77 607 108503766 108503232 0.000000e+00 769
17 TraesCS6A01G310500 chr5B 88.167 600 55 9 17 604 212205735 212206330 0.000000e+00 701
18 TraesCS6A01G310500 chr5B 89.394 462 32 5 1 451 457457119 457456664 1.480000e-157 566
19 TraesCS6A01G310500 chr4A 89.313 393 29 8 1499 1887 445280620 445280237 5.530000e-132 481
20 TraesCS6A01G310500 chr4A 87.277 393 37 8 1499 1887 110273623 110273240 1.210000e-118 436
21 TraesCS6A01G310500 chr4A 79.310 348 33 15 1150 1482 593482581 593482904 1.040000e-49 207
22 TraesCS6A01G310500 chr4A 93.966 116 3 2 1951 2066 110273226 110273115 3.780000e-39 172
23 TraesCS6A01G310500 chr4A 93.966 116 3 2 1951 2066 445280223 445280112 3.780000e-39 172
24 TraesCS6A01G310500 chr4A 90.551 127 8 2 1948 2073 167814146 167814269 6.330000e-37 165
25 TraesCS6A01G310500 chr3A 92.790 319 19 4 287 603 742905884 742905568 2.590000e-125 459
26 TraesCS6A01G310500 chr5A 87.532 393 36 8 1499 1887 407308286 407308669 2.610000e-120 442
27 TraesCS6A01G310500 chr7A 88.988 336 27 6 1556 1887 53341648 53341977 9.520000e-110 407
28 TraesCS6A01G310500 chr7A 91.870 123 6 2 1951 2073 53341991 53342109 4.890000e-38 169
29 TraesCS6A01G310500 chr1B 83.171 410 29 9 1504 1880 732560 732158 3.520000e-89 339
30 TraesCS6A01G310500 chr1B 75.499 351 48 22 1150 1486 732946 732620 1.380000e-28 137
31 TraesCS6A01G310500 chr2A 87.712 236 19 6 1656 1887 461740731 461740502 1.690000e-67 267
32 TraesCS6A01G310500 chr3D 90.385 104 10 0 21 124 2029033 2028930 1.380000e-28 137


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 TraesCS6A01G310500 chr6A 546600036 546602889 2853 True 5271.0 5271 100.000000 1 2854 1 chr6A.!!$R1 2853
1 TraesCS6A01G310500 chr6D 400651716 400653967 2251 True 1301.0 1674 88.104500 614 2854 2 chr6D.!!$R3 2240
2 TraesCS6A01G310500 chr6D 114803725 114804313 588 True 660.0 660 87.037000 17 603 1 chr6D.!!$R1 586
3 TraesCS6A01G310500 chr6B 599694291 599696799 2508 True 813.0 1653 89.669667 605 2853 3 chr6B.!!$R1 2248
4 TraesCS6A01G310500 chr6B 267748889 267749936 1047 False 347.5 521 85.079000 998 2073 2 chr6B.!!$F2 1075
5 TraesCS6A01G310500 chr1A 110063528 110064144 616 True 833.0 833 91.438000 1 604 1 chr1A.!!$R1 603
6 TraesCS6A01G310500 chr1A 487615694 487616305 611 False 833.0 833 91.558000 1 603 1 chr1A.!!$F1 602
7 TraesCS6A01G310500 chr1A 63974069 63974569 500 True 303.5 435 90.781500 1505 2066 2 chr1A.!!$R2 561
8 TraesCS6A01G310500 chr2B 108503232 108503766 534 True 769.0 769 92.724000 77 607 1 chr2B.!!$R1 530
9 TraesCS6A01G310500 chr5B 212205735 212206330 595 False 701.0 701 88.167000 17 604 1 chr5B.!!$F1 587
10 TraesCS6A01G310500 chr4A 445280112 445280620 508 True 326.5 481 91.639500 1499 2066 2 chr4A.!!$R2 567
11 TraesCS6A01G310500 chr4A 110273115 110273623 508 True 304.0 436 90.621500 1499 2066 2 chr4A.!!$R1 567
12 TraesCS6A01G310500 chr1B 732158 732946 788 True 238.0 339 79.335000 1150 1880 2 chr1B.!!$R1 730

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
855 876 0.309922 TCCCGACTTCTTATAGCGCG 59.69 55.0 0.0 0.0 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2620 3076 1.06706 TGGTGAACGTCAGTGAGTCTG 59.933 52.381 0.0 0.0 44.85 3.51 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
102 110 6.803807 GCAATTCCTGATAGTCAAGAACAAAC 59.196 38.462 0.00 0.00 30.49 2.93
190 202 1.078143 ATTCTTCCGTGCTGCTCCC 60.078 57.895 0.00 0.00 0.00 4.30
380 397 9.517868 AAGAGAGAGTTTGAATGAAAGATGATT 57.482 29.630 0.00 0.00 0.00 2.57
410 427 8.295288 CAGTCTTTATTGATGATAGAAATGGGC 58.705 37.037 0.00 0.00 0.00 5.36
427 444 1.626825 GGGCTATTTATACCCAGGCGA 59.373 52.381 0.00 0.00 43.64 5.54
477 497 7.469537 AGTAAGCACATAGTTACTTGAGAGT 57.530 36.000 0.00 0.00 36.29 3.24
505 525 7.398024 AGAAATTACATAGTTGCCTTGAGAGT 58.602 34.615 0.00 0.00 0.00 3.24
533 553 6.014156 AGGAAGTACATAGTTGCTTGAGAACT 60.014 38.462 0.00 0.00 34.21 3.01
649 670 1.452108 GGATTCCTGCTTGTCCCCG 60.452 63.158 0.00 0.00 0.00 5.73
657 678 3.015145 CTTGTCCCCGGACCCCAT 61.015 66.667 0.73 0.00 43.97 4.00
667 688 2.673523 GACCCCATCAGCAGCAGT 59.326 61.111 0.00 0.00 0.00 4.40
668 689 1.626356 GGACCCCATCAGCAGCAGTA 61.626 60.000 0.00 0.00 0.00 2.74
669 690 0.462759 GACCCCATCAGCAGCAGTAC 60.463 60.000 0.00 0.00 0.00 2.73
713 734 3.189285 CACTCCAACAAGTTTGCAAAGG 58.811 45.455 13.26 9.33 0.00 3.11
731 752 2.633509 GCAAAGGCCACAGCTCCAG 61.634 63.158 5.01 0.00 39.73 3.86
732 753 2.282745 AAAGGCCACAGCTCCAGC 60.283 61.111 5.01 0.00 39.73 4.85
734 755 3.857309 AAGGCCACAGCTCCAGCAC 62.857 63.158 5.01 0.00 45.16 4.40
738 759 4.994471 CACAGCTCCAGCACCGCA 62.994 66.667 0.48 0.00 45.16 5.69
740 761 2.979676 CAGCTCCAGCACCGCAAA 60.980 61.111 0.48 0.00 45.16 3.68
741 762 2.203337 AGCTCCAGCACCGCAAAA 60.203 55.556 0.48 0.00 45.16 2.44
742 763 2.256461 GCTCCAGCACCGCAAAAG 59.744 61.111 0.00 0.00 41.59 2.27
743 764 2.256461 CTCCAGCACCGCAAAAGC 59.744 61.111 0.00 0.00 0.00 3.51
744 765 3.273080 CTCCAGCACCGCAAAAGCC 62.273 63.158 0.00 0.00 0.00 4.35
747 768 2.832661 AGCACCGCAAAAGCCACA 60.833 55.556 0.00 0.00 0.00 4.17
761 782 1.821936 CCACAAAAGCCCTGCACAA 59.178 52.632 0.00 0.00 0.00 3.33
855 876 0.309922 TCCCGACTTCTTATAGCGCG 59.690 55.000 0.00 0.00 0.00 6.86
888 909 3.069300 CCTGAATCCTGATCACATCGTCT 59.931 47.826 0.00 0.00 0.00 4.18
889 910 4.297510 CTGAATCCTGATCACATCGTCTC 58.702 47.826 0.00 0.00 0.00 3.36
890 911 3.956848 TGAATCCTGATCACATCGTCTCT 59.043 43.478 0.00 0.00 0.00 3.10
891 912 4.037327 TGAATCCTGATCACATCGTCTCTC 59.963 45.833 0.00 0.00 0.00 3.20
990 1012 3.267860 GCTGAGATCGGCCTTGCG 61.268 66.667 0.00 0.00 42.27 4.85
1069 1092 4.467084 GCGCCGTGGAAGATCCCA 62.467 66.667 0.00 0.00 35.03 4.37
1078 1101 3.406595 GAAGATCCCACCGCCCTGG 62.407 68.421 0.00 0.00 46.41 4.45
1116 1139 1.553690 TTCTACTGCCCAGGGTGAGC 61.554 60.000 7.55 0.00 0.00 4.26
1120 1143 3.618780 CTGCCCAGGGTGAGCTCAC 62.619 68.421 34.25 34.25 45.72 3.51
1176 1199 0.606401 TTCCTGCCTTGCCTTCTTCG 60.606 55.000 0.00 0.00 0.00 3.79
1188 1211 1.804151 CCTTCTTCGGCGTTTCATTCA 59.196 47.619 6.85 0.00 0.00 2.57
1215 1243 2.108168 AGCGCCACACTATTCTAGGAA 58.892 47.619 2.29 0.00 0.00 3.36
1223 1251 6.183360 GCCACACTATTCTAGGAATCTTCAGA 60.183 42.308 0.00 0.00 0.00 3.27
1224 1252 7.633772 GCCACACTATTCTAGGAATCTTCAGAA 60.634 40.741 0.00 0.00 0.00 3.02
1225 1253 7.925483 CCACACTATTCTAGGAATCTTCAGAAG 59.075 40.741 3.45 3.45 31.00 2.85
1254 1294 1.536922 CCACTACCATGTAGCAGAGCG 60.537 57.143 1.28 0.00 0.00 5.03
1260 1300 2.294791 ACCATGTAGCAGAGCGATCTAC 59.705 50.000 1.25 0.00 34.74 2.59
1269 1309 3.433709 CAGAGCGATCTACTGTTGTGAG 58.566 50.000 1.25 0.00 0.00 3.51
1289 1329 4.406326 TGAGTTTGTCCAAGTGGTAGTGTA 59.594 41.667 0.00 0.00 36.34 2.90
1299 1339 5.163723 CCAAGTGGTAGTGTATTCTTGCATG 60.164 44.000 0.00 0.00 33.37 4.06
1313 1353 1.179152 TGCATGGTGAATTGCAGAGG 58.821 50.000 0.00 0.00 43.54 3.69
1319 1359 4.202245 TGGTGAATTGCAGAGGTAGTAC 57.798 45.455 0.00 0.00 0.00 2.73
1320 1360 3.838317 TGGTGAATTGCAGAGGTAGTACT 59.162 43.478 0.00 0.00 0.00 2.73
1321 1361 4.184629 GGTGAATTGCAGAGGTAGTACTG 58.815 47.826 5.39 0.00 37.22 2.74
1322 1362 4.081642 GGTGAATTGCAGAGGTAGTACTGA 60.082 45.833 5.39 0.00 36.38 3.41
1323 1363 5.479306 GTGAATTGCAGAGGTAGTACTGAA 58.521 41.667 5.39 0.00 36.38 3.02
1324 1364 5.348997 GTGAATTGCAGAGGTAGTACTGAAC 59.651 44.000 5.39 0.00 36.38 3.18
1325 1365 5.246203 TGAATTGCAGAGGTAGTACTGAACT 59.754 40.000 5.39 0.22 42.62 3.01
1326 1366 6.436218 TGAATTGCAGAGGTAGTACTGAACTA 59.564 38.462 5.39 0.00 39.80 2.24
1362 1403 8.507249 AGATGTGATGTAAAAAGACTGCTAAAC 58.493 33.333 0.00 0.00 0.00 2.01
1373 1457 8.926092 AAAAGACTGCTAAACTTCTAGGAAAT 57.074 30.769 0.00 0.00 0.00 2.17
1378 1462 7.680730 ACTGCTAAACTTCTAGGAAATCAGAA 58.319 34.615 0.00 0.00 0.00 3.02
1407 1684 2.743928 GCAGAACAGTCGGCAGGG 60.744 66.667 0.00 0.00 43.64 4.45
1428 1771 4.155462 GGGCAGTGCATATGAATGATGTAG 59.845 45.833 18.61 0.00 34.84 2.74
1429 1772 4.999311 GGCAGTGCATATGAATGATGTAGA 59.001 41.667 18.61 0.00 34.84 2.59
1430 1773 5.121925 GGCAGTGCATATGAATGATGTAGAG 59.878 44.000 18.61 0.00 34.84 2.43
1431 1774 5.930569 GCAGTGCATATGAATGATGTAGAGA 59.069 40.000 11.09 0.00 34.84 3.10
1432 1775 6.426025 GCAGTGCATATGAATGATGTAGAGAA 59.574 38.462 11.09 0.00 34.84 2.87
1433 1776 7.041576 GCAGTGCATATGAATGATGTAGAGAAA 60.042 37.037 11.09 0.00 34.84 2.52
1434 1777 9.000486 CAGTGCATATGAATGATGTAGAGAAAT 58.000 33.333 6.97 0.00 34.84 2.17
1435 1778 9.000486 AGTGCATATGAATGATGTAGAGAAATG 58.000 33.333 6.97 0.00 34.84 2.32
1436 1779 8.781196 GTGCATATGAATGATGTAGAGAAATGT 58.219 33.333 6.97 0.00 34.84 2.71
1437 1780 9.346005 TGCATATGAATGATGTAGAGAAATGTT 57.654 29.630 6.97 0.00 34.84 2.71
1438 1781 9.823098 GCATATGAATGATGTAGAGAAATGTTC 57.177 33.333 6.97 0.00 34.84 3.18
1441 1784 7.854557 TGAATGATGTAGAGAAATGTTCAGG 57.145 36.000 0.00 0.00 0.00 3.86
1442 1785 7.397221 TGAATGATGTAGAGAAATGTTCAGGT 58.603 34.615 0.00 0.00 0.00 4.00
1443 1786 7.335171 TGAATGATGTAGAGAAATGTTCAGGTG 59.665 37.037 0.00 0.00 0.00 4.00
1492 1849 6.120905 AGTCCAGTGTACATACTACTACAGG 58.879 44.000 0.00 0.00 0.00 4.00
1539 1942 9.057089 CAGTGTGTTCTATAACCTTTCTCTTTT 57.943 33.333 0.00 0.00 34.49 2.27
1552 1955 8.877808 ACCTTTCTCTTTTTCATGTGATTTTC 57.122 30.769 0.00 0.00 0.00 2.29
1702 2105 1.536943 AAGGAGACGGTGCAGGAGAC 61.537 60.000 0.00 0.00 0.00 3.36
1790 2222 4.390264 GGGAGGTACCATCAGAAATAAGC 58.610 47.826 15.94 0.00 41.20 3.09
1887 2334 1.429930 TGTCAACCACTAGGCTTGGA 58.570 50.000 12.14 0.00 39.06 3.53
1888 2335 1.347707 TGTCAACCACTAGGCTTGGAG 59.652 52.381 12.14 4.51 39.06 3.86
1890 2337 2.565834 GTCAACCACTAGGCTTGGAGTA 59.434 50.000 12.14 0.00 39.06 2.59
2066 2517 3.082698 GCACTTTGCAAGAATGTCACA 57.917 42.857 0.00 0.00 44.26 3.58
2088 2539 2.744202 GGATGTGTAAAGCTCTGGTGTG 59.256 50.000 0.00 0.00 0.00 3.82
2092 2543 2.037251 GTGTAAAGCTCTGGTGTGGAGA 59.963 50.000 0.00 0.00 33.03 3.71
2117 2572 4.959596 ACTGAAAAGATACATGCAGCAG 57.040 40.909 0.00 0.00 0.00 4.24
2128 2583 1.614160 TGCAGCAGGGGATAATGCA 59.386 52.632 0.00 0.00 45.01 3.96
2151 2606 4.161189 ACTGTGACTTGACTATCAGATGGG 59.839 45.833 0.00 0.00 0.00 4.00
2152 2607 3.118629 TGTGACTTGACTATCAGATGGGC 60.119 47.826 0.00 0.00 0.00 5.36
2154 2609 3.133542 TGACTTGACTATCAGATGGGCAG 59.866 47.826 2.03 0.61 27.35 4.85
2155 2610 3.378512 ACTTGACTATCAGATGGGCAGA 58.621 45.455 2.03 0.00 27.35 4.26
2156 2611 3.972638 ACTTGACTATCAGATGGGCAGAT 59.027 43.478 2.03 0.00 27.35 2.90
2158 2613 3.580039 TGACTATCAGATGGGCAGATGA 58.420 45.455 0.00 0.00 0.00 2.92
2160 2615 2.298446 ACTATCAGATGGGCAGATGACG 59.702 50.000 0.00 0.00 0.00 4.35
2172 2627 2.478134 GCAGATGACGATGGCTCATAAC 59.522 50.000 0.00 0.00 0.00 1.89
2174 2629 4.559502 GCAGATGACGATGGCTCATAACTA 60.560 45.833 0.00 0.00 0.00 2.24
2180 2635 4.887748 ACGATGGCTCATAACTAATCTGG 58.112 43.478 0.00 0.00 0.00 3.86
2221 2676 3.429085 GAATCCATCATGTCAACAACGC 58.571 45.455 0.00 0.00 0.00 4.84
2223 2678 0.179192 CCATCATGTCAACAACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
2242 2697 2.414138 CCGTTTAGGTGAAATCGTGTCC 59.586 50.000 0.00 0.00 34.51 4.02
2268 2723 4.731773 GCCAATGTTCTTCCAGCGAAATAG 60.732 45.833 0.00 0.00 0.00 1.73
2278 2734 2.289002 CCAGCGAAATAGGAGTTGATGC 59.711 50.000 0.00 0.00 0.00 3.91
2289 2745 1.662629 GAGTTGATGCACTCCACATCG 59.337 52.381 0.00 0.00 45.61 3.84
2312 2768 4.831698 CAGCTGGACTGCTAGAGC 57.168 61.111 5.57 0.00 41.98 4.09
2313 2769 1.143620 CAGCTGGACTGCTAGAGCC 59.856 63.158 5.57 0.00 41.98 4.70
2314 2770 1.001503 AGCTGGACTGCTAGAGCCT 59.998 57.895 1.63 0.00 42.10 4.58
2315 2771 0.260230 AGCTGGACTGCTAGAGCCTA 59.740 55.000 1.63 0.00 42.10 3.93
2316 2772 0.673437 GCTGGACTGCTAGAGCCTAG 59.327 60.000 0.00 5.20 41.18 3.02
2317 2773 1.752436 GCTGGACTGCTAGAGCCTAGA 60.752 57.143 11.96 0.00 41.18 2.43
2318 2774 2.229792 CTGGACTGCTAGAGCCTAGAG 58.770 57.143 11.96 9.04 41.18 2.43
2380 2836 1.193203 CTCGTGTGTGACATGAACTGC 59.807 52.381 0.00 0.00 42.90 4.40
2399 2855 6.500589 ACTGCTTACATGATTGGGTACTAT 57.499 37.500 0.00 0.00 0.00 2.12
2401 2857 8.207350 ACTGCTTACATGATTGGGTACTATAT 57.793 34.615 0.00 0.00 0.00 0.86
2435 2891 4.322080 ACACGACTGAAGATGACAGAAA 57.678 40.909 0.00 0.00 38.55 2.52
2494 2950 8.604035 ACTCTACAAGCATTATCATACAAAACG 58.396 33.333 0.00 0.00 0.00 3.60
2614 3070 1.729284 TCCTTTACCGTTCGGATTGC 58.271 50.000 18.28 0.00 0.00 3.56
2615 3071 1.002201 TCCTTTACCGTTCGGATTGCA 59.998 47.619 18.28 0.00 0.00 4.08
2616 3072 1.129811 CCTTTACCGTTCGGATTGCAC 59.870 52.381 18.28 0.00 0.00 4.57
2617 3073 2.073816 CTTTACCGTTCGGATTGCACT 58.926 47.619 18.28 0.00 0.00 4.40
2618 3074 1.717194 TTACCGTTCGGATTGCACTC 58.283 50.000 18.28 0.00 0.00 3.51
2619 3075 0.604073 TACCGTTCGGATTGCACTCA 59.396 50.000 18.28 0.00 0.00 3.41
2620 3076 0.949105 ACCGTTCGGATTGCACTCAC 60.949 55.000 18.28 0.00 0.00 3.51
2621 3077 0.948623 CCGTTCGGATTGCACTCACA 60.949 55.000 5.19 0.00 0.00 3.58
2622 3078 0.439985 CGTTCGGATTGCACTCACAG 59.560 55.000 6.38 0.00 0.00 3.66
2623 3079 1.795768 GTTCGGATTGCACTCACAGA 58.204 50.000 6.38 0.00 0.00 3.41
2624 3080 1.461127 GTTCGGATTGCACTCACAGAC 59.539 52.381 6.38 0.00 0.00 3.51
2625 3081 0.969149 TCGGATTGCACTCACAGACT 59.031 50.000 6.38 0.00 0.00 3.24
2664 3124 4.021104 TCTCAGTAGTTGAATGGTCACTGG 60.021 45.833 0.00 0.00 34.81 4.00
2689 3149 8.076781 GGGTTTATTCTTCTGAGTTGAACTTTC 58.923 37.037 0.00 0.00 0.00 2.62
2698 3158 6.513180 TCTGAGTTGAACTTTCGAGTAATGT 58.487 36.000 0.00 0.00 0.00 2.71
2709 3169 9.751542 AACTTTCGAGTAATGTTCCATATAGAG 57.248 33.333 0.00 0.00 31.67 2.43
2712 3172 6.549242 TCGAGTAATGTTCCATATAGAGGGA 58.451 40.000 0.00 0.00 32.35 4.20
2717 3177 4.689612 TGTTCCATATAGAGGGACAAGC 57.310 45.455 5.80 0.00 41.65 4.01
2762 3222 5.726308 TCTTCTGAATCCCACCATCTCTAAA 59.274 40.000 0.00 0.00 0.00 1.85
2773 3233 5.163683 CCACCATCTCTAAAAATGTCTGCAG 60.164 44.000 7.63 7.63 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 110 7.545615 TCATATGCTAGTGCGATTTACCTAATG 59.454 37.037 0.00 0.00 43.34 1.90
157 165 3.306019 GGAAGAATCGCACCAAACCAAAT 60.306 43.478 0.00 0.00 0.00 2.32
190 202 2.455674 TCTGTCGGAATCAACACCTG 57.544 50.000 0.00 0.00 0.00 4.00
218 230 9.036671 GGTCTAGAAGAACAGATAAATAGCAAC 57.963 37.037 0.00 0.00 30.64 4.17
355 371 9.165035 GAATCATCTTTCATTCAAACTCTCTCT 57.835 33.333 0.00 0.00 0.00 3.10
410 427 6.423001 GTGTACTTTCGCCTGGGTATAAATAG 59.577 42.308 0.00 0.00 0.00 1.73
427 444 2.162208 CGCCAAGCATCATGTGTACTTT 59.838 45.455 0.00 0.00 0.00 2.66
458 478 6.639671 CTTGACTCTCAAGTAACTATGTGC 57.360 41.667 4.13 0.00 46.50 4.57
505 525 6.014584 TCTCAAGCAACTATGTACTTCCTTGA 60.015 38.462 0.00 0.00 36.82 3.02
649 670 1.626356 TACTGCTGCTGATGGGGTCC 61.626 60.000 13.69 0.00 0.00 4.46
657 678 6.280855 TGAATTTACTAGTACTGCTGCTGA 57.719 37.500 13.69 0.00 0.00 4.26
667 688 5.521010 CGTGGCCGATTTGAATTTACTAGTA 59.479 40.000 0.00 0.00 35.63 1.82
668 689 4.331717 CGTGGCCGATTTGAATTTACTAGT 59.668 41.667 0.00 0.00 35.63 2.57
669 690 4.785341 GCGTGGCCGATTTGAATTTACTAG 60.785 45.833 0.00 0.00 35.63 2.57
713 734 2.598394 TGGAGCTGTGGCCTTTGC 60.598 61.111 3.32 5.22 39.73 3.68
738 759 0.179048 GCAGGGCTTTTGTGGCTTTT 60.179 50.000 0.00 0.00 0.00 2.27
740 761 1.761667 TGCAGGGCTTTTGTGGCTT 60.762 52.632 0.00 0.00 0.00 4.35
741 762 2.123338 TGCAGGGCTTTTGTGGCT 60.123 55.556 0.00 0.00 0.00 4.75
742 763 2.029518 GTGCAGGGCTTTTGTGGC 59.970 61.111 0.00 0.00 0.00 5.01
743 764 0.530431 GTTGTGCAGGGCTTTTGTGG 60.530 55.000 0.00 0.00 0.00 4.17
744 765 0.461135 AGTTGTGCAGGGCTTTTGTG 59.539 50.000 0.00 0.00 0.00 3.33
747 768 1.455383 CGGAGTTGTGCAGGGCTTTT 61.455 55.000 0.00 0.00 0.00 2.27
761 782 4.827087 CGAGCTGGCATGCGGAGT 62.827 66.667 12.44 0.00 38.13 3.85
855 876 1.169034 GGATTCAGGAGCCGCCATTC 61.169 60.000 0.00 0.00 40.02 2.67
888 909 2.823152 CGATAGGGATGGGGATGTGAGA 60.823 54.545 0.00 0.00 0.00 3.27
889 910 1.552337 CGATAGGGATGGGGATGTGAG 59.448 57.143 0.00 0.00 0.00 3.51
890 911 1.644509 CGATAGGGATGGGGATGTGA 58.355 55.000 0.00 0.00 0.00 3.58
891 912 0.036010 GCGATAGGGATGGGGATGTG 60.036 60.000 0.00 0.00 0.00 3.21
985 1007 2.587322 TTCATCCCCTACGCCGCAAG 62.587 60.000 0.00 0.00 0.00 4.01
990 1012 2.280186 CGCTTCATCCCCTACGCC 60.280 66.667 0.00 0.00 0.00 5.68
1061 1084 3.411517 CCAGGGCGGTGGGATCTT 61.412 66.667 0.00 0.00 33.46 2.40
1176 1199 0.810648 TGCCAGATGAATGAAACGCC 59.189 50.000 0.00 0.00 0.00 5.68
1203 1226 9.930158 ACTACTTCTGAAGATTCCTAGAATAGT 57.070 33.333 23.36 12.71 36.82 2.12
1215 1243 8.735692 GTAGTGGTACTACTACTTCTGAAGAT 57.264 38.462 31.36 10.39 45.70 2.40
1254 1294 5.297547 TGGACAAACTCACAACAGTAGATC 58.702 41.667 0.00 0.00 0.00 2.75
1260 1300 3.181497 CCACTTGGACAAACTCACAACAG 60.181 47.826 0.00 0.00 37.39 3.16
1269 1309 5.995897 AGAATACACTACCACTTGGACAAAC 59.004 40.000 1.14 0.00 38.94 2.93
1299 1339 4.081642 TCAGTACTACCTCTGCAATTCACC 60.082 45.833 0.00 0.00 0.00 4.02
1319 1359 7.326968 TCACATCTCTCACATAGTAGTTCAG 57.673 40.000 0.00 0.00 0.00 3.02
1320 1360 7.340487 ACATCACATCTCTCACATAGTAGTTCA 59.660 37.037 0.00 0.00 0.00 3.18
1321 1361 7.711846 ACATCACATCTCTCACATAGTAGTTC 58.288 38.462 0.00 0.00 0.00 3.01
1322 1362 7.652524 ACATCACATCTCTCACATAGTAGTT 57.347 36.000 0.00 0.00 0.00 2.24
1323 1363 8.753497 TTACATCACATCTCTCACATAGTAGT 57.247 34.615 0.00 0.00 0.00 2.73
1326 1366 9.376075 CTTTTTACATCACATCTCTCACATAGT 57.624 33.333 0.00 0.00 0.00 2.12
1327 1367 9.591792 TCTTTTTACATCACATCTCTCACATAG 57.408 33.333 0.00 0.00 0.00 2.23
1332 1372 6.369890 GCAGTCTTTTTACATCACATCTCTCA 59.630 38.462 0.00 0.00 0.00 3.27
1373 1457 6.061441 TGTTCTGCCTTCTTAAACATTCTGA 58.939 36.000 0.00 0.00 0.00 3.27
1378 1462 4.452455 CGACTGTTCTGCCTTCTTAAACAT 59.548 41.667 0.00 0.00 0.00 2.71
1407 1684 5.930569 TCTCTACATCATTCATATGCACTGC 59.069 40.000 0.00 0.00 0.00 4.40
1428 1771 2.887152 ACTTGCCACCTGAACATTTCTC 59.113 45.455 0.00 0.00 0.00 2.87
1429 1772 2.887152 GACTTGCCACCTGAACATTTCT 59.113 45.455 0.00 0.00 0.00 2.52
1430 1773 2.350772 CGACTTGCCACCTGAACATTTC 60.351 50.000 0.00 0.00 0.00 2.17
1431 1774 1.608590 CGACTTGCCACCTGAACATTT 59.391 47.619 0.00 0.00 0.00 2.32
1432 1775 1.202758 TCGACTTGCCACCTGAACATT 60.203 47.619 0.00 0.00 0.00 2.71
1433 1776 0.396435 TCGACTTGCCACCTGAACAT 59.604 50.000 0.00 0.00 0.00 2.71
1434 1777 0.179234 TTCGACTTGCCACCTGAACA 59.821 50.000 0.00 0.00 0.00 3.18
1435 1778 1.197721 CATTCGACTTGCCACCTGAAC 59.802 52.381 0.00 0.00 0.00 3.18
1436 1779 1.202758 ACATTCGACTTGCCACCTGAA 60.203 47.619 0.00 0.00 0.00 3.02
1437 1780 0.396435 ACATTCGACTTGCCACCTGA 59.604 50.000 0.00 0.00 0.00 3.86
1438 1781 0.518636 CACATTCGACTTGCCACCTG 59.481 55.000 0.00 0.00 0.00 4.00
1439 1782 1.237285 GCACATTCGACTTGCCACCT 61.237 55.000 1.41 0.00 0.00 4.00
1440 1783 1.210155 GCACATTCGACTTGCCACC 59.790 57.895 1.41 0.00 0.00 4.61
1441 1784 0.110056 CTGCACATTCGACTTGCCAC 60.110 55.000 9.06 0.00 35.26 5.01
1442 1785 1.236616 CCTGCACATTCGACTTGCCA 61.237 55.000 9.06 0.71 35.26 4.92
1443 1786 1.237285 ACCTGCACATTCGACTTGCC 61.237 55.000 9.06 0.00 35.26 4.52
1492 1849 5.360144 ACTGTCAGATGTACCACTATGTACC 59.640 44.000 6.91 0.00 40.29 3.34
1539 1942 4.764823 GTGGTACTGGGAAAATCACATGAA 59.235 41.667 0.00 0.00 0.00 2.57
1549 1952 1.616865 CTGTCGAGTGGTACTGGGAAA 59.383 52.381 0.00 0.00 0.00 3.13
1552 1955 0.811915 CTCTGTCGAGTGGTACTGGG 59.188 60.000 0.00 0.00 32.47 4.45
1607 2010 1.014564 CCGTCGTTCTTGCCTTCTCC 61.015 60.000 0.00 0.00 0.00 3.71
1673 2076 2.436824 GTCTCCTTTGCGCCCTCC 60.437 66.667 4.18 0.00 0.00 4.30
1702 2105 2.747855 GAGCACCGCTTCCTTGGG 60.748 66.667 0.00 0.00 39.88 4.12
1887 2334 6.845758 TTACACATACAGTAGCACCTTACT 57.154 37.500 0.00 0.00 34.26 2.24
1888 2335 7.039882 ACATTACACATACAGTAGCACCTTAC 58.960 38.462 0.00 0.00 0.00 2.34
1890 2337 6.049955 ACATTACACATACAGTAGCACCTT 57.950 37.500 0.00 0.00 0.00 3.50
2015 2466 9.706691 AAGTTCAGTCGAGAAGAAAAATACATA 57.293 29.630 0.00 0.00 0.00 2.29
2016 2467 8.499162 CAAGTTCAGTCGAGAAGAAAAATACAT 58.501 33.333 0.00 0.00 0.00 2.29
2017 2468 7.042051 CCAAGTTCAGTCGAGAAGAAAAATACA 60.042 37.037 0.00 0.00 0.00 2.29
2018 2469 7.170998 TCCAAGTTCAGTCGAGAAGAAAAATAC 59.829 37.037 0.00 0.00 0.00 1.89
2066 2517 2.639839 ACACCAGAGCTTTACACATCCT 59.360 45.455 0.00 0.00 0.00 3.24
2088 2539 6.818644 TGCATGTATCTTTTCAGTTACTCTCC 59.181 38.462 0.00 0.00 0.00 3.71
2092 2543 5.939883 TGCTGCATGTATCTTTTCAGTTACT 59.060 36.000 0.00 0.00 0.00 2.24
2117 2572 2.684881 CAAGTCACAGTGCATTATCCCC 59.315 50.000 0.00 0.00 0.00 4.81
2128 2583 4.161189 CCCATCTGATAGTCAAGTCACAGT 59.839 45.833 0.00 0.00 0.00 3.55
2151 2606 2.445565 TATGAGCCATCGTCATCTGC 57.554 50.000 0.00 0.00 36.11 4.26
2152 2607 3.987547 AGTTATGAGCCATCGTCATCTG 58.012 45.455 0.00 0.00 36.11 2.90
2154 2609 6.309980 CAGATTAGTTATGAGCCATCGTCATC 59.690 42.308 0.00 0.00 36.11 2.92
2155 2610 6.162079 CAGATTAGTTATGAGCCATCGTCAT 58.838 40.000 0.00 0.00 38.26 3.06
2156 2611 5.509670 CCAGATTAGTTATGAGCCATCGTCA 60.510 44.000 0.00 0.00 0.00 4.35
2158 2613 4.345257 ACCAGATTAGTTATGAGCCATCGT 59.655 41.667 0.00 0.00 0.00 3.73
2160 2615 6.514048 GCAAACCAGATTAGTTATGAGCCATC 60.514 42.308 0.00 0.00 0.00 3.51
2172 2627 6.970484 ACTAACAAAGTGCAAACCAGATTAG 58.030 36.000 0.00 0.00 36.93 1.73
2174 2629 5.359576 TGACTAACAAAGTGCAAACCAGATT 59.640 36.000 0.00 0.00 39.07 2.40
2180 2635 4.267357 TCGTGACTAACAAAGTGCAAAC 57.733 40.909 0.00 0.00 39.07 2.93
2221 2676 2.414138 GGACACGATTTCACCTAAACGG 59.586 50.000 0.00 0.00 39.35 4.44
2223 2678 4.612939 GCAAGGACACGATTTCACCTAAAC 60.613 45.833 0.00 0.00 0.00 2.01
2235 2690 1.202758 AGAACATTGGCAAGGACACGA 60.203 47.619 19.84 0.00 0.00 4.35
2242 2697 1.401931 CGCTGGAAGAACATTGGCAAG 60.402 52.381 5.96 0.50 34.07 4.01
2278 2734 1.642037 CTGCTTGCCGATGTGGAGTG 61.642 60.000 0.00 0.00 42.00 3.51
2312 2768 4.098654 CACACTGACTAACCATCCTCTAGG 59.901 50.000 0.00 0.00 0.00 3.02
2313 2769 4.440802 GCACACTGACTAACCATCCTCTAG 60.441 50.000 0.00 0.00 0.00 2.43
2314 2770 3.447586 GCACACTGACTAACCATCCTCTA 59.552 47.826 0.00 0.00 0.00 2.43
2315 2771 2.234908 GCACACTGACTAACCATCCTCT 59.765 50.000 0.00 0.00 0.00 3.69
2316 2772 2.028112 TGCACACTGACTAACCATCCTC 60.028 50.000 0.00 0.00 0.00 3.71
2317 2773 1.977854 TGCACACTGACTAACCATCCT 59.022 47.619 0.00 0.00 0.00 3.24
2318 2774 2.472695 TGCACACTGACTAACCATCC 57.527 50.000 0.00 0.00 0.00 3.51
2399 2855 9.093970 CTTCAGTCGTGTACCAATTCATTTATA 57.906 33.333 0.00 0.00 0.00 0.98
2401 2857 7.156000 TCTTCAGTCGTGTACCAATTCATTTA 58.844 34.615 0.00 0.00 0.00 1.40
2403 2859 5.547465 TCTTCAGTCGTGTACCAATTCATT 58.453 37.500 0.00 0.00 0.00 2.57
2404 2860 5.147330 TCTTCAGTCGTGTACCAATTCAT 57.853 39.130 0.00 0.00 0.00 2.57
2450 2906 6.605594 TGTAGAGTCACCCAATTTTTCACTTT 59.394 34.615 0.00 0.00 0.00 2.66
2528 2984 5.509832 TGATGCTCATAGAAAGCCCATAT 57.490 39.130 0.00 0.00 39.05 1.78
2614 3070 1.335182 ACGTCAGTGAGTCTGTGAGTG 59.665 52.381 0.00 0.00 43.97 3.51
2615 3071 1.681538 ACGTCAGTGAGTCTGTGAGT 58.318 50.000 0.00 0.00 43.97 3.41
2616 3072 2.033424 TGAACGTCAGTGAGTCTGTGAG 59.967 50.000 0.00 0.00 43.97 3.51
2617 3073 2.021457 TGAACGTCAGTGAGTCTGTGA 58.979 47.619 0.00 0.00 43.97 3.58
2618 3074 2.120232 GTGAACGTCAGTGAGTCTGTG 58.880 52.381 0.00 0.00 43.97 3.66
2619 3075 1.067212 GGTGAACGTCAGTGAGTCTGT 59.933 52.381 0.00 0.00 43.97 3.41
2620 3076 1.067060 TGGTGAACGTCAGTGAGTCTG 59.933 52.381 0.00 0.00 44.85 3.51
2621 3077 1.399714 TGGTGAACGTCAGTGAGTCT 58.600 50.000 0.00 0.00 0.00 3.24
2622 3078 2.029828 AGATGGTGAACGTCAGTGAGTC 60.030 50.000 0.00 0.00 37.58 3.36
2623 3079 1.964223 AGATGGTGAACGTCAGTGAGT 59.036 47.619 0.00 0.00 37.58 3.41
2624 3080 2.029918 TGAGATGGTGAACGTCAGTGAG 60.030 50.000 0.00 0.00 37.58 3.51
2625 3081 1.960689 TGAGATGGTGAACGTCAGTGA 59.039 47.619 0.00 0.00 37.58 3.41
2664 3124 7.798982 CGAAAGTTCAACTCAGAAGAATAAACC 59.201 37.037 0.00 0.00 0.00 3.27
2698 3158 4.505566 GCATGCTTGTCCCTCTATATGGAA 60.506 45.833 11.37 0.00 31.03 3.53
2709 3169 3.874392 AAATAGTTGCATGCTTGTCCC 57.126 42.857 20.33 0.18 0.00 4.46
2712 3172 6.573664 TGTCTAAAATAGTTGCATGCTTGT 57.426 33.333 20.33 5.36 0.00 3.16
2750 3210 5.675575 GCTGCAGACATTTTTAGAGATGGTG 60.676 44.000 20.43 0.00 0.00 4.17
2762 3222 1.550524 TCCGTAGAGCTGCAGACATTT 59.449 47.619 20.43 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.