Multiple sequence alignment - TraesCS3B01G149900

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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 TraesCS3B01G149900 chr3B 100.000 2782 0 0 1 2782 141131557 141134338 0.000000e+00 5138.0
1 TraesCS3B01G149900 chr3B 85.965 285 40 0 1006 1290 71328901 71328617 3.480000e-79 305.0
2 TraesCS3B01G149900 chr3B 82.239 259 46 0 1032 1290 71356113 71355855 1.000000e-54 224.0
3 TraesCS3B01G149900 chr3B 88.288 111 8 2 559 669 354923195 354923090 8.090000e-26 128.0
4 TraesCS3B01G149900 chr3B 83.704 135 21 1 1648 1782 71350502 71350369 2.910000e-25 126.0
5 TraesCS3B01G149900 chr3B 86.555 119 11 2 553 671 164032691 164032578 2.910000e-25 126.0
6 TraesCS3B01G149900 chr3B 86.885 61 7 1 1500 1559 71328431 71328371 1.790000e-07 67.6
7 TraesCS3B01G149900 chr3D 92.214 655 42 4 659 1307 91678248 91678899 0.000000e+00 918.0
8 TraesCS3B01G149900 chr3D 92.185 563 41 1 1 560 91677687 91678249 0.000000e+00 793.0
9 TraesCS3B01G149900 chr3D 93.474 475 27 4 2302 2773 91681746 91682219 0.000000e+00 702.0
10 TraesCS3B01G149900 chr3D 87.765 613 56 10 1405 2004 91679060 91679666 0.000000e+00 699.0
11 TraesCS3B01G149900 chr3D 88.987 227 25 0 1006 1232 45666670 45666444 5.870000e-72 281.0
12 TraesCS3B01G149900 chr3D 83.275 287 48 0 1004 1290 45686799 45686513 5.910000e-67 265.0
13 TraesCS3B01G149900 chr3D 88.525 61 7 0 1493 1553 45686268 45686208 1.070000e-09 75.0
14 TraesCS3B01G149900 chr3A 90.455 660 47 5 659 1307 107743715 107744369 0.000000e+00 856.0
15 TraesCS3B01G149900 chr3A 88.655 714 51 12 1444 2134 107754865 107755571 0.000000e+00 843.0
16 TraesCS3B01G149900 chr3A 93.269 416 23 1 145 560 107743306 107743716 2.370000e-170 608.0
17 TraesCS3B01G149900 chr3A 88.985 463 26 15 2317 2773 107755848 107756291 1.460000e-152 549.0
18 TraesCS3B01G149900 chr3A 86.667 285 38 0 1006 1290 57226878 57226594 1.610000e-82 316.0
19 TraesCS3B01G149900 chr3A 83.793 290 47 0 1004 1293 57244680 57244391 2.730000e-70 276.0
20 TraesCS3B01G149900 chr3A 84.028 288 42 4 1004 1289 545900337 545900052 9.820000e-70 274.0
21 TraesCS3B01G149900 chr3A 90.351 114 9 2 1 112 107743197 107743310 6.210000e-32 148.0
22 TraesCS3B01G149900 chr3A 82.963 135 22 1 1648 1782 57244009 57243876 1.350000e-23 121.0
23 TraesCS3B01G149900 chr3A 97.727 44 1 0 1405 1448 107744530 107744573 2.970000e-10 76.8
24 TraesCS3B01G149900 chr7B 87.931 116 10 3 553 667 354415272 354415160 1.740000e-27 134.0
25 TraesCS3B01G149900 chr2A 89.189 111 6 3 558 668 68155823 68155927 1.740000e-27 134.0
26 TraesCS3B01G149900 chr2A 85.366 123 12 3 557 679 23539849 23539965 3.760000e-24 122.0
27 TraesCS3B01G149900 chr1B 88.596 114 7 3 555 668 328139786 328139679 1.740000e-27 134.0
28 TraesCS3B01G149900 chr1A 86.992 123 10 3 557 679 77163685 77163569 1.740000e-27 134.0
29 TraesCS3B01G149900 chr6D 88.288 111 7 3 559 668 466538228 466538123 8.090000e-26 128.0
30 TraesCS3B01G149900 chr6B 86.667 120 6 6 553 672 113454741 113454850 1.050000e-24 124.0


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 TraesCS3B01G149900 chr3B 141131557 141134338 2781 False 5138.0 5138 100.0000 1 2782 1 chr3B.!!$F1 2781
1 TraesCS3B01G149900 chr3D 91677687 91682219 4532 False 778.0 918 91.4095 1 2773 4 chr3D.!!$F1 2772
2 TraesCS3B01G149900 chr3A 107754865 107756291 1426 False 696.0 843 88.8200 1444 2773 2 chr3A.!!$F2 1329
3 TraesCS3B01G149900 chr3A 107743197 107744573 1376 False 422.2 856 92.9505 1 1448 4 chr3A.!!$F1 1447

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
211 214 0.323633 CTGGATGGGCACATGTTGGA 60.324 55.0 5.94 0.00 37.47 3.53 F
1144 1155 1.608717 CCTACTGACCAAGGAGCGCT 61.609 60.0 11.27 11.27 35.17 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1292 1303 0.324943 GGCTCCACATGTGTAGGTGT 59.675 55.0 23.79 0.0 36.9 4.16 R
2218 2392 0.245539 TTCGACTTCCCTAACAGCCG 59.754 55.0 0.00 0.0 0.0 5.52 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
73 76 4.508128 CGGTGAGGCGCATACGGT 62.508 66.667 10.83 0.00 40.57 4.83
75 78 2.183300 GTGAGGCGCATACGGTCA 59.817 61.111 10.83 0.00 40.57 4.02
81 84 1.587876 GCGCATACGGTCATCGACA 60.588 57.895 0.30 0.00 42.43 4.35
107 110 4.736896 GACGTGGTCGGTGAGCCC 62.737 72.222 0.00 0.00 41.85 5.19
143 146 4.620723 ACTGACATGAATAGGGAGTACCA 58.379 43.478 0.00 0.00 43.89 3.25
175 178 3.951563 TGGATTAATGGAGGTCAAGGG 57.048 47.619 0.00 0.00 0.00 3.95
177 180 2.091885 GGATTAATGGAGGTCAAGGGCA 60.092 50.000 0.00 0.00 0.00 5.36
181 184 0.706433 ATGGAGGTCAAGGGCAACAT 59.294 50.000 0.00 0.00 39.74 2.71
211 214 0.323633 CTGGATGGGCACATGTTGGA 60.324 55.000 5.94 0.00 37.47 3.53
472 478 4.578871 TCATGCACTAACAACACTAGCAT 58.421 39.130 0.00 0.00 41.42 3.79
477 483 5.584649 TGCACTAACAACACTAGCATTATCC 59.415 40.000 0.00 0.00 0.00 2.59
482 488 6.500684 AACAACACTAGCATTATCCAACAG 57.499 37.500 0.00 0.00 0.00 3.16
487 493 6.900194 ACACTAGCATTATCCAACAGGTATT 58.100 36.000 0.00 0.00 0.00 1.89
514 520 5.945155 ACAAGCACGTTGAAAAACTCTTAA 58.055 33.333 0.00 0.00 38.60 1.85
521 527 7.431084 GCACGTTGAAAAACTCTTAAAATCTCA 59.569 33.333 0.00 0.00 0.00 3.27
568 574 8.904099 ATCTAAACCATTTAATACTCCTTCCG 57.096 34.615 0.00 0.00 0.00 4.30
569 575 7.854337 TCTAAACCATTTAATACTCCTTCCGT 58.146 34.615 0.00 0.00 0.00 4.69
570 576 6.997239 AAACCATTTAATACTCCTTCCGTC 57.003 37.500 0.00 0.00 0.00 4.79
571 577 5.032327 ACCATTTAATACTCCTTCCGTCC 57.968 43.478 0.00 0.00 0.00 4.79
572 578 4.141551 ACCATTTAATACTCCTTCCGTCCC 60.142 45.833 0.00 0.00 0.00 4.46
573 579 4.141574 CCATTTAATACTCCTTCCGTCCCA 60.142 45.833 0.00 0.00 0.00 4.37
574 580 5.433526 CATTTAATACTCCTTCCGTCCCAA 58.566 41.667 0.00 0.00 0.00 4.12
575 581 5.502089 TTTAATACTCCTTCCGTCCCAAA 57.498 39.130 0.00 0.00 0.00 3.28
576 582 5.502089 TTAATACTCCTTCCGTCCCAAAA 57.498 39.130 0.00 0.00 0.00 2.44
577 583 4.376225 AATACTCCTTCCGTCCCAAAAA 57.624 40.909 0.00 0.00 0.00 1.94
605 611 8.747538 AAATGTCTTGACCTTAGTACAACTTT 57.252 30.769 0.00 0.00 0.00 2.66
606 612 7.730364 ATGTCTTGACCTTAGTACAACTTTG 57.270 36.000 0.00 0.00 0.00 2.77
607 613 6.646267 TGTCTTGACCTTAGTACAACTTTGT 58.354 36.000 0.00 0.00 44.86 2.83
608 614 7.784037 TGTCTTGACCTTAGTACAACTTTGTA 58.216 34.615 0.00 0.00 42.35 2.41
621 627 6.760161 ACAACTTTGTACGAAAGCTAGTAC 57.240 37.500 15.82 15.82 40.16 2.73
622 628 6.510536 ACAACTTTGTACGAAAGCTAGTACT 58.489 36.000 20.43 0.00 42.53 2.73
623 629 7.651808 ACAACTTTGTACGAAAGCTAGTACTA 58.348 34.615 20.43 14.02 42.53 1.82
624 630 8.302438 ACAACTTTGTACGAAAGCTAGTACTAT 58.698 33.333 20.43 0.00 42.53 2.12
625 631 9.778993 CAACTTTGTACGAAAGCTAGTACTATA 57.221 33.333 20.43 9.22 42.53 1.31
631 637 9.778993 TGTACGAAAGCTAGTACTATAAAGTTG 57.221 33.333 20.43 0.00 42.53 3.16
632 638 9.994432 GTACGAAAGCTAGTACTATAAAGTTGA 57.006 33.333 15.55 0.00 39.86 3.18
634 640 8.954350 ACGAAAGCTAGTACTATAAAGTTGAGA 58.046 33.333 2.33 0.00 37.15 3.27
635 641 9.224058 CGAAAGCTAGTACTATAAAGTTGAGAC 57.776 37.037 2.33 0.00 37.15 3.36
637 643 9.857957 AAAGCTAGTACTATAAAGTTGAGACAC 57.142 33.333 2.33 0.00 37.15 3.67
638 644 8.810990 AGCTAGTACTATAAAGTTGAGACACT 57.189 34.615 2.33 0.00 37.15 3.55
639 645 9.245481 AGCTAGTACTATAAAGTTGAGACACTT 57.755 33.333 2.33 0.00 38.74 3.16
648 654 8.934023 ATAAAGTTGAGACACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
649 655 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
650 656 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
651 657 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
652 658 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
653 659 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
654 660 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
655 661 2.640826 ACACTTATTTTGGGACGGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
656 662 3.073356 ACACTTATTTTGGGACGGAGGAA 59.927 43.478 0.00 0.00 0.00 3.36
657 663 3.689649 CACTTATTTTGGGACGGAGGAAG 59.310 47.826 0.00 0.00 0.00 3.46
691 697 6.098679 TGCATTACACAAAGCATCCATTTAC 58.901 36.000 0.00 0.00 31.05 2.01
765 771 8.519799 AATGTTTATCTAGTGGTATTGGTTGG 57.480 34.615 0.00 0.00 0.00 3.77
769 775 3.522759 TCTAGTGGTATTGGTTGGGTGA 58.477 45.455 0.00 0.00 0.00 4.02
777 783 4.142556 GGTATTGGTTGGGTGATTTGTACG 60.143 45.833 0.00 0.00 0.00 3.67
797 803 3.749609 ACGTAGCTTGTGGGTTACATTTC 59.250 43.478 0.00 0.00 39.48 2.17
834 840 3.876914 TCTGAAATTTTCTGCTCACACGT 59.123 39.130 10.33 0.00 0.00 4.49
898 904 7.961351 TCCATCTGCTTTAATTCTTGGAAAAA 58.039 30.769 0.00 0.00 0.00 1.94
923 929 7.818493 TCAACTTCTTTTCGATGATACAGAG 57.182 36.000 0.00 0.00 0.00 3.35
940 946 5.779529 ACAGAGATGCATGTTTTCTTGTT 57.220 34.783 2.46 0.00 0.00 2.83
956 962 7.901874 TTTCTTGTTAATTAACGTTGCTCAC 57.098 32.000 20.51 1.95 39.00 3.51
1038 1049 2.417924 GCTCATGATCGACACCAAGTCT 60.418 50.000 0.00 0.00 45.32 3.24
1053 1064 3.209410 CAAGTCTCAGAAGGTGTGCTTT 58.791 45.455 0.00 0.00 0.00 3.51
1087 1098 1.848932 CGACGTCGTGGAGTTCCTCA 61.849 60.000 29.08 0.00 36.82 3.86
1144 1155 1.608717 CCTACTGACCAAGGAGCGCT 61.609 60.000 11.27 11.27 35.17 5.92
1159 1170 2.747460 GCTTGGTCGGCAGCATCA 60.747 61.111 0.00 0.00 35.95 3.07
1210 1221 2.812358 TGCGAACTACAAGAGCAAGA 57.188 45.000 0.00 0.00 34.66 3.02
1211 1222 3.319137 TGCGAACTACAAGAGCAAGAT 57.681 42.857 0.00 0.00 34.66 2.40
1235 1246 4.090588 CCTTAGCCCGGCCGTCAA 62.091 66.667 26.12 10.86 0.00 3.18
1291 1302 0.027979 CACACAACTCAGCAACGGTG 59.972 55.000 0.00 0.00 0.00 4.94
1292 1303 0.107897 ACACAACTCAGCAACGGTGA 60.108 50.000 3.55 0.00 37.74 4.02
1293 1304 0.304705 CACAACTCAGCAACGGTGAC 59.695 55.000 3.55 0.00 35.04 3.67
1294 1305 0.107897 ACAACTCAGCAACGGTGACA 60.108 50.000 3.55 0.00 35.04 3.58
1295 1306 0.304705 CAACTCAGCAACGGTGACAC 59.695 55.000 3.55 0.00 35.04 3.67
1307 1324 1.808411 GGTGACACCTACACATGTGG 58.192 55.000 28.64 14.54 39.65 4.17
1310 1327 1.001974 TGACACCTACACATGTGGAGC 59.998 52.381 29.74 17.61 40.22 4.70
1328 1381 1.827969 AGCCTGTGGATATCTATCGGC 59.172 52.381 18.05 18.05 36.41 5.54
1333 1386 4.023622 CCTGTGGATATCTATCGGCGATAG 60.024 50.000 38.37 38.37 42.22 2.08
1370 1423 5.674569 GCCCTAGATGCAAATGTTATATGCG 60.675 44.000 0.00 0.00 42.91 4.73
1384 1437 2.434658 TATGCGCAGGGCTATGACGG 62.435 60.000 18.32 0.00 44.05 4.79
1452 1559 1.961180 CTGTCGGGGATGACCTGTCC 61.961 65.000 0.00 0.00 46.44 4.02
1503 1610 1.033746 CGCTGTTGGGCATCAAGGAT 61.034 55.000 0.00 0.00 35.80 3.24
1554 1661 1.810030 CGGCAAGGAAGAGGTACGC 60.810 63.158 0.00 0.00 0.00 4.42
1572 1679 5.579511 GGTACGCAGTGCTCTAATTTCTTTA 59.420 40.000 14.33 0.00 45.73 1.85
1623 1741 6.463995 TTGCTCAAGTTGGTGATTTACTTT 57.536 33.333 2.34 0.00 30.08 2.66
1653 1772 7.139896 TGTGTGTTTGTGTATGTATGGATTC 57.860 36.000 0.00 0.00 0.00 2.52
1724 1843 2.422479 CGTCCTGTCGGATGTCTTTCTA 59.578 50.000 0.00 0.00 42.43 2.10
1760 1879 1.472376 CGCCTCAAGAGAGAACATCCC 60.472 57.143 0.00 0.00 44.98 3.85
1775 1894 2.591915 TCCCGAGGGAGTCATTCAC 58.408 57.895 6.80 0.00 39.76 3.18
1776 1895 0.252057 TCCCGAGGGAGTCATTCACA 60.252 55.000 6.80 0.00 39.76 3.58
1791 1910 4.877823 TCATTCACATATGACTTGGTGCTC 59.122 41.667 10.38 0.00 33.38 4.26
1792 1911 3.266510 TCACATATGACTTGGTGCTCC 57.733 47.619 10.38 0.00 0.00 4.70
1807 1926 5.445964 TGGTGCTCCCTATTTTAGAATTCC 58.554 41.667 0.65 0.00 0.00 3.01
1849 1968 9.480861 TCGATATCATATTTATGAGGAAGGAGT 57.519 33.333 3.12 0.00 45.01 3.85
1850 1969 9.743057 CGATATCATATTTATGAGGAAGGAGTC 57.257 37.037 3.12 0.00 45.01 3.36
1873 1992 6.531948 GTCATATGTGAGTGACTTGGAACTAC 59.468 42.308 1.90 0.00 41.10 2.73
1877 1996 5.357257 TGTGAGTGACTTGGAACTACTTTC 58.643 41.667 0.00 0.00 0.00 2.62
1885 2004 6.984474 TGACTTGGAACTACTTTCACTTACTG 59.016 38.462 0.00 0.00 35.70 2.74
1898 2025 8.947115 ACTTTCACTTACTGCCATAAGTTATTC 58.053 33.333 6.92 0.00 41.62 1.75
1923 2052 8.966868 TCATAGTGAATTCCAAATTTTACTCCC 58.033 33.333 2.27 0.00 0.00 4.30
1951 2080 5.812127 GTGTCAATTTGGGATATTTCTTGCC 59.188 40.000 0.00 0.00 0.00 4.52
2010 2139 6.407202 ACCATAGTTAAGCAAGTTGGTCTAG 58.593 40.000 8.24 0.00 29.70 2.43
2043 2172 5.820926 TTTAATGTTTTGCATCGTTCTGC 57.179 34.783 0.00 1.35 42.62 4.26
2047 2176 1.786579 GTTTTGCATCGTTCTGCCAAC 59.213 47.619 0.00 5.03 41.58 3.77
2049 2178 2.177394 TTGCATCGTTCTGCCAACTA 57.823 45.000 0.00 0.00 41.58 2.24
2053 2182 1.066143 CATCGTTCTGCCAACTAGGGT 60.066 52.381 0.00 0.00 38.09 4.34
2066 2195 5.186992 GCCAACTAGGGTCCATTGTTAATTT 59.813 40.000 3.05 0.00 38.09 1.82
2108 2237 2.322355 CTCACATCGGCAGAGGAATT 57.678 50.000 5.30 0.00 31.71 2.17
2159 2323 3.151022 GAGCCAGTCCCCTCTCCG 61.151 72.222 0.00 0.00 0.00 4.63
2179 2353 1.479730 GTCGACCGAGGTAGGGATTTT 59.520 52.381 3.51 0.00 35.02 1.82
2180 2354 2.689983 GTCGACCGAGGTAGGGATTTTA 59.310 50.000 3.51 0.00 35.02 1.52
2183 2357 3.867493 CGACCGAGGTAGGGATTTTAAAC 59.133 47.826 0.00 0.00 35.02 2.01
2185 2359 3.588396 ACCGAGGTAGGGATTTTAAACCA 59.412 43.478 0.00 0.00 35.02 3.67
2189 2363 3.264964 AGGTAGGGATTTTAAACCAGCGA 59.735 43.478 0.00 0.00 32.43 4.93
2209 2383 0.251787 TGGTGACAGCAGCTAGAGGA 60.252 55.000 2.50 0.00 42.84 3.71
2210 2384 0.898320 GGTGACAGCAGCTAGAGGAA 59.102 55.000 0.00 0.00 39.38 3.36
2212 2386 0.534412 TGACAGCAGCTAGAGGAAGC 59.466 55.000 0.00 0.00 43.11 3.86
2218 2392 2.278923 GCTAGAGGAAGCGACGGC 60.279 66.667 0.00 0.00 40.37 5.68
2219 2393 2.024871 CTAGAGGAAGCGACGGCG 59.975 66.667 6.12 6.12 46.35 6.46
2220 2394 3.471244 CTAGAGGAAGCGACGGCGG 62.471 68.421 15.06 0.00 46.35 6.13
2234 4128 1.449778 GGCGGCTGTTAGGGAAGTC 60.450 63.158 0.00 0.00 0.00 3.01
2239 4133 2.677037 CGGCTGTTAGGGAAGTCGAATT 60.677 50.000 0.00 0.00 44.07 2.17
2301 4197 8.732746 ATGCTTATATTAGTTTTCGTGTCCTT 57.267 30.769 0.00 0.00 0.00 3.36
2302 4198 8.556213 TGCTTATATTAGTTTTCGTGTCCTTT 57.444 30.769 0.00 0.00 0.00 3.11
2303 4199 9.005777 TGCTTATATTAGTTTTCGTGTCCTTTT 57.994 29.630 0.00 0.00 0.00 2.27
2304 4200 9.274065 GCTTATATTAGTTTTCGTGTCCTTTTG 57.726 33.333 0.00 0.00 0.00 2.44
2307 4203 5.883503 TTAGTTTTCGTGTCCTTTTGTGT 57.116 34.783 0.00 0.00 0.00 3.72
2308 4204 4.776795 AGTTTTCGTGTCCTTTTGTGTT 57.223 36.364 0.00 0.00 0.00 3.32
2309 4205 4.481463 AGTTTTCGTGTCCTTTTGTGTTG 58.519 39.130 0.00 0.00 0.00 3.33
2310 4206 4.216687 AGTTTTCGTGTCCTTTTGTGTTGA 59.783 37.500 0.00 0.00 0.00 3.18
2311 4207 4.768130 TTTCGTGTCCTTTTGTGTTGAA 57.232 36.364 0.00 0.00 0.00 2.69
2312 4208 4.768130 TTCGTGTCCTTTTGTGTTGAAA 57.232 36.364 0.00 0.00 0.00 2.69
2313 4209 4.974368 TCGTGTCCTTTTGTGTTGAAAT 57.026 36.364 0.00 0.00 0.00 2.17
2315 4211 6.055231 TCGTGTCCTTTTGTGTTGAAATAG 57.945 37.500 0.00 0.00 0.00 1.73
2353 4310 7.880105 AGTTTCAATGAAATCTGGAGAAAGTC 58.120 34.615 11.87 0.00 33.97 3.01
2354 4311 6.486253 TTCAATGAAATCTGGAGAAAGTCG 57.514 37.500 0.00 0.00 0.00 4.18
2355 4312 5.793817 TCAATGAAATCTGGAGAAAGTCGA 58.206 37.500 0.00 0.00 0.00 4.20
2370 4327 6.226787 AGAAAGTCGAAAGATCTCAACACAT 58.773 36.000 0.00 0.00 45.19 3.21
2393 4350 5.482006 TCCACAACATCACTAATGAGACAG 58.518 41.667 0.00 0.00 38.57 3.51
2432 4389 3.349022 ACGGTTTTCACTTTTCAGACCA 58.651 40.909 0.00 0.00 0.00 4.02
2477 4434 3.003897 TCAAATGGTTCGTTAGGTTGTGC 59.996 43.478 0.00 0.00 0.00 4.57
2515 4476 9.726034 CATTATTGCAAGTAAAAATCAAACGAC 57.274 29.630 4.94 0.00 0.00 4.34
2554 4516 3.882888 GGAGATCACCAAACACTTCAACA 59.117 43.478 4.05 0.00 0.00 3.33
2628 4590 2.816958 CGCATCAGCTCGTTGGCT 60.817 61.111 0.00 0.00 44.10 4.75
2715 4677 0.327000 CCTTCCCCATCTCCCTCAGT 60.327 60.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 51 1.815421 GCGCCTCACCGTCATTCAT 60.815 57.895 0.00 0.00 0.00 2.57
53 56 2.183300 GTATGCGCCTCACCGTCA 59.817 61.111 4.18 0.00 0.00 4.35
59 62 1.067416 GATGACCGTATGCGCCTCA 59.933 57.895 4.18 0.84 36.67 3.86
73 76 2.194800 GTCGAATGCTCTGTCGATGA 57.805 50.000 0.00 0.00 46.91 2.92
75 78 0.452184 ACGTCGAATGCTCTGTCGAT 59.548 50.000 0.00 0.00 46.91 3.59
81 84 4.891566 GACCACGTCGAATGCTCT 57.108 55.556 0.00 0.00 0.00 4.09
107 110 2.946564 TGTCAGTCTTCTGCACATACG 58.053 47.619 0.00 0.00 41.10 3.06
143 146 8.502738 ACCTCCATTAATCCAACTACAATATGT 58.497 33.333 0.00 0.00 0.00 2.29
177 180 3.056393 CCATCCAGCAACATGTTCATGTT 60.056 43.478 20.87 20.87 44.79 2.71
181 184 1.548081 CCCATCCAGCAACATGTTCA 58.452 50.000 8.48 0.00 0.00 3.18
211 214 1.766461 CCCCCTCTACCCTTGCGAT 60.766 63.158 0.00 0.00 0.00 4.58
381 384 6.550163 AGGTTAGTTAGGTACTTCTCACTCA 58.450 40.000 0.00 0.00 41.75 3.41
472 478 7.282224 GTGCTTGTATGAATACCTGTTGGATAA 59.718 37.037 0.00 0.00 37.04 1.75
477 483 4.391830 ACGTGCTTGTATGAATACCTGTTG 59.608 41.667 0.00 0.00 32.33 3.33
482 488 5.539582 TTCAACGTGCTTGTATGAATACC 57.460 39.130 0.00 0.00 32.33 2.73
487 493 5.295787 AGAGTTTTTCAACGTGCTTGTATGA 59.704 36.000 0.00 0.00 38.03 2.15
514 520 3.589288 AGTTTAGACTGGGGCTGAGATTT 59.411 43.478 0.00 0.00 33.99 2.17
521 527 3.517612 TGTAAGAGTTTAGACTGGGGCT 58.482 45.455 0.00 0.00 35.88 5.19
579 585 9.841295 AAAGTTGTACTAAGGTCAAGACATTTA 57.159 29.630 5.39 1.73 36.63 1.40
580 586 8.621286 CAAAGTTGTACTAAGGTCAAGACATTT 58.379 33.333 5.39 0.65 36.63 2.32
581 587 7.773690 ACAAAGTTGTACTAAGGTCAAGACATT 59.226 33.333 5.41 5.41 40.16 2.71
582 588 7.280356 ACAAAGTTGTACTAAGGTCAAGACAT 58.720 34.615 2.29 0.00 40.16 3.06
583 589 6.646267 ACAAAGTTGTACTAAGGTCAAGACA 58.354 36.000 2.29 0.00 40.16 3.41
597 603 7.651808 AGTACTAGCTTTCGTACAAAGTTGTA 58.348 34.615 17.43 0.00 42.35 2.41
598 604 6.510536 AGTACTAGCTTTCGTACAAAGTTGT 58.489 36.000 17.43 1.75 44.86 3.32
599 605 8.684973 ATAGTACTAGCTTTCGTACAAAGTTG 57.315 34.615 8.85 9.99 38.69 3.16
605 611 9.778993 CAACTTTATAGTACTAGCTTTCGTACA 57.221 33.333 8.85 8.32 38.69 2.90
606 612 9.994432 TCAACTTTATAGTACTAGCTTTCGTAC 57.006 33.333 8.85 1.81 36.98 3.67
608 614 8.954350 TCTCAACTTTATAGTACTAGCTTTCGT 58.046 33.333 8.85 0.00 33.17 3.85
609 615 9.224058 GTCTCAACTTTATAGTACTAGCTTTCG 57.776 37.037 8.85 0.00 33.17 3.46
611 617 9.857957 GTGTCTCAACTTTATAGTACTAGCTTT 57.142 33.333 8.85 0.00 33.17 3.51
612 618 9.245481 AGTGTCTCAACTTTATAGTACTAGCTT 57.755 33.333 8.85 0.00 33.17 3.74
613 619 8.810990 AGTGTCTCAACTTTATAGTACTAGCT 57.189 34.615 8.85 0.00 33.17 3.32
623 629 8.793592 GTCCCAAAATAAGTGTCTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
624 630 7.041644 CGTCCCAAAATAAGTGTCTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
625 631 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
626 632 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
627 633 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
628 634 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
629 635 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
630 636 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
631 637 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
632 638 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
633 639 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
634 640 2.640826 TCCTCCGTCCCAAAATAAGTGT 59.359 45.455 0.00 0.00 0.00 3.55
635 641 3.343941 TCCTCCGTCCCAAAATAAGTG 57.656 47.619 0.00 0.00 0.00 3.16
636 642 3.329814 ACTTCCTCCGTCCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
637 643 3.951663 ACTTCCTCCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
638 644 4.533311 ACTACTTCCTCCGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
639 645 4.098894 ACTACTTCCTCCGTCCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
640 646 2.910977 ACTACTTCCTCCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
641 647 2.332117 ACTACTTCCTCCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
642 648 2.019807 ACTACTTCCTCCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
643 649 2.905415 TACTACTTCCTCCGTCCCAA 57.095 50.000 0.00 0.00 0.00 4.12
644 650 4.736611 ATATACTACTTCCTCCGTCCCA 57.263 45.455 0.00 0.00 0.00 4.37
645 651 5.067544 GCATATATACTACTTCCTCCGTCCC 59.932 48.000 0.00 0.00 0.00 4.46
646 652 5.651139 TGCATATATACTACTTCCTCCGTCC 59.349 44.000 0.00 0.00 0.00 4.79
647 653 6.754702 TGCATATATACTACTTCCTCCGTC 57.245 41.667 0.00 0.00 0.00 4.79
648 654 7.719871 AATGCATATATACTACTTCCTCCGT 57.280 36.000 0.00 0.00 0.00 4.69
649 655 8.683615 TGTAATGCATATATACTACTTCCTCCG 58.316 37.037 0.00 0.00 0.00 4.63
650 656 9.804758 GTGTAATGCATATATACTACTTCCTCC 57.195 37.037 0.00 0.00 0.00 4.30
656 662 9.996554 TGCTTTGTGTAATGCATATATACTACT 57.003 29.630 0.00 0.00 40.67 2.57
765 771 3.124636 CCACAAGCTACGTACAAATCACC 59.875 47.826 0.00 0.00 0.00 4.02
769 775 3.412237 ACCCACAAGCTACGTACAAAT 57.588 42.857 0.00 0.00 0.00 2.32
777 783 5.897377 ATGAAATGTAACCCACAAGCTAC 57.103 39.130 0.00 0.00 41.55 3.58
821 827 3.348119 AGAGATCTACGTGTGAGCAGAA 58.652 45.455 0.00 0.00 0.00 3.02
898 904 8.253810 TCTCTGTATCATCGAAAAGAAGTTGAT 58.746 33.333 0.00 0.00 33.15 2.57
923 929 8.911662 ACGTTAATTAACAAGAAAACATGCATC 58.088 29.630 24.27 0.00 35.99 3.91
940 946 5.637810 CCTTCTGAGTGAGCAACGTTAATTA 59.362 40.000 0.00 0.00 0.00 1.40
956 962 7.496529 TGTAGTTCAATTCAAACCTTCTGAG 57.503 36.000 0.00 0.00 0.00 3.35
1038 1049 1.165907 CGGCAAAGCACACCTTCTGA 61.166 55.000 0.00 0.00 31.99 3.27
1144 1155 2.747460 GCTGATGCTGCCGACCAA 60.747 61.111 0.00 0.00 36.03 3.67
1171 1182 1.257743 TCTAGCTTCTCCACGCTGTT 58.742 50.000 0.00 0.00 37.05 3.16
1172 1183 1.135915 CATCTAGCTTCTCCACGCTGT 59.864 52.381 0.00 0.00 37.05 4.40
1210 1221 4.856801 CGGGCTAAGGCACCGCAT 62.857 66.667 5.24 0.00 42.10 4.73
1243 1254 3.541713 CTGTAGGAGGGGGAGCGC 61.542 72.222 0.00 0.00 0.00 5.92
1271 1282 0.392461 ACCGTTGCTGAGTTGTGTGT 60.392 50.000 0.00 0.00 0.00 3.72
1291 1302 1.676014 GGCTCCACATGTGTAGGTGTC 60.676 57.143 23.79 8.21 36.90 3.67
1292 1303 0.324943 GGCTCCACATGTGTAGGTGT 59.675 55.000 23.79 0.00 36.90 4.16
1293 1304 0.615331 AGGCTCCACATGTGTAGGTG 59.385 55.000 23.79 11.13 38.28 4.00
1294 1305 0.615331 CAGGCTCCACATGTGTAGGT 59.385 55.000 23.79 2.34 0.00 3.08
1295 1306 0.615331 ACAGGCTCCACATGTGTAGG 59.385 55.000 23.79 13.88 0.00 3.18
1307 1324 2.159170 GCCGATAGATATCCACAGGCTC 60.159 54.545 17.47 0.00 40.12 4.70
1310 1327 2.092323 TCGCCGATAGATATCCACAGG 58.908 52.381 0.00 0.00 39.76 4.00
1328 1381 2.030363 GGGCAGACTCTGTCATCTATCG 60.030 54.545 12.70 0.00 37.90 2.92
1333 1386 2.660572 TCTAGGGCAGACTCTGTCATC 58.339 52.381 12.70 0.00 37.90 2.92
1334 1387 2.836636 TCTAGGGCAGACTCTGTCAT 57.163 50.000 12.70 8.00 37.90 3.06
1336 1389 1.068434 GCATCTAGGGCAGACTCTGTC 59.932 57.143 7.89 4.95 35.62 3.51
1370 1423 2.279517 CGACCGTCATAGCCCTGC 60.280 66.667 0.00 0.00 0.00 4.85
1452 1559 1.226746 AAAAAGAGGCCGAAGTCACG 58.773 50.000 0.00 0.00 0.00 4.35
1572 1679 6.318900 CCACCACTTAAAAGTTCAAAGACTCT 59.681 38.462 4.62 0.00 37.08 3.24
1590 1697 2.143876 ACTTGAGCAAAACCACCACT 57.856 45.000 0.00 0.00 0.00 4.00
1623 1741 9.684448 CCATACATACACAAACACACATAAAAA 57.316 29.630 0.00 0.00 0.00 1.94
1628 1746 7.611467 AGAATCCATACATACACAAACACACAT 59.389 33.333 0.00 0.00 0.00 3.21
1724 1843 0.741221 GGCGAGCATTCTTCTTCGGT 60.741 55.000 0.00 0.00 0.00 4.69
1760 1879 4.590850 TCATATGTGAATGACTCCCTCG 57.409 45.455 1.90 0.00 30.92 4.63
1775 1894 4.630644 ATAGGGAGCACCAAGTCATATG 57.369 45.455 1.58 0.00 43.89 1.78
1776 1895 5.653255 AAATAGGGAGCACCAAGTCATAT 57.347 39.130 1.58 0.00 43.89 1.78
1784 1903 5.044476 TGGAATTCTAAAATAGGGAGCACCA 60.044 40.000 5.23 0.00 43.89 4.17
1849 1968 5.745312 AGTTCCAAGTCACTCACATATGA 57.255 39.130 10.38 0.00 0.00 2.15
1850 1969 6.634805 AGTAGTTCCAAGTCACTCACATATG 58.365 40.000 0.00 0.00 0.00 1.78
1851 1970 6.859112 AGTAGTTCCAAGTCACTCACATAT 57.141 37.500 0.00 0.00 0.00 1.78
1855 1974 5.234543 GTGAAAGTAGTTCCAAGTCACTCAC 59.765 44.000 5.25 0.00 35.12 3.51
1868 1987 7.450903 ACTTATGGCAGTAAGTGAAAGTAGTT 58.549 34.615 16.36 0.00 41.90 2.24
1873 1992 8.946085 TGAATAACTTATGGCAGTAAGTGAAAG 58.054 33.333 17.26 4.52 42.48 2.62
1877 1996 9.547753 ACTATGAATAACTTATGGCAGTAAGTG 57.452 33.333 17.26 8.99 42.48 3.16
1885 2004 9.066892 TGGAATTCACTATGAATAACTTATGGC 57.933 33.333 7.93 0.00 45.57 4.40
1898 2025 8.971073 AGGGAGTAAAATTTGGAATTCACTATG 58.029 33.333 7.93 0.00 0.00 2.23
1923 2052 9.793252 CAAGAAATATCCCAAATTGACACTTAG 57.207 33.333 0.00 0.00 0.00 2.18
1984 2113 6.958767 AGACCAACTTGCTTAACTATGGTAT 58.041 36.000 0.00 0.00 39.65 2.73
1986 2115 5.242795 AGACCAACTTGCTTAACTATGGT 57.757 39.130 0.00 0.00 42.09 3.55
2037 2166 0.690762 TGGACCCTAGTTGGCAGAAC 59.309 55.000 0.00 0.00 0.00 3.01
2043 2172 6.435904 TCAAATTAACAATGGACCCTAGTTGG 59.564 38.462 0.00 0.00 0.00 3.77
2047 2176 7.645058 ATGTCAAATTAACAATGGACCCTAG 57.355 36.000 0.00 0.00 0.00 3.02
2049 2178 7.410174 TCTATGTCAAATTAACAATGGACCCT 58.590 34.615 0.00 0.00 0.00 4.34
2066 2195 4.769488 GGGCTGACTCATCTATCTATGTCA 59.231 45.833 0.00 0.00 34.04 3.58
2100 2229 2.297033 ACGCATTTTGCACAATTCCTCT 59.703 40.909 0.00 0.00 45.36 3.69
2101 2230 2.663119 GACGCATTTTGCACAATTCCTC 59.337 45.455 0.00 0.00 45.36 3.71
2106 2235 0.388391 CCGGACGCATTTTGCACAAT 60.388 50.000 0.00 0.00 45.36 2.71
2108 2237 2.642129 CCGGACGCATTTTGCACA 59.358 55.556 0.00 0.00 45.36 4.57
2159 2323 1.109609 AAATCCCTACCTCGGTCGAC 58.890 55.000 7.13 7.13 0.00 4.20
2185 2359 1.607801 TAGCTGCTGTCACCATCGCT 61.608 55.000 13.43 0.00 0.00 4.93
2189 2363 0.829333 CCTCTAGCTGCTGTCACCAT 59.171 55.000 13.43 0.00 0.00 3.55
2209 2383 4.367023 TAACAGCCGCCGTCGCTT 62.367 61.111 0.00 0.00 0.00 4.68
2210 2384 4.796231 CTAACAGCCGCCGTCGCT 62.796 66.667 0.00 0.00 0.00 4.93
2213 2387 3.305177 TTCCCTAACAGCCGCCGTC 62.305 63.158 0.00 0.00 0.00 4.79
2214 2388 3.310860 CTTCCCTAACAGCCGCCGT 62.311 63.158 0.00 0.00 0.00 5.68
2215 2389 2.511600 CTTCCCTAACAGCCGCCG 60.512 66.667 0.00 0.00 0.00 6.46
2216 2390 1.449778 GACTTCCCTAACAGCCGCC 60.450 63.158 0.00 0.00 0.00 6.13
2217 2391 1.810030 CGACTTCCCTAACAGCCGC 60.810 63.158 0.00 0.00 0.00 6.53
2218 2392 0.245539 TTCGACTTCCCTAACAGCCG 59.754 55.000 0.00 0.00 0.00 5.52
2219 2393 2.678336 CAATTCGACTTCCCTAACAGCC 59.322 50.000 0.00 0.00 0.00 4.85
2220 2394 2.096013 GCAATTCGACTTCCCTAACAGC 59.904 50.000 0.00 0.00 0.00 4.40
2221 2395 3.600388 AGCAATTCGACTTCCCTAACAG 58.400 45.455 0.00 0.00 0.00 3.16
2228 4122 9.736023 AAATAATTTATGAGCAATTCGACTTCC 57.264 29.630 0.00 0.00 0.00 3.46
2276 4172 8.732746 AAGGACACGAAAACTAATATAAGCAT 57.267 30.769 0.00 0.00 0.00 3.79
2284 4180 6.445357 ACACAAAAGGACACGAAAACTAAT 57.555 33.333 0.00 0.00 0.00 1.73
2293 4189 5.816919 ACTATTTCAACACAAAAGGACACG 58.183 37.500 0.00 0.00 0.00 4.49
2336 4293 5.853936 TCTTTCGACTTTCTCCAGATTTCA 58.146 37.500 0.00 0.00 0.00 2.69
2353 4310 3.996363 TGTGGATGTGTTGAGATCTTTCG 59.004 43.478 0.00 0.00 0.00 3.46
2354 4311 5.239306 TGTTGTGGATGTGTTGAGATCTTTC 59.761 40.000 0.00 0.00 0.00 2.62
2355 4312 5.132502 TGTTGTGGATGTGTTGAGATCTTT 58.867 37.500 0.00 0.00 0.00 2.52
2370 4327 5.482006 CTGTCTCATTAGTGATGTTGTGGA 58.518 41.667 0.00 0.00 37.06 4.02
2393 4350 2.604914 CCGTATGTGAGATGTTCTGTGC 59.395 50.000 0.00 0.00 0.00 4.57
2466 4423 0.676782 ATCCAGCCGCACAACCTAAC 60.677 55.000 0.00 0.00 0.00 2.34
2477 4434 4.566545 TGCAATAATGTAAATCCAGCCG 57.433 40.909 0.00 0.00 0.00 5.52
2515 4476 3.415212 TCTCCTGATCCTTTTGTGCAAG 58.585 45.455 0.00 0.00 0.00 4.01
2554 4516 3.624861 CGTAATAGTACGTCCCACTGAGT 59.375 47.826 14.24 0.00 46.49 3.41
2584 4546 0.386476 AAGCGGTTCGTGTACACAGA 59.614 50.000 24.98 18.92 0.00 3.41
2595 4557 2.668280 GCGTGTCCTCAAGCGGTTC 61.668 63.158 0.00 0.00 38.97 3.62


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

AutoCloner maintained by Alex Coulton.