Multiple sequence alignment - TraesCS5A01G048600

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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 TraesCS5A01G048600 chr5A 100.000 5929 0 0 1 5929 44943356 44949284 0.000000e+00 10949.0
1 TraesCS5A01G048600 chr5A 90.909 44 4 0 5381 5424 10900 10857 6.420000e-05 60.2
2 TraesCS5A01G048600 chr5D 92.479 3816 214 43 1626 5414 56121909 56125678 0.000000e+00 5389.0
3 TraesCS5A01G048600 chr5D 92.973 1608 81 19 1 1597 56119979 56121565 0.000000e+00 2314.0
4 TraesCS5A01G048600 chr5D 94.412 519 24 3 5414 5929 56125719 56126235 0.000000e+00 793.0
5 TraesCS5A01G048600 chr5D 97.368 38 1 0 5381 5418 69354257 69354220 1.380000e-06 65.8
6 TraesCS5A01G048600 chr5D 100.000 35 0 0 5381 5415 381914482 381914448 1.380000e-06 65.8
7 TraesCS5A01G048600 chr5B 91.705 1941 108 21 1669 3601 58891618 58893513 0.000000e+00 2643.0
8 TraesCS5A01G048600 chr5B 94.743 1655 71 9 3648 5290 58893507 58895157 0.000000e+00 2560.0
9 TraesCS5A01G048600 chr5B 92.308 1417 88 12 1 1404 58890150 58891558 0.000000e+00 1993.0
10 TraesCS5A01G048600 chr5B 91.803 671 34 10 5272 5929 58895337 58895999 0.000000e+00 915.0
11 TraesCS5A01G048600 chr5B 90.909 44 4 0 5381 5424 1739562 1739519 6.420000e-05 60.2
12 TraesCS5A01G048600 chr2D 82.413 489 58 19 5445 5928 112871209 112871674 9.260000e-108 401.0
13 TraesCS5A01G048600 chr2A 81.836 512 61 22 5424 5929 114310649 114311134 9.260000e-108 401.0
14 TraesCS5A01G048600 chr2A 92.683 41 3 0 5381 5421 675304133 675304173 6.420000e-05 60.2
15 TraesCS5A01G048600 chr3B 81.081 518 70 16 5417 5929 103246265 103245771 7.210000e-104 388.0
16 TraesCS5A01G048600 chr4B 97.561 41 1 0 5381 5421 70256638 70256678 2.960000e-08 71.3
17 TraesCS5A01G048600 chr4A 95.122 41 2 0 5381 5421 549879049 549879009 1.380000e-06 65.8
18 TraesCS5A01G048600 chr2B 100.000 35 0 0 5381 5415 587169380 587169346 1.380000e-06 65.8


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 TraesCS5A01G048600 chr5A 44943356 44949284 5928 False 10949.00 10949 100.00000 1 5929 1 chr5A.!!$F1 5928
1 TraesCS5A01G048600 chr5D 56119979 56126235 6256 False 2832.00 5389 93.28800 1 5929 3 chr5D.!!$F1 5928
2 TraesCS5A01G048600 chr5B 58890150 58895999 5849 False 2027.75 2643 92.63975 1 5929 4 chr5B.!!$F1 5928

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
435 439 0.329596 GGTTGGGTGGCTCTTCTCAT 59.670 55.0 0.00 0.0 0.00 2.90 F
817 827 1.138047 GGTGTGCGACTCGATAACCG 61.138 60.0 1.63 0.0 40.25 4.44 F
1454 1470 0.041535 TTGCAAATCCATCCAGGGCT 59.958 50.0 0.00 0.0 38.24 5.19 F
2605 2947 0.108472 TTCATGAGTGCTCAGGCTCG 60.108 55.0 8.76 0.0 43.61 5.03 F
2947 3290 1.048601 ATGCCCACAGTAGTATCCGG 58.951 55.0 0.00 0.0 0.00 5.14 F
4646 5000 1.130054 AGTGTCCTGTGGAGCATGGT 61.130 55.0 0.00 0.0 29.39 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1451 0.041535 AGCCCTGGATGGATTTGCAA 59.958 50.000 0.00 0.0 38.35 4.08 R
2342 2684 0.818040 AAACGCAGCCGAAAGAACCT 60.818 50.000 0.00 0.0 38.29 3.50 R
2947 3290 0.954452 CCCTTGTGCTCCAGTCAAAC 59.046 55.000 0.00 0.0 0.00 2.93 R
4142 4493 0.320771 AGCTTCGTCGGTGCTGAAAT 60.321 50.000 11.04 0.0 35.54 2.17 R
4666 5020 2.348998 GCCTGGTGTAGCTGTGCT 59.651 61.111 0.00 0.0 43.41 4.40 R
5868 6486 1.877443 GCGCAACTTAAAGAGGGAACA 59.123 47.619 0.30 0.0 0.00 3.18 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
156 157 4.455606 CCCTCATTTGTTATGTCTCCCTC 58.544 47.826 0.00 0.00 0.00 4.30
222 226 5.050363 TCGTCTTCGCAAGGCAATTATAATC 60.050 40.000 0.00 0.00 36.96 1.75
244 248 2.233271 CAGGGCACTTGTGTCATTTCT 58.767 47.619 7.67 0.00 0.00 2.52
259 263 5.525012 TGTCATTTCTGCTCAAAGATATCCG 59.475 40.000 0.00 0.00 0.00 4.18
295 299 1.164411 TAATTTCTGTGGCCTGCGTG 58.836 50.000 3.32 0.00 0.00 5.34
319 323 3.028850 TCGACGAAGGGGAATGTATCTT 58.971 45.455 0.00 0.00 0.00 2.40
435 439 0.329596 GGTTGGGTGGCTCTTCTCAT 59.670 55.000 0.00 0.00 0.00 2.90
589 594 1.653667 CACTGCGTGCCATGAAACA 59.346 52.632 0.00 0.00 0.00 2.83
604 609 7.981789 TGCCATGAAACACAAAAGTTGTTATTA 59.018 29.630 0.00 0.00 43.23 0.98
632 637 3.680642 CCATGAGGTGAAATACAAGCG 57.319 47.619 0.00 0.00 0.00 4.68
635 640 1.804151 TGAGGTGAAATACAAGCGTGC 59.196 47.619 0.00 0.00 0.00 5.34
712 717 7.786046 TGTAAACTGAAGACTAACTATGGGA 57.214 36.000 0.00 0.00 0.00 4.37
713 718 7.837863 TGTAAACTGAAGACTAACTATGGGAG 58.162 38.462 0.00 0.00 0.00 4.30
817 827 1.138047 GGTGTGCGACTCGATAACCG 61.138 60.000 1.63 0.00 40.25 4.44
859 869 8.414778 ACTATAGCAATACTAAAGTCAGGACAC 58.585 37.037 0.00 0.00 33.57 3.67
878 888 3.214328 CACGGGCATTAAGAATAAGCCT 58.786 45.455 0.00 0.00 44.60 4.58
880 890 5.003804 CACGGGCATTAAGAATAAGCCTAT 58.996 41.667 0.00 0.00 44.60 2.57
881 891 6.170506 CACGGGCATTAAGAATAAGCCTATA 58.829 40.000 0.00 0.00 44.60 1.31
1074 1085 7.001674 CCTCTGCCTGGACTAGTATATATAGG 58.998 46.154 0.00 0.00 0.00 2.57
1080 1091 7.531317 CCTGGACTAGTATATATAGGGAGCAT 58.469 42.308 0.00 0.00 0.00 3.79
1098 1109 3.131046 AGCATATTGTAGCACCCTTTTGC 59.869 43.478 0.00 0.00 43.34 3.68
1162 1174 7.106239 CCACCATCATCCAGGACTTATATTAC 58.894 42.308 0.00 0.00 0.00 1.89
1196 1208 2.477845 TCATACACACTGCAGCACAT 57.522 45.000 15.27 0.00 0.00 3.21
1245 1257 2.484947 CGCCTAATCCTTGGGTAGGTTC 60.485 54.545 14.51 3.70 45.03 3.62
1272 1288 4.792068 TCTCTCCTTTTCTCCTTTTTGCA 58.208 39.130 0.00 0.00 0.00 4.08
1375 1391 1.539827 CCCTTTTGCTGAAACTACCCG 59.460 52.381 0.00 0.00 0.00 5.28
1379 1395 4.022329 CCTTTTGCTGAAACTACCCGATTT 60.022 41.667 0.00 0.00 0.00 2.17
1386 1402 1.665137 AACTACCCGATTTCCCTGGT 58.335 50.000 0.00 0.00 34.85 4.00
1392 1408 2.850568 ACCCGATTTCCCTGGTTAGATT 59.149 45.455 0.00 0.00 0.00 2.40
1404 1420 6.836527 TCCCTGGTTAGATTTGTTTTGAGAAA 59.163 34.615 0.00 0.00 0.00 2.52
1405 1421 7.343316 TCCCTGGTTAGATTTGTTTTGAGAAAA 59.657 33.333 0.00 0.00 0.00 2.29
1407 1423 9.196552 CCTGGTTAGATTTGTTTTGAGAAAATC 57.803 33.333 0.00 0.00 39.52 2.17
1409 1425 9.748708 TGGTTAGATTTGTTTTGAGAAAATCAG 57.251 29.630 9.33 0.00 40.95 2.90
1414 1430 9.657419 AGATTTGTTTTGAGAAAATCAGTTGTT 57.343 25.926 9.33 0.00 40.95 2.83
1450 1466 3.663995 TTGTGTTGCAAATCCATCCAG 57.336 42.857 0.00 0.00 33.53 3.86
1453 1469 0.176449 GTTGCAAATCCATCCAGGGC 59.824 55.000 0.00 0.00 38.24 5.19
1454 1470 0.041535 TTGCAAATCCATCCAGGGCT 59.958 50.000 0.00 0.00 38.24 5.19
1455 1471 0.685131 TGCAAATCCATCCAGGGCTG 60.685 55.000 0.00 0.00 38.24 4.85
1456 1472 0.685458 GCAAATCCATCCAGGGCTGT 60.685 55.000 0.00 0.00 38.24 4.40
1457 1473 1.856629 CAAATCCATCCAGGGCTGTT 58.143 50.000 0.00 0.00 38.24 3.16
1458 1474 2.181975 CAAATCCATCCAGGGCTGTTT 58.818 47.619 0.00 0.00 38.24 2.83
1459 1475 2.149973 AATCCATCCAGGGCTGTTTC 57.850 50.000 0.00 0.00 38.24 2.78
1460 1476 1.302907 ATCCATCCAGGGCTGTTTCT 58.697 50.000 0.00 0.00 38.24 2.52
1461 1477 0.620556 TCCATCCAGGGCTGTTTCTC 59.379 55.000 0.00 0.00 38.24 2.87
1462 1478 0.329261 CCATCCAGGGCTGTTTCTCA 59.671 55.000 0.00 0.00 0.00 3.27
1463 1479 1.064166 CCATCCAGGGCTGTTTCTCAT 60.064 52.381 0.00 0.00 0.00 2.90
1464 1480 2.022195 CATCCAGGGCTGTTTCTCATG 58.978 52.381 0.00 0.00 0.00 3.07
1465 1481 1.361204 TCCAGGGCTGTTTCTCATGA 58.639 50.000 0.00 0.00 0.00 3.07
1468 1484 2.892852 CCAGGGCTGTTTCTCATGAAAA 59.107 45.455 0.00 0.00 42.94 2.29
1484 1500 5.568677 TCATGAAAACATTTGATTCGCTTCG 59.431 36.000 0.00 0.00 0.00 3.79
1493 1509 2.607187 TGATTCGCTTCGAGTTCCTTC 58.393 47.619 0.00 0.00 37.14 3.46
1494 1510 2.029380 TGATTCGCTTCGAGTTCCTTCA 60.029 45.455 0.00 0.00 37.14 3.02
1495 1511 2.065993 TTCGCTTCGAGTTCCTTCAG 57.934 50.000 0.00 0.00 37.14 3.02
1498 1514 1.457303 CGCTTCGAGTTCCTTCAGTTG 59.543 52.381 0.00 0.00 0.00 3.16
1510 1529 5.975693 TCCTTCAGTTGTTGTGTTTCTTT 57.024 34.783 0.00 0.00 0.00 2.52
1529 1548 8.567948 GTTTCTTTAACCATCAAGTTCATCTGA 58.432 33.333 0.00 0.00 0.00 3.27
1537 1556 7.397221 ACCATCAAGTTCATCTGATTCTGTTA 58.603 34.615 0.00 0.00 0.00 2.41
1538 1557 7.551974 ACCATCAAGTTCATCTGATTCTGTTAG 59.448 37.037 0.00 0.00 0.00 2.34
1552 1572 7.901029 TGATTCTGTTAGAAGATCTCAGTTGT 58.099 34.615 0.00 0.00 37.69 3.32
1553 1573 8.370940 TGATTCTGTTAGAAGATCTCAGTTGTT 58.629 33.333 0.00 0.00 37.69 2.83
1554 1574 7.953158 TTCTGTTAGAAGATCTCAGTTGTTG 57.047 36.000 0.00 0.00 29.50 3.33
1597 1617 3.449737 CAGGGATCATGCTGAAAATGGTT 59.550 43.478 0.00 0.00 0.00 3.67
1598 1618 4.081309 CAGGGATCATGCTGAAAATGGTTT 60.081 41.667 0.00 0.00 0.00 3.27
1599 1619 4.161001 AGGGATCATGCTGAAAATGGTTTC 59.839 41.667 0.00 0.00 43.04 2.78
1600 1620 4.436332 GGATCATGCTGAAAATGGTTTCC 58.564 43.478 0.00 0.00 42.20 3.13
1601 1621 3.959535 TCATGCTGAAAATGGTTTCCC 57.040 42.857 0.00 0.00 42.20 3.97
1602 1622 2.566724 TCATGCTGAAAATGGTTTCCCC 59.433 45.455 0.00 0.00 42.20 4.81
1603 1623 1.347062 TGCTGAAAATGGTTTCCCCC 58.653 50.000 0.00 0.00 42.20 5.40
1604 1624 1.132881 TGCTGAAAATGGTTTCCCCCT 60.133 47.619 0.00 0.00 42.20 4.79
1605 1625 1.276138 GCTGAAAATGGTTTCCCCCTG 59.724 52.381 0.00 0.00 42.20 4.45
1606 1626 2.608623 CTGAAAATGGTTTCCCCCTGT 58.391 47.619 0.00 0.00 42.20 4.00
1607 1627 3.773560 CTGAAAATGGTTTCCCCCTGTA 58.226 45.455 0.00 0.00 42.20 2.74
1608 1628 4.352893 CTGAAAATGGTTTCCCCCTGTAT 58.647 43.478 0.00 0.00 42.20 2.29
1609 1629 5.515106 CTGAAAATGGTTTCCCCCTGTATA 58.485 41.667 0.00 0.00 42.20 1.47
1610 1630 5.515106 TGAAAATGGTTTCCCCCTGTATAG 58.485 41.667 0.00 0.00 42.20 1.31
1611 1631 4.536295 AAATGGTTTCCCCCTGTATAGG 57.464 45.455 0.00 0.00 44.18 2.57
1612 1632 6.160801 GAAAATGGTTTCCCCCTGTATAGGG 61.161 48.000 17.59 17.59 46.49 3.53
1643 1978 7.495279 TCTTTTCCCATTGATTTTGTTGTTCAG 59.505 33.333 0.00 0.00 0.00 3.02
1683 2018 9.507280 CACACAAAATATTCTTCATATGTCCAC 57.493 33.333 1.90 0.00 0.00 4.02
1727 2062 9.599866 CTTAATTTTGTCATTATCTTTTCCCCC 57.400 33.333 0.00 0.00 0.00 5.40
1730 2065 8.909423 ATTTTGTCATTATCTTTTCCCCCTAA 57.091 30.769 0.00 0.00 0.00 2.69
1731 2066 7.954666 TTTGTCATTATCTTTTCCCCCTAAG 57.045 36.000 0.00 0.00 0.00 2.18
1732 2067 6.652205 TGTCATTATCTTTTCCCCCTAAGT 57.348 37.500 0.00 0.00 0.00 2.24
1738 2073 5.669798 ATCTTTTCCCCCTAAGTATGCAT 57.330 39.130 3.79 3.79 0.00 3.96
1741 2076 5.670361 TCTTTTCCCCCTAAGTATGCATAGT 59.330 40.000 6.67 7.56 0.00 2.12
1742 2077 4.974645 TTCCCCCTAAGTATGCATAGTG 57.025 45.455 14.79 3.59 0.00 2.74
1745 2080 5.661565 TCCCCCTAAGTATGCATAGTGTAT 58.338 41.667 14.79 2.35 0.00 2.29
1747 2082 6.561070 TCCCCCTAAGTATGCATAGTGTATTT 59.439 38.462 14.79 1.63 0.00 1.40
1748 2083 7.073215 TCCCCCTAAGTATGCATAGTGTATTTT 59.927 37.037 14.79 0.93 0.00 1.82
1749 2084 7.724061 CCCCCTAAGTATGCATAGTGTATTTTT 59.276 37.037 14.79 0.23 0.00 1.94
1750 2085 9.787435 CCCCTAAGTATGCATAGTGTATTTTTA 57.213 33.333 14.79 1.39 0.00 1.52
1797 2132 6.370166 CAGAGGAAGAAGAAACATACCAGAAC 59.630 42.308 0.00 0.00 0.00 3.01
1801 2136 9.268282 AGGAAGAAGAAACATACCAGAACTATA 57.732 33.333 0.00 0.00 0.00 1.31
1818 2153 8.483218 CAGAACTATATGTTTGAGTTATGAGCG 58.517 37.037 4.60 0.00 42.34 5.03
2091 2433 6.734104 TCTGAAGCTTCTAAGAAGCAAATC 57.266 37.500 26.09 17.14 45.30 2.17
2126 2468 2.288666 TGACTTGCTTTCGTTTGCTCT 58.711 42.857 0.00 0.00 0.00 4.09
2168 2510 2.162681 GCCAAATTGTACAGCAGGACT 58.837 47.619 9.15 0.00 0.00 3.85
2177 2519 5.143376 TGTACAGCAGGACTTAGGTAAAC 57.857 43.478 0.00 0.00 0.00 2.01
2227 2569 4.657814 TCTGAAGCATCCTAAAACCCTT 57.342 40.909 0.00 0.00 0.00 3.95
2232 2574 3.956744 AGCATCCTAAAACCCTTCTGAC 58.043 45.455 0.00 0.00 0.00 3.51
2248 2590 6.325028 CCCTTCTGACTCATCCTATTCTGTTA 59.675 42.308 0.00 0.00 0.00 2.41
2342 2684 3.130340 GCTCAGGAAACAAACTTGGACAA 59.870 43.478 0.00 0.00 0.00 3.18
2418 2760 6.934056 TGCACCATATAAGCTTTGACATTTT 58.066 32.000 3.20 0.00 0.00 1.82
2448 2790 5.710099 TCAAACACCACAATCTCTTTATCCC 59.290 40.000 0.00 0.00 0.00 3.85
2456 2798 7.147620 ACCACAATCTCTTTATCCCGTAACATA 60.148 37.037 0.00 0.00 0.00 2.29
2458 2800 9.273016 CACAATCTCTTTATCCCGTAACATATT 57.727 33.333 0.00 0.00 0.00 1.28
2459 2801 9.273016 ACAATCTCTTTATCCCGTAACATATTG 57.727 33.333 0.00 0.00 0.00 1.90
2540 2882 3.130516 TCTTCCTGCTGTAGTGATTACCG 59.869 47.826 0.00 0.00 0.00 4.02
2579 2921 5.863935 GGACCAGCTATCAAAATTCAAACAC 59.136 40.000 0.00 0.00 0.00 3.32
2605 2947 0.108472 TTCATGAGTGCTCAGGCTCG 60.108 55.000 8.76 0.00 43.61 5.03
2611 2953 2.052690 GTGCTCAGGCTCGGGTCTA 61.053 63.158 0.00 0.00 39.59 2.59
2660 3002 4.038642 GGTCAAAAAGTTGCCATCAAGGTA 59.961 41.667 0.00 0.00 40.61 3.08
2669 3011 2.292521 TGCCATCAAGGTACTCTCCTCT 60.293 50.000 0.00 0.00 38.49 3.69
2741 3083 2.684881 CAGCATAACCCATCACAACCTC 59.315 50.000 0.00 0.00 0.00 3.85
2744 3086 3.343617 CATAACCCATCACAACCTCGTT 58.656 45.455 0.00 0.00 0.00 3.85
2816 3158 4.640771 TTATCTGGAGAACAACAGCCTT 57.359 40.909 0.00 0.00 34.76 4.35
2840 3182 3.721087 AGGACCCTCTTTGGTATGTTG 57.279 47.619 0.00 0.00 39.24 3.33
2893 3236 6.757897 AAATCGCTGGTAAATTCATTCTCA 57.242 33.333 0.00 0.00 0.00 3.27
2947 3290 1.048601 ATGCCCACAGTAGTATCCGG 58.951 55.000 0.00 0.00 0.00 5.14
3025 3368 1.356624 GCATGAAGAAATCCGGCCG 59.643 57.895 21.04 21.04 0.00 6.13
3549 3892 5.649557 ACAGCTATGATAGATCGAAGATGC 58.350 41.667 3.13 0.00 45.12 3.91
3557 3900 3.834489 AGATCGAAGATGCTCCACATT 57.166 42.857 0.00 0.00 45.12 2.71
3567 3910 3.548745 TGCTCCACATTAGACCATGAG 57.451 47.619 0.00 0.00 0.00 2.90
3570 3913 3.873952 GCTCCACATTAGACCATGAGAAC 59.126 47.826 0.00 0.00 0.00 3.01
3621 3964 7.812191 TGCACATGGTTGAACAATTTAGATAAC 59.188 33.333 0.00 0.00 0.00 1.89
3747 4093 7.518188 AGTTTCCTCTCTGTCCTGAAAATTAA 58.482 34.615 0.00 0.00 0.00 1.40
3891 4242 8.580720 TCTCATTCTTAGGACATATCTGTTAGC 58.419 37.037 0.00 0.00 35.14 3.09
4032 4383 5.526115 AGCATTGTTTCTTGACATTGTCAG 58.474 37.500 18.27 12.98 43.69 3.51
4142 4493 5.186992 TCATCGACAGGACCTTAAAAGATGA 59.813 40.000 15.36 15.36 39.39 2.92
4227 4578 2.300967 GGTCAGGCCCTCCATGTCA 61.301 63.158 0.00 0.00 33.74 3.58
4257 4608 3.560025 CCAAGATGCTAAAGGGTGAGTGT 60.560 47.826 0.00 0.00 0.00 3.55
4512 4863 5.770663 TGTAAATTGGAGGGATGACGAAAAA 59.229 36.000 0.00 0.00 0.00 1.94
4646 5000 1.130054 AGTGTCCTGTGGAGCATGGT 61.130 55.000 0.00 0.00 29.39 3.55
4666 5020 6.945636 TGGTTTATAGGTGAAGGAAGAAGA 57.054 37.500 0.00 0.00 0.00 2.87
4848 5206 4.034394 CACACGGATAATGACATGACTTGG 59.966 45.833 0.00 0.00 0.00 3.61
4872 5230 3.817084 TCTGCATGAAAGACCTGTGAAAG 59.183 43.478 0.00 0.00 0.00 2.62
4878 5236 4.792068 TGAAAGACCTGTGAAAGTTCCAT 58.208 39.130 0.00 0.00 0.00 3.41
5006 5364 8.458573 AGTGAAGATATCTAGGTACAGAAGTG 57.541 38.462 5.46 0.00 0.00 3.16
5035 5393 7.417496 AAAAATATATCTTACCGAACGAGGC 57.583 36.000 0.00 0.00 33.69 4.70
5055 5413 3.198872 GCCTTGAATCTAAGAGGAACCG 58.801 50.000 0.00 0.00 0.00 4.44
5227 5588 0.598065 ATGGTTTCCGCAGCTTGAAC 59.402 50.000 0.00 0.00 0.00 3.18
5255 5616 6.988522 ACAAGTTAAACCAAACAAACAGTCT 58.011 32.000 0.00 0.00 0.00 3.24
5331 5891 4.094294 CACAGTAATAACCCAACCATGTCG 59.906 45.833 0.00 0.00 0.00 4.35
5333 5893 4.331717 CAGTAATAACCCAACCATGTCGTC 59.668 45.833 0.00 0.00 0.00 4.20
5377 5937 5.068855 TCACAGCAAAAACTTTCATCCATCA 59.931 36.000 0.00 0.00 0.00 3.07
5422 6028 7.756558 AGACGTTTTAGGTCACTAGTACATAC 58.243 38.462 0.00 0.00 35.60 2.39
5423 6029 7.609532 AGACGTTTTAGGTCACTAGTACATACT 59.390 37.037 0.00 0.00 35.60 2.12
5500 6109 3.208922 TCCTAGTGGGGGACATTCTGATA 59.791 47.826 0.00 0.00 35.33 2.15
5532 6141 6.978080 GGAAACACAGCAAGAAATGAACTTAA 59.022 34.615 0.00 0.00 0.00 1.85
5544 6153 8.702163 AGAAATGAACTTAACAAAACAACAGG 57.298 30.769 0.00 0.00 0.00 4.00
5632 6250 5.601313 AGATTATTCATTCTTGGGCAGCAAT 59.399 36.000 0.00 0.00 0.00 3.56
5682 6300 6.906659 AGAAAATCACATTCAGACACATCAC 58.093 36.000 0.00 0.00 0.00 3.06
5702 6320 7.339466 ACATCACCAGAAACTTTGTTCTTTAGT 59.661 33.333 0.00 0.00 35.63 2.24
5844 6462 3.181476 GGTTCATTTCCAGCAGTTGTGTT 60.181 43.478 0.00 0.00 0.00 3.32
5868 6486 5.765510 AGAGACACAGAACTCCATCTATCT 58.234 41.667 0.00 0.00 34.13 1.98
5879 6497 5.284582 ACTCCATCTATCTGTTCCCTCTTT 58.715 41.667 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 8.034804 GGGCATTTGGGTAATTATCATCATTAC 58.965 37.037 0.00 0.00 36.67 1.89
222 226 1.321474 AATGACACAAGTGCCCTGTG 58.679 50.000 8.02 8.02 39.26 3.66
244 248 8.559536 GTGATAAAATTCGGATATCTTTGAGCA 58.440 33.333 2.05 0.00 0.00 4.26
295 299 0.531200 ACATTCCCCTTCGTCGACTC 59.469 55.000 14.70 0.00 0.00 3.36
319 323 3.585862 GAGAAAGTAATCAGCGTGACCA 58.414 45.455 0.00 0.00 0.00 4.02
612 617 3.009723 ACGCTTGTATTTCACCTCATGG 58.990 45.455 0.00 0.00 39.83 3.66
632 637 2.762535 TTAAGTGAGGTAGGCTGCAC 57.237 50.000 4.64 4.39 0.00 4.57
635 640 5.812642 CACAGTAATTAAGTGAGGTAGGCTG 59.187 44.000 11.88 2.68 35.33 4.85
638 643 5.116882 GGCACAGTAATTAAGTGAGGTAGG 58.883 45.833 18.50 0.00 35.33 3.18
696 701 6.937392 ACTTTGTCTCCCATAGTTAGTCTTC 58.063 40.000 0.00 0.00 32.19 2.87
703 708 6.875972 ATGTCTACTTTGTCTCCCATAGTT 57.124 37.500 0.00 0.00 36.79 2.24
709 714 8.794335 AAAGAAATATGTCTACTTTGTCTCCC 57.206 34.615 0.00 0.00 31.11 4.30
751 761 9.783256 ATAAACTAAACACTGTGACTTGAAAAC 57.217 29.630 15.86 0.00 0.00 2.43
859 869 7.552687 TCATTATAGGCTTATTCTTAATGCCCG 59.447 37.037 0.00 0.00 44.19 6.13
1074 1085 2.938956 AGGGTGCTACAATATGCTCC 57.061 50.000 0.00 0.00 40.78 4.70
1098 1109 6.215121 CACATGTATCTCCTAGCTTCAGAAG 58.785 44.000 5.72 5.72 0.00 2.85
1103 1114 4.280677 AGAGCACATGTATCTCCTAGCTTC 59.719 45.833 18.37 7.40 0.00 3.86
1245 1257 6.951062 AAAAGGAGAAAAGGAGAGAAACTG 57.049 37.500 0.00 0.00 0.00 3.16
1272 1288 4.641868 TCCAGGGTAATTGGGTAGATTCT 58.358 43.478 0.00 0.00 36.34 2.40
1375 1391 7.666623 TCAAAACAAATCTAACCAGGGAAATC 58.333 34.615 0.00 0.00 0.00 2.17
1379 1395 5.947663 TCTCAAAACAAATCTAACCAGGGA 58.052 37.500 0.00 0.00 0.00 4.20
1431 1447 1.894466 CCTGGATGGATTTGCAACACA 59.106 47.619 0.00 0.00 38.35 3.72
1432 1448 1.205417 CCCTGGATGGATTTGCAACAC 59.795 52.381 0.00 0.00 38.35 3.32
1435 1451 0.041535 AGCCCTGGATGGATTTGCAA 59.958 50.000 0.00 0.00 38.35 4.08
1436 1452 0.685131 CAGCCCTGGATGGATTTGCA 60.685 55.000 0.00 0.00 38.35 4.08
1437 1453 0.685458 ACAGCCCTGGATGGATTTGC 60.685 55.000 6.37 0.00 38.35 3.68
1438 1454 1.856629 AACAGCCCTGGATGGATTTG 58.143 50.000 6.37 0.00 38.35 2.32
1439 1455 2.043526 AGAAACAGCCCTGGATGGATTT 59.956 45.455 6.37 0.00 38.35 2.17
1450 1466 4.525912 ATGTTTTCATGAGAAACAGCCC 57.474 40.909 25.83 8.05 43.09 5.19
1453 1469 8.422457 CGAATCAAATGTTTTCATGAGAAACAG 58.578 33.333 25.83 18.42 43.09 3.16
1454 1470 7.096106 GCGAATCAAATGTTTTCATGAGAAACA 60.096 33.333 24.94 24.94 43.09 2.83
1455 1471 7.115378 AGCGAATCAAATGTTTTCATGAGAAAC 59.885 33.333 18.62 18.62 43.09 2.78
1456 1472 7.147312 AGCGAATCAAATGTTTTCATGAGAAA 58.853 30.769 0.00 0.14 41.78 2.52
1457 1473 6.680810 AGCGAATCAAATGTTTTCATGAGAA 58.319 32.000 0.00 0.00 40.79 2.87
1458 1474 6.258230 AGCGAATCAAATGTTTTCATGAGA 57.742 33.333 0.00 0.00 40.79 3.27
1459 1475 6.237123 CGAAGCGAATCAAATGTTTTCATGAG 60.237 38.462 0.00 0.00 40.79 2.90
1460 1476 5.568677 CGAAGCGAATCAAATGTTTTCATGA 59.431 36.000 0.00 0.00 40.79 3.07
1461 1477 5.568677 TCGAAGCGAATCAAATGTTTTCATG 59.431 36.000 0.00 0.00 35.09 3.07
1462 1478 5.698832 TCGAAGCGAATCAAATGTTTTCAT 58.301 33.333 0.00 0.00 35.91 2.57
1463 1479 5.102020 TCGAAGCGAATCAAATGTTTTCA 57.898 34.783 0.00 0.00 31.06 2.69
1464 1480 5.147162 ACTCGAAGCGAATCAAATGTTTTC 58.853 37.500 0.00 0.00 34.74 2.29
1465 1481 5.108385 ACTCGAAGCGAATCAAATGTTTT 57.892 34.783 0.00 0.00 34.74 2.43
1468 1484 3.125316 GGAACTCGAAGCGAATCAAATGT 59.875 43.478 0.00 0.00 34.74 2.71
1484 1500 4.965119 AACACAACAACTGAAGGAACTC 57.035 40.909 0.00 0.00 38.49 3.01
1493 1509 7.032580 TGATGGTTAAAGAAACACAACAACTG 58.967 34.615 0.00 0.00 40.08 3.16
1494 1510 7.164230 TGATGGTTAAAGAAACACAACAACT 57.836 32.000 0.00 0.00 40.08 3.16
1495 1511 7.544217 ACTTGATGGTTAAAGAAACACAACAAC 59.456 33.333 0.00 0.00 40.08 3.32
1498 1514 7.757624 TGAACTTGATGGTTAAAGAAACACAAC 59.242 33.333 0.00 0.00 40.08 3.32
1510 1529 7.397221 ACAGAATCAGATGAACTTGATGGTTA 58.603 34.615 0.00 0.00 0.00 2.85
1529 1548 7.118971 GCAACAACTGAGATCTTCTAACAGAAT 59.881 37.037 13.67 1.91 33.13 2.40
1537 1556 3.072184 ACAGGCAACAACTGAGATCTTCT 59.928 43.478 0.00 0.00 39.24 2.85
1538 1557 3.406764 ACAGGCAACAACTGAGATCTTC 58.593 45.455 0.00 0.00 39.24 2.87
1552 1572 4.734398 ACTTCAAATGTTCAACAGGCAA 57.266 36.364 0.00 0.00 0.00 4.52
1553 1573 4.681744 GAACTTCAAATGTTCAACAGGCA 58.318 39.130 0.00 0.00 42.22 4.75
1611 1631 6.992123 ACAAAATCAATGGGAAAAGAAAGTCC 59.008 34.615 0.00 0.00 0.00 3.85
1612 1632 8.337532 CAACAAAATCAATGGGAAAAGAAAGTC 58.662 33.333 0.00 0.00 0.00 3.01
1613 1633 7.828717 ACAACAAAATCAATGGGAAAAGAAAGT 59.171 29.630 0.00 0.00 0.00 2.66
1614 1634 8.212317 ACAACAAAATCAATGGGAAAAGAAAG 57.788 30.769 0.00 0.00 0.00 2.62
1615 1635 8.572855 AACAACAAAATCAATGGGAAAAGAAA 57.427 26.923 0.00 0.00 0.00 2.52
1616 1636 7.826252 TGAACAACAAAATCAATGGGAAAAGAA 59.174 29.630 0.00 0.00 0.00 2.52
1617 1637 7.334090 TGAACAACAAAATCAATGGGAAAAGA 58.666 30.769 0.00 0.00 0.00 2.52
1618 1638 7.495279 TCTGAACAACAAAATCAATGGGAAAAG 59.505 33.333 0.00 0.00 0.00 2.27
1619 1639 7.334090 TCTGAACAACAAAATCAATGGGAAAA 58.666 30.769 0.00 0.00 0.00 2.29
1620 1640 6.882656 TCTGAACAACAAAATCAATGGGAAA 58.117 32.000 0.00 0.00 0.00 3.13
1621 1641 6.477053 TCTGAACAACAAAATCAATGGGAA 57.523 33.333 0.00 0.00 0.00 3.97
1622 1642 6.477053 TTCTGAACAACAAAATCAATGGGA 57.523 33.333 0.00 0.00 0.00 4.37
1623 1643 5.178067 GCTTCTGAACAACAAAATCAATGGG 59.822 40.000 0.00 0.00 0.00 4.00
1624 1644 5.754406 TGCTTCTGAACAACAAAATCAATGG 59.246 36.000 0.00 0.00 0.00 3.16
1643 1978 4.882671 TTTGTGTGAAGAACTCTGCTTC 57.117 40.909 0.00 0.00 41.57 3.86
1711 2046 7.147213 TGCATACTTAGGGGGAAAAGATAATGA 60.147 37.037 0.00 0.00 0.00 2.57
1718 2053 5.765182 CACTATGCATACTTAGGGGGAAAAG 59.235 44.000 1.16 0.00 0.00 2.27
1720 2055 4.724798 ACACTATGCATACTTAGGGGGAAA 59.275 41.667 1.16 0.00 32.50 3.13
1724 2059 8.691661 AAAAATACACTATGCATACTTAGGGG 57.308 34.615 1.16 0.00 32.50 4.79
1741 2076 8.987890 GCAGCAGGAAAAGAAAATAAAAATACA 58.012 29.630 0.00 0.00 0.00 2.29
1742 2077 8.162245 CGCAGCAGGAAAAGAAAATAAAAATAC 58.838 33.333 0.00 0.00 0.00 1.89
1745 2080 6.523676 CGCAGCAGGAAAAGAAAATAAAAA 57.476 33.333 0.00 0.00 0.00 1.94
1797 2132 7.115520 CACTCCGCTCATAACTCAAACATATAG 59.884 40.741 0.00 0.00 0.00 1.31
1801 2136 3.935203 CACTCCGCTCATAACTCAAACAT 59.065 43.478 0.00 0.00 0.00 2.71
1812 2147 3.695606 ACGTGGCACTCCGCTCAT 61.696 61.111 16.72 0.00 40.70 2.90
1828 2163 3.654414 AGAGAGGAAAATGACACGACAC 58.346 45.455 0.00 0.00 0.00 3.67
1844 2179 6.460953 GCTGGTAAGATGTCCTCTTAAGAGAG 60.461 46.154 30.17 20.43 45.72 3.20
1859 2194 5.045578 TCCAAAGAAGCTAAGCTGGTAAGAT 60.046 40.000 0.00 0.00 39.62 2.40
1917 2258 9.628500 AAAAACTCACTCTTAAACTTCCTACAT 57.372 29.630 0.00 0.00 0.00 2.29
2008 2350 6.455690 AAGAACCTGAGGGTAAAGAAGAAT 57.544 37.500 2.38 0.00 46.67 2.40
2177 2519 7.775120 ACAAAAGTTAAATGAGATATGCAGGG 58.225 34.615 0.00 0.00 0.00 4.45
2227 2569 7.615757 TGTCTTAACAGAATAGGATGAGTCAGA 59.384 37.037 0.00 0.00 0.00 3.27
2232 2574 8.642432 TGGTATGTCTTAACAGAATAGGATGAG 58.358 37.037 0.00 0.00 39.20 2.90
2342 2684 0.818040 AAACGCAGCCGAAAGAACCT 60.818 50.000 0.00 0.00 38.29 3.50
2403 2745 8.868916 GTTTGAACTTGAAAATGTCAAAGCTTA 58.131 29.630 0.00 0.00 45.67 3.09
2418 2760 5.192927 AGAGATTGTGGTGTTTGAACTTGA 58.807 37.500 0.00 0.00 0.00 3.02
2448 2790 6.953843 TGATTGGTGCATACAATATGTTACG 58.046 36.000 16.50 0.00 38.57 3.18
2456 2798 4.592942 AGTGACTGATTGGTGCATACAAT 58.407 39.130 16.49 16.49 40.98 2.71
2458 2800 3.599343 GAGTGACTGATTGGTGCATACA 58.401 45.455 0.00 0.00 0.00 2.29
2459 2801 2.939103 GGAGTGACTGATTGGTGCATAC 59.061 50.000 0.00 0.00 0.00 2.39
2499 2841 1.138266 GAGTATAACCTGCCGCTTCCA 59.862 52.381 0.00 0.00 0.00 3.53
2501 2843 2.892784 AGAGTATAACCTGCCGCTTC 57.107 50.000 0.00 0.00 0.00 3.86
2540 2882 1.070134 TGGTCCAAGTGCTACAGTGAC 59.930 52.381 0.00 0.00 0.00 3.67
2579 2921 3.931468 CCTGAGCACTCATGAAACACTAG 59.069 47.826 0.00 0.00 39.13 2.57
2605 2947 4.038042 GCTTTCCCTGCATAATTTAGACCC 59.962 45.833 0.00 0.00 0.00 4.46
2611 2953 5.018809 TCTTCAGCTTTCCCTGCATAATTT 58.981 37.500 0.00 0.00 32.87 1.82
2669 3011 2.951642 CCTTGTTCCTTGCTTTGACTCA 59.048 45.455 0.00 0.00 0.00 3.41
2741 3083 4.818417 CAGCCGTGCAGTTTAACG 57.182 55.556 0.00 0.00 39.48 3.18
2816 3158 1.440618 TACCAAAGAGGGTCCTTGCA 58.559 50.000 0.00 0.00 43.89 4.08
2840 3182 9.411801 GTTCTGAGGAAAATAGAAATTTGGTTC 57.588 33.333 0.00 0.00 35.46 3.62
2852 3194 8.450964 CAGCGATTTAAAGTTCTGAGGAAAATA 58.549 33.333 7.28 0.00 32.81 1.40
2859 3201 6.721571 TTACCAGCGATTTAAAGTTCTGAG 57.278 37.500 12.28 7.24 0.00 3.35
2870 3212 6.599244 TCTGAGAATGAATTTACCAGCGATTT 59.401 34.615 0.00 0.00 0.00 2.17
2947 3290 0.954452 CCCTTGTGCTCCAGTCAAAC 59.046 55.000 0.00 0.00 0.00 2.93
3504 3847 9.843334 GCTGTATTCCATACTATTGTACTAGAC 57.157 37.037 0.00 0.00 36.70 2.59
3520 3863 7.611855 TCTTCGATCTATCATAGCTGTATTCCA 59.388 37.037 0.00 0.00 0.00 3.53
3541 3884 3.126831 GGTCTAATGTGGAGCATCTTCG 58.873 50.000 0.00 0.00 36.67 3.79
3542 3885 4.142609 TGGTCTAATGTGGAGCATCTTC 57.857 45.455 0.00 0.00 36.67 2.87
3549 3892 4.080919 TGGTTCTCATGGTCTAATGTGGAG 60.081 45.833 0.00 0.00 0.00 3.86
3567 3910 4.357918 AGGTATATGTCTGGCATGGTTC 57.642 45.455 4.74 0.00 38.47 3.62
3570 3913 6.155221 ACATAGTAGGTATATGTCTGGCATGG 59.845 42.308 4.74 0.00 39.13 3.66
3621 3964 6.813649 AGTATATTATGCGCATCTACTTGTGG 59.186 38.462 29.11 0.00 0.00 4.17
3747 4093 5.755849 AGCTGGCAGTACTACCAAAAATAT 58.244 37.500 15.80 0.00 34.96 1.28
3811 4157 6.697019 ACATTTTCAGAAACAAATCCAGAACG 59.303 34.615 0.00 0.00 0.00 3.95
3891 4242 9.467258 CAGGTGCATATAATAATTGGACAAAAG 57.533 33.333 0.00 0.00 33.87 2.27
3929 4280 7.244166 AGATCTCTCATAAATCGCTGTTTTG 57.756 36.000 0.00 0.00 0.00 2.44
3965 4316 3.885297 CCTTTTGACTTCTCTTTGCAGGA 59.115 43.478 0.00 0.00 0.00 3.86
4062 4413 1.047801 CCTGGGAAAAACAAGTGGGG 58.952 55.000 0.00 0.00 0.00 4.96
4063 4414 0.392706 GCCTGGGAAAAACAAGTGGG 59.607 55.000 0.00 0.00 0.00 4.61
4142 4493 0.320771 AGCTTCGTCGGTGCTGAAAT 60.321 50.000 11.04 0.00 35.54 2.17
4227 4578 2.472695 TTAGCATCTTGGCGACTGTT 57.527 45.000 0.00 0.00 39.27 3.16
4441 4792 5.841810 TCCTTCATGTGCCTTTTTAACTTG 58.158 37.500 0.00 0.00 0.00 3.16
4512 4863 4.025040 TCAAATGCCTCTCTTGACATGT 57.975 40.909 0.00 0.00 0.00 3.21
4646 5000 6.013725 TGTGCTCTTCTTCCTTCACCTATAAA 60.014 38.462 0.00 0.00 0.00 1.40
4666 5020 2.348998 GCCTGGTGTAGCTGTGCT 59.651 61.111 0.00 0.00 43.41 4.40
4698 5052 3.008375 AGCAAATCTCTGTAAGTCCAGCA 59.992 43.478 0.00 0.00 33.76 4.41
4805 5163 8.186163 CCGTGTGAGATTTGTACTGTATACTTA 58.814 37.037 4.17 0.00 0.00 2.24
4848 5206 3.603532 TCACAGGTCTTTCATGCAGATC 58.396 45.455 0.00 0.00 0.00 2.75
4872 5230 7.765360 TGAATTATTGGCATTTCAGAATGGAAC 59.235 33.333 0.00 0.00 35.60 3.62
4878 5236 8.366401 TCAGTTTGAATTATTGGCATTTCAGAA 58.634 29.630 0.00 0.00 30.45 3.02
4916 5274 6.741992 TCTGCTGACGTATTTGATTGAAAT 57.258 33.333 0.00 0.00 37.96 2.17
4921 5279 8.437360 TCAATAATCTGCTGACGTATTTGATT 57.563 30.769 0.00 0.00 0.00 2.57
4931 5289 6.485984 ACAATCATCCTCAATAATCTGCTGAC 59.514 38.462 0.00 0.00 0.00 3.51
5019 5377 1.134788 CAAGGCCTCGTTCGGTAAGAT 60.135 52.381 5.23 0.00 0.00 2.40
5027 5385 4.116238 CTCTTAGATTCAAGGCCTCGTTC 58.884 47.826 5.23 0.74 0.00 3.95
5030 5388 2.695666 TCCTCTTAGATTCAAGGCCTCG 59.304 50.000 5.23 0.00 0.00 4.63
5035 5393 4.184629 CACGGTTCCTCTTAGATTCAAGG 58.815 47.826 0.00 0.00 0.00 3.61
5227 5588 7.810759 ACTGTTTGTTTGGTTTAACTTGTACTG 59.189 33.333 0.00 0.00 0.00 2.74
5302 5862 3.510531 TGGGTTATTACTGTGGTGCAA 57.489 42.857 0.00 0.00 0.00 4.08
5331 5891 7.172532 TGTGATACCATGTTCAACTGTTAAGAC 59.827 37.037 0.00 0.00 0.00 3.01
5333 5893 7.433708 TGTGATACCATGTTCAACTGTTAAG 57.566 36.000 0.00 0.00 0.00 1.85
5377 5937 8.205131 ACGTCTTACATTTGTTTACAGAGTTT 57.795 30.769 0.00 0.00 0.00 2.66
5496 6105 4.650734 TGCTGTGTTTCCTGACATTATCA 58.349 39.130 0.00 0.00 35.45 2.15
5500 6109 3.554934 TCTTGCTGTGTTTCCTGACATT 58.445 40.909 0.00 0.00 0.00 2.71
5532 6141 4.770010 TCTTGAGGTTTCCTGTTGTTTTGT 59.230 37.500 0.00 0.00 31.76 2.83
5544 6153 9.124807 CCGTATTTGTTTATTTCTTGAGGTTTC 57.875 33.333 0.00 0.00 0.00 2.78
5717 6335 4.282703 AGAATGTGGCTTTTGAGAGCATTT 59.717 37.500 0.00 0.00 44.49 2.32
5719 6337 3.192844 CAGAATGTGGCTTTTGAGAGCAT 59.807 43.478 0.00 0.00 44.49 3.79
5844 6462 6.770303 CAGATAGATGGAGTTCTGTGTCTCTA 59.230 42.308 0.00 0.00 32.73 2.43
5868 6486 1.877443 GCGCAACTTAAAGAGGGAACA 59.123 47.619 0.30 0.00 0.00 3.18
5879 6497 3.791122 GCGACTACTCTATGCGCAACTTA 60.791 47.826 17.11 0.50 46.19 2.24


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

AutoCloner maintained by Alex Coulton.