Multiple sequence alignment - TraesCS3B01G162900

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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 TraesCS3B01G162900 chr3B 100.000 3385 0 0 1 3385 160620364 160623748 0.000000e+00 6252.0
1 TraesCS3B01G162900 chr3B 80.603 232 42 3 2063 2292 807316812 807316582 3.470000e-40 176.0
2 TraesCS3B01G162900 chr3D 95.004 1241 38 7 1373 2598 109262969 109264200 0.000000e+00 1927.0
3 TraesCS3B01G162900 chr3D 87.353 1273 83 30 78 1323 109261296 109262517 0.000000e+00 1387.0
4 TraesCS3B01G162900 chr3D 80.508 118 22 1 1512 1629 419387094 419387210 4.650000e-14 89.8
5 TraesCS3B01G162900 chr3A 94.522 1150 38 9 1440 2580 121328590 121327457 0.000000e+00 1751.0
6 TraesCS3B01G162900 chr3A 99.361 782 5 0 2604 3385 102266912 102266131 0.000000e+00 1417.0
7 TraesCS3B01G162900 chr3A 97.980 792 14 2 2594 3385 658604730 658603941 0.000000e+00 1373.0
8 TraesCS3B01G162900 chr3A 90.302 629 34 4 613 1234 121329302 121328694 0.000000e+00 798.0
9 TraesCS3B01G162900 chr3A 96.183 131 5 0 488 618 121329462 121329332 7.360000e-52 215.0
10 TraesCS3B01G162900 chr4B 99.107 784 7 0 2602 3385 529324925 529325708 0.000000e+00 1410.0
11 TraesCS3B01G162900 chr4B 98.981 785 7 1 2602 3385 101958096 101957312 0.000000e+00 1404.0
12 TraesCS3B01G162900 chr1B 98.977 782 7 1 2604 3385 529277029 529276249 0.000000e+00 1399.0
13 TraesCS3B01G162900 chr1B 98.346 786 11 2 2600 3385 26176760 26177543 0.000000e+00 1378.0
14 TraesCS3B01G162900 chr5A 98.338 782 13 0 2604 3385 433385030 433384249 0.000000e+00 1373.0
15 TraesCS3B01G162900 chr7B 98.092 786 13 2 2601 3385 100046013 100046797 0.000000e+00 1367.0
16 TraesCS3B01G162900 chr6B 97.967 787 13 3 2599 3385 25990899 25990116 0.000000e+00 1362.0
17 TraesCS3B01G162900 chr6B 100.000 37 0 0 242 278 9165438 9165474 6.060000e-08 69.4
18 TraesCS3B01G162900 chr4A 83.690 374 61 0 1513 1886 666637918 666637545 1.490000e-93 353.0
19 TraesCS3B01G162900 chr7D 82.620 374 65 0 1513 1886 52000048 52000421 7.000000e-87 331.0
20 TraesCS3B01G162900 chr2D 75.493 355 72 12 1509 1853 95645119 95645468 3.500000e-35 159.0
21 TraesCS3B01G162900 chr2D 77.064 109 19 5 1524 1629 96293619 96293724 1.310000e-04 58.4
22 TraesCS3B01G162900 chr6A 75.974 308 62 10 1514 1815 50034987 50035288 7.570000e-32 148.0
23 TraesCS3B01G162900 chr2A 82.857 105 18 0 1525 1629 94204671 94204567 1.000000e-15 95.3


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 TraesCS3B01G162900 chr3B 160620364 160623748 3384 False 6252.000000 6252 100.0000 1 3385 1 chr3B.!!$F1 3384
1 TraesCS3B01G162900 chr3D 109261296 109264200 2904 False 1657.000000 1927 91.1785 78 2598 2 chr3D.!!$F2 2520
2 TraesCS3B01G162900 chr3A 102266131 102266912 781 True 1417.000000 1417 99.3610 2604 3385 1 chr3A.!!$R1 781
3 TraesCS3B01G162900 chr3A 658603941 658604730 789 True 1373.000000 1373 97.9800 2594 3385 1 chr3A.!!$R2 791
4 TraesCS3B01G162900 chr3A 121327457 121329462 2005 True 921.333333 1751 93.6690 488 2580 3 chr3A.!!$R3 2092
5 TraesCS3B01G162900 chr4B 529324925 529325708 783 False 1410.000000 1410 99.1070 2602 3385 1 chr4B.!!$F1 783
6 TraesCS3B01G162900 chr4B 101957312 101958096 784 True 1404.000000 1404 98.9810 2602 3385 1 chr4B.!!$R1 783
7 TraesCS3B01G162900 chr1B 529276249 529277029 780 True 1399.000000 1399 98.9770 2604 3385 1 chr1B.!!$R1 781
8 TraesCS3B01G162900 chr1B 26176760 26177543 783 False 1378.000000 1378 98.3460 2600 3385 1 chr1B.!!$F1 785
9 TraesCS3B01G162900 chr5A 433384249 433385030 781 True 1373.000000 1373 98.3380 2604 3385 1 chr5A.!!$R1 781
10 TraesCS3B01G162900 chr7B 100046013 100046797 784 False 1367.000000 1367 98.0920 2601 3385 1 chr7B.!!$F1 784
11 TraesCS3B01G162900 chr6B 25990116 25990899 783 True 1362.000000 1362 97.9670 2599 3385 1 chr6B.!!$R1 786

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
165 166 0.109913 AAACCAAACCTCTCCGACCC 59.890 55.0 0.00 0.00 0.0 4.46 F
1353 1430 0.107703 TCTTCCCGGATGCATCACAC 60.108 55.0 27.25 9.98 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 1440 0.095245 CCAAAGTGTAGCATCGCACG 59.905 55.0 0.00 0.0 40.26 5.34 R
2430 2918 0.310543 GGACGAAGCATGCAAACACA 59.689 50.0 21.98 0.0 0.00 3.72 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
23 24 6.385649 GTCCTTGTTCCAAATAGTCAACAA 57.614 37.500 0.00 0.00 36.60 2.83
24 25 6.981722 GTCCTTGTTCCAAATAGTCAACAAT 58.018 36.000 0.00 0.00 37.92 2.71
25 26 7.433680 GTCCTTGTTCCAAATAGTCAACAATT 58.566 34.615 0.00 0.00 37.92 2.32
26 27 7.926018 GTCCTTGTTCCAAATAGTCAACAATTT 59.074 33.333 0.00 0.00 37.92 1.82
27 28 8.482128 TCCTTGTTCCAAATAGTCAACAATTTT 58.518 29.630 0.00 0.00 37.92 1.82
28 29 8.764287 CCTTGTTCCAAATAGTCAACAATTTTC 58.236 33.333 0.00 0.00 37.92 2.29
29 30 9.533253 CTTGTTCCAAATAGTCAACAATTTTCT 57.467 29.630 0.00 0.00 37.92 2.52
30 31 9.883142 TTGTTCCAAATAGTCAACAATTTTCTT 57.117 25.926 0.00 0.00 34.56 2.52
31 32 9.883142 TGTTCCAAATAGTCAACAATTTTCTTT 57.117 25.926 0.00 0.00 0.00 2.52
39 40 7.654022 AGTCAACAATTTTCTTTAGGAACCA 57.346 32.000 0.00 0.00 33.13 3.67
40 41 8.250143 AGTCAACAATTTTCTTTAGGAACCAT 57.750 30.769 0.00 0.00 33.13 3.55
41 42 8.143835 AGTCAACAATTTTCTTTAGGAACCATG 58.856 33.333 0.00 0.00 33.13 3.66
42 43 7.926018 GTCAACAATTTTCTTTAGGAACCATGT 59.074 33.333 0.00 0.00 33.13 3.21
43 44 8.482128 TCAACAATTTTCTTTAGGAACCATGTT 58.518 29.630 0.00 0.00 35.37 2.71
44 45 9.108284 CAACAATTTTCTTTAGGAACCATGTTT 57.892 29.630 0.00 0.00 34.08 2.83
45 46 9.679661 AACAATTTTCTTTAGGAACCATGTTTT 57.320 25.926 0.00 0.00 33.29 2.43
46 47 9.679661 ACAATTTTCTTTAGGAACCATGTTTTT 57.320 25.926 0.00 0.00 33.13 1.94
68 69 3.546002 TTTTGCGAAATAGGAACCACG 57.454 42.857 0.00 0.00 0.00 4.94
69 70 1.444836 TTGCGAAATAGGAACCACGG 58.555 50.000 0.00 0.00 0.00 4.94
70 71 0.609151 TGCGAAATAGGAACCACGGA 59.391 50.000 0.00 0.00 0.00 4.69
71 72 1.208535 TGCGAAATAGGAACCACGGAT 59.791 47.619 0.00 0.00 0.00 4.18
72 73 1.597663 GCGAAATAGGAACCACGGATG 59.402 52.381 0.00 0.00 0.00 3.51
73 74 2.740580 GCGAAATAGGAACCACGGATGA 60.741 50.000 0.00 0.00 0.00 2.92
74 75 3.527533 CGAAATAGGAACCACGGATGAA 58.472 45.455 0.00 0.00 0.00 2.57
75 76 4.127171 CGAAATAGGAACCACGGATGAAT 58.873 43.478 0.00 0.00 0.00 2.57
76 77 4.574828 CGAAATAGGAACCACGGATGAATT 59.425 41.667 0.00 0.00 0.00 2.17
77 78 5.756347 CGAAATAGGAACCACGGATGAATTA 59.244 40.000 0.00 0.00 0.00 1.40
78 79 6.426937 CGAAATAGGAACCACGGATGAATTAT 59.573 38.462 0.00 0.00 0.00 1.28
79 80 7.510549 AAATAGGAACCACGGATGAATTATG 57.489 36.000 0.00 0.00 0.00 1.90
80 81 4.771114 AGGAACCACGGATGAATTATGA 57.229 40.909 0.00 0.00 0.00 2.15
81 82 5.310409 AGGAACCACGGATGAATTATGAT 57.690 39.130 0.00 0.00 0.00 2.45
89 90 8.156820 ACCACGGATGAATTATGATTTATGAGA 58.843 33.333 0.00 0.00 0.00 3.27
165 166 0.109913 AAACCAAACCTCTCCGACCC 59.890 55.000 0.00 0.00 0.00 4.46
166 167 0.767060 AACCAAACCTCTCCGACCCT 60.767 55.000 0.00 0.00 0.00 4.34
167 168 0.115745 ACCAAACCTCTCCGACCCTA 59.884 55.000 0.00 0.00 0.00 3.53
209 210 4.507756 TCAATCACACGCAACTAGATATGC 59.492 41.667 0.00 3.26 39.17 3.14
216 217 1.139989 CAACTAGATATGCGCACCGG 58.860 55.000 14.90 0.00 0.00 5.28
217 218 1.037493 AACTAGATATGCGCACCGGA 58.963 50.000 14.90 0.00 0.00 5.14
218 219 0.598562 ACTAGATATGCGCACCGGAG 59.401 55.000 14.90 9.52 0.00 4.63
219 220 0.881796 CTAGATATGCGCACCGGAGA 59.118 55.000 14.90 0.00 0.00 3.71
220 221 0.596577 TAGATATGCGCACCGGAGAC 59.403 55.000 14.90 0.00 0.00 3.36
231 256 0.816825 ACCGGAGACATGCATGCATC 60.817 55.000 30.07 20.79 33.90 3.91
232 257 1.568025 CGGAGACATGCATGCATCG 59.432 57.895 30.07 24.32 33.90 3.84
233 258 0.877213 CGGAGACATGCATGCATCGA 60.877 55.000 30.07 3.65 33.90 3.59
234 259 1.520494 GGAGACATGCATGCATCGAT 58.480 50.000 30.07 18.23 33.90 3.59
235 260 1.197036 GGAGACATGCATGCATCGATG 59.803 52.381 30.07 22.27 33.90 3.84
265 290 4.238514 CGGAAATTCCTAATAGAGCTCGG 58.761 47.826 10.64 2.90 33.30 4.63
267 292 3.686916 AATTCCTAATAGAGCTCGGGC 57.313 47.619 8.37 0.00 39.06 6.13
332 357 8.433421 TTCTAAGTTTCAGAAAAATCTGACGT 57.567 30.769 7.98 0.00 45.32 4.34
340 365 8.651391 TTCAGAAAAATCTGACGTAAACTACA 57.349 30.769 7.98 0.00 45.32 2.74
351 376 8.017373 TCTGACGTAAACTACACATGTACTTAC 58.983 37.037 0.00 1.88 0.00 2.34
407 432 7.108194 TGATGAAATACTTTCTGATGTGAGCT 58.892 34.615 0.00 0.00 40.32 4.09
450 475 8.958119 TTTATAACACATGGACTATTCACTCC 57.042 34.615 0.00 0.00 0.00 3.85
451 476 4.908601 AACACATGGACTATTCACTCCA 57.091 40.909 0.00 0.00 40.92 3.86
452 477 4.908601 ACACATGGACTATTCACTCCAA 57.091 40.909 0.00 0.00 40.05 3.53
453 478 5.241403 ACACATGGACTATTCACTCCAAA 57.759 39.130 0.00 0.00 40.05 3.28
454 479 5.248640 ACACATGGACTATTCACTCCAAAG 58.751 41.667 0.00 0.00 40.05 2.77
455 480 5.221925 ACACATGGACTATTCACTCCAAAGT 60.222 40.000 0.00 0.00 40.05 2.66
458 483 4.566004 TGGACTATTCACTCCAAAGTTCG 58.434 43.478 0.00 0.00 33.39 3.95
459 484 3.371285 GGACTATTCACTCCAAAGTTCGC 59.629 47.826 0.00 0.00 31.71 4.70
461 486 2.163818 ATTCACTCCAAAGTTCGCGA 57.836 45.000 3.71 3.71 31.71 5.87
463 488 1.214367 TCACTCCAAAGTTCGCGAAC 58.786 50.000 38.00 38.00 41.45 3.95
464 489 0.934496 CACTCCAAAGTTCGCGAACA 59.066 50.000 42.89 26.59 43.47 3.18
465 490 1.531149 CACTCCAAAGTTCGCGAACAT 59.469 47.619 42.89 33.90 43.47 2.71
466 491 2.032030 CACTCCAAAGTTCGCGAACATT 60.032 45.455 42.89 36.77 43.47 2.71
467 492 2.616842 ACTCCAAAGTTCGCGAACATTT 59.383 40.909 42.89 34.51 43.47 2.32
468 493 3.066203 ACTCCAAAGTTCGCGAACATTTT 59.934 39.130 42.89 33.51 43.47 1.82
548 576 7.812648 TGTATGCTATGTTTGTACCTTTTCAC 58.187 34.615 0.00 0.00 0.00 3.18
657 721 1.239968 GCTGCAAGGGTGGTCAAGAG 61.240 60.000 0.00 0.00 0.00 2.85
664 728 1.694696 AGGGTGGTCAAGAGAACTGTC 59.305 52.381 0.00 0.00 30.86 3.51
703 771 2.494059 CCATCCACGAGAACAAGTTGT 58.506 47.619 1.64 1.64 0.00 3.32
839 907 4.745649 GTGTATGGACTCACCTCAACTAC 58.254 47.826 0.00 0.00 39.86 2.73
840 908 4.463186 GTGTATGGACTCACCTCAACTACT 59.537 45.833 0.00 0.00 39.86 2.57
841 909 5.047235 GTGTATGGACTCACCTCAACTACTT 60.047 44.000 0.00 0.00 39.86 2.24
842 910 4.543590 ATGGACTCACCTCAACTACTTG 57.456 45.455 0.00 0.00 39.86 3.16
843 911 3.572642 TGGACTCACCTCAACTACTTGA 58.427 45.455 0.00 0.00 39.86 3.02
844 912 3.964688 TGGACTCACCTCAACTACTTGAA 59.035 43.478 0.00 0.00 35.92 2.69
845 913 4.039245 TGGACTCACCTCAACTACTTGAAG 59.961 45.833 0.00 0.00 35.92 3.02
846 914 3.991121 GACTCACCTCAACTACTTGAAGC 59.009 47.826 0.00 0.00 35.92 3.86
847 915 3.388024 ACTCACCTCAACTACTTGAAGCA 59.612 43.478 0.00 0.00 35.92 3.91
848 916 3.993081 CTCACCTCAACTACTTGAAGCAG 59.007 47.826 0.00 0.00 35.92 4.24
849 917 3.641436 TCACCTCAACTACTTGAAGCAGA 59.359 43.478 0.00 0.00 35.92 4.26
850 918 3.993081 CACCTCAACTACTTGAAGCAGAG 59.007 47.826 0.00 0.00 35.92 3.35
851 919 3.007398 ACCTCAACTACTTGAAGCAGAGG 59.993 47.826 13.69 13.69 42.36 3.69
852 920 3.259374 CCTCAACTACTTGAAGCAGAGGA 59.741 47.826 11.22 3.13 40.60 3.71
853 921 4.493547 CTCAACTACTTGAAGCAGAGGAG 58.506 47.826 0.00 2.21 35.92 3.69
854 922 3.898123 TCAACTACTTGAAGCAGAGGAGT 59.102 43.478 0.00 0.00 38.71 3.85
855 923 4.345257 TCAACTACTTGAAGCAGAGGAGTT 59.655 41.667 0.00 0.00 45.60 3.01
885 953 3.365472 ACAAAACCCTCTGCTTCAAGTT 58.635 40.909 0.00 0.00 0.00 2.66
886 954 3.131046 ACAAAACCCTCTGCTTCAAGTTG 59.869 43.478 0.00 0.00 0.00 3.16
907 981 7.696017 AGTTGTATATAAACCCCTCAAACTGT 58.304 34.615 0.00 0.00 0.00 3.55
908 982 7.610305 AGTTGTATATAAACCCCTCAAACTGTG 59.390 37.037 0.00 0.00 0.00 3.66
994 1068 2.037208 CCAAAGCCCCCAACGGAT 59.963 61.111 0.00 0.00 0.00 4.18
1224 1301 0.179032 TCCGGGTACGTATCGCCTAA 60.179 55.000 0.00 0.30 38.78 2.69
1236 1313 0.178941 TCGCCTAACCCCTAGATCCC 60.179 60.000 0.00 0.00 0.00 3.85
1249 1326 3.004944 CCTAGATCCCTTACGCTCTTGTC 59.995 52.174 0.00 0.00 0.00 3.18
1251 1328 3.899726 AGATCCCTTACGCTCTTGTCTA 58.100 45.455 0.00 0.00 0.00 2.59
1254 1331 1.476891 CCCTTACGCTCTTGTCTAGCA 59.523 52.381 0.00 0.00 40.08 3.49
1279 1356 3.324846 TCAATATCCATCCTCCCGAGTTG 59.675 47.826 0.00 0.00 0.00 3.16
1282 1359 0.902531 TCCATCCTCCCGAGTTGTTC 59.097 55.000 0.00 0.00 0.00 3.18
1292 1369 0.391263 CGAGTTGTTCCCTAGCCACC 60.391 60.000 0.00 0.00 0.00 4.61
1313 1390 5.750067 CACCTTGGCTGCAATCAAAATATAC 59.250 40.000 0.50 0.00 0.00 1.47
1342 1419 8.904099 ACAGTATTATTTTCTTATCTTCCCGG 57.096 34.615 0.00 0.00 0.00 5.73
1343 1420 8.711170 ACAGTATTATTTTCTTATCTTCCCGGA 58.289 33.333 0.73 0.00 0.00 5.14
1344 1421 9.726438 CAGTATTATTTTCTTATCTTCCCGGAT 57.274 33.333 0.73 0.00 0.00 4.18
1345 1422 9.726438 AGTATTATTTTCTTATCTTCCCGGATG 57.274 33.333 0.73 0.00 0.00 3.51
1347 1424 3.924114 TTTCTTATCTTCCCGGATGCA 57.076 42.857 0.73 0.00 0.00 3.96
1349 1426 3.685139 TCTTATCTTCCCGGATGCATC 57.315 47.619 18.81 18.81 0.00 3.91
1350 1427 2.972021 TCTTATCTTCCCGGATGCATCA 59.028 45.455 27.25 6.06 0.00 3.07
1351 1428 2.839486 TATCTTCCCGGATGCATCAC 57.161 50.000 27.25 15.61 0.00 3.06
1352 1429 0.839277 ATCTTCCCGGATGCATCACA 59.161 50.000 27.25 5.58 0.00 3.58
1353 1430 0.107703 TCTTCCCGGATGCATCACAC 60.108 55.000 27.25 9.98 0.00 3.82
1355 1432 2.867793 TTCCCGGATGCATCACACCG 62.868 60.000 27.25 21.14 40.47 4.94
1356 1433 2.186644 CCGGATGCATCACACCGA 59.813 61.111 27.25 0.00 42.17 4.69
1357 1434 1.884464 CCGGATGCATCACACCGAG 60.884 63.158 27.25 12.45 42.17 4.63
1367 1444 4.883026 ACACCGAGTGATACGTGC 57.117 55.556 10.46 0.00 36.96 5.34
1369 1446 1.135939 CACCGAGTGATACGTGCGA 59.864 57.895 0.00 0.00 35.23 5.10
1371 1448 0.248498 ACCGAGTGATACGTGCGATG 60.248 55.000 0.00 0.00 0.00 3.84
1380 1859 2.357327 TACGTGCGATGCTACACTTT 57.643 45.000 0.00 0.00 34.58 2.66
1412 1891 9.443283 GATCTTTACATGATTTGATGTTACTGC 57.557 33.333 0.00 0.00 37.70 4.40
1413 1892 8.565896 TCTTTACATGATTTGATGTTACTGCT 57.434 30.769 0.00 0.00 37.70 4.24
1414 1893 9.665719 TCTTTACATGATTTGATGTTACTGCTA 57.334 29.630 0.00 0.00 37.70 3.49
1415 1894 9.926751 CTTTACATGATTTGATGTTACTGCTAG 57.073 33.333 0.00 0.00 37.70 3.42
1416 1895 9.448438 TTTACATGATTTGATGTTACTGCTAGT 57.552 29.630 0.00 0.00 37.70 2.57
1418 1897 8.425577 ACATGATTTGATGTTACTGCTAGTAC 57.574 34.615 0.00 0.00 32.38 2.73
1419 1898 8.260818 ACATGATTTGATGTTACTGCTAGTACT 58.739 33.333 0.00 0.00 32.38 2.73
1700 2179 1.258445 ACGGCAACTTCTCCCTCGAT 61.258 55.000 0.00 0.00 0.00 3.59
1896 2375 1.099879 CGTACGTCCTCCGATCCCTT 61.100 60.000 7.22 0.00 40.70 3.95
1904 2385 1.831736 CCTCCGATCCCTTGTAACACT 59.168 52.381 0.00 0.00 0.00 3.55
1910 2391 3.412386 GATCCCTTGTAACACTTGCAGT 58.588 45.455 0.00 0.00 0.00 4.40
1912 2393 4.425180 TCCCTTGTAACACTTGCAGTTA 57.575 40.909 0.00 0.00 0.00 2.24
2210 2697 2.333014 CTCTGGAAGCAGAAGTTCGTC 58.667 52.381 0.00 0.00 0.00 4.20
2426 2914 0.605319 TGCAATTCGTCCCACCACTC 60.605 55.000 0.00 0.00 0.00 3.51
2427 2915 0.321653 GCAATTCGTCCCACCACTCT 60.322 55.000 0.00 0.00 0.00 3.24
2428 2916 1.066430 GCAATTCGTCCCACCACTCTA 60.066 52.381 0.00 0.00 0.00 2.43
2429 2917 2.420129 GCAATTCGTCCCACCACTCTAT 60.420 50.000 0.00 0.00 0.00 1.98
2430 2918 3.873910 CAATTCGTCCCACCACTCTATT 58.126 45.455 0.00 0.00 0.00 1.73
2431 2919 3.543680 ATTCGTCCCACCACTCTATTG 57.456 47.619 0.00 0.00 0.00 1.90
2432 2920 1.933021 TCGTCCCACCACTCTATTGT 58.067 50.000 0.00 0.00 0.00 2.71
2433 2921 1.548719 TCGTCCCACCACTCTATTGTG 59.451 52.381 0.00 0.00 37.66 3.33
2525 3035 3.871594 ACGCATATGTACCTCTGCTTTTC 59.128 43.478 4.29 0.00 32.48 2.29
2548 3058 2.153680 ACGCGTGAATAAAACGATGC 57.846 45.000 12.93 0.00 43.68 3.91
2599 3109 1.272704 GGAAGCAGTCCCCCTGAATTT 60.273 52.381 0.00 0.00 44.49 1.82
2905 3417 4.258543 AGACAAAAGAAACCACTTCACGA 58.741 39.130 0.00 0.00 36.40 4.35
3091 3603 2.230992 CCTCGATGGCAATTTTGTTCCA 59.769 45.455 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.362151 TGGTTCCTAAAGAAAATTGTTGACTAT 57.638 29.630 0.00 0.00 35.85 2.12
14 15 8.754991 TGGTTCCTAAAGAAAATTGTTGACTA 57.245 30.769 0.00 0.00 35.85 2.59
15 16 7.654022 TGGTTCCTAAAGAAAATTGTTGACT 57.346 32.000 0.00 0.00 35.85 3.41
16 17 7.926018 ACATGGTTCCTAAAGAAAATTGTTGAC 59.074 33.333 0.00 0.00 35.85 3.18
17 18 8.017418 ACATGGTTCCTAAAGAAAATTGTTGA 57.983 30.769 0.00 0.00 35.85 3.18
18 19 8.661352 AACATGGTTCCTAAAGAAAATTGTTG 57.339 30.769 0.00 0.00 35.85 3.33
19 20 9.679661 AAAACATGGTTCCTAAAGAAAATTGTT 57.320 25.926 0.00 0.00 35.85 2.83
20 21 9.679661 AAAAACATGGTTCCTAAAGAAAATTGT 57.320 25.926 0.00 0.00 35.85 2.71
47 48 3.304794 CCGTGGTTCCTATTTCGCAAAAA 60.305 43.478 0.00 0.00 0.00 1.94
48 49 2.226912 CCGTGGTTCCTATTTCGCAAAA 59.773 45.455 0.00 0.00 0.00 2.44
49 50 1.807742 CCGTGGTTCCTATTTCGCAAA 59.192 47.619 0.00 0.00 0.00 3.68
50 51 1.002201 TCCGTGGTTCCTATTTCGCAA 59.998 47.619 0.00 0.00 0.00 4.85
51 52 0.609151 TCCGTGGTTCCTATTTCGCA 59.391 50.000 0.00 0.00 0.00 5.10
52 53 1.597663 CATCCGTGGTTCCTATTTCGC 59.402 52.381 0.00 0.00 0.00 4.70
53 54 3.173668 TCATCCGTGGTTCCTATTTCG 57.826 47.619 0.00 0.00 0.00 3.46
54 55 7.444183 TCATAATTCATCCGTGGTTCCTATTTC 59.556 37.037 0.00 0.00 0.00 2.17
55 56 7.287061 TCATAATTCATCCGTGGTTCCTATTT 58.713 34.615 0.00 0.00 0.00 1.40
56 57 6.837312 TCATAATTCATCCGTGGTTCCTATT 58.163 36.000 0.00 0.00 0.00 1.73
57 58 6.433847 TCATAATTCATCCGTGGTTCCTAT 57.566 37.500 0.00 0.00 0.00 2.57
58 59 5.880164 TCATAATTCATCCGTGGTTCCTA 57.120 39.130 0.00 0.00 0.00 2.94
59 60 4.771114 TCATAATTCATCCGTGGTTCCT 57.229 40.909 0.00 0.00 0.00 3.36
60 61 6.391227 AAATCATAATTCATCCGTGGTTCC 57.609 37.500 0.00 0.00 0.00 3.62
61 62 8.783093 TCATAAATCATAATTCATCCGTGGTTC 58.217 33.333 0.00 0.00 0.00 3.62
62 63 8.690203 TCATAAATCATAATTCATCCGTGGTT 57.310 30.769 0.00 0.00 0.00 3.67
63 64 8.156820 TCTCATAAATCATAATTCATCCGTGGT 58.843 33.333 0.00 0.00 0.00 4.16
64 65 8.446273 GTCTCATAAATCATAATTCATCCGTGG 58.554 37.037 0.00 0.00 0.00 4.94
65 66 8.992073 TGTCTCATAAATCATAATTCATCCGTG 58.008 33.333 0.00 0.00 0.00 4.94
66 67 9.559732 TTGTCTCATAAATCATAATTCATCCGT 57.440 29.630 0.00 0.00 0.00 4.69
71 72 8.623903 GCACCTTGTCTCATAAATCATAATTCA 58.376 33.333 0.00 0.00 0.00 2.57
72 73 8.844244 AGCACCTTGTCTCATAAATCATAATTC 58.156 33.333 0.00 0.00 0.00 2.17
73 74 8.757982 AGCACCTTGTCTCATAAATCATAATT 57.242 30.769 0.00 0.00 0.00 1.40
74 75 9.277783 GTAGCACCTTGTCTCATAAATCATAAT 57.722 33.333 0.00 0.00 0.00 1.28
75 76 8.486210 AGTAGCACCTTGTCTCATAAATCATAA 58.514 33.333 0.00 0.00 0.00 1.90
76 77 8.023021 AGTAGCACCTTGTCTCATAAATCATA 57.977 34.615 0.00 0.00 0.00 2.15
77 78 6.893583 AGTAGCACCTTGTCTCATAAATCAT 58.106 36.000 0.00 0.00 0.00 2.45
78 79 6.299805 AGTAGCACCTTGTCTCATAAATCA 57.700 37.500 0.00 0.00 0.00 2.57
79 80 7.617041 AAAGTAGCACCTTGTCTCATAAATC 57.383 36.000 0.00 0.00 0.00 2.17
80 81 7.094205 CCAAAAGTAGCACCTTGTCTCATAAAT 60.094 37.037 0.00 0.00 0.00 1.40
81 82 6.206634 CCAAAAGTAGCACCTTGTCTCATAAA 59.793 38.462 0.00 0.00 0.00 1.40
89 90 2.949644 GTGACCAAAAGTAGCACCTTGT 59.050 45.455 0.00 0.00 0.00 3.16
165 166 1.160137 GCCTTTGACTGTGGCTGTAG 58.840 55.000 0.01 0.00 43.05 2.74
166 167 0.472044 TGCCTTTGACTGTGGCTGTA 59.528 50.000 8.16 0.00 46.23 2.74
167 168 0.178981 ATGCCTTTGACTGTGGCTGT 60.179 50.000 8.16 0.00 46.23 4.40
186 187 4.507756 GCATATCTAGTTGCGTGTGATTGA 59.492 41.667 0.00 0.00 0.00 2.57
209 210 2.512286 ATGCATGTCTCCGGTGCG 60.512 61.111 0.00 0.00 41.61 5.34
216 217 2.596263 CATCGATGCATGCATGTCTC 57.404 50.000 36.73 22.01 36.70 3.36
231 256 3.935203 AGGAATTTCCGCTATATGCATCG 59.065 43.478 0.19 0.00 42.75 3.84
232 257 6.985188 TTAGGAATTTCCGCTATATGCATC 57.015 37.500 0.19 0.00 42.75 3.91
233 258 8.486210 TCTATTAGGAATTTCCGCTATATGCAT 58.514 33.333 3.79 3.79 42.75 3.96
234 259 7.847096 TCTATTAGGAATTTCCGCTATATGCA 58.153 34.615 9.77 0.00 42.75 3.96
235 260 7.042389 GCTCTATTAGGAATTTCCGCTATATGC 60.042 40.741 9.77 7.72 42.75 3.14
236 261 8.200792 AGCTCTATTAGGAATTTCCGCTATATG 58.799 37.037 9.77 2.07 42.75 1.78
237 262 8.312669 AGCTCTATTAGGAATTTCCGCTATAT 57.687 34.615 9.77 3.64 42.75 0.86
238 263 7.415318 CGAGCTCTATTAGGAATTTCCGCTATA 60.415 40.741 12.85 8.00 42.75 1.31
239 264 6.613153 AGCTCTATTAGGAATTTCCGCTAT 57.387 37.500 9.77 7.34 42.75 2.97
267 292 8.782339 ATTTTGAAAAATTAAGCTCCATGGAG 57.218 30.769 33.73 33.73 38.99 3.86
305 330 9.374960 CGTCAGATTTTTCTGAAACTTAGAAAG 57.625 33.333 7.23 0.00 46.81 2.62
307 332 8.433421 ACGTCAGATTTTTCTGAAACTTAGAA 57.567 30.769 7.23 0.00 46.81 2.10
319 344 8.280497 ACATGTGTAGTTTACGTCAGATTTTTC 58.720 33.333 0.00 0.00 0.00 2.29
324 349 7.154435 AGTACATGTGTAGTTTACGTCAGAT 57.846 36.000 9.11 0.00 30.42 2.90
330 355 6.314018 TCCGTAAGTACATGTGTAGTTTACG 58.686 40.000 24.77 24.77 44.32 3.18
332 357 7.829725 ACATCCGTAAGTACATGTGTAGTTTA 58.170 34.615 16.01 5.98 42.37 2.01
420 445 9.952030 TGAATAGTCCATGTGTTATAAAAGTCA 57.048 29.630 0.00 0.00 0.00 3.41
444 469 1.214367 GTTCGCGAACTTTGGAGTGA 58.786 50.000 37.61 4.57 38.25 3.41
449 474 3.549873 ACAAAAATGTTCGCGAACTTTGG 59.450 39.130 39.03 33.53 41.67 3.28
450 475 4.495289 CACAAAAATGTTCGCGAACTTTG 58.505 39.130 37.19 37.19 41.67 2.77
451 476 3.549873 CCACAAAAATGTTCGCGAACTTT 59.450 39.130 41.46 37.73 41.67 2.66
452 477 3.112580 CCACAAAAATGTTCGCGAACTT 58.887 40.909 41.46 35.17 41.67 2.66
453 478 2.726633 CCACAAAAATGTTCGCGAACT 58.273 42.857 41.46 28.39 41.67 3.01
454 479 1.189227 GCCACAAAAATGTTCGCGAAC 59.811 47.619 38.12 38.12 41.50 3.95
455 480 1.482278 GCCACAAAAATGTTCGCGAA 58.518 45.000 19.38 19.38 0.00 4.70
458 483 1.792367 GAAGGCCACAAAAATGTTCGC 59.208 47.619 5.01 0.00 0.00 4.70
459 484 3.090952 TGAAGGCCACAAAAATGTTCG 57.909 42.857 5.01 0.00 0.00 3.95
461 486 4.190772 CAGTTGAAGGCCACAAAAATGTT 58.809 39.130 15.16 0.00 0.00 2.71
463 488 3.795877 ACAGTTGAAGGCCACAAAAATG 58.204 40.909 15.16 15.30 0.00 2.32
464 489 3.181466 GGACAGTTGAAGGCCACAAAAAT 60.181 43.478 15.16 5.56 0.00 1.82
465 490 2.167487 GGACAGTTGAAGGCCACAAAAA 59.833 45.455 15.16 0.00 0.00 1.94
466 491 1.754226 GGACAGTTGAAGGCCACAAAA 59.246 47.619 15.16 0.00 0.00 2.44
467 492 1.398692 GGACAGTTGAAGGCCACAAA 58.601 50.000 15.16 0.00 0.00 2.83
468 493 0.817634 CGGACAGTTGAAGGCCACAA 60.818 55.000 5.01 8.54 0.00 3.33
510 535 3.692257 AGCATACAAGACTGCAACTCT 57.308 42.857 0.00 0.00 40.88 3.24
513 538 5.551760 AACATAGCATACAAGACTGCAAC 57.448 39.130 0.00 0.00 40.88 4.17
614 643 1.437986 CGGAGCCTCGGGAACTAAG 59.562 63.158 0.00 0.00 0.00 2.18
638 702 1.228245 TCTTGACCACCCTTGCAGC 60.228 57.895 0.00 0.00 0.00 5.25
639 703 0.397941 TCTCTTGACCACCCTTGCAG 59.602 55.000 0.00 0.00 0.00 4.41
644 708 1.694696 GACAGTTCTCTTGACCACCCT 59.305 52.381 0.00 0.00 0.00 4.34
648 712 1.538204 GCGTGACAGTTCTCTTGACCA 60.538 52.381 0.00 0.00 0.00 4.02
657 721 2.198406 TGTGTACTTGCGTGACAGTTC 58.802 47.619 0.00 0.00 0.00 3.01
664 728 1.263217 GGGTCTTTGTGTACTTGCGTG 59.737 52.381 0.00 0.00 0.00 5.34
675 739 1.348064 TCTCGTGGATGGGTCTTTGT 58.652 50.000 0.00 0.00 0.00 2.83
703 771 9.203421 GGCTTTAGCTTTGCTTTCTTAAAATTA 57.797 29.630 0.00 0.00 40.44 1.40
794 862 4.870991 CCTCTGCCAAAAGTAGTTAGCTAC 59.129 45.833 8.59 8.59 45.96 3.58
796 864 3.328050 ACCTCTGCCAAAAGTAGTTAGCT 59.672 43.478 0.00 0.00 0.00 3.32
839 907 2.847327 TGGAACTCCTCTGCTTCAAG 57.153 50.000 0.00 0.00 36.82 3.02
840 908 3.072915 TGAATGGAACTCCTCTGCTTCAA 59.927 43.478 0.00 0.00 36.82 2.69
841 909 2.639347 TGAATGGAACTCCTCTGCTTCA 59.361 45.455 0.00 0.00 36.82 3.02
842 910 3.340814 TGAATGGAACTCCTCTGCTTC 57.659 47.619 0.00 0.00 36.82 3.86
843 911 4.225942 TGTATGAATGGAACTCCTCTGCTT 59.774 41.667 0.00 0.00 36.82 3.91
844 912 3.776969 TGTATGAATGGAACTCCTCTGCT 59.223 43.478 0.00 0.00 36.82 4.24
845 913 4.142609 TGTATGAATGGAACTCCTCTGC 57.857 45.455 0.00 0.00 36.82 4.26
846 914 6.127897 GGTTTTGTATGAATGGAACTCCTCTG 60.128 42.308 0.00 0.00 36.82 3.35
847 915 5.946377 GGTTTTGTATGAATGGAACTCCTCT 59.054 40.000 0.00 0.00 36.82 3.69
848 916 5.125578 GGGTTTTGTATGAATGGAACTCCTC 59.874 44.000 0.00 0.00 36.82 3.71
849 917 5.016831 GGGTTTTGTATGAATGGAACTCCT 58.983 41.667 0.00 0.00 36.82 3.69
850 918 5.016831 AGGGTTTTGTATGAATGGAACTCC 58.983 41.667 0.00 0.00 0.00 3.85
851 919 5.946377 AGAGGGTTTTGTATGAATGGAACTC 59.054 40.000 0.00 0.00 0.00 3.01
852 920 5.711976 CAGAGGGTTTTGTATGAATGGAACT 59.288 40.000 0.00 0.00 0.00 3.01
853 921 5.622233 GCAGAGGGTTTTGTATGAATGGAAC 60.622 44.000 0.00 0.00 0.00 3.62
854 922 4.462483 GCAGAGGGTTTTGTATGAATGGAA 59.538 41.667 0.00 0.00 0.00 3.53
855 923 4.016444 GCAGAGGGTTTTGTATGAATGGA 58.984 43.478 0.00 0.00 0.00 3.41
885 953 5.883673 GCACAGTTTGAGGGGTTTATATACA 59.116 40.000 0.00 0.00 0.00 2.29
886 954 5.298527 GGCACAGTTTGAGGGGTTTATATAC 59.701 44.000 0.00 0.00 0.00 1.47
907 981 1.001887 TGATGCAGCTCACATGGCA 60.002 52.632 2.53 0.00 41.00 4.92
908 982 1.432251 GTGATGCAGCTCACATGGC 59.568 57.895 14.23 0.00 44.03 4.40
994 1068 2.695561 TGGCAGCCACCATCTCTAA 58.304 52.632 11.22 0.00 33.75 2.10
1224 1301 0.561680 AGCGTAAGGGATCTAGGGGT 59.438 55.000 0.00 0.00 38.28 4.95
1236 1313 3.217599 TGTGCTAGACAAGAGCGTAAG 57.782 47.619 0.00 0.00 43.19 2.34
1249 1326 5.426504 GGAGGATGGATATTGATGTGCTAG 58.573 45.833 0.00 0.00 0.00 3.42
1251 1328 3.009916 GGGAGGATGGATATTGATGTGCT 59.990 47.826 0.00 0.00 0.00 4.40
1254 1331 3.517100 CTCGGGAGGATGGATATTGATGT 59.483 47.826 0.00 0.00 0.00 3.06
1292 1369 5.581605 ACGTATATTTTGATTGCAGCCAAG 58.418 37.500 0.00 0.00 33.80 3.61
1323 1400 6.361433 TGCATCCGGGAAGATAAGAAAATAA 58.639 36.000 0.00 0.00 0.00 1.40
1325 1402 4.792068 TGCATCCGGGAAGATAAGAAAAT 58.208 39.130 0.00 0.00 0.00 1.82
1326 1403 4.229304 TGCATCCGGGAAGATAAGAAAA 57.771 40.909 0.00 0.00 0.00 2.29
1327 1404 3.924114 TGCATCCGGGAAGATAAGAAA 57.076 42.857 0.00 0.00 0.00 2.52
1328 1405 3.390967 TGATGCATCCGGGAAGATAAGAA 59.609 43.478 23.67 0.00 0.00 2.52
1329 1406 2.972021 TGATGCATCCGGGAAGATAAGA 59.028 45.455 23.67 0.00 0.00 2.10
1330 1407 3.070018 GTGATGCATCCGGGAAGATAAG 58.930 50.000 23.67 0.00 0.00 1.73
1333 1410 0.839277 TGTGATGCATCCGGGAAGAT 59.161 50.000 23.67 0.00 0.00 2.40
1335 1412 1.097547 GGTGTGATGCATCCGGGAAG 61.098 60.000 23.67 0.00 0.00 3.46
1336 1413 1.077787 GGTGTGATGCATCCGGGAA 60.078 57.895 23.67 1.57 0.00 3.97
1337 1414 2.589540 GGTGTGATGCATCCGGGA 59.410 61.111 23.67 0.00 0.00 5.14
1338 1415 2.896854 CGGTGTGATGCATCCGGG 60.897 66.667 23.67 5.22 37.78 5.73
1340 1417 1.153568 ACTCGGTGTGATGCATCCG 60.154 57.895 23.67 19.71 40.54 4.18
1341 1418 4.941609 ACTCGGTGTGATGCATCC 57.058 55.556 23.67 15.02 0.00 3.51
1350 1427 1.154093 CGCACGTATCACTCGGTGT 60.154 57.895 0.00 0.00 34.79 4.16
1351 1428 0.248498 ATCGCACGTATCACTCGGTG 60.248 55.000 0.00 0.00 34.45 4.94
1352 1429 0.248498 CATCGCACGTATCACTCGGT 60.248 55.000 0.00 0.00 0.00 4.69
1353 1430 1.540607 GCATCGCACGTATCACTCGG 61.541 60.000 0.00 0.00 0.00 4.63
1355 1432 2.044860 GTAGCATCGCACGTATCACTC 58.955 52.381 0.00 0.00 0.00 3.51
1356 1433 1.404035 TGTAGCATCGCACGTATCACT 59.596 47.619 0.00 0.00 0.00 3.41
1357 1434 1.517276 GTGTAGCATCGCACGTATCAC 59.483 52.381 0.00 0.00 0.00 3.06
1359 1436 2.121116 AGTGTAGCATCGCACGTATC 57.879 50.000 0.00 0.00 40.26 2.24
1360 1437 2.579207 AAGTGTAGCATCGCACGTAT 57.421 45.000 0.00 0.00 40.26 3.06
1362 1439 0.790207 CAAAGTGTAGCATCGCACGT 59.210 50.000 0.00 0.00 40.26 4.49
1363 1440 0.095245 CCAAAGTGTAGCATCGCACG 59.905 55.000 0.00 0.00 40.26 5.34
1366 1443 1.394917 CTGTCCAAAGTGTAGCATCGC 59.605 52.381 0.00 0.00 0.00 4.58
1367 1444 2.959516 TCTGTCCAAAGTGTAGCATCG 58.040 47.619 0.00 0.00 0.00 3.84
1369 1446 4.833478 AGATCTGTCCAAAGTGTAGCAT 57.167 40.909 0.00 0.00 0.00 3.79
1371 1448 5.932303 TGTAAAGATCTGTCCAAAGTGTAGC 59.068 40.000 0.00 0.00 0.00 3.58
1380 1859 7.830697 ACATCAAATCATGTAAAGATCTGTCCA 59.169 33.333 0.00 0.00 35.10 4.02
1700 2179 1.954146 GTTGTTGAGCGCGTCCTGA 60.954 57.895 8.43 0.00 0.00 3.86
1904 2385 1.876799 CATGGACGGTTGTAACTGCAA 59.123 47.619 3.57 0.00 38.89 4.08
1910 2391 1.270947 GGTCACCATGGACGGTTGTAA 60.271 52.381 21.47 0.00 37.07 2.41
1912 2393 1.072505 GGTCACCATGGACGGTTGT 59.927 57.895 21.47 0.00 37.07 3.32
1915 2396 3.820425 ATGGTCACCATGGACGGT 58.180 55.556 21.47 0.00 43.39 4.83
1939 2420 0.110823 CACGCACGCCAGTAGTTTTC 60.111 55.000 0.00 0.00 0.00 2.29
1940 2421 1.938861 CACGCACGCCAGTAGTTTT 59.061 52.632 0.00 0.00 0.00 2.43
2192 2679 1.063806 CGACGAACTTCTGCTTCCAG 58.936 55.000 0.00 0.00 40.54 3.86
2210 2697 2.514592 ATCTTCACCATGGCCGCG 60.515 61.111 13.04 0.00 0.00 6.46
2426 2914 3.825308 ACGAAGCATGCAAACACAATAG 58.175 40.909 21.98 1.46 0.00 1.73
2427 2915 3.365868 GGACGAAGCATGCAAACACAATA 60.366 43.478 21.98 0.00 0.00 1.90
2428 2916 2.607771 GGACGAAGCATGCAAACACAAT 60.608 45.455 21.98 0.00 0.00 2.71
2429 2917 1.268999 GGACGAAGCATGCAAACACAA 60.269 47.619 21.98 0.00 0.00 3.33
2430 2918 0.310543 GGACGAAGCATGCAAACACA 59.689 50.000 21.98 0.00 0.00 3.72
2431 2919 0.387239 GGGACGAAGCATGCAAACAC 60.387 55.000 21.98 8.00 0.00 3.32
2432 2920 0.821301 TGGGACGAAGCATGCAAACA 60.821 50.000 21.98 5.83 0.00 2.83
2433 2921 0.387239 GTGGGACGAAGCATGCAAAC 60.387 55.000 21.98 9.47 0.00 2.93
2548 3058 3.374988 TCAATCAAGGTGCGCAAATAGAG 59.625 43.478 14.00 0.00 0.00 2.43
2612 3122 1.511768 GCTCCTAGCGTCTCCGTTT 59.488 57.895 0.00 0.00 36.15 3.60
2813 3323 2.945668 AGACTCGCTTTGCTCACTTTTT 59.054 40.909 0.00 0.00 0.00 1.94
2905 3417 4.796231 CGCCAGCCGCTTCTACGT 62.796 66.667 0.00 0.00 34.21 3.57


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

AutoCloner maintained by Alex Coulton.