Multiple sequence alignment - TraesCS1D01G319700

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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 TraesCS1D01G319700 chr1D 100.000 4506 0 0 1 4506 413728322 413732827 0.000000e+00 8322.0
1 TraesCS1D01G319700 chr1D 91.000 400 34 2 2721 3119 413778757 413779155 5.130000e-149 538.0
2 TraesCS1D01G319700 chr1D 91.880 234 18 1 1110 1343 413772205 413772437 4.350000e-85 326.0
3 TraesCS1D01G319700 chr1D 89.535 86 9 0 2597 2682 413778604 413778689 4.770000e-20 110.0
4 TraesCS1D01G319700 chr1A 89.753 2225 130 38 2332 4503 510672715 510674894 0.000000e+00 2756.0
5 TraesCS1D01G319700 chr1A 89.232 1198 64 11 203 1343 510671534 510672723 0.000000e+00 1437.0
6 TraesCS1D01G319700 chr1A 91.500 400 32 2 2721 3119 510803903 510804301 2.370000e-152 549.0
7 TraesCS1D01G319700 chr1A 84.646 495 65 4 3129 3621 510804490 510804975 2.440000e-132 483.0
8 TraesCS1D01G319700 chr1A 89.939 328 22 7 2365 2682 510803509 510803835 3.240000e-111 412.0
9 TraesCS1D01G319700 chr1A 91.880 234 18 1 1110 1343 510803178 510803410 4.350000e-85 326.0
10 TraesCS1D01G319700 chr1A 92.258 155 12 0 1 155 510617428 510617582 2.110000e-53 220.0
11 TraesCS1D01G319700 chr1B 91.336 1362 85 14 2688 4036 558285072 558286413 0.000000e+00 1831.0
12 TraesCS1D01G319700 chr1B 81.312 1418 141 49 5 1343 558283291 558284663 0.000000e+00 1037.0
13 TraesCS1D01G319700 chr1B 90.421 428 33 3 2692 3119 558496279 558496698 1.420000e-154 556.0
14 TraesCS1D01G319700 chr1B 95.253 316 15 0 2371 2686 558284719 558285034 6.730000e-138 501.0
15 TraesCS1D01G319700 chr1B 88.379 327 28 5 2365 2682 558495903 558496228 7.070000e-103 385.0
16 TraesCS1D01G319700 chr1B 92.308 234 17 1 1110 1343 558495621 558495853 9.340000e-87 331.0
17 TraesCS1D01G319700 chr1B 88.770 187 13 5 4282 4467 558286754 558286933 5.870000e-54 222.0
18 TraesCS1D01G319700 chr7D 99.493 987 5 0 1341 2327 163196541 163197527 0.000000e+00 1796.0
19 TraesCS1D01G319700 chr7D 98.796 997 12 0 1331 2327 562126070 562127066 0.000000e+00 1775.0
20 TraesCS1D01G319700 chr7D 98.780 984 9 2 1344 2327 418953162 418952182 0.000000e+00 1748.0
21 TraesCS1D01G319700 chr7D 98.176 987 18 0 1341 2327 491881513 491880527 0.000000e+00 1724.0
22 TraesCS1D01G319700 chr7D 77.842 695 131 13 2403 3076 23510076 23510768 4.200000e-110 409.0
23 TraesCS1D01G319700 chr7D 79.673 428 58 17 3863 4263 428013422 428012997 9.540000e-72 281.0
24 TraesCS1D01G319700 chr7D 79.822 337 57 9 3217 3547 26002055 26001724 7.540000e-58 235.0
25 TraesCS1D01G319700 chr3D 99.191 989 7 1 1340 2327 607831635 607832623 0.000000e+00 1781.0
26 TraesCS1D01G319700 chr3D 84.649 228 29 6 4049 4273 267785802 267786026 5.870000e-54 222.0
27 TraesCS1D01G319700 chr5D 98.887 988 10 1 1341 2327 303832975 303831988 0.000000e+00 1762.0
28 TraesCS1D01G319700 chr5D 77.419 155 30 3 548 702 565672465 565672316 2.230000e-13 87.9
29 TraesCS1D01G319700 chr6D 98.690 992 13 0 1336 2327 420729690 420728699 0.000000e+00 1760.0
30 TraesCS1D01G319700 chr4B 97.885 993 20 1 1336 2327 467912855 467913847 0.000000e+00 1716.0
31 TraesCS1D01G319700 chr7B 97.976 988 19 1 1340 2327 448657609 448656623 0.000000e+00 1712.0
32 TraesCS1D01G319700 chr7B 77.111 533 91 15 3764 4269 616922152 616922680 3.430000e-71 279.0
33 TraesCS1D01G319700 chr7B 94.444 36 2 0 131 166 74484776 74484741 6.300000e-04 56.5
34 TraesCS1D01G319700 chr7A 77.988 686 128 13 2412 3076 24627212 24627895 4.200000e-110 409.0
35 TraesCS1D01G319700 chr7A 82.517 286 41 7 3217 3496 26838580 26838298 4.500000e-60 243.0
36 TraesCS1D01G319700 chr4A 84.783 368 54 2 2738 3104 710413235 710412869 7.120000e-98 368.0
37 TraesCS1D01G319700 chr4A 82.482 274 41 5 3217 3485 710412541 710412270 2.710000e-57 233.0
38 TraesCS1D01G319700 chrUn 80.402 398 73 5 2718 3111 90118076 90117680 9.480000e-77 298.0
39 TraesCS1D01G319700 chr6B 77.491 542 91 18 3759 4273 371615204 371615741 3.410000e-76 296.0
40 TraesCS1D01G319700 chr5B 77.111 533 91 15 3764 4269 465273704 465273176 3.430000e-71 279.0
41 TraesCS1D01G319700 chr5B 95.349 43 2 0 665 707 18950569 18950527 8.090000e-08 69.4
42 TraesCS1D01G319700 chr2A 77.165 508 79 24 3762 4239 702560881 702560381 1.240000e-65 261.0
43 TraesCS1D01G319700 chr3B 73.518 506 112 14 266 757 245357004 245357501 5.990000e-39 172.0
44 TraesCS1D01G319700 chr6A 97.368 38 1 0 3277 3314 445776081 445776118 1.050000e-06 65.8
45 TraesCS1D01G319700 chr2B 96.970 33 1 0 29 61 457107815 457107783 6.300000e-04 56.5


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 TraesCS1D01G319700 chr1D 413728322 413732827 4505 False 8322.00 8322 100.000000 1 4506 1 chr1D.!!$F1 4505
1 TraesCS1D01G319700 chr1D 413778604 413779155 551 False 324.00 538 90.267500 2597 3119 2 chr1D.!!$F3 522
2 TraesCS1D01G319700 chr1A 510671534 510674894 3360 False 2096.50 2756 89.492500 203 4503 2 chr1A.!!$F2 4300
3 TraesCS1D01G319700 chr1A 510803178 510804975 1797 False 442.50 549 89.491250 1110 3621 4 chr1A.!!$F3 2511
4 TraesCS1D01G319700 chr1B 558283291 558286933 3642 False 897.75 1831 89.167750 5 4467 4 chr1B.!!$F1 4462
5 TraesCS1D01G319700 chr1B 558495621 558496698 1077 False 424.00 556 90.369333 1110 3119 3 chr1B.!!$F2 2009
6 TraesCS1D01G319700 chr7D 163196541 163197527 986 False 1796.00 1796 99.493000 1341 2327 1 chr7D.!!$F2 986
7 TraesCS1D01G319700 chr7D 562126070 562127066 996 False 1775.00 1775 98.796000 1331 2327 1 chr7D.!!$F3 996
8 TraesCS1D01G319700 chr7D 418952182 418953162 980 True 1748.00 1748 98.780000 1344 2327 1 chr7D.!!$R2 983
9 TraesCS1D01G319700 chr7D 491880527 491881513 986 True 1724.00 1724 98.176000 1341 2327 1 chr7D.!!$R4 986
10 TraesCS1D01G319700 chr7D 23510076 23510768 692 False 409.00 409 77.842000 2403 3076 1 chr7D.!!$F1 673
11 TraesCS1D01G319700 chr3D 607831635 607832623 988 False 1781.00 1781 99.191000 1340 2327 1 chr3D.!!$F2 987
12 TraesCS1D01G319700 chr5D 303831988 303832975 987 True 1762.00 1762 98.887000 1341 2327 1 chr5D.!!$R1 986
13 TraesCS1D01G319700 chr6D 420728699 420729690 991 True 1760.00 1760 98.690000 1336 2327 1 chr6D.!!$R1 991
14 TraesCS1D01G319700 chr4B 467912855 467913847 992 False 1716.00 1716 97.885000 1336 2327 1 chr4B.!!$F1 991
15 TraesCS1D01G319700 chr7B 448656623 448657609 986 True 1712.00 1712 97.976000 1340 2327 1 chr7B.!!$R2 987
16 TraesCS1D01G319700 chr7B 616922152 616922680 528 False 279.00 279 77.111000 3764 4269 1 chr7B.!!$F1 505
17 TraesCS1D01G319700 chr7A 24627212 24627895 683 False 409.00 409 77.988000 2412 3076 1 chr7A.!!$F1 664
18 TraesCS1D01G319700 chr4A 710412270 710413235 965 True 300.50 368 83.632500 2738 3485 2 chr4A.!!$R1 747
19 TraesCS1D01G319700 chr6B 371615204 371615741 537 False 296.00 296 77.491000 3759 4273 1 chr6B.!!$F1 514
20 TraesCS1D01G319700 chr5B 465273176 465273704 528 True 279.00 279 77.111000 3764 4269 1 chr5B.!!$R2 505
21 TraesCS1D01G319700 chr2A 702560381 702560881 500 True 261.00 261 77.165000 3762 4239 1 chr2A.!!$R1 477

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
269 315 0.034863 GAAGGGGTTGCGGTTCCATA 60.035 55.0 0.00 0.00 0.00 2.74 F
581 642 0.104304 CTAGGGTTTCGTCCGGGATG 59.896 60.0 10.10 10.10 0.00 3.51 F
644 705 0.176680 AGCTTGATCCGAAGACGCAT 59.823 50.0 0.00 0.00 38.29 4.73 F
1003 1104 0.256752 TCCCAGTTCATCCTGCATGG 59.743 55.0 0.00 0.00 32.64 3.66 F
1332 1441 0.531532 GGTCAGCCATCGAGTCATGG 60.532 60.0 14.03 14.03 45.70 3.66 F
2327 2436 0.545787 ATCACACGGGTTCCCACCTA 60.546 55.0 8.70 0.00 43.65 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2155 0.107703 CCTATGGACGCTGCTCCAAA 60.108 55.0 19.68 3.68 43.79 3.28 R
2565 2761 0.678048 GGATTTGGTCCAGCGAGCTT 60.678 55.0 0.00 0.00 46.96 3.74 R
2686 2885 1.293924 CATGATCAGTCAACGCTCCC 58.706 55.0 0.09 0.00 38.01 4.30 R
2795 3052 0.323360 AGCTTCGCCATTGCCCTTAA 60.323 50.0 0.00 0.00 0.00 1.85 R
2966 3223 0.391661 CCAACCCTGTCATCGACCAG 60.392 60.0 0.00 0.00 0.00 4.00 R
3809 4305 0.743345 GTAAGGCGGCCACTACAAGG 60.743 60.0 23.09 0.00 0.00 3.61 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
29 30 4.100084 TGGCCAGGATGTCGCTGG 62.100 66.667 0.00 11.10 37.37 4.85
46 47 2.567049 GTCGAGGTGAGGTCCACG 59.433 66.667 0.00 0.00 46.62 4.94
62 63 1.269102 CCACGATAGACATGGACGGAC 60.269 57.143 0.00 0.00 35.33 4.79
66 67 1.745320 ATAGACATGGACGGACGGGC 61.745 60.000 0.00 0.00 0.00 6.13
84 85 4.082523 CCGCCTCATGGTCACCGT 62.083 66.667 0.00 0.00 35.27 4.83
86 87 2.347490 GCCTCATGGTCACCGTGT 59.653 61.111 16.05 0.00 41.03 4.49
88 89 1.371183 CCTCATGGTCACCGTGTGT 59.629 57.895 16.05 0.00 41.03 3.72
90 91 0.950555 CTCATGGTCACCGTGTGTGG 60.951 60.000 16.05 1.90 45.48 4.17
103 104 4.720902 TGTGGGTCCGCCAGCATG 62.721 66.667 0.00 0.00 36.17 4.06
153 178 3.005539 ACACCCTCTGCCTCGCAT 61.006 61.111 0.00 0.00 38.13 4.73
170 195 2.369633 ATGGCGGGCACATCTCTCA 61.370 57.895 6.33 0.00 0.00 3.27
173 198 1.445095 GCGGGCACATCTCTCATCT 59.555 57.895 0.00 0.00 0.00 2.90
268 314 1.304134 GAAGGGGTTGCGGTTCCAT 60.304 57.895 0.00 0.00 0.00 3.41
269 315 0.034863 GAAGGGGTTGCGGTTCCATA 60.035 55.000 0.00 0.00 0.00 2.74
384 430 0.252421 TGCTGGATGGAGTCTGACCT 60.252 55.000 3.76 0.00 0.00 3.85
386 432 1.857965 CTGGATGGAGTCTGACCTCA 58.142 55.000 3.76 3.73 32.91 3.86
502 548 3.639094 AGGAGATCTTGGAGTTGTATCCG 59.361 47.826 0.00 0.00 42.77 4.18
517 563 3.196901 TGTATCCGTTGTCTGTTATGCCT 59.803 43.478 0.00 0.00 0.00 4.75
525 581 2.131183 GTCTGTTATGCCTGAGATCGC 58.869 52.381 0.00 0.00 0.00 4.58
557 618 1.076485 GGGGGCGTAGTAGAGTGGA 60.076 63.158 0.00 0.00 0.00 4.02
558 619 1.108132 GGGGGCGTAGTAGAGTGGAG 61.108 65.000 0.00 0.00 0.00 3.86
559 620 0.395448 GGGGCGTAGTAGAGTGGAGT 60.395 60.000 0.00 0.00 0.00 3.85
560 621 0.739561 GGGCGTAGTAGAGTGGAGTG 59.260 60.000 0.00 0.00 0.00 3.51
561 622 0.739561 GGCGTAGTAGAGTGGAGTGG 59.260 60.000 0.00 0.00 0.00 4.00
581 642 0.104304 CTAGGGTTTCGTCCGGGATG 59.896 60.000 10.10 10.10 0.00 3.51
621 682 2.361230 GGGTTGTGGTGGGCTAGC 60.361 66.667 6.04 6.04 0.00 3.42
644 705 0.176680 AGCTTGATCCGAAGACGCAT 59.823 50.000 0.00 0.00 38.29 4.73
646 707 1.212616 CTTGATCCGAAGACGCATCC 58.787 55.000 0.00 0.00 36.04 3.51
650 711 4.143333 CCGAAGACGCATCCGGGT 62.143 66.667 0.00 0.00 41.78 5.28
704 766 3.401342 TGGACTAGATATGAGGGGTGCTA 59.599 47.826 0.00 0.00 0.00 3.49
707 769 5.081032 GACTAGATATGAGGGGTGCTAGTT 58.919 45.833 0.00 0.00 38.78 2.24
709 771 6.621394 ACTAGATATGAGGGGTGCTAGTTAA 58.379 40.000 0.00 0.00 36.16 2.01
757 819 2.614481 GGTGCAGTTGGGTCGAGATTTA 60.614 50.000 0.00 0.00 0.00 1.40
758 820 3.071479 GTGCAGTTGGGTCGAGATTTAA 58.929 45.455 0.00 0.00 0.00 1.52
786 848 0.739462 CACTTACCGAGCAATCCGCA 60.739 55.000 0.00 0.00 46.13 5.69
962 1061 1.946768 CCGTCTCTGATCTCTCTCCAC 59.053 57.143 0.00 0.00 0.00 4.02
1003 1104 0.256752 TCCCAGTTCATCCTGCATGG 59.743 55.000 0.00 0.00 32.64 3.66
1058 1159 7.386059 TGTATGAGCATTTGTACTGAAAGAGA 58.614 34.615 0.00 0.00 37.43 3.10
1066 1167 3.702792 TGTACTGAAAGAGAGAGGGGAG 58.297 50.000 0.00 0.00 37.43 4.30
1076 1177 4.884961 AGAGAGAGGGGAGCTATTTTGTA 58.115 43.478 0.00 0.00 0.00 2.41
1330 1439 1.439228 CGGTCAGCCATCGAGTCAT 59.561 57.895 0.00 0.00 34.09 3.06
1331 1440 0.873312 CGGTCAGCCATCGAGTCATG 60.873 60.000 0.00 0.00 34.09 3.07
1332 1441 0.531532 GGTCAGCCATCGAGTCATGG 60.532 60.000 14.03 14.03 45.70 3.66
1333 1442 0.531532 GTCAGCCATCGAGTCATGGG 60.532 60.000 17.83 5.46 43.42 4.00
1334 1443 1.227764 CAGCCATCGAGTCATGGGG 60.228 63.158 17.83 3.96 43.42 4.96
1950 2059 2.674220 GGGAGAGGACCAAGCCCAG 61.674 68.421 9.91 0.00 38.68 4.45
1989 2098 1.305381 AGGCTGCGGAGTAGTTCCT 60.305 57.895 5.62 0.00 43.91 3.36
2327 2436 0.545787 ATCACACGGGTTCCCACCTA 60.546 55.000 8.70 0.00 43.65 3.08
2360 2469 6.499350 TCCTTATGGTAAGTAACAACTCCACT 59.501 38.462 0.00 0.00 34.23 4.00
2547 2743 2.434359 CGGTTCCAGTTCGAGGGC 60.434 66.667 0.00 0.00 0.00 5.19
2565 2761 1.117150 GCTATGGGAACGACTGGGTA 58.883 55.000 0.00 0.00 0.00 3.69
2573 2769 1.533469 AACGACTGGGTAAGCTCGCT 61.533 55.000 0.00 0.00 34.68 4.93
2795 3052 1.550976 GGGAAGTGAAGGACGATCTGT 59.449 52.381 0.00 0.00 0.00 3.41
2797 3054 3.194968 GGGAAGTGAAGGACGATCTGTTA 59.805 47.826 0.00 0.00 0.00 2.41
3122 3379 9.927668 ATATCCTGAAAAAGTGTTGTTTTATGG 57.072 29.630 0.00 0.00 0.00 2.74
3126 3386 8.603181 CCTGAAAAAGTGTTGTTTTATGGAAAG 58.397 33.333 0.00 0.00 0.00 2.62
3149 3623 6.998802 AGGTTATATGAAGGGAATCTCGAAG 58.001 40.000 0.00 0.00 0.00 3.79
3158 3632 5.359194 AGGGAATCTCGAAGCTTCAAATA 57.641 39.130 25.47 8.56 0.00 1.40
3163 3637 7.040823 GGGAATCTCGAAGCTTCAAATATTCAT 60.041 37.037 25.47 2.89 0.00 2.57
3215 3692 4.100189 CCTCTCGGACTGATGAAGGTTAAT 59.900 45.833 0.00 0.00 0.00 1.40
3219 3697 6.605995 TCTCGGACTGATGAAGGTTAATCTTA 59.394 38.462 0.00 0.00 0.00 2.10
3308 3786 1.112315 AGAGAGGCTATCGGTGGCAG 61.112 60.000 6.30 0.00 32.73 4.85
3341 3819 6.556974 ATGTTGATCCTGAGAGAGAAATCA 57.443 37.500 0.00 0.00 0.00 2.57
3380 3858 1.153549 AATGAGAAGAGACCGGCGC 60.154 57.895 0.00 0.00 0.00 6.53
3523 4004 9.491675 TTCAATAAAATGTTGTCATTCTGCAAT 57.508 25.926 0.00 0.00 42.60 3.56
3563 4056 8.827177 TTTATTCATGTATCGTTACATCCCTC 57.173 34.615 14.75 0.00 45.27 4.30
3621 4114 3.617263 GTCTCGGTTAGCATGGTTTACAG 59.383 47.826 1.12 3.30 0.00 2.74
3650 4143 4.073052 TGGAACATGGTTCCACGC 57.927 55.556 23.13 2.18 43.17 5.34
3651 4144 1.963855 TGGAACATGGTTCCACGCG 60.964 57.895 23.13 3.53 43.17 6.01
3674 4167 7.088272 GCGGGAACACTTATGAAAAGTAAATT 58.912 34.615 0.00 0.00 0.00 1.82
3678 4171 9.626045 GGAACACTTATGAAAAGTAAATTCAGG 57.374 33.333 0.00 0.00 39.92 3.86
3738 4231 9.469807 TGAATTTGTTTTGTAACATACATGGTC 57.530 29.630 0.00 0.00 43.43 4.02
3739 4232 9.469807 GAATTTGTTTTGTAACATACATGGTCA 57.530 29.630 0.00 0.00 43.43 4.02
3742 4235 7.575414 TGTTTTGTAACATACATGGTCAACT 57.425 32.000 0.00 0.00 39.29 3.16
3743 4236 7.421599 TGTTTTGTAACATACATGGTCAACTG 58.578 34.615 0.00 0.00 39.29 3.16
3744 4237 6.567687 TTTGTAACATACATGGTCAACTGG 57.432 37.500 0.00 0.00 38.68 4.00
3745 4238 5.235850 TGTAACATACATGGTCAACTGGT 57.764 39.130 0.00 0.00 32.89 4.00
3746 4239 6.361768 TGTAACATACATGGTCAACTGGTA 57.638 37.500 0.00 0.00 32.89 3.25
3747 4240 6.953101 TGTAACATACATGGTCAACTGGTAT 58.047 36.000 0.00 0.00 32.89 2.73
3748 4241 8.080363 TGTAACATACATGGTCAACTGGTATA 57.920 34.615 0.00 0.00 32.89 1.47
3774 4267 3.255642 TGTATGAAGTTTGGCAAAGAGGC 59.744 43.478 13.94 1.22 44.50 4.70
3784 4277 1.202222 GGCAAAGAGGCAACATGATCG 60.202 52.381 0.00 0.00 43.51 3.69
3809 4305 7.795272 CGTATGTGTTTTTACCTTGAAGTACAC 59.205 37.037 0.00 0.00 0.00 2.90
3815 4311 7.828223 TGTTTTTACCTTGAAGTACACCTTGTA 59.172 33.333 0.00 0.00 32.03 2.41
3825 4321 2.928396 ACCTTGTAGTGGCCGCCT 60.928 61.111 14.07 6.30 0.00 5.52
3852 4348 1.806542 CTGTGGTGGGAAAGAATGACG 59.193 52.381 0.00 0.00 0.00 4.35
3860 4356 4.876107 GTGGGAAAGAATGACGTGTATCAT 59.124 41.667 0.00 0.00 41.20 2.45
3971 4468 5.355350 ACCTCAAGTGCAATGTTTCTATAGC 59.645 40.000 0.00 0.00 0.00 2.97
4036 4534 3.434309 AGTACCAAGCTCTTACCCGTTA 58.566 45.455 0.00 0.00 0.00 3.18
4037 4535 3.446516 AGTACCAAGCTCTTACCCGTTAG 59.553 47.826 0.00 0.00 0.00 2.34
4099 4648 5.070313 AGCAATTACCAAGTGACCAAACAAT 59.930 36.000 0.00 0.00 0.00 2.71
4229 4779 1.205179 TGCGGGCAATCGACTAGTAAA 59.795 47.619 0.00 0.00 0.00 2.01
4327 4920 2.632512 TGTGATGTGGTAGTCAAGCTCA 59.367 45.455 0.00 0.00 33.96 4.26
4330 4923 3.070878 TGATGTGGTAGTCAAGCTCACAA 59.929 43.478 6.28 0.00 40.92 3.33
4331 4924 2.833794 TGTGGTAGTCAAGCTCACAAC 58.166 47.619 0.06 0.00 35.72 3.32
4332 4925 1.792949 GTGGTAGTCAAGCTCACAACG 59.207 52.381 0.00 0.00 0.00 4.10
4333 4926 1.411246 TGGTAGTCAAGCTCACAACGT 59.589 47.619 0.00 0.00 0.00 3.99
4395 4989 1.341383 CCCCAAAACAGATGCTAGCCT 60.341 52.381 13.29 1.02 0.00 4.58
4405 4999 2.707791 AGATGCTAGCCTGCCTGATTTA 59.292 45.455 13.29 0.00 0.00 1.40
4414 5008 4.774200 AGCCTGCCTGATTTAATTTTCACT 59.226 37.500 0.00 0.00 0.00 3.41
4468 5062 3.196039 TGTCAAGCCGGTTACTAGCAATA 59.804 43.478 1.90 0.00 0.00 1.90
4477 5071 5.438972 CGGTTACTAGCAATAGAGACGTAC 58.561 45.833 0.00 0.00 0.00 3.67
4478 5072 5.236047 CGGTTACTAGCAATAGAGACGTACT 59.764 44.000 0.00 0.00 0.00 2.73
4482 5076 8.772705 GTTACTAGCAATAGAGACGTACTACAT 58.227 37.037 4.46 0.00 0.00 2.29
4485 5079 8.772705 ACTAGCAATAGAGACGTACTACATAAC 58.227 37.037 4.46 0.00 0.00 1.89
4497 5091 9.435802 GACGTACTACATAACTTAGATCAACAG 57.564 37.037 0.00 0.00 0.00 3.16
4503 5097 7.259088 ACATAACTTAGATCAACAGGGACTT 57.741 36.000 0.00 0.00 34.60 3.01
4504 5098 7.106239 ACATAACTTAGATCAACAGGGACTTG 58.894 38.462 0.00 0.00 34.60 3.16
4505 5099 5.825593 AACTTAGATCAACAGGGACTTGA 57.174 39.130 0.00 0.00 34.60 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.760047 GCGACATCCTGGCCACGT 62.760 66.667 0.00 0.00 0.00 4.49
29 30 1.970114 TCGTGGACCTCACCTCGAC 60.970 63.158 0.00 0.00 46.14 4.20
46 47 0.314302 CCCGTCCGTCCATGTCTATC 59.686 60.000 0.00 0.00 0.00 2.08
66 67 4.838152 CGGTGACCATGAGGCGGG 62.838 72.222 1.11 0.00 39.06 6.13
86 87 4.720902 CATGCTGGCGGACCCACA 62.721 66.667 0.00 0.00 39.18 4.17
136 161 3.005539 ATGCGAGGCAGAGGGTGT 61.006 61.111 0.00 0.00 43.65 4.16
153 178 2.315781 GATGAGAGATGTGCCCGCCA 62.316 60.000 0.00 0.00 0.00 5.69
163 188 0.388659 GTCCGCTGCAGATGAGAGAT 59.611 55.000 20.43 0.00 0.00 2.75
164 189 1.812525 GTCCGCTGCAGATGAGAGA 59.187 57.895 20.43 0.58 0.00 3.10
198 223 0.456653 TAGTCGAAGGTAAACGCCGC 60.457 55.000 0.00 0.00 0.00 6.53
199 224 1.542544 CTAGTCGAAGGTAAACGCCG 58.457 55.000 0.00 0.00 0.00 6.46
230 255 1.530419 GTGGCATGTTGTCCCCACA 60.530 57.895 11.67 0.00 45.41 4.17
240 265 3.256960 ACCCCTTCGGTGGCATGT 61.257 61.111 0.00 0.00 46.09 3.21
384 430 1.692762 GGGAGGAGTCAGCCCTATTGA 60.693 57.143 11.31 0.00 38.85 2.57
386 432 0.760945 CGGGAGGAGTCAGCCCTATT 60.761 60.000 15.29 0.00 39.79 1.73
473 519 1.484240 CTCCAAGATCTCCTGACCCAC 59.516 57.143 0.00 0.00 0.00 4.61
477 523 3.971245 ACAACTCCAAGATCTCCTGAC 57.029 47.619 0.00 0.00 0.00 3.51
502 548 3.553511 CGATCTCAGGCATAACAGACAAC 59.446 47.826 0.00 0.00 0.00 3.32
517 563 1.138883 CTTCGTTCCGGCGATCTCA 59.861 57.895 9.30 0.00 40.76 3.27
525 581 2.746277 CCCCAAGCTTCGTTCCGG 60.746 66.667 0.00 0.00 0.00 5.14
557 618 1.885163 CGGACGAAACCCTAGCCACT 61.885 60.000 0.00 0.00 0.00 4.00
558 619 1.447314 CGGACGAAACCCTAGCCAC 60.447 63.158 0.00 0.00 0.00 5.01
559 620 2.652095 CCGGACGAAACCCTAGCCA 61.652 63.158 0.00 0.00 0.00 4.75
560 621 2.186125 CCGGACGAAACCCTAGCC 59.814 66.667 0.00 0.00 0.00 3.93
561 622 1.683418 ATCCCGGACGAAACCCTAGC 61.683 60.000 0.73 0.00 0.00 3.42
581 642 6.219473 CCCACATATATTCATCTCTATCCGC 58.781 44.000 0.00 0.00 0.00 5.54
621 682 1.272781 GTCTTCGGATCAAGCTCACG 58.727 55.000 0.00 0.00 0.00 4.35
661 723 4.626042 CATATCTAAGGCGGATATGGAGC 58.374 47.826 20.10 0.00 44.21 4.70
704 766 5.250774 CCAGCCCTATATGTATGGGTTAACT 59.749 44.000 5.42 0.00 42.77 2.24
707 769 4.770193 ACCAGCCCTATATGTATGGGTTA 58.230 43.478 0.00 0.00 42.77 2.85
709 771 3.291626 ACCAGCCCTATATGTATGGGT 57.708 47.619 0.00 0.00 42.77 4.51
714 776 4.574172 CCCCTCATACCAGCCCTATATGTA 60.574 50.000 0.00 0.00 0.00 2.29
786 848 3.949754 TCGAACACTCCATATAAGTCCGT 59.050 43.478 0.00 0.00 0.00 4.69
932 1031 3.976169 GATCAGAGACGGATCTTGGAAG 58.024 50.000 0.00 0.00 38.47 3.46
962 1061 6.371825 GGGAGACAGTATTACCTTCAAACAAG 59.628 42.308 0.00 0.00 0.00 3.16
1003 1104 4.246458 ACATGTAGGAAAAGCTCGAAGAC 58.754 43.478 0.00 0.00 0.00 3.01
1058 1159 4.362677 TCAGTACAAAATAGCTCCCCTCT 58.637 43.478 0.00 0.00 0.00 3.69
1066 1167 6.604735 ATGTCCGATTCAGTACAAAATAGC 57.395 37.500 0.00 0.00 0.00 2.97
1171 1280 3.730761 CTGAGCTGGCACGTTGGC 61.731 66.667 0.00 4.92 44.03 4.52
1174 1283 0.321671 ATGTACTGAGCTGGCACGTT 59.678 50.000 0.00 0.00 0.00 3.99
1244 1353 2.005960 GACGAGGTCGATGACAGGGG 62.006 65.000 6.35 0.00 43.02 4.79
1950 2059 3.165498 CGTACAGGGCGCAGTTTC 58.835 61.111 10.83 1.23 0.00 2.78
2046 2155 0.107703 CCTATGGACGCTGCTCCAAA 60.108 55.000 19.68 3.68 43.79 3.28
2327 2436 2.065799 CTTACCATAAGGAGGCCCCAT 58.934 52.381 12.24 3.44 38.69 4.00
2337 2446 8.529476 ACTAGTGGAGTTGTTACTTACCATAAG 58.471 37.037 0.00 0.00 33.13 1.73
2360 2469 6.164417 TGGTGTTGCTTCAAAGTAGTACTA 57.836 37.500 2.50 0.00 0.00 1.82
2547 2743 2.483188 GCTTACCCAGTCGTTCCCATAG 60.483 54.545 0.00 0.00 0.00 2.23
2565 2761 0.678048 GGATTTGGTCCAGCGAGCTT 60.678 55.000 0.00 0.00 46.96 3.74
2686 2885 1.293924 CATGATCAGTCAACGCTCCC 58.706 55.000 0.09 0.00 38.01 4.30
2795 3052 0.323360 AGCTTCGCCATTGCCCTTAA 60.323 50.000 0.00 0.00 0.00 1.85
2797 3054 2.036256 AGCTTCGCCATTGCCCTT 59.964 55.556 0.00 0.00 0.00 3.95
2966 3223 0.391661 CCAACCCTGTCATCGACCAG 60.392 60.000 0.00 0.00 0.00 4.00
3055 3312 5.524284 CGTACCTCAGTTTGATCTCCTATG 58.476 45.833 0.00 0.00 0.00 2.23
3122 3379 7.442656 TCGAGATTCCCTTCATATAACCTTTC 58.557 38.462 0.00 0.00 0.00 2.62
3126 3386 5.639931 GCTTCGAGATTCCCTTCATATAACC 59.360 44.000 0.00 0.00 0.00 2.85
3135 3609 3.703001 TTGAAGCTTCGAGATTCCCTT 57.297 42.857 21.11 0.00 39.71 3.95
3149 3623 8.922058 AACTCACAATGATGAATATTTGAAGC 57.078 30.769 0.00 0.00 0.00 3.86
3158 3632 6.669125 TGGGAAAAACTCACAATGATGAAT 57.331 33.333 0.00 0.00 33.21 2.57
3163 3637 6.648192 ACATTTTGGGAAAAACTCACAATGA 58.352 32.000 13.18 0.00 46.94 2.57
3215 3692 6.877236 TGCTCATTATCTGTGTCACATAAGA 58.123 36.000 6.03 0.73 0.00 2.10
3219 3697 5.298527 CCATTGCTCATTATCTGTGTCACAT 59.701 40.000 6.03 0.00 0.00 3.21
3272 3750 6.038714 AGCCTCTCTTTCTTTGTGTTTGTTAG 59.961 38.462 0.00 0.00 0.00 2.34
3274 3752 4.706962 AGCCTCTCTTTCTTTGTGTTTGTT 59.293 37.500 0.00 0.00 0.00 2.83
3308 3786 7.934665 TCTCTCAGGATCAACATAGTAGTCTAC 59.065 40.741 1.39 1.39 0.00 2.59
3380 3858 7.813627 GTCCTTAACCTTCACTTTAGAGTACAG 59.186 40.741 0.00 0.00 33.90 2.74
3621 4114 3.194116 ACCATGTTCCACAAATCTGCATC 59.806 43.478 0.00 0.00 0.00 3.91
3650 4143 8.293867 TGAATTTACTTTTCATAAGTGTTCCCG 58.706 33.333 0.00 0.00 0.00 5.14
3651 4144 9.626045 CTGAATTTACTTTTCATAAGTGTTCCC 57.374 33.333 0.00 0.00 32.94 3.97
3721 4214 6.065374 ACCAGTTGACCATGTATGTTACAAA 58.935 36.000 0.00 0.00 42.76 2.83
3738 4231 8.328146 CAAACTTCATACACGATATACCAGTTG 58.672 37.037 0.00 0.00 0.00 3.16
3739 4232 7.494625 CCAAACTTCATACACGATATACCAGTT 59.505 37.037 0.00 0.00 0.00 3.16
3742 4235 5.756347 GCCAAACTTCATACACGATATACCA 59.244 40.000 0.00 0.00 0.00 3.25
3743 4236 5.756347 TGCCAAACTTCATACACGATATACC 59.244 40.000 0.00 0.00 0.00 2.73
3744 4237 6.838198 TGCCAAACTTCATACACGATATAC 57.162 37.500 0.00 0.00 0.00 1.47
3745 4238 7.766738 TCTTTGCCAAACTTCATACACGATATA 59.233 33.333 0.00 0.00 0.00 0.86
3746 4239 6.597672 TCTTTGCCAAACTTCATACACGATAT 59.402 34.615 0.00 0.00 0.00 1.63
3747 4240 5.935206 TCTTTGCCAAACTTCATACACGATA 59.065 36.000 0.00 0.00 0.00 2.92
3748 4241 4.759693 TCTTTGCCAAACTTCATACACGAT 59.240 37.500 0.00 0.00 0.00 3.73
3774 4267 7.526608 AGGTAAAAACACATACGATCATGTTG 58.473 34.615 0.00 0.00 37.02 3.33
3784 4277 8.071967 GGTGTACTTCAAGGTAAAAACACATAC 58.928 37.037 0.00 0.00 0.00 2.39
3809 4305 0.743345 GTAAGGCGGCCACTACAAGG 60.743 60.000 23.09 0.00 0.00 3.61
3815 4311 1.918800 AGAAGGTAAGGCGGCCACT 60.919 57.895 23.09 10.42 0.00 4.00
3825 4321 3.050089 TCTTTCCCACCACAGAAGGTAA 58.950 45.455 0.00 0.00 40.77 2.85
3852 4348 6.484643 AGATGACTTGCCATACAATGATACAC 59.515 38.462 0.00 0.00 37.72 2.90
3860 4356 2.575735 TGGGAGATGACTTGCCATACAA 59.424 45.455 0.00 0.00 36.62 2.41
3971 4468 1.486211 CCCACCACCTCCTAGTAGTG 58.514 60.000 0.00 0.00 0.00 2.74
4099 4648 9.787435 ACCAAGTTCTACTTTTCATATTGTACA 57.213 29.630 0.00 0.00 36.03 2.90
4116 4665 5.223449 TGAGGAAATCGTAACCAAGTTCT 57.777 39.130 0.00 0.00 0.00 3.01
4119 4668 4.969484 AGTTGAGGAAATCGTAACCAAGT 58.031 39.130 0.00 0.00 0.00 3.16
4200 4750 1.737696 CGATTGCCCGCACTAGTTACA 60.738 52.381 0.00 0.00 0.00 2.41
4245 4795 4.142138 ACTCACTTGATTCAGTATCGGGTC 60.142 45.833 0.00 0.00 35.94 4.46
4276 4827 5.006746 CGGTTTGAGCTTCATTATACTCCAC 59.993 44.000 0.00 0.00 0.00 4.02
4327 4920 3.630312 ACATCCTTTTTGCTGTACGTTGT 59.370 39.130 0.00 0.00 0.00 3.32
4330 4923 3.740115 AGACATCCTTTTTGCTGTACGT 58.260 40.909 0.00 0.00 0.00 3.57
4331 4924 5.856126 TTAGACATCCTTTTTGCTGTACG 57.144 39.130 0.00 0.00 0.00 3.67
4332 4925 7.422399 TGTTTTAGACATCCTTTTTGCTGTAC 58.578 34.615 0.00 0.00 32.00 2.90
4333 4926 7.500892 TCTGTTTTAGACATCCTTTTTGCTGTA 59.499 33.333 0.00 0.00 37.69 2.74
4395 4989 9.612066 AAGAAAAAGTGAAAATTAAATCAGGCA 57.388 25.926 0.00 0.00 0.00 4.75
4414 5008 9.639601 GACAAAAAGAGAGAAGGAAAAGAAAAA 57.360 29.630 0.00 0.00 0.00 1.94
4468 5062 9.610705 TTGATCTAAGTTATGTAGTACGTCTCT 57.389 33.333 0.00 0.00 0.00 3.10
4477 5071 8.012957 AGTCCCTGTTGATCTAAGTTATGTAG 57.987 38.462 0.00 0.00 0.00 2.74
4478 5072 7.973048 AGTCCCTGTTGATCTAAGTTATGTA 57.027 36.000 0.00 0.00 0.00 2.29
4482 5076 6.928348 TCAAGTCCCTGTTGATCTAAGTTA 57.072 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.