Multiple sequence alignment - TraesCS7A01G318300

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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 TraesCS7A01G318300 chr7A 100.000 3287 0 0 1 3287 458772697 458775983 0.000000e+00 6071.0
1 TraesCS7A01G318300 chr7A 88.971 1360 145 2 941 2295 458835353 458836712 0.000000e+00 1676.0
2 TraesCS7A01G318300 chr7B 91.866 1463 88 15 839 2300 409890758 409892190 0.000000e+00 2013.0
3 TraesCS7A01G318300 chr7B 89.400 1283 118 5 1016 2295 410022759 410024026 0.000000e+00 1600.0
4 TraesCS7A01G318300 chr7B 90.421 522 26 10 45 560 409890097 409890600 0.000000e+00 665.0
5 TraesCS7A01G318300 chr7B 87.975 474 36 9 44 514 409917671 409918126 1.040000e-149 540.0
6 TraesCS7A01G318300 chr7D 89.291 1326 137 3 979 2300 401068003 401069327 0.000000e+00 1657.0
7 TraesCS7A01G318300 chr7D 92.828 488 35 0 1457 1944 400938360 400938847 0.000000e+00 708.0
8 TraesCS7A01G318300 chr7D 82.690 855 65 54 23 838 400907527 400908337 0.000000e+00 682.0
9 TraesCS7A01G318300 chr7D 94.318 264 13 2 2078 2340 400942425 400942687 1.420000e-108 403.0
10 TraesCS7A01G318300 chr7D 93.750 160 7 2 2377 2534 400942769 400942927 1.520000e-58 237.0
11 TraesCS7A01G318300 chr7D 95.270 148 7 0 1939 2086 400941045 400941192 5.480000e-58 235.0
12 TraesCS7A01G318300 chr7D 95.000 60 3 0 840 899 400908403 400908462 9.710000e-16 95.3
13 TraesCS7A01G318300 chr3A 86.686 1367 158 13 946 2290 683450148 683448784 0.000000e+00 1495.0
14 TraesCS7A01G318300 chr3D 85.041 1464 189 17 852 2290 546710781 546709323 0.000000e+00 1463.0
15 TraesCS7A01G318300 chr2B 95.029 523 22 2 2762 3284 388942035 388942553 0.000000e+00 819.0
16 TraesCS7A01G318300 chr2B 90.529 454 15 3 2834 3287 128365008 128365433 2.840000e-160 575.0
17 TraesCS7A01G318300 chr2B 96.135 207 8 0 2534 2740 128364805 128365011 4.060000e-89 339.0
18 TraesCS7A01G318300 chr4D 74.371 835 163 35 1450 2260 1198336 1199143 3.190000e-80 309.0
19 TraesCS7A01G318300 chr4D 74.306 432 69 26 1016 1432 1197813 1198217 9.510000e-31 145.0
20 TraesCS7A01G318300 chr6D 92.344 209 16 0 2532 2740 229384713 229384505 6.900000e-77 298.0
21 TraesCS7A01G318300 chr3B 92.271 207 16 0 2532 2738 795971664 795971458 8.920000e-76 294.0
22 TraesCS7A01G318300 chr3B 90.777 206 19 0 2535 2740 312164403 312164608 3.230000e-70 276.0
23 TraesCS7A01G318300 chr1B 92.647 204 15 0 2535 2738 89439041 89439244 8.920000e-76 294.0
24 TraesCS7A01G318300 chr1D 80.139 433 51 25 2538 2960 121619874 121620281 1.150000e-74 291.0
25 TraesCS7A01G318300 chr2D 91.346 208 17 1 2532 2738 555034691 555034898 1.930000e-72 283.0
26 TraesCS7A01G318300 chr5D 83.974 312 22 10 2762 3056 234036022 234035722 1.160000e-69 274.0
27 TraesCS7A01G318300 chr4A 73.264 864 176 38 1450 2287 603649221 603648387 6.990000e-67 265.0
28 TraesCS7A01G318300 chr5B 83.158 285 44 3 3000 3282 270758715 270758997 1.170000e-64 257.0
29 TraesCS7A01G318300 chr5B 89.163 203 12 5 2762 2960 270758417 270758613 9.110000e-61 244.0
30 TraesCS7A01G318300 chr5B 88.557 201 21 2 2539 2738 554655917 554656116 3.280000e-60 243.0
31 TraesCS7A01G318300 chr5B 88.060 201 24 0 2538 2738 33544770 33544570 4.240000e-59 239.0
32 TraesCS7A01G318300 chr4B 74.365 433 76 20 1016 1432 825916 825503 5.680000e-33 152.0


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 TraesCS7A01G318300 chr7A 458772697 458775983 3286 False 6071.00 6071 100.0000 1 3287 1 chr7A.!!$F1 3286
1 TraesCS7A01G318300 chr7A 458835353 458836712 1359 False 1676.00 1676 88.9710 941 2295 1 chr7A.!!$F2 1354
2 TraesCS7A01G318300 chr7B 410022759 410024026 1267 False 1600.00 1600 89.4000 1016 2295 1 chr7B.!!$F2 1279
3 TraesCS7A01G318300 chr7B 409890097 409892190 2093 False 1339.00 2013 91.1435 45 2300 2 chr7B.!!$F3 2255
4 TraesCS7A01G318300 chr7D 401068003 401069327 1324 False 1657.00 1657 89.2910 979 2300 1 chr7D.!!$F1 1321
5 TraesCS7A01G318300 chr7D 400938360 400942927 4567 False 395.75 708 94.0415 1457 2534 4 chr7D.!!$F3 1077
6 TraesCS7A01G318300 chr7D 400907527 400908462 935 False 388.65 682 88.8450 23 899 2 chr7D.!!$F2 876
7 TraesCS7A01G318300 chr3A 683448784 683450148 1364 True 1495.00 1495 86.6860 946 2290 1 chr3A.!!$R1 1344
8 TraesCS7A01G318300 chr3D 546709323 546710781 1458 True 1463.00 1463 85.0410 852 2290 1 chr3D.!!$R1 1438
9 TraesCS7A01G318300 chr2B 388942035 388942553 518 False 819.00 819 95.0290 2762 3284 1 chr2B.!!$F1 522
10 TraesCS7A01G318300 chr2B 128364805 128365433 628 False 457.00 575 93.3320 2534 3287 2 chr2B.!!$F2 753
11 TraesCS7A01G318300 chr4D 1197813 1199143 1330 False 227.00 309 74.3385 1016 2260 2 chr4D.!!$F1 1244
12 TraesCS7A01G318300 chr4A 603648387 603649221 834 True 265.00 265 73.2640 1450 2287 1 chr4A.!!$R1 837
13 TraesCS7A01G318300 chr5B 270758417 270758997 580 False 250.50 257 86.1605 2762 3282 2 chr5B.!!$F2 520

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
997 1132 0.401356 TTGGCTCATTGCTCAGTCCA 59.599 50.0 0.0 0.0 42.39 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2972 6790 0.178068 TACCGCCTGCCATCTTCTTC 59.822 55.0 0.0 0.0 0.0 2.87 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
241 245 1.082756 GCTGTTCTTGTTCGTGCCG 60.083 57.895 0.00 0.00 0.00 5.69
244 248 1.278637 GTTCTTGTTCGTGCCGGTG 59.721 57.895 1.90 0.00 0.00 4.94
327 331 0.880718 GCGCCATCCTACTTGTAGCC 60.881 60.000 0.00 0.00 0.00 3.93
434 460 1.363885 GCTATCGCGGGGTTCGTTTT 61.364 55.000 6.13 0.00 41.72 2.43
482 514 9.052759 GGAGATTTTGCTCGGACTAATTAATTA 57.947 33.333 7.66 7.66 35.74 1.40
494 526 9.450807 CGGACTAATTAATTAATTTCTTGCTGG 57.549 33.333 24.53 7.07 37.16 4.85
517 552 3.840124 AAAAAGTGTCTCCGGAAGAGT 57.160 42.857 5.23 0.00 43.71 3.24
519 554 4.522722 AAAAGTGTCTCCGGAAGAGTAG 57.477 45.455 5.23 0.00 43.71 2.57
520 555 3.436577 AAGTGTCTCCGGAAGAGTAGA 57.563 47.619 5.23 0.00 43.71 2.59
521 556 2.993937 AGTGTCTCCGGAAGAGTAGAG 58.006 52.381 5.23 0.00 43.71 2.43
522 557 2.306512 AGTGTCTCCGGAAGAGTAGAGT 59.693 50.000 5.23 0.00 43.71 3.24
523 558 3.083293 GTGTCTCCGGAAGAGTAGAGTT 58.917 50.000 5.23 0.00 43.71 3.01
524 559 3.082548 TGTCTCCGGAAGAGTAGAGTTG 58.917 50.000 5.23 0.00 43.71 3.16
525 560 3.083293 GTCTCCGGAAGAGTAGAGTTGT 58.917 50.000 5.23 0.00 43.71 3.32
526 561 4.260170 GTCTCCGGAAGAGTAGAGTTGTA 58.740 47.826 5.23 0.00 43.71 2.41
527 562 4.094739 GTCTCCGGAAGAGTAGAGTTGTAC 59.905 50.000 5.23 0.00 43.71 2.90
567 602 4.974645 AACCACAAGACAGTCAGGATTA 57.025 40.909 2.66 0.00 0.00 1.75
568 603 5.505181 AACCACAAGACAGTCAGGATTAT 57.495 39.130 2.66 0.00 0.00 1.28
577 612 7.673641 AGACAGTCAGGATTATCTCTGAATT 57.326 36.000 12.57 4.90 41.07 2.17
581 616 8.859090 ACAGTCAGGATTATCTCTGAATTCTAG 58.141 37.037 7.05 4.65 41.07 2.43
594 629 7.338196 TCTCTGAATTCTAGTCTGATCTTCGTT 59.662 37.037 7.05 0.00 0.00 3.85
602 637 3.194542 AGTCTGATCTTCGTTGAGGGAAG 59.805 47.826 0.00 0.00 41.74 3.46
612 647 3.583086 TCGTTGAGGGAAGGAAGAGAAAT 59.417 43.478 0.00 0.00 0.00 2.17
623 658 5.190357 AGGAAGAGAAATCAAAGGCATCT 57.810 39.130 0.00 0.00 0.00 2.90
624 659 6.319048 AGGAAGAGAAATCAAAGGCATCTA 57.681 37.500 0.00 0.00 0.00 1.98
625 660 6.118852 AGGAAGAGAAATCAAAGGCATCTAC 58.881 40.000 0.00 0.00 0.00 2.59
640 683 6.381801 AGGCATCTACGAAAATTTTGTGAAG 58.618 36.000 8.47 0.00 0.00 3.02
658 702 1.471119 AGAACACGGCTCTATCGGAA 58.529 50.000 0.00 0.00 0.00 4.30
721 766 3.812156 TCTCTCGTGGAGAAACACAAA 57.188 42.857 8.03 0.00 46.85 2.83
728 773 1.748493 TGGAGAAACACAAACACCAGC 59.252 47.619 0.00 0.00 0.00 4.85
738 783 3.251004 CACAAACACCAGCTAGGAAAGAC 59.749 47.826 8.91 0.00 41.22 3.01
750 795 2.889852 AGGAAAGACGAGGATTAACGC 58.110 47.619 0.00 0.00 0.00 4.84
753 798 3.062234 GGAAAGACGAGGATTAACGCTTG 59.938 47.826 0.00 0.00 0.00 4.01
754 799 1.641577 AGACGAGGATTAACGCTTGC 58.358 50.000 0.00 0.00 0.00 4.01
755 800 1.204941 AGACGAGGATTAACGCTTGCT 59.795 47.619 0.00 0.00 0.00 3.91
756 801 2.000447 GACGAGGATTAACGCTTGCTT 59.000 47.619 0.00 0.00 0.00 3.91
757 802 1.732259 ACGAGGATTAACGCTTGCTTG 59.268 47.619 0.00 0.00 0.00 4.01
758 803 1.999735 CGAGGATTAACGCTTGCTTGA 59.000 47.619 0.00 0.00 0.00 3.02
759 804 2.029728 CGAGGATTAACGCTTGCTTGAG 59.970 50.000 0.00 0.00 0.00 3.02
760 805 1.740025 AGGATTAACGCTTGCTTGAGC 59.260 47.619 0.00 0.00 42.50 4.26
761 806 1.202188 GGATTAACGCTTGCTTGAGCC 60.202 52.381 0.00 0.00 39.51 4.70
762 807 1.468520 GATTAACGCTTGCTTGAGCCA 59.531 47.619 0.00 0.00 39.51 4.75
763 808 1.313772 TTAACGCTTGCTTGAGCCAA 58.686 45.000 0.00 0.00 39.51 4.52
785 830 3.826524 TGGTCAAGTAGCCAAACAATGA 58.173 40.909 0.00 0.00 0.00 2.57
794 839 6.116126 AGTAGCCAAACAATGATACTCTTCC 58.884 40.000 0.00 0.00 30.20 3.46
808 853 7.806690 TGATACTCTTCCGAAAATTCAAACAG 58.193 34.615 0.00 0.00 0.00 3.16
809 854 5.438761 ACTCTTCCGAAAATTCAAACAGG 57.561 39.130 0.00 0.00 0.00 4.00
810 855 4.887655 ACTCTTCCGAAAATTCAAACAGGT 59.112 37.500 0.00 0.00 0.00 4.00
850 976 2.725203 TTTCTCTCCCACCGTTGCCG 62.725 60.000 0.00 0.00 0.00 5.69
899 1031 5.938322 TGAAAATTCAAAGATGCGGAGTAC 58.062 37.500 0.00 0.00 33.55 2.73
900 1032 5.471797 TGAAAATTCAAAGATGCGGAGTACA 59.528 36.000 0.00 0.00 33.55 2.90
901 1033 5.551760 AAATTCAAAGATGCGGAGTACAG 57.448 39.130 0.00 0.00 0.00 2.74
902 1034 3.678056 TTCAAAGATGCGGAGTACAGT 57.322 42.857 0.00 0.00 0.00 3.55
903 1035 4.794278 TTCAAAGATGCGGAGTACAGTA 57.206 40.909 0.00 0.00 0.00 2.74
912 1044 5.099484 TGCGGAGTACAGTATAATACACG 57.901 43.478 0.00 0.00 0.00 4.49
915 1047 5.277974 GCGGAGTACAGTATAATACACGGAA 60.278 44.000 0.00 0.00 0.00 4.30
930 1062 0.749454 CGGAAGGGGGCAAATCTCTG 60.749 60.000 0.00 0.00 0.00 3.35
977 1111 1.526986 CGAACGCTACATTTTGCCTCG 60.527 52.381 0.00 0.00 0.00 4.63
995 1130 0.445436 CGTTGGCTCATTGCTCAGTC 59.555 55.000 0.00 0.00 42.39 3.51
997 1132 0.401356 TTGGCTCATTGCTCAGTCCA 59.599 50.000 0.00 0.00 42.39 4.02
999 1134 0.807496 GGCTCATTGCTCAGTCCAAC 59.193 55.000 0.00 0.00 42.39 3.77
1006 1141 0.320683 TGCTCAGTCCAACATGACCG 60.321 55.000 0.00 0.00 35.83 4.79
1011 1152 1.599518 GTCCAACATGACCGGCACA 60.600 57.895 0.00 2.06 0.00 4.57
1012 1153 1.149401 TCCAACATGACCGGCACAA 59.851 52.632 0.00 0.00 0.00 3.33
1013 1154 0.466372 TCCAACATGACCGGCACAAA 60.466 50.000 0.00 0.00 0.00 2.83
1014 1155 0.387202 CCAACATGACCGGCACAAAA 59.613 50.000 0.00 0.00 0.00 2.44
1054 1195 3.701604 GAGCTCATCGTTCCGGCGT 62.702 63.158 9.40 0.00 0.00 5.68
1057 1198 1.445410 CTCATCGTTCCGGCGTTGA 60.445 57.895 6.01 12.64 37.98 3.18
1059 1200 2.024868 CATCGTTCCGGCGTTGACA 61.025 57.895 6.01 0.00 34.58 3.58
1099 1240 1.741732 CGCTCTCCTCCATTGACAAGG 60.742 57.143 0.00 0.00 0.00 3.61
1101 1242 1.280133 CTCTCCTCCATTGACAAGGCA 59.720 52.381 0.00 0.00 0.00 4.75
1169 1310 2.202703 GTTCACCGCCGCTCGTAT 60.203 61.111 0.00 0.00 36.19 3.06
1171 1312 2.702788 TTCACCGCCGCTCGTATGA 61.703 57.895 0.00 0.00 36.19 2.15
1172 1313 2.607668 TTCACCGCCGCTCGTATGAG 62.608 60.000 7.65 7.65 45.49 2.90
1719 1988 4.953010 TTCAAGCAGGCTGCCGCA 62.953 61.111 34.33 16.36 46.52 5.69
1725 1994 3.057548 CAGGCTGCCGCAACATCA 61.058 61.111 13.96 0.00 38.10 3.07
1756 2025 4.090057 GCTCCACCTTTGACGCGC 62.090 66.667 5.73 0.00 0.00 6.86
2172 5906 1.724929 CGTCAACTTCGTCGCGTCT 60.725 57.895 5.77 0.00 0.00 4.18
2307 6041 2.926420 GCAACGGACGCCCCATTTT 61.926 57.895 0.00 0.00 34.14 1.82
2335 6069 0.969409 AAAATGGAGAGGCAGCCTGC 60.969 55.000 22.26 8.55 44.08 4.85
2352 6101 2.645411 GCATTTCGATGCTGCACAC 58.355 52.632 3.57 1.12 43.79 3.82
2378 6127 8.988934 CCATCAACAGTGTATATATACAACACC 58.011 37.037 23.88 13.37 44.11 4.16
2453 6232 7.602644 TCACATAGTTGGTTCAAAGATCTACAC 59.397 37.037 0.00 0.00 0.00 2.90
2519 6299 5.903764 TTTTTCTTTCGAATTGTGCATGG 57.096 34.783 0.00 0.00 0.00 3.66
2530 6310 1.175654 TGTGCATGGCAATACACCTG 58.824 50.000 13.23 0.00 41.47 4.00
2534 6314 2.752354 TGCATGGCAATACACCTGTAAC 59.248 45.455 0.00 0.00 34.76 2.50
2535 6315 2.223249 GCATGGCAATACACCTGTAACG 60.223 50.000 0.00 0.00 33.76 3.18
2536 6316 2.843401 TGGCAATACACCTGTAACGT 57.157 45.000 0.00 0.00 33.76 3.99
2537 6317 3.128852 TGGCAATACACCTGTAACGTT 57.871 42.857 5.88 5.88 33.76 3.99
2538 6318 2.809119 TGGCAATACACCTGTAACGTTG 59.191 45.455 11.99 0.00 33.76 4.10
2611 6391 5.190132 TCAATTCGGGGAGGAAACTGTAATA 59.810 40.000 0.00 0.00 44.43 0.98
2698 6478 6.422776 AATCATGTTCGGATGACAAACTAC 57.577 37.500 0.00 0.00 35.17 2.73
2700 6480 3.646611 TGTTCGGATGACAAACTACGA 57.353 42.857 0.00 0.00 0.00 3.43
2709 6489 6.456315 CGGATGACAAACTACGAAATTGCATA 60.456 38.462 0.00 0.00 0.00 3.14
2720 6500 5.229423 ACGAAATTGCATATGCTTTGTGTT 58.771 33.333 27.13 12.87 42.66 3.32
2736 6516 7.226128 TGCTTTGTGTTTTATGCATCAAATCAA 59.774 29.630 0.19 11.69 0.00 2.57
2737 6517 8.068977 GCTTTGTGTTTTATGCATCAAATCAAA 58.931 29.630 22.74 22.74 0.00 2.69
2738 6518 9.932699 CTTTGTGTTTTATGCATCAAATCAAAA 57.067 25.926 23.46 14.88 0.00 2.44
2740 6520 9.880064 TTGTGTTTTATGCATCAAATCAAAATG 57.120 25.926 0.19 0.00 0.00 2.32
2741 6521 9.269453 TGTGTTTTATGCATCAAATCAAAATGA 57.731 25.926 0.19 0.00 0.00 2.57
2746 6526 6.978343 ATGCATCAAATCAAAATGAACAGG 57.022 33.333 0.00 0.00 0.00 4.00
2747 6527 5.856156 TGCATCAAATCAAAATGAACAGGT 58.144 33.333 0.00 0.00 0.00 4.00
2748 6528 6.289834 TGCATCAAATCAAAATGAACAGGTT 58.710 32.000 0.00 0.00 0.00 3.50
2749 6529 6.424509 TGCATCAAATCAAAATGAACAGGTTC 59.575 34.615 5.23 5.23 39.91 3.62
2750 6530 6.647895 GCATCAAATCAAAATGAACAGGTTCT 59.352 34.615 12.86 0.00 40.14 3.01
2751 6531 7.814107 GCATCAAATCAAAATGAACAGGTTCTA 59.186 33.333 12.86 1.18 40.14 2.10
2752 6532 9.695526 CATCAAATCAAAATGAACAGGTTCTAA 57.304 29.630 12.86 0.00 40.14 2.10
2754 6534 9.912634 TCAAATCAAAATGAACAGGTTCTAATC 57.087 29.630 12.86 0.00 40.14 1.75
2755 6535 9.695526 CAAATCAAAATGAACAGGTTCTAATCA 57.304 29.630 12.86 0.00 40.14 2.57
2871 6655 3.498661 GGACAACAGGGGAAGAACAGAAT 60.499 47.826 0.00 0.00 0.00 2.40
2903 6687 3.370633 GGAGAAACTTGGCTAGGTAAGGG 60.371 52.174 0.20 0.00 0.00 3.95
2904 6688 2.576648 AGAAACTTGGCTAGGTAAGGGG 59.423 50.000 0.20 0.00 0.00 4.79
2905 6689 2.354261 AACTTGGCTAGGTAAGGGGA 57.646 50.000 0.20 0.00 0.00 4.81
2966 6784 1.577736 ACATGGAAGAGGAGGTCAGG 58.422 55.000 0.00 0.00 0.00 3.86
2967 6785 1.079490 ACATGGAAGAGGAGGTCAGGA 59.921 52.381 0.00 0.00 0.00 3.86
2968 6786 1.761784 CATGGAAGAGGAGGTCAGGAG 59.238 57.143 0.00 0.00 0.00 3.69
2969 6787 0.041833 TGGAAGAGGAGGTCAGGAGG 59.958 60.000 0.00 0.00 0.00 4.30
2970 6788 0.689412 GGAAGAGGAGGTCAGGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
2971 6789 0.689412 GAAGAGGAGGTCAGGAGGGG 60.689 65.000 0.00 0.00 0.00 4.79
2972 6790 2.041405 GAGGAGGTCAGGAGGGGG 60.041 72.222 0.00 0.00 0.00 5.40
2973 6791 2.540910 AGGAGGTCAGGAGGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
2974 6792 2.182858 GAGGAGGTCAGGAGGGGGAA 62.183 65.000 0.00 0.00 0.00 3.97
2975 6793 1.690985 GGAGGTCAGGAGGGGGAAG 60.691 68.421 0.00 0.00 0.00 3.46
2976 6794 1.392534 GAGGTCAGGAGGGGGAAGA 59.607 63.158 0.00 0.00 0.00 2.87
2977 6795 0.252742 GAGGTCAGGAGGGGGAAGAA 60.253 60.000 0.00 0.00 0.00 2.52
2978 6796 0.252927 AGGTCAGGAGGGGGAAGAAG 60.253 60.000 0.00 0.00 0.00 2.85
2979 6797 0.252742 GGTCAGGAGGGGGAAGAAGA 60.253 60.000 0.00 0.00 0.00 2.87
2980 6798 1.626631 GGTCAGGAGGGGGAAGAAGAT 60.627 57.143 0.00 0.00 0.00 2.40
2981 6799 1.488393 GTCAGGAGGGGGAAGAAGATG 59.512 57.143 0.00 0.00 0.00 2.90
2982 6800 0.842635 CAGGAGGGGGAAGAAGATGG 59.157 60.000 0.00 0.00 0.00 3.51
3060 6924 2.124085 TCGGGATGGAGGGGTTGT 59.876 61.111 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.902759 GAAAGTACCGGCCGCTCCTC 62.903 65.000 22.85 8.45 0.00 3.71
31 32 2.510918 GGAAAGTACCGGCCGCTC 60.511 66.667 22.85 12.06 0.00 5.03
111 115 3.650298 TACCCTCCACCTCCGTCGG 62.650 68.421 4.39 4.39 0.00 4.79
119 123 3.027675 GCCCGAAGTACCCTCCACC 62.028 68.421 0.00 0.00 0.00 4.61
120 124 2.582978 GCCCGAAGTACCCTCCAC 59.417 66.667 0.00 0.00 0.00 4.02
121 125 2.686106 GGCCCGAAGTACCCTCCA 60.686 66.667 0.00 0.00 0.00 3.86
343 347 2.281498 CGAGCGCACGATTTGATTTAGA 59.719 45.455 23.01 0.00 35.09 2.10
344 348 2.618419 CGAGCGCACGATTTGATTTAG 58.382 47.619 23.01 0.00 35.09 1.85
434 460 6.837312 TCCATCAACTAGTCTCCAAGAAAAA 58.163 36.000 0.00 0.00 0.00 1.94
513 548 7.922278 CAGAGATACTACGTACAACTCTACTCT 59.078 40.741 10.24 0.00 31.16 3.24
515 550 7.780064 TCAGAGATACTACGTACAACTCTACT 58.220 38.462 10.24 0.00 31.16 2.57
517 552 9.610705 AATTCAGAGATACTACGTACAACTCTA 57.389 33.333 10.24 0.86 31.16 2.43
519 554 9.570488 AAAATTCAGAGATACTACGTACAACTC 57.430 33.333 0.00 0.00 0.00 3.01
523 558 9.793252 GGTTAAAATTCAGAGATACTACGTACA 57.207 33.333 0.00 0.00 0.00 2.90
524 559 9.793252 TGGTTAAAATTCAGAGATACTACGTAC 57.207 33.333 0.00 0.00 0.00 3.67
525 560 9.793252 GTGGTTAAAATTCAGAGATACTACGTA 57.207 33.333 0.00 0.00 0.00 3.57
526 561 8.308931 TGTGGTTAAAATTCAGAGATACTACGT 58.691 33.333 0.00 0.00 0.00 3.57
527 562 8.697846 TGTGGTTAAAATTCAGAGATACTACG 57.302 34.615 0.00 0.00 0.00 3.51
567 602 7.502226 ACGAAGATCAGACTAGAATTCAGAGAT 59.498 37.037 8.44 9.14 0.00 2.75
568 603 6.826231 ACGAAGATCAGACTAGAATTCAGAGA 59.174 38.462 8.44 5.44 0.00 3.10
577 612 3.948473 CCCTCAACGAAGATCAGACTAGA 59.052 47.826 0.00 0.00 0.00 2.43
581 616 3.516615 CTTCCCTCAACGAAGATCAGAC 58.483 50.000 0.00 0.00 39.29 3.51
594 629 5.515534 CCTTTGATTTCTCTTCCTTCCCTCA 60.516 44.000 0.00 0.00 0.00 3.86
602 637 5.007136 CGTAGATGCCTTTGATTTCTCTTCC 59.993 44.000 0.00 0.00 0.00 3.46
612 647 6.640499 CACAAAATTTTCGTAGATGCCTTTGA 59.360 34.615 0.00 0.00 35.04 2.69
623 658 5.966503 CCGTGTTCTTCACAAAATTTTCGTA 59.033 36.000 0.00 0.00 46.44 3.43
624 659 4.796312 CCGTGTTCTTCACAAAATTTTCGT 59.204 37.500 0.00 0.60 46.44 3.85
625 660 4.317069 GCCGTGTTCTTCACAAAATTTTCG 60.317 41.667 0.00 0.00 46.44 3.46
640 683 1.134560 ACTTCCGATAGAGCCGTGTTC 59.865 52.381 0.00 0.00 39.76 3.18
645 689 1.932604 GCATCACTTCCGATAGAGCCG 60.933 57.143 0.00 0.00 39.76 5.52
658 702 0.512952 GAACGCAACGAAGCATCACT 59.487 50.000 0.00 0.00 0.00 3.41
720 765 1.968493 TCGTCTTTCCTAGCTGGTGTT 59.032 47.619 0.00 0.00 37.07 3.32
721 766 1.546476 CTCGTCTTTCCTAGCTGGTGT 59.454 52.381 0.00 0.00 37.07 4.16
728 773 4.043073 GCGTTAATCCTCGTCTTTCCTAG 58.957 47.826 0.00 0.00 0.00 3.02
738 783 1.999735 TCAAGCAAGCGTTAATCCTCG 59.000 47.619 0.00 0.00 0.00 4.63
750 795 1.250328 TGACCATTGGCTCAAGCAAG 58.750 50.000 1.54 0.00 44.36 4.01
753 798 1.251251 ACTTGACCATTGGCTCAAGC 58.749 50.000 28.79 0.00 40.74 4.01
754 799 2.421424 GCTACTTGACCATTGGCTCAAG 59.579 50.000 28.01 28.01 41.71 3.02
755 800 2.436417 GCTACTTGACCATTGGCTCAA 58.564 47.619 15.39 15.39 0.00 3.02
756 801 1.340017 GGCTACTTGACCATTGGCTCA 60.340 52.381 1.54 3.36 0.00 4.26
757 802 1.340017 TGGCTACTTGACCATTGGCTC 60.340 52.381 1.54 0.62 0.00 4.70
758 803 0.698238 TGGCTACTTGACCATTGGCT 59.302 50.000 1.54 0.00 0.00 4.75
759 804 1.544724 TTGGCTACTTGACCATTGGC 58.455 50.000 1.54 0.00 35.42 4.52
760 805 2.890311 TGTTTGGCTACTTGACCATTGG 59.110 45.455 0.00 0.00 35.42 3.16
761 806 4.582701 TTGTTTGGCTACTTGACCATTG 57.417 40.909 0.00 0.00 35.42 2.82
762 807 4.832266 TCATTGTTTGGCTACTTGACCATT 59.168 37.500 0.00 0.00 35.42 3.16
763 808 4.406456 TCATTGTTTGGCTACTTGACCAT 58.594 39.130 0.00 0.00 35.42 3.55
774 819 3.938963 TCGGAAGAGTATCATTGTTTGGC 59.061 43.478 0.00 0.00 37.82 4.52
785 830 6.715264 ACCTGTTTGAATTTTCGGAAGAGTAT 59.285 34.615 0.00 0.00 43.69 2.12
794 839 4.041723 GTCACCACCTGTTTGAATTTTCG 58.958 43.478 0.00 0.00 0.00 3.46
809 854 2.032071 CCCCTTCGGTGTCACCAC 59.968 66.667 21.91 0.96 38.47 4.16
810 855 3.948719 GCCCCTTCGGTGTCACCA 61.949 66.667 21.91 6.45 38.47 4.17
822 867 0.253347 TGGGAGAGAAATCTGCCCCT 60.253 55.000 12.54 0.00 46.11 4.79
826 871 0.250513 ACGGTGGGAGAGAAATCTGC 59.749 55.000 0.00 0.00 0.00 4.26
829 874 1.087501 GCAACGGTGGGAGAGAAATC 58.912 55.000 0.90 0.00 0.00 2.17
869 995 5.285607 CGCATCTTTGAATTTTCAGAAGAGC 59.714 40.000 15.99 16.22 37.54 4.09
899 1031 3.556423 GCCCCCTTCCGTGTATTATACTG 60.556 52.174 3.92 0.00 0.00 2.74
900 1032 2.636403 GCCCCCTTCCGTGTATTATACT 59.364 50.000 3.92 0.00 0.00 2.12
901 1033 2.369532 TGCCCCCTTCCGTGTATTATAC 59.630 50.000 0.00 0.00 0.00 1.47
902 1034 2.692024 TGCCCCCTTCCGTGTATTATA 58.308 47.619 0.00 0.00 0.00 0.98
903 1035 1.513858 TGCCCCCTTCCGTGTATTAT 58.486 50.000 0.00 0.00 0.00 1.28
912 1044 1.039785 GCAGAGATTTGCCCCCTTCC 61.040 60.000 0.00 0.00 38.13 3.46
915 1047 2.273449 CGCAGAGATTTGCCCCCT 59.727 61.111 0.00 0.00 41.01 4.79
995 1130 0.387202 TTTTGTGCCGGTCATGTTGG 59.613 50.000 1.90 0.00 0.00 3.77
997 1132 1.202475 GGTTTTTGTGCCGGTCATGTT 60.202 47.619 1.90 0.00 0.00 2.71
999 1134 0.662970 CGGTTTTTGTGCCGGTCATG 60.663 55.000 1.90 0.00 43.85 3.07
1006 1141 2.159212 ACTTGGTAACGGTTTTTGTGCC 60.159 45.455 0.00 0.00 42.51 5.01
1011 1152 1.334556 GGCGACTTGGTAACGGTTTTT 59.665 47.619 0.00 0.00 42.51 1.94
1012 1153 0.946528 GGCGACTTGGTAACGGTTTT 59.053 50.000 0.00 0.00 42.51 2.43
1013 1154 1.223417 CGGCGACTTGGTAACGGTTT 61.223 55.000 0.00 0.00 42.51 3.27
1014 1155 1.665599 CGGCGACTTGGTAACGGTT 60.666 57.895 0.00 0.00 42.51 4.44
1046 1187 2.592287 GGGTTGTCAACGCCGGAA 60.592 61.111 19.34 0.00 38.30 4.30
1164 1305 4.221422 GCGCCCTGGCTCATACGA 62.221 66.667 6.60 0.00 39.32 3.43
1701 1970 4.112341 GCGGCAGCCTGCTTGAAG 62.112 66.667 17.55 4.65 44.28 3.02
1719 1988 1.378762 CACCTCCCCCGTTGATGTT 59.621 57.895 0.00 0.00 0.00 2.71
1725 1994 3.637273 GAGCACACCTCCCCCGTT 61.637 66.667 0.00 0.00 34.35 4.44
1756 2025 3.041940 GAACACCACGGCCGTCAG 61.042 66.667 31.80 25.19 0.00 3.51
1875 2147 2.044650 TAGTAGCCGTCCACCGCT 60.045 61.111 0.00 0.00 34.38 5.52
2335 6069 0.522626 TGGTGTGCAGCATCGAAATG 59.477 50.000 0.00 0.00 33.39 2.32
2352 6101 8.988934 GGTGTTGTATATATACACTGTTGATGG 58.011 37.037 22.44 0.00 42.48 3.51
2378 6127 7.801716 TTCCCTCCGTTTCATAATTCTTATG 57.198 36.000 1.30 1.30 43.41 1.90
2453 6232 8.553459 ACAAAATGTACCTAGAAATCTGAGTG 57.447 34.615 0.00 0.00 0.00 3.51
2502 6282 2.350899 TGCCATGCACAATTCGAAAG 57.649 45.000 0.00 0.00 31.71 2.62
2503 6283 2.808523 TTGCCATGCACAATTCGAAA 57.191 40.000 0.00 0.00 38.71 3.46
2506 6286 2.853594 GTGTATTGCCATGCACAATTCG 59.146 45.455 13.10 0.00 43.56 3.34
2514 6294 2.223249 CGTTACAGGTGTATTGCCATGC 60.223 50.000 0.00 0.00 0.00 4.06
2519 6299 3.249080 ACACAACGTTACAGGTGTATTGC 59.751 43.478 17.54 0.00 40.58 3.56
2530 6310 3.054878 AGACATCCGAACACAACGTTAC 58.945 45.455 0.00 0.00 38.19 2.50
2534 6314 1.497991 ACAGACATCCGAACACAACG 58.502 50.000 0.00 0.00 0.00 4.10
2535 6315 4.142902 CCAATACAGACATCCGAACACAAC 60.143 45.833 0.00 0.00 0.00 3.32
2536 6316 4.000325 CCAATACAGACATCCGAACACAA 59.000 43.478 0.00 0.00 0.00 3.33
2537 6317 3.259625 TCCAATACAGACATCCGAACACA 59.740 43.478 0.00 0.00 0.00 3.72
2538 6318 3.857052 TCCAATACAGACATCCGAACAC 58.143 45.455 0.00 0.00 0.00 3.32
2587 6367 1.702957 ACAGTTTCCTCCCCGAATTGA 59.297 47.619 0.00 0.00 0.00 2.57
2698 6478 5.766702 AACACAAAGCATATGCAATTTCG 57.233 34.783 28.62 16.73 45.16 3.46
2700 6480 7.964011 GCATAAAACACAAAGCATATGCAATTT 59.036 29.630 28.62 18.07 43.04 1.82
2709 6489 7.388224 TGATTTGATGCATAAAACACAAAGCAT 59.612 29.630 17.92 0.00 44.50 3.79
2720 6500 8.937884 CCTGTTCATTTTGATTTGATGCATAAA 58.062 29.630 0.00 0.00 0.00 1.40
2736 6516 8.149647 TGCATTTTGATTAGAACCTGTTCATTT 58.850 29.630 12.21 0.00 41.84 2.32
2737 6517 7.599998 GTGCATTTTGATTAGAACCTGTTCATT 59.400 33.333 12.21 0.00 41.84 2.57
2738 6518 7.092716 GTGCATTTTGATTAGAACCTGTTCAT 58.907 34.615 12.21 0.00 41.84 2.57
2739 6519 6.040278 TGTGCATTTTGATTAGAACCTGTTCA 59.960 34.615 12.21 0.00 41.84 3.18
2740 6520 6.446318 TGTGCATTTTGATTAGAACCTGTTC 58.554 36.000 1.75 1.75 39.78 3.18
2741 6521 6.403866 TGTGCATTTTGATTAGAACCTGTT 57.596 33.333 0.00 0.00 0.00 3.16
2742 6522 6.403866 TTGTGCATTTTGATTAGAACCTGT 57.596 33.333 0.00 0.00 0.00 4.00
2743 6523 7.318141 AGATTGTGCATTTTGATTAGAACCTG 58.682 34.615 0.00 0.00 0.00 4.00
2744 6524 7.472334 AGATTGTGCATTTTGATTAGAACCT 57.528 32.000 0.00 0.00 0.00 3.50
2745 6525 8.243426 TGTAGATTGTGCATTTTGATTAGAACC 58.757 33.333 0.00 0.00 0.00 3.62
2746 6526 9.282247 CTGTAGATTGTGCATTTTGATTAGAAC 57.718 33.333 0.00 0.00 0.00 3.01
2747 6527 9.013229 ACTGTAGATTGTGCATTTTGATTAGAA 57.987 29.630 0.00 0.00 0.00 2.10
2748 6528 8.565896 ACTGTAGATTGTGCATTTTGATTAGA 57.434 30.769 0.00 0.00 0.00 2.10
2749 6529 8.453320 TGACTGTAGATTGTGCATTTTGATTAG 58.547 33.333 0.00 0.00 0.00 1.73
2750 6530 8.236586 GTGACTGTAGATTGTGCATTTTGATTA 58.763 33.333 0.00 0.00 0.00 1.75
2751 6531 7.086376 GTGACTGTAGATTGTGCATTTTGATT 58.914 34.615 0.00 0.00 0.00 2.57
2752 6532 6.207221 TGTGACTGTAGATTGTGCATTTTGAT 59.793 34.615 0.00 0.00 0.00 2.57
2753 6533 5.530543 TGTGACTGTAGATTGTGCATTTTGA 59.469 36.000 0.00 0.00 0.00 2.69
2754 6534 5.761003 TGTGACTGTAGATTGTGCATTTTG 58.239 37.500 0.00 0.00 0.00 2.44
2755 6535 6.579666 ATGTGACTGTAGATTGTGCATTTT 57.420 33.333 0.00 0.00 0.00 1.82
2756 6536 7.362056 GGTTATGTGACTGTAGATTGTGCATTT 60.362 37.037 0.00 0.00 0.00 2.32
2757 6537 6.094048 GGTTATGTGACTGTAGATTGTGCATT 59.906 38.462 0.00 0.00 0.00 3.56
2758 6538 5.586243 GGTTATGTGACTGTAGATTGTGCAT 59.414 40.000 0.00 0.00 0.00 3.96
2759 6539 4.935205 GGTTATGTGACTGTAGATTGTGCA 59.065 41.667 0.00 0.00 0.00 4.57
2760 6540 4.935205 TGGTTATGTGACTGTAGATTGTGC 59.065 41.667 0.00 0.00 0.00 4.57
2871 6655 3.497942 GCCAAGTTTCTCCTGTTCCCTTA 60.498 47.826 0.00 0.00 0.00 2.69
2966 6784 0.182299 CTGCCATCTTCTTCCCCCTC 59.818 60.000 0.00 0.00 0.00 4.30
2967 6785 1.284841 CCTGCCATCTTCTTCCCCCT 61.285 60.000 0.00 0.00 0.00 4.79
2968 6786 1.228510 CCTGCCATCTTCTTCCCCC 59.771 63.158 0.00 0.00 0.00 5.40
2969 6787 1.454663 GCCTGCCATCTTCTTCCCC 60.455 63.158 0.00 0.00 0.00 4.81
2970 6788 1.821332 CGCCTGCCATCTTCTTCCC 60.821 63.158 0.00 0.00 0.00 3.97
2971 6789 1.821332 CCGCCTGCCATCTTCTTCC 60.821 63.158 0.00 0.00 0.00 3.46
2972 6790 0.178068 TACCGCCTGCCATCTTCTTC 59.822 55.000 0.00 0.00 0.00 2.87
2973 6791 0.179000 CTACCGCCTGCCATCTTCTT 59.821 55.000 0.00 0.00 0.00 2.52
2974 6792 1.690219 CCTACCGCCTGCCATCTTCT 61.690 60.000 0.00 0.00 0.00 2.85
2975 6793 1.227674 CCTACCGCCTGCCATCTTC 60.228 63.158 0.00 0.00 0.00 2.87
2976 6794 2.746375 CCCTACCGCCTGCCATCTT 61.746 63.158 0.00 0.00 0.00 2.40
2977 6795 3.164269 CCCTACCGCCTGCCATCT 61.164 66.667 0.00 0.00 0.00 2.90
2978 6796 4.256180 CCCCTACCGCCTGCCATC 62.256 72.222 0.00 0.00 0.00 3.51
2979 6797 4.815973 TCCCCTACCGCCTGCCAT 62.816 66.667 0.00 0.00 0.00 4.40
2982 6800 3.851128 GACTCCCCTACCGCCTGC 61.851 72.222 0.00 0.00 0.00 4.85
2998 6862 1.829970 ATCTCGGCCATCTCGCTGA 60.830 57.895 2.24 0.00 41.89 4.26
3060 6924 2.203195 GACTGCATATGGCCGGCA 60.203 61.111 30.85 15.30 43.89 5.69
3223 7089 2.281484 GCGAGACACAAGCCCCAA 60.281 61.111 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.