Multiple sequence alignment - TraesCS2B01G569100

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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 TraesCS2B01G569100 chr2B 100.000 2585 0 0 1 2585 759740757 759743341 0.000000e+00 4774.0
1 TraesCS2B01G569100 chr2B 86.969 683 53 11 1228 1882 759677051 759677725 0.000000e+00 736.0
2 TraesCS2B01G569100 chr2B 90.691 333 22 3 2196 2527 759677762 759678086 3.950000e-118 435.0
3 TraesCS2B01G569100 chr2B 74.684 711 99 55 1083 1731 759817808 759818499 9.240000e-60 241.0
4 TraesCS2B01G569100 chr2B 89.157 166 10 3 545 710 759674258 759674415 1.570000e-47 200.0
5 TraesCS2B01G569100 chr2B 76.506 332 46 19 1273 1587 760259230 760259546 4.460000e-33 152.0
6 TraesCS2B01G569100 chr2B 77.544 285 36 15 1311 1572 759882145 759882424 2.070000e-31 147.0
7 TraesCS2B01G569100 chr2B 79.085 153 26 5 1487 1637 760119307 760119455 1.640000e-17 100.0
8 TraesCS2B01G569100 chr2B 82.857 70 10 2 2421 2488 759766569 759766638 7.720000e-06 62.1
9 TraesCS2B01G569100 chr2A 85.219 1556 138 24 1000 2527 751546619 751548110 0.000000e+00 1515.0
10 TraesCS2B01G569100 chr2A 82.247 445 25 17 543 943 751546168 751546602 4.120000e-88 335.0
11 TraesCS2B01G569100 chr2A 79.104 402 50 16 1083 1457 751609017 751609411 1.990000e-61 246.0
12 TraesCS2B01G569100 chr2A 75.711 387 52 24 1311 1655 751662861 751663247 3.440000e-34 156.0
13 TraesCS2B01G569100 chr2A 82.993 147 17 4 1083 1226 751662671 751662812 2.700000e-25 126.0
14 TraesCS2B01G569100 chr2A 92.208 77 6 0 1123 1199 752048322 752048398 2.720000e-20 110.0
15 TraesCS2B01G569100 chr2A 86.170 94 9 4 1544 1637 751892687 751892598 5.890000e-17 99.0
16 TraesCS2B01G569100 chr2D 85.158 1361 74 31 531 1804 620153099 620154418 0.000000e+00 1277.0
17 TraesCS2B01G569100 chr2D 88.620 703 35 13 1846 2528 620154416 620155093 0.000000e+00 813.0
18 TraesCS2B01G569100 chr2D 77.249 567 75 35 1083 1604 620198943 620199500 1.510000e-72 283.0
19 TraesCS2B01G569100 chr2D 75.415 663 80 44 1078 1687 620193755 620194387 7.150000e-61 244.0
20 TraesCS2B01G569100 chr2D 90.909 77 7 0 1123 1199 620295785 620295861 1.270000e-18 104.0
21 TraesCS2B01G569100 chr2D 89.744 78 8 0 1123 1200 620447877 620447954 1.640000e-17 100.0
22 TraesCS2B01G569100 chr2D 85.714 70 7 3 2421 2488 620194853 620194921 1.280000e-08 71.3
23 TraesCS2B01G569100 chrUn 86.969 683 53 11 1228 1882 23148936 23148262 0.000000e+00 736.0
24 TraesCS2B01G569100 chrUn 85.513 711 52 14 545 1220 23151388 23150694 0.000000e+00 695.0
25 TraesCS2B01G569100 chrUn 90.691 333 22 3 2196 2527 23148225 23147901 3.950000e-118 435.0
26 TraesCS2B01G569100 chr1B 89.655 377 25 4 1 374 544803060 544803425 3.890000e-128 468.0
27 TraesCS2B01G569100 chr7B 89.572 374 22 2 1 374 327803934 327804290 2.340000e-125 459.0
28 TraesCS2B01G569100 chr7B 94.545 55 2 1 373 426 327804317 327804371 1.650000e-12 84.2
29 TraesCS2B01G569100 chr6B 88.919 370 37 3 6 374 115519502 115519136 1.090000e-123 453.0
30 TraesCS2B01G569100 chr6B 92.958 213 14 1 1 212 114971713 114971501 2.500000e-80 309.0
31 TraesCS2B01G569100 chr6D 93.385 257 16 1 1 256 46439397 46439141 1.880000e-101 379.0
32 TraesCS2B01G569100 chr6D 96.429 56 1 1 372 426 46438926 46438871 9.850000e-15 91.6
33 TraesCS2B01G569100 chr3A 86.275 357 32 8 20 373 95897547 95897205 3.140000e-99 372.0
34 TraesCS2B01G569100 chr3A 90.254 236 19 2 1 232 62449397 62449162 3.230000e-79 305.0
35 TraesCS2B01G569100 chr3A 82.553 235 38 3 1 232 30556443 30556209 1.210000e-48 204.0
36 TraesCS2B01G569100 chr3D 85.215 372 40 3 6 374 632722 632363 4.060000e-98 368.0
37 TraesCS2B01G569100 chr3D 77.869 122 23 4 255 374 554922479 554922360 3.570000e-09 73.1
38 TraesCS2B01G569100 chr1A 82.906 234 33 3 3 233 338744991 338745220 1.210000e-48 204.0


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 TraesCS2B01G569100 chr2B 759740757 759743341 2584 False 4774.0 4774 100.000000 1 2585 1 chr2B.!!$F1 2584
1 TraesCS2B01G569100 chr2B 759674258 759678086 3828 False 457.0 736 88.939000 545 2527 3 chr2B.!!$F7 1982
2 TraesCS2B01G569100 chr2B 759817808 759818499 691 False 241.0 241 74.684000 1083 1731 1 chr2B.!!$F3 648
3 TraesCS2B01G569100 chr2A 751546168 751548110 1942 False 925.0 1515 83.733000 543 2527 2 chr2A.!!$F3 1984
4 TraesCS2B01G569100 chr2D 620153099 620155093 1994 False 1045.0 1277 86.889000 531 2528 2 chr2D.!!$F4 1997
5 TraesCS2B01G569100 chr2D 620198943 620199500 557 False 283.0 283 77.249000 1083 1604 1 chr2D.!!$F1 521
6 TraesCS2B01G569100 chrUn 23147901 23151388 3487 True 622.0 736 87.724333 545 2527 3 chrUn.!!$R1 1982
7 TraesCS2B01G569100 chr6D 46438871 46439397 526 True 235.3 379 94.907000 1 426 2 chr6D.!!$R1 425

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
368 428 0.033504 ACTACCACTGGTGACAAGCG 59.966 55.0 11.32 0.0 42.06 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 4454 0.247814 GCATCCGCGTCAAGTTCATG 60.248 55.0 4.92 0.0 0.0 3.07 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
56 58 4.766404 ACTTTTCTTGAATAGGGCAACG 57.234 40.909 5.96 0.00 37.60 4.10
93 95 6.523676 TCATGAACTTTTTCCGAAATTTGC 57.476 33.333 0.00 0.00 0.00 3.68
100 102 5.231357 ACTTTTTCCGAAATTTGCGAAGTTC 59.769 36.000 15.40 15.40 36.71 3.01
132 134 6.930722 TCTTGCAGAAAATCATATATGAGCGA 59.069 34.615 19.73 14.43 40.64 4.93
149 151 6.612247 TGAGCGACTATGAAAGTTTTTCAA 57.388 33.333 8.16 0.00 39.07 2.69
167 169 8.699749 GTTTTTCAAGTATTAGCGCTCAATTTT 58.300 29.630 16.34 1.26 0.00 1.82
188 190 0.528017 TCAGTTGCAAAAACACGCCA 59.472 45.000 0.00 0.00 0.00 5.69
193 195 2.697431 TGCAAAAACACGCCATAGTC 57.303 45.000 0.00 0.00 0.00 2.59
219 221 2.674177 GCTGAACGCATGTAGGTAGTGT 60.674 50.000 0.00 0.00 38.92 3.55
225 227 2.286831 CGCATGTAGGTAGTGTAGGTCG 60.287 54.545 0.00 0.00 0.00 4.79
240 242 6.654161 AGTGTAGGTCGCGAGTTCTATATATT 59.346 38.462 10.24 0.00 0.00 1.28
314 374 6.015940 AGAGTGGTTTTCTAATTTCAAGCCAG 60.016 38.462 1.33 0.00 32.10 4.85
316 376 6.775629 AGTGGTTTTCTAATTTCAAGCCAGTA 59.224 34.615 5.76 0.00 33.89 2.74
337 397 2.594592 GGTCTTGGCGCAGTGGTT 60.595 61.111 10.83 0.00 0.00 3.67
338 398 2.639286 GTCTTGGCGCAGTGGTTG 59.361 61.111 10.83 0.00 0.00 3.77
361 421 2.628178 TCTGTTGAGACTACCACTGGTG 59.372 50.000 11.32 3.77 36.19 4.17
365 425 2.673258 TGAGACTACCACTGGTGACAA 58.327 47.619 11.32 0.00 42.06 3.18
368 428 0.033504 ACTACCACTGGTGACAAGCG 59.966 55.000 11.32 0.00 42.06 4.68
374 434 1.071471 CTGGTGACAAGCGGGTTCT 59.929 57.895 0.00 0.00 42.06 3.01
375 435 0.535102 CTGGTGACAAGCGGGTTCTT 60.535 55.000 0.00 0.00 42.06 2.52
376 436 0.106918 TGGTGACAAGCGGGTTCTTT 60.107 50.000 0.00 0.00 37.44 2.52
378 438 1.407618 GGTGACAAGCGGGTTCTTTTT 59.592 47.619 0.00 0.00 0.00 1.94
429 530 3.272334 CCCACTAGCGGCGCATTC 61.272 66.667 35.02 4.02 0.00 2.67
430 531 2.511373 CCACTAGCGGCGCATTCA 60.511 61.111 35.02 14.66 0.00 2.57
431 532 2.528743 CCACTAGCGGCGCATTCAG 61.529 63.158 35.02 24.72 0.00 3.02
432 533 2.892425 ACTAGCGGCGCATTCAGC 60.892 61.111 35.02 6.32 40.87 4.26
441 542 3.313750 GCATTCAGCGCCGAGTAG 58.686 61.111 2.29 0.00 0.00 2.57
442 543 2.240500 GCATTCAGCGCCGAGTAGG 61.241 63.158 2.29 0.00 44.97 3.18
443 544 1.437573 CATTCAGCGCCGAGTAGGA 59.562 57.895 2.29 0.00 45.00 2.94
444 545 0.596083 CATTCAGCGCCGAGTAGGAG 60.596 60.000 2.29 0.00 45.00 3.69
449 550 3.597728 CGCCGAGTAGGAGCTCCC 61.598 72.222 29.54 15.08 45.00 4.30
450 551 3.228017 GCCGAGTAGGAGCTCCCC 61.228 72.222 29.54 19.74 45.00 4.81
451 552 2.279073 CCGAGTAGGAGCTCCCCA 59.721 66.667 29.54 15.01 45.00 4.96
452 553 1.152440 CCGAGTAGGAGCTCCCCAT 60.152 63.158 29.54 15.03 45.00 4.00
453 554 1.182385 CCGAGTAGGAGCTCCCCATC 61.182 65.000 29.54 21.38 45.00 3.51
454 555 0.178975 CGAGTAGGAGCTCCCCATCT 60.179 60.000 29.54 20.45 36.42 2.90
455 556 1.627864 GAGTAGGAGCTCCCCATCTC 58.372 60.000 29.54 23.85 36.42 2.75
456 557 0.937441 AGTAGGAGCTCCCCATCTCA 59.063 55.000 29.54 3.09 36.42 3.27
457 558 1.133199 AGTAGGAGCTCCCCATCTCAG 60.133 57.143 29.54 0.00 36.42 3.35
458 559 1.133325 GTAGGAGCTCCCCATCTCAGA 60.133 57.143 29.54 0.65 36.42 3.27
459 560 0.105555 AGGAGCTCCCCATCTCAGAG 60.106 60.000 29.54 0.00 36.42 3.35
461 562 2.420890 GCTCCCCATCTCAGAGCG 59.579 66.667 0.00 0.00 43.18 5.03
462 563 3.136750 CTCCCCATCTCAGAGCGG 58.863 66.667 0.00 0.00 0.00 5.52
463 564 1.456518 CTCCCCATCTCAGAGCGGA 60.457 63.158 7.19 2.29 0.00 5.54
464 565 1.001631 TCCCCATCTCAGAGCGGAA 59.998 57.895 7.19 0.00 0.00 4.30
465 566 0.399091 TCCCCATCTCAGAGCGGAAT 60.399 55.000 7.19 0.00 0.00 3.01
466 567 0.034616 CCCCATCTCAGAGCGGAATC 59.965 60.000 7.19 0.00 0.00 2.52
467 568 0.319383 CCCATCTCAGAGCGGAATCG 60.319 60.000 7.19 0.00 39.81 3.34
477 578 4.798288 CGGAATCGCACGGTCTTA 57.202 55.556 0.00 0.00 0.00 2.10
478 579 3.038946 CGGAATCGCACGGTCTTAA 57.961 52.632 0.00 0.00 0.00 1.85
479 580 1.352114 CGGAATCGCACGGTCTTAAA 58.648 50.000 0.00 0.00 0.00 1.52
480 581 1.727880 CGGAATCGCACGGTCTTAAAA 59.272 47.619 0.00 0.00 0.00 1.52
481 582 2.350498 CGGAATCGCACGGTCTTAAAAT 59.650 45.455 0.00 0.00 0.00 1.82
482 583 3.543460 CGGAATCGCACGGTCTTAAAATC 60.543 47.826 0.00 0.00 0.00 2.17
483 584 3.543460 GGAATCGCACGGTCTTAAAATCG 60.543 47.826 0.00 0.00 0.00 3.34
484 585 2.350899 TCGCACGGTCTTAAAATCGA 57.649 45.000 0.00 0.00 0.00 3.59
485 586 1.987770 TCGCACGGTCTTAAAATCGAC 59.012 47.619 0.00 0.00 0.00 4.20
486 587 1.990563 CGCACGGTCTTAAAATCGACT 59.009 47.619 0.00 0.00 0.00 4.18
487 588 2.222508 CGCACGGTCTTAAAATCGACTG 60.223 50.000 0.00 0.00 41.24 3.51
488 589 2.991190 GCACGGTCTTAAAATCGACTGA 59.009 45.455 8.06 0.00 38.50 3.41
489 590 3.181533 GCACGGTCTTAAAATCGACTGAC 60.182 47.826 8.06 0.00 38.50 3.51
490 591 3.367025 CACGGTCTTAAAATCGACTGACC 59.633 47.826 8.06 0.00 38.50 4.02
491 592 2.928116 CGGTCTTAAAATCGACTGACCC 59.072 50.000 0.00 0.00 40.37 4.46
492 593 3.615592 CGGTCTTAAAATCGACTGACCCA 60.616 47.826 0.00 0.00 40.37 4.51
493 594 4.320870 GGTCTTAAAATCGACTGACCCAA 58.679 43.478 0.00 0.00 38.31 4.12
494 595 4.758165 GGTCTTAAAATCGACTGACCCAAA 59.242 41.667 0.00 0.00 38.31 3.28
495 596 5.239963 GGTCTTAAAATCGACTGACCCAAAA 59.760 40.000 0.00 0.00 38.31 2.44
496 597 6.371389 GTCTTAAAATCGACTGACCCAAAAG 58.629 40.000 0.00 0.00 0.00 2.27
497 598 6.204108 GTCTTAAAATCGACTGACCCAAAAGA 59.796 38.462 0.00 0.00 0.00 2.52
498 599 6.768861 TCTTAAAATCGACTGACCCAAAAGAA 59.231 34.615 0.00 0.00 0.00 2.52
499 600 7.447238 TCTTAAAATCGACTGACCCAAAAGAAT 59.553 33.333 0.00 0.00 0.00 2.40
500 601 6.405278 AAAATCGACTGACCCAAAAGAATT 57.595 33.333 0.00 0.00 0.00 2.17
501 602 6.405278 AAATCGACTGACCCAAAAGAATTT 57.595 33.333 0.00 0.00 42.41 1.82
523 624 2.669300 AGCTGACTGACATGTAGCTG 57.331 50.000 17.25 4.84 42.63 4.24
524 625 2.174360 AGCTGACTGACATGTAGCTGA 58.826 47.619 17.25 0.00 42.63 4.26
525 626 2.564504 AGCTGACTGACATGTAGCTGAA 59.435 45.455 17.25 0.00 42.63 3.02
526 627 2.928757 GCTGACTGACATGTAGCTGAAG 59.071 50.000 9.79 0.96 0.00 3.02
527 628 3.616076 GCTGACTGACATGTAGCTGAAGT 60.616 47.826 9.79 2.71 0.00 3.01
528 629 3.917988 TGACTGACATGTAGCTGAAGTG 58.082 45.455 0.00 0.00 0.00 3.16
529 630 3.321968 TGACTGACATGTAGCTGAAGTGT 59.678 43.478 0.00 0.00 0.00 3.55
538 639 8.396272 ACATGTAGCTGAAGTGTAAAGAAAAT 57.604 30.769 0.00 0.00 0.00 1.82
540 641 9.683069 CATGTAGCTGAAGTGTAAAGAAAATTT 57.317 29.630 0.00 0.00 0.00 1.82
548 649 9.130661 TGAAGTGTAAAGAAAATTTCAGGATCA 57.869 29.630 8.55 0.00 0.00 2.92
551 652 8.912988 AGTGTAAAGAAAATTTCAGGATCAACA 58.087 29.630 8.55 0.38 0.00 3.33
562 663 6.737720 TTCAGGATCAACATAGTAGCATCT 57.262 37.500 0.00 0.00 0.00 2.90
572 673 9.481340 TCAACATAGTAGCATCTAAATCATGAC 57.519 33.333 0.00 0.00 0.00 3.06
577 678 4.156455 AGCATCTAAATCATGACCGGTT 57.844 40.909 9.42 0.00 0.00 4.44
604 705 5.144359 GTCACGCAATGAACTCGTAATTTT 58.856 37.500 0.00 0.00 39.72 1.82
920 1071 1.664321 ATCGTCGCCCAGACCTACAC 61.664 60.000 0.00 0.00 46.92 2.90
988 1139 2.800544 CAACGATCTCTGTTGGTTTCGT 59.199 45.455 4.55 0.00 42.27 3.85
1017 1168 1.148273 GATGGCCGCCATGAAGGTA 59.852 57.895 29.86 0.00 45.26 3.08
1021 1172 0.385390 GGCCGCCATGAAGGTAATTG 59.615 55.000 3.91 0.00 40.61 2.32
1033 1184 2.076863 AGGTAATTGCTTGCAGTCGAC 58.923 47.619 7.70 7.70 0.00 4.20
1038 1189 1.495584 TTGCTTGCAGTCGACCGAAC 61.496 55.000 13.01 0.00 0.00 3.95
1043 1194 2.261671 CAGTCGACCGAACTGGGG 59.738 66.667 13.01 0.00 44.64 4.96
1058 1209 1.205893 CTGGGGTTTCTCTCCTCTTCG 59.794 57.143 0.00 0.00 37.63 3.79
1063 1214 3.431068 GGGTTTCTCTCCTCTTCGGATTC 60.431 52.174 0.00 0.00 42.12 2.52
1115 1266 2.570442 TTTGTTCTTTGACGGTTGCC 57.430 45.000 0.00 0.00 0.00 4.52
1116 1267 0.741915 TTGTTCTTTGACGGTTGCCC 59.258 50.000 0.00 0.00 0.00 5.36
1126 1277 1.178534 ACGGTTGCCCAATTCAGGTG 61.179 55.000 0.00 0.00 0.00 4.00
1195 1346 4.148825 GTGGTCTCCGCGCTCCAT 62.149 66.667 5.56 0.00 32.45 3.41
1249 3471 3.778618 CTCTGCTTCGTCTTGATCATGA 58.221 45.455 7.19 7.19 0.00 3.07
1254 3476 3.715495 CTTCGTCTTGATCATGAGGGAG 58.285 50.000 23.33 21.43 0.00 4.30
1283 3508 4.577693 CGGTCATCCATGTCTGAATTTGAT 59.422 41.667 0.00 0.00 0.00 2.57
1338 3570 0.318784 GGATAGACCACATCGCCGTC 60.319 60.000 0.00 0.00 38.79 4.79
1473 3738 2.355481 GACAAGAACGACGCGGGT 60.355 61.111 12.47 4.12 0.00 5.28
1655 3969 0.750249 TTCCTGCTTGCCGATCGATA 59.250 50.000 18.66 1.36 0.00 2.92
1658 3972 1.143305 CTGCTTGCCGATCGATAAGG 58.857 55.000 18.66 13.44 0.00 2.69
1669 3983 1.776662 TCGATAAGGCTACCTGCACT 58.223 50.000 0.00 0.00 45.15 4.40
1734 4053 3.554692 GAGTTGCGCCGGTGATCG 61.555 66.667 21.76 7.07 38.88 3.69
1789 4110 6.652900 TGTGCATCTGCTTAGTTTGTAATGTA 59.347 34.615 3.53 0.00 42.66 2.29
1792 4113 7.174080 TGCATCTGCTTAGTTTGTAATGTACAA 59.826 33.333 0.00 0.00 43.24 2.41
1861 4221 6.090129 TCAAGTTGTTACAAGAAAAGTGTGC 58.910 36.000 0.00 0.00 0.00 4.57
1865 4225 5.484173 TGTTACAAGAAAAGTGTGCAGAG 57.516 39.130 0.00 0.00 0.00 3.35
1869 4229 2.262423 AGAAAAGTGTGCAGAGGGAC 57.738 50.000 0.00 0.00 35.66 4.46
1887 4247 2.615912 GGACCAGATAGAATTGCTGCAC 59.384 50.000 0.00 0.00 0.00 4.57
1930 4295 8.442632 TTGATGGATTGATCTTCAATAGTGAC 57.557 34.615 2.87 0.00 46.20 3.67
1977 4342 0.959372 GCACAGCTGCTCATCCAGTT 60.959 55.000 15.27 0.00 40.63 3.16
1987 4352 4.401022 TGCTCATCCAGTTTTCAGTTGAT 58.599 39.130 0.00 0.00 0.00 2.57
1988 4353 4.216902 TGCTCATCCAGTTTTCAGTTGATG 59.783 41.667 0.00 0.00 0.00 3.07
2009 4374 9.895138 TTGATGATCTGAATAGAAAGTTGATGA 57.105 29.630 0.00 0.00 36.32 2.92
2075 4446 2.202395 GCAAAACCAGCCTGCCAGA 61.202 57.895 0.00 0.00 0.00 3.86
2083 4454 1.303155 AGCCTGCCAGAGTTCAAGC 60.303 57.895 0.00 0.00 0.00 4.01
2256 4633 3.444034 CGGACAACTAGATTGGTCTCTCA 59.556 47.826 0.00 0.00 43.20 3.27
2260 4637 4.469227 ACAACTAGATTGGTCTCTCATGCT 59.531 41.667 0.00 0.00 43.20 3.79
2278 4655 9.023962 TCTCATGCTTCTTTACATTTACCAATT 57.976 29.630 0.00 0.00 0.00 2.32
2286 4663 9.974980 TTCTTTACATTTACCAATTGAAACTCC 57.025 29.630 7.12 0.00 0.00 3.85
2298 4675 2.846193 TGAAACTCCGAACTCCAAAGG 58.154 47.619 0.00 0.00 0.00 3.11
2411 4795 5.801350 ACTCATGTATGTTTTCATCGGTG 57.199 39.130 0.00 0.00 41.25 4.94
2412 4796 4.094887 ACTCATGTATGTTTTCATCGGTGC 59.905 41.667 0.00 0.00 41.25 5.01
2413 4797 3.063316 TCATGTATGTTTTCATCGGTGCG 59.937 43.478 0.00 0.00 41.25 5.34
2414 4798 2.689646 TGTATGTTTTCATCGGTGCGA 58.310 42.857 0.00 0.00 41.25 5.10
2415 4799 2.413796 TGTATGTTTTCATCGGTGCGAC 59.586 45.455 0.00 0.00 39.18 5.19
2416 4800 0.802494 ATGTTTTCATCGGTGCGACC 59.198 50.000 0.00 0.00 39.18 4.79
2528 4913 6.316390 GCTGCTCCAACTACACATAGTATTTT 59.684 38.462 0.00 0.00 41.00 1.82
2529 4914 7.494625 GCTGCTCCAACTACACATAGTATTTTA 59.505 37.037 0.00 0.00 41.00 1.52
2530 4915 9.547753 CTGCTCCAACTACACATAGTATTTTAT 57.452 33.333 0.00 0.00 41.00 1.40
2531 4916 9.899661 TGCTCCAACTACACATAGTATTTTATT 57.100 29.630 0.00 0.00 41.00 1.40
2534 4919 9.037737 TCCAACTACACATAGTATTTTATTCGC 57.962 33.333 0.00 0.00 41.00 4.70
2535 4920 8.822855 CCAACTACACATAGTATTTTATTCGCA 58.177 33.333 0.00 0.00 41.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 17 9.753669 GAAAAGTTCAATGATTTTGAAAAACGT 57.246 25.926 2.58 0.00 39.76 3.99
93 95 4.858935 TCTGCAAGAAAAATGGAACTTCG 58.141 39.130 0.00 0.00 42.31 3.79
167 169 1.996191 GGCGTGTTTTTGCAACTGAAA 59.004 42.857 0.00 0.00 0.00 2.69
219 221 5.942236 ACCAATATATAGAACTCGCGACCTA 59.058 40.000 3.71 7.66 0.00 3.08
225 227 9.037737 TGTTTTGTACCAATATATAGAACTCGC 57.962 33.333 0.00 0.00 0.00 5.03
240 242 9.781633 ACACTAACATATACTTGTTTTGTACCA 57.218 29.630 0.00 0.00 40.25 3.25
273 333 6.847421 ACCACTCTATTTAGTACTTCCGTT 57.153 37.500 0.00 0.00 0.00 4.44
294 354 6.208797 ACCTACTGGCTTGAAATTAGAAAACC 59.791 38.462 0.00 0.00 36.63 3.27
307 367 1.611673 CCAAGACCACCTACTGGCTTG 60.612 57.143 12.72 12.72 45.32 4.01
309 369 1.842381 GCCAAGACCACCTACTGGCT 61.842 60.000 4.16 0.00 45.32 4.75
310 370 1.377333 GCCAAGACCACCTACTGGC 60.377 63.158 0.00 0.00 45.32 4.85
314 374 1.741770 CTGCGCCAAGACCACCTAC 60.742 63.158 4.18 0.00 0.00 3.18
316 376 3.560251 ACTGCGCCAAGACCACCT 61.560 61.111 4.18 0.00 0.00 4.00
337 397 2.297315 CAGTGGTAGTCTCAACAGAGCA 59.703 50.000 0.00 0.00 0.00 4.26
338 398 2.353208 CCAGTGGTAGTCTCAACAGAGC 60.353 54.545 0.00 0.00 0.00 4.09
361 421 1.924629 GCGAAAAAGAACCCGCTTGTC 60.925 52.381 0.00 0.00 43.75 3.18
365 425 1.838568 GACGCGAAAAAGAACCCGCT 61.839 55.000 15.93 0.00 44.77 5.52
368 428 0.385598 GCAGACGCGAAAAAGAACCC 60.386 55.000 15.93 0.00 0.00 4.11
374 434 3.138205 TCAAAAAGCAGACGCGAAAAA 57.862 38.095 15.93 0.00 45.49 1.94
375 435 2.834574 TCAAAAAGCAGACGCGAAAA 57.165 40.000 15.93 0.00 45.49 2.29
376 436 2.096819 ACTTCAAAAAGCAGACGCGAAA 59.903 40.909 15.93 0.00 45.49 3.46
378 438 1.295792 ACTTCAAAAAGCAGACGCGA 58.704 45.000 15.93 0.00 45.49 5.87
424 525 2.240500 CCTACTCGGCGCTGAATGC 61.241 63.158 21.34 0.00 38.57 3.56
425 526 0.596083 CTCCTACTCGGCGCTGAATG 60.596 60.000 21.34 12.21 0.00 2.67
426 527 1.736586 CTCCTACTCGGCGCTGAAT 59.263 57.895 21.34 13.75 0.00 2.57
427 528 3.064987 GCTCCTACTCGGCGCTGAA 62.065 63.158 21.34 5.30 40.41 3.02
428 529 3.518998 GCTCCTACTCGGCGCTGA 61.519 66.667 19.73 19.73 40.41 4.26
431 532 4.273257 GGAGCTCCTACTCGGCGC 62.273 72.222 26.25 0.00 43.98 6.53
432 533 3.597728 GGGAGCTCCTACTCGGCG 61.598 72.222 31.36 0.00 37.57 6.46
433 534 3.228017 GGGGAGCTCCTACTCGGC 61.228 72.222 31.36 13.25 37.57 5.54
434 535 1.152440 ATGGGGAGCTCCTACTCGG 60.152 63.158 31.36 0.00 37.57 4.63
435 536 0.178975 AGATGGGGAGCTCCTACTCG 60.179 60.000 31.36 0.00 37.57 4.18
436 537 1.133325 TGAGATGGGGAGCTCCTACTC 60.133 57.143 31.36 28.03 35.95 2.59
437 538 0.937441 TGAGATGGGGAGCTCCTACT 59.063 55.000 31.36 22.78 35.95 2.57
438 539 1.133325 TCTGAGATGGGGAGCTCCTAC 60.133 57.143 31.36 23.77 35.95 3.18
439 540 1.146774 CTCTGAGATGGGGAGCTCCTA 59.853 57.143 31.36 20.96 35.95 2.94
440 541 0.105555 CTCTGAGATGGGGAGCTCCT 60.106 60.000 31.36 13.11 35.95 3.69
441 542 1.757423 GCTCTGAGATGGGGAGCTCC 61.757 65.000 25.59 25.59 46.04 4.70
442 543 1.747774 GCTCTGAGATGGGGAGCTC 59.252 63.158 9.28 4.71 46.04 4.09
443 544 2.132996 CGCTCTGAGATGGGGAGCT 61.133 63.158 9.28 0.00 46.96 4.09
444 545 2.420890 CGCTCTGAGATGGGGAGC 59.579 66.667 9.28 0.00 46.06 4.70
445 546 1.045350 TTCCGCTCTGAGATGGGGAG 61.045 60.000 9.28 0.00 44.23 4.30
446 547 0.399091 ATTCCGCTCTGAGATGGGGA 60.399 55.000 9.28 11.62 42.35 4.81
447 548 0.034616 GATTCCGCTCTGAGATGGGG 59.965 60.000 9.28 3.68 37.59 4.96
448 549 0.319383 CGATTCCGCTCTGAGATGGG 60.319 60.000 9.28 6.20 0.00 4.00
449 550 3.191903 CGATTCCGCTCTGAGATGG 57.808 57.895 9.28 9.35 0.00 3.51
460 561 1.352114 TTTAAGACCGTGCGATTCCG 58.648 50.000 0.00 0.00 39.16 4.30
461 562 3.543460 CGATTTTAAGACCGTGCGATTCC 60.543 47.826 0.00 0.00 0.00 3.01
462 563 3.305094 TCGATTTTAAGACCGTGCGATTC 59.695 43.478 0.00 0.00 0.00 2.52
463 564 3.061697 GTCGATTTTAAGACCGTGCGATT 59.938 43.478 0.00 0.00 0.00 3.34
464 565 2.601763 GTCGATTTTAAGACCGTGCGAT 59.398 45.455 0.00 0.00 0.00 4.58
465 566 1.987770 GTCGATTTTAAGACCGTGCGA 59.012 47.619 0.00 0.00 0.00 5.10
466 567 1.990563 AGTCGATTTTAAGACCGTGCG 59.009 47.619 0.00 0.00 38.08 5.34
467 568 2.991190 TCAGTCGATTTTAAGACCGTGC 59.009 45.455 0.00 0.00 38.08 5.34
468 569 3.367025 GGTCAGTCGATTTTAAGACCGTG 59.633 47.826 0.00 0.00 36.55 4.94
469 570 3.582780 GGTCAGTCGATTTTAAGACCGT 58.417 45.455 0.00 0.00 36.55 4.83
470 571 2.928116 GGGTCAGTCGATTTTAAGACCG 59.072 50.000 8.45 0.00 44.89 4.79
471 572 3.934068 TGGGTCAGTCGATTTTAAGACC 58.066 45.455 6.61 6.61 43.60 3.85
472 573 5.934935 TTTGGGTCAGTCGATTTTAAGAC 57.065 39.130 0.00 0.00 37.63 3.01
473 574 6.292923 TCTTTTGGGTCAGTCGATTTTAAGA 58.707 36.000 0.00 0.00 0.00 2.10
474 575 6.554334 TCTTTTGGGTCAGTCGATTTTAAG 57.446 37.500 0.00 0.00 0.00 1.85
475 576 6.945938 TTCTTTTGGGTCAGTCGATTTTAA 57.054 33.333 0.00 0.00 0.00 1.52
476 577 7.519032 AATTCTTTTGGGTCAGTCGATTTTA 57.481 32.000 0.00 0.00 0.00 1.52
477 578 6.405278 AATTCTTTTGGGTCAGTCGATTTT 57.595 33.333 0.00 0.00 0.00 1.82
478 579 6.405278 AAATTCTTTTGGGTCAGTCGATTT 57.595 33.333 0.00 0.00 0.00 2.17
479 580 6.040391 TGAAAATTCTTTTGGGTCAGTCGATT 59.960 34.615 0.00 0.00 31.94 3.34
480 581 5.534654 TGAAAATTCTTTTGGGTCAGTCGAT 59.465 36.000 0.00 0.00 31.94 3.59
481 582 4.884744 TGAAAATTCTTTTGGGTCAGTCGA 59.115 37.500 0.00 0.00 31.94 4.20
482 583 5.181690 TGAAAATTCTTTTGGGTCAGTCG 57.818 39.130 0.00 0.00 31.94 4.18
483 584 4.984785 GCTGAAAATTCTTTTGGGTCAGTC 59.015 41.667 0.00 0.00 33.02 3.51
484 585 4.651045 AGCTGAAAATTCTTTTGGGTCAGT 59.349 37.500 0.00 0.00 33.02 3.41
485 586 4.986659 CAGCTGAAAATTCTTTTGGGTCAG 59.013 41.667 8.42 0.00 33.35 3.51
486 587 4.648762 TCAGCTGAAAATTCTTTTGGGTCA 59.351 37.500 15.67 0.00 31.94 4.02
487 588 4.984785 GTCAGCTGAAAATTCTTTTGGGTC 59.015 41.667 20.19 0.00 31.94 4.46
488 589 4.651045 AGTCAGCTGAAAATTCTTTTGGGT 59.349 37.500 20.19 0.00 31.94 4.51
489 590 4.986659 CAGTCAGCTGAAAATTCTTTTGGG 59.013 41.667 20.19 0.00 45.28 4.12
503 604 2.669300 AGCTACATGTCAGTCAGCTG 57.331 50.000 17.25 7.63 40.92 4.24
504 605 2.174360 TCAGCTACATGTCAGTCAGCT 58.826 47.619 13.19 13.19 43.16 4.24
505 606 2.662006 TCAGCTACATGTCAGTCAGC 57.338 50.000 0.00 5.39 0.00 4.26
506 607 3.925299 CACTTCAGCTACATGTCAGTCAG 59.075 47.826 0.00 0.00 0.00 3.51
507 608 3.321968 ACACTTCAGCTACATGTCAGTCA 59.678 43.478 0.00 0.00 0.00 3.41
508 609 3.919216 ACACTTCAGCTACATGTCAGTC 58.081 45.455 0.00 0.00 0.00 3.51
509 610 5.468540 TTACACTTCAGCTACATGTCAGT 57.531 39.130 0.00 0.00 0.00 3.41
510 611 6.159293 TCTTTACACTTCAGCTACATGTCAG 58.841 40.000 0.00 0.00 0.00 3.51
511 612 6.096673 TCTTTACACTTCAGCTACATGTCA 57.903 37.500 0.00 0.00 0.00 3.58
512 613 7.421530 TTTCTTTACACTTCAGCTACATGTC 57.578 36.000 0.00 0.00 0.00 3.06
513 614 7.801716 TTTTCTTTACACTTCAGCTACATGT 57.198 32.000 2.69 2.69 0.00 3.21
514 615 9.683069 AAATTTTCTTTACACTTCAGCTACATG 57.317 29.630 0.00 0.00 0.00 3.21
515 616 9.899226 GAAATTTTCTTTACACTTCAGCTACAT 57.101 29.630 1.79 0.00 0.00 2.29
516 617 8.898761 TGAAATTTTCTTTACACTTCAGCTACA 58.101 29.630 10.33 0.00 0.00 2.74
517 618 9.387123 CTGAAATTTTCTTTACACTTCAGCTAC 57.613 33.333 10.33 0.00 33.95 3.58
518 619 8.567948 CCTGAAATTTTCTTTACACTTCAGCTA 58.432 33.333 10.33 0.00 37.86 3.32
519 620 7.285401 TCCTGAAATTTTCTTTACACTTCAGCT 59.715 33.333 10.33 0.00 37.86 4.24
520 621 7.425606 TCCTGAAATTTTCTTTACACTTCAGC 58.574 34.615 10.33 0.00 37.86 4.26
521 622 9.617975 GATCCTGAAATTTTCTTTACACTTCAG 57.382 33.333 10.33 0.00 38.55 3.02
522 623 9.130661 TGATCCTGAAATTTTCTTTACACTTCA 57.869 29.630 10.33 1.56 0.00 3.02
523 624 9.965824 TTGATCCTGAAATTTTCTTTACACTTC 57.034 29.630 10.33 0.00 0.00 3.01
524 625 9.750125 GTTGATCCTGAAATTTTCTTTACACTT 57.250 29.630 10.33 0.00 0.00 3.16
525 626 8.912988 TGTTGATCCTGAAATTTTCTTTACACT 58.087 29.630 10.33 0.00 0.00 3.55
526 627 9.696917 ATGTTGATCCTGAAATTTTCTTTACAC 57.303 29.630 10.33 0.79 0.00 2.90
538 639 7.129457 AGATGCTACTATGTTGATCCTGAAA 57.871 36.000 0.00 0.00 0.00 2.69
540 641 7.839680 TTAGATGCTACTATGTTGATCCTGA 57.160 36.000 0.00 0.00 0.00 3.86
548 649 7.600375 CGGTCATGATTTAGATGCTACTATGTT 59.400 37.037 0.00 0.00 0.00 2.71
551 652 6.211584 ACCGGTCATGATTTAGATGCTACTAT 59.788 38.462 0.00 0.00 0.00 2.12
562 663 3.244596 TGACACCAACCGGTCATGATTTA 60.245 43.478 8.04 0.00 44.71 1.40
572 673 2.258013 ATTGCGTGACACCAACCGG 61.258 57.895 0.00 0.00 38.77 5.28
577 678 1.225855 GAGTTCATTGCGTGACACCA 58.774 50.000 0.00 0.00 36.32 4.17
604 705 2.304221 TGGTCGGAGAAAAGAGAGGA 57.696 50.000 0.00 0.00 39.69 3.71
647 748 2.388232 CGCGTGGTTAGGCAGGAAC 61.388 63.158 0.00 0.00 37.55 3.62
944 1095 0.906775 TAGGAATGGTGGGACGGAAC 59.093 55.000 0.00 0.00 0.00 3.62
988 1139 1.451207 CGGCCATCGGTCCAAATGA 60.451 57.895 2.24 0.00 34.75 2.57
1017 1168 0.602638 TCGGTCGACTGCAAGCAATT 60.603 50.000 19.89 0.00 37.60 2.32
1021 1172 1.664965 AGTTCGGTCGACTGCAAGC 60.665 57.895 19.89 5.68 37.60 4.01
1033 1184 0.036294 GGAGAGAAACCCCAGTTCGG 60.036 60.000 0.00 0.00 34.19 4.30
1038 1189 1.205893 CGAAGAGGAGAGAAACCCCAG 59.794 57.143 0.00 0.00 0.00 4.45
1063 1214 3.197790 CCGGCCGTCTGCAATCAG 61.198 66.667 26.12 0.00 43.89 2.90
1115 1266 1.619654 TTCAGCACCACCTGAATTGG 58.380 50.000 0.81 0.00 44.49 3.16
1126 1277 2.031163 ACGTCCAGCTTCAGCACC 59.969 61.111 0.75 0.00 45.16 5.01
1195 1346 4.695606 AGAGAAACAGGGGATTACTACCA 58.304 43.478 0.00 0.00 0.00 3.25
1249 3471 1.343069 GGATGACCGCTAATCTCCCT 58.657 55.000 0.00 0.00 0.00 4.20
1254 3476 3.062763 CAGACATGGATGACCGCTAATC 58.937 50.000 0.00 0.00 39.42 1.75
1283 3508 4.261741 GGGTTGTTGTCGTCAGAACTAGTA 60.262 45.833 0.00 0.00 0.00 1.82
1323 3555 3.060000 TCGACGGCGATGTGGTCT 61.060 61.111 10.67 0.00 42.51 3.85
1338 3570 5.226396 GTCATCTTCTGGTCCTTCATATCG 58.774 45.833 0.00 0.00 0.00 2.92
1341 3573 3.384789 CCGTCATCTTCTGGTCCTTCATA 59.615 47.826 0.00 0.00 0.00 2.15
1655 3969 1.127567 TCACCAGTGCAGGTAGCCTT 61.128 55.000 0.00 0.00 44.83 4.35
1658 3972 0.250234 TGATCACCAGTGCAGGTAGC 59.750 55.000 0.00 0.00 40.77 3.58
1669 3983 3.047280 GCACGCCGTTGATCACCA 61.047 61.111 0.00 0.00 0.00 4.17
1804 4125 9.959749 TCCTTTTTGAACAACATACTGTAATTC 57.040 29.630 0.00 0.00 0.00 2.17
1809 4130 9.313118 GATTTTCCTTTTTGAACAACATACTGT 57.687 29.630 0.00 0.00 0.00 3.55
1810 4131 9.311916 TGATTTTCCTTTTTGAACAACATACTG 57.688 29.630 0.00 0.00 0.00 2.74
1824 4145 9.883142 TTGTAACAACTTGATGATTTTCCTTTT 57.117 25.926 0.00 0.00 0.00 2.27
1848 4169 2.291741 GTCCCTCTGCACACTTTTCTTG 59.708 50.000 0.00 0.00 0.00 3.02
1861 4221 3.390639 AGCAATTCTATCTGGTCCCTCTG 59.609 47.826 0.00 0.00 0.00 3.35
1865 4225 2.225467 GCAGCAATTCTATCTGGTCCC 58.775 52.381 0.00 0.00 0.00 4.46
1869 4229 6.630444 AATAAGTGCAGCAATTCTATCTGG 57.370 37.500 12.20 0.00 0.00 3.86
1968 4333 6.373495 CAGATCATCAACTGAAAACTGGATGA 59.627 38.462 0.00 0.00 43.46 2.92
2009 4374 5.465724 GTGTGCTTAGTTTGCAGTAGTACTT 59.534 40.000 0.00 0.00 41.41 2.24
2067 4438 0.809385 CATGCTTGAACTCTGGCAGG 59.191 55.000 15.73 8.05 38.11 4.85
2083 4454 0.247814 GCATCCGCGTCAAGTTCATG 60.248 55.000 4.92 0.00 0.00 3.07
2120 4497 5.983540 AGTAGAGCCGAAGAATCTGAAATT 58.016 37.500 0.00 0.00 0.00 1.82
2256 4633 9.995003 TTTCAATTGGTAAATGTAAAGAAGCAT 57.005 25.926 5.42 0.00 0.00 3.79
2260 4637 9.974980 GGAGTTTCAATTGGTAAATGTAAAGAA 57.025 29.630 5.42 0.00 0.00 2.52
2278 4655 2.171870 ACCTTTGGAGTTCGGAGTTTCA 59.828 45.455 0.00 0.00 0.00 2.69
2286 4663 2.093447 AGCTGGATACCTTTGGAGTTCG 60.093 50.000 0.00 0.00 0.00 3.95
2298 4675 1.415659 AGATGGAGCACAGCTGGATAC 59.584 52.381 19.93 7.20 45.73 2.24
2411 4795 3.332493 TTAGGACTCGCACGGTCGC 62.332 63.158 0.00 0.00 34.82 5.19
2412 4796 1.513586 GTTAGGACTCGCACGGTCG 60.514 63.158 0.00 0.00 34.82 4.79
2413 4797 0.731855 GTGTTAGGACTCGCACGGTC 60.732 60.000 0.00 3.90 0.00 4.79
2414 4798 1.288127 GTGTTAGGACTCGCACGGT 59.712 57.895 0.00 0.00 0.00 4.83
2415 4799 0.108804 ATGTGTTAGGACTCGCACGG 60.109 55.000 0.00 0.00 34.86 4.94
2416 4800 0.992072 CATGTGTTAGGACTCGCACG 59.008 55.000 0.00 0.00 34.86 5.34
2417 4801 2.363788 TCATGTGTTAGGACTCGCAC 57.636 50.000 0.00 0.00 0.00 5.34
2418 4802 3.610040 AATCATGTGTTAGGACTCGCA 57.390 42.857 0.00 0.00 0.00 5.10
2419 4803 3.486108 CGTAATCATGTGTTAGGACTCGC 59.514 47.826 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.