Multiple sequence alignment - TraesCS3A01G242000

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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 TraesCS3A01G242000 chr3A 100.000 5277 0 0 1 5277 454176481 454171205 0.000000e+00 9745
1 TraesCS3A01G242000 chr3A 82.936 545 53 18 1 511 643177064 643177602 6.230000e-124 455
2 TraesCS3A01G242000 chr3D 94.831 3173 116 24 556 3723 336840220 336837091 0.000000e+00 4907
3 TraesCS3A01G242000 chr3D 95.380 736 29 3 3710 4441 336832812 336832078 0.000000e+00 1166
4 TraesCS3A01G242000 chr3D 89.163 729 52 13 4425 5128 336832065 336831339 0.000000e+00 883
5 TraesCS3A01G242000 chr3D 91.824 159 10 3 5119 5277 336831318 336831163 8.900000e-53 219
6 TraesCS3A01G242000 chr3B 95.491 2218 78 13 556 2768 434673833 434671633 0.000000e+00 3522
7 TraesCS3A01G242000 chr3B 94.363 958 38 6 2948 3891 434670960 434670005 0.000000e+00 1456
8 TraesCS3A01G242000 chr3B 91.754 861 58 7 4425 5277 434669479 434668624 0.000000e+00 1184
9 TraesCS3A01G242000 chr3B 95.278 360 15 2 3876 4234 434669992 434669634 2.130000e-158 569
10 TraesCS3A01G242000 chr3B 98.630 73 1 0 4369 4441 434669564 434669492 4.290000e-26 130
11 TraesCS3A01G242000 chr7D 86.000 550 41 11 1 515 271756883 271757431 1.660000e-154 556
12 TraesCS3A01G242000 chr4A 85.660 530 60 9 1 515 471006282 471006810 1.290000e-150 544
13 TraesCS3A01G242000 chr4A 90.411 292 21 3 1 292 660682968 660683252 1.390000e-100 377
14 TraesCS3A01G242000 chr1A 85.929 533 48 14 1 515 232332748 232332225 1.290000e-150 544
15 TraesCS3A01G242000 chr7A 83.992 531 48 13 1 504 324941476 324941996 4.780000e-130 475
16 TraesCS3A01G242000 chr7A 86.638 232 28 3 284 513 708491486 708491716 2.440000e-63 254
17 TraesCS3A01G242000 chr2D 83.303 545 50 14 1 511 512454457 512453920 1.040000e-126 464
18 TraesCS3A01G242000 chr1B 82.385 545 59 15 1 514 642486668 642486130 1.740000e-119 440
19 TraesCS3A01G242000 chr1B 81.901 547 57 22 3 515 604626049 604626587 1.760000e-114 424
20 TraesCS3A01G242000 chr2B 91.034 290 20 2 1 290 117697363 117697646 2.300000e-103 387
21 TraesCS3A01G242000 chr1D 91.342 231 16 2 284 511 218271681 218271910 3.970000e-81 313
22 TraesCS3A01G242000 chr5A 88.511 235 23 3 284 516 690019911 690019679 1.120000e-71 281
23 TraesCS3A01G242000 chr5B 87.607 234 26 2 284 515 233443328 233443560 8.710000e-68 268
24 TraesCS3A01G242000 chr6B 86.638 232 28 1 285 513 207432171 207431940 2.440000e-63 254


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 TraesCS3A01G242000 chr3A 454171205 454176481 5276 True 9745.0 9745 100.000000 1 5277 1 chr3A.!!$R1 5276
1 TraesCS3A01G242000 chr3A 643177064 643177602 538 False 455.0 455 82.936000 1 511 1 chr3A.!!$F1 510
2 TraesCS3A01G242000 chr3D 336837091 336840220 3129 True 4907.0 4907 94.831000 556 3723 1 chr3D.!!$R1 3167
3 TraesCS3A01G242000 chr3D 336831163 336832812 1649 True 756.0 1166 92.122333 3710 5277 3 chr3D.!!$R2 1567
4 TraesCS3A01G242000 chr3B 434668624 434673833 5209 True 1372.2 3522 95.103200 556 5277 5 chr3B.!!$R1 4721
5 TraesCS3A01G242000 chr7D 271756883 271757431 548 False 556.0 556 86.000000 1 515 1 chr7D.!!$F1 514
6 TraesCS3A01G242000 chr4A 471006282 471006810 528 False 544.0 544 85.660000 1 515 1 chr4A.!!$F1 514
7 TraesCS3A01G242000 chr1A 232332225 232332748 523 True 544.0 544 85.929000 1 515 1 chr1A.!!$R1 514
8 TraesCS3A01G242000 chr7A 324941476 324941996 520 False 475.0 475 83.992000 1 504 1 chr7A.!!$F1 503
9 TraesCS3A01G242000 chr2D 512453920 512454457 537 True 464.0 464 83.303000 1 511 1 chr2D.!!$R1 510
10 TraesCS3A01G242000 chr1B 642486130 642486668 538 True 440.0 440 82.385000 1 514 1 chr1B.!!$R1 513
11 TraesCS3A01G242000 chr1B 604626049 604626587 538 False 424.0 424 81.901000 3 515 1 chr1B.!!$F1 512

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
922 980 0.398696 ACACGCCCACTGGTAAATCA 59.601 50.000 0.0 0.0 0.00 2.57 F
2326 2388 0.823460 AAAGCACCAACACAACCCAG 59.177 50.000 0.0 0.0 0.00 4.45 F
3034 3588 1.140589 CACTGGAGCAGGTAGAGCG 59.859 63.158 0.0 0.0 35.51 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 2570 0.623723 ATGGTCATAAGCGGGTGGTT 59.376 50.0 0.0 0.0 39.56 3.67 R
3828 4393 0.698238 AACTGTGCAGCCCCAAGATA 59.302 50.0 0.0 0.0 0.00 1.98 R
4441 5040 0.531657 TTGCAATACCATGCTGTGCC 59.468 50.0 0.0 0.0 46.54 5.01 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
186 198 2.462782 CGACTCCTCCGACTCCGAC 61.463 68.421 0.00 0.00 38.22 4.79
187 199 1.078285 GACTCCTCCGACTCCGACT 60.078 63.158 0.00 0.00 38.22 4.18
188 200 1.078285 ACTCCTCCGACTCCGACTC 60.078 63.158 0.00 0.00 38.22 3.36
189 201 1.820481 CTCCTCCGACTCCGACTCC 60.820 68.421 0.00 0.00 38.22 3.85
190 202 3.203412 CCTCCGACTCCGACTCCG 61.203 72.222 0.00 0.00 38.22 4.63
191 203 2.125229 CTCCGACTCCGACTCCGA 60.125 66.667 0.00 0.00 38.22 4.55
229 244 3.827898 GCTACCGCACGAGCTCCT 61.828 66.667 8.47 0.00 39.10 3.69
431 481 1.418342 GCTCTGTCGCCGCGATTTTA 61.418 55.000 20.03 5.37 38.42 1.52
451 501 2.188829 GCCTGCATAAGCGCCATCA 61.189 57.895 2.29 0.00 46.23 3.07
493 547 2.178273 GTTCGGCGAAATGTGGGC 59.822 61.111 25.48 6.13 0.00 5.36
511 565 3.028130 GGGCTCTGCTAGAGTTACTCTT 58.972 50.000 20.59 5.00 44.12 2.85
515 569 5.450826 GGCTCTGCTAGAGTTACTCTTAACC 60.451 48.000 20.59 8.89 44.12 2.85
516 570 5.450826 GCTCTGCTAGAGTTACTCTTAACCC 60.451 48.000 20.59 5.54 44.12 4.11
517 571 4.954826 TCTGCTAGAGTTACTCTTAACCCC 59.045 45.833 20.59 3.94 41.50 4.95
518 572 4.028825 TGCTAGAGTTACTCTTAACCCCC 58.971 47.826 20.59 2.67 41.50 5.40
519 573 3.067883 GCTAGAGTTACTCTTAACCCCCG 59.932 52.174 20.59 1.30 41.50 5.73
520 574 3.181393 AGAGTTACTCTTAACCCCCGT 57.819 47.619 9.37 0.00 37.60 5.28
521 575 4.322057 AGAGTTACTCTTAACCCCCGTA 57.678 45.455 9.37 0.00 37.60 4.02
522 576 4.876580 AGAGTTACTCTTAACCCCCGTAT 58.123 43.478 9.37 0.00 37.60 3.06
523 577 4.892345 AGAGTTACTCTTAACCCCCGTATC 59.108 45.833 9.37 0.00 37.60 2.24
524 578 4.613437 AGTTACTCTTAACCCCCGTATCA 58.387 43.478 0.00 0.00 38.79 2.15
525 579 5.214293 AGTTACTCTTAACCCCCGTATCAT 58.786 41.667 0.00 0.00 38.79 2.45
526 580 5.303845 AGTTACTCTTAACCCCCGTATCATC 59.696 44.000 0.00 0.00 38.79 2.92
527 581 2.970640 ACTCTTAACCCCCGTATCATCC 59.029 50.000 0.00 0.00 0.00 3.51
528 582 2.969950 CTCTTAACCCCCGTATCATCCA 59.030 50.000 0.00 0.00 0.00 3.41
529 583 3.386063 TCTTAACCCCCGTATCATCCAA 58.614 45.455 0.00 0.00 0.00 3.53
530 584 3.135167 TCTTAACCCCCGTATCATCCAAC 59.865 47.826 0.00 0.00 0.00 3.77
531 585 1.291109 AACCCCCGTATCATCCAACA 58.709 50.000 0.00 0.00 0.00 3.33
532 586 1.291109 ACCCCCGTATCATCCAACAA 58.709 50.000 0.00 0.00 0.00 2.83
533 587 1.850345 ACCCCCGTATCATCCAACAAT 59.150 47.619 0.00 0.00 0.00 2.71
534 588 2.158667 ACCCCCGTATCATCCAACAATC 60.159 50.000 0.00 0.00 0.00 2.67
535 589 2.158682 CCCCCGTATCATCCAACAATCA 60.159 50.000 0.00 0.00 0.00 2.57
536 590 3.498481 CCCCCGTATCATCCAACAATCAT 60.498 47.826 0.00 0.00 0.00 2.45
537 591 4.144297 CCCCGTATCATCCAACAATCATT 58.856 43.478 0.00 0.00 0.00 2.57
538 592 5.312895 CCCCGTATCATCCAACAATCATTA 58.687 41.667 0.00 0.00 0.00 1.90
539 593 5.181245 CCCCGTATCATCCAACAATCATTAC 59.819 44.000 0.00 0.00 0.00 1.89
540 594 5.107104 CCCGTATCATCCAACAATCATTACG 60.107 44.000 0.00 0.00 0.00 3.18
541 595 5.107104 CCGTATCATCCAACAATCATTACGG 60.107 44.000 0.00 0.00 42.19 4.02
542 596 5.465390 CGTATCATCCAACAATCATTACGGT 59.535 40.000 0.00 0.00 0.00 4.83
543 597 5.756195 ATCATCCAACAATCATTACGGTG 57.244 39.130 0.00 0.00 0.00 4.94
544 598 4.584874 TCATCCAACAATCATTACGGTGT 58.415 39.130 0.00 0.00 0.00 4.16
545 599 4.634004 TCATCCAACAATCATTACGGTGTC 59.366 41.667 0.00 0.00 0.00 3.67
546 600 3.340034 TCCAACAATCATTACGGTGTCC 58.660 45.455 0.00 0.00 0.00 4.02
547 601 2.422127 CCAACAATCATTACGGTGTCCC 59.578 50.000 0.00 0.00 0.00 4.46
548 602 3.343617 CAACAATCATTACGGTGTCCCT 58.656 45.455 0.00 0.00 0.00 4.20
549 603 4.509616 CAACAATCATTACGGTGTCCCTA 58.490 43.478 0.00 0.00 0.00 3.53
550 604 4.829872 ACAATCATTACGGTGTCCCTAA 57.170 40.909 0.00 0.00 0.00 2.69
551 605 5.168647 ACAATCATTACGGTGTCCCTAAA 57.831 39.130 0.00 0.00 0.00 1.85
552 606 5.562635 ACAATCATTACGGTGTCCCTAAAA 58.437 37.500 0.00 0.00 0.00 1.52
553 607 6.005198 ACAATCATTACGGTGTCCCTAAAAA 58.995 36.000 0.00 0.00 0.00 1.94
603 657 1.616628 ATCTGTCCACCCACCCTCC 60.617 63.158 0.00 0.00 0.00 4.30
604 658 2.415962 ATCTGTCCACCCACCCTCCA 62.416 60.000 0.00 0.00 0.00 3.86
605 659 1.925455 CTGTCCACCCACCCTCCAT 60.925 63.158 0.00 0.00 0.00 3.41
611 668 2.268920 CCCACCCTCCATCACACG 59.731 66.667 0.00 0.00 0.00 4.49
643 700 0.984230 TCGCAAACCCCTCTCATCTT 59.016 50.000 0.00 0.00 0.00 2.40
781 839 2.820787 CTCTTCAGGTACTCACGGTCTT 59.179 50.000 0.00 0.00 34.60 3.01
782 840 4.008330 CTCTTCAGGTACTCACGGTCTTA 58.992 47.826 0.00 0.00 34.60 2.10
828 886 2.746472 GCCGGGTATGAGAAATGCTCTT 60.746 50.000 2.18 0.00 44.27 2.85
856 914 5.048434 CCATTTGTTCAGAGTTCCTCCTTTC 60.048 44.000 0.00 0.00 0.00 2.62
857 915 3.386768 TGTTCAGAGTTCCTCCTTTCG 57.613 47.619 0.00 0.00 0.00 3.46
858 916 2.963101 TGTTCAGAGTTCCTCCTTTCGA 59.037 45.455 0.00 0.00 0.00 3.71
859 917 3.578716 TGTTCAGAGTTCCTCCTTTCGAT 59.421 43.478 0.00 0.00 0.00 3.59
860 918 4.177783 GTTCAGAGTTCCTCCTTTCGATC 58.822 47.826 0.00 0.00 0.00 3.69
861 919 2.761208 TCAGAGTTCCTCCTTTCGATCC 59.239 50.000 0.00 0.00 0.00 3.36
862 920 2.112190 AGAGTTCCTCCTTTCGATCCC 58.888 52.381 0.00 0.00 0.00 3.85
914 972 1.148157 GATCGATCACACGCCCACTG 61.148 60.000 20.52 0.00 0.00 3.66
922 980 0.398696 ACACGCCCACTGGTAAATCA 59.601 50.000 0.00 0.00 0.00 2.57
927 985 4.156922 CACGCCCACTGGTAAATCATTTTA 59.843 41.667 0.00 0.00 0.00 1.52
974 1036 5.043248 GTCAGCAAAATTTACTTGTGTGCT 58.957 37.500 5.63 5.63 41.33 4.40
976 1038 5.009854 AGCAAAATTTACTTGTGTGCTGT 57.990 34.783 9.81 0.00 39.29 4.40
977 1039 5.043248 AGCAAAATTTACTTGTGTGCTGTC 58.957 37.500 9.81 0.00 39.29 3.51
998 1060 5.100943 GTCCGTCTGTTAGTTAGTTCATCC 58.899 45.833 0.00 0.00 0.00 3.51
1008 1070 1.294041 TAGTTCATCCCATGGTGGCA 58.706 50.000 11.73 0.00 35.79 4.92
1101 1163 4.554036 GGCAGGGATCACGGAGCC 62.554 72.222 12.31 12.31 37.39 4.70
1203 1265 2.049063 AAGGTGTGCTCGCTCGTC 60.049 61.111 0.00 0.00 0.00 4.20
1218 1280 2.661979 GCTCGTCGGCAAGTTTAACAAG 60.662 50.000 0.00 0.00 0.00 3.16
1326 1388 3.190874 GTGGCTAATGGAAAGAGTCGAG 58.809 50.000 0.00 0.00 0.00 4.04
1440 1502 1.676529 AGATCGATATGCCCCGATACG 59.323 52.381 0.00 0.00 44.40 3.06
1454 1516 2.985486 GATACGACCGAGCCGTCTGC 62.985 65.000 0.00 0.00 40.95 4.26
1614 1676 5.065859 AGCCTTTGTTATTTTTGTTGTTGGC 59.934 36.000 0.00 0.00 34.90 4.52
1632 1694 1.379044 CCACCTGTTGGCTCCATCC 60.379 63.158 0.00 0.00 39.07 3.51
1671 1733 0.890996 CCATAGATTTCTGGGCCGCC 60.891 60.000 0.00 0.00 0.00 6.13
1803 1865 2.094675 GTACATCTTGTTGGCTGCCAT 58.905 47.619 24.03 7.33 31.53 4.40
2073 2135 4.785376 AGTGTGAGACCTCTCCCATTTAAT 59.215 41.667 0.00 0.00 42.20 1.40
2164 2226 2.475111 CAGTGGTCATGTACACGTTCAC 59.525 50.000 0.00 5.47 42.25 3.18
2166 2228 3.064207 GTGGTCATGTACACGTTCACAT 58.936 45.455 0.00 6.05 35.79 3.21
2326 2388 0.823460 AAAGCACCAACACAACCCAG 59.177 50.000 0.00 0.00 0.00 4.45
2369 2431 2.291741 GCTTCACTGAAACTGGACAAGG 59.708 50.000 0.00 0.00 0.00 3.61
2466 2528 6.493449 TTCTTCATGTTACATCGAATTGCA 57.507 33.333 0.00 0.00 0.00 4.08
2479 2541 4.637276 TCGAATTGCACTCCTTCTGTTTA 58.363 39.130 0.00 0.00 0.00 2.01
2480 2542 5.245531 TCGAATTGCACTCCTTCTGTTTAT 58.754 37.500 0.00 0.00 0.00 1.40
2615 2677 3.428452 CGATGTCTACCTTAGCGGACAAA 60.428 47.826 0.00 0.00 41.14 2.83
2669 2731 2.600769 AGAGCGGTGGGACGAACT 60.601 61.111 0.00 0.00 35.47 3.01
2688 2750 4.602340 ACTGATTGTTTACTGAGGTCGT 57.398 40.909 0.00 0.00 0.00 4.34
2764 2826 5.010282 ACCCCTTCTTGCATAACTAACAAG 58.990 41.667 0.00 0.00 41.70 3.16
2765 2827 4.142381 CCCCTTCTTGCATAACTAACAAGC 60.142 45.833 0.00 0.00 40.45 4.01
2828 3134 6.241207 ACAACACGTCAATCCTGATTTTAG 57.759 37.500 0.00 0.00 33.05 1.85
2901 3207 6.607019 TGTTCTTATGGTTCCCTGTTAGTTT 58.393 36.000 0.00 0.00 0.00 2.66
2909 3215 1.987368 TCCCTGTTAGTTTACCACCCC 59.013 52.381 0.00 0.00 0.00 4.95
2911 3217 1.706305 CCTGTTAGTTTACCACCCCCA 59.294 52.381 0.00 0.00 0.00 4.96
3034 3588 1.140589 CACTGGAGCAGGTAGAGCG 59.859 63.158 0.00 0.00 35.51 5.03
3162 3716 5.277250 TGGGTAGGACATCACAAGAAGATA 58.723 41.667 0.00 0.00 0.00 1.98
3228 3782 3.679389 ACCTGGATGCTCAACTAACAAG 58.321 45.455 0.00 0.00 0.00 3.16
3304 3858 4.142622 CCAGATGAGCGTCTTTATTTTGCA 60.143 41.667 0.00 0.00 0.00 4.08
3334 3888 6.598525 CATCAACTTTCACGCTGTATGTAAA 58.401 36.000 0.00 0.00 0.00 2.01
3356 3910 1.897615 GGATCAGCAGCCCTCATGC 60.898 63.158 0.00 0.00 44.18 4.06
3390 3944 3.192001 TCCGTTGTCTTCGTAGCATAGTT 59.808 43.478 0.00 0.00 0.00 2.24
3403 3957 5.234543 CGTAGCATAGTTTCTTAGGCTTTCC 59.765 44.000 0.00 0.00 40.69 3.13
3418 3972 2.023673 CTTTCCTCACCAACTTGCACA 58.976 47.619 0.00 0.00 0.00 4.57
3451 4005 2.932614 CTCTGATTGTTCACGGCTTAGG 59.067 50.000 0.00 0.00 0.00 2.69
3487 4041 1.463056 CTTAAGCGATCGTTTGGTGCA 59.537 47.619 25.00 3.80 0.00 4.57
3499 4053 3.674997 GTTTGGTGCACATTCTCTAGGA 58.325 45.455 20.43 0.00 0.00 2.94
3515 4069 5.973124 TCTCTAGGATCCCAAAGAAATTCCT 59.027 40.000 8.55 0.00 37.38 3.36
3558 4112 3.562176 CCAGGCTAACATGTTTCTCCCTT 60.562 47.826 17.78 0.00 0.00 3.95
3613 4167 1.382522 CAATGTCCCGGTGAGATTGG 58.617 55.000 23.58 12.44 46.05 3.16
3670 4225 4.070630 AGCATGACTGAGGCTTATTCTC 57.929 45.455 0.00 0.00 39.11 2.87
3744 4309 2.222027 GTCTCAACACCTCCAAACCAG 58.778 52.381 0.00 0.00 0.00 4.00
3767 4332 5.066505 AGGTTGTGTGTGAAAAGCTAAAGAG 59.933 40.000 0.00 0.00 30.28 2.85
3798 4363 5.389859 TGTGAAGGCTTTCAATTACCATG 57.610 39.130 13.42 0.00 44.49 3.66
3892 4488 6.073003 GCTCCATTAGGTATAAATCAGCACAC 60.073 42.308 0.00 0.00 35.89 3.82
4007 4604 4.365514 TGTTCATTCCTAGCTGGTTCAA 57.634 40.909 0.00 0.00 37.07 2.69
4147 4745 0.456142 GCAGAACCGCGATTTTTCCC 60.456 55.000 8.23 0.00 0.00 3.97
4251 4849 3.748568 GGCAAACTCAAACTCTCTACAGG 59.251 47.826 0.00 0.00 0.00 4.00
4287 4885 1.138859 TGTTGTGTGAGACTGGGACTG 59.861 52.381 0.00 0.00 0.00 3.51
4327 4926 3.177228 AGGAGTTGTCTGCTTAGGATGT 58.823 45.455 0.00 0.00 39.28 3.06
4447 5075 3.188048 GTGAAGAGATGAACTTGGCACAG 59.812 47.826 0.00 0.00 42.39 3.66
4451 5079 1.816835 AGATGAACTTGGCACAGCATG 59.183 47.619 0.00 0.00 42.39 4.06
4453 5081 0.467844 TGAACTTGGCACAGCATGGT 60.468 50.000 0.00 0.00 43.62 3.55
4519 5149 3.054878 GTTGTCAAGCTTCAAGCAATGG 58.945 45.455 13.10 0.00 45.56 3.16
4550 5185 5.112686 ACAGCATACTTTGTAGAGCTAAGC 58.887 41.667 0.00 0.00 34.10 3.09
4551 5186 5.105146 ACAGCATACTTTGTAGAGCTAAGCT 60.105 40.000 0.00 0.00 43.88 3.74
4552 5187 6.096987 ACAGCATACTTTGTAGAGCTAAGCTA 59.903 38.462 0.00 0.00 39.88 3.32
4553 5188 6.980978 CAGCATACTTTGTAGAGCTAAGCTAA 59.019 38.462 0.00 0.00 39.88 3.09
4554 5189 7.492669 CAGCATACTTTGTAGAGCTAAGCTAAA 59.507 37.037 0.00 0.00 39.88 1.85
4555 5190 8.041323 AGCATACTTTGTAGAGCTAAGCTAAAA 58.959 33.333 0.00 0.00 39.88 1.52
4560 5195 4.174009 TGTAGAGCTAAGCTAAAACTGCG 58.826 43.478 0.00 0.00 39.88 5.18
4568 5203 3.319137 AGCTAAAACTGCGTGATCAGA 57.681 42.857 0.00 0.00 37.51 3.27
4585 5221 8.331022 CGTGATCAGAACATCCACTTATTTTAG 58.669 37.037 0.00 0.00 0.00 1.85
4598 5234 8.358148 TCCACTTATTTTAGAGTATAAGGAGCG 58.642 37.037 0.00 0.00 38.21 5.03
4599 5235 8.142551 CCACTTATTTTAGAGTATAAGGAGCGT 58.857 37.037 0.00 0.00 38.21 5.07
4689 5332 7.501559 AGTTTGCATCTGATGAGCATTAGTATT 59.498 33.333 21.30 0.00 38.19 1.89
4731 5382 1.228988 AGCTTCAAGGGGCCCTTTG 60.229 57.895 35.11 35.11 41.69 2.77
4744 5395 0.545071 CCCTTTGGGCTTGTTGGGAT 60.545 55.000 0.00 0.00 35.35 3.85
5072 5731 5.646360 CGATATAAGTGGTGACTTTTTGGGT 59.354 40.000 0.00 0.00 39.56 4.51
5127 5816 2.500098 TCCTGTGAGTACCCATACAAGC 59.500 50.000 0.00 0.00 33.30 4.01
5135 5824 1.821216 ACCCATACAAGCTTGGAACG 58.179 50.000 29.18 16.67 34.81 3.95
5173 5862 1.668826 TACACCCAAGAGGCCAAGAT 58.331 50.000 5.01 0.00 40.58 2.40
5263 5952 7.528307 CCTTCATTCTGATCTTGAGTTTCTTG 58.472 38.462 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.310904 GGAGGAAGAGTCGCTCGTAT 58.689 55.000 1.98 0.00 35.36 3.06
204 216 4.082523 GTGCGGTAGCTGCCCAGA 62.083 66.667 15.92 0.00 45.42 3.86
229 244 5.122519 TCACTACACAAAATTGAGCTCACA 58.877 37.500 18.03 8.50 0.00 3.58
268 283 2.042259 TTCGCCGGAGCTAGAACGA 61.042 57.895 5.05 0.00 36.60 3.85
365 413 1.744374 TTAAAACTTGTTTCGCGCGG 58.256 45.000 31.69 15.29 0.00 6.46
407 457 3.184683 GCGGCGACAGAGCAGAAG 61.185 66.667 12.98 0.00 39.27 2.85
431 481 1.450531 GATGGCGCTTATGCAGGCTT 61.451 55.000 7.64 11.27 39.64 4.35
469 523 3.119990 CCACATTTCGCCGAACTGTAAAT 60.120 43.478 20.21 0.00 34.13 1.40
511 565 2.479340 TGTTGGATGATACGGGGGTTA 58.521 47.619 0.00 0.00 0.00 2.85
515 569 3.207265 TGATTGTTGGATGATACGGGG 57.793 47.619 0.00 0.00 0.00 5.73
516 570 5.107104 CGTAATGATTGTTGGATGATACGGG 60.107 44.000 0.00 0.00 0.00 5.28
517 571 5.107104 CCGTAATGATTGTTGGATGATACGG 60.107 44.000 6.20 6.20 39.32 4.02
518 572 5.465390 ACCGTAATGATTGTTGGATGATACG 59.535 40.000 0.00 0.00 0.00 3.06
519 573 6.260050 ACACCGTAATGATTGTTGGATGATAC 59.740 38.462 0.00 0.00 0.00 2.24
520 574 6.353323 ACACCGTAATGATTGTTGGATGATA 58.647 36.000 0.00 0.00 0.00 2.15
521 575 5.192927 ACACCGTAATGATTGTTGGATGAT 58.807 37.500 0.00 0.00 0.00 2.45
522 576 4.584874 ACACCGTAATGATTGTTGGATGA 58.415 39.130 0.00 0.00 0.00 2.92
523 577 4.201910 GGACACCGTAATGATTGTTGGATG 60.202 45.833 0.00 0.00 0.00 3.51
524 578 3.945285 GGACACCGTAATGATTGTTGGAT 59.055 43.478 0.00 0.00 0.00 3.41
525 579 3.340034 GGACACCGTAATGATTGTTGGA 58.660 45.455 0.00 0.00 0.00 3.53
526 580 2.422127 GGGACACCGTAATGATTGTTGG 59.578 50.000 0.00 0.00 0.00 3.77
527 581 3.343617 AGGGACACCGTAATGATTGTTG 58.656 45.455 0.00 0.00 43.47 3.33
528 582 3.713826 AGGGACACCGTAATGATTGTT 57.286 42.857 0.00 0.00 43.47 2.83
529 583 4.829872 TTAGGGACACCGTAATGATTGT 57.170 40.909 0.00 0.00 43.47 2.71
530 584 6.503589 TTTTTAGGGACACCGTAATGATTG 57.496 37.500 0.00 0.00 43.47 2.67
552 606 7.014422 TGGAGAACCACCGTAATAATTGTTTTT 59.986 33.333 0.00 0.00 41.77 1.94
553 607 6.490721 TGGAGAACCACCGTAATAATTGTTTT 59.509 34.615 0.00 0.00 41.77 2.43
554 608 6.005198 TGGAGAACCACCGTAATAATTGTTT 58.995 36.000 0.00 0.00 41.77 2.83
603 657 0.950555 CAGGGGTGTGTCGTGTGATG 60.951 60.000 0.00 0.00 0.00 3.07
604 658 1.371183 CAGGGGTGTGTCGTGTGAT 59.629 57.895 0.00 0.00 0.00 3.06
605 659 2.818841 CAGGGGTGTGTCGTGTGA 59.181 61.111 0.00 0.00 0.00 3.58
611 668 3.825160 TTGCGAGCAGGGGTGTGTC 62.825 63.158 0.00 0.00 0.00 3.67
643 700 1.406180 CAATTGCCATGGATTGCGAGA 59.594 47.619 18.40 0.00 0.00 4.04
734 792 2.106332 CCGTAACTGGCCTAGGCG 59.894 66.667 27.24 16.92 43.06 5.52
761 819 2.581216 AGACCGTGAGTACCTGAAGA 57.419 50.000 0.00 0.00 0.00 2.87
782 840 8.351461 GCAGTAAGAACCTACTTAGATTCGTAT 58.649 37.037 0.00 0.00 33.79 3.06
828 886 4.792068 AGGAACTCTGAACAAATGGACAA 58.208 39.130 0.00 0.00 0.00 3.18
856 914 1.887198 ACTAGCTGATAACGGGGATCG 59.113 52.381 0.00 0.00 45.88 3.69
857 915 4.338379 AAACTAGCTGATAACGGGGATC 57.662 45.455 0.00 0.00 0.00 3.36
858 916 5.881923 TTAAACTAGCTGATAACGGGGAT 57.118 39.130 0.00 0.00 0.00 3.85
859 917 5.188359 AGTTTAAACTAGCTGATAACGGGGA 59.812 40.000 19.26 0.00 37.52 4.81
860 918 5.425630 AGTTTAAACTAGCTGATAACGGGG 58.574 41.667 19.26 0.00 37.52 5.73
861 919 6.592607 TCAAGTTTAAACTAGCTGATAACGGG 59.407 38.462 20.83 0.00 38.57 5.28
862 920 7.591006 TCAAGTTTAAACTAGCTGATAACGG 57.409 36.000 20.83 0.96 38.57 4.44
914 972 4.209080 GGCGCTGCAATAAAATGATTTACC 59.791 41.667 7.64 0.00 33.98 2.85
922 980 3.056607 AGAACAAGGCGCTGCAATAAAAT 60.057 39.130 7.64 0.00 0.00 1.82
927 985 1.089920 CTAGAACAAGGCGCTGCAAT 58.910 50.000 7.64 0.00 0.00 3.56
974 1036 5.336213 GGATGAACTAACTAACAGACGGACA 60.336 44.000 0.00 0.00 0.00 4.02
975 1037 5.100943 GGATGAACTAACTAACAGACGGAC 58.899 45.833 0.00 0.00 0.00 4.79
976 1038 4.159135 GGGATGAACTAACTAACAGACGGA 59.841 45.833 0.00 0.00 0.00 4.69
977 1039 4.081862 TGGGATGAACTAACTAACAGACGG 60.082 45.833 0.00 0.00 0.00 4.79
1101 1163 3.238260 GCATCTGCTATGTCGGCG 58.762 61.111 0.00 0.00 38.21 6.46
1203 1265 4.915704 TCTTGAACTTGTTAAACTTGCCG 58.084 39.130 0.00 0.00 0.00 5.69
1218 1280 3.003480 CTCGACCAAATCCCTCTTGAAC 58.997 50.000 0.00 0.00 0.00 3.18
1326 1388 1.373497 CAGTGTGCTGGACTCGACC 60.373 63.158 0.00 0.00 39.01 4.79
1335 1397 3.181526 GCTCGTCTATTTTCAGTGTGCTG 60.182 47.826 0.00 0.00 43.87 4.41
1338 1400 4.990543 TTGCTCGTCTATTTTCAGTGTG 57.009 40.909 0.00 0.00 0.00 3.82
1454 1516 1.402456 GCATGAACTCTTTGCAGGCTG 60.402 52.381 10.94 10.94 36.51 4.85
1506 1568 1.519455 CTCCGCGGCCTTTAGACTG 60.519 63.158 23.51 0.00 0.00 3.51
1632 1694 4.758688 TGGTGATGTAGTCATGCTTAGTG 58.241 43.478 0.00 0.00 39.48 2.74
1671 1733 6.525121 TTAATTTGCGAGATATCGTTGAGG 57.475 37.500 11.90 0.00 35.26 3.86
1803 1865 4.503714 AACAAGGACCTGAAGAAACAGA 57.496 40.909 0.00 0.00 39.94 3.41
2098 2160 6.079763 CGAACACTATTCAGTCATTTTGTGG 58.920 40.000 0.00 0.00 30.46 4.17
2103 2165 5.995282 TGAACCGAACACTATTCAGTCATTT 59.005 36.000 0.00 0.00 30.46 2.32
2110 2172 4.219944 AGCTACTGAACCGAACACTATTCA 59.780 41.667 0.00 0.00 0.00 2.57
2142 2204 2.362717 TGAACGTGTACATGACCACTGA 59.637 45.455 21.82 0.00 0.00 3.41
2178 2240 4.584327 AAACTGGCATGTAAAACAGGAC 57.416 40.909 0.00 0.00 38.63 3.85
2326 2388 2.202566 GCTTCGTAGCATGGGAGTAAC 58.797 52.381 9.38 0.00 46.95 2.50
2369 2431 3.133003 TCGGAGATGGTTGGAGAAATCTC 59.867 47.826 1.68 1.68 42.79 2.75
2479 2541 7.445402 CCTGCCTTTGCACTATTAGTTACATAT 59.555 37.037 0.00 0.00 44.23 1.78
2480 2542 6.765989 CCTGCCTTTGCACTATTAGTTACATA 59.234 38.462 0.00 0.00 44.23 2.29
2508 2570 0.623723 ATGGTCATAAGCGGGTGGTT 59.376 50.000 0.00 0.00 39.56 3.67
2615 2677 7.309499 CGGTTCTCAGATATATAGCCAAGAAGT 60.309 40.741 11.07 0.00 0.00 3.01
2669 2731 3.571571 CGACGACCTCAGTAAACAATCA 58.428 45.455 0.00 0.00 0.00 2.57
2688 2750 1.805943 CTCACCATGAATTGTGTGCGA 59.194 47.619 0.00 0.00 34.14 5.10
2746 2808 6.800543 TGTTTGCTTGTTAGTTATGCAAGAA 58.199 32.000 7.58 0.00 43.13 2.52
2765 2827 6.128063 TGTTTCCTTGGAAGCAAAAATGTTTG 60.128 34.615 14.93 3.80 45.88 2.93
2828 3134 2.128771 ATGACTACATTGTGCCCCAC 57.871 50.000 0.00 0.00 32.21 4.61
2918 3228 9.457436 AAACAAATCAGTACCCTATCGTAATTT 57.543 29.630 0.00 0.00 0.00 1.82
2926 3236 7.166167 ACGAGAAAAACAAATCAGTACCCTAT 58.834 34.615 0.00 0.00 0.00 2.57
3034 3588 4.058124 TGTCTGAAATCTGCTGTGTACAC 58.942 43.478 19.36 19.36 0.00 2.90
3162 3716 1.229082 TAGAGGCTGGTTCACCCGT 60.229 57.895 0.00 0.00 35.15 5.28
3228 3782 3.851128 GGACTGCGGGGTAGGCTC 61.851 72.222 0.00 0.00 0.00 4.70
3304 3858 2.816087 AGCGTGAAAGTTGATGCTGAAT 59.184 40.909 0.00 0.00 35.32 2.57
3334 3888 1.203441 TGAGGGCTGCTGATCCAGTT 61.203 55.000 0.00 0.00 35.28 3.16
3356 3910 2.167281 AGACAACGGACATCTCTGATGG 59.833 50.000 11.55 0.00 31.29 3.51
3403 3957 6.441093 ACATATATTGTGCAAGTTGGTGAG 57.559 37.500 4.75 0.00 37.11 3.51
3451 4005 4.406943 GCTTAAGACAGTATGCAGCAAAC 58.593 43.478 6.67 0.00 42.53 2.93
3487 4041 6.642733 TTTCTTTGGGATCCTAGAGAATGT 57.357 37.500 25.60 0.00 0.00 2.71
3499 4053 6.842807 AGCATTATCAGGAATTTCTTTGGGAT 59.157 34.615 0.00 0.00 0.00 3.85
3515 4069 6.233905 TGGCTAGAGTTTACAGCATTATCA 57.766 37.500 0.00 0.00 37.02 2.15
3558 4112 9.959749 CAAAAGACTTAATTGGTTAAGCAACTA 57.040 29.630 21.50 13.04 46.97 2.24
3613 4167 3.188159 TGTGGAGAGGTGTTGTGTTAC 57.812 47.619 0.00 0.00 0.00 2.50
3656 4211 5.083533 AGTGAACAGAGAATAAGCCTCAG 57.916 43.478 0.00 0.00 33.25 3.35
3670 4225 8.948631 ATAATGGACAGTACATTAGTGAACAG 57.051 34.615 20.73 0.00 42.21 3.16
3708 4267 8.674607 GGTGTTGAGACCGAAAAGAATATAAAT 58.325 33.333 0.00 0.00 0.00 1.40
3744 4309 5.243426 TCTTTAGCTTTTCACACACAACC 57.757 39.130 0.00 0.00 0.00 3.77
3767 4332 1.734388 AAGCCTTCACAAACCGGTGC 61.734 55.000 8.52 4.10 38.66 5.01
3798 4363 5.722021 ATGTAGAAACCAATTCCCACAAC 57.278 39.130 0.00 0.00 37.17 3.32
3828 4393 0.698238 AACTGTGCAGCCCCAAGATA 59.302 50.000 0.00 0.00 0.00 1.98
3865 4433 6.148480 GTGCTGATTTATACCTAATGGAGCAG 59.852 42.308 0.00 0.00 32.20 4.24
3869 4437 5.989168 CGTGTGCTGATTTATACCTAATGGA 59.011 40.000 0.00 0.00 37.04 3.41
3892 4488 2.095853 ACACTTTCAAGCAACTGTGACG 59.904 45.455 0.00 0.00 0.00 4.35
4007 4604 3.920231 TCTTCCACATTCAGCTATGCT 57.080 42.857 0.00 0.00 40.77 3.79
4287 4885 5.126061 ACTCCTTGTATTTGATGGTCAATGC 59.874 40.000 0.00 0.00 36.11 3.56
4327 4926 5.130975 ACAATGATGGTACTCCTTATCTGCA 59.869 40.000 0.00 0.00 34.23 4.41
4441 5040 0.531657 TTGCAATACCATGCTGTGCC 59.468 50.000 0.00 0.00 46.54 5.01
4447 5075 3.855689 AGTCAACTTGCAATACCATGC 57.144 42.857 0.00 0.00 46.58 4.06
4496 5126 3.865011 TTGCTTGAAGCTTGACAACAA 57.135 38.095 18.94 7.57 42.97 2.83
4519 5149 3.356290 ACAAAGTATGCTGTCCCATTCC 58.644 45.455 0.00 0.00 0.00 3.01
4550 5185 4.990543 TGTTCTGATCACGCAGTTTTAG 57.009 40.909 0.00 0.00 41.61 1.85
4551 5186 4.391830 GGATGTTCTGATCACGCAGTTTTA 59.608 41.667 0.00 0.00 41.61 1.52
4552 5187 3.189287 GGATGTTCTGATCACGCAGTTTT 59.811 43.478 0.00 0.00 41.61 2.43
4553 5188 2.744202 GGATGTTCTGATCACGCAGTTT 59.256 45.455 0.00 0.00 41.61 2.66
4554 5189 2.289631 TGGATGTTCTGATCACGCAGTT 60.290 45.455 0.00 0.00 41.61 3.16
4560 5195 9.383519 TCTAAAATAAGTGGATGTTCTGATCAC 57.616 33.333 0.00 0.00 0.00 3.06
4585 5221 9.344309 GTTGAATTATCTACGCTCCTTATACTC 57.656 37.037 0.00 0.00 0.00 2.59
4652 5295 5.005740 TCAGATGCAAACTTCAGCTTATGT 58.994 37.500 0.00 0.00 31.56 2.29
4689 5332 2.901192 TCGACCAAAACTCCAGGTATCA 59.099 45.455 0.00 0.00 35.36 2.15
4731 5382 3.065462 TGGAAATCCCAACAAGCCC 57.935 52.632 0.00 0.00 43.29 5.19
4744 5395 3.447040 GCTGCAGCAAGGTGGAAA 58.553 55.556 33.36 0.00 41.59 3.13
5187 5876 1.982958 ACTGTCTTTTCCCGGTACCAT 59.017 47.619 13.54 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.