Multiple sequence alignment - TraesCS7D01G261800

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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 TraesCS7D01G261800 chr7D 100.000 4617 0 0 1 4617 238968619 238973235 0.000000e+00 8527.0
1 TraesCS7D01G261800 chr7D 96.482 1990 54 3 2186 4175 239348087 239350060 0.000000e+00 3273.0
2 TraesCS7D01G261800 chr7D 93.376 468 26 4 4155 4617 239350084 239350551 0.000000e+00 688.0
3 TraesCS7D01G261800 chr7D 84.179 335 51 1 188 520 80268162 80267828 1.600000e-84 324.0
4 TraesCS7D01G261800 chr7A 94.941 3242 103 19 840 4024 254384764 254388001 0.000000e+00 5022.0
5 TraesCS7D01G261800 chr7A 90.468 598 47 6 4019 4612 254388025 254388616 0.000000e+00 780.0
6 TraesCS7D01G261800 chr7A 86.531 245 25 8 609 845 91928083 91928327 3.540000e-66 263.0
7 TraesCS7D01G261800 chr7A 90.256 195 17 2 609 801 232743804 232743998 2.130000e-63 254.0
8 TraesCS7D01G261800 chr7B 95.593 2791 80 10 1261 4024 215927449 215930223 0.000000e+00 4433.0
9 TraesCS7D01G261800 chr7B 90.563 604 51 5 4019 4617 215930247 215930849 0.000000e+00 795.0
10 TraesCS7D01G261800 chr7B 81.924 603 94 10 1 590 562479331 562478731 3.210000e-136 496.0
11 TraesCS7D01G261800 chr7B 94.839 310 11 3 858 1162 215926872 215927181 3.230000e-131 479.0
12 TraesCS7D01G261800 chr3B 83.446 592 87 7 1 586 628719130 628719716 1.460000e-149 540.0
13 TraesCS7D01G261800 chr3B 90.000 50 5 0 539 588 724943550 724943501 1.070000e-06 65.8
14 TraesCS7D01G261800 chr1B 86.145 498 64 2 1 493 641871900 641871403 2.450000e-147 532.0
15 TraesCS7D01G261800 chr1B 85.263 95 13 1 2102 2196 629772993 629772900 3.800000e-16 97.1
16 TraesCS7D01G261800 chr5D 85.102 490 64 4 1 485 371632241 371632726 4.150000e-135 492.0
17 TraesCS7D01G261800 chr5D 91.282 195 15 2 609 801 279292870 279293064 9.850000e-67 265.0
18 TraesCS7D01G261800 chr5D 92.000 50 4 0 537 586 466560248 466560297 2.300000e-08 71.3
19 TraesCS7D01G261800 chr5B 83.636 550 63 10 1 524 510831927 510831379 4.150000e-135 492.0
20 TraesCS7D01G261800 chr1A 81.926 592 70 19 1 586 374023755 374024315 2.520000e-127 466.0
21 TraesCS7D01G261800 chr1A 77.703 592 79 24 1 586 564343229 564342685 3.470000e-81 313.0
22 TraesCS7D01G261800 chr1D 81.636 599 70 10 1 593 460172239 460171675 1.170000e-125 460.0
23 TraesCS7D01G261800 chr1D 90.722 194 15 3 610 801 11958664 11958472 5.930000e-64 255.0
24 TraesCS7D01G261800 chr2B 82.231 529 86 6 1 523 641874136 641874662 2.530000e-122 449.0
25 TraesCS7D01G261800 chr2B 81.183 558 75 10 1 530 564824860 564825415 5.520000e-114 422.0
26 TraesCS7D01G261800 chr2B 89.163 203 20 2 610 811 218284960 218285161 7.670000e-63 252.0
27 TraesCS7D01G261800 chr4B 81.982 555 68 14 1 524 623175502 623176055 4.240000e-120 442.0
28 TraesCS7D01G261800 chr4B 87.712 236 23 6 610 842 107235041 107235273 2.120000e-68 270.0
29 TraesCS7D01G261800 chr3A 80.444 496 91 3 1 491 726405156 726405650 1.570000e-99 374.0
30 TraesCS7D01G261800 chr3A 81.905 105 17 1 2100 2202 359357226 359357330 2.290000e-13 87.9
31 TraesCS7D01G261800 chr2A 76.667 600 103 19 1 590 779639600 779639028 9.710000e-77 298.0
32 TraesCS7D01G261800 chr2A 90.306 196 15 4 609 801 606519062 606519256 2.130000e-63 254.0
33 TraesCS7D01G261800 chr4D 83.654 312 43 6 288 591 502727923 502727612 2.100000e-73 287.0
34 TraesCS7D01G261800 chr2D 90.000 200 17 2 610 806 455942225 455942424 5.930000e-64 255.0
35 TraesCS7D01G261800 chr2D 84.946 93 14 0 2109 2201 445896315 445896407 1.370000e-15 95.3
36 TraesCS7D01G261800 chr2D 84.043 94 15 0 2109 2202 446082917 446083010 1.770000e-14 91.6
37 TraesCS7D01G261800 chr6D 84.362 243 28 7 608 842 334030901 334031141 3.590000e-56 230.0
38 TraesCS7D01G261800 chr4A 87.234 94 12 0 2109 2202 631960054 631960147 1.760000e-19 108.0
39 TraesCS7D01G261800 chr4A 87.356 87 10 1 2101 2187 718869878 718869963 1.060000e-16 99.0
40 TraesCS7D01G261800 chr6B 82.075 106 16 3 2101 2204 185669334 185669438 2.290000e-13 87.9


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 TraesCS7D01G261800 chr7D 238968619 238973235 4616 False 8527.000000 8527 100.0000 1 4617 1 chr7D.!!$F1 4616
1 TraesCS7D01G261800 chr7D 239348087 239350551 2464 False 1980.500000 3273 94.9290 2186 4617 2 chr7D.!!$F2 2431
2 TraesCS7D01G261800 chr7A 254384764 254388616 3852 False 2901.000000 5022 92.7045 840 4612 2 chr7A.!!$F3 3772
3 TraesCS7D01G261800 chr7B 215926872 215930849 3977 False 1902.333333 4433 93.6650 858 4617 3 chr7B.!!$F1 3759
4 TraesCS7D01G261800 chr7B 562478731 562479331 600 True 496.000000 496 81.9240 1 590 1 chr7B.!!$R1 589
5 TraesCS7D01G261800 chr3B 628719130 628719716 586 False 540.000000 540 83.4460 1 586 1 chr3B.!!$F1 585
6 TraesCS7D01G261800 chr5B 510831379 510831927 548 True 492.000000 492 83.6360 1 524 1 chr5B.!!$R1 523
7 TraesCS7D01G261800 chr1A 374023755 374024315 560 False 466.000000 466 81.9260 1 586 1 chr1A.!!$F1 585
8 TraesCS7D01G261800 chr1A 564342685 564343229 544 True 313.000000 313 77.7030 1 586 1 chr1A.!!$R1 585
9 TraesCS7D01G261800 chr1D 460171675 460172239 564 True 460.000000 460 81.6360 1 593 1 chr1D.!!$R2 592
10 TraesCS7D01G261800 chr2B 641874136 641874662 526 False 449.000000 449 82.2310 1 523 1 chr2B.!!$F3 522
11 TraesCS7D01G261800 chr2B 564824860 564825415 555 False 422.000000 422 81.1830 1 530 1 chr2B.!!$F2 529
12 TraesCS7D01G261800 chr4B 623175502 623176055 553 False 442.000000 442 81.9820 1 524 1 chr4B.!!$F2 523
13 TraesCS7D01G261800 chr2A 779639028 779639600 572 True 298.000000 298 76.6670 1 590 1 chr2A.!!$R1 589

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
598 667 0.182299 ATGCTCTAAGCTTGAGGGCC 59.818 55.0 18.95 0.0 42.97 5.80 F
624 693 0.322648 CCCGTACTCCCTCCGTTTTT 59.677 55.0 0.00 0.0 0.00 1.94 F
2399 2676 0.251297 TGTGGGATCAAACTGCTGGG 60.251 55.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 2661 1.303309 CGATCCCAGCAGTTTGATCC 58.697 55.000 0.0 0.0 31.94 3.36 R
2531 2808 4.846779 TCACCTGAATTAAACACAAGCC 57.153 40.909 0.0 0.0 0.00 4.35 R
3875 4153 1.000717 ACAACGGTTACATTTGCTGGC 60.001 47.619 0.0 0.0 0.00 4.85 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
43 46 4.054359 AGAGCTTGAGAAGGAGAGGTTA 57.946 45.455 0.00 0.00 0.00 2.85
61 64 0.664224 TACAACTCGCACGAGACACA 59.336 50.000 25.53 6.14 44.53 3.72
82 85 5.587443 CACAGAAGATGCAAGGATCATGTTA 59.413 40.000 4.40 0.00 29.14 2.41
92 95 1.132588 GATCATGTTAGCGGACGAGC 58.867 55.000 0.00 0.00 37.41 5.03
107 110 1.133325 ACGAGCCCCTCTATGATGAGT 60.133 52.381 0.00 0.00 32.50 3.41
126 130 2.028112 AGTATGCGAAGAAGTGGCTTGA 60.028 45.455 0.00 0.00 0.00 3.02
150 160 4.245660 GACAAGATGAAGATCAACGACCA 58.754 43.478 0.00 0.00 0.00 4.02
343 402 2.106938 GCCATCCGTCATGCTCGA 59.893 61.111 10.73 0.00 0.00 4.04
368 429 1.173043 GACCATTTTGCCATGTCCGA 58.827 50.000 0.00 0.00 0.00 4.55
372 433 3.766591 ACCATTTTGCCATGTCCGATTTA 59.233 39.130 0.00 0.00 0.00 1.40
378 439 5.850557 TTGCCATGTCCGATTTATTGAAT 57.149 34.783 0.00 0.00 0.00 2.57
405 468 5.289675 TGATTTGTTTTGCGTTGTTTCGAAT 59.710 32.000 0.00 0.00 0.00 3.34
411 474 3.152261 TGCGTTGTTTCGAATTTTGGT 57.848 38.095 0.00 0.00 0.00 3.67
479 542 5.095490 GGATTTGAGAATCGAAATTTGCGT 58.905 37.500 0.00 0.00 42.82 5.24
496 559 2.675844 TGCGTTATGTAGATGTGCAACC 59.324 45.455 0.00 0.00 34.36 3.77
524 587 3.626924 GGGGTGTCCGCTCAGTGT 61.627 66.667 0.00 0.00 33.42 3.55
532 599 2.250939 CCGCTCAGTGTCCGCAAAA 61.251 57.895 0.00 0.00 0.00 2.44
533 600 1.646540 CGCTCAGTGTCCGCAAAAA 59.353 52.632 0.00 0.00 0.00 1.94
540 608 4.615834 GTCCGCAAAAACGCCGCA 62.616 61.111 0.00 0.00 0.00 5.69
542 610 4.320928 CCGCAAAAACGCCGCAGA 62.321 61.111 0.00 0.00 0.00 4.26
552 621 2.357034 GCCGCAGACGTTTGAGGA 60.357 61.111 28.94 0.00 40.07 3.71
564 633 1.305219 TTTGAGGAGCCGGATTTGCG 61.305 55.000 5.05 0.00 0.00 4.85
567 636 1.002624 AGGAGCCGGATTTGCGAAA 60.003 52.632 5.05 0.00 0.00 3.46
586 655 4.499188 CGAAATCCGGTTGTAGATGCTCTA 60.499 45.833 0.00 0.00 33.91 2.43
591 660 3.430929 CCGGTTGTAGATGCTCTAAGCTT 60.431 47.826 3.48 3.48 42.97 3.74
592 661 3.553511 CGGTTGTAGATGCTCTAAGCTTG 59.446 47.826 9.86 0.00 42.97 4.01
593 662 4.678044 CGGTTGTAGATGCTCTAAGCTTGA 60.678 45.833 9.86 3.84 42.97 3.02
594 663 4.808364 GGTTGTAGATGCTCTAAGCTTGAG 59.192 45.833 9.86 14.35 42.97 3.02
595 664 4.662468 TGTAGATGCTCTAAGCTTGAGG 57.338 45.455 20.36 8.25 42.97 3.86
596 665 3.386078 TGTAGATGCTCTAAGCTTGAGGG 59.614 47.826 20.36 11.34 42.97 4.30
597 666 1.140652 AGATGCTCTAAGCTTGAGGGC 59.859 52.381 20.36 18.45 42.97 5.19
598 667 0.182299 ATGCTCTAAGCTTGAGGGCC 59.818 55.000 18.95 0.00 42.97 5.80
599 668 1.200760 TGCTCTAAGCTTGAGGGCCA 61.201 55.000 18.95 10.72 42.97 5.36
600 669 0.182299 GCTCTAAGCTTGAGGGCCAT 59.818 55.000 20.36 0.00 38.45 4.40
601 670 1.813477 GCTCTAAGCTTGAGGGCCATC 60.813 57.143 11.34 11.34 38.45 3.51
602 671 1.767681 CTCTAAGCTTGAGGGCCATCT 59.232 52.381 19.75 0.00 0.00 2.90
603 672 1.487976 TCTAAGCTTGAGGGCCATCTG 59.512 52.381 19.75 12.38 0.00 2.90
604 673 0.548031 TAAGCTTGAGGGCCATCTGG 59.452 55.000 19.75 11.96 38.53 3.86
614 683 2.822399 CCATCTGGCCCGTACTCC 59.178 66.667 0.00 0.00 0.00 3.85
615 684 2.808206 CCATCTGGCCCGTACTCCC 61.808 68.421 0.00 0.00 0.00 4.30
616 685 1.762460 CATCTGGCCCGTACTCCCT 60.762 63.158 0.00 0.00 0.00 4.20
617 686 1.457831 ATCTGGCCCGTACTCCCTC 60.458 63.158 0.00 0.00 0.00 4.30
618 687 2.948801 ATCTGGCCCGTACTCCCTCC 62.949 65.000 0.00 0.00 0.00 4.30
621 690 3.073101 GCCCGTACTCCCTCCGTT 61.073 66.667 0.00 0.00 0.00 4.44
622 691 2.653087 GCCCGTACTCCCTCCGTTT 61.653 63.158 0.00 0.00 0.00 3.60
623 692 1.977685 CCCGTACTCCCTCCGTTTT 59.022 57.895 0.00 0.00 0.00 2.43
624 693 0.322648 CCCGTACTCCCTCCGTTTTT 59.677 55.000 0.00 0.00 0.00 1.94
625 694 1.550072 CCCGTACTCCCTCCGTTTTTA 59.450 52.381 0.00 0.00 0.00 1.52
626 695 2.169144 CCCGTACTCCCTCCGTTTTTAT 59.831 50.000 0.00 0.00 0.00 1.40
627 696 3.369787 CCCGTACTCCCTCCGTTTTTATT 60.370 47.826 0.00 0.00 0.00 1.40
628 697 4.256110 CCGTACTCCCTCCGTTTTTATTT 58.744 43.478 0.00 0.00 0.00 1.40
629 698 5.418676 CCGTACTCCCTCCGTTTTTATTTA 58.581 41.667 0.00 0.00 0.00 1.40
630 699 5.521372 CCGTACTCCCTCCGTTTTTATTTAG 59.479 44.000 0.00 0.00 0.00 1.85
631 700 6.101997 CGTACTCCCTCCGTTTTTATTTAGT 58.898 40.000 0.00 0.00 0.00 2.24
632 701 6.254373 CGTACTCCCTCCGTTTTTATTTAGTC 59.746 42.308 0.00 0.00 0.00 2.59
633 702 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
634 703 5.013391 ACTCCCTCCGTTTTTATTTAGTCCA 59.987 40.000 0.00 0.00 0.00 4.02
635 704 6.069705 TCCCTCCGTTTTTATTTAGTCCAT 57.930 37.500 0.00 0.00 0.00 3.41
636 705 5.883673 TCCCTCCGTTTTTATTTAGTCCATG 59.116 40.000 0.00 0.00 0.00 3.66
637 706 5.650703 CCCTCCGTTTTTATTTAGTCCATGT 59.349 40.000 0.00 0.00 0.00 3.21
638 707 6.824704 CCCTCCGTTTTTATTTAGTCCATGTA 59.175 38.462 0.00 0.00 0.00 2.29
639 708 7.501225 CCCTCCGTTTTTATTTAGTCCATGTAT 59.499 37.037 0.00 0.00 0.00 2.29
640 709 8.899771 CCTCCGTTTTTATTTAGTCCATGTATT 58.100 33.333 0.00 0.00 0.00 1.89
643 712 9.940166 CCGTTTTTATTTAGTCCATGTATTACC 57.060 33.333 0.00 0.00 0.00 2.85
650 719 8.747538 ATTTAGTCCATGTATTACCTTTGGTC 57.252 34.615 0.00 3.55 37.09 4.02
651 720 5.772393 AGTCCATGTATTACCTTTGGTCA 57.228 39.130 0.00 0.00 37.09 4.02
652 721 6.134535 AGTCCATGTATTACCTTTGGTCAA 57.865 37.500 0.00 0.00 37.09 3.18
653 722 6.548321 AGTCCATGTATTACCTTTGGTCAAA 58.452 36.000 0.00 0.00 37.09 2.69
654 723 6.659242 AGTCCATGTATTACCTTTGGTCAAAG 59.341 38.462 14.56 14.56 45.47 2.77
655 724 6.433093 GTCCATGTATTACCTTTGGTCAAAGT 59.567 38.462 18.52 11.18 44.66 2.66
656 725 6.657541 TCCATGTATTACCTTTGGTCAAAGTC 59.342 38.462 18.52 6.12 44.66 3.01
657 726 6.432783 CCATGTATTACCTTTGGTCAAAGTCA 59.567 38.462 18.52 6.46 44.66 3.41
658 727 7.040062 CCATGTATTACCTTTGGTCAAAGTCAA 60.040 37.037 18.52 13.12 44.66 3.18
659 728 7.504924 TGTATTACCTTTGGTCAAAGTCAAG 57.495 36.000 18.52 8.58 44.66 3.02
660 729 4.911514 TTACCTTTGGTCAAAGTCAAGC 57.088 40.909 18.52 0.00 44.66 4.01
661 730 3.018423 ACCTTTGGTCAAAGTCAAGCT 57.982 42.857 18.52 0.00 44.66 3.74
662 731 3.365472 ACCTTTGGTCAAAGTCAAGCTT 58.635 40.909 18.52 0.00 44.66 3.74
663 732 4.953579 TACCTTTGGTCAAAGTCAAGCTTT 59.046 37.500 18.52 0.00 44.66 3.51
675 744 7.812309 AAAGTCAAGCTTTGTAAACTTTGAC 57.188 32.000 14.76 14.88 45.00 3.18
676 745 6.509418 AGTCAAGCTTTGTAAACTTTGACA 57.491 33.333 20.02 0.00 30.59 3.58
677 746 6.919721 AGTCAAGCTTTGTAAACTTTGACAA 58.080 32.000 20.02 0.88 33.81 3.18
678 747 7.375053 AGTCAAGCTTTGTAAACTTTGACAAA 58.625 30.769 20.02 0.00 41.90 2.83
849 918 6.374417 AAATACAGAGGGAGTACAACACAT 57.626 37.500 0.00 0.00 0.00 3.21
850 919 6.374417 AATACAGAGGGAGTACAACACATT 57.626 37.500 0.00 0.00 0.00 2.71
851 920 4.273148 ACAGAGGGAGTACAACACATTC 57.727 45.455 0.00 0.00 0.00 2.67
852 921 3.008049 ACAGAGGGAGTACAACACATTCC 59.992 47.826 0.00 0.00 0.00 3.01
889 958 0.850856 AAACGACGTTCTTCTCACGC 59.149 50.000 14.58 0.00 41.53 5.34
937 1013 1.228552 CCACCAAACCCCTCACCAG 60.229 63.158 0.00 0.00 0.00 4.00
1170 1250 1.478510 TCTGAGGAGATCTTCAACGCC 59.521 52.381 3.21 0.00 31.40 5.68
1192 1295 1.750778 CCAAGGTGCTCTCTCTCTCTC 59.249 57.143 0.00 0.00 0.00 3.20
1196 1299 2.041620 AGGTGCTCTCTCTCTCTCTGTT 59.958 50.000 0.00 0.00 0.00 3.16
1210 1313 5.630121 TCTCTCTGTTTGTCTCTCTCTCTT 58.370 41.667 0.00 0.00 0.00 2.85
1219 1326 4.152647 TGTCTCTCTCTCTTTTAGTGCCA 58.847 43.478 0.00 0.00 0.00 4.92
1239 1346 4.702392 CCACGTTTGAGATTTTCTCTTCG 58.298 43.478 6.13 9.42 43.73 3.79
1246 1353 2.347731 AGATTTTCTCTTCGCGGTTCC 58.652 47.619 6.13 0.00 0.00 3.62
1247 1354 1.397343 GATTTTCTCTTCGCGGTTCCC 59.603 52.381 6.13 0.00 0.00 3.97
1696 1946 3.055891 GGCCAGTGCATTTAACCATTCTT 60.056 43.478 0.00 0.00 40.13 2.52
1977 2235 1.523758 GTGCCTTCAAATCAGTCGGT 58.476 50.000 0.00 0.00 0.00 4.69
2028 2286 2.551721 GGGCTCTCATATGTGGGATGTG 60.552 54.545 8.85 0.00 33.46 3.21
2094 2352 4.262036 GCAATCATTGGTCATGCAGATGAT 60.262 41.667 0.00 7.44 40.78 2.45
2131 2389 3.420893 CTCTGTCCCAAAATAAGTGCCA 58.579 45.455 0.00 0.00 0.00 4.92
2384 2661 6.728200 ACATGCGTTATTCATTAGATTGTGG 58.272 36.000 0.00 0.00 0.00 4.17
2399 2676 0.251297 TGTGGGATCAAACTGCTGGG 60.251 55.000 0.00 0.00 0.00 4.45
2420 2697 4.339814 GGGATCGCCTAATACTATCTCAGG 59.660 50.000 0.00 0.00 0.00 3.86
2506 2783 6.818644 GCAAGATAGAAACTGACTGACCATTA 59.181 38.462 0.00 0.00 0.00 1.90
2531 2808 6.664515 TGAACCAAATTCAGCGTTACTAAAG 58.335 36.000 0.00 0.00 42.62 1.85
3181 3458 2.175035 CTTACGGTGGGCGGAAGGAA 62.175 60.000 0.00 0.00 0.00 3.36
3355 3632 1.678970 GGGGATATTGGATGCGGGC 60.679 63.158 0.00 0.00 0.00 6.13
3665 3942 5.301555 AGCTTTTCCTTCTGTTGTACTCTC 58.698 41.667 0.00 0.00 0.00 3.20
3803 4081 8.275632 GTGATTTTGTCTTGGCAATAAAACTTC 58.724 33.333 14.96 11.76 0.00 3.01
3866 4144 6.164876 TGTTCAATGGATATTTTTGCACCAG 58.835 36.000 0.00 0.00 34.08 4.00
3875 4153 7.035612 GGATATTTTTGCACCAGGTAAAGAAG 58.964 38.462 0.00 0.00 32.54 2.85
3979 4257 4.681483 CGCTAAAGCCAAAGAAGGAAAAAG 59.319 41.667 0.00 0.00 37.91 2.27
3984 4264 5.039920 AGCCAAAGAAGGAAAAAGCAAAT 57.960 34.783 0.00 0.00 0.00 2.32
4264 4655 4.008933 AAGCTGCCTCCGTCGCTT 62.009 61.111 0.00 0.00 37.84 4.68
4266 4657 4.443266 GCTGCCTCCGTCGCTTCT 62.443 66.667 0.00 0.00 0.00 2.85
4308 4699 2.523015 GAAATCTTCATGCAAGTGCCG 58.477 47.619 0.00 0.00 41.18 5.69
4348 4739 4.763279 TCTCACTTGTAGTCGTCACCAATA 59.237 41.667 0.00 0.00 0.00 1.90
4450 4843 6.327365 TCCCAAGAAGACTGCATGAATCTATA 59.673 38.462 0.00 0.00 0.00 1.31
4474 4867 5.123227 TCAAAACTCCATCGACTTTGTTCT 58.877 37.500 0.00 0.00 0.00 3.01
4494 4887 0.179097 GATGGACGAACTGGAGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
4497 4890 0.250513 GGACGAACTGGAGGAGCATT 59.749 55.000 0.00 0.00 0.00 3.56
4498 4891 1.480954 GGACGAACTGGAGGAGCATTA 59.519 52.381 0.00 0.00 0.00 1.90
4550 4943 3.716195 CCATCCGCCACCTCACCA 61.716 66.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.382158 TCTCAAGCTCTATGTCGCCG 59.618 55.000 0.00 0.00 0.00 6.46
43 46 0.595053 CTGTGTCTCGTGCGAGTTGT 60.595 55.000 19.20 0.00 42.49 3.32
61 64 4.820716 GCTAACATGATCCTTGCATCTTCT 59.179 41.667 0.00 0.00 0.00 2.85
92 95 3.092301 TCGCATACTCATCATAGAGGGG 58.908 50.000 0.00 0.00 39.97 4.79
107 110 2.621338 CTCAAGCCACTTCTTCGCATA 58.379 47.619 0.00 0.00 0.00 3.14
126 130 4.499183 GTCGTTGATCTTCATCTTGTCCT 58.501 43.478 0.00 0.00 0.00 3.85
150 160 1.793134 CGCCGCCTCGTACTTCCTAT 61.793 60.000 0.00 0.00 0.00 2.57
343 402 4.317488 GACATGGCAAAATGGTCAATGTT 58.683 39.130 0.00 0.00 31.46 2.71
372 433 8.772705 ACAACGCAAAACAAATCATAATTCAAT 58.227 25.926 0.00 0.00 0.00 2.57
378 439 6.472486 TCGAAACAACGCAAAACAAATCATAA 59.528 30.769 0.00 0.00 0.00 1.90
394 456 7.646130 TGTCTGAATACCAAAATTCGAAACAAC 59.354 33.333 0.00 0.00 38.47 3.32
397 459 8.742554 ATTGTCTGAATACCAAAATTCGAAAC 57.257 30.769 0.00 0.00 38.47 2.78
405 468 7.013464 ACGGTACAAATTGTCTGAATACCAAAA 59.987 33.333 0.22 0.00 0.00 2.44
411 474 9.256477 GATCATACGGTACAAATTGTCTGAATA 57.744 33.333 0.22 0.00 0.00 1.75
479 542 4.657013 TGTTGGGTTGCACATCTACATAA 58.343 39.130 0.00 0.00 0.00 1.90
496 559 1.256812 GGACACCCCTCAAATGTTGG 58.743 55.000 0.00 0.00 0.00 3.77
524 587 4.320928 CTGCGGCGTTTTTGCGGA 62.321 61.111 9.37 0.00 37.16 5.54
533 600 3.036084 CTCAAACGTCTGCGGCGT 61.036 61.111 9.37 8.85 45.07 5.68
540 608 1.258445 ATCCGGCTCCTCAAACGTCT 61.258 55.000 0.00 0.00 0.00 4.18
542 610 0.036306 AAATCCGGCTCCTCAAACGT 59.964 50.000 0.00 0.00 0.00 3.99
586 655 1.305623 CCAGATGGCCCTCAAGCTT 59.694 57.895 10.92 0.00 0.00 3.74
597 666 2.808206 GGGAGTACGGGCCAGATGG 61.808 68.421 10.86 0.00 38.53 3.51
598 667 1.749334 GAGGGAGTACGGGCCAGATG 61.749 65.000 10.86 0.00 0.00 2.90
599 668 1.457831 GAGGGAGTACGGGCCAGAT 60.458 63.158 10.86 0.00 0.00 2.90
600 669 2.043248 GAGGGAGTACGGGCCAGA 60.043 66.667 10.86 0.00 0.00 3.86
601 670 3.155167 GGAGGGAGTACGGGCCAG 61.155 72.222 4.39 1.85 0.00 4.85
604 673 2.176314 AAAACGGAGGGAGTACGGGC 62.176 60.000 0.00 0.00 0.00 6.13
605 674 0.322648 AAAAACGGAGGGAGTACGGG 59.677 55.000 0.00 0.00 0.00 5.28
606 675 3.531934 ATAAAAACGGAGGGAGTACGG 57.468 47.619 0.00 0.00 0.00 4.02
607 676 6.101997 ACTAAATAAAAACGGAGGGAGTACG 58.898 40.000 0.00 0.00 0.00 3.67
608 677 6.536582 GGACTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
609 678 6.213195 TGGACTAAATAAAAACGGAGGGAGTA 59.787 38.462 0.00 0.00 0.00 2.59
610 679 5.013391 TGGACTAAATAAAAACGGAGGGAGT 59.987 40.000 0.00 0.00 0.00 3.85
611 680 5.493809 TGGACTAAATAAAAACGGAGGGAG 58.506 41.667 0.00 0.00 0.00 4.30
612 681 5.502089 TGGACTAAATAAAAACGGAGGGA 57.498 39.130 0.00 0.00 0.00 4.20
613 682 5.650703 ACATGGACTAAATAAAAACGGAGGG 59.349 40.000 0.00 0.00 0.00 4.30
614 683 6.753107 ACATGGACTAAATAAAAACGGAGG 57.247 37.500 0.00 0.00 0.00 4.30
617 686 9.940166 GGTAATACATGGACTAAATAAAAACGG 57.060 33.333 0.00 0.00 0.00 4.44
624 693 9.841295 GACCAAAGGTAATACATGGACTAAATA 57.159 33.333 13.58 0.00 35.25 1.40
625 694 8.333235 TGACCAAAGGTAATACATGGACTAAAT 58.667 33.333 13.58 0.00 35.25 1.40
626 695 7.691213 TGACCAAAGGTAATACATGGACTAAA 58.309 34.615 13.58 0.00 35.25 1.85
627 696 7.260387 TGACCAAAGGTAATACATGGACTAA 57.740 36.000 13.58 0.00 35.25 2.24
628 697 6.877668 TGACCAAAGGTAATACATGGACTA 57.122 37.500 13.58 0.00 35.25 2.59
629 698 5.772393 TGACCAAAGGTAATACATGGACT 57.228 39.130 13.58 0.00 35.25 3.85
630 699 6.827586 TTTGACCAAAGGTAATACATGGAC 57.172 37.500 13.58 9.27 35.25 4.02
652 721 6.919721 TGTCAAAGTTTACAAAGCTTGACTT 58.080 32.000 19.48 3.36 39.29 3.01
653 722 6.509418 TGTCAAAGTTTACAAAGCTTGACT 57.491 33.333 19.48 0.00 39.29 3.41
654 723 7.575332 TTTGTCAAAGTTTACAAAGCTTGAC 57.425 32.000 0.00 15.49 39.88 3.18
813 882 9.950496 CTCCCTCTGTATTTATTAACTATGCAT 57.050 33.333 3.79 3.79 0.00 3.96
814 883 8.934697 ACTCCCTCTGTATTTATTAACTATGCA 58.065 33.333 0.00 0.00 0.00 3.96
820 889 9.880157 TGTTGTACTCCCTCTGTATTTATTAAC 57.120 33.333 0.00 0.00 0.00 2.01
821 890 9.880157 GTGTTGTACTCCCTCTGTATTTATTAA 57.120 33.333 0.00 0.00 0.00 1.40
822 891 9.038072 TGTGTTGTACTCCCTCTGTATTTATTA 57.962 33.333 0.00 0.00 0.00 0.98
823 892 7.913789 TGTGTTGTACTCCCTCTGTATTTATT 58.086 34.615 0.00 0.00 0.00 1.40
824 893 7.490657 TGTGTTGTACTCCCTCTGTATTTAT 57.509 36.000 0.00 0.00 0.00 1.40
825 894 6.921486 TGTGTTGTACTCCCTCTGTATTTA 57.079 37.500 0.00 0.00 0.00 1.40
826 895 5.818678 TGTGTTGTACTCCCTCTGTATTT 57.181 39.130 0.00 0.00 0.00 1.40
827 896 6.374417 AATGTGTTGTACTCCCTCTGTATT 57.626 37.500 0.00 0.00 0.00 1.89
828 897 5.104900 GGAATGTGTTGTACTCCCTCTGTAT 60.105 44.000 0.00 0.00 0.00 2.29
829 898 4.222145 GGAATGTGTTGTACTCCCTCTGTA 59.778 45.833 0.00 0.00 0.00 2.74
830 899 3.008049 GGAATGTGTTGTACTCCCTCTGT 59.992 47.826 0.00 0.00 0.00 3.41
831 900 3.007940 TGGAATGTGTTGTACTCCCTCTG 59.992 47.826 0.00 0.00 0.00 3.35
832 901 3.248024 TGGAATGTGTTGTACTCCCTCT 58.752 45.455 0.00 0.00 0.00 3.69
833 902 3.695830 TGGAATGTGTTGTACTCCCTC 57.304 47.619 0.00 0.00 0.00 4.30
834 903 3.846588 AGATGGAATGTGTTGTACTCCCT 59.153 43.478 0.00 0.00 0.00 4.20
835 904 4.222124 AGATGGAATGTGTTGTACTCCC 57.778 45.455 0.00 0.00 0.00 4.30
836 905 5.491982 AGAAGATGGAATGTGTTGTACTCC 58.508 41.667 0.00 0.00 0.00 3.85
837 906 6.091441 GTGAGAAGATGGAATGTGTTGTACTC 59.909 42.308 0.00 0.00 0.00 2.59
838 907 5.934625 GTGAGAAGATGGAATGTGTTGTACT 59.065 40.000 0.00 0.00 0.00 2.73
871 940 1.266786 CGCGTGAGAAGAACGTCGTT 61.267 55.000 11.08 11.08 42.93 3.85
937 1013 4.488770 AGATGAGGAGGGGATAAGAGAAC 58.511 47.826 0.00 0.00 0.00 3.01
984 1060 1.409241 GCCATGATGCTTCCTTCTCCA 60.409 52.381 0.00 0.00 0.00 3.86
1035 1115 2.049985 CGGATCGAGATGCCGGAC 60.050 66.667 5.05 0.00 41.29 4.79
1170 1250 1.153667 GAGAGAGAGCACCTTGGCG 60.154 63.158 0.00 0.00 39.27 5.69
1192 1295 6.145371 GCACTAAAAGAGAGAGAGACAAACAG 59.855 42.308 0.00 0.00 0.00 3.16
1196 1299 4.588951 TGGCACTAAAAGAGAGAGAGACAA 59.411 41.667 0.00 0.00 0.00 3.18
1210 1313 5.298276 AGAAAATCTCAAACGTGGCACTAAA 59.702 36.000 16.72 0.00 0.00 1.85
1219 1326 3.120991 CGCGAAGAGAAAATCTCAAACGT 60.121 43.478 0.00 0.00 45.73 3.99
1246 1353 2.442087 GCATTTTCCTCCCCCGGG 60.442 66.667 15.80 15.80 0.00 5.73
1247 1354 2.828549 CGCATTTTCCTCCCCCGG 60.829 66.667 0.00 0.00 0.00 5.73
1321 1571 0.406361 TTGCCCCAAGTTTACCCGAT 59.594 50.000 0.00 0.00 0.00 4.18
1524 1774 2.729360 CTGTGCGTGAAACTTGACGATA 59.271 45.455 5.62 0.00 40.22 2.92
1696 1946 8.160765 TGATCTAAGACCCAAAACATGACTAAA 58.839 33.333 0.00 0.00 0.00 1.85
1710 1960 3.451178 TGCCAACTACTGATCTAAGACCC 59.549 47.826 0.00 0.00 0.00 4.46
1888 2146 7.490725 AGTGAGACATCAATCAGTAAAAGATCG 59.509 37.037 0.00 0.00 37.14 3.69
1892 2150 8.545229 AGAAGTGAGACATCAATCAGTAAAAG 57.455 34.615 0.00 0.00 37.14 2.27
2113 2371 4.021544 GTCAATGGCACTTATTTTGGGACA 60.022 41.667 0.00 0.00 0.00 4.02
2171 2429 5.279255 TCCGTCCCGAAATAAATATCACA 57.721 39.130 0.00 0.00 0.00 3.58
2173 2431 4.262721 CCCTCCGTCCCGAAATAAATATCA 60.263 45.833 0.00 0.00 0.00 2.15
2384 2661 1.303309 CGATCCCAGCAGTTTGATCC 58.697 55.000 0.00 0.00 31.94 3.36
2399 2676 5.648526 TGACCTGAGATAGTATTAGGCGATC 59.351 44.000 8.26 0.00 31.69 3.69
2420 2697 7.922811 ACTTCATGATTCCTCAAAAGTTTTGAC 59.077 33.333 23.91 15.45 37.82 3.18
2506 2783 6.811253 TTAGTAACGCTGAATTTGGTTCAT 57.189 33.333 0.00 0.00 45.36 2.57
2531 2808 4.846779 TCACCTGAATTAAACACAAGCC 57.153 40.909 0.00 0.00 0.00 4.35
3355 3632 1.737838 TCTCATGCCCTGTTTTAGCG 58.262 50.000 0.00 0.00 0.00 4.26
3665 3942 3.650139 ACTTCAGCCACGTACAACTAAG 58.350 45.455 0.00 0.00 0.00 2.18
3803 4081 2.618053 AGAAAATTGAGGTCGTAGCCG 58.382 47.619 0.00 0.00 0.00 5.52
3866 4144 3.942130 ACATTTGCTGGCTTCTTTACC 57.058 42.857 0.00 0.00 0.00 2.85
3875 4153 1.000717 ACAACGGTTACATTTGCTGGC 60.001 47.619 0.00 0.00 0.00 4.85
3979 4257 4.537015 ACGTGCTCAAGTAGAAAATTTGC 58.463 39.130 0.00 0.00 0.00 3.68
3984 4264 5.986741 TGACATAACGTGCTCAAGTAGAAAA 59.013 36.000 0.00 0.00 0.00 2.29
4264 4655 1.502690 TAGGCCGGCTCCATTAAAGA 58.497 50.000 28.56 0.00 0.00 2.52
4266 4657 1.270625 CGATAGGCCGGCTCCATTAAA 60.271 52.381 28.56 3.20 0.00 1.52
4308 4699 5.831997 AGTGAGAAAATGTTGGTTGTTAGC 58.168 37.500 0.00 0.00 0.00 3.09
4348 4739 5.351189 GCGCTTCAAATCAATTTATGGGTTT 59.649 36.000 0.00 0.00 0.00 3.27
4450 4843 5.765182 AGAACAAAGTCGATGGAGTTTTGAT 59.235 36.000 16.49 8.52 41.86 2.57
4474 4867 1.186200 CTCCTCCAGTTCGTCCATCA 58.814 55.000 0.00 0.00 0.00 3.07
4494 4887 6.533012 TCAAGTTGATCTTTCGAGCTCTAATG 59.467 38.462 12.85 9.66 33.63 1.90
4497 4890 5.644977 TCAAGTTGATCTTTCGAGCTCTA 57.355 39.130 12.85 0.00 33.63 2.43
4498 4891 4.527509 TCAAGTTGATCTTTCGAGCTCT 57.472 40.909 12.85 0.00 33.63 4.09
4550 4943 7.184067 AGAGTTTATTATTTCTCGTGGGAGT 57.816 36.000 0.00 0.00 41.26 3.85


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

AutoCloner maintained by Alex Coulton.