Multiple sequence alignment - TraesCS3D01G206200

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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 TraesCS3D01G206200 chr3D 100.000 3195 0 0 1 3195 268144688 268141494 0.000000e+00 5901.0
1 TraesCS3D01G206200 chr3D 100.000 1891 0 0 3453 5343 268141236 268139346 0.000000e+00 3493.0
2 TraesCS3D01G206200 chr3D 99.330 597 4 0 1 597 268151498 268150902 0.000000e+00 1081.0
3 TraesCS3D01G206200 chr3D 95.515 602 19 5 1 595 21206969 21206369 0.000000e+00 955.0
4 TraesCS3D01G206200 chr3D 81.951 205 28 8 2942 3143 570500795 570500597 1.190000e-36 165.0
5 TraesCS3D01G206200 chr3D 81.068 206 29 9 2942 3143 35710707 35710906 7.160000e-34 156.0
6 TraesCS3D01G206200 chr3B 97.600 2458 41 6 743 3195 292020405 292022849 0.000000e+00 4196.0
7 TraesCS3D01G206200 chr3B 97.036 1282 24 5 3453 4728 292023106 292024379 0.000000e+00 2145.0
8 TraesCS3D01G206200 chr3B 95.775 142 6 0 4727 4868 161826630 161826489 4.160000e-56 230.0
9 TraesCS3D01G206200 chr3A 97.102 1622 27 10 671 2278 343234210 343232595 0.000000e+00 2717.0
10 TraesCS3D01G206200 chr3A 97.047 1287 18 6 3455 4732 343230074 343228799 0.000000e+00 2148.0
11 TraesCS3D01G206200 chr3A 95.660 553 23 1 4727 5279 111801273 111801824 0.000000e+00 887.0
12 TraesCS3D01G206200 chr3A 98.698 461 6 0 2592 3052 343231018 343230558 0.000000e+00 819.0
13 TraesCS3D01G206200 chr3A 96.639 357 10 2 2267 2622 343231539 343231184 4.610000e-165 592.0
14 TraesCS3D01G206200 chr3A 100.000 106 0 0 3054 3159 343230431 343230326 4.220000e-46 196.0
15 TraesCS3D01G206200 chr3A 92.063 63 4 1 601 662 676202252 676202314 2.650000e-13 87.9
16 TraesCS3D01G206200 chr1D 96.013 602 19 4 1 597 29701070 29700469 0.000000e+00 974.0
17 TraesCS3D01G206200 chr1D 95.993 599 22 1 1 597 169609277 169608679 0.000000e+00 972.0
18 TraesCS3D01G206200 chr6D 95.826 599 22 2 1 597 182396264 182396861 0.000000e+00 965.0
19 TraesCS3D01G206200 chr6D 80.851 94 10 7 601 688 468141479 468141570 3.450000e-07 67.6
20 TraesCS3D01G206200 chr2D 95.167 600 24 5 1 597 629878654 629878057 0.000000e+00 942.0
21 TraesCS3D01G206200 chr2D 95.167 600 22 6 1 597 72634213 72633618 0.000000e+00 941.0
22 TraesCS3D01G206200 chr2A 95.159 599 25 3 1 597 446057482 446058078 0.000000e+00 942.0
23 TraesCS3D01G206200 chr7D 95.310 597 20 6 1 597 148362497 148361909 0.000000e+00 941.0
24 TraesCS3D01G206200 chr7D 100.000 54 0 0 5290 5343 419800887 419800834 3.410000e-17 100.0
25 TraesCS3D01G206200 chr7D 100.000 54 0 0 5290 5343 552317778 552317831 3.410000e-17 100.0
26 TraesCS3D01G206200 chr7D 85.870 92 6 5 601 686 287673733 287673643 2.050000e-14 91.6
27 TraesCS3D01G206200 chr7A 96.739 552 17 1 4728 5279 575617710 575617160 0.000000e+00 918.0
28 TraesCS3D01G206200 chr7A 89.919 496 46 2 4788 5279 65054373 65054868 2.100000e-178 636.0
29 TraesCS3D01G206200 chr7A 78.541 233 34 13 4979 5202 715335187 715334962 7.220000e-29 139.0
30 TraesCS3D01G206200 chr4A 95.290 552 26 0 4728 5279 348120332 348119781 0.000000e+00 876.0
31 TraesCS3D01G206200 chr4A 94.794 557 29 0 4723 5279 374360339 374359783 0.000000e+00 869.0
32 TraesCS3D01G206200 chrUn 97.085 446 12 1 4728 5173 217819745 217820189 0.000000e+00 750.0
33 TraesCS3D01G206200 chrUn 83.516 182 21 9 5029 5203 17532709 17532888 1.540000e-35 161.0
34 TraesCS3D01G206200 chr5B 96.479 142 5 0 4727 4868 608364673 608364814 8.950000e-58 235.0
35 TraesCS3D01G206200 chr5B 83.333 228 31 6 4986 5207 91204361 91204587 2.520000e-48 204.0
36 TraesCS3D01G206200 chr5B 97.059 34 1 0 614 647 693425425 693425392 2.080000e-04 58.4
37 TraesCS3D01G206200 chr5B 100.000 29 0 0 4147 4175 402435585 402435557 3.000000e-03 54.7
38 TraesCS3D01G206200 chr6B 96.454 141 5 0 4728 4868 700952108 700952248 3.220000e-57 233.0
39 TraesCS3D01G206200 chr4D 81.463 205 29 8 2942 3143 23910481 23910283 5.540000e-35 159.0
40 TraesCS3D01G206200 chr7B 78.838 241 42 8 4969 5202 662669205 662668967 2.580000e-33 154.0
41 TraesCS3D01G206200 chr7B 98.148 54 1 0 5290 5343 463841349 463841402 1.580000e-15 95.3
42 TraesCS3D01G206200 chr7B 97.143 35 1 0 608 642 711478583 711478617 5.780000e-05 60.2
43 TraesCS3D01G206200 chr2B 83.673 98 9 6 598 688 642792856 642792953 9.530000e-13 86.1
44 TraesCS3D01G206200 chr2B 92.105 38 3 0 610 647 463853907 463853870 3.000000e-03 54.7
45 TraesCS3D01G206200 chr6A 100.000 32 0 0 608 639 459682185 459682154 5.780000e-05 60.2
46 TraesCS3D01G206200 chr5D 92.857 42 2 1 607 647 426972661 426972702 5.780000e-05 60.2
47 TraesCS3D01G206200 chr1A 97.059 34 1 0 2942 2975 77099302 77099335 2.080000e-04 58.4
48 TraesCS3D01G206200 chr4B 100.000 29 0 0 4147 4175 61624139 61624111 3.000000e-03 54.7


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 TraesCS3D01G206200 chr3D 268139346 268144688 5342 True 4697.0 5901 100.0000 1 5343 2 chr3D.!!$R4 5342
1 TraesCS3D01G206200 chr3D 268150902 268151498 596 True 1081.0 1081 99.3300 1 597 1 chr3D.!!$R2 596
2 TraesCS3D01G206200 chr3D 21206369 21206969 600 True 955.0 955 95.5150 1 595 1 chr3D.!!$R1 594
3 TraesCS3D01G206200 chr3B 292020405 292024379 3974 False 3170.5 4196 97.3180 743 4728 2 chr3B.!!$F1 3985
4 TraesCS3D01G206200 chr3A 343228799 343234210 5411 True 1294.4 2717 97.8972 671 4732 5 chr3A.!!$R1 4061
5 TraesCS3D01G206200 chr3A 111801273 111801824 551 False 887.0 887 95.6600 4727 5279 1 chr3A.!!$F1 552
6 TraesCS3D01G206200 chr1D 29700469 29701070 601 True 974.0 974 96.0130 1 597 1 chr1D.!!$R1 596
7 TraesCS3D01G206200 chr1D 169608679 169609277 598 True 972.0 972 95.9930 1 597 1 chr1D.!!$R2 596
8 TraesCS3D01G206200 chr6D 182396264 182396861 597 False 965.0 965 95.8260 1 597 1 chr6D.!!$F1 596
9 TraesCS3D01G206200 chr2D 629878057 629878654 597 True 942.0 942 95.1670 1 597 1 chr2D.!!$R2 596
10 TraesCS3D01G206200 chr2D 72633618 72634213 595 True 941.0 941 95.1670 1 597 1 chr2D.!!$R1 596
11 TraesCS3D01G206200 chr2A 446057482 446058078 596 False 942.0 942 95.1590 1 597 1 chr2A.!!$F1 596
12 TraesCS3D01G206200 chr7D 148361909 148362497 588 True 941.0 941 95.3100 1 597 1 chr7D.!!$R1 596
13 TraesCS3D01G206200 chr7A 575617160 575617710 550 True 918.0 918 96.7390 4728 5279 1 chr7A.!!$R1 551
14 TraesCS3D01G206200 chr4A 348119781 348120332 551 True 876.0 876 95.2900 4728 5279 1 chr4A.!!$R1 551
15 TraesCS3D01G206200 chr4A 374359783 374360339 556 True 869.0 869 94.7940 4723 5279 1 chr4A.!!$R2 556

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
703 726 0.953960 AAAAGACAACCCTAGCGCGG 60.954 55.0 8.83 0.0 0.00 6.46 F
1018 1049 0.036388 CATGGCAGGTACCACGAACT 60.036 55.0 15.94 0.0 44.17 3.01 F
2414 3513 1.135094 CACCCACAGCCCATAGAGAT 58.865 55.0 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 3480 0.254462 TGGGTGCTGTTGTCAGTTCA 59.746 50.0 0.0 0.0 43.05 3.18 R
2464 3563 1.434188 TGTGGCTCAAGAGGGAGAAA 58.566 50.0 0.0 0.0 37.05 2.52 R
4394 5821 1.909700 ATGTCAACACATCGGGCTTT 58.090 45.0 0.0 0.0 39.15 3.51 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
322 340 8.530311 CCTATGACTATGAGATTATGCAACTCT 58.470 37.037 0.00 0.00 0.00 3.24
598 616 5.069501 GGTAACGAGATTGAACTAGGTGT 57.930 43.478 0.00 0.00 0.00 4.16
599 617 6.199937 GGTAACGAGATTGAACTAGGTGTA 57.800 41.667 0.00 0.00 0.00 2.90
600 618 6.624423 GGTAACGAGATTGAACTAGGTGTAA 58.376 40.000 0.00 0.00 0.00 2.41
601 619 6.750963 GGTAACGAGATTGAACTAGGTGTAAG 59.249 42.308 0.00 0.00 0.00 2.34
602 620 5.326200 ACGAGATTGAACTAGGTGTAAGG 57.674 43.478 0.00 0.00 0.00 2.69
603 621 5.014858 ACGAGATTGAACTAGGTGTAAGGA 58.985 41.667 0.00 0.00 0.00 3.36
604 622 5.105837 ACGAGATTGAACTAGGTGTAAGGAC 60.106 44.000 0.00 0.00 0.00 3.85
605 623 5.125739 CGAGATTGAACTAGGTGTAAGGACT 59.874 44.000 0.00 0.00 0.00 3.85
606 624 6.350277 CGAGATTGAACTAGGTGTAAGGACTT 60.350 42.308 0.00 0.00 0.00 3.01
607 625 7.317722 AGATTGAACTAGGTGTAAGGACTTT 57.682 36.000 0.00 0.00 0.00 2.66
608 626 7.162082 AGATTGAACTAGGTGTAAGGACTTTG 58.838 38.462 0.00 0.00 0.00 2.77
609 627 5.881923 TGAACTAGGTGTAAGGACTTTGT 57.118 39.130 0.00 0.00 0.00 2.83
610 628 6.243216 TGAACTAGGTGTAAGGACTTTGTT 57.757 37.500 0.00 0.00 0.00 2.83
611 629 6.053005 TGAACTAGGTGTAAGGACTTTGTTG 58.947 40.000 0.00 0.00 0.00 3.33
612 630 5.881923 ACTAGGTGTAAGGACTTTGTTGA 57.118 39.130 0.00 0.00 0.00 3.18
613 631 6.435292 ACTAGGTGTAAGGACTTTGTTGAT 57.565 37.500 0.00 0.00 0.00 2.57
614 632 6.838382 ACTAGGTGTAAGGACTTTGTTGATT 58.162 36.000 0.00 0.00 0.00 2.57
615 633 6.710744 ACTAGGTGTAAGGACTTTGTTGATTG 59.289 38.462 0.00 0.00 0.00 2.67
616 634 5.445964 AGGTGTAAGGACTTTGTTGATTGT 58.554 37.500 0.00 0.00 0.00 2.71
617 635 5.299279 AGGTGTAAGGACTTTGTTGATTGTG 59.701 40.000 0.00 0.00 0.00 3.33
618 636 5.067283 GGTGTAAGGACTTTGTTGATTGTGT 59.933 40.000 0.00 0.00 0.00 3.72
619 637 5.971202 GTGTAAGGACTTTGTTGATTGTGTG 59.029 40.000 0.00 0.00 0.00 3.82
620 638 3.715628 AGGACTTTGTTGATTGTGTGC 57.284 42.857 0.00 0.00 0.00 4.57
621 639 3.023119 AGGACTTTGTTGATTGTGTGCA 58.977 40.909 0.00 0.00 0.00 4.57
622 640 3.638160 AGGACTTTGTTGATTGTGTGCAT 59.362 39.130 0.00 0.00 0.00 3.96
623 641 3.983344 GGACTTTGTTGATTGTGTGCATC 59.017 43.478 0.00 0.00 0.00 3.91
624 642 4.261741 GGACTTTGTTGATTGTGTGCATCT 60.262 41.667 0.00 0.00 0.00 2.90
625 643 5.266733 ACTTTGTTGATTGTGTGCATCTT 57.733 34.783 0.00 0.00 0.00 2.40
626 644 6.389830 ACTTTGTTGATTGTGTGCATCTTA 57.610 33.333 0.00 0.00 0.00 2.10
627 645 6.441274 ACTTTGTTGATTGTGTGCATCTTAG 58.559 36.000 0.00 0.00 0.00 2.18
628 646 6.039717 ACTTTGTTGATTGTGTGCATCTTAGT 59.960 34.615 0.00 0.00 0.00 2.24
629 647 6.389830 TTGTTGATTGTGTGCATCTTAGTT 57.610 33.333 0.00 0.00 0.00 2.24
630 648 7.503521 TTGTTGATTGTGTGCATCTTAGTTA 57.496 32.000 0.00 0.00 0.00 2.24
631 649 7.686438 TGTTGATTGTGTGCATCTTAGTTAT 57.314 32.000 0.00 0.00 0.00 1.89
632 650 7.529158 TGTTGATTGTGTGCATCTTAGTTATG 58.471 34.615 0.00 0.00 0.00 1.90
643 661 6.355397 CATCTTAGTTATGCAGAGGTTGTG 57.645 41.667 0.00 0.00 0.00 3.33
644 662 5.483685 TCTTAGTTATGCAGAGGTTGTGT 57.516 39.130 0.00 0.00 0.00 3.72
645 663 5.237815 TCTTAGTTATGCAGAGGTTGTGTG 58.762 41.667 0.00 0.00 0.00 3.82
646 664 3.492102 AGTTATGCAGAGGTTGTGTGT 57.508 42.857 0.00 0.00 0.00 3.72
647 665 4.617253 AGTTATGCAGAGGTTGTGTGTA 57.383 40.909 0.00 0.00 0.00 2.90
648 666 4.968259 AGTTATGCAGAGGTTGTGTGTAA 58.032 39.130 0.00 0.00 0.00 2.41
649 667 5.560724 AGTTATGCAGAGGTTGTGTGTAAT 58.439 37.500 0.00 0.00 0.00 1.89
650 668 5.412594 AGTTATGCAGAGGTTGTGTGTAATG 59.587 40.000 0.00 0.00 0.00 1.90
651 669 3.483808 TGCAGAGGTTGTGTGTAATGA 57.516 42.857 0.00 0.00 0.00 2.57
652 670 4.019792 TGCAGAGGTTGTGTGTAATGAT 57.980 40.909 0.00 0.00 0.00 2.45
653 671 4.397420 TGCAGAGGTTGTGTGTAATGATT 58.603 39.130 0.00 0.00 0.00 2.57
654 672 5.555966 TGCAGAGGTTGTGTGTAATGATTA 58.444 37.500 0.00 0.00 0.00 1.75
655 673 6.000840 TGCAGAGGTTGTGTGTAATGATTAA 58.999 36.000 0.00 0.00 0.00 1.40
656 674 6.488344 TGCAGAGGTTGTGTGTAATGATTAAA 59.512 34.615 0.00 0.00 0.00 1.52
657 675 6.801862 GCAGAGGTTGTGTGTAATGATTAAAC 59.198 38.462 0.00 0.00 0.00 2.01
658 676 7.305474 CAGAGGTTGTGTGTAATGATTAAACC 58.695 38.462 3.20 5.54 36.83 3.27
659 677 7.174946 CAGAGGTTGTGTGTAATGATTAAACCT 59.825 37.037 14.78 14.78 46.66 3.50
660 678 7.724061 AGAGGTTGTGTGTAATGATTAAACCTT 59.276 33.333 15.59 6.96 44.63 3.50
661 679 8.245195 AGGTTGTGTGTAATGATTAAACCTTT 57.755 30.769 10.84 0.00 42.63 3.11
662 680 9.357161 AGGTTGTGTGTAATGATTAAACCTTTA 57.643 29.630 10.84 0.00 42.63 1.85
663 681 9.968870 GGTTGTGTGTAATGATTAAACCTTTAA 57.031 29.630 3.20 0.00 37.08 1.52
674 692 6.378848 TGATTAAACCTTTAATAAAGCGCCCT 59.621 34.615 2.29 0.00 41.88 5.19
703 726 0.953960 AAAAGACAACCCTAGCGCGG 60.954 55.000 8.83 0.00 0.00 6.46
711 734 1.453197 CCCTAGCGCGGGGATTTTT 60.453 57.895 29.29 0.31 46.50 1.94
1011 1042 2.189521 CCCGTCATGGCAGGTACC 59.810 66.667 2.73 2.73 35.87 3.34
1018 1049 0.036388 CATGGCAGGTACCACGAACT 60.036 55.000 15.94 0.00 44.17 3.01
1149 1180 2.754552 GCAATTGGCATGGAAGACTACA 59.245 45.455 7.72 0.00 43.97 2.74
1320 1351 1.489481 TTGATGCAGAGATCGACCCT 58.511 50.000 0.00 0.00 0.00 4.34
1428 1459 2.350192 CACCATTTGTAGCACGCGATTA 59.650 45.455 15.93 0.00 0.00 1.75
1444 1475 3.800604 GCGATTAAGTTCTCCCTAGGCAG 60.801 52.174 2.05 0.00 0.00 4.85
1589 1621 2.163390 CGACGAGGCAGCTCATGTG 61.163 63.158 0.00 0.00 0.00 3.21
1858 1890 6.675541 TGGATACTCTTGCTTTTGGTGCAAA 61.676 40.000 0.00 0.00 43.21 3.68
1994 2026 4.082408 GGTATGTAAGACTTGGTTTTGGCC 60.082 45.833 0.00 0.00 0.00 5.36
2349 3448 4.150098 GTCTAGCTAACCACAAGAACAACG 59.850 45.833 0.00 0.00 0.00 4.10
2381 3480 2.679930 GCTTAGCGACCCACAATAACCT 60.680 50.000 0.00 0.00 0.00 3.50
2414 3513 1.135094 CACCCACAGCCCATAGAGAT 58.865 55.000 0.00 0.00 0.00 2.75
2464 3563 1.308998 CACCGCAGAAAACTGGTTCT 58.691 50.000 0.00 0.00 38.41 3.01
2788 4083 7.013750 TGCTCAAATACCAACACAACTCATTAA 59.986 33.333 0.00 0.00 0.00 1.40
2840 4135 3.680169 TCCCCCTCATTCACCTGATATT 58.320 45.455 0.00 0.00 0.00 1.28
3024 4319 6.807789 AGGAGGTATTCTTAGCTTTAGTTCG 58.192 40.000 0.00 0.00 36.32 3.95
3186 4606 0.889994 TGGTGCATTCATTCAGTGGC 59.110 50.000 0.00 0.00 0.00 5.01
3812 5233 6.893554 TCATGGAAAATGAATCTTCCTCACAT 59.106 34.615 0.00 0.00 41.52 3.21
4175 5599 2.091333 AGATGAGGAAGAGGAGGAGGAC 60.091 54.545 0.00 0.00 0.00 3.85
4394 5821 4.202010 GCTGCGCAAAATCTATTTTAGGGA 60.202 41.667 13.05 0.00 37.86 4.20
4470 5897 0.396435 TCATTCAGTTGCCTCGTGGT 59.604 50.000 5.26 0.00 35.27 4.16
4581 6010 5.479306 AGCATCTGTGTAATGTACTTCGTT 58.521 37.500 0.00 0.00 0.00 3.85
4920 6349 3.384146 TGTTGTGAATGTCCATGCTTTGT 59.616 39.130 0.00 0.00 0.00 2.83
5032 6461 6.987992 CGTGCCCCACTTTAACTATAGATTTA 59.012 38.462 6.78 0.00 31.34 1.40
5279 6708 5.181245 GCAACTCACTAAAGGATACAAAGCA 59.819 40.000 0.00 0.00 41.41 3.91
5280 6709 6.127897 GCAACTCACTAAAGGATACAAAGCAT 60.128 38.462 0.00 0.00 41.41 3.79
5281 6710 7.467623 CAACTCACTAAAGGATACAAAGCATC 58.532 38.462 0.00 0.00 41.41 3.91
5282 6711 5.812642 ACTCACTAAAGGATACAAAGCATCG 59.187 40.000 0.00 0.00 41.41 3.84
5283 6712 5.972935 TCACTAAAGGATACAAAGCATCGA 58.027 37.500 0.00 0.00 41.41 3.59
5284 6713 6.403049 TCACTAAAGGATACAAAGCATCGAA 58.597 36.000 0.00 0.00 41.41 3.71
5285 6714 7.047891 TCACTAAAGGATACAAAGCATCGAAT 58.952 34.615 0.00 0.00 41.41 3.34
5286 6715 7.552687 TCACTAAAGGATACAAAGCATCGAATT 59.447 33.333 0.00 0.00 41.41 2.17
5287 6716 8.184192 CACTAAAGGATACAAAGCATCGAATTT 58.816 33.333 0.00 0.00 41.41 1.82
5288 6717 9.391006 ACTAAAGGATACAAAGCATCGAATTTA 57.609 29.630 0.00 0.00 41.41 1.40
5291 6720 7.807977 AGGATACAAAGCATCGAATTTATGT 57.192 32.000 0.00 0.00 41.41 2.29
5292 6721 7.642669 AGGATACAAAGCATCGAATTTATGTG 58.357 34.615 0.00 0.00 41.41 3.21
5293 6722 6.857964 GGATACAAAGCATCGAATTTATGTGG 59.142 38.462 0.00 0.00 0.00 4.17
5294 6723 4.997565 ACAAAGCATCGAATTTATGTGGG 58.002 39.130 0.00 0.00 0.00 4.61
5295 6724 4.142182 ACAAAGCATCGAATTTATGTGGGG 60.142 41.667 0.00 0.00 0.00 4.96
5296 6725 3.576078 AGCATCGAATTTATGTGGGGA 57.424 42.857 0.00 0.00 0.00 4.81
5297 6726 4.104383 AGCATCGAATTTATGTGGGGAT 57.896 40.909 0.00 0.00 0.00 3.85
5298 6727 4.473444 AGCATCGAATTTATGTGGGGATT 58.527 39.130 0.00 0.00 0.00 3.01
5299 6728 4.520492 AGCATCGAATTTATGTGGGGATTC 59.480 41.667 0.00 0.00 0.00 2.52
5300 6729 4.278170 GCATCGAATTTATGTGGGGATTCA 59.722 41.667 0.00 0.00 0.00 2.57
5301 6730 5.221224 GCATCGAATTTATGTGGGGATTCAA 60.221 40.000 0.00 0.00 0.00 2.69
5302 6731 6.517194 GCATCGAATTTATGTGGGGATTCAAT 60.517 38.462 0.00 0.00 0.00 2.57
5303 6732 6.633500 TCGAATTTATGTGGGGATTCAATC 57.367 37.500 0.00 0.00 0.00 2.67
5313 6742 2.629336 GGATTCAATCCGAGGCTCTT 57.371 50.000 13.50 0.00 40.13 2.85
5314 6743 3.753294 GGATTCAATCCGAGGCTCTTA 57.247 47.619 13.50 0.09 40.13 2.10
5315 6744 3.658709 GGATTCAATCCGAGGCTCTTAG 58.341 50.000 13.50 1.24 40.13 2.18
5316 6745 3.070302 GGATTCAATCCGAGGCTCTTAGT 59.930 47.826 13.50 0.00 40.13 2.24
5317 6746 3.526931 TTCAATCCGAGGCTCTTAGTG 57.473 47.619 13.50 9.71 0.00 2.74
5318 6747 2.735151 TCAATCCGAGGCTCTTAGTGA 58.265 47.619 13.50 11.86 0.00 3.41
5319 6748 3.096852 TCAATCCGAGGCTCTTAGTGAA 58.903 45.455 13.50 0.00 0.00 3.18
5320 6749 3.119101 TCAATCCGAGGCTCTTAGTGAAC 60.119 47.826 13.50 0.00 0.00 3.18
5321 6750 0.809385 TCCGAGGCTCTTAGTGAACG 59.191 55.000 13.50 0.00 0.00 3.95
5322 6751 0.809385 CCGAGGCTCTTAGTGAACGA 59.191 55.000 13.50 0.00 0.00 3.85
5323 6752 1.405821 CCGAGGCTCTTAGTGAACGAT 59.594 52.381 13.50 0.00 0.00 3.73
5324 6753 2.617308 CCGAGGCTCTTAGTGAACGATA 59.383 50.000 13.50 0.00 0.00 2.92
5325 6754 3.253677 CCGAGGCTCTTAGTGAACGATAT 59.746 47.826 13.50 0.00 0.00 1.63
5326 6755 4.261656 CCGAGGCTCTTAGTGAACGATATT 60.262 45.833 13.50 0.00 0.00 1.28
5327 6756 5.282510 CGAGGCTCTTAGTGAACGATATTT 58.717 41.667 13.50 0.00 0.00 1.40
5328 6757 5.174035 CGAGGCTCTTAGTGAACGATATTTG 59.826 44.000 13.50 0.00 0.00 2.32
5329 6758 5.360591 AGGCTCTTAGTGAACGATATTTGG 58.639 41.667 0.00 0.00 0.00 3.28
5330 6759 4.511826 GGCTCTTAGTGAACGATATTTGGG 59.488 45.833 0.00 0.00 0.00 4.12
5331 6760 4.024809 GCTCTTAGTGAACGATATTTGGGC 60.025 45.833 0.00 0.00 0.00 5.36
5332 6761 4.448210 TCTTAGTGAACGATATTTGGGCC 58.552 43.478 0.00 0.00 0.00 5.80
5333 6762 4.163458 TCTTAGTGAACGATATTTGGGCCT 59.837 41.667 4.53 0.00 0.00 5.19
5334 6763 2.919228 AGTGAACGATATTTGGGCCTC 58.081 47.619 4.53 0.00 0.00 4.70
5335 6764 1.947456 GTGAACGATATTTGGGCCTCC 59.053 52.381 4.53 0.00 0.00 4.30
5336 6765 1.133915 TGAACGATATTTGGGCCTCCC 60.134 52.381 4.53 0.00 45.71 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
564 582 1.741706 CTCGTTACCGGCAAGTCTCTA 59.258 52.381 0.00 0.00 33.95 2.43
597 615 4.976116 GCACACAATCAACAAAGTCCTTAC 59.024 41.667 0.00 0.00 0.00 2.34
598 616 4.642437 TGCACACAATCAACAAAGTCCTTA 59.358 37.500 0.00 0.00 0.00 2.69
599 617 3.446873 TGCACACAATCAACAAAGTCCTT 59.553 39.130 0.00 0.00 0.00 3.36
600 618 3.023119 TGCACACAATCAACAAAGTCCT 58.977 40.909 0.00 0.00 0.00 3.85
601 619 3.435105 TGCACACAATCAACAAAGTCC 57.565 42.857 0.00 0.00 0.00 3.85
602 620 4.863491 AGATGCACACAATCAACAAAGTC 58.137 39.130 0.00 0.00 0.00 3.01
603 621 4.924305 AGATGCACACAATCAACAAAGT 57.076 36.364 0.00 0.00 0.00 2.66
604 622 6.441274 ACTAAGATGCACACAATCAACAAAG 58.559 36.000 0.00 0.00 0.00 2.77
605 623 6.389830 ACTAAGATGCACACAATCAACAAA 57.610 33.333 0.00 0.00 0.00 2.83
606 624 6.389830 AACTAAGATGCACACAATCAACAA 57.610 33.333 0.00 0.00 0.00 2.83
607 625 7.529158 CATAACTAAGATGCACACAATCAACA 58.471 34.615 0.00 0.00 0.00 3.33
608 626 7.959718 CATAACTAAGATGCACACAATCAAC 57.040 36.000 0.00 0.00 0.00 3.18
620 638 5.877012 ACACAACCTCTGCATAACTAAGATG 59.123 40.000 0.00 0.00 0.00 2.90
621 639 5.877012 CACACAACCTCTGCATAACTAAGAT 59.123 40.000 0.00 0.00 0.00 2.40
622 640 5.221641 ACACACAACCTCTGCATAACTAAGA 60.222 40.000 0.00 0.00 0.00 2.10
623 641 4.997395 ACACACAACCTCTGCATAACTAAG 59.003 41.667 0.00 0.00 0.00 2.18
624 642 4.968259 ACACACAACCTCTGCATAACTAA 58.032 39.130 0.00 0.00 0.00 2.24
625 643 4.617253 ACACACAACCTCTGCATAACTA 57.383 40.909 0.00 0.00 0.00 2.24
626 644 3.492102 ACACACAACCTCTGCATAACT 57.508 42.857 0.00 0.00 0.00 2.24
627 645 5.411361 TCATTACACACAACCTCTGCATAAC 59.589 40.000 0.00 0.00 0.00 1.89
628 646 5.555966 TCATTACACACAACCTCTGCATAA 58.444 37.500 0.00 0.00 0.00 1.90
629 647 5.159273 TCATTACACACAACCTCTGCATA 57.841 39.130 0.00 0.00 0.00 3.14
630 648 4.019792 TCATTACACACAACCTCTGCAT 57.980 40.909 0.00 0.00 0.00 3.96
631 649 3.483808 TCATTACACACAACCTCTGCA 57.516 42.857 0.00 0.00 0.00 4.41
632 650 6.494893 TTAATCATTACACACAACCTCTGC 57.505 37.500 0.00 0.00 0.00 4.26
633 651 7.174946 AGGTTTAATCATTACACACAACCTCTG 59.825 37.037 5.06 0.00 38.74 3.35
634 652 7.231467 AGGTTTAATCATTACACACAACCTCT 58.769 34.615 5.06 0.00 38.74 3.69
635 653 7.448748 AGGTTTAATCATTACACACAACCTC 57.551 36.000 5.06 0.00 38.74 3.85
636 654 7.833285 AAGGTTTAATCATTACACACAACCT 57.167 32.000 5.06 5.06 43.72 3.50
637 655 9.968870 TTAAAGGTTTAATCATTACACACAACC 57.031 29.630 1.09 1.09 33.90 3.77
646 664 9.738832 GGCGCTTTATTAAAGGTTTAATCATTA 57.261 29.630 16.02 0.00 41.17 1.90
647 665 7.709182 GGGCGCTTTATTAAAGGTTTAATCATT 59.291 33.333 16.02 0.00 41.17 2.57
648 666 7.069455 AGGGCGCTTTATTAAAGGTTTAATCAT 59.931 33.333 16.02 0.00 41.17 2.45
649 667 6.378848 AGGGCGCTTTATTAAAGGTTTAATCA 59.621 34.615 16.02 0.00 41.17 2.57
650 668 6.802608 AGGGCGCTTTATTAAAGGTTTAATC 58.197 36.000 16.02 0.00 41.17 1.75
651 669 6.785337 AGGGCGCTTTATTAAAGGTTTAAT 57.215 33.333 16.02 11.46 43.57 1.40
652 670 6.593268 AAGGGCGCTTTATTAAAGGTTTAA 57.407 33.333 10.73 0.00 38.93 1.52
653 671 6.434965 AGAAAGGGCGCTTTATTAAAGGTTTA 59.565 34.615 26.64 0.00 38.93 2.01
654 672 5.245301 AGAAAGGGCGCTTTATTAAAGGTTT 59.755 36.000 26.64 2.19 38.93 3.27
655 673 4.770531 AGAAAGGGCGCTTTATTAAAGGTT 59.229 37.500 26.64 2.73 38.93 3.50
656 674 4.341487 AGAAAGGGCGCTTTATTAAAGGT 58.659 39.130 26.64 3.49 38.93 3.50
657 675 4.495844 CGAGAAAGGGCGCTTTATTAAAGG 60.496 45.833 26.64 9.71 38.93 3.11
658 676 4.495844 CCGAGAAAGGGCGCTTTATTAAAG 60.496 45.833 26.64 15.89 41.46 1.85
659 677 3.375922 CCGAGAAAGGGCGCTTTATTAAA 59.624 43.478 26.64 0.00 0.00 1.52
660 678 2.940410 CCGAGAAAGGGCGCTTTATTAA 59.060 45.455 26.64 0.00 0.00 1.40
661 679 2.168936 TCCGAGAAAGGGCGCTTTATTA 59.831 45.455 26.64 11.90 0.00 0.98
662 680 1.065709 TCCGAGAAAGGGCGCTTTATT 60.066 47.619 26.64 18.27 0.00 1.40
663 681 0.539986 TCCGAGAAAGGGCGCTTTAT 59.460 50.000 26.64 24.14 0.00 1.40
664 682 0.322322 TTCCGAGAAAGGGCGCTTTA 59.678 50.000 26.64 9.91 0.00 1.85
665 683 0.536460 TTTCCGAGAAAGGGCGCTTT 60.536 50.000 26.87 26.87 0.00 3.51
666 684 0.536460 TTTTCCGAGAAAGGGCGCTT 60.536 50.000 10.73 10.73 0.00 4.68
667 685 0.536460 TTTTTCCGAGAAAGGGCGCT 60.536 50.000 7.64 0.00 0.00 5.92
668 686 1.953772 TTTTTCCGAGAAAGGGCGC 59.046 52.632 0.00 0.00 0.00 6.53
711 734 8.697507 AAAAATTCAGAAGGCTAGAGAAAGAA 57.302 30.769 0.00 0.00 0.00 2.52
712 735 9.965902 ATAAAAATTCAGAAGGCTAGAGAAAGA 57.034 29.630 0.00 0.00 0.00 2.52
728 751 8.924691 CGCAAGGATTTTTCTCATAAAAATTCA 58.075 29.630 13.82 0.00 39.23 2.57
1011 1042 1.264288 GAAGCAGGGTTTGAGTTCGTG 59.736 52.381 0.00 0.00 0.00 4.35
1018 1049 0.693049 GAGGAGGAAGCAGGGTTTGA 59.307 55.000 0.00 0.00 0.00 2.69
1149 1180 1.558756 CTCCATCTCCTGTTCCTGCTT 59.441 52.381 0.00 0.00 0.00 3.91
1320 1351 1.065273 GTCGATCCCGCTTTCGCTA 59.935 57.895 0.00 0.00 35.39 4.26
1428 1459 1.003696 GTTGCTGCCTAGGGAGAACTT 59.996 52.381 32.59 0.00 35.50 2.66
1589 1621 7.954788 TTTGTACAAAATCAATTTACCTGGC 57.045 32.000 18.54 0.00 0.00 4.85
1858 1890 6.380095 TTTAGAAAACAATAAGCACACGGT 57.620 33.333 0.00 0.00 0.00 4.83
1994 2026 2.554032 GTGAACTGAACACAGGATTGGG 59.446 50.000 0.00 0.00 38.05 4.12
2079 2111 7.790782 ATAACTGTCCATGGTTATTTGGTTT 57.209 32.000 12.58 0.00 35.80 3.27
2381 3480 0.254462 TGGGTGCTGTTGTCAGTTCA 59.746 50.000 0.00 0.00 43.05 3.18
2414 3513 3.685139 TGGCTGTTTTGTTGTTTGGAA 57.315 38.095 0.00 0.00 0.00 3.53
2464 3563 1.434188 TGTGGCTCAAGAGGGAGAAA 58.566 50.000 0.00 0.00 37.05 2.52
2840 4135 6.071952 GGAAGGTTGCACATAAATGAGAAGAA 60.072 38.462 0.00 0.00 0.00 2.52
3812 5233 7.208777 ACAAATGCTATGAAAAACATGTCACA 58.791 30.769 0.00 0.00 39.77 3.58
4093 5517 9.862371 ACAACTTATGTAATGAGAGAGTTACAG 57.138 33.333 4.57 0.00 42.21 2.74
4394 5821 1.909700 ATGTCAACACATCGGGCTTT 58.090 45.000 0.00 0.00 39.15 3.51
4470 5897 1.209383 GCAGCTACGTCGTCAGTCA 59.791 57.895 0.00 0.00 0.00 3.41
4581 6010 7.794810 CAGACGAAAAACACGATAAATTACACA 59.205 33.333 0.00 0.00 34.70 3.72
4920 6349 3.751518 GGCAACTGGAGTTTCCTCTTAA 58.248 45.455 1.38 0.00 38.13 1.85
4967 6396 9.268282 ACCAATAAATCAGGACGGATATAGTAT 57.732 33.333 0.00 0.00 0.00 2.12
4973 6402 4.041198 GGGACCAATAAATCAGGACGGATA 59.959 45.833 0.00 0.00 0.00 2.59
5265 6694 8.686334 ACATAAATTCGATGCTTTGTATCCTTT 58.314 29.630 0.00 0.00 0.00 3.11
5279 6708 6.209391 GGATTGAATCCCCACATAAATTCGAT 59.791 38.462 13.26 0.00 43.88 3.59
5280 6709 5.534654 GGATTGAATCCCCACATAAATTCGA 59.465 40.000 13.26 0.00 43.88 3.71
5281 6710 5.772521 GGATTGAATCCCCACATAAATTCG 58.227 41.667 13.26 0.00 43.88 3.34
5294 6723 2.629336 AAGAGCCTCGGATTGAATCC 57.371 50.000 14.21 14.21 46.22 3.01
5295 6724 4.054671 CACTAAGAGCCTCGGATTGAATC 58.945 47.826 0.00 0.00 0.00 2.52
5296 6725 3.706594 TCACTAAGAGCCTCGGATTGAAT 59.293 43.478 0.00 0.00 0.00 2.57
5297 6726 3.096852 TCACTAAGAGCCTCGGATTGAA 58.903 45.455 0.00 0.00 0.00 2.69
5298 6727 2.735151 TCACTAAGAGCCTCGGATTGA 58.265 47.619 0.00 0.00 0.00 2.57
5299 6728 3.190874 GTTCACTAAGAGCCTCGGATTG 58.809 50.000 0.00 0.00 0.00 2.67
5300 6729 2.159226 CGTTCACTAAGAGCCTCGGATT 60.159 50.000 0.00 0.00 0.00 3.01
5301 6730 1.405821 CGTTCACTAAGAGCCTCGGAT 59.594 52.381 0.00 0.00 0.00 4.18
5302 6731 0.809385 CGTTCACTAAGAGCCTCGGA 59.191 55.000 0.00 0.00 0.00 4.55
5303 6732 0.809385 TCGTTCACTAAGAGCCTCGG 59.191 55.000 0.00 0.00 0.00 4.63
5304 6733 2.853731 ATCGTTCACTAAGAGCCTCG 57.146 50.000 0.00 0.00 0.00 4.63
5305 6734 5.463724 CCAAATATCGTTCACTAAGAGCCTC 59.536 44.000 0.00 0.00 0.00 4.70
5306 6735 5.360591 CCAAATATCGTTCACTAAGAGCCT 58.639 41.667 0.00 0.00 0.00 4.58
5307 6736 4.511826 CCCAAATATCGTTCACTAAGAGCC 59.488 45.833 0.00 0.00 0.00 4.70
5308 6737 4.024809 GCCCAAATATCGTTCACTAAGAGC 60.025 45.833 0.00 0.00 0.00 4.09
5309 6738 4.511826 GGCCCAAATATCGTTCACTAAGAG 59.488 45.833 0.00 0.00 0.00 2.85
5310 6739 4.163458 AGGCCCAAATATCGTTCACTAAGA 59.837 41.667 0.00 0.00 0.00 2.10
5311 6740 4.451900 AGGCCCAAATATCGTTCACTAAG 58.548 43.478 0.00 0.00 0.00 2.18
5312 6741 4.448210 GAGGCCCAAATATCGTTCACTAA 58.552 43.478 0.00 0.00 0.00 2.24
5313 6742 3.181458 GGAGGCCCAAATATCGTTCACTA 60.181 47.826 0.00 0.00 0.00 2.74
5314 6743 2.421529 GGAGGCCCAAATATCGTTCACT 60.422 50.000 0.00 0.00 0.00 3.41
5315 6744 1.947456 GGAGGCCCAAATATCGTTCAC 59.053 52.381 0.00 0.00 0.00 3.18
5316 6745 1.133915 GGGAGGCCCAAATATCGTTCA 60.134 52.381 0.00 0.00 44.65 3.18
5317 6746 1.605753 GGGAGGCCCAAATATCGTTC 58.394 55.000 0.00 0.00 44.65 3.95
5318 6747 3.821306 GGGAGGCCCAAATATCGTT 57.179 52.632 0.00 0.00 44.65 3.85


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

AutoCloner maintained by Alex Coulton.