Multiple sequence alignment - TraesCS2B01G465900

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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 TraesCS2B01G465900 chr2B 100.000 3242 0 0 1 3242 661444006 661447247 0.000000e+00 5987.0
1 TraesCS2B01G465900 chr2B 89.610 539 49 5 4 539 745776929 745776395 0.000000e+00 678.0
2 TraesCS2B01G465900 chr2B 100.000 362 0 0 3516 3877 661447521 661447882 0.000000e+00 669.0
3 TraesCS2B01G465900 chr2B 81.016 669 104 17 995 1660 661175712 661176360 9.610000e-141 510.0
4 TraesCS2B01G465900 chr2B 85.751 386 44 4 943 1324 661191806 661192184 7.800000e-107 398.0
5 TraesCS2B01G465900 chr2B 88.000 50 6 0 3613 3662 747347160 747347111 4.180000e-05 60.2
6 TraesCS2B01G465900 chr2B 100.000 31 0 0 3613 3643 661447522 661447552 1.500000e-04 58.4
7 TraesCS2B01G465900 chr2B 100.000 31 0 0 3517 3547 661447618 661447648 1.500000e-04 58.4
8 TraesCS2B01G465900 chr2B 100.000 31 0 0 3516 3546 747347161 747347131 1.500000e-04 58.4
9 TraesCS2B01G465900 chrUn 92.769 2199 120 22 1038 3226 26257763 26259932 0.000000e+00 3144.0
10 TraesCS2B01G465900 chrUn 84.974 386 47 4 943 1324 26244801 26245179 7.860000e-102 381.0
11 TraesCS2B01G465900 chrUn 94.872 156 7 1 804 959 26257608 26257762 3.870000e-60 243.0
12 TraesCS2B01G465900 chrUn 82.759 290 26 12 3591 3868 26261334 26261611 1.800000e-58 237.0
13 TraesCS2B01G465900 chrUn 87.234 141 18 0 1493 1633 26245225 26245365 1.110000e-35 161.0
14 TraesCS2B01G465900 chrUn 85.816 141 18 1 632 770 26255173 26255313 8.680000e-32 148.0
15 TraesCS2B01G465900 chr2A 92.302 1390 76 11 1848 3235 694902806 694904166 0.000000e+00 1945.0
16 TraesCS2B01G465900 chr2A 94.130 988 52 4 769 1751 694901825 694902811 0.000000e+00 1498.0
17 TraesCS2B01G465900 chr2A 81.832 677 111 10 995 1670 694839903 694840568 3.380000e-155 558.0
18 TraesCS2B01G465900 chr2A 89.971 349 15 2 3543 3871 694904528 694904876 2.140000e-117 433.0
19 TraesCS2B01G465900 chr2A 86.269 386 42 4 943 1324 694864528 694864906 3.610000e-110 409.0
20 TraesCS2B01G465900 chr2A 86.096 187 26 0 1484 1670 694864943 694865129 6.570000e-48 202.0
21 TraesCS2B01G465900 chr2A 85.981 107 13 1 632 736 694900302 694900408 3.170000e-21 113.0
22 TraesCS2B01G465900 chr2A 78.571 168 32 3 3587 3754 491538510 491538673 1.470000e-19 108.0
23 TraesCS2B01G465900 chr2A 97.826 46 1 0 725 770 694901674 694901719 3.210000e-11 80.5
24 TraesCS2B01G465900 chr2A 100.000 32 0 0 3516 3547 694904597 694904628 4.180000e-05 60.2
25 TraesCS2B01G465900 chr3D 89.758 537 52 3 4 537 2339740 2339204 0.000000e+00 684.0
26 TraesCS2B01G465900 chr1B 89.869 533 47 5 5 535 463821610 463822137 0.000000e+00 678.0
27 TraesCS2B01G465900 chr6A 89.179 536 56 1 4 537 111557678 111557143 0.000000e+00 667.0
28 TraesCS2B01G465900 chr6D 89.159 535 53 5 4 536 455914336 455913805 0.000000e+00 662.0
29 TraesCS2B01G465900 chr4B 88.312 539 59 4 1 536 535326496 535327033 0.000000e+00 643.0
30 TraesCS2B01G465900 chr3B 88.577 534 56 5 4 534 252592750 252592219 0.000000e+00 643.0
31 TraesCS2B01G465900 chr3B 91.250 80 7 0 3587 3666 764769009 764769088 4.100000e-20 110.0
32 TraesCS2B01G465900 chr3B 86.585 82 8 3 3587 3666 764785670 764785750 1.920000e-13 87.9
33 TraesCS2B01G465900 chr3B 83.333 84 7 4 3783 3861 737660150 737660231 1.930000e-08 71.3
34 TraesCS2B01G465900 chr5D 88.051 544 62 3 4 544 432445049 432444506 3.270000e-180 641.0
35 TraesCS2B01G465900 chr5D 92.857 56 4 0 3539 3594 363320116 363320171 8.930000e-12 82.4
36 TraesCS2B01G465900 chr2D 88.051 544 56 7 1 537 19606905 19607446 1.520000e-178 636.0
37 TraesCS2B01G465900 chr1A 75.588 1020 195 39 1825 2820 568697268 568698257 4.570000e-124 455.0
38 TraesCS2B01G465900 chr1D 78.042 378 58 17 2462 2820 474354075 474354446 8.440000e-52 215.0
39 TraesCS2B01G465900 chr6B 74.593 307 43 19 3587 3861 225322060 225322363 6.850000e-18 102.0
40 TraesCS2B01G465900 chr6B 86.667 75 3 5 1818 1885 457468951 457469025 4.150000e-10 76.8
41 TraesCS2B01G465900 chr3A 89.474 76 8 0 3587 3662 710443903 710443978 3.190000e-16 97.1
42 TraesCS2B01G465900 chr3A 87.805 82 8 2 3587 3666 710383158 710383239 1.150000e-15 95.3
43 TraesCS2B01G465900 chr3A 89.041 73 8 0 3587 3659 710331493 710331565 1.480000e-14 91.6


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 TraesCS2B01G465900 chr2B 661444006 661447882 3876 False 1693.200000 5987 100.000000 1 3877 4 chr2B.!!$F3 3876
1 TraesCS2B01G465900 chr2B 745776395 745776929 534 True 678.000000 678 89.610000 4 539 1 chr2B.!!$R1 535
2 TraesCS2B01G465900 chr2B 661175712 661176360 648 False 510.000000 510 81.016000 995 1660 1 chr2B.!!$F1 665
3 TraesCS2B01G465900 chrUn 26255173 26261611 6438 False 943.000000 3144 89.054000 632 3868 4 chrUn.!!$F2 3236
4 TraesCS2B01G465900 chrUn 26244801 26245365 564 False 271.000000 381 86.104000 943 1633 2 chrUn.!!$F1 690
5 TraesCS2B01G465900 chr2A 694900302 694904876 4574 False 688.283333 1945 93.368333 632 3871 6 chr2A.!!$F4 3239
6 TraesCS2B01G465900 chr2A 694839903 694840568 665 False 558.000000 558 81.832000 995 1670 1 chr2A.!!$F2 675
7 TraesCS2B01G465900 chr2A 694864528 694865129 601 False 305.500000 409 86.182500 943 1670 2 chr2A.!!$F3 727
8 TraesCS2B01G465900 chr3D 2339204 2339740 536 True 684.000000 684 89.758000 4 537 1 chr3D.!!$R1 533
9 TraesCS2B01G465900 chr1B 463821610 463822137 527 False 678.000000 678 89.869000 5 535 1 chr1B.!!$F1 530
10 TraesCS2B01G465900 chr6A 111557143 111557678 535 True 667.000000 667 89.179000 4 537 1 chr6A.!!$R1 533
11 TraesCS2B01G465900 chr6D 455913805 455914336 531 True 662.000000 662 89.159000 4 536 1 chr6D.!!$R1 532
12 TraesCS2B01G465900 chr4B 535326496 535327033 537 False 643.000000 643 88.312000 1 536 1 chr4B.!!$F1 535
13 TraesCS2B01G465900 chr3B 252592219 252592750 531 True 643.000000 643 88.577000 4 534 1 chr3B.!!$R1 530
14 TraesCS2B01G465900 chr5D 432444506 432445049 543 True 641.000000 641 88.051000 4 544 1 chr5D.!!$R1 540
15 TraesCS2B01G465900 chr2D 19606905 19607446 541 False 636.000000 636 88.051000 1 537 1 chr2D.!!$F1 536
16 TraesCS2B01G465900 chr1A 568697268 568698257 989 False 455.000000 455 75.588000 1825 2820 1 chr1A.!!$F1 995

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
158 160 0.176680 GTCTGGATGGACGAGCACAT 59.823 55.0 0.00 0.0 0.00 3.21 F
564 569 0.323629 CGGGTGGCTCCAGAGTAAAA 59.676 55.0 8.03 0.0 38.11 1.52 F
1490 5072 0.110373 GGTGGTGATTTTGACGTCGC 60.110 55.0 11.62 0.0 0.00 5.19 F
2158 5745 0.240945 GGAAGTGCACATCAAACGGG 59.759 55.0 22.37 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 5050 0.941542 ACGTCAAAATCACCACCACG 59.058 50.000 0.0 0.0 0.00 4.94 R
2230 5817 0.320697 GCAAGTTCGGGGACAGTAGT 59.679 55.000 0.0 0.0 0.00 2.73 R
2760 6358 2.040278 TCACCAAGGCAGCTTTCAGTAT 59.960 45.455 0.0 0.0 0.00 2.12 R
3596 8286 1.068588 GCCCTTGTCAAAAGGAACACC 59.931 52.381 0.0 0.0 39.81 4.16 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
132 134 2.419159 CGCATGACAGATCCTCCAGAAA 60.419 50.000 0.00 0.00 0.00 2.52
137 139 3.103742 GACAGATCCTCCAGAAACTCCT 58.896 50.000 0.00 0.00 0.00 3.69
158 160 0.176680 GTCTGGATGGACGAGCACAT 59.823 55.000 0.00 0.00 0.00 3.21
304 307 4.099727 TGCATGTGGTATACGCTTTAGGTA 59.900 41.667 0.00 0.00 0.00 3.08
350 353 2.833794 ACGTTATGTGGATGAATCGGG 58.166 47.619 0.00 0.00 0.00 5.14
419 422 6.844696 TTGAGTTTTGTAGATGTGAGTGAC 57.155 37.500 0.00 0.00 0.00 3.67
431 434 0.880278 TGAGTGACGGCTTTGAGTGC 60.880 55.000 0.00 0.00 0.00 4.40
444 447 5.997746 GGCTTTGAGTGCCTTGATGTATATA 59.002 40.000 0.00 0.00 46.38 0.86
510 515 1.750399 GATTGATGCAGTGCCGGGT 60.750 57.895 13.72 0.00 0.00 5.28
553 558 3.434940 AAAATTAAGAGTCGGGTGGCT 57.565 42.857 0.00 0.00 0.00 4.75
554 559 2.693267 AATTAAGAGTCGGGTGGCTC 57.307 50.000 0.00 0.00 0.00 4.70
555 560 0.831307 ATTAAGAGTCGGGTGGCTCC 59.169 55.000 0.00 0.00 32.47 4.70
556 561 0.543410 TTAAGAGTCGGGTGGCTCCA 60.543 55.000 8.03 0.00 38.11 3.86
557 562 0.970937 TAAGAGTCGGGTGGCTCCAG 60.971 60.000 8.03 3.44 38.11 3.86
558 563 2.680352 GAGTCGGGTGGCTCCAGA 60.680 66.667 8.03 6.11 38.04 3.86
559 564 2.681778 AGTCGGGTGGCTCCAGAG 60.682 66.667 8.71 0.00 40.80 3.35
560 565 2.997897 GTCGGGTGGCTCCAGAGT 60.998 66.667 8.71 0.00 40.80 3.24
561 566 1.681327 GTCGGGTGGCTCCAGAGTA 60.681 63.158 8.71 0.00 40.80 2.59
562 567 1.077805 TCGGGTGGCTCCAGAGTAA 59.922 57.895 8.03 0.00 35.59 2.24
563 568 0.543410 TCGGGTGGCTCCAGAGTAAA 60.543 55.000 8.03 0.00 35.59 2.01
564 569 0.323629 CGGGTGGCTCCAGAGTAAAA 59.676 55.000 8.03 0.00 38.11 1.52
565 570 1.271163 CGGGTGGCTCCAGAGTAAAAA 60.271 52.381 8.03 0.00 38.11 1.94
589 594 8.649973 AAAAATTACTCCTCTAACTGCGATAG 57.350 34.615 0.00 0.00 0.00 2.08
590 595 5.968528 ATTACTCCTCTAACTGCGATAGG 57.031 43.478 0.00 0.00 0.00 2.57
591 596 2.588620 ACTCCTCTAACTGCGATAGGG 58.411 52.381 0.00 0.00 0.00 3.53
592 597 1.889829 CTCCTCTAACTGCGATAGGGG 59.110 57.143 3.36 3.36 41.62 4.79
593 598 1.497716 TCCTCTAACTGCGATAGGGGA 59.502 52.381 7.55 7.55 45.71 4.81
594 599 2.091499 TCCTCTAACTGCGATAGGGGAA 60.091 50.000 8.87 0.00 45.09 3.97
595 600 2.036089 CCTCTAACTGCGATAGGGGAAC 59.964 54.545 3.63 0.00 42.69 3.62
596 601 1.679680 TCTAACTGCGATAGGGGAACG 59.320 52.381 0.00 0.00 0.00 3.95
597 602 1.679680 CTAACTGCGATAGGGGAACGA 59.320 52.381 0.00 0.00 0.00 3.85
598 603 1.120530 AACTGCGATAGGGGAACGAT 58.879 50.000 0.00 0.00 0.00 3.73
599 604 1.120530 ACTGCGATAGGGGAACGATT 58.879 50.000 0.00 0.00 0.00 3.34
600 605 2.313317 ACTGCGATAGGGGAACGATTA 58.687 47.619 0.00 0.00 0.00 1.75
601 606 2.296471 ACTGCGATAGGGGAACGATTAG 59.704 50.000 0.00 0.00 0.00 1.73
602 607 1.616865 TGCGATAGGGGAACGATTAGG 59.383 52.381 0.00 0.00 0.00 2.69
603 608 1.617357 GCGATAGGGGAACGATTAGGT 59.383 52.381 0.00 0.00 0.00 3.08
604 609 2.609737 GCGATAGGGGAACGATTAGGTG 60.610 54.545 0.00 0.00 0.00 4.00
605 610 2.609737 CGATAGGGGAACGATTAGGTGC 60.610 54.545 0.00 0.00 0.00 5.01
612 617 4.813296 GGAACGATTAGGTGCCATTTAG 57.187 45.455 0.00 0.00 35.50 1.85
613 618 4.448210 GGAACGATTAGGTGCCATTTAGA 58.552 43.478 0.00 0.00 35.50 2.10
614 619 4.511826 GGAACGATTAGGTGCCATTTAGAG 59.488 45.833 0.00 0.00 35.50 2.43
615 620 5.353394 AACGATTAGGTGCCATTTAGAGA 57.647 39.130 0.00 0.00 0.00 3.10
616 621 5.552870 ACGATTAGGTGCCATTTAGAGAT 57.447 39.130 0.00 0.00 0.00 2.75
617 622 5.930135 ACGATTAGGTGCCATTTAGAGATT 58.070 37.500 0.00 0.00 0.00 2.40
618 623 7.062749 ACGATTAGGTGCCATTTAGAGATTA 57.937 36.000 0.00 0.00 0.00 1.75
619 624 7.506114 ACGATTAGGTGCCATTTAGAGATTAA 58.494 34.615 0.00 0.00 0.00 1.40
620 625 7.441458 ACGATTAGGTGCCATTTAGAGATTAAC 59.559 37.037 0.00 0.00 0.00 2.01
621 626 7.657761 CGATTAGGTGCCATTTAGAGATTAACT 59.342 37.037 0.00 0.00 0.00 2.24
622 627 8.910351 ATTAGGTGCCATTTAGAGATTAACTC 57.090 34.615 0.00 0.00 45.22 3.01
653 658 4.336280 AGGTGCCATTTAGAGAAGGAAAC 58.664 43.478 0.00 0.00 0.00 2.78
659 664 5.193679 CCATTTAGAGAAGGAAACCCGAAT 58.806 41.667 0.00 0.00 0.00 3.34
660 665 5.066505 CCATTTAGAGAAGGAAACCCGAATG 59.933 44.000 0.00 0.00 0.00 2.67
674 679 7.121611 GGAAACCCGAATGTTTATTCCTCTAAA 59.878 37.037 0.00 0.00 39.63 1.85
677 682 5.588648 CCCGAATGTTTATTCCTCTAAAGCA 59.411 40.000 0.00 0.00 39.63 3.91
690 695 5.931441 CTCTAAAGCATTTTAGGGGATCG 57.069 43.478 5.82 0.00 43.83 3.69
691 696 4.134563 TCTAAAGCATTTTAGGGGATCGC 58.865 43.478 0.06 0.06 43.83 4.58
694 699 2.024414 AGCATTTTAGGGGATCGCAAC 58.976 47.619 12.32 0.00 0.00 4.17
763 2047 7.928908 TGAGAAAAGAAAAATCAAATGACCG 57.071 32.000 0.00 0.00 0.00 4.79
785 2180 4.499183 GTCAAGTAACTGATCCACTCCAG 58.501 47.826 0.00 0.00 36.53 3.86
864 4441 3.305608 GGAAAACTGCAGGACCAATTCAG 60.306 47.826 19.93 0.00 0.00 3.02
881 4458 1.956170 AGTTCTGCACACGAAGCCG 60.956 57.895 0.00 0.00 42.50 5.52
969 4547 2.771089 AGACGACATTCTGCAACACAT 58.229 42.857 0.00 0.00 0.00 3.21
1161 4742 2.654079 CCTCCTCGGCAAGCAGTCT 61.654 63.158 0.00 0.00 0.00 3.24
1200 4781 2.539953 CGAGATCTACAAGAGCGTGGAC 60.540 54.545 0.00 0.00 35.43 4.02
1223 4805 1.535444 TCCCCACTCGCCTCTTCAA 60.535 57.895 0.00 0.00 0.00 2.69
1450 5032 0.761802 GGAGAGGCCGGAGAATGATT 59.238 55.000 5.05 0.00 0.00 2.57
1468 5050 0.458543 TTGTAGCACTAGCGCTGCTC 60.459 55.000 23.86 16.08 44.07 4.26
1481 5063 1.237285 GCTGCTCGTGGTGGTGATTT 61.237 55.000 0.00 0.00 0.00 2.17
1490 5072 0.110373 GGTGGTGATTTTGACGTCGC 60.110 55.000 11.62 0.00 0.00 5.19
1739 5321 9.730420 GAAACTTCTAATTTACTGCACTTTTCA 57.270 29.630 0.00 0.00 0.00 2.69
1812 5395 9.771534 TTAAATTTGCTGTACTTTGCCTAAAAT 57.228 25.926 0.00 0.00 0.00 1.82
1930 5513 2.877043 ATTTTGATCTTGCCATCGCC 57.123 45.000 0.00 0.00 0.00 5.54
1931 5514 1.838112 TTTTGATCTTGCCATCGCCT 58.162 45.000 0.00 0.00 0.00 5.52
1966 5549 4.283722 GTCACAGATATTCTCCCCGGTAAT 59.716 45.833 0.00 0.00 0.00 1.89
1997 5583 3.876914 TCAACAAGAAAACGATGCTGAGT 59.123 39.130 0.00 0.00 0.00 3.41
2082 5668 0.733909 GAAGCTGGTGCCGATTTTGC 60.734 55.000 0.00 0.00 40.80 3.68
2133 5720 4.230502 ACCACTGGGATCCATAGTGAAAAT 59.769 41.667 33.32 20.20 43.35 1.82
2155 5742 3.505680 TGTATGGGAAGTGCACATCAAAC 59.494 43.478 22.37 14.09 40.61 2.93
2158 5745 0.240945 GGAAGTGCACATCAAACGGG 59.759 55.000 22.37 0.00 0.00 5.28
2165 5752 1.599419 GCACATCAAACGGGTGTGTTC 60.599 52.381 9.22 0.00 43.80 3.18
2185 5772 7.095229 TGTGTTCACAATCTTTACAGTAGCATC 60.095 37.037 2.99 0.00 0.00 3.91
2186 5773 6.934083 TGTTCACAATCTTTACAGTAGCATCA 59.066 34.615 0.00 0.00 0.00 3.07
2230 5817 1.834996 GCCAGGATGCCAGATCTCA 59.165 57.895 0.00 0.00 31.97 3.27
2242 5829 1.678627 CAGATCTCACTACTGTCCCCG 59.321 57.143 0.00 0.00 0.00 5.73
2269 5856 1.410932 CCACCCTTCTTTGGTTGTGGA 60.411 52.381 0.00 0.00 39.95 4.02
2273 5860 2.362077 CCCTTCTTTGGTTGTGGAACTG 59.638 50.000 0.00 0.00 38.04 3.16
2274 5861 2.223805 CCTTCTTTGGTTGTGGAACTGC 60.224 50.000 0.00 0.00 38.04 4.40
2284 5871 4.253685 GTTGTGGAACTGCTAAGATGCTA 58.746 43.478 0.00 0.00 38.04 3.49
2676 6263 4.311520 AACCCCAGGTTGGTATTTCTAC 57.688 45.455 0.00 0.00 45.07 2.59
2760 6358 4.075682 TGATTTTGCAACGGTTATGGAGA 58.924 39.130 0.00 0.00 0.00 3.71
2913 6511 6.179756 TGCTCTACCATTGCAGAATAAGAAA 58.820 36.000 0.00 0.00 32.55 2.52
2972 6570 5.841237 TCCCAATACCCTTGTTGAATTTGAA 59.159 36.000 0.00 0.00 0.00 2.69
2981 6586 6.424812 CCCTTGTTGAATTTGAATTTGGAGTC 59.575 38.462 0.00 0.00 0.00 3.36
3079 6684 5.221501 GCAGGCCCACAAACATTATATTCAT 60.222 40.000 0.00 0.00 0.00 2.57
3142 6747 5.546526 ACAACACAACCAAATCAACAAAGT 58.453 33.333 0.00 0.00 0.00 2.66
3235 6840 3.873801 GCCTTCCATTTAGCACTTCTCCA 60.874 47.826 0.00 0.00 0.00 3.86
3236 6841 4.530875 CCTTCCATTTAGCACTTCTCCAT 58.469 43.478 0.00 0.00 0.00 3.41
3237 6842 4.337555 CCTTCCATTTAGCACTTCTCCATG 59.662 45.833 0.00 0.00 0.00 3.66
3238 6843 3.282021 TCCATTTAGCACTTCTCCATGC 58.718 45.455 0.00 0.00 42.39 4.06
3240 6845 3.181493 CCATTTAGCACTTCTCCATGCAC 60.181 47.826 0.00 0.00 44.59 4.57
3241 6846 1.725641 TTAGCACTTCTCCATGCACG 58.274 50.000 0.00 0.00 44.59 5.34
3581 8271 7.722949 TTTGATGAGGGCTTTGAAATAAGAT 57.277 32.000 0.00 0.00 0.00 2.40
3584 8274 6.891361 TGATGAGGGCTTTGAAATAAGATCAA 59.109 34.615 0.00 0.00 35.11 2.57
3611 8301 6.968263 TGAATATTGGTGTTCCTTTTGACA 57.032 33.333 0.00 0.00 34.23 3.58
3740 8437 8.028938 CAGAACTGAAACTTAAAACCATATGGG 58.971 37.037 25.55 9.13 44.81 4.00
3779 8496 9.730420 TGACAAGTTTTAAAATCAGTAAGCTTC 57.270 29.630 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.828145 GCTCCATCTCCTGCCTCC 59.172 66.667 0.00 0.00 0.00 4.30
13 14 1.298859 GCAAGACGAAACCGCTCCAT 61.299 55.000 0.00 0.00 0.00 3.41
132 134 0.898320 CGTCCATCCAGACAAGGAGT 59.102 55.000 0.00 0.00 41.90 3.85
137 139 0.037326 GTGCTCGTCCATCCAGACAA 60.037 55.000 0.00 0.00 36.52 3.18
186 188 2.126071 CGTCCATCCGTTGACGCT 60.126 61.111 0.00 0.00 46.41 5.07
304 307 1.889105 CGAATAGCCGGTGCAGCAT 60.889 57.895 17.33 3.57 41.13 3.79
350 353 4.809426 CCATATCTAAAACTGGTGTCGTCC 59.191 45.833 0.00 0.00 0.00 4.79
397 400 4.982295 CGTCACTCACATCTACAAAACTCA 59.018 41.667 0.00 0.00 0.00 3.41
541 546 2.680352 TCTGGAGCCACCCGACTC 60.680 66.667 0.00 0.00 38.00 3.36
542 547 2.151307 TACTCTGGAGCCACCCGACT 62.151 60.000 0.00 0.00 38.00 4.18
543 548 1.255667 TTACTCTGGAGCCACCCGAC 61.256 60.000 0.00 0.00 38.00 4.79
544 549 0.543410 TTTACTCTGGAGCCACCCGA 60.543 55.000 0.00 0.00 38.00 5.14
545 550 0.323629 TTTTACTCTGGAGCCACCCG 59.676 55.000 0.00 0.00 38.00 5.28
546 551 2.579410 TTTTTACTCTGGAGCCACCC 57.421 50.000 0.00 0.00 38.00 4.61
564 569 7.711339 CCTATCGCAGTTAGAGGAGTAATTTTT 59.289 37.037 0.00 0.00 0.00 1.94
565 570 7.210873 CCTATCGCAGTTAGAGGAGTAATTTT 58.789 38.462 0.00 0.00 0.00 1.82
566 571 6.239345 CCCTATCGCAGTTAGAGGAGTAATTT 60.239 42.308 0.00 0.00 0.00 1.82
567 572 5.244178 CCCTATCGCAGTTAGAGGAGTAATT 59.756 44.000 0.00 0.00 0.00 1.40
568 573 4.767928 CCCTATCGCAGTTAGAGGAGTAAT 59.232 45.833 0.00 0.00 0.00 1.89
569 574 4.142790 CCCTATCGCAGTTAGAGGAGTAA 58.857 47.826 0.00 0.00 0.00 2.24
570 575 3.498121 CCCCTATCGCAGTTAGAGGAGTA 60.498 52.174 0.00 0.00 0.00 2.59
571 576 2.588620 CCCTATCGCAGTTAGAGGAGT 58.411 52.381 0.00 0.00 0.00 3.85
572 577 1.889829 CCCCTATCGCAGTTAGAGGAG 59.110 57.143 0.00 0.00 0.00 3.69
573 578 1.497716 TCCCCTATCGCAGTTAGAGGA 59.502 52.381 0.00 0.00 0.00 3.71
574 579 1.996798 TCCCCTATCGCAGTTAGAGG 58.003 55.000 0.00 0.00 0.00 3.69
575 580 2.287668 CGTTCCCCTATCGCAGTTAGAG 60.288 54.545 0.00 0.00 0.00 2.43
576 581 1.679680 CGTTCCCCTATCGCAGTTAGA 59.320 52.381 0.00 0.00 0.00 2.10
577 582 1.679680 TCGTTCCCCTATCGCAGTTAG 59.320 52.381 0.00 0.00 0.00 2.34
578 583 1.766494 TCGTTCCCCTATCGCAGTTA 58.234 50.000 0.00 0.00 0.00 2.24
579 584 1.120530 ATCGTTCCCCTATCGCAGTT 58.879 50.000 0.00 0.00 0.00 3.16
580 585 1.120530 AATCGTTCCCCTATCGCAGT 58.879 50.000 0.00 0.00 0.00 4.40
581 586 2.352814 CCTAATCGTTCCCCTATCGCAG 60.353 54.545 0.00 0.00 0.00 5.18
582 587 1.616865 CCTAATCGTTCCCCTATCGCA 59.383 52.381 0.00 0.00 0.00 5.10
583 588 1.617357 ACCTAATCGTTCCCCTATCGC 59.383 52.381 0.00 0.00 0.00 4.58
584 589 2.609737 GCACCTAATCGTTCCCCTATCG 60.610 54.545 0.00 0.00 0.00 2.92
585 590 2.289506 GGCACCTAATCGTTCCCCTATC 60.290 54.545 0.00 0.00 0.00 2.08
586 591 1.697982 GGCACCTAATCGTTCCCCTAT 59.302 52.381 0.00 0.00 0.00 2.57
587 592 1.125633 GGCACCTAATCGTTCCCCTA 58.874 55.000 0.00 0.00 0.00 3.53
588 593 0.912487 TGGCACCTAATCGTTCCCCT 60.912 55.000 0.00 0.00 0.00 4.79
589 594 0.182775 ATGGCACCTAATCGTTCCCC 59.817 55.000 0.00 0.00 0.00 4.81
590 595 2.052782 AATGGCACCTAATCGTTCCC 57.947 50.000 0.00 0.00 0.00 3.97
591 596 4.448210 TCTAAATGGCACCTAATCGTTCC 58.552 43.478 0.00 0.00 0.00 3.62
592 597 5.357257 TCTCTAAATGGCACCTAATCGTTC 58.643 41.667 0.00 0.00 0.00 3.95
593 598 5.353394 TCTCTAAATGGCACCTAATCGTT 57.647 39.130 0.00 0.00 0.00 3.85
594 599 5.552870 ATCTCTAAATGGCACCTAATCGT 57.447 39.130 0.00 0.00 0.00 3.73
595 600 7.657761 AGTTAATCTCTAAATGGCACCTAATCG 59.342 37.037 0.00 0.00 0.00 3.34
596 601 8.910351 AGTTAATCTCTAAATGGCACCTAATC 57.090 34.615 0.00 0.00 0.00 1.75
597 602 8.494433 TGAGTTAATCTCTAAATGGCACCTAAT 58.506 33.333 0.00 0.00 43.13 1.73
598 603 7.857456 TGAGTTAATCTCTAAATGGCACCTAA 58.143 34.615 0.00 0.00 43.13 2.69
599 604 7.432148 TGAGTTAATCTCTAAATGGCACCTA 57.568 36.000 0.00 0.00 43.13 3.08
600 605 6.313519 TGAGTTAATCTCTAAATGGCACCT 57.686 37.500 0.00 0.00 43.13 4.00
601 606 7.391148 TTTGAGTTAATCTCTAAATGGCACC 57.609 36.000 0.00 0.00 43.13 5.01
627 632 5.393866 TCCTTCTCTAAATGGCACCTTTTT 58.606 37.500 5.93 0.00 0.00 1.94
628 633 4.998051 TCCTTCTCTAAATGGCACCTTTT 58.002 39.130 5.92 5.92 0.00 2.27
629 634 4.657814 TCCTTCTCTAAATGGCACCTTT 57.342 40.909 0.00 0.00 0.00 3.11
630 635 4.657814 TTCCTTCTCTAAATGGCACCTT 57.342 40.909 0.00 0.00 0.00 3.50
638 643 5.816682 ACATTCGGGTTTCCTTCTCTAAAT 58.183 37.500 0.00 0.00 0.00 1.40
643 648 6.404403 GGAATAAACATTCGGGTTTCCTTCTC 60.404 42.308 4.47 2.68 41.07 2.87
653 658 5.588648 TGCTTTAGAGGAATAAACATTCGGG 59.411 40.000 0.00 0.00 0.00 5.14
659 664 8.966868 CCCTAAAATGCTTTAGAGGAATAAACA 58.033 33.333 11.89 0.00 44.70 2.83
660 665 8.414003 CCCCTAAAATGCTTTAGAGGAATAAAC 58.586 37.037 11.89 0.00 42.76 2.01
674 679 2.024414 GTTGCGATCCCCTAAAATGCT 58.976 47.619 0.00 0.00 0.00 3.79
677 682 2.702592 TCGTTGCGATCCCCTAAAAT 57.297 45.000 0.00 0.00 0.00 1.82
691 696 3.439293 ACTCGTTATCTGAGCATCGTTG 58.561 45.455 0.00 0.00 38.61 4.10
694 699 5.172232 CACTTAACTCGTTATCTGAGCATCG 59.828 44.000 0.00 0.00 38.61 3.84
763 2047 4.021016 ACTGGAGTGGATCAGTTACTTGAC 60.021 45.833 0.00 0.00 40.91 3.18
864 4441 1.495584 TTCGGCTTCGTGTGCAGAAC 61.496 55.000 0.00 0.00 39.06 3.01
881 4458 2.602322 GCGGCAGATGGATCGCTTC 61.602 63.158 0.00 0.00 44.10 3.86
969 4547 1.003839 GGTGATCCGGTCAAGTGCA 60.004 57.895 0.00 0.00 38.90 4.57
976 4554 3.221222 CTGGAGGGTGATCCGGTC 58.779 66.667 0.00 0.00 42.77 4.79
1223 4805 1.600916 GTCTTGCAGGCCTCGGTTT 60.601 57.895 0.00 0.00 0.00 3.27
1277 4859 1.230324 GACCTTGAGTTGACAGCACC 58.770 55.000 0.00 0.00 0.00 5.01
1468 5050 0.941542 ACGTCAAAATCACCACCACG 59.058 50.000 0.00 0.00 0.00 4.94
1481 5063 1.732809 TGACAAAAACAGCGACGTCAA 59.267 42.857 17.16 0.00 30.88 3.18
1490 5072 4.094294 TCACGTCCTCTTTGACAAAAACAG 59.906 41.667 1.62 0.00 34.88 3.16
1581 5163 6.000840 GGAGAGATCCTGAACTTCAAACTTT 58.999 40.000 0.00 0.00 0.00 2.66
1626 5208 5.163652 ACAAACCTTGTCTGAACTAAGTTGC 60.164 40.000 0.00 0.00 40.56 4.17
1966 5549 4.097135 TCGTTTTCTTGTTGAGGATGCAAA 59.903 37.500 0.00 0.00 0.00 3.68
2082 5668 2.158842 AGCAATCCCAAGAGAAGATCCG 60.159 50.000 0.00 0.00 0.00 4.18
2133 5720 3.431673 TTGATGTGCACTTCCCATACA 57.568 42.857 25.08 7.67 0.00 2.29
2155 5742 3.562141 TGTAAAGATTGTGAACACACCCG 59.438 43.478 7.16 0.00 41.67 5.28
2158 5745 6.018262 TGCTACTGTAAAGATTGTGAACACAC 60.018 38.462 7.16 0.00 41.67 3.82
2165 5752 7.066163 TCCATTGATGCTACTGTAAAGATTGTG 59.934 37.037 0.00 0.00 0.00 3.33
2185 5772 3.889538 AGAATCCATCAGCACATCCATTG 59.110 43.478 0.00 0.00 0.00 2.82
2186 5773 4.180377 AGAATCCATCAGCACATCCATT 57.820 40.909 0.00 0.00 0.00 3.16
2200 5787 1.213678 CATCCTGGCCTCAAGAATCCA 59.786 52.381 3.32 0.00 0.00 3.41
2230 5817 0.320697 GCAAGTTCGGGGACAGTAGT 59.679 55.000 0.00 0.00 0.00 2.73
2242 5829 1.341209 CCAAAGAAGGGTGGCAAGTTC 59.659 52.381 0.00 0.00 0.00 3.01
2269 5856 5.551233 TCAACTTGTAGCATCTTAGCAGTT 58.449 37.500 0.00 0.00 36.85 3.16
2273 5860 6.370166 AGTTCTTCAACTTGTAGCATCTTAGC 59.630 38.462 0.00 0.00 40.16 3.09
2274 5861 7.897575 AGTTCTTCAACTTGTAGCATCTTAG 57.102 36.000 0.00 0.00 40.16 2.18
2760 6358 2.040278 TCACCAAGGCAGCTTTCAGTAT 59.960 45.455 0.00 0.00 0.00 2.12
2994 6599 6.283694 AGCGTCTTGAAATAGCAGATCATAA 58.716 36.000 0.00 0.00 0.00 1.90
2998 6603 3.492756 GGAGCGTCTTGAAATAGCAGATC 59.507 47.826 0.00 0.00 0.00 2.75
3001 6606 2.621338 TGGAGCGTCTTGAAATAGCAG 58.379 47.619 0.00 0.00 0.00 4.24
3002 6607 2.760634 TGGAGCGTCTTGAAATAGCA 57.239 45.000 0.00 0.00 0.00 3.49
3003 6608 4.811557 AGTATTGGAGCGTCTTGAAATAGC 59.188 41.667 0.00 0.00 0.00 2.97
3004 6609 5.812642 ACAGTATTGGAGCGTCTTGAAATAG 59.187 40.000 0.00 0.00 0.00 1.73
3005 6610 5.580691 CACAGTATTGGAGCGTCTTGAAATA 59.419 40.000 0.00 0.00 0.00 1.40
3006 6611 4.393062 CACAGTATTGGAGCGTCTTGAAAT 59.607 41.667 0.00 0.00 0.00 2.17
3007 6612 3.745975 CACAGTATTGGAGCGTCTTGAAA 59.254 43.478 0.00 0.00 0.00 2.69
3008 6613 3.006430 TCACAGTATTGGAGCGTCTTGAA 59.994 43.478 0.00 0.00 0.00 2.69
3009 6614 2.560981 TCACAGTATTGGAGCGTCTTGA 59.439 45.455 0.00 0.00 0.00 3.02
3010 6615 2.959516 TCACAGTATTGGAGCGTCTTG 58.040 47.619 0.00 0.00 0.00 3.02
3079 6684 7.279615 CCTGATGTACCAATTAACTATGGTCA 58.720 38.462 11.53 10.28 46.94 4.02
3142 6747 4.320861 CGTGGATTTGGTTGTGCTCATTAA 60.321 41.667 0.00 0.00 0.00 1.40
3515 7120 5.921962 ATTGGTCTTATTTCAAAGCCCTC 57.078 39.130 0.00 0.00 0.00 4.30
3516 7121 6.686484 AAATTGGTCTTATTTCAAAGCCCT 57.314 33.333 0.00 0.00 0.00 5.19
3529 7134 9.271828 GGAACACAAATATTCAAAATTGGTCTT 57.728 29.630 0.00 0.00 0.00 3.01
3530 7135 8.650490 AGGAACACAAATATTCAAAATTGGTCT 58.350 29.630 0.00 0.00 0.00 3.85
3532 7137 9.625747 AAAGGAACACAAATATTCAAAATTGGT 57.374 25.926 0.00 0.00 0.00 3.67
3539 7144 9.695526 CTCATCAAAAGGAACACAAATATTCAA 57.304 29.630 0.00 0.00 0.00 2.69
3540 7145 8.306038 CCTCATCAAAAGGAACACAAATATTCA 58.694 33.333 0.00 0.00 35.83 2.57
3541 7146 7.761249 CCCTCATCAAAAGGAACACAAATATTC 59.239 37.037 0.00 0.00 35.83 1.75
3562 8252 7.722949 AATTGATCTTATTTCAAAGCCCTCA 57.277 32.000 0.00 0.00 36.72 3.86
3581 8271 9.844257 AAAAGGAACACCAATATTCAAAATTGA 57.156 25.926 0.00 0.00 36.61 2.57
3584 8274 9.271828 GTCAAAAGGAACACCAATATTCAAAAT 57.728 29.630 0.00 0.00 0.00 1.82
3596 8286 1.068588 GCCCTTGTCAAAAGGAACACC 59.931 52.381 0.00 0.00 39.81 4.16
3611 8301 6.686484 AATTGGTCTTATTTCAAAGCCCTT 57.314 33.333 0.00 0.00 0.00 3.95
3735 8432 4.991776 TGTCAAAATGTTGGAGTCCCATA 58.008 39.130 6.74 0.00 43.12 2.74
3740 8437 8.696410 TTAAAACTTGTCAAAATGTTGGAGTC 57.304 30.769 0.00 0.00 35.29 3.36


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

AutoCloner maintained by Alex Coulton.