Multiple sequence alignment - TraesCS1D01G203700

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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 TraesCS1D01G203700 chr1D 100.000 2827 0 0 1 2827 288544857 288547683 0.000000e+00 5221.0
1 TraesCS1D01G203700 chr1D 100.000 144 0 0 3143 3286 288547999 288548142 1.940000e-67 267.0
2 TraesCS1D01G203700 chr1B 94.103 2357 83 27 489 2822 389979654 389981977 0.000000e+00 3531.0
3 TraesCS1D01G203700 chr1B 87.309 457 27 17 1 441 389979207 389979648 8.190000e-136 494.0
4 TraesCS1D01G203700 chr1B 96.429 56 2 0 3174 3229 389983544 389983599 3.490000e-15 93.5
5 TraesCS1D01G203700 chr1B 100.000 47 0 0 3144 3190 389982016 389982062 1.620000e-13 87.9
6 TraesCS1D01G203700 chr1B 100.000 37 0 0 447 483 109734428 109734392 5.880000e-08 69.4
7 TraesCS1D01G203700 chr1A 90.615 2408 97 45 489 2815 360008944 360011303 0.000000e+00 3075.0
8 TraesCS1D01G203700 chr1A 85.683 454 25 19 12 447 360008511 360008942 3.010000e-120 442.0
9 TraesCS1D01G203700 chr1A 96.703 91 3 0 3144 3234 360011744 360011834 5.680000e-33 152.0
10 TraesCS1D01G203700 chr1A 97.222 36 1 0 447 482 6156536 6156501 9.850000e-06 62.1
11 TraesCS1D01G203700 chr7B 75.068 369 71 20 1080 1435 578438666 578439026 5.680000e-33 152.0
12 TraesCS1D01G203700 chr7B 77.670 206 41 5 1192 1396 200022365 200022566 1.600000e-23 121.0
13 TraesCS1D01G203700 chr7D 78.008 241 40 13 1203 1435 535967294 535967529 4.420000e-29 139.0
14 TraesCS1D01G203700 chr7D 77.184 206 42 5 1192 1396 229769541 229769742 7.450000e-22 115.0
15 TraesCS1D01G203700 chr2D 77.184 206 42 5 1198 1402 324015918 324015717 7.450000e-22 115.0
16 TraesCS1D01G203700 chr2B 77.184 206 42 5 1198 1402 392530381 392530180 7.450000e-22 115.0
17 TraesCS1D01G203700 chr7A 76.699 206 43 5 1192 1396 241367121 241367322 3.470000e-20 110.0
18 TraesCS1D01G203700 chr5A 80.282 142 26 2 1097 1237 679722225 679722365 4.480000e-19 106.0
19 TraesCS1D01G203700 chr4D 80.420 143 24 4 1097 1237 498906599 498906739 4.480000e-19 106.0
20 TraesCS1D01G203700 chr4B 80.420 143 24 4 1097 1237 641407786 641407926 4.480000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G203700 chr1D 288544857 288548142 3285 False 2744.0 5221 100.000000 1 3286 2 chr1D.!!$F1 3285
1 TraesCS1D01G203700 chr1B 389979207 389983599 4392 False 1051.6 3531 94.460250 1 3229 4 chr1B.!!$F1 3228
2 TraesCS1D01G203700 chr1A 360008511 360011834 3323 False 1223.0 3075 91.000333 12 3234 3 chr1A.!!$F1 3222

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
630 653 0.749091 TGGCATGCATACACAGCTCC 60.749 55.0 21.36 0.0 32.33 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2540 1.227527 CACACACACCTCAGCCGAA 60.228 57.895 0.0 0.0 0.0 4.3 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
64 66 3.455327 CATGCATCTCTACACTGACTGG 58.545 50.000 0.00 0.00 0.00 4.00
65 67 2.807676 TGCATCTCTACACTGACTGGA 58.192 47.619 0.00 0.00 0.00 3.86
66 68 3.369175 TGCATCTCTACACTGACTGGAT 58.631 45.455 0.00 0.00 0.00 3.41
67 69 3.771479 TGCATCTCTACACTGACTGGATT 59.229 43.478 0.00 0.00 0.00 3.01
68 70 4.118410 GCATCTCTACACTGACTGGATTG 58.882 47.826 0.00 0.00 0.00 2.67
111 113 1.416030 TCGGGATTTGCTAGCTATGCA 59.584 47.619 17.23 12.13 38.80 3.96
112 114 2.038952 TCGGGATTTGCTAGCTATGCAT 59.961 45.455 17.23 3.79 40.34 3.96
113 115 2.161012 CGGGATTTGCTAGCTATGCATG 59.839 50.000 17.23 7.45 40.34 4.06
114 116 2.094854 GGGATTTGCTAGCTATGCATGC 60.095 50.000 17.23 11.82 40.34 4.06
115 117 2.094854 GGATTTGCTAGCTATGCATGCC 60.095 50.000 16.68 13.33 40.34 4.40
116 118 0.946528 TTTGCTAGCTATGCATGCCG 59.053 50.000 16.68 4.74 40.34 5.69
300 307 4.141711 ACGAGGCCTCAATGATTAAGCTTA 60.142 41.667 31.67 0.86 0.00 3.09
302 309 4.140536 AGGCCTCAATGATTAAGCTTAGC 58.859 43.478 0.00 0.00 0.00 3.09
316 323 3.863041 AGCTTAGCTTGCTAACAGGTAC 58.137 45.455 10.62 0.00 39.21 3.34
317 324 3.515901 AGCTTAGCTTGCTAACAGGTACT 59.484 43.478 10.62 0.92 39.21 2.73
334 352 4.477581 AGGTACTGGTGGAGTATCTCACTA 59.522 45.833 0.00 0.00 44.18 2.74
337 355 3.011369 ACTGGTGGAGTATCTCACTACCA 59.989 47.826 14.22 14.22 37.28 3.25
342 360 4.819630 GTGGAGTATCTCACTACCAGAGAG 59.180 50.000 0.00 0.00 44.60 3.20
347 365 2.712709 TCTCACTACCAGAGAGGAACG 58.287 52.381 1.60 0.00 41.22 3.95
369 387 2.041081 AGACTACCAGCTCAGACAGAGT 59.959 50.000 0.00 0.00 46.47 3.24
411 429 2.094494 AGACGCAGGTCATACTTCAGTG 60.094 50.000 0.00 0.00 45.92 3.66
419 437 3.557054 GGTCATACTTCAGTGTTGGCAGA 60.557 47.826 0.00 0.00 0.00 4.26
422 444 4.515191 TCATACTTCAGTGTTGGCAGAAAC 59.485 41.667 0.00 0.00 0.00 2.78
441 463 6.413818 CAGAAACTAAATCGTCCAAACAACAC 59.586 38.462 0.00 0.00 0.00 3.32
442 464 5.821516 AACTAAATCGTCCAAACAACACA 57.178 34.783 0.00 0.00 0.00 3.72
443 465 5.164606 ACTAAATCGTCCAAACAACACAC 57.835 39.130 0.00 0.00 0.00 3.82
444 466 4.636648 ACTAAATCGTCCAAACAACACACA 59.363 37.500 0.00 0.00 0.00 3.72
446 468 3.691049 ATCGTCCAAACAACACACAAG 57.309 42.857 0.00 0.00 0.00 3.16
447 469 2.428491 TCGTCCAAACAACACACAAGT 58.572 42.857 0.00 0.00 0.00 3.16
448 470 3.597255 TCGTCCAAACAACACACAAGTA 58.403 40.909 0.00 0.00 0.00 2.24
449 471 3.371591 TCGTCCAAACAACACACAAGTAC 59.628 43.478 0.00 0.00 0.00 2.73
450 472 3.372822 CGTCCAAACAACACACAAGTACT 59.627 43.478 0.00 0.00 0.00 2.73
451 473 4.567558 CGTCCAAACAACACACAAGTACTA 59.432 41.667 0.00 0.00 0.00 1.82
452 474 5.063691 CGTCCAAACAACACACAAGTACTAA 59.936 40.000 0.00 0.00 0.00 2.24
453 475 6.253013 GTCCAAACAACACACAAGTACTAAC 58.747 40.000 0.00 0.00 0.00 2.34
454 476 6.093082 GTCCAAACAACACACAAGTACTAACT 59.907 38.462 0.00 0.00 37.65 2.24
456 478 7.175293 TCCAAACAACACACAAGTACTAACTTT 59.825 33.333 0.00 0.00 43.60 2.66
457 479 7.272515 CCAAACAACACACAAGTACTAACTTTG 59.727 37.037 0.00 0.00 43.60 2.77
458 480 7.443259 AACAACACACAAGTACTAACTTTGT 57.557 32.000 0.00 0.00 43.60 2.83
459 481 8.550710 AACAACACACAAGTACTAACTTTGTA 57.449 30.769 0.00 0.00 43.60 2.41
460 482 7.967178 ACAACACACAAGTACTAACTTTGTAC 58.033 34.615 0.00 5.63 43.60 2.90
461 483 7.603404 ACAACACACAAGTACTAACTTTGTACA 59.397 33.333 13.70 0.00 43.60 2.90
462 484 8.444715 CAACACACAAGTACTAACTTTGTACAA 58.555 33.333 3.59 3.59 43.60 2.41
463 485 8.550710 ACACACAAGTACTAACTTTGTACAAA 57.449 30.769 19.53 19.53 43.60 2.83
464 486 9.001542 ACACACAAGTACTAACTTTGTACAAAA 57.998 29.630 20.89 6.75 43.60 2.44
465 487 9.997482 CACACAAGTACTAACTTTGTACAAAAT 57.003 29.630 20.89 9.56 43.60 1.82
469 491 9.382244 CAAGTACTAACTTTGTACAAAATCAGC 57.618 33.333 20.89 8.99 43.60 4.26
470 492 7.793902 AGTACTAACTTTGTACAAAATCAGCG 58.206 34.615 20.89 11.18 41.76 5.18
471 493 6.854496 ACTAACTTTGTACAAAATCAGCGA 57.146 33.333 20.89 0.00 0.00 4.93
472 494 6.656003 ACTAACTTTGTACAAAATCAGCGAC 58.344 36.000 20.89 0.00 0.00 5.19
473 495 5.493133 AACTTTGTACAAAATCAGCGACA 57.507 34.783 20.89 0.00 0.00 4.35
474 496 4.844267 ACTTTGTACAAAATCAGCGACAC 58.156 39.130 20.89 0.00 0.00 3.67
475 497 4.574828 ACTTTGTACAAAATCAGCGACACT 59.425 37.500 20.89 0.00 0.00 3.55
476 498 5.065988 ACTTTGTACAAAATCAGCGACACTT 59.934 36.000 20.89 0.00 0.00 3.16
477 499 6.259167 ACTTTGTACAAAATCAGCGACACTTA 59.741 34.615 20.89 0.00 0.00 2.24
478 500 6.795098 TTGTACAAAATCAGCGACACTTAT 57.205 33.333 5.64 0.00 0.00 1.73
479 501 6.795098 TGTACAAAATCAGCGACACTTATT 57.205 33.333 0.00 0.00 0.00 1.40
480 502 7.197071 TGTACAAAATCAGCGACACTTATTT 57.803 32.000 0.00 0.00 34.37 1.40
481 503 7.644490 TGTACAAAATCAGCGACACTTATTTT 58.356 30.769 0.00 0.00 40.98 1.82
485 507 7.858052 AAAATCAGCGACACTTATTTTGAAG 57.142 32.000 0.00 0.00 39.57 3.02
486 508 5.551760 ATCAGCGACACTTATTTTGAAGG 57.448 39.130 0.00 0.00 0.00 3.46
487 509 4.637276 TCAGCGACACTTATTTTGAAGGA 58.363 39.130 0.00 0.00 0.00 3.36
503 525 5.957771 TGAAGGAAGTAGTATCTGCCAAT 57.042 39.130 0.00 0.00 35.63 3.16
505 527 6.349300 TGAAGGAAGTAGTATCTGCCAATTC 58.651 40.000 0.00 0.00 35.63 2.17
509 531 7.406104 AGGAAGTAGTATCTGCCAATTCTTTT 58.594 34.615 0.00 0.00 35.63 2.27
510 532 7.890655 AGGAAGTAGTATCTGCCAATTCTTTTT 59.109 33.333 0.00 0.00 35.63 1.94
511 533 9.174166 GGAAGTAGTATCTGCCAATTCTTTTTA 57.826 33.333 0.00 0.00 33.44 1.52
586 608 1.234821 TCACAAGATGCGGGAACAAC 58.765 50.000 0.00 0.00 0.00 3.32
604 626 3.650942 ACAACCACCACTTCATCTTCCTA 59.349 43.478 0.00 0.00 0.00 2.94
605 627 4.104102 ACAACCACCACTTCATCTTCCTAA 59.896 41.667 0.00 0.00 0.00 2.69
606 628 4.559862 ACCACCACTTCATCTTCCTAAG 57.440 45.455 0.00 0.00 0.00 2.18
608 630 4.223923 ACCACCACTTCATCTTCCTAAGAG 59.776 45.833 0.00 0.00 41.61 2.85
615 638 5.190528 ACTTCATCTTCCTAAGAGAATGGCA 59.809 40.000 0.00 0.00 41.61 4.92
623 646 4.102996 TCCTAAGAGAATGGCATGCATACA 59.897 41.667 21.36 8.94 0.00 2.29
630 653 0.749091 TGGCATGCATACACAGCTCC 60.749 55.000 21.36 0.00 32.33 4.70
647 670 2.113986 CGGGGGAATCCATGGCTC 59.886 66.667 6.96 5.97 37.22 4.70
651 674 1.227973 GGGAATCCATGGCTCGACC 60.228 63.158 6.96 5.84 39.84 4.79
652 675 1.595382 GGAATCCATGGCTCGACCG 60.595 63.158 6.96 0.00 43.94 4.79
653 676 2.203070 AATCCATGGCTCGACCGC 60.203 61.111 6.96 0.00 43.94 5.68
674 697 1.274770 CGTACTGCATGCATCTGCG 59.725 57.895 22.97 19.52 45.30 5.18
675 698 1.010350 GTACTGCATGCATCTGCGC 60.010 57.895 22.97 0.00 45.30 6.09
696 719 2.811431 CGCAGGTGAAAACATTGGAGTA 59.189 45.455 0.00 0.00 0.00 2.59
697 720 3.364964 CGCAGGTGAAAACATTGGAGTAC 60.365 47.826 0.00 0.00 0.00 2.73
698 721 3.057526 GCAGGTGAAAACATTGGAGTACC 60.058 47.826 0.00 0.00 0.00 3.34
699 722 3.188460 CAGGTGAAAACATTGGAGTACCG 59.812 47.826 0.00 0.00 39.42 4.02
700 723 3.071892 AGGTGAAAACATTGGAGTACCGA 59.928 43.478 0.00 0.00 39.42 4.69
701 724 4.007659 GGTGAAAACATTGGAGTACCGAT 58.992 43.478 0.00 0.00 40.68 4.18
869 897 1.499007 TCCCCTTAATCCCTCCAATGC 59.501 52.381 0.00 0.00 0.00 3.56
875 903 5.840693 CCCTTAATCCCTCCAATGCTTAATT 59.159 40.000 0.00 0.00 0.00 1.40
880 908 6.715347 ATCCCTCCAATGCTTAATTGTAAC 57.285 37.500 0.00 0.00 43.66 2.50
1272 1331 2.734591 GTGCTGGTCGACTCCACA 59.265 61.111 16.46 6.28 33.55 4.17
1350 1409 1.595382 CATCGACCGGATCAAGGCC 60.595 63.158 9.46 0.00 31.28 5.19
1445 1507 1.925946 GCTGGTACGTGCAAAGCAAAG 60.926 52.381 20.41 0.00 41.47 2.77
1516 1595 7.745620 ATAAACTGTCACTTTAGGAAACCAG 57.254 36.000 0.00 0.00 0.00 4.00
1563 1642 4.995124 TCAGAATCTCAGTACGTAAAGCC 58.005 43.478 0.00 0.00 0.00 4.35
1682 1762 2.218603 CCTGCCGTTGTTTAGTCTGTT 58.781 47.619 0.00 0.00 0.00 3.16
2273 2353 0.610232 GCAAGATCAGGGCCAACTGT 60.610 55.000 6.18 0.00 39.48 3.55
2339 2419 5.289917 GGTCATCTTTCTCGTTTAGAAGAGC 59.710 44.000 0.00 0.00 44.95 4.09
2344 2424 1.743855 CTCGTTTAGAAGAGCGGCGC 61.744 60.000 26.86 26.86 0.00 6.53
2348 2428 2.852495 TTTAGAAGAGCGGCGCTGGG 62.852 60.000 41.51 3.64 39.88 4.45
2411 2491 6.507456 GCGTTCTTATTTGACCATGTACGTAG 60.507 42.308 0.00 0.00 0.00 3.51
2449 2529 2.412421 TGCTCATCGATCGATCTGTG 57.588 50.000 27.20 19.42 31.62 3.66
2460 2540 5.869344 TCGATCGATCTGTGTTGATTCTTTT 59.131 36.000 22.43 0.00 0.00 2.27
2585 2672 7.377766 ACAACGTTAATTATCTTGCAGTGAT 57.622 32.000 0.00 8.88 0.00 3.06
2602 2713 6.128661 TGCAGTGATATTAAGACGTGTTTGAC 60.129 38.462 2.22 0.00 0.00 3.18
2801 2914 1.080501 ATCACCTCACGCACTCACG 60.081 57.895 0.00 0.00 39.50 4.35
2803 2916 3.911698 ACCTCACGCACTCACGCA 61.912 61.111 0.00 0.00 36.19 5.24
2815 2928 1.003118 ACTCACGCACTCTCTCTCTCT 59.997 52.381 0.00 0.00 0.00 3.10
2816 2929 1.665679 CTCACGCACTCTCTCTCTCTC 59.334 57.143 0.00 0.00 0.00 3.20
2817 2930 1.277842 TCACGCACTCTCTCTCTCTCT 59.722 52.381 0.00 0.00 0.00 3.10
2818 2931 1.665679 CACGCACTCTCTCTCTCTCTC 59.334 57.143 0.00 0.00 0.00 3.20
2820 2933 2.205074 CGCACTCTCTCTCTCTCTCTC 58.795 57.143 0.00 0.00 0.00 3.20
2823 2936 3.133721 GCACTCTCTCTCTCTCTCTCTCT 59.866 52.174 0.00 0.00 0.00 3.10
2824 2937 4.739137 GCACTCTCTCTCTCTCTCTCTCTC 60.739 54.167 0.00 0.00 0.00 3.20
2825 2938 4.648762 CACTCTCTCTCTCTCTCTCTCTCT 59.351 50.000 0.00 0.00 0.00 3.10
2826 2939 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
3217 4940 2.623915 GGTTGTGGCAGCTCAGCAG 61.624 63.158 0.00 0.00 35.83 4.24
3234 4957 3.635373 CAGCAGCCCAATAAATCATCTGT 59.365 43.478 0.00 0.00 0.00 3.41
3235 4958 4.098960 CAGCAGCCCAATAAATCATCTGTT 59.901 41.667 0.00 0.00 0.00 3.16
3236 4959 4.098960 AGCAGCCCAATAAATCATCTGTTG 59.901 41.667 0.00 0.00 0.00 3.33
3237 4960 4.365723 CAGCCCAATAAATCATCTGTTGC 58.634 43.478 0.00 0.00 0.00 4.17
3238 4961 3.385755 AGCCCAATAAATCATCTGTTGCC 59.614 43.478 0.00 0.00 0.00 4.52
3239 4962 3.132646 GCCCAATAAATCATCTGTTGCCA 59.867 43.478 0.00 0.00 0.00 4.92
3240 4963 4.685924 CCCAATAAATCATCTGTTGCCAC 58.314 43.478 0.00 0.00 0.00 5.01
3241 4964 4.353737 CCAATAAATCATCTGTTGCCACG 58.646 43.478 0.00 0.00 0.00 4.94
3242 4965 4.142403 CCAATAAATCATCTGTTGCCACGT 60.142 41.667 0.00 0.00 0.00 4.49
3243 4966 5.401550 CAATAAATCATCTGTTGCCACGTT 58.598 37.500 0.00 0.00 0.00 3.99
3244 4967 2.995466 AATCATCTGTTGCCACGTTG 57.005 45.000 0.00 0.00 0.00 4.10
3245 4968 1.896220 ATCATCTGTTGCCACGTTGT 58.104 45.000 0.00 0.00 0.00 3.32
3246 4969 2.535012 TCATCTGTTGCCACGTTGTA 57.465 45.000 0.00 0.00 0.00 2.41
3247 4970 2.839975 TCATCTGTTGCCACGTTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
3248 4971 2.805671 TCATCTGTTGCCACGTTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
3249 4972 1.588674 TCTGTTGCCACGTTGTAAGG 58.411 50.000 0.00 0.00 0.00 2.69
3250 4973 1.139256 TCTGTTGCCACGTTGTAAGGA 59.861 47.619 0.00 0.00 0.00 3.36
3251 4974 1.944024 CTGTTGCCACGTTGTAAGGAA 59.056 47.619 0.00 0.00 0.00 3.36
3252 4975 1.944024 TGTTGCCACGTTGTAAGGAAG 59.056 47.619 0.00 0.00 0.00 3.46
3253 4976 2.215196 GTTGCCACGTTGTAAGGAAGA 58.785 47.619 0.00 0.00 0.00 2.87
3254 4977 2.614983 GTTGCCACGTTGTAAGGAAGAA 59.385 45.455 0.00 0.00 0.00 2.52
3255 4978 3.134574 TGCCACGTTGTAAGGAAGAAT 57.865 42.857 0.00 0.00 0.00 2.40
3256 4979 3.482436 TGCCACGTTGTAAGGAAGAATT 58.518 40.909 0.00 0.00 0.00 2.17
3257 4980 3.886505 TGCCACGTTGTAAGGAAGAATTT 59.113 39.130 0.00 0.00 0.00 1.82
3258 4981 4.339814 TGCCACGTTGTAAGGAAGAATTTT 59.660 37.500 0.00 0.00 0.00 1.82
3259 4982 5.163499 TGCCACGTTGTAAGGAAGAATTTTT 60.163 36.000 0.00 0.00 0.00 1.94
3260 4983 6.039493 TGCCACGTTGTAAGGAAGAATTTTTA 59.961 34.615 0.00 0.00 0.00 1.52
3261 4984 7.088272 GCCACGTTGTAAGGAAGAATTTTTAT 58.912 34.615 0.00 0.00 0.00 1.40
3262 4985 7.061789 GCCACGTTGTAAGGAAGAATTTTTATG 59.938 37.037 0.00 0.00 0.00 1.90
3263 4986 8.293867 CCACGTTGTAAGGAAGAATTTTTATGA 58.706 33.333 0.00 0.00 0.00 2.15
3264 4987 9.113876 CACGTTGTAAGGAAGAATTTTTATGAC 57.886 33.333 0.00 0.00 0.00 3.06
3265 4988 9.063615 ACGTTGTAAGGAAGAATTTTTATGACT 57.936 29.630 0.00 0.00 0.00 3.41
3266 4989 9.893305 CGTTGTAAGGAAGAATTTTTATGACTT 57.107 29.630 0.00 0.00 0.00 3.01
3272 4995 8.463930 AGGAAGAATTTTTATGACTTGTGTGA 57.536 30.769 0.00 0.00 0.00 3.58
3273 4996 8.912988 AGGAAGAATTTTTATGACTTGTGTGAA 58.087 29.630 0.00 0.00 0.00 3.18
3274 4997 9.696917 GGAAGAATTTTTATGACTTGTGTGAAT 57.303 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 66 1.030457 CAGGCAAGCTCCATCCAATC 58.970 55.000 0.00 0.00 0.00 2.67
65 67 0.333993 ACAGGCAAGCTCCATCCAAT 59.666 50.000 0.00 0.00 0.00 3.16
66 68 0.322816 GACAGGCAAGCTCCATCCAA 60.323 55.000 0.00 0.00 0.00 3.53
67 69 1.300963 GACAGGCAAGCTCCATCCA 59.699 57.895 0.00 0.00 0.00 3.41
68 70 0.747283 CTGACAGGCAAGCTCCATCC 60.747 60.000 0.00 0.00 0.00 3.51
111 113 0.880278 GATACACACGGCATCGGCAT 60.880 55.000 0.00 0.00 43.71 4.40
112 114 1.520564 GATACACACGGCATCGGCA 60.521 57.895 0.00 0.00 43.71 5.69
113 115 2.244651 GGATACACACGGCATCGGC 61.245 63.158 0.00 0.00 41.39 5.54
114 116 1.949133 CGGATACACACGGCATCGG 60.949 63.158 0.00 0.00 41.39 4.18
115 117 0.318699 ATCGGATACACACGGCATCG 60.319 55.000 0.00 0.00 43.02 3.84
116 118 1.139989 CATCGGATACACACGGCATC 58.860 55.000 0.00 0.00 0.00 3.91
265 272 0.664166 GGCCTCGTTGCATGTTGTTG 60.664 55.000 0.00 0.00 0.00 3.33
266 273 0.823356 AGGCCTCGTTGCATGTTGTT 60.823 50.000 0.00 0.00 0.00 2.83
267 274 1.228245 AGGCCTCGTTGCATGTTGT 60.228 52.632 0.00 0.00 0.00 3.32
300 307 1.978580 ACCAGTACCTGTTAGCAAGCT 59.021 47.619 0.00 0.00 0.00 3.74
302 309 2.301870 TCCACCAGTACCTGTTAGCAAG 59.698 50.000 0.00 0.00 0.00 4.01
306 313 5.202004 AGATACTCCACCAGTACCTGTTAG 58.798 45.833 0.00 0.00 40.60 2.34
308 315 4.024670 GAGATACTCCACCAGTACCTGTT 58.975 47.826 0.00 0.00 40.60 3.16
312 319 3.633418 AGTGAGATACTCCACCAGTACC 58.367 50.000 0.00 0.00 40.60 3.34
313 320 4.579753 GGTAGTGAGATACTCCACCAGTAC 59.420 50.000 0.00 0.00 40.60 2.73
316 323 3.632333 TGGTAGTGAGATACTCCACCAG 58.368 50.000 10.65 0.00 40.89 4.00
317 324 3.268595 TCTGGTAGTGAGATACTCCACCA 59.731 47.826 12.74 12.74 40.89 4.17
319 326 4.783055 TCTCTGGTAGTGAGATACTCCAC 58.217 47.826 0.00 0.00 40.89 4.02
320 327 4.141367 CCTCTCTGGTAGTGAGATACTCCA 60.141 50.000 8.92 0.00 37.89 3.86
322 329 5.298989 TCCTCTCTGGTAGTGAGATACTC 57.701 47.826 8.92 0.00 37.89 2.59
324 331 4.273969 CGTTCCTCTCTGGTAGTGAGATAC 59.726 50.000 8.92 6.12 37.89 2.24
334 352 2.618559 GGTAGTCTCGTTCCTCTCTGGT 60.619 54.545 0.00 0.00 37.07 4.00
337 355 2.942306 GCTGGTAGTCTCGTTCCTCTCT 60.942 54.545 0.00 0.00 0.00 3.10
342 360 1.133407 CTGAGCTGGTAGTCTCGTTCC 59.867 57.143 0.00 0.00 32.20 3.62
347 365 2.682856 CTCTGTCTGAGCTGGTAGTCTC 59.317 54.545 0.00 0.00 35.84 3.36
369 387 4.349636 TCTCCTTGACACCTGGTAATTCAA 59.650 41.667 13.86 13.86 0.00 2.69
397 415 2.744202 CTGCCAACACTGAAGTATGACC 59.256 50.000 0.00 0.00 0.00 4.02
411 429 3.500680 TGGACGATTTAGTTTCTGCCAAC 59.499 43.478 0.00 0.00 0.00 3.77
419 437 6.031471 GTGTGTTGTTTGGACGATTTAGTTT 58.969 36.000 0.00 0.00 0.00 2.66
422 444 5.163302 TGTGTGTTGTTTGGACGATTTAG 57.837 39.130 0.00 0.00 0.00 1.85
443 465 9.382244 GCTGATTTTGTACAAAGTTAGTACTTG 57.618 33.333 25.94 10.07 43.74 3.16
444 466 8.280497 CGCTGATTTTGTACAAAGTTAGTACTT 58.720 33.333 25.94 6.88 46.44 2.24
446 468 7.739043 GTCGCTGATTTTGTACAAAGTTAGTAC 59.261 37.037 25.94 21.61 41.63 2.73
447 469 7.438757 TGTCGCTGATTTTGTACAAAGTTAGTA 59.561 33.333 25.94 16.92 30.15 1.82
448 470 6.259167 TGTCGCTGATTTTGTACAAAGTTAGT 59.741 34.615 25.94 12.18 30.15 2.24
449 471 6.573725 GTGTCGCTGATTTTGTACAAAGTTAG 59.426 38.462 23.19 23.19 30.46 2.34
450 472 6.259167 AGTGTCGCTGATTTTGTACAAAGTTA 59.741 34.615 19.72 13.46 0.00 2.24
451 473 5.065988 AGTGTCGCTGATTTTGTACAAAGTT 59.934 36.000 19.72 12.36 0.00 2.66
452 474 4.574828 AGTGTCGCTGATTTTGTACAAAGT 59.425 37.500 19.72 17.59 0.00 2.66
453 475 5.095691 AGTGTCGCTGATTTTGTACAAAG 57.904 39.130 19.72 10.43 0.00 2.77
454 476 5.493133 AAGTGTCGCTGATTTTGTACAAA 57.507 34.783 17.01 17.01 0.00 2.83
455 477 6.795098 ATAAGTGTCGCTGATTTTGTACAA 57.205 33.333 3.59 3.59 0.00 2.41
456 478 6.795098 AATAAGTGTCGCTGATTTTGTACA 57.205 33.333 0.00 0.00 0.00 2.90
461 483 6.863126 CCTTCAAAATAAGTGTCGCTGATTTT 59.137 34.615 13.65 13.65 44.96 1.82
462 484 6.206634 TCCTTCAAAATAAGTGTCGCTGATTT 59.793 34.615 3.21 3.21 39.41 2.17
463 485 5.705441 TCCTTCAAAATAAGTGTCGCTGATT 59.295 36.000 0.00 0.00 29.37 2.57
464 486 5.245531 TCCTTCAAAATAAGTGTCGCTGAT 58.754 37.500 0.00 0.00 0.00 2.90
465 487 4.637276 TCCTTCAAAATAAGTGTCGCTGA 58.363 39.130 0.00 0.00 0.00 4.26
466 488 5.049405 ACTTCCTTCAAAATAAGTGTCGCTG 60.049 40.000 0.00 0.00 31.20 5.18
467 489 5.063880 ACTTCCTTCAAAATAAGTGTCGCT 58.936 37.500 0.00 0.00 31.20 4.93
468 490 5.358298 ACTTCCTTCAAAATAAGTGTCGC 57.642 39.130 0.00 0.00 31.20 5.19
469 491 7.653767 ACTACTTCCTTCAAAATAAGTGTCG 57.346 36.000 0.00 0.00 34.23 4.35
473 495 9.384764 GCAGATACTACTTCCTTCAAAATAAGT 57.615 33.333 0.00 0.00 36.26 2.24
474 496 8.831550 GGCAGATACTACTTCCTTCAAAATAAG 58.168 37.037 0.00 0.00 0.00 1.73
475 497 8.325787 TGGCAGATACTACTTCCTTCAAAATAA 58.674 33.333 0.00 0.00 0.00 1.40
476 498 7.857456 TGGCAGATACTACTTCCTTCAAAATA 58.143 34.615 0.00 0.00 0.00 1.40
477 499 6.721318 TGGCAGATACTACTTCCTTCAAAAT 58.279 36.000 0.00 0.00 0.00 1.82
478 500 6.121776 TGGCAGATACTACTTCCTTCAAAA 57.878 37.500 0.00 0.00 0.00 2.44
479 501 5.755409 TGGCAGATACTACTTCCTTCAAA 57.245 39.130 0.00 0.00 0.00 2.69
480 502 5.755409 TTGGCAGATACTACTTCCTTCAA 57.245 39.130 0.00 0.00 0.00 2.69
481 503 5.957771 ATTGGCAGATACTACTTCCTTCA 57.042 39.130 0.00 0.00 0.00 3.02
482 504 6.587273 AGAATTGGCAGATACTACTTCCTTC 58.413 40.000 0.00 0.00 0.00 3.46
483 505 6.567602 AGAATTGGCAGATACTACTTCCTT 57.432 37.500 0.00 0.00 0.00 3.36
484 506 6.567602 AAGAATTGGCAGATACTACTTCCT 57.432 37.500 0.00 0.00 0.00 3.36
485 507 7.631717 AAAAGAATTGGCAGATACTACTTCC 57.368 36.000 0.00 0.00 0.00 3.46
568 590 0.240945 GGTTGTTCCCGCATCTTGTG 59.759 55.000 0.00 0.00 0.00 3.33
578 600 1.886542 GATGAAGTGGTGGTTGTTCCC 59.113 52.381 0.00 0.00 34.77 3.97
580 602 3.253432 GGAAGATGAAGTGGTGGTTGTTC 59.747 47.826 0.00 0.00 0.00 3.18
586 608 4.467795 TCTCTTAGGAAGATGAAGTGGTGG 59.532 45.833 0.00 0.00 36.82 4.61
604 626 3.623703 TGTGTATGCATGCCATTCTCTT 58.376 40.909 16.68 0.00 35.34 2.85
605 627 3.211865 CTGTGTATGCATGCCATTCTCT 58.788 45.455 16.68 0.00 35.34 3.10
606 628 2.287427 GCTGTGTATGCATGCCATTCTC 60.287 50.000 16.68 8.20 35.34 2.87
608 630 1.679680 AGCTGTGTATGCATGCCATTC 59.320 47.619 16.68 7.42 35.34 2.67
615 638 1.146930 CCCGGAGCTGTGTATGCAT 59.853 57.895 0.73 3.79 0.00 3.96
623 646 3.090532 GGATTCCCCCGGAGCTGT 61.091 66.667 0.73 0.00 31.21 4.40
630 653 2.113986 GAGCCATGGATTCCCCCG 59.886 66.667 18.40 0.00 0.00 5.73
652 675 3.512287 GATGCATGCAGTACGCCGC 62.512 63.158 26.69 3.96 41.33 6.53
653 676 1.884464 AGATGCATGCAGTACGCCG 60.884 57.895 26.69 0.00 41.33 6.46
655 678 1.010350 GCAGATGCATGCAGTACGC 60.010 57.895 26.69 20.29 45.77 4.42
656 679 1.274770 CGCAGATGCATGCAGTACG 59.725 57.895 26.69 21.10 46.87 3.67
657 680 1.010350 GCGCAGATGCATGCAGTAC 60.010 57.895 26.69 18.51 46.87 2.73
658 681 2.527867 CGCGCAGATGCATGCAGTA 61.528 57.895 26.69 1.91 46.87 2.74
659 682 3.872728 CGCGCAGATGCATGCAGT 61.873 61.111 26.69 13.10 46.87 4.40
674 697 0.313672 TCCAATGTTTTCACCTGCGC 59.686 50.000 0.00 0.00 0.00 6.09
675 698 1.608590 ACTCCAATGTTTTCACCTGCG 59.391 47.619 0.00 0.00 0.00 5.18
696 719 0.669077 GAGATCTGCGGTACATCGGT 59.331 55.000 0.00 0.00 0.00 4.69
697 720 0.386100 CGAGATCTGCGGTACATCGG 60.386 60.000 0.00 0.00 0.00 4.18
698 721 0.999228 GCGAGATCTGCGGTACATCG 60.999 60.000 0.00 0.00 0.00 3.84
699 722 0.030773 TGCGAGATCTGCGGTACATC 59.969 55.000 0.00 0.00 34.24 3.06
700 723 0.031314 CTGCGAGATCTGCGGTACAT 59.969 55.000 0.00 0.00 33.99 2.29
701 724 1.433471 CTGCGAGATCTGCGGTACA 59.567 57.895 0.00 0.00 33.99 2.90
702 725 1.946650 GCTGCGAGATCTGCGGTAC 60.947 63.158 20.17 7.43 40.87 3.34
703 726 2.413351 GCTGCGAGATCTGCGGTA 59.587 61.111 20.17 2.87 40.87 4.02
704 727 4.521062 GGCTGCGAGATCTGCGGT 62.521 66.667 20.17 0.00 40.87 5.68
768 791 2.607750 TGGTGGAGAGAGTGGGGC 60.608 66.667 0.00 0.00 0.00 5.80
834 857 0.464452 GGGGAATCTCGACCGATTGT 59.536 55.000 4.76 0.00 33.96 2.71
875 903 5.797051 AGCGTGTTAAATAGAAGGGTTACA 58.203 37.500 0.00 0.00 0.00 2.41
880 908 3.621715 GTGGAGCGTGTTAAATAGAAGGG 59.378 47.826 0.00 0.00 0.00 3.95
1055 1105 2.181021 GCACCACGTAGGAGACCG 59.819 66.667 10.46 0.00 41.22 4.79
1272 1331 4.572571 TCCGCCGTGTTGCCCTTT 62.573 61.111 0.00 0.00 0.00 3.11
1445 1507 2.985847 GCCGGGGCTAATGATGGC 60.986 66.667 2.18 0.00 38.26 4.40
1516 1595 3.748083 ACCCATATGATCATGTGCTGTC 58.252 45.455 23.09 0.00 0.00 3.51
1563 1642 4.056740 GACACAGATGGCAGATCACATAG 58.943 47.826 0.00 0.00 32.03 2.23
1664 1744 4.150980 CGATTAACAGACTAAACAACGGCA 59.849 41.667 0.00 0.00 0.00 5.69
1665 1745 4.151157 ACGATTAACAGACTAAACAACGGC 59.849 41.667 0.00 0.00 0.00 5.68
1666 1746 5.834239 ACGATTAACAGACTAAACAACGG 57.166 39.130 0.00 0.00 0.00 4.44
1667 1747 5.558888 GCAACGATTAACAGACTAAACAACG 59.441 40.000 0.00 0.00 0.00 4.10
1682 1762 3.261580 CAGTCACCATCAGCAACGATTA 58.738 45.455 0.00 0.00 0.00 1.75
2273 2353 3.480505 TGGACCGATCATACGACTCTA 57.519 47.619 0.00 0.00 35.09 2.43
2316 2396 5.003967 CGCTCTTCTAAACGAGAAAGATGAC 59.996 44.000 0.00 0.00 43.75 3.06
2339 2419 2.179018 CAAATCAACCCAGCGCCG 59.821 61.111 2.29 0.00 0.00 6.46
2344 2424 2.164219 CGTCCAATCCAAATCAACCCAG 59.836 50.000 0.00 0.00 0.00 4.45
2348 2428 2.817258 TCCACGTCCAATCCAAATCAAC 59.183 45.455 0.00 0.00 0.00 3.18
2351 2431 1.743394 GGTCCACGTCCAATCCAAATC 59.257 52.381 0.00 0.00 0.00 2.17
2411 2491 2.612672 GCAAAAGAATAGGCGGAGTACC 59.387 50.000 0.00 0.00 0.00 3.34
2449 2529 3.253432 ACCTCAGCCGAAAAAGAATCAAC 59.747 43.478 0.00 0.00 0.00 3.18
2460 2540 1.227527 CACACACACCTCAGCCGAA 60.228 57.895 0.00 0.00 0.00 4.30
2579 2666 6.590292 AGGTCAAACACGTCTTAATATCACTG 59.410 38.462 0.00 0.00 0.00 3.66
2585 2672 7.280428 TGTTCAAAGGTCAAACACGTCTTAATA 59.720 33.333 0.00 0.00 0.00 0.98
2602 2713 4.122776 CCGGATCATACTCTGTTCAAAGG 58.877 47.826 0.00 0.00 0.00 3.11
2712 2823 9.906660 TTTTCCTTTGATATGTAACATGTTGAC 57.093 29.630 21.42 14.49 0.00 3.18
2801 2914 3.133721 AGAGAGAGAGAGAGAGAGAGTGC 59.866 52.174 0.00 0.00 0.00 4.40
2803 2916 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
3142 3255 2.103263 AGTGTGGTCTTCTTCCTGTGTC 59.897 50.000 0.00 0.00 0.00 3.67
3217 4940 3.132646 TGGCAACAGATGATTTATTGGGC 59.867 43.478 0.00 0.00 46.17 5.36
3234 4957 2.623878 TCTTCCTTACAACGTGGCAA 57.376 45.000 0.00 0.00 0.00 4.52
3235 4958 2.623878 TTCTTCCTTACAACGTGGCA 57.376 45.000 0.00 0.00 0.00 4.92
3236 4959 4.499037 AAATTCTTCCTTACAACGTGGC 57.501 40.909 0.00 0.00 0.00 5.01
3237 4960 8.293867 TCATAAAAATTCTTCCTTACAACGTGG 58.706 33.333 0.00 0.00 0.00 4.94
3238 4961 9.113876 GTCATAAAAATTCTTCCTTACAACGTG 57.886 33.333 0.00 0.00 0.00 4.49
3239 4962 9.063615 AGTCATAAAAATTCTTCCTTACAACGT 57.936 29.630 0.00 0.00 0.00 3.99
3240 4963 9.893305 AAGTCATAAAAATTCTTCCTTACAACG 57.107 29.630 0.00 0.00 0.00 4.10
3246 4969 8.912988 TCACACAAGTCATAAAAATTCTTCCTT 58.087 29.630 0.00 0.00 0.00 3.36
3247 4970 8.463930 TCACACAAGTCATAAAAATTCTTCCT 57.536 30.769 0.00 0.00 0.00 3.36
3248 4971 9.696917 ATTCACACAAGTCATAAAAATTCTTCC 57.303 29.630 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.