Multiple sequence alignment - TraesCS2B01G515400

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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 TraesCS2B01G515400 chr2B 100.000 2498 0 0 1 2498 710279174 710281671 0.000000e+00 4614.0
1 TraesCS2B01G515400 chr2B 97.222 36 1 0 476 511 495136002 495136037 7.460000e-06 62.1
2 TraesCS2B01G515400 chr2D 88.674 2013 113 61 525 2498 587695671 587697607 0.000000e+00 2348.0
3 TraesCS2B01G515400 chr2D 85.922 412 55 3 16 425 587695246 587695656 1.060000e-118 436.0
4 TraesCS2B01G515400 chr2D 84.289 401 56 4 3 397 617956532 617956931 3.900000e-103 385.0
5 TraesCS2B01G515400 chr2A 88.823 1843 97 35 702 2498 722517768 722519547 0.000000e+00 2161.0
6 TraesCS2B01G515400 chr2A 91.753 194 12 4 1663 1854 32974152 32974343 1.470000e-67 267.0
7 TraesCS2B01G515400 chr4D 87.928 994 58 28 1486 2441 344373768 344372799 0.000000e+00 1114.0
8 TraesCS2B01G515400 chr3A 86.067 811 43 28 1486 2254 195452298 195451516 0.000000e+00 808.0
9 TraesCS2B01G515400 chr3A 85.204 392 55 3 1 391 16154255 16154644 1.390000e-107 399.0
10 TraesCS2B01G515400 chr3A 85.714 343 43 6 9 349 523760229 523759891 8.500000e-95 357.0
11 TraesCS2B01G515400 chr3A 92.308 182 11 2 2260 2441 195447607 195447429 3.190000e-64 255.0
12 TraesCS2B01G515400 chr6B 84.694 392 57 2 2 391 482469637 482470027 3.010000e-104 388.0
13 TraesCS2B01G515400 chr5B 84.615 390 56 4 1 388 63546446 63546059 3.900000e-103 385.0
14 TraesCS2B01G515400 chr4B 82.576 396 63 5 3 397 22950744 22950354 6.610000e-91 344.0
15 TraesCS2B01G515400 chr7A 82.353 391 64 5 1 389 280020335 280019948 3.980000e-88 335.0
16 TraesCS2B01G515400 chr1B 82.031 384 64 5 4 385 618552438 618552818 3.100000e-84 322.0
17 TraesCS2B01G515400 chr1B 97.222 36 1 0 478 513 114434107 114434142 7.460000e-06 62.1
18 TraesCS2B01G515400 chr1D 93.377 151 8 1 2291 2441 2480366 2480514 3.230000e-54 222.0
19 TraesCS2B01G515400 chr7D 97.222 36 1 0 476 511 518568932 518568897 7.460000e-06 62.1
20 TraesCS2B01G515400 chr6A 97.222 36 1 0 476 511 380939702 380939737 7.460000e-06 62.1
21 TraesCS2B01G515400 chr4A 97.222 36 1 0 477 512 362108319 362108354 7.460000e-06 62.1
22 TraesCS2B01G515400 chr3D 97.222 36 1 0 476 511 166518491 166518456 7.460000e-06 62.1
23 TraesCS2B01G515400 chr3D 97.222 36 1 0 476 511 292887737 292887772 7.460000e-06 62.1
24 TraesCS2B01G515400 chr3B 97.222 36 1 0 476 511 242209250 242209215 7.460000e-06 62.1
25 TraesCS2B01G515400 chr3B 97.222 36 1 0 476 511 386056423 386056388 7.460000e-06 62.1


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 TraesCS2B01G515400 chr2B 710279174 710281671 2497 False 4614.0 4614 100.0000 1 2498 1 chr2B.!!$F2 2497
1 TraesCS2B01G515400 chr2D 587695246 587697607 2361 False 1392.0 2348 87.2980 16 2498 2 chr2D.!!$F2 2482
2 TraesCS2B01G515400 chr2A 722517768 722519547 1779 False 2161.0 2161 88.8230 702 2498 1 chr2A.!!$F2 1796
3 TraesCS2B01G515400 chr4D 344372799 344373768 969 True 1114.0 1114 87.9280 1486 2441 1 chr4D.!!$R1 955
4 TraesCS2B01G515400 chr3A 195447429 195452298 4869 True 531.5 808 89.1875 1486 2441 2 chr3A.!!$R2 955

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
100 102 0.038744 CACAGCCCCAAAGAGATGGT 59.961 55.0 0.0 0.0 38.91 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1867 1.133606 CACCTACCTCTCCCTCTCTCC 60.134 61.905 0.0 0.0 0.0 3.71 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
28 29 0.591170 CGTCGTTTGAACCCTTGCAT 59.409 50.000 0.00 0.00 0.00 3.96
41 42 3.137913 ACCCTTGCATAGATCTGAAGCAT 59.862 43.478 16.05 2.82 34.87 3.79
42 43 3.752222 CCCTTGCATAGATCTGAAGCATC 59.248 47.826 16.05 0.00 34.87 3.91
52 53 2.771089 TCTGAAGCATCTGACACCAAC 58.229 47.619 0.00 0.00 0.00 3.77
66 67 0.687354 ACCAACTCTCGCCACAAGAT 59.313 50.000 0.00 0.00 0.00 2.40
84 86 6.483307 CACAAGATGAGAAAACTAACCTCACA 59.517 38.462 0.00 0.00 39.43 3.58
90 92 1.145571 AAACTAACCTCACAGCCCCA 58.854 50.000 0.00 0.00 0.00 4.96
97 99 0.622665 CCTCACAGCCCCAAAGAGAT 59.377 55.000 0.00 0.00 0.00 2.75
99 101 0.329261 TCACAGCCCCAAAGAGATGG 59.671 55.000 0.00 0.00 40.35 3.51
100 102 0.038744 CACAGCCCCAAAGAGATGGT 59.961 55.000 0.00 0.00 38.91 3.55
110 112 5.221742 CCCCAAAGAGATGGTAGGAATCTAC 60.222 48.000 0.00 0.00 43.82 2.59
113 115 4.107127 AGAGATGGTAGGAATCTACGCT 57.893 45.455 0.00 0.00 45.10 5.07
114 116 3.823873 AGAGATGGTAGGAATCTACGCTG 59.176 47.826 0.00 0.00 45.10 5.18
160 162 0.818296 ACAAACTCGAGGAGGATCGG 59.182 55.000 18.41 0.00 42.93 4.18
162 164 1.476891 CAAACTCGAGGAGGATCGGAA 59.523 52.381 18.41 0.00 42.93 4.30
163 165 2.074729 AACTCGAGGAGGATCGGAAT 57.925 50.000 18.41 0.00 42.93 3.01
164 166 1.611519 ACTCGAGGAGGATCGGAATC 58.388 55.000 18.41 0.00 42.93 2.52
193 195 0.601558 AACTCGAAGAAGTAGCGCCA 59.398 50.000 2.29 0.00 34.09 5.69
197 199 0.669318 CGAAGAAGTAGCGCCACCAA 60.669 55.000 2.29 0.00 0.00 3.67
254 256 4.102367 ACCCTAGACTAGACTACTAACCGG 59.898 50.000 11.27 0.00 0.00 5.28
258 260 2.543430 GACTAGACTACTAACCGGAGCG 59.457 54.545 9.46 0.00 0.00 5.03
274 276 1.079405 GCGAAGACACCGGGATTCA 60.079 57.895 6.32 0.00 0.00 2.57
275 277 1.359459 GCGAAGACACCGGGATTCAC 61.359 60.000 6.32 0.00 0.00 3.18
286 288 2.757124 GGATTCACCTCCCCGCCAT 61.757 63.158 0.00 0.00 35.41 4.40
322 324 1.153147 GGCGGAAGGGAGGTGAATC 60.153 63.158 0.00 0.00 0.00 2.52
323 325 1.153147 GCGGAAGGGAGGTGAATCC 60.153 63.158 0.00 0.00 38.76 3.01
326 328 2.047061 CGGAAGGGAGGTGAATCCATA 58.953 52.381 0.00 0.00 41.52 2.74
333 335 0.394565 AGGTGAATCCATAGGCTCGC 59.605 55.000 0.00 0.00 39.02 5.03
335 337 0.946221 GTGAATCCATAGGCTCGCCG 60.946 60.000 1.69 0.00 41.95 6.46
337 339 2.788191 GAATCCATAGGCTCGCCGGG 62.788 65.000 2.18 6.18 41.95 5.73
346 348 2.345991 CTCGCCGGGGAAGTTTGA 59.654 61.111 22.77 0.00 0.00 2.69
350 352 1.977009 GCCGGGGAAGTTTGAAGGG 60.977 63.158 2.18 0.00 0.00 3.95
351 353 1.304134 CCGGGGAAGTTTGAAGGGG 60.304 63.158 0.00 0.00 0.00 4.79
352 354 1.304134 CGGGGAAGTTTGAAGGGGG 60.304 63.158 0.00 0.00 0.00 5.40
370 372 2.824489 GAGTTTGCCCTAGCCGCC 60.824 66.667 0.00 0.00 38.69 6.13
392 394 5.479027 GCCTAGGGTTATGGAAGAAAAACAA 59.521 40.000 11.72 0.00 0.00 2.83
394 396 6.946009 CCTAGGGTTATGGAAGAAAAACAAGA 59.054 38.462 0.00 0.00 0.00 3.02
398 400 6.239317 GGGTTATGGAAGAAAAACAAGAAGCT 60.239 38.462 0.00 0.00 0.00 3.74
433 435 9.986833 ACTAACAAAATGAAAATCAAAAGCAAC 57.013 25.926 0.00 0.00 0.00 4.17
434 436 9.985318 CTAACAAAATGAAAATCAAAAGCAACA 57.015 25.926 0.00 0.00 0.00 3.33
436 438 9.857957 AACAAAATGAAAATCAAAAGCAACATT 57.142 22.222 0.00 0.00 0.00 2.71
437 439 9.291664 ACAAAATGAAAATCAAAAGCAACATTG 57.708 25.926 0.00 0.00 0.00 2.82
438 440 9.291664 CAAAATGAAAATCAAAAGCAACATTGT 57.708 25.926 0.00 0.00 0.00 2.71
454 456 9.567848 AGCAACATTGTAAATTTAAGAATACGG 57.432 29.630 0.00 0.00 0.00 4.02
455 457 9.562583 GCAACATTGTAAATTTAAGAATACGGA 57.437 29.630 0.00 0.00 0.00 4.69
476 478 5.973565 CGGAAACCGTAGATCTATTTACGTT 59.026 40.000 17.97 7.29 42.73 3.99
477 479 7.132213 CGGAAACCGTAGATCTATTTACGTTA 58.868 38.462 17.97 0.00 42.73 3.18
478 480 7.805071 CGGAAACCGTAGATCTATTTACGTTAT 59.195 37.037 17.97 4.69 42.73 1.89
492 494 9.852091 CTATTTACGTTATTATGTACTCCCTCC 57.148 37.037 0.00 0.00 0.00 4.30
493 495 4.843220 ACGTTATTATGTACTCCCTCCG 57.157 45.455 0.00 0.00 0.00 4.63
494 496 4.210331 ACGTTATTATGTACTCCCTCCGT 58.790 43.478 0.00 0.00 0.00 4.69
495 497 4.276926 ACGTTATTATGTACTCCCTCCGTC 59.723 45.833 0.00 0.00 0.00 4.79
496 498 4.320788 CGTTATTATGTACTCCCTCCGTCC 60.321 50.000 0.00 0.00 0.00 4.79
497 499 2.077687 TTATGTACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
498 500 0.928505 TATGTACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
499 501 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
500 502 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
501 503 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
502 504 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
503 505 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
504 506 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
505 507 2.645797 ACTCCCTCCGTCCCAAAATAAA 59.354 45.455 0.00 0.00 0.00 1.40
506 508 3.268595 ACTCCCTCCGTCCCAAAATAAAT 59.731 43.478 0.00 0.00 0.00 1.40
507 509 3.626930 TCCCTCCGTCCCAAAATAAATG 58.373 45.455 0.00 0.00 0.00 2.32
508 510 3.010808 TCCCTCCGTCCCAAAATAAATGT 59.989 43.478 0.00 0.00 0.00 2.71
509 511 3.380320 CCCTCCGTCCCAAAATAAATGTC 59.620 47.826 0.00 0.00 0.00 3.06
510 512 4.270008 CCTCCGTCCCAAAATAAATGTCT 58.730 43.478 0.00 0.00 0.00 3.41
511 513 4.705023 CCTCCGTCCCAAAATAAATGTCTT 59.295 41.667 0.00 0.00 0.00 3.01
512 514 5.393027 CCTCCGTCCCAAAATAAATGTCTTG 60.393 44.000 0.00 0.00 0.00 3.02
513 515 4.461081 TCCGTCCCAAAATAAATGTCTTGG 59.539 41.667 0.00 0.00 38.45 3.61
519 521 6.543430 CCAAAATAAATGTCTTGGGATGGA 57.457 37.500 0.00 0.00 35.65 3.41
520 522 6.576185 CCAAAATAAATGTCTTGGGATGGAG 58.424 40.000 0.00 0.00 35.65 3.86
521 523 6.407299 CCAAAATAAATGTCTTGGGATGGAGG 60.407 42.308 0.00 0.00 35.65 4.30
522 524 5.732331 AATAAATGTCTTGGGATGGAGGA 57.268 39.130 0.00 0.00 0.00 3.71
523 525 5.732331 ATAAATGTCTTGGGATGGAGGAA 57.268 39.130 0.00 0.00 0.00 3.36
524 526 3.659183 AATGTCTTGGGATGGAGGAAG 57.341 47.619 0.00 0.00 0.00 3.46
525 527 2.044793 TGTCTTGGGATGGAGGAAGT 57.955 50.000 0.00 0.00 0.00 3.01
526 528 3.199442 TGTCTTGGGATGGAGGAAGTA 57.801 47.619 0.00 0.00 0.00 2.24
527 529 3.736094 TGTCTTGGGATGGAGGAAGTAT 58.264 45.455 0.00 0.00 0.00 2.12
528 530 4.890988 TGTCTTGGGATGGAGGAAGTATA 58.109 43.478 0.00 0.00 0.00 1.47
529 531 5.476983 TGTCTTGGGATGGAGGAAGTATAT 58.523 41.667 0.00 0.00 0.00 0.86
530 532 5.911178 TGTCTTGGGATGGAGGAAGTATATT 59.089 40.000 0.00 0.00 0.00 1.28
531 533 6.183361 TGTCTTGGGATGGAGGAAGTATATTG 60.183 42.308 0.00 0.00 0.00 1.90
532 534 5.911178 TCTTGGGATGGAGGAAGTATATTGT 59.089 40.000 0.00 0.00 0.00 2.71
533 535 7.016268 GTCTTGGGATGGAGGAAGTATATTGTA 59.984 40.741 0.00 0.00 0.00 2.41
534 536 7.739444 TCTTGGGATGGAGGAAGTATATTGTAT 59.261 37.037 0.00 0.00 0.00 2.29
535 537 8.982471 TTGGGATGGAGGAAGTATATTGTATA 57.018 34.615 0.00 0.00 0.00 1.47
536 538 8.609617 TGGGATGGAGGAAGTATATTGTATAG 57.390 38.462 0.00 0.00 0.00 1.31
537 539 7.125811 TGGGATGGAGGAAGTATATTGTATAGC 59.874 40.741 0.00 0.00 0.00 2.97
538 540 7.125811 GGGATGGAGGAAGTATATTGTATAGCA 59.874 40.741 0.00 0.00 0.00 3.49
561 563 8.682710 AGCATGGTTTTATAATAAACATCGTGT 58.317 29.630 0.00 0.00 39.27 4.49
586 588 5.103000 GTGTATGTCACATAGTCCAGTCAC 58.897 45.833 0.00 0.00 45.51 3.67
616 618 8.303876 TGGACCTGCAAAGTATTTTTCTTAATC 58.696 33.333 0.00 0.00 35.03 1.75
630 632 9.692325 ATTTTTCTTAATCTAGAAGCATGGTCT 57.308 29.630 0.00 0.00 35.69 3.85
644 646 9.064706 AGAAGCATGGTCTTAAAATCATCTATG 57.935 33.333 0.00 0.00 0.00 2.23
645 647 7.756395 AGCATGGTCTTAAAATCATCTATGG 57.244 36.000 0.00 0.00 0.00 2.74
717 720 7.656137 TCAATACTTGAGATTTATTAGGACGCC 59.344 37.037 0.00 0.00 34.08 5.68
721 724 3.382227 TGAGATTTATTAGGACGCCGACA 59.618 43.478 0.00 0.00 0.00 4.35
725 728 3.872511 TTATTAGGACGCCGACAAGAA 57.127 42.857 0.00 0.00 0.00 2.52
729 732 0.319641 AGGACGCCGACAAGAAGAAC 60.320 55.000 0.00 0.00 0.00 3.01
738 741 4.454504 GCCGACAAGAAGAACTAAATCCAA 59.545 41.667 0.00 0.00 0.00 3.53
779 782 9.276590 AGAAAAAGGAAGGCATTAAATTCTTTG 57.723 29.630 0.00 0.00 0.00 2.77
819 822 5.636543 AGTGCTAAAAATACACTGGACGTAC 59.363 40.000 0.00 0.00 42.83 3.67
970 973 1.913762 CACCACCGTCTTCCTCCCT 60.914 63.158 0.00 0.00 0.00 4.20
977 980 1.180029 CGTCTTCCTCCCTTCCGTTA 58.820 55.000 0.00 0.00 0.00 3.18
978 981 1.135170 CGTCTTCCTCCCTTCCGTTAC 60.135 57.143 0.00 0.00 0.00 2.50
979 982 2.177734 GTCTTCCTCCCTTCCGTTACT 58.822 52.381 0.00 0.00 0.00 2.24
980 983 3.359950 GTCTTCCTCCCTTCCGTTACTA 58.640 50.000 0.00 0.00 0.00 1.82
1159 1167 0.175989 GGAGGTGATCAAGACGGACC 59.824 60.000 0.00 0.00 0.00 4.46
1241 1258 2.648102 CTCGCCGTCATCGTCGTC 60.648 66.667 0.00 0.00 39.43 4.20
1379 1408 0.336737 GAGGTGAAGGAGGAGGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
1385 1414 2.123640 GGAGGAGGAGGAGGACGG 60.124 72.222 0.00 0.00 0.00 4.79
1498 1527 2.203015 TCGGCGGATGGCTTTAGC 60.203 61.111 7.21 0.00 42.94 3.09
1540 1569 2.821991 CCCCCATTAGAGCTAAGTCG 57.178 55.000 0.00 0.00 0.00 4.18
1659 1694 3.644966 ATAGAATTGGGTTTCCTGCGA 57.355 42.857 0.00 0.00 0.00 5.10
1694 1730 9.567776 TTCTCCAGTTTGTTGATATTTCAGTTA 57.432 29.630 0.00 0.00 32.27 2.24
1747 1788 4.846779 TGGCAGATTAGTTTGGTTGTTC 57.153 40.909 0.00 0.00 0.00 3.18
1789 1830 2.392662 TCCAACCTTCATTGTTTGCCA 58.607 42.857 0.00 0.00 0.00 4.92
1824 1867 2.697751 CTGGGTGAACTAGAGGGAGATG 59.302 54.545 0.00 0.00 0.00 2.90
1846 1891 1.076632 AGAGGGAGAGGTAGGTGCG 60.077 63.158 0.00 0.00 0.00 5.34
2040 2101 8.091449 ACTAAACATTCTTCAGTTCAGGTAGAG 58.909 37.037 0.00 0.00 0.00 2.43
2045 2106 0.888619 TCAGTTCAGGTAGAGTGCCG 59.111 55.000 0.00 0.00 0.00 5.69
2049 2118 2.089980 GTTCAGGTAGAGTGCCGTCTA 58.910 52.381 0.00 0.00 0.00 2.59
2082 2151 9.731819 ATGACGGCTTATACTATGATTATTACG 57.268 33.333 0.00 0.00 0.00 3.18
2083 2152 8.733458 TGACGGCTTATACTATGATTATTACGT 58.267 33.333 0.00 0.00 0.00 3.57
2085 2154 9.994432 ACGGCTTATACTATGATTATTACGTAC 57.006 33.333 0.00 0.00 0.00 3.67
2096 2165 6.811954 TGATTATTACGTACTCCTGATGCAA 58.188 36.000 0.00 0.00 0.00 4.08
2097 2166 7.441836 TGATTATTACGTACTCCTGATGCAAT 58.558 34.615 0.00 0.00 0.00 3.56
2098 2167 7.598869 TGATTATTACGTACTCCTGATGCAATC 59.401 37.037 0.00 0.00 45.83 2.67
2099 2168 2.604046 ACGTACTCCTGATGCAATCC 57.396 50.000 0.00 0.00 44.73 3.01
2120 2192 5.321927 TCCAACAAGGGGAAGATTTTAGAC 58.678 41.667 0.00 0.00 38.24 2.59
2128 2200 5.016831 GGGGAAGATTTTAGACACAATGGT 58.983 41.667 0.00 0.00 0.00 3.55
2181 2269 2.291735 TGGCCACATGATCCACATTTCT 60.292 45.455 0.00 0.00 37.07 2.52
2182 2270 3.053768 TGGCCACATGATCCACATTTCTA 60.054 43.478 0.00 0.00 37.07 2.10
2184 2272 3.316308 GCCACATGATCCACATTTCTACC 59.684 47.826 0.00 0.00 37.07 3.18
2211 2299 6.441093 TGCTGGATGTTTGTATTTGAGATC 57.559 37.500 0.00 0.00 0.00 2.75
2324 6318 2.939460 ATTTACTGCCCATTTCGCAC 57.061 45.000 0.00 0.00 31.61 5.34
2326 6320 1.164411 TTACTGCCCATTTCGCACAG 58.836 50.000 0.00 0.00 31.61 3.66
2348 6342 5.680229 CAGCTAATTTTTCATCGCATCTGAC 59.320 40.000 0.00 0.00 0.00 3.51
2354 6348 0.248784 TCATCGCATCTGACTGCTCG 60.249 55.000 9.33 0.00 40.06 5.03
2375 6369 3.181471 CGAGTATTGCTCAACTCCAGGAT 60.181 47.826 2.63 0.00 44.33 3.24
2376 6370 4.038042 CGAGTATTGCTCAACTCCAGGATA 59.962 45.833 2.63 0.00 44.33 2.59
2457 6451 6.535150 TGACTGCTAACATATGCACTACTTTC 59.465 38.462 1.58 0.00 35.20 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.781787 TTCAAACGACGATGACTGCG 59.218 50.000 0.00 0.00 0.00 5.18
1 2 1.136336 GGTTCAAACGACGATGACTGC 60.136 52.381 0.00 0.00 0.00 4.40
2 3 1.459592 GGGTTCAAACGACGATGACTG 59.540 52.381 0.00 0.00 0.00 3.51
3 4 1.343465 AGGGTTCAAACGACGATGACT 59.657 47.619 0.00 0.00 0.00 3.41
4 5 1.792006 AGGGTTCAAACGACGATGAC 58.208 50.000 0.00 1.48 0.00 3.06
5 6 2.139917 CAAGGGTTCAAACGACGATGA 58.860 47.619 0.00 2.67 0.00 2.92
6 7 1.399727 GCAAGGGTTCAAACGACGATG 60.400 52.381 0.00 0.00 0.00 3.84
7 8 0.872388 GCAAGGGTTCAAACGACGAT 59.128 50.000 0.00 0.00 0.00 3.73
8 9 0.462225 TGCAAGGGTTCAAACGACGA 60.462 50.000 0.00 0.00 0.00 4.20
9 10 0.591170 ATGCAAGGGTTCAAACGACG 59.409 50.000 0.00 0.00 0.00 5.12
10 11 3.071479 TCTATGCAAGGGTTCAAACGAC 58.929 45.455 0.00 0.00 0.00 4.34
11 12 3.410631 TCTATGCAAGGGTTCAAACGA 57.589 42.857 0.00 0.00 0.00 3.85
12 13 3.941483 AGATCTATGCAAGGGTTCAAACG 59.059 43.478 0.00 0.00 0.00 3.60
13 14 4.943705 TCAGATCTATGCAAGGGTTCAAAC 59.056 41.667 0.00 0.00 0.00 2.93
14 15 5.178096 TCAGATCTATGCAAGGGTTCAAA 57.822 39.130 0.00 0.00 0.00 2.69
28 29 4.026052 TGGTGTCAGATGCTTCAGATCTA 58.974 43.478 0.00 0.00 0.00 1.98
41 42 1.112916 TGGCGAGAGTTGGTGTCAGA 61.113 55.000 0.00 0.00 0.00 3.27
42 43 0.946221 GTGGCGAGAGTTGGTGTCAG 60.946 60.000 0.00 0.00 0.00 3.51
52 53 2.662006 TTCTCATCTTGTGGCGAGAG 57.338 50.000 0.00 0.00 35.99 3.20
66 67 3.496160 GGGCTGTGAGGTTAGTTTTCTCA 60.496 47.826 0.00 0.00 35.45 3.27
84 86 1.216990 CCTACCATCTCTTTGGGGCT 58.783 55.000 0.00 0.00 41.35 5.19
90 92 4.896482 AGCGTAGATTCCTACCATCTCTTT 59.104 41.667 0.00 0.00 41.68 2.52
97 99 2.307768 CTCCAGCGTAGATTCCTACCA 58.692 52.381 0.00 0.00 41.68 3.25
99 101 2.425578 GCTCCAGCGTAGATTCCTAC 57.574 55.000 0.00 0.00 41.38 3.18
113 115 3.900855 GTAGTCGACGGAGCTCCA 58.099 61.111 31.67 10.19 35.14 3.86
141 143 0.818296 CCGATCCTCCTCGAGTTTGT 59.182 55.000 12.31 0.00 41.12 2.83
143 145 1.848652 TTCCGATCCTCCTCGAGTTT 58.151 50.000 12.31 0.00 41.12 2.66
160 162 2.955614 TCGAGTTTGTCTTCCGGATTC 58.044 47.619 4.15 0.00 0.00 2.52
162 164 2.561419 TCTTCGAGTTTGTCTTCCGGAT 59.439 45.455 4.15 0.00 0.00 4.18
163 165 1.958579 TCTTCGAGTTTGTCTTCCGGA 59.041 47.619 0.00 0.00 0.00 5.14
164 166 2.433868 TCTTCGAGTTTGTCTTCCGG 57.566 50.000 0.00 0.00 0.00 5.14
232 234 4.346418 TCCGGTTAGTAGTCTAGTCTAGGG 59.654 50.000 0.00 0.00 0.00 3.53
233 235 5.540911 CTCCGGTTAGTAGTCTAGTCTAGG 58.459 50.000 0.00 0.00 0.00 3.02
237 239 2.543430 CGCTCCGGTTAGTAGTCTAGTC 59.457 54.545 0.00 0.00 0.00 2.59
238 240 2.169352 TCGCTCCGGTTAGTAGTCTAGT 59.831 50.000 0.00 0.00 0.00 2.57
242 244 2.012673 TCTTCGCTCCGGTTAGTAGTC 58.987 52.381 0.00 0.00 0.00 2.59
254 256 0.806492 GAATCCCGGTGTCTTCGCTC 60.806 60.000 0.00 0.00 0.00 5.03
258 260 0.613777 AGGTGAATCCCGGTGTCTTC 59.386 55.000 0.00 0.00 36.75 2.87
307 309 2.373502 CCTATGGATTCACCTCCCTTCC 59.626 54.545 0.00 0.00 39.86 3.46
310 312 1.061033 AGCCTATGGATTCACCTCCCT 60.061 52.381 0.00 0.00 39.86 4.20
317 319 1.367471 CGGCGAGCCTATGGATTCA 59.633 57.895 12.70 0.00 0.00 2.57
323 325 3.521529 CTTCCCCGGCGAGCCTATG 62.522 68.421 9.30 0.68 0.00 2.23
333 335 1.304134 CCCCTTCAAACTTCCCCGG 60.304 63.158 0.00 0.00 0.00 5.73
335 337 4.865629 CCCCCTTCAAACTTCCCC 57.134 61.111 0.00 0.00 0.00 4.81
351 353 2.124695 CGGCTAGGGCAAACTCCC 60.125 66.667 0.00 0.00 46.93 4.30
352 354 2.824489 GCGGCTAGGGCAAACTCC 60.824 66.667 0.00 0.00 40.87 3.85
370 372 7.996098 TCTTGTTTTTCTTCCATAACCCTAG 57.004 36.000 0.00 0.00 0.00 3.02
379 381 6.357367 ACTCTAGCTTCTTGTTTTTCTTCCA 58.643 36.000 0.00 0.00 0.00 3.53
408 410 9.985318 TGTTGCTTTTGATTTTCATTTTGTTAG 57.015 25.926 0.00 0.00 0.00 2.34
411 413 9.291664 CAATGTTGCTTTTGATTTTCATTTTGT 57.708 25.926 0.00 0.00 0.00 2.83
428 430 9.567848 CCGTATTCTTAAATTTACAATGTTGCT 57.432 29.630 0.00 0.00 0.00 3.91
429 431 9.562583 TCCGTATTCTTAAATTTACAATGTTGC 57.437 29.630 0.00 0.00 0.00 4.17
434 436 9.777575 CGGTTTCCGTATTCTTAAATTTACAAT 57.222 29.630 0.00 2.60 42.73 2.71
453 455 9.468532 AATAACGTAAATAGATCTACGGTTTCC 57.531 33.333 17.53 1.47 44.01 3.13
476 478 3.140707 TGGGACGGAGGGAGTACATAATA 59.859 47.826 0.00 0.00 0.00 0.98
477 479 2.090943 TGGGACGGAGGGAGTACATAAT 60.091 50.000 0.00 0.00 0.00 1.28
478 480 1.288633 TGGGACGGAGGGAGTACATAA 59.711 52.381 0.00 0.00 0.00 1.90
480 482 0.042131 TTGGGACGGAGGGAGTACAT 59.958 55.000 0.00 0.00 0.00 2.29
481 483 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
482 484 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
483 485 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
484 486 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
486 488 3.010808 ACATTTATTTTGGGACGGAGGGA 59.989 43.478 0.00 0.00 0.00 4.20
487 489 3.361786 ACATTTATTTTGGGACGGAGGG 58.638 45.455 0.00 0.00 0.00 4.30
488 490 4.270008 AGACATTTATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 0.00 4.30
489 491 5.393027 CCAAGACATTTATTTTGGGACGGAG 60.393 44.000 0.00 0.00 37.11 4.63
490 492 4.461081 CCAAGACATTTATTTTGGGACGGA 59.539 41.667 0.00 0.00 37.11 4.69
491 493 4.743493 CCAAGACATTTATTTTGGGACGG 58.257 43.478 0.00 0.00 37.11 4.79
496 498 6.407299 CCTCCATCCCAAGACATTTATTTTGG 60.407 42.308 0.00 0.00 39.77 3.28
497 499 6.380846 TCCTCCATCCCAAGACATTTATTTTG 59.619 38.462 0.00 0.00 0.00 2.44
498 500 6.502138 TCCTCCATCCCAAGACATTTATTTT 58.498 36.000 0.00 0.00 0.00 1.82
499 501 6.091076 TCCTCCATCCCAAGACATTTATTT 57.909 37.500 0.00 0.00 0.00 1.40
500 502 5.732331 TCCTCCATCCCAAGACATTTATT 57.268 39.130 0.00 0.00 0.00 1.40
501 503 5.194537 ACTTCCTCCATCCCAAGACATTTAT 59.805 40.000 0.00 0.00 0.00 1.40
502 504 4.540099 ACTTCCTCCATCCCAAGACATTTA 59.460 41.667 0.00 0.00 0.00 1.40
503 505 3.334881 ACTTCCTCCATCCCAAGACATTT 59.665 43.478 0.00 0.00 0.00 2.32
504 506 2.922283 ACTTCCTCCATCCCAAGACATT 59.078 45.455 0.00 0.00 0.00 2.71
505 507 2.566746 ACTTCCTCCATCCCAAGACAT 58.433 47.619 0.00 0.00 0.00 3.06
506 508 2.044793 ACTTCCTCCATCCCAAGACA 57.955 50.000 0.00 0.00 0.00 3.41
507 509 6.183361 ACAATATACTTCCTCCATCCCAAGAC 60.183 42.308 0.00 0.00 0.00 3.01
508 510 5.911178 ACAATATACTTCCTCCATCCCAAGA 59.089 40.000 0.00 0.00 0.00 3.02
509 511 6.192970 ACAATATACTTCCTCCATCCCAAG 57.807 41.667 0.00 0.00 0.00 3.61
510 512 7.888514 ATACAATATACTTCCTCCATCCCAA 57.111 36.000 0.00 0.00 0.00 4.12
511 513 7.125811 GCTATACAATATACTTCCTCCATCCCA 59.874 40.741 0.00 0.00 0.00 4.37
512 514 7.125811 TGCTATACAATATACTTCCTCCATCCC 59.874 40.741 0.00 0.00 0.00 3.85
513 515 8.079211 TGCTATACAATATACTTCCTCCATCC 57.921 38.462 0.00 0.00 0.00 3.51
514 516 9.539825 CATGCTATACAATATACTTCCTCCATC 57.460 37.037 0.00 0.00 0.00 3.51
515 517 8.489489 CCATGCTATACAATATACTTCCTCCAT 58.511 37.037 0.00 0.00 0.00 3.41
516 518 7.457852 ACCATGCTATACAATATACTTCCTCCA 59.542 37.037 0.00 0.00 0.00 3.86
517 519 7.852263 ACCATGCTATACAATATACTTCCTCC 58.148 38.462 0.00 0.00 0.00 4.30
518 520 9.726438 AAACCATGCTATACAATATACTTCCTC 57.274 33.333 0.00 0.00 0.00 3.71
535 537 8.682710 ACACGATGTTTATTATAAAACCATGCT 58.317 29.630 0.00 0.00 38.35 3.79
536 538 8.850454 ACACGATGTTTATTATAAAACCATGC 57.150 30.769 0.00 0.00 38.35 4.06
569 571 4.393062 CCATTTGTGACTGGACTATGTGAC 59.607 45.833 0.00 0.00 34.24 3.67
571 573 4.578871 TCCATTTGTGACTGGACTATGTG 58.421 43.478 0.00 0.00 36.63 3.21
580 582 1.608055 TGCAGGTCCATTTGTGACTG 58.392 50.000 0.00 0.00 33.22 3.51
582 584 2.362077 ACTTTGCAGGTCCATTTGTGAC 59.638 45.455 0.00 0.00 0.00 3.67
586 588 6.930722 AGAAAAATACTTTGCAGGTCCATTTG 59.069 34.615 0.00 0.00 0.00 2.32
616 618 8.674263 AGATGATTTTAAGACCATGCTTCTAG 57.326 34.615 0.00 0.00 0.00 2.43
623 625 8.469309 AACCCATAGATGATTTTAAGACCATG 57.531 34.615 0.00 0.00 0.00 3.66
638 640 3.305403 CGCGTGTGAGATAACCCATAGAT 60.305 47.826 0.00 0.00 0.00 1.98
643 645 1.447140 GCGCGTGTGAGATAACCCA 60.447 57.895 8.43 0.00 0.00 4.51
644 646 0.101759 TAGCGCGTGTGAGATAACCC 59.898 55.000 8.43 0.00 0.00 4.11
645 647 1.065102 TCTAGCGCGTGTGAGATAACC 59.935 52.381 8.43 0.00 0.00 2.85
652 654 1.136085 GCAAAAATCTAGCGCGTGTGA 60.136 47.619 8.43 3.56 0.00 3.58
696 699 4.098960 TCGGCGTCCTAATAAATCTCAAGT 59.901 41.667 6.85 0.00 0.00 3.16
717 720 7.806690 TCAATTGGATTTAGTTCTTCTTGTCG 58.193 34.615 5.42 0.00 0.00 4.35
721 724 6.623767 GCGCTCAATTGGATTTAGTTCTTCTT 60.624 38.462 5.42 0.00 0.00 2.52
725 728 3.063997 CGCGCTCAATTGGATTTAGTTCT 59.936 43.478 5.56 0.00 0.00 3.01
729 732 4.024893 ACATACGCGCTCAATTGGATTTAG 60.025 41.667 5.73 0.00 0.00 1.85
738 741 4.034048 CCTTTTTCTACATACGCGCTCAAT 59.966 41.667 5.73 0.00 0.00 2.57
793 796 6.403878 ACGTCCAGTGTATTTTTAGCACTAT 58.596 36.000 0.00 0.00 40.99 2.12
811 814 2.563620 TGGCACTGATTTAGTACGTCCA 59.436 45.455 0.00 0.00 37.60 4.02
819 822 7.639850 CGTGTGTAATATTTGGCACTGATTTAG 59.360 37.037 14.33 0.00 33.44 1.85
970 973 2.463553 CGATGCGAGTAGTAACGGAA 57.536 50.000 0.00 0.00 33.29 4.30
977 980 2.491022 GCCTCCCGATGCGAGTAGT 61.491 63.158 0.00 0.00 0.00 2.73
978 981 2.336809 GCCTCCCGATGCGAGTAG 59.663 66.667 0.00 0.00 0.00 2.57
1110 1118 1.203928 CGTGCACGATCCTGATCTTC 58.796 55.000 34.93 0.00 43.02 2.87
1219 1236 4.271816 CGATGACGGCGAGGAGGG 62.272 72.222 16.62 0.00 35.72 4.30
1659 1694 6.591935 TCAACAAACTGGAGAAGTAACAGAT 58.408 36.000 0.00 0.00 38.56 2.90
1712 1748 1.303970 TGCCATTTCCATGTGCGGA 60.304 52.632 0.00 0.00 32.24 5.54
1747 1788 3.124921 GACACCCAATGCCGTCGG 61.125 66.667 6.99 6.99 0.00 4.79
1789 1830 6.368805 AGTTCACCCAGAAGAGAAGAAAAAT 58.631 36.000 0.00 0.00 36.78 1.82
1824 1867 1.133606 CACCTACCTCTCCCTCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
1857 1902 3.056536 TCTTCCTTCATCGTCAGTTCAGG 60.057 47.826 0.00 0.00 0.00 3.86
2040 2101 2.474816 GTCATTCCTCATAGACGGCAC 58.525 52.381 0.00 0.00 0.00 5.01
2045 2106 3.460857 AAGCCGTCATTCCTCATAGAC 57.539 47.619 0.00 0.00 0.00 2.59
2049 2118 6.437477 TCATAGTATAAGCCGTCATTCCTCAT 59.563 38.462 0.00 0.00 0.00 2.90
2082 2151 3.609853 TGTTGGATTGCATCAGGAGTAC 58.390 45.455 0.00 0.00 0.00 2.73
2083 2152 3.998913 TGTTGGATTGCATCAGGAGTA 57.001 42.857 0.00 0.00 0.00 2.59
2084 2153 2.885135 TGTTGGATTGCATCAGGAGT 57.115 45.000 0.00 0.00 0.00 3.85
2085 2154 2.426024 CCTTGTTGGATTGCATCAGGAG 59.574 50.000 0.00 0.00 38.35 3.69
2096 2165 5.952347 GTCTAAAATCTTCCCCTTGTTGGAT 59.048 40.000 0.00 0.00 38.35 3.41
2097 2166 5.163034 TGTCTAAAATCTTCCCCTTGTTGGA 60.163 40.000 0.00 0.00 38.35 3.53
2098 2167 5.048013 GTGTCTAAAATCTTCCCCTTGTTGG 60.048 44.000 0.00 0.00 0.00 3.77
2099 2168 5.534654 TGTGTCTAAAATCTTCCCCTTGTTG 59.465 40.000 0.00 0.00 0.00 3.33
2120 2192 2.193447 CGGTGATCTACGACCATTGTG 58.807 52.381 3.97 0.00 31.97 3.33
2128 2200 1.259142 TTTGGGCCGGTGATCTACGA 61.259 55.000 1.90 0.00 0.00 3.43
2165 2253 4.723789 AGGAGGTAGAAATGTGGATCATGT 59.276 41.667 0.00 0.00 36.81 3.21
2211 2299 5.684626 CCAAAGTAAGTTAGCTCGGTATACG 59.315 44.000 0.00 0.00 46.11 3.06
2277 6271 8.739972 ACTCTGAACTGTAATTTGTTTTGTTCT 58.260 29.630 0.00 0.00 35.00 3.01
2324 6318 5.680229 GTCAGATGCGATGAAAAATTAGCTG 59.320 40.000 0.00 0.00 0.00 4.24
2326 6320 5.680229 CAGTCAGATGCGATGAAAAATTAGC 59.320 40.000 0.00 0.00 0.00 3.09
2354 6348 3.895232 TCCTGGAGTTGAGCAATACTC 57.105 47.619 0.00 0.00 46.45 2.59
2375 6369 5.706369 GCTGGCTAGAGTAGTTACTGCTATA 59.294 44.000 2.37 3.80 36.50 1.31
2376 6370 4.521256 GCTGGCTAGAGTAGTTACTGCTAT 59.479 45.833 2.37 2.64 36.50 2.97
2457 6451 3.270027 TCCAGGTTTTCGCATACATGAG 58.730 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.