Multiple sequence alignment - TraesCS4B01G144400

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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 TraesCS4B01G144400 chr4B 100.000 2383 0 0 1 2383 193561296 193563678 0.000000e+00 4401.0
1 TraesCS4B01G144400 chr4B 82.544 338 32 15 1 338 618085917 618085607 3.020000e-69 272.0
2 TraesCS4B01G144400 chr4B 81.250 304 46 6 335 631 644709606 644709905 3.960000e-58 235.0
3 TraesCS4B01G144400 chr4D 93.348 1368 49 20 663 1993 134686210 134687572 0.000000e+00 1984.0
4 TraesCS4B01G144400 chr4D 95.202 396 18 1 1988 2383 134687644 134688038 2.010000e-175 625.0
5 TraesCS4B01G144400 chr4A 90.465 839 28 20 633 1435 396756507 396757329 0.000000e+00 1059.0
6 TraesCS4B01G144400 chr4A 93.583 561 33 3 1434 1993 396757411 396757969 0.000000e+00 833.0
7 TraesCS4B01G144400 chr4A 95.041 363 15 2 2023 2383 396758145 396758506 3.440000e-158 568.0
8 TraesCS4B01G144400 chr4A 100.000 28 0 0 1347 1374 57438717 57438744 4.000000e-03 52.8
9 TraesCS4B01G144400 chr7B 79.880 666 59 40 1 631 134308275 134307650 3.660000e-113 418.0
10 TraesCS4B01G144400 chr7B 81.214 346 29 24 1 342 551894195 551893882 1.830000e-61 246.0
11 TraesCS4B01G144400 chr7B 87.845 181 20 1 155 335 743980693 743980871 6.670000e-51 211.0
12 TraesCS4B01G144400 chr7B 95.833 96 3 1 1 96 642514785 642514691 1.140000e-33 154.0
13 TraesCS4B01G144400 chr7B 90.625 96 9 0 1 96 5201735 5201830 6.910000e-26 128.0
14 TraesCS4B01G144400 chr5B 77.273 682 73 35 1 631 547004133 547004783 2.280000e-85 326.0
15 TraesCS4B01G144400 chr5B 82.635 334 30 17 2 335 527790586 527790891 1.090000e-68 270.0
16 TraesCS4B01G144400 chr5B 78.779 344 30 22 1 327 63552170 63551853 8.690000e-45 191.0
17 TraesCS4B01G144400 chr3D 85.714 308 35 6 331 631 15453423 15453728 1.370000e-82 316.0
18 TraesCS4B01G144400 chr1B 84.810 316 30 6 333 631 114599902 114600216 3.850000e-78 302.0
19 TraesCS4B01G144400 chr1B 85.083 181 19 5 155 335 512620858 512621030 6.770000e-41 178.0
20 TraesCS4B01G144400 chr2B 83.136 338 30 20 1 338 775131910 775131600 1.390000e-72 283.0
21 TraesCS4B01G144400 chr2B 81.845 336 33 14 1 335 58539386 58539694 8.450000e-65 257.0
22 TraesCS4B01G144400 chr2B 82.410 307 39 11 334 631 682866953 682866653 1.090000e-63 254.0
23 TraesCS4B01G144400 chr2B 82.246 276 40 5 334 601 761277217 761276943 1.840000e-56 230.0
24 TraesCS4B01G144400 chr2B 81.633 98 13 3 239 335 772380962 772381055 2.540000e-10 76.8
25 TraesCS4B01G144400 chr1D 83.226 310 39 9 331 631 463926027 463926332 3.020000e-69 272.0
26 TraesCS4B01G144400 chr6B 82.779 331 30 16 1 331 204325088 204324785 1.090000e-68 270.0
27 TraesCS4B01G144400 chr5D 81.672 311 43 11 334 634 322821102 322820796 1.830000e-61 246.0
28 TraesCS4B01G144400 chr7D 81.046 306 46 9 334 631 539121186 539120885 1.420000e-57 233.0
29 TraesCS4B01G144400 chr6D 81.230 309 41 10 331 631 352856570 352856869 1.420000e-57 233.0
30 TraesCS4B01G144400 chrUn 79.205 327 35 21 1 327 53436206 53436499 1.870000e-46 196.0
31 TraesCS4B01G144400 chr2D 78.736 348 33 22 1 335 629483171 629483490 6.720000e-46 195.0
32 TraesCS4B01G144400 chr2A 100.000 36 0 0 334 369 158027737 158027702 1.530000e-07 67.6


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 TraesCS4B01G144400 chr4B 193561296 193563678 2382 False 4401.0 4401 100.000000 1 2383 1 chr4B.!!$F1 2382
1 TraesCS4B01G144400 chr4D 134686210 134688038 1828 False 1304.5 1984 94.275000 663 2383 2 chr4D.!!$F1 1720
2 TraesCS4B01G144400 chr4A 396756507 396758506 1999 False 820.0 1059 93.029667 633 2383 3 chr4A.!!$F2 1750
3 TraesCS4B01G144400 chr7B 134307650 134308275 625 True 418.0 418 79.880000 1 631 1 chr7B.!!$R1 630
4 TraesCS4B01G144400 chr5B 547004133 547004783 650 False 326.0 326 77.273000 1 631 1 chr5B.!!$F2 630

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
634 658 0.095935 CGCGACTGGAGATGCTTTTG 59.904 55.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 2068 1.000283 CGTGGCAGCTATCTAGGAAGG 60.0 57.143 0.0 0.0 0.0 3.46 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
106 107 2.576298 GCTCTTGGCCATCTTTGCT 58.424 52.632 6.09 0.00 34.27 3.91
107 108 0.893447 GCTCTTGGCCATCTTTGCTT 59.107 50.000 6.09 0.00 34.27 3.91
109 110 1.131883 CTCTTGGCCATCTTTGCTTCG 59.868 52.381 6.09 0.00 0.00 3.79
110 111 0.457337 CTTGGCCATCTTTGCTTCGC 60.457 55.000 6.09 0.00 0.00 4.70
111 112 0.895100 TTGGCCATCTTTGCTTCGCT 60.895 50.000 6.09 0.00 0.00 4.93
112 113 1.308069 TGGCCATCTTTGCTTCGCTC 61.308 55.000 0.00 0.00 0.00 5.03
114 115 1.061570 CCATCTTTGCTTCGCTCGC 59.938 57.895 0.00 0.00 0.00 5.03
115 116 1.061570 CATCTTTGCTTCGCTCGCC 59.938 57.895 0.00 0.00 0.00 5.54
116 117 2.456119 ATCTTTGCTTCGCTCGCCG 61.456 57.895 0.00 0.00 38.61 6.46
117 118 3.414700 CTTTGCTTCGCTCGCCGT 61.415 61.111 0.00 0.00 38.35 5.68
118 119 3.635734 CTTTGCTTCGCTCGCCGTG 62.636 63.158 0.00 0.00 38.35 4.94
132 133 4.758251 CGTGCCACCATCGCCTGA 62.758 66.667 0.00 0.00 0.00 3.86
133 134 2.124570 GTGCCACCATCGCCTGAT 60.125 61.111 0.00 0.00 34.28 2.90
188 189 1.012841 CTCTCGGCCATCTTTGCTTC 58.987 55.000 2.24 0.00 0.00 3.86
195 196 0.798776 CCATCTTTGCTTCGCTCGTT 59.201 50.000 0.00 0.00 0.00 3.85
207 208 4.778143 CTCGTTGGCGGGAAGGGG 62.778 72.222 0.00 0.00 42.12 4.79
229 230 1.227674 GGGATGGCTTTCGCGAGAT 60.228 57.895 9.59 0.00 41.60 2.75
237 238 2.650813 CTTTCGCGAGATGGGGAGGG 62.651 65.000 9.59 0.00 41.60 4.30
271 272 1.301623 CGGGGAGTGGGTGCATTTA 59.698 57.895 0.00 0.00 0.00 1.40
275 276 3.222603 GGGGAGTGGGTGCATTTAATAG 58.777 50.000 0.00 0.00 0.00 1.73
314 315 3.945434 GCAGCATGTCGGGCGATG 61.945 66.667 0.00 0.00 39.31 3.84
315 316 3.945434 CAGCATGTCGGGCGATGC 61.945 66.667 8.35 8.35 44.49 3.91
380 404 4.626081 AGCGCGACAACCTTGGCT 62.626 61.111 12.10 0.00 32.73 4.75
381 405 3.660111 GCGCGACAACCTTGGCTT 61.660 61.111 12.10 0.00 32.73 4.35
382 406 3.030652 CGCGACAACCTTGGCTTT 58.969 55.556 0.00 0.00 32.73 3.51
383 407 1.370414 CGCGACAACCTTGGCTTTG 60.370 57.895 0.00 0.00 32.73 2.77
384 408 1.781025 CGCGACAACCTTGGCTTTGA 61.781 55.000 0.00 0.00 32.73 2.69
385 409 0.598065 GCGACAACCTTGGCTTTGAT 59.402 50.000 0.00 0.00 32.73 2.57
386 410 1.000274 GCGACAACCTTGGCTTTGATT 60.000 47.619 0.00 0.00 32.73 2.57
387 411 2.227865 GCGACAACCTTGGCTTTGATTA 59.772 45.455 0.00 0.00 32.73 1.75
388 412 3.821841 CGACAACCTTGGCTTTGATTAC 58.178 45.455 0.00 0.00 32.73 1.89
389 413 3.365969 CGACAACCTTGGCTTTGATTACC 60.366 47.826 0.00 0.00 32.73 2.85
390 414 2.556622 ACAACCTTGGCTTTGATTACCG 59.443 45.455 0.00 0.00 0.00 4.02
391 415 1.173913 ACCTTGGCTTTGATTACCGC 58.826 50.000 0.00 0.00 0.00 5.68
392 416 0.098728 CCTTGGCTTTGATTACCGCG 59.901 55.000 0.00 0.00 0.00 6.46
393 417 0.098728 CTTGGCTTTGATTACCGCGG 59.901 55.000 26.86 26.86 0.00 6.46
394 418 1.309499 TTGGCTTTGATTACCGCGGG 61.309 55.000 31.76 11.88 0.00 6.13
395 419 1.450669 GGCTTTGATTACCGCGGGA 60.451 57.895 31.76 21.43 0.00 5.14
396 420 1.027792 GGCTTTGATTACCGCGGGAA 61.028 55.000 28.14 28.14 0.00 3.97
397 421 0.098200 GCTTTGATTACCGCGGGAAC 59.902 55.000 28.60 19.59 0.00 3.62
409 433 4.752514 GGGAACCGAGGCGATAAG 57.247 61.111 0.00 0.00 40.86 1.73
410 434 1.069258 GGGAACCGAGGCGATAAGG 59.931 63.158 0.00 0.00 40.86 2.69
411 435 1.069258 GGAACCGAGGCGATAAGGG 59.931 63.158 0.00 0.00 0.00 3.95
412 436 1.594564 GAACCGAGGCGATAAGGGC 60.595 63.158 0.00 0.00 0.00 5.19
413 437 3.441011 AACCGAGGCGATAAGGGCG 62.441 63.158 0.00 0.00 37.59 6.13
414 438 3.602677 CCGAGGCGATAAGGGCGA 61.603 66.667 0.00 0.00 37.59 5.54
415 439 2.354773 CGAGGCGATAAGGGCGAC 60.355 66.667 0.00 0.00 37.59 5.19
416 440 2.354773 GAGGCGATAAGGGCGACG 60.355 66.667 0.00 0.00 42.78 5.12
417 441 2.831742 AGGCGATAAGGGCGACGA 60.832 61.111 0.00 0.00 42.78 4.20
418 442 2.105528 GGCGATAAGGGCGACGAA 59.894 61.111 0.00 0.00 0.00 3.85
419 443 1.949631 GGCGATAAGGGCGACGAAG 60.950 63.158 0.00 0.00 0.00 3.79
420 444 2.586773 GCGATAAGGGCGACGAAGC 61.587 63.158 0.00 0.00 0.00 3.86
421 445 2.293627 CGATAAGGGCGACGAAGCG 61.294 63.158 0.00 0.00 38.18 4.68
422 446 1.949631 GATAAGGGCGACGAAGCGG 60.950 63.158 0.00 0.00 38.18 5.52
440 464 2.409651 CGTCTCGCTGACTAGGCC 59.590 66.667 0.00 0.00 43.25 5.19
441 465 2.809010 GTCTCGCTGACTAGGCCC 59.191 66.667 0.00 0.00 42.21 5.80
442 466 2.442272 TCTCGCTGACTAGGCCCC 60.442 66.667 0.00 0.00 0.00 5.80
443 467 3.541713 CTCGCTGACTAGGCCCCC 61.542 72.222 0.00 0.00 0.00 5.40
457 481 3.674906 CCCCCATTCGCGTCAAAA 58.325 55.556 5.77 0.00 0.00 2.44
458 482 1.211709 CCCCCATTCGCGTCAAAAC 59.788 57.895 5.77 0.00 0.00 2.43
459 483 1.211709 CCCCATTCGCGTCAAAACC 59.788 57.895 5.77 0.00 0.00 3.27
460 484 1.154301 CCCATTCGCGTCAAAACCG 60.154 57.895 5.77 0.00 0.00 4.44
467 491 4.084888 CGTCAAAACCGCTCGCCC 62.085 66.667 0.00 0.00 0.00 6.13
468 492 3.733960 GTCAAAACCGCTCGCCCC 61.734 66.667 0.00 0.00 0.00 5.80
505 529 4.717313 GGTTCGGCCTGGGTCCAC 62.717 72.222 0.00 0.00 0.00 4.02
506 530 4.717313 GTTCGGCCTGGGTCCACC 62.717 72.222 0.00 0.00 40.81 4.61
513 537 3.000819 CTGGGTCCACCGGCACTA 61.001 66.667 0.00 0.00 44.64 2.74
514 538 2.527123 TGGGTCCACCGGCACTAA 60.527 61.111 0.00 0.00 44.64 2.24
515 539 2.046604 GGGTCCACCGGCACTAAC 60.047 66.667 0.00 0.00 36.71 2.34
516 540 2.590114 GGGTCCACCGGCACTAACT 61.590 63.158 0.00 0.00 36.71 2.24
517 541 1.373812 GGTCCACCGGCACTAACTT 59.626 57.895 0.00 0.00 0.00 2.66
518 542 0.672711 GGTCCACCGGCACTAACTTC 60.673 60.000 0.00 0.00 0.00 3.01
519 543 1.012486 GTCCACCGGCACTAACTTCG 61.012 60.000 0.00 0.00 0.00 3.79
520 544 1.180456 TCCACCGGCACTAACTTCGA 61.180 55.000 0.00 0.00 0.00 3.71
521 545 1.012486 CCACCGGCACTAACTTCGAC 61.012 60.000 0.00 0.00 0.00 4.20
522 546 1.012486 CACCGGCACTAACTTCGACC 61.012 60.000 0.00 0.00 0.00 4.79
523 547 1.447314 CCGGCACTAACTTCGACCC 60.447 63.158 0.00 0.00 0.00 4.46
524 548 1.290955 CGGCACTAACTTCGACCCA 59.709 57.895 0.00 0.00 0.00 4.51
525 549 0.320073 CGGCACTAACTTCGACCCAA 60.320 55.000 0.00 0.00 0.00 4.12
526 550 1.874739 CGGCACTAACTTCGACCCAAA 60.875 52.381 0.00 0.00 0.00 3.28
527 551 1.534163 GGCACTAACTTCGACCCAAAC 59.466 52.381 0.00 0.00 0.00 2.93
528 552 1.534163 GCACTAACTTCGACCCAAACC 59.466 52.381 0.00 0.00 0.00 3.27
529 553 1.796459 CACTAACTTCGACCCAAACCG 59.204 52.381 0.00 0.00 0.00 4.44
530 554 1.688197 ACTAACTTCGACCCAAACCGA 59.312 47.619 0.00 0.00 0.00 4.69
531 555 2.064014 CTAACTTCGACCCAAACCGAC 58.936 52.381 0.00 0.00 34.26 4.79
532 556 0.877213 AACTTCGACCCAAACCGACG 60.877 55.000 0.00 0.00 34.26 5.12
533 557 1.007038 CTTCGACCCAAACCGACGA 60.007 57.895 0.00 0.00 34.26 4.20
534 558 0.598158 CTTCGACCCAAACCGACGAA 60.598 55.000 0.00 0.00 39.89 3.85
535 559 0.179089 TTCGACCCAAACCGACGAAA 60.179 50.000 0.00 0.00 39.39 3.46
536 560 0.179089 TCGACCCAAACCGACGAAAA 60.179 50.000 0.00 0.00 0.00 2.29
537 561 0.656785 CGACCCAAACCGACGAAAAA 59.343 50.000 0.00 0.00 0.00 1.94
538 562 1.595246 CGACCCAAACCGACGAAAAAC 60.595 52.381 0.00 0.00 0.00 2.43
550 574 0.872388 CGAAAAACGGACTCTTGGGG 59.128 55.000 0.00 0.00 38.46 4.96
551 575 1.244816 GAAAAACGGACTCTTGGGGG 58.755 55.000 0.00 0.00 0.00 5.40
552 576 0.826256 AAAAACGGACTCTTGGGGGC 60.826 55.000 0.00 0.00 0.00 5.80
553 577 3.546714 AAACGGACTCTTGGGGGCG 62.547 63.158 0.00 0.00 0.00 6.13
555 579 4.760047 CGGACTCTTGGGGGCGTG 62.760 72.222 0.00 0.00 0.00 5.34
556 580 3.319198 GGACTCTTGGGGGCGTGA 61.319 66.667 0.00 0.00 0.00 4.35
557 581 2.047179 GACTCTTGGGGGCGTGAC 60.047 66.667 0.00 0.00 0.00 3.67
558 582 2.526873 ACTCTTGGGGGCGTGACT 60.527 61.111 0.00 0.00 0.00 3.41
559 583 2.046892 CTCTTGGGGGCGTGACTG 60.047 66.667 0.00 0.00 0.00 3.51
560 584 3.612247 CTCTTGGGGGCGTGACTGG 62.612 68.421 0.00 0.00 0.00 4.00
561 585 3.636231 CTTGGGGGCGTGACTGGA 61.636 66.667 0.00 0.00 0.00 3.86
562 586 3.901797 CTTGGGGGCGTGACTGGAC 62.902 68.421 0.00 0.00 0.00 4.02
566 590 4.309950 GGGCGTGACTGGACCGTT 62.310 66.667 0.00 0.00 0.00 4.44
567 591 2.280592 GGCGTGACTGGACCGTTT 60.281 61.111 0.00 0.00 0.00 3.60
568 592 1.890510 GGCGTGACTGGACCGTTTT 60.891 57.895 0.00 0.00 0.00 2.43
569 593 1.441732 GGCGTGACTGGACCGTTTTT 61.442 55.000 0.00 0.00 0.00 1.94
628 652 4.899239 GGGGCGCGACTGGAGATG 62.899 72.222 13.91 0.00 0.00 2.90
630 654 4.521062 GGCGCGACTGGAGATGCT 62.521 66.667 12.10 0.00 0.00 3.79
631 655 2.510238 GCGCGACTGGAGATGCTT 60.510 61.111 12.10 0.00 0.00 3.91
632 656 2.103042 GCGCGACTGGAGATGCTTT 61.103 57.895 12.10 0.00 0.00 3.51
633 657 1.639298 GCGCGACTGGAGATGCTTTT 61.639 55.000 12.10 0.00 0.00 2.27
634 658 0.095935 CGCGACTGGAGATGCTTTTG 59.904 55.000 0.00 0.00 0.00 2.44
674 698 1.822990 CCGGCCTTTCAGTACTAGTCA 59.177 52.381 0.00 0.00 0.00 3.41
677 701 4.261656 CCGGCCTTTCAGTACTAGTCATAG 60.262 50.000 0.00 0.00 34.96 2.23
689 713 9.042008 CAGTACTAGTCATAGTTCTCTCTTCTC 57.958 40.741 0.00 0.00 42.39 2.87
690 714 8.764558 AGTACTAGTCATAGTTCTCTCTTCTCA 58.235 37.037 0.00 0.00 42.39 3.27
730 756 9.701098 AGTCGTAGTTCTCATATTTTGTTGTTA 57.299 29.630 0.00 0.00 0.00 2.41
941 972 1.755380 GCCTACGTCCTACCACATCTT 59.245 52.381 0.00 0.00 0.00 2.40
1048 1089 4.085733 TCTCTGCTTTCTTCTGCTAGTCT 58.914 43.478 0.00 0.00 0.00 3.24
1051 1092 2.899900 TGCTTTCTTCTGCTAGTCTCCA 59.100 45.455 0.00 0.00 0.00 3.86
1097 1138 1.227321 TTTCAGCGGACGGTTCGTT 60.227 52.632 10.98 0.56 41.37 3.85
1102 1150 2.378084 GCGGACGGTTCGTTTCTCC 61.378 63.158 10.98 0.00 41.37 3.71
1104 1152 1.375140 GGACGGTTCGTTTCTCCCC 60.375 63.158 0.00 0.00 41.37 4.81
1121 1169 1.078214 CCCTCTGCGCCATTCTTGA 60.078 57.895 4.18 0.00 0.00 3.02
1402 1666 7.201839 CCAATGAAACACATACATCATCCATCA 60.202 37.037 0.00 0.00 38.38 3.07
1403 1667 8.357402 CAATGAAACACATACATCATCCATCAT 58.643 33.333 0.00 0.00 38.38 2.45
1467 1822 4.141287 TCAAACATTCCTCATCCACGTTT 58.859 39.130 0.00 0.00 0.00 3.60
1599 1959 5.012893 GTCCCAGTTTGGAGATTGAATTCT 58.987 41.667 7.05 0.00 40.96 2.40
1601 1961 5.014544 TCCCAGTTTGGAGATTGAATTCTCT 59.985 40.000 7.05 1.75 40.96 3.10
1632 2085 1.051812 TGCCTTCCTAGATAGCTGCC 58.948 55.000 0.00 0.00 0.00 4.85
1639 2092 1.032794 CTAGATAGCTGCCACGACCA 58.967 55.000 0.00 0.00 0.00 4.02
1788 2243 7.730067 TGTCAATTCTTGTATACGTAACTCG 57.270 36.000 0.00 0.00 46.00 4.18
1813 2268 1.201647 ACCATCCTACGTGTCACTTCG 59.798 52.381 0.00 0.00 0.00 3.79
1895 2350 2.555227 GCCCTTGGAATCCAACAGAAGA 60.555 50.000 11.23 0.00 38.75 2.87
1983 2439 2.159240 TCATGTCTTTGGAGATCGACCG 60.159 50.000 0.00 0.00 33.70 4.79
2003 2623 3.612860 CCGTGCTACTTAGTTACTGCTTG 59.387 47.826 0.00 0.00 0.00 4.01
2033 2653 2.851263 TCAGTTGTCCACCACATACC 57.149 50.000 0.00 0.00 33.90 2.73
2041 2661 3.010027 TGTCCACCACATACCACATGATT 59.990 43.478 0.00 0.00 0.00 2.57
2069 2689 5.514914 ACATAACATAAGGAAATTTTGCGCG 59.485 36.000 0.00 0.00 0.00 6.86
2319 2941 6.658816 ACTCAATCTACACATTAACAATGCCA 59.341 34.615 0.00 0.00 42.69 4.92
2342 2964 7.224167 GCCACGCTAGTTTAGTTTTATCTATGT 59.776 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 4.758251 TCAGGCGATGGTGGCACG 62.758 66.667 12.17 0.57 36.77 5.34
116 117 2.124570 ATCAGGCGATGGTGGCAC 60.125 61.111 9.70 9.70 36.77 5.01
117 118 2.124612 CATCAGGCGATGGTGGCA 60.125 61.111 10.25 0.00 44.59 4.92
222 223 4.227134 CACCCTCCCCATCTCGCG 62.227 72.222 0.00 0.00 0.00 5.87
331 335 0.992431 AGCCTCCATTGATGCCTCCT 60.992 55.000 0.00 0.00 33.08 3.69
363 387 4.626081 AGCCAAGGTTGTCGCGCT 62.626 61.111 5.56 0.00 0.00 5.92
372 396 1.173913 GCGGTAATCAAAGCCAAGGT 58.826 50.000 0.00 0.00 0.00 3.50
380 404 1.020333 CGGTTCCCGCGGTAATCAAA 61.020 55.000 26.12 5.33 41.17 2.69
381 405 1.448189 CGGTTCCCGCGGTAATCAA 60.448 57.895 26.12 5.50 41.17 2.57
382 406 2.184836 CGGTTCCCGCGGTAATCA 59.815 61.111 26.12 0.00 41.17 2.57
383 407 2.966182 CCTCGGTTCCCGCGGTAATC 62.966 65.000 26.12 14.97 45.61 1.75
384 408 3.085119 CCTCGGTTCCCGCGGTAAT 62.085 63.158 26.12 0.00 45.61 1.89
385 409 3.762247 CCTCGGTTCCCGCGGTAA 61.762 66.667 26.12 12.90 45.61 2.85
392 416 1.069258 CCTTATCGCCTCGGTTCCC 59.931 63.158 0.00 0.00 0.00 3.97
393 417 1.069258 CCCTTATCGCCTCGGTTCC 59.931 63.158 0.00 0.00 0.00 3.62
394 418 1.594564 GCCCTTATCGCCTCGGTTC 60.595 63.158 0.00 0.00 0.00 3.62
395 419 2.504519 GCCCTTATCGCCTCGGTT 59.495 61.111 0.00 0.00 0.00 4.44
396 420 3.912907 CGCCCTTATCGCCTCGGT 61.913 66.667 0.00 0.00 0.00 4.69
397 421 3.602677 TCGCCCTTATCGCCTCGG 61.603 66.667 0.00 0.00 0.00 4.63
398 422 2.354773 GTCGCCCTTATCGCCTCG 60.355 66.667 0.00 0.00 0.00 4.63
399 423 2.345880 TTCGTCGCCCTTATCGCCTC 62.346 60.000 0.00 0.00 0.00 4.70
400 424 2.351336 CTTCGTCGCCCTTATCGCCT 62.351 60.000 0.00 0.00 0.00 5.52
401 425 1.949631 CTTCGTCGCCCTTATCGCC 60.950 63.158 0.00 0.00 0.00 5.54
402 426 2.586773 GCTTCGTCGCCCTTATCGC 61.587 63.158 0.00 0.00 0.00 4.58
403 427 2.293627 CGCTTCGTCGCCCTTATCG 61.294 63.158 0.00 0.00 0.00 2.92
404 428 1.949631 CCGCTTCGTCGCCCTTATC 60.950 63.158 0.00 0.00 0.00 1.75
405 429 2.106332 CCGCTTCGTCGCCCTTAT 59.894 61.111 0.00 0.00 0.00 1.73
406 430 4.807039 GCCGCTTCGTCGCCCTTA 62.807 66.667 0.00 0.00 0.00 2.69
425 449 2.442272 GGGGCCTAGTCAGCGAGA 60.442 66.667 0.84 0.00 0.00 4.04
426 450 3.541713 GGGGGCCTAGTCAGCGAG 61.542 72.222 0.84 0.00 0.00 5.03
440 464 1.211709 GTTTTGACGCGAATGGGGG 59.788 57.895 15.93 0.00 0.00 5.40
441 465 1.211709 GGTTTTGACGCGAATGGGG 59.788 57.895 15.93 0.00 0.00 4.96
442 466 1.154301 CGGTTTTGACGCGAATGGG 60.154 57.895 15.93 0.00 0.00 4.00
443 467 4.433102 CGGTTTTGACGCGAATGG 57.567 55.556 15.93 0.00 0.00 3.16
450 474 4.084888 GGGCGAGCGGTTTTGACG 62.085 66.667 0.00 0.00 0.00 4.35
451 475 3.733960 GGGGCGAGCGGTTTTGAC 61.734 66.667 0.00 0.00 0.00 3.18
488 512 4.717313 GTGGACCCAGGCCGAACC 62.717 72.222 0.00 0.00 39.61 3.62
489 513 4.717313 GGTGGACCCAGGCCGAAC 62.717 72.222 0.00 0.00 0.00 3.95
496 520 2.589157 TTAGTGCCGGTGGACCCAG 61.589 63.158 1.90 0.00 0.00 4.45
497 521 2.527123 TTAGTGCCGGTGGACCCA 60.527 61.111 1.90 0.00 0.00 4.51
498 522 2.046604 GTTAGTGCCGGTGGACCC 60.047 66.667 1.90 0.00 0.00 4.46
499 523 0.672711 GAAGTTAGTGCCGGTGGACC 60.673 60.000 1.90 0.00 0.00 4.46
500 524 1.012486 CGAAGTTAGTGCCGGTGGAC 61.012 60.000 1.90 0.00 0.00 4.02
501 525 1.180456 TCGAAGTTAGTGCCGGTGGA 61.180 55.000 1.90 0.00 0.00 4.02
502 526 1.012486 GTCGAAGTTAGTGCCGGTGG 61.012 60.000 1.90 0.00 0.00 4.61
503 527 1.012486 GGTCGAAGTTAGTGCCGGTG 61.012 60.000 1.90 0.00 0.00 4.94
504 528 1.291272 GGTCGAAGTTAGTGCCGGT 59.709 57.895 1.90 0.00 0.00 5.28
505 529 1.447314 GGGTCGAAGTTAGTGCCGG 60.447 63.158 0.00 0.00 0.00 6.13
506 530 0.320073 TTGGGTCGAAGTTAGTGCCG 60.320 55.000 0.00 0.00 0.00 5.69
507 531 1.534163 GTTTGGGTCGAAGTTAGTGCC 59.466 52.381 0.00 0.00 0.00 5.01
508 532 1.534163 GGTTTGGGTCGAAGTTAGTGC 59.466 52.381 0.00 0.00 0.00 4.40
509 533 1.796459 CGGTTTGGGTCGAAGTTAGTG 59.204 52.381 0.00 0.00 0.00 2.74
510 534 1.688197 TCGGTTTGGGTCGAAGTTAGT 59.312 47.619 0.00 0.00 32.11 2.24
511 535 2.064014 GTCGGTTTGGGTCGAAGTTAG 58.936 52.381 0.00 0.00 37.14 2.34
512 536 1.602668 CGTCGGTTTGGGTCGAAGTTA 60.603 52.381 0.00 0.00 37.14 2.24
513 537 0.877213 CGTCGGTTTGGGTCGAAGTT 60.877 55.000 0.00 0.00 37.14 2.66
514 538 1.300388 CGTCGGTTTGGGTCGAAGT 60.300 57.895 0.00 0.00 37.14 3.01
515 539 0.598158 TTCGTCGGTTTGGGTCGAAG 60.598 55.000 0.00 0.00 37.14 3.79
516 540 0.179089 TTTCGTCGGTTTGGGTCGAA 60.179 50.000 0.00 0.00 37.14 3.71
517 541 0.179089 TTTTCGTCGGTTTGGGTCGA 60.179 50.000 0.00 0.00 0.00 4.20
518 542 0.656785 TTTTTCGTCGGTTTGGGTCG 59.343 50.000 0.00 0.00 0.00 4.79
519 543 1.595246 CGTTTTTCGTCGGTTTGGGTC 60.595 52.381 0.00 0.00 34.52 4.46
520 544 0.377905 CGTTTTTCGTCGGTTTGGGT 59.622 50.000 0.00 0.00 34.52 4.51
521 545 0.317186 CCGTTTTTCGTCGGTTTGGG 60.317 55.000 0.00 0.00 41.58 4.12
522 546 0.656785 TCCGTTTTTCGTCGGTTTGG 59.343 50.000 3.64 0.00 45.88 3.28
523 547 1.328374 AGTCCGTTTTTCGTCGGTTTG 59.672 47.619 3.64 0.00 45.88 2.93
524 548 1.594397 GAGTCCGTTTTTCGTCGGTTT 59.406 47.619 3.64 0.00 45.88 3.27
525 549 1.202452 AGAGTCCGTTTTTCGTCGGTT 60.202 47.619 3.64 0.00 45.88 4.44
526 550 0.386838 AGAGTCCGTTTTTCGTCGGT 59.613 50.000 3.64 0.00 45.88 4.69
527 551 1.191647 CAAGAGTCCGTTTTTCGTCGG 59.808 52.381 0.00 0.00 46.93 4.79
528 552 1.191647 CCAAGAGTCCGTTTTTCGTCG 59.808 52.381 0.00 0.00 37.94 5.12
529 553 1.529865 CCCAAGAGTCCGTTTTTCGTC 59.470 52.381 0.00 0.00 37.94 4.20
530 554 1.589803 CCCAAGAGTCCGTTTTTCGT 58.410 50.000 0.00 0.00 37.94 3.85
531 555 0.872388 CCCCAAGAGTCCGTTTTTCG 59.128 55.000 0.00 0.00 39.52 3.46
532 556 1.244816 CCCCCAAGAGTCCGTTTTTC 58.755 55.000 0.00 0.00 0.00 2.29
533 557 0.826256 GCCCCCAAGAGTCCGTTTTT 60.826 55.000 0.00 0.00 0.00 1.94
534 558 1.228459 GCCCCCAAGAGTCCGTTTT 60.228 57.895 0.00 0.00 0.00 2.43
535 559 2.434774 GCCCCCAAGAGTCCGTTT 59.565 61.111 0.00 0.00 0.00 3.60
536 560 4.016706 CGCCCCCAAGAGTCCGTT 62.017 66.667 0.00 0.00 0.00 4.44
538 562 4.760047 CACGCCCCCAAGAGTCCG 62.760 72.222 0.00 0.00 0.00 4.79
539 563 3.319198 TCACGCCCCCAAGAGTCC 61.319 66.667 0.00 0.00 0.00 3.85
540 564 2.047179 GTCACGCCCCCAAGAGTC 60.047 66.667 0.00 0.00 0.00 3.36
541 565 2.526873 AGTCACGCCCCCAAGAGT 60.527 61.111 0.00 0.00 0.00 3.24
542 566 2.046892 CAGTCACGCCCCCAAGAG 60.047 66.667 0.00 0.00 0.00 2.85
543 567 3.636231 CCAGTCACGCCCCCAAGA 61.636 66.667 0.00 0.00 0.00 3.02
544 568 3.636231 TCCAGTCACGCCCCCAAG 61.636 66.667 0.00 0.00 0.00 3.61
545 569 3.948719 GTCCAGTCACGCCCCCAA 61.949 66.667 0.00 0.00 0.00 4.12
549 573 3.819877 AAACGGTCCAGTCACGCCC 62.820 63.158 0.00 0.00 0.00 6.13
550 574 1.441732 AAAAACGGTCCAGTCACGCC 61.442 55.000 0.00 0.00 0.00 5.68
551 575 2.019337 AAAAACGGTCCAGTCACGC 58.981 52.632 0.00 0.00 0.00 5.34
611 635 4.899239 CATCTCCAGTCGCGCCCC 62.899 72.222 0.00 0.00 0.00 5.80
613 637 4.521062 AGCATCTCCAGTCGCGCC 62.521 66.667 0.00 0.00 0.00 6.53
614 638 1.639298 AAAAGCATCTCCAGTCGCGC 61.639 55.000 0.00 0.00 0.00 6.86
615 639 0.095935 CAAAAGCATCTCCAGTCGCG 59.904 55.000 0.00 0.00 0.00 5.87
616 640 0.449388 CCAAAAGCATCTCCAGTCGC 59.551 55.000 0.00 0.00 0.00 5.19
617 641 1.813513 ACCAAAAGCATCTCCAGTCG 58.186 50.000 0.00 0.00 0.00 4.18
618 642 3.010420 GGTACCAAAAGCATCTCCAGTC 58.990 50.000 7.15 0.00 0.00 3.51
619 643 2.615493 CGGTACCAAAAGCATCTCCAGT 60.615 50.000 13.54 0.00 0.00 4.00
620 644 2.009774 CGGTACCAAAAGCATCTCCAG 58.990 52.381 13.54 0.00 0.00 3.86
621 645 1.948611 GCGGTACCAAAAGCATCTCCA 60.949 52.381 13.54 0.00 0.00 3.86
622 646 0.733150 GCGGTACCAAAAGCATCTCC 59.267 55.000 13.54 0.00 0.00 3.71
623 647 1.130561 GTGCGGTACCAAAAGCATCTC 59.869 52.381 13.54 0.00 41.88 2.75
624 648 1.165270 GTGCGGTACCAAAAGCATCT 58.835 50.000 13.54 0.00 41.88 2.90
625 649 0.179200 CGTGCGGTACCAAAAGCATC 60.179 55.000 13.54 7.23 41.88 3.91
626 650 1.873165 CGTGCGGTACCAAAAGCAT 59.127 52.632 13.54 0.00 41.88 3.79
627 651 2.899044 GCGTGCGGTACCAAAAGCA 61.899 57.895 13.54 10.47 37.26 3.91
628 652 2.127003 GCGTGCGGTACCAAAAGC 60.127 61.111 13.54 9.25 0.00 3.51
629 653 2.172419 CGCGTGCGGTACCAAAAG 59.828 61.111 13.54 2.51 35.56 2.27
730 756 7.612677 AGATCAAAGGTACGACTAGTCAAATT 58.387 34.615 22.37 6.81 0.00 1.82
941 972 1.476110 CGTTGGGTTGGGTTTCTCAGA 60.476 52.381 0.00 0.00 0.00 3.27
1048 1089 3.561313 GGGTTGCCTTGTAAGAAGATGGA 60.561 47.826 0.00 0.00 0.00 3.41
1051 1092 4.288626 TGTAGGGTTGCCTTGTAAGAAGAT 59.711 41.667 0.00 0.00 0.00 2.40
1102 1150 2.117156 CAAGAATGGCGCAGAGGGG 61.117 63.158 10.83 0.00 0.00 4.79
1104 1152 1.712977 GCTCAAGAATGGCGCAGAGG 61.713 60.000 10.83 0.00 0.00 3.69
1166 1214 7.470900 ACGTACTAGATCAGTAAGTAACTTGC 58.529 38.462 16.22 0.00 46.52 4.01
1402 1666 0.530744 TACTGGACGAGCGAGCAAAT 59.469 50.000 0.00 0.00 0.00 2.32
1403 1667 0.109272 CTACTGGACGAGCGAGCAAA 60.109 55.000 0.00 0.00 0.00 3.68
1451 1806 2.496899 AGCAAACGTGGATGAGGAAT 57.503 45.000 0.00 0.00 0.00 3.01
1608 2061 4.201960 GCAGCTATCTAGGAAGGCAAAAAC 60.202 45.833 0.00 0.00 0.00 2.43
1615 2068 1.000283 CGTGGCAGCTATCTAGGAAGG 60.000 57.143 0.00 0.00 0.00 3.46
1632 2085 3.002791 AGCAAGACATTACATGGTCGTG 58.997 45.455 10.03 10.03 43.40 4.35
1682 2135 5.577164 AGTTACGCAGAGACAATCATGTAAC 59.423 40.000 4.28 4.28 40.74 2.50
1685 2138 3.928992 CAGTTACGCAGAGACAATCATGT 59.071 43.478 0.00 0.00 44.25 3.21
1686 2139 4.176271 TCAGTTACGCAGAGACAATCATG 58.824 43.478 0.00 0.00 0.00 3.07
1692 2145 2.736721 GCATTTCAGTTACGCAGAGACA 59.263 45.455 0.00 0.00 0.00 3.41
1693 2146 2.996621 AGCATTTCAGTTACGCAGAGAC 59.003 45.455 0.00 0.00 0.00 3.36
1720 2173 6.309980 GTGACATACTGACATCTCTGAAACAG 59.690 42.308 0.00 0.00 0.00 3.16
1788 2243 5.007385 AGTGACACGTAGGATGGTTAATC 57.993 43.478 0.00 0.00 34.19 1.75
1895 2350 7.206687 TGGCTGAAGATATTTTGAAACGTTTT 58.793 30.769 15.89 0.82 0.00 2.43
1983 2439 4.246458 AGCAAGCAGTAACTAAGTAGCAC 58.754 43.478 0.00 0.00 0.00 4.40
2003 2623 5.105473 TGGTGGACAACTGAATACTAGTAGC 60.105 44.000 8.85 3.88 0.00 3.58
2067 2687 3.181510 CCTTATTTCTTGGTAGTGTGCGC 60.182 47.826 0.00 0.00 0.00 6.09
2069 2689 3.694566 CCCCTTATTTCTTGGTAGTGTGC 59.305 47.826 0.00 0.00 0.00 4.57
2319 2941 8.472413 TGGACATAGATAAAACTAAACTAGCGT 58.528 33.333 0.00 0.00 0.00 5.07
2355 2977 8.786826 AGCTTATTTTGTACATGTAGCTAACA 57.213 30.769 12.61 4.19 43.86 2.41


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

AutoCloner maintained by Alex Coulton.