Multiple sequence alignment - TraesCS3B01G411100

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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 TraesCS3B01G411100 chr3B 100.000 2731 0 0 1 2731 647697685 647700415 0.000000e+00 5044
1 TraesCS3B01G411100 chr3B 81.653 496 76 11 1 482 112391505 112391011 5.480000e-107 398
2 TraesCS3B01G411100 chr3D 92.619 1138 56 14 509 1639 484827598 484828714 0.000000e+00 1611
3 TraesCS3B01G411100 chr3D 88.732 568 46 8 1636 2202 484828743 484829293 0.000000e+00 678
4 TraesCS3B01G411100 chr3D 92.733 344 24 1 1 344 484827178 484827520 1.890000e-136 496
5 TraesCS3B01G411100 chr3D 89.062 384 38 2 2346 2729 484829286 484829665 8.850000e-130 473
6 TraesCS3B01G411100 chr3A 91.904 1124 60 13 537 1639 627929268 627930381 0.000000e+00 1543
7 TraesCS3B01G411100 chr3A 92.703 603 38 5 1917 2518 627948167 627948764 0.000000e+00 865
8 TraesCS3B01G411100 chr3A 92.063 189 15 0 2541 2729 627949081 627949269 1.610000e-67 267
9 TraesCS3B01G411100 chr3A 87.755 196 23 1 1728 1923 627930654 627930848 7.610000e-56 228
10 TraesCS3B01G411100 chr2D 83.367 493 70 7 1 482 650949955 650950446 1.930000e-121 446
11 TraesCS3B01G411100 chr2D 77.989 527 77 16 1 505 1612782 1613291 7.400000e-76 294
12 TraesCS3B01G411100 chr2D 80.162 247 45 4 2435 2680 441590736 441590493 6.010000e-42 182
13 TraesCS3B01G411100 chr1B 82.806 506 75 7 1 494 678205565 678205060 2.500000e-120 442
14 TraesCS3B01G411100 chr1B 80.925 519 73 12 13 507 47628476 47627960 1.190000e-103 387
15 TraesCS3B01G411100 chr1B 80.716 503 74 11 1 482 32420195 32419695 1.190000e-98 370
16 TraesCS3B01G411100 chrUn 82.353 527 68 10 1 505 46070196 46069673 4.180000e-118 435
17 TraesCS3B01G411100 chr1D 82.961 493 71 8 2 482 106293057 106292566 1.500000e-117 433
18 TraesCS3B01G411100 chr1D 82.283 508 76 9 13 507 487023142 487022636 6.990000e-116 427
19 TraesCS3B01G411100 chr1D 81.200 250 41 6 2435 2680 278422139 278421892 2.150000e-46 196
20 TraesCS3B01G411100 chr1D 78.767 292 61 1 2431 2722 271661333 271661043 7.720000e-46 195
21 TraesCS3B01G411100 chr2B 84.475 438 60 7 73 505 155031820 155032254 2.510000e-115 425
22 TraesCS3B01G411100 chr2B 85.496 131 14 5 262 389 741185444 741185572 6.140000e-27 132
23 TraesCS3B01G411100 chr7D 81.748 515 81 8 4 505 82607816 82608330 4.210000e-113 418
24 TraesCS3B01G411100 chr7D 77.667 300 61 6 2429 2725 41436029 41436325 7.770000e-41 178
25 TraesCS3B01G411100 chr6D 81.629 528 73 10 1 505 68328774 68329300 1.510000e-112 416
26 TraesCS3B01G411100 chr5D 84.300 414 54 6 1 403 566043227 566042814 7.090000e-106 394
27 TraesCS3B01G411100 chr5D 79.452 292 58 2 2435 2726 127153444 127153155 3.560000e-49 206
28 TraesCS3B01G411100 chr5B 80.502 518 69 15 1 505 397947220 397947718 4.300000e-98 368
29 TraesCS3B01G411100 chr4B 78.337 517 77 27 1 507 672201230 672200739 4.420000e-78 302
30 TraesCS3B01G411100 chr6A 76.316 532 92 21 1 507 497988002 497988524 1.260000e-63 254
31 TraesCS3B01G411100 chr4D 79.920 249 46 3 2435 2680 326576421 326576174 2.160000e-41 180
32 TraesCS3B01G411100 chr5A 77.104 297 57 11 2435 2725 265014259 265014550 7.830000e-36 161


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 TraesCS3B01G411100 chr3B 647697685 647700415 2730 False 5044.0 5044 100.0000 1 2731 1 chr3B.!!$F1 2730
1 TraesCS3B01G411100 chr3D 484827178 484829665 2487 False 814.5 1611 90.7865 1 2729 4 chr3D.!!$F1 2728
2 TraesCS3B01G411100 chr3A 627929268 627930848 1580 False 885.5 1543 89.8295 537 1923 2 chr3A.!!$F1 1386
3 TraesCS3B01G411100 chr3A 627948167 627949269 1102 False 566.0 865 92.3830 1917 2729 2 chr3A.!!$F2 812
4 TraesCS3B01G411100 chr2D 1612782 1613291 509 False 294.0 294 77.9890 1 505 1 chr2D.!!$F1 504
5 TraesCS3B01G411100 chr1B 678205060 678205565 505 True 442.0 442 82.8060 1 494 1 chr1B.!!$R3 493
6 TraesCS3B01G411100 chr1B 47627960 47628476 516 True 387.0 387 80.9250 13 507 1 chr1B.!!$R2 494
7 TraesCS3B01G411100 chr1B 32419695 32420195 500 True 370.0 370 80.7160 1 482 1 chr1B.!!$R1 481
8 TraesCS3B01G411100 chrUn 46069673 46070196 523 True 435.0 435 82.3530 1 505 1 chrUn.!!$R1 504
9 TraesCS3B01G411100 chr1D 487022636 487023142 506 True 427.0 427 82.2830 13 507 1 chr1D.!!$R4 494
10 TraesCS3B01G411100 chr7D 82607816 82608330 514 False 418.0 418 81.7480 4 505 1 chr7D.!!$F2 501
11 TraesCS3B01G411100 chr6D 68328774 68329300 526 False 416.0 416 81.6290 1 505 1 chr6D.!!$F1 504
12 TraesCS3B01G411100 chr6A 497988002 497988524 522 False 254.0 254 76.3160 1 507 1 chr6A.!!$F1 506

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
83 84 0.037882 CACTGAAGCGAGCTGAAGGA 60.038 55.0 0.0 0.0 0.0 3.36 F
489 549 0.107017 CCATCGGCAAGGACTGGAAT 60.107 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1138 1.227674 GGTAGGGCTGCGATGGAAG 60.228 63.158 0.0 0.0 0.0 3.46 R
2261 2575 0.033405 TCGGGGAGAGAGATCGGTTT 60.033 55.000 0.0 0.0 0.0 3.27 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
83 84 0.037882 CACTGAAGCGAGCTGAAGGA 60.038 55.000 0.00 0.00 0.00 3.36
150 152 5.534207 TTTTGTAGTAGACAGTCGGGAAA 57.466 39.130 0.00 0.00 39.88 3.13
183 185 1.564348 GACCCCATAGGACCAACACAT 59.436 52.381 0.00 0.00 39.89 3.21
197 201 3.758023 CCAACACATCAGAATAGCAACCA 59.242 43.478 0.00 0.00 0.00 3.67
222 226 7.921214 CACTGCCGATAAAGAGAAGTTTAGATA 59.079 37.037 0.00 0.00 0.00 1.98
289 323 2.807676 GGATCCACCAAAGACAACCAT 58.192 47.619 6.95 0.00 38.79 3.55
290 324 2.493278 GGATCCACCAAAGACAACCATG 59.507 50.000 6.95 0.00 38.79 3.66
294 328 2.958355 CCACCAAAGACAACCATGAACT 59.042 45.455 0.00 0.00 0.00 3.01
310 344 6.328410 ACCATGAACTGAATCCTATGAGATCA 59.672 38.462 0.00 0.00 0.00 2.92
348 400 4.814294 CGCCCTAGACGCACCACC 62.814 72.222 0.00 0.00 0.00 4.61
397 449 2.859165 TTCCATCTTCAAGAAGCCGT 57.141 45.000 4.95 0.00 38.28 5.68
412 464 1.285023 CCGTCACCGTCTCGTCTTT 59.715 57.895 0.00 0.00 0.00 2.52
425 482 3.574396 TCTCGTCTTTCTGAACAGGACAT 59.426 43.478 13.72 0.00 0.00 3.06
479 539 0.975556 TGTAGCTCTCCCATCGGCAA 60.976 55.000 0.00 0.00 0.00 4.52
480 540 0.249657 GTAGCTCTCCCATCGGCAAG 60.250 60.000 0.00 0.00 0.00 4.01
481 541 1.402896 TAGCTCTCCCATCGGCAAGG 61.403 60.000 0.00 0.00 0.00 3.61
482 542 2.735772 GCTCTCCCATCGGCAAGGA 61.736 63.158 0.00 0.00 0.00 3.36
483 543 1.144936 CTCTCCCATCGGCAAGGAC 59.855 63.158 0.00 0.00 0.00 3.85
484 544 1.306141 TCTCCCATCGGCAAGGACT 60.306 57.895 0.00 0.00 0.00 3.85
485 545 1.153289 CTCCCATCGGCAAGGACTG 60.153 63.158 0.00 0.00 0.00 3.51
486 546 2.124570 CCCATCGGCAAGGACTGG 60.125 66.667 0.00 0.00 0.00 4.00
487 547 2.669133 CCCATCGGCAAGGACTGGA 61.669 63.158 0.00 0.00 0.00 3.86
488 548 1.299648 CCATCGGCAAGGACTGGAA 59.700 57.895 0.00 0.00 0.00 3.53
489 549 0.107017 CCATCGGCAAGGACTGGAAT 60.107 55.000 0.00 0.00 0.00 3.01
490 550 1.683011 CCATCGGCAAGGACTGGAATT 60.683 52.381 0.00 0.00 0.00 2.17
491 551 1.672881 CATCGGCAAGGACTGGAATTC 59.327 52.381 0.00 0.00 0.00 2.17
492 552 0.690192 TCGGCAAGGACTGGAATTCA 59.310 50.000 7.93 0.00 0.00 2.57
493 553 0.804989 CGGCAAGGACTGGAATTCAC 59.195 55.000 7.93 0.00 0.00 3.18
494 554 0.804989 GGCAAGGACTGGAATTCACG 59.195 55.000 7.93 0.00 0.00 4.35
495 555 0.169009 GCAAGGACTGGAATTCACGC 59.831 55.000 7.93 0.00 0.00 5.34
496 556 1.813513 CAAGGACTGGAATTCACGCT 58.186 50.000 7.93 0.00 0.00 5.07
497 557 1.734465 CAAGGACTGGAATTCACGCTC 59.266 52.381 7.93 0.00 0.00 5.03
498 558 0.976641 AGGACTGGAATTCACGCTCA 59.023 50.000 7.93 0.00 0.00 4.26
499 559 1.079503 GGACTGGAATTCACGCTCAC 58.920 55.000 7.93 0.00 0.00 3.51
500 560 1.079503 GACTGGAATTCACGCTCACC 58.920 55.000 7.93 0.00 0.00 4.02
501 561 0.321653 ACTGGAATTCACGCTCACCC 60.322 55.000 7.93 0.00 0.00 4.61
502 562 0.321564 CTGGAATTCACGCTCACCCA 60.322 55.000 7.93 0.00 0.00 4.51
503 563 0.327924 TGGAATTCACGCTCACCCAT 59.672 50.000 7.93 0.00 0.00 4.00
504 564 0.734889 GGAATTCACGCTCACCCATG 59.265 55.000 7.93 0.00 0.00 3.66
505 565 1.678728 GGAATTCACGCTCACCCATGA 60.679 52.381 7.93 0.00 0.00 3.07
506 566 1.398390 GAATTCACGCTCACCCATGAC 59.602 52.381 0.00 0.00 0.00 3.06
507 567 0.324614 ATTCACGCTCACCCATGACA 59.675 50.000 0.00 0.00 0.00 3.58
508 568 0.602638 TTCACGCTCACCCATGACAC 60.603 55.000 0.00 0.00 0.00 3.67
509 569 1.301637 CACGCTCACCCATGACACA 60.302 57.895 0.00 0.00 0.00 3.72
510 570 1.301716 ACGCTCACCCATGACACAC 60.302 57.895 0.00 0.00 0.00 3.82
511 571 1.301637 CGCTCACCCATGACACACA 60.302 57.895 0.00 0.00 0.00 3.72
512 572 0.674581 CGCTCACCCATGACACACAT 60.675 55.000 0.00 0.00 40.17 3.21
513 573 1.405391 CGCTCACCCATGACACACATA 60.405 52.381 0.00 0.00 37.46 2.29
514 574 2.710377 GCTCACCCATGACACACATAA 58.290 47.619 0.00 0.00 37.46 1.90
515 575 3.081061 GCTCACCCATGACACACATAAA 58.919 45.455 0.00 0.00 37.46 1.40
516 576 3.505680 GCTCACCCATGACACACATAAAA 59.494 43.478 0.00 0.00 37.46 1.52
517 577 4.158394 GCTCACCCATGACACACATAAAAT 59.842 41.667 0.00 0.00 37.46 1.82
518 578 5.677091 GCTCACCCATGACACACATAAAATC 60.677 44.000 0.00 0.00 37.46 2.17
519 579 4.394610 TCACCCATGACACACATAAAATCG 59.605 41.667 0.00 0.00 37.46 3.34
520 580 4.155826 CACCCATGACACACATAAAATCGT 59.844 41.667 0.00 0.00 37.46 3.73
521 581 5.352846 CACCCATGACACACATAAAATCGTA 59.647 40.000 0.00 0.00 37.46 3.43
522 582 5.584649 ACCCATGACACACATAAAATCGTAG 59.415 40.000 0.00 0.00 37.46 3.51
523 583 5.501715 CCATGACACACATAAAATCGTAGC 58.498 41.667 0.00 0.00 37.46 3.58
524 584 5.501715 CATGACACACATAAAATCGTAGCC 58.498 41.667 0.00 0.00 37.46 3.93
525 585 3.936453 TGACACACATAAAATCGTAGCCC 59.064 43.478 0.00 0.00 0.00 5.19
526 586 4.189231 GACACACATAAAATCGTAGCCCT 58.811 43.478 0.00 0.00 0.00 5.19
527 587 4.189231 ACACACATAAAATCGTAGCCCTC 58.811 43.478 0.00 0.00 0.00 4.30
528 588 3.560068 CACACATAAAATCGTAGCCCTCC 59.440 47.826 0.00 0.00 0.00 4.30
529 589 3.454812 ACACATAAAATCGTAGCCCTCCT 59.545 43.478 0.00 0.00 0.00 3.69
530 590 4.652421 ACACATAAAATCGTAGCCCTCCTA 59.348 41.667 0.00 0.00 0.00 2.94
531 591 5.307196 ACACATAAAATCGTAGCCCTCCTAT 59.693 40.000 0.00 0.00 0.00 2.57
532 592 5.869888 CACATAAAATCGTAGCCCTCCTATC 59.130 44.000 0.00 0.00 0.00 2.08
533 593 3.662247 AAAATCGTAGCCCTCCTATCG 57.338 47.619 0.00 0.00 0.00 2.92
534 594 1.546961 AATCGTAGCCCTCCTATCGG 58.453 55.000 0.00 0.00 0.00 4.18
569 629 0.532573 ACGCTCACCCATGACACTAG 59.467 55.000 0.00 0.00 0.00 2.57
594 655 1.378646 AGGAGACGTGGCAGATCGA 60.379 57.895 0.00 0.00 0.00 3.59
595 656 0.753479 AGGAGACGTGGCAGATCGAT 60.753 55.000 0.00 0.00 0.00 3.59
598 659 0.955178 AGACGTGGCAGATCGATAGG 59.045 55.000 0.00 0.00 0.00 2.57
606 667 1.908793 AGATCGATAGGGCCACCGG 60.909 63.158 6.18 0.00 43.47 5.28
630 694 1.887707 GGCAGAAACCCTATCCGCG 60.888 63.158 0.00 0.00 0.00 6.46
673 740 0.685097 TGTGGCTTCTTCCGCTTAGT 59.315 50.000 0.00 0.00 37.51 2.24
674 741 1.071699 TGTGGCTTCTTCCGCTTAGTT 59.928 47.619 0.00 0.00 37.51 2.24
853 928 2.095847 GTGCCGCCGTTGATCGTTA 61.096 57.895 0.00 0.00 37.94 3.18
981 1061 3.672295 CTGGCACTTCTCCTCGGCC 62.672 68.421 0.00 0.00 44.82 6.13
1091 1171 3.181458 GCCCTACCGGTTGATAATTCAGA 60.181 47.826 15.04 0.00 32.27 3.27
1186 1269 3.003763 AGGGAGGAGACAACGGCC 61.004 66.667 0.00 0.00 0.00 6.13
1266 1361 2.279517 GATCAGCGGCGGTACAGG 60.280 66.667 12.74 0.00 0.00 4.00
1362 1457 0.252881 AGATCAGGAAGTGGGCCAGA 60.253 55.000 6.40 0.00 0.00 3.86
1425 1520 2.119611 TCCTCCCCTCGCAAGTCA 59.880 61.111 0.00 0.00 39.48 3.41
1475 1570 3.384532 GGCCGTCCGGTCCAAGTA 61.385 66.667 7.66 0.00 37.65 2.24
1583 1678 1.958715 CGGTTGCGTGTGACCATGA 60.959 57.895 0.00 0.00 35.63 3.07
1707 2020 7.813148 GCGTAGATACCAGATATGTACATGTTT 59.187 37.037 18.81 4.09 39.11 2.83
1743 2056 2.437281 AGTCCTACCATGGATGCTTCAG 59.563 50.000 21.47 3.38 38.52 3.02
1753 2066 0.239347 GATGCTTCAGTTGCAGCGTT 59.761 50.000 0.25 0.00 44.04 4.84
1758 2071 2.478894 GCTTCAGTTGCAGCGTTACTAA 59.521 45.455 0.00 0.00 0.00 2.24
1844 2157 5.395324 CGGTGATATTCTACCACCTTTCACT 60.395 44.000 0.00 0.00 46.03 3.41
1845 2158 6.183360 CGGTGATATTCTACCACCTTTCACTA 60.183 42.308 0.00 0.00 46.03 2.74
1850 2163 4.737855 TCTACCACCTTTCACTATGAGC 57.262 45.455 0.00 0.00 0.00 4.26
1859 2172 7.436933 CACCTTTCACTATGAGCAGTATCATA 58.563 38.462 0.00 0.00 40.40 2.15
1931 2244 6.959639 TTTATGATAAGAACTCCCCAATGC 57.040 37.500 0.00 0.00 0.00 3.56
2147 2461 7.452562 TGCCAATGCTTATGATACTCTCATTA 58.547 34.615 0.00 0.00 40.83 1.90
2195 2509 6.367969 TCCTTTGCTCGTAACTTTAATCACTC 59.632 38.462 0.00 0.00 0.00 3.51
2204 2518 6.090898 CGTAACTTTAATCACTCAGACCAAGG 59.909 42.308 0.00 0.00 0.00 3.61
2215 2529 2.958355 TCAGACCAAGGAAAGCAAAAGG 59.042 45.455 0.00 0.00 0.00 3.11
2241 2555 6.683974 ACTTAGAATCAAATTGGATGGACG 57.316 37.500 0.00 0.00 0.00 4.79
2242 2556 6.414732 ACTTAGAATCAAATTGGATGGACGA 58.585 36.000 0.00 0.00 0.00 4.20
2260 2574 5.839063 TGGACGATTATATCCCTCAGTTCTT 59.161 40.000 0.00 0.00 33.69 2.52
2261 2575 7.008332 TGGACGATTATATCCCTCAGTTCTTA 58.992 38.462 0.00 0.00 33.69 2.10
2264 2578 9.194271 GACGATTATATCCCTCAGTTCTTAAAC 57.806 37.037 0.00 0.00 35.50 2.01
2275 2589 6.197364 TCAGTTCTTAAACCGATCTCTCTC 57.803 41.667 0.00 0.00 35.92 3.20
2277 2591 4.403113 AGTTCTTAAACCGATCTCTCTCCC 59.597 45.833 0.00 0.00 35.92 4.30
2314 2629 5.630061 CAATAACTGTTGTTGCATGATCGA 58.370 37.500 15.44 0.00 37.59 3.59
2363 2678 3.245229 TGTTGCATACCATCTCCAAACCT 60.245 43.478 0.00 0.00 0.00 3.50
2392 2707 0.385751 CATACCCGATGTCGTCAGCT 59.614 55.000 1.44 0.00 37.74 4.24
2398 2713 1.079543 GATGTCGTCAGCTGCCACT 60.080 57.895 9.47 0.00 0.00 4.00
2417 2732 5.504665 GCCACTTGTCTAATTGAATCATCGG 60.505 44.000 0.00 0.00 0.00 4.18
2423 2738 6.169800 TGTCTAATTGAATCATCGGACAACA 58.830 36.000 6.46 0.00 31.00 3.33
2433 2748 1.522668 TCGGACAACATGCTTTCCTG 58.477 50.000 0.10 0.00 0.00 3.86
2437 2752 3.149196 GGACAACATGCTTTCCTGAGAA 58.851 45.455 0.00 0.00 0.00 2.87
2505 2820 9.725019 ATATAATATTTTCGCTGAGTTGGATGA 57.275 29.630 0.00 0.00 0.00 2.92
2506 2821 5.998454 ATATTTTCGCTGAGTTGGATGAG 57.002 39.130 0.00 0.00 0.00 2.90
2507 2822 3.401033 TTTTCGCTGAGTTGGATGAGA 57.599 42.857 0.00 0.00 0.00 3.27
2508 2823 2.662006 TTCGCTGAGTTGGATGAGAG 57.338 50.000 0.00 0.00 0.00 3.20
2509 2824 1.550327 TCGCTGAGTTGGATGAGAGT 58.450 50.000 0.00 0.00 0.00 3.24
2510 2825 1.203287 TCGCTGAGTTGGATGAGAGTG 59.797 52.381 0.00 0.00 0.00 3.51
2511 2826 1.203287 CGCTGAGTTGGATGAGAGTGA 59.797 52.381 0.00 0.00 0.00 3.41
2538 2865 4.021981 TGAGAGAGAATGAAAGCGAGTTGA 60.022 41.667 0.00 0.00 0.00 3.18
2547 3178 5.283060 TGAAAGCGAGTTGAAGAATAAGC 57.717 39.130 0.00 0.00 0.00 3.09
2549 3180 2.960819 AGCGAGTTGAAGAATAAGCGT 58.039 42.857 0.00 0.00 0.00 5.07
2601 3232 6.201226 TGTGAGAGTGTAAGATGAGTCATC 57.799 41.667 23.20 23.20 40.80 2.92
2698 3329 6.059484 GGCAACAAGGTATGGCTATAACTTA 58.941 40.000 18.80 0.00 43.30 2.24
2729 3360 6.763610 ACTATTAACCAATGCTCTAAGCTCAC 59.236 38.462 0.11 0.00 42.97 3.51
2730 3361 2.015736 ACCAATGCTCTAAGCTCACG 57.984 50.000 0.11 0.00 42.97 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.243434 CGTCGCTAGGTGGTCTATGAATT 60.243 47.826 0.00 0.00 0.00 2.17
150 152 0.968901 TGGGGTCTTAGCACGACGAT 60.969 55.000 0.00 0.00 32.24 3.73
197 201 6.282199 TCTAAACTTCTCTTTATCGGCAGT 57.718 37.500 0.00 0.00 0.00 4.40
222 226 7.496346 TGTGTCTTCAGGTTATATCCTTCTT 57.504 36.000 0.00 0.00 35.37 2.52
232 236 5.008613 GCTTTGTTCATGTGTCTTCAGGTTA 59.991 40.000 0.00 0.00 0.00 2.85
289 323 5.221601 GCCTGATCTCATAGGATTCAGTTCA 60.222 44.000 13.31 0.00 36.11 3.18
290 324 5.237048 GCCTGATCTCATAGGATTCAGTTC 58.763 45.833 13.31 4.91 36.11 3.01
294 328 3.500343 TCGCCTGATCTCATAGGATTCA 58.500 45.455 1.03 0.00 36.11 2.57
354 406 1.001760 TTCTTCTCGCCTAGCCCCT 59.998 57.895 0.00 0.00 0.00 4.79
366 418 7.922382 TCTTGAAGATGGAATAAGGTTCTTCT 58.078 34.615 11.07 0.00 41.69 2.85
397 449 1.601166 TCAGAAAGACGAGACGGTGA 58.399 50.000 0.00 0.00 0.00 4.02
412 464 4.047627 TGGAGTCTATGTCCTGTTCAGA 57.952 45.455 1.00 0.00 34.86 3.27
425 482 7.500892 TGCTTATTCAAGTTTTGTTGGAGTCTA 59.499 33.333 0.00 0.00 34.00 2.59
462 520 1.402896 CCTTGCCGATGGGAGAGCTA 61.403 60.000 0.00 0.00 34.06 3.32
479 539 0.976641 TGAGCGTGAATTCCAGTCCT 59.023 50.000 2.27 0.00 0.00 3.85
480 540 1.079503 GTGAGCGTGAATTCCAGTCC 58.920 55.000 2.27 0.00 0.00 3.85
481 541 1.079503 GGTGAGCGTGAATTCCAGTC 58.920 55.000 2.27 0.00 0.00 3.51
482 542 0.321653 GGGTGAGCGTGAATTCCAGT 60.322 55.000 2.27 0.00 0.00 4.00
483 543 0.321564 TGGGTGAGCGTGAATTCCAG 60.322 55.000 2.27 0.00 0.00 3.86
484 544 0.327924 ATGGGTGAGCGTGAATTCCA 59.672 50.000 2.27 0.00 0.00 3.53
485 545 0.734889 CATGGGTGAGCGTGAATTCC 59.265 55.000 2.27 0.00 0.00 3.01
486 546 1.398390 GTCATGGGTGAGCGTGAATTC 59.602 52.381 0.00 0.00 34.36 2.17
487 547 1.271325 TGTCATGGGTGAGCGTGAATT 60.271 47.619 0.00 0.00 34.36 2.17
488 548 0.324614 TGTCATGGGTGAGCGTGAAT 59.675 50.000 0.00 0.00 34.36 2.57
489 549 0.602638 GTGTCATGGGTGAGCGTGAA 60.603 55.000 0.00 0.00 34.36 3.18
490 550 1.005037 GTGTCATGGGTGAGCGTGA 60.005 57.895 0.00 0.00 34.36 4.35
491 551 1.301637 TGTGTCATGGGTGAGCGTG 60.302 57.895 0.00 0.00 34.36 5.34
492 552 1.301716 GTGTGTCATGGGTGAGCGT 60.302 57.895 0.00 0.00 34.36 5.07
493 553 0.674581 ATGTGTGTCATGGGTGAGCG 60.675 55.000 0.00 0.00 34.36 5.03
494 554 2.401583 TATGTGTGTCATGGGTGAGC 57.598 50.000 0.00 0.00 37.91 4.26
495 555 5.447683 CGATTTTATGTGTGTCATGGGTGAG 60.448 44.000 0.00 0.00 37.91 3.51
496 556 4.394610 CGATTTTATGTGTGTCATGGGTGA 59.605 41.667 0.00 0.00 37.91 4.02
497 557 4.155826 ACGATTTTATGTGTGTCATGGGTG 59.844 41.667 0.00 0.00 37.91 4.61
498 558 4.331968 ACGATTTTATGTGTGTCATGGGT 58.668 39.130 0.00 0.00 37.91 4.51
499 559 4.963276 ACGATTTTATGTGTGTCATGGG 57.037 40.909 0.00 0.00 37.91 4.00
500 560 5.501715 GCTACGATTTTATGTGTGTCATGG 58.498 41.667 0.00 0.00 37.91 3.66
501 561 5.501715 GGCTACGATTTTATGTGTGTCATG 58.498 41.667 0.00 0.00 37.91 3.07
502 562 4.574828 GGGCTACGATTTTATGTGTGTCAT 59.425 41.667 0.00 0.00 40.25 3.06
503 563 3.936453 GGGCTACGATTTTATGTGTGTCA 59.064 43.478 0.00 0.00 0.00 3.58
504 564 4.189231 AGGGCTACGATTTTATGTGTGTC 58.811 43.478 0.00 0.00 0.00 3.67
505 565 4.189231 GAGGGCTACGATTTTATGTGTGT 58.811 43.478 0.00 0.00 0.00 3.72
506 566 3.560068 GGAGGGCTACGATTTTATGTGTG 59.440 47.826 0.00 0.00 0.00 3.82
507 567 3.454812 AGGAGGGCTACGATTTTATGTGT 59.545 43.478 0.00 0.00 0.00 3.72
508 568 4.073293 AGGAGGGCTACGATTTTATGTG 57.927 45.455 0.00 0.00 0.00 3.21
509 569 5.336531 CGATAGGAGGGCTACGATTTTATGT 60.337 44.000 0.00 0.00 0.00 2.29
510 570 5.103000 CGATAGGAGGGCTACGATTTTATG 58.897 45.833 0.00 0.00 0.00 1.90
511 571 5.326200 CGATAGGAGGGCTACGATTTTAT 57.674 43.478 0.00 0.00 0.00 1.40
512 572 4.778534 CGATAGGAGGGCTACGATTTTA 57.221 45.455 0.00 0.00 0.00 1.52
513 573 3.662247 CGATAGGAGGGCTACGATTTT 57.338 47.619 0.00 0.00 0.00 1.82
533 593 1.644786 CGTGAATTCCGGTCCTTGCC 61.645 60.000 0.00 0.00 0.00 4.52
534 594 1.794222 CGTGAATTCCGGTCCTTGC 59.206 57.895 0.00 0.00 0.00 4.01
611 675 1.223487 GCGGATAGGGTTTCTGCCA 59.777 57.895 0.00 0.00 39.16 4.92
625 689 0.393267 CCCCTTTTGTAATCCGCGGA 60.393 55.000 33.12 33.12 0.00 5.54
630 694 0.683179 AGCGGCCCCTTTTGTAATCC 60.683 55.000 0.00 0.00 0.00 3.01
673 740 2.798283 GTGGACGAACAATGAACTCGAA 59.202 45.455 10.06 0.00 36.45 3.71
674 741 2.400399 GTGGACGAACAATGAACTCGA 58.600 47.619 10.06 0.00 36.45 4.04
853 928 3.053170 ACGCTTAATATTCCCTGGGGTTT 60.053 43.478 14.00 4.41 36.47 3.27
919 999 0.109272 CGTGCGAGGTTGCTTCTAGA 60.109 55.000 0.00 0.00 35.36 2.43
1058 1138 1.227674 GGTAGGGCTGCGATGGAAG 60.228 63.158 0.00 0.00 0.00 3.46
1091 1171 1.432251 CCTACCGACATCGACGCTT 59.568 57.895 2.09 0.00 43.02 4.68
1209 1292 2.793160 TTCTGCTGCCGCTCTCCTTG 62.793 60.000 0.70 0.00 36.97 3.61
1222 1317 4.767255 CTTCCCGCCGCTTCTGCT 62.767 66.667 0.00 0.00 36.97 4.24
1223 1318 4.760047 TCTTCCCGCCGCTTCTGC 62.760 66.667 0.00 0.00 0.00 4.26
1224 1319 2.047274 TTCTTCCCGCCGCTTCTG 60.047 61.111 0.00 0.00 0.00 3.02
1225 1320 2.266055 CTTCTTCCCGCCGCTTCT 59.734 61.111 0.00 0.00 0.00 2.85
1226 1321 2.820037 CCTTCTTCCCGCCGCTTC 60.820 66.667 0.00 0.00 0.00 3.86
1329 1424 1.743958 CTGATCTGGCCTTTCAGCTTG 59.256 52.381 14.44 0.00 34.91 4.01
1335 1430 2.363683 CACTTCCTGATCTGGCCTTTC 58.636 52.381 13.60 0.00 0.00 2.62
1514 1609 3.286751 GCTTTCACGGTGGCAGCA 61.287 61.111 17.80 0.00 0.00 4.41
1544 1639 2.164017 GACCGGTCAAGGAGTACTCTTC 59.836 54.545 29.75 6.92 34.73 2.87
1583 1678 4.566426 AGGAAGAAGCTGCATAACTCTT 57.434 40.909 1.02 0.00 0.00 2.85
1656 1783 8.915654 GCACGAACAATTAAATCAAAGAATCTT 58.084 29.630 0.00 0.00 0.00 2.40
1723 2036 2.171448 ACTGAAGCATCCATGGTAGGAC 59.829 50.000 12.58 1.45 41.30 3.85
1743 2056 4.616181 ATGGATTTAGTAACGCTGCAAC 57.384 40.909 0.00 0.00 0.00 4.17
1753 2066 5.138276 AGACTGCTCCGTATGGATTTAGTA 58.862 41.667 3.55 0.00 45.33 1.82
1758 2071 1.338337 CGAGACTGCTCCGTATGGATT 59.662 52.381 3.55 0.00 45.33 3.01
1901 2214 8.278639 TGGGGAGTTCTTATCATAAATTAGCAA 58.721 33.333 0.00 0.00 0.00 3.91
1903 2216 8.691661 TTGGGGAGTTCTTATCATAAATTAGC 57.308 34.615 0.00 0.00 0.00 3.09
1909 2222 6.012337 TGCATTGGGGAGTTCTTATCATAA 57.988 37.500 0.00 0.00 0.00 1.90
2195 2509 2.695147 ACCTTTTGCTTTCCTTGGTCTG 59.305 45.455 0.00 0.00 0.00 3.51
2204 2518 9.744468 TTTGATTCTAAGTTACCTTTTGCTTTC 57.256 29.630 0.00 0.00 31.89 2.62
2215 2529 8.122952 CGTCCATCCAATTTGATTCTAAGTTAC 58.877 37.037 0.00 0.00 0.00 2.50
2241 2555 8.365647 TCGGTTTAAGAACTGAGGGATATAATC 58.634 37.037 0.00 0.00 44.24 1.75
2242 2556 8.258850 TCGGTTTAAGAACTGAGGGATATAAT 57.741 34.615 0.00 0.00 44.24 1.28
2260 2574 1.213678 TCGGGGAGAGAGATCGGTTTA 59.786 52.381 0.00 0.00 0.00 2.01
2261 2575 0.033405 TCGGGGAGAGAGATCGGTTT 60.033 55.000 0.00 0.00 0.00 3.27
2264 2578 2.255172 CGTCGGGGAGAGAGATCGG 61.255 68.421 0.00 0.00 0.00 4.18
2277 2591 0.742990 TTATTGCTGAAGGCCGTCGG 60.743 55.000 21.92 21.92 40.92 4.79
2363 2678 1.118965 ATCGGGTATGCACGGATGGA 61.119 55.000 5.38 0.00 42.74 3.41
2392 2707 5.065090 CGATGATTCAATTAGACAAGTGGCA 59.935 40.000 0.00 0.00 30.72 4.92
2398 2713 6.652900 TGTTGTCCGATGATTCAATTAGACAA 59.347 34.615 15.26 15.26 39.83 3.18
2417 2732 3.565482 TGTTCTCAGGAAAGCATGTTGTC 59.435 43.478 0.00 0.00 32.81 3.18
2423 2738 9.905713 TTATTATACTTGTTCTCAGGAAAGCAT 57.094 29.630 0.00 0.00 32.81 3.79
2483 2798 6.115446 TCTCATCCAACTCAGCGAAAATATT 58.885 36.000 0.00 0.00 0.00 1.28
2492 2807 2.495270 TCTCACTCTCATCCAACTCAGC 59.505 50.000 0.00 0.00 0.00 4.26
2500 2815 5.132502 TCTCTCTCATTCTCACTCTCATCC 58.867 45.833 0.00 0.00 0.00 3.51
2501 2816 6.698008 TTCTCTCTCATTCTCACTCTCATC 57.302 41.667 0.00 0.00 0.00 2.92
2502 2817 6.834969 TCATTCTCTCTCATTCTCACTCTCAT 59.165 38.462 0.00 0.00 0.00 2.90
2503 2818 6.186234 TCATTCTCTCTCATTCTCACTCTCA 58.814 40.000 0.00 0.00 0.00 3.27
2504 2819 6.698008 TCATTCTCTCTCATTCTCACTCTC 57.302 41.667 0.00 0.00 0.00 3.20
2505 2820 7.479352 TTTCATTCTCTCTCATTCTCACTCT 57.521 36.000 0.00 0.00 0.00 3.24
2506 2821 6.256321 GCTTTCATTCTCTCTCATTCTCACTC 59.744 42.308 0.00 0.00 0.00 3.51
2507 2822 6.108015 GCTTTCATTCTCTCTCATTCTCACT 58.892 40.000 0.00 0.00 0.00 3.41
2508 2823 5.005586 CGCTTTCATTCTCTCTCATTCTCAC 59.994 44.000 0.00 0.00 0.00 3.51
2509 2824 5.105595 TCGCTTTCATTCTCTCTCATTCTCA 60.106 40.000 0.00 0.00 0.00 3.27
2510 2825 5.347342 TCGCTTTCATTCTCTCTCATTCTC 58.653 41.667 0.00 0.00 0.00 2.87
2511 2826 5.105392 ACTCGCTTTCATTCTCTCTCATTCT 60.105 40.000 0.00 0.00 0.00 2.40
2547 3178 4.056125 TCCGTGCTGGAGCTGACG 62.056 66.667 0.00 2.57 43.74 4.35
2558 3189 1.523758 ATGTTTCTTGGAGTCCGTGC 58.476 50.000 4.30 0.00 0.00 5.34
2698 3329 6.739331 AGAGCATTGGTTAATAGTAGAGCT 57.261 37.500 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.