Multiple sequence alignment - TraesCS5B01G465000

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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 TraesCS5B01G465000 chr5B 100.000 4190 0 0 1 4190 639674655 639678844 0.000000e+00 7738.0
1 TraesCS5B01G465000 chr5B 91.557 687 38 9 1001 1675 639649621 639648943 0.000000e+00 929.0
2 TraesCS5B01G465000 chr5B 81.766 872 109 33 2335 3202 639620901 639620076 0.000000e+00 684.0
3 TraesCS5B01G465000 chr5B 83.595 573 56 15 1671 2205 639621582 639621010 1.740000e-138 503.0
4 TraesCS5B01G465000 chr5B 77.725 211 27 10 487 682 694526918 694526713 1.230000e-20 111.0
5 TraesCS5B01G465000 chr5A 92.312 3421 164 42 847 4190 636411490 636414888 0.000000e+00 4769.0
6 TraesCS5B01G465000 chr5A 87.232 1261 95 31 1001 2205 636308174 636306924 0.000000e+00 1376.0
7 TraesCS5B01G465000 chr5A 85.965 456 48 6 1116 1571 636409602 636410041 1.360000e-129 473.0
8 TraesCS5B01G465000 chr5A 83.164 493 59 15 2343 2833 636306759 636306289 2.990000e-116 429.0
9 TraesCS5B01G465000 chr5A 93.262 282 18 1 2924 3205 636306229 636305949 8.380000e-112 414.0
10 TraesCS5B01G465000 chr5A 75.488 563 78 21 2258 2816 636311401 636310895 1.960000e-53 220.0
11 TraesCS5B01G465000 chr5A 87.302 63 7 1 669 731 426721050 426720989 2.090000e-08 71.3
12 TraesCS5B01G465000 chr5D 91.758 3482 185 46 793 4190 509134458 509137921 0.000000e+00 4747.0
13 TraesCS5B01G465000 chr5D 87.540 1260 96 33 1001 2205 509022491 509021238 0.000000e+00 1400.0
14 TraesCS5B01G465000 chr5D 87.050 556 53 11 2637 3192 509020830 509020294 9.960000e-171 610.0
15 TraesCS5B01G465000 chr5D 83.133 249 39 2 2570 2816 509023215 509022968 1.520000e-54 224.0
16 TraesCS5B01G465000 chr5D 88.889 81 8 1 3125 3205 509019531 509019452 9.590000e-17 99.0
17 TraesCS5B01G465000 chr1B 87.755 490 56 3 1 488 410308967 410308480 1.690000e-158 569.0
18 TraesCS5B01G465000 chr1B 85.646 418 54 5 58 472 410314704 410314290 6.430000e-118 435.0
19 TraesCS5B01G465000 chr7D 87.474 487 55 5 1 484 585195083 585194600 1.320000e-154 556.0
20 TraesCS5B01G465000 chr7D 83.666 551 72 14 1210 1753 88148025 88148564 1.740000e-138 503.0
21 TraesCS5B01G465000 chr7D 89.034 383 33 8 107 483 379770822 379770443 2.280000e-127 466.0
22 TraesCS5B01G465000 chr7D 84.742 485 49 11 1 473 112010737 112010266 2.950000e-126 462.0
23 TraesCS5B01G465000 chr7D 87.566 378 44 3 108 483 465162094 465162470 6.430000e-118 435.0
24 TraesCS5B01G465000 chr7D 80.124 322 38 9 490 786 178705134 178704814 2.540000e-52 217.0
25 TraesCS5B01G465000 chr7D 76.444 225 35 4 573 781 59084286 59084508 5.730000e-19 106.0
26 TraesCS5B01G465000 chr7D 87.097 93 12 0 487 579 635708456 635708548 5.730000e-19 106.0
27 TraesCS5B01G465000 chr7D 87.097 93 12 0 487 579 636303450 636303358 5.730000e-19 106.0
28 TraesCS5B01G465000 chr7A 84.239 552 65 14 1210 1753 89833884 89834421 6.210000e-143 518.0
29 TraesCS5B01G465000 chr7A 86.364 264 34 2 2928 3190 89835456 89835718 1.910000e-73 287.0
30 TraesCS5B01G465000 chr3D 83.434 495 62 9 1 480 402498056 402497567 3.840000e-120 442.0
31 TraesCS5B01G465000 chr3D 95.238 42 2 0 487 528 79598059 79598100 2.700000e-07 67.6
32 TraesCS5B01G465000 chr2B 87.533 377 38 5 108 480 747575543 747575172 1.080000e-115 427.0
33 TraesCS5B01G465000 chr2B 87.268 377 39 5 108 480 747604145 747603774 5.010000e-114 422.0
34 TraesCS5B01G465000 chr2D 87.466 367 42 3 108 472 555476756 555476392 1.800000e-113 420.0
35 TraesCS5B01G465000 chr2D 82.143 504 66 8 1 482 572644248 572643747 1.080000e-110 411.0
36 TraesCS5B01G465000 chr2D 89.381 113 11 1 669 781 610169146 610169257 1.570000e-29 141.0
37 TraesCS5B01G465000 chr7B 84.017 463 41 17 6 437 241541924 241542384 8.380000e-112 414.0
38 TraesCS5B01G465000 chr7B 90.909 297 24 1 1210 1506 37359832 37360125 3.040000e-106 396.0
39 TraesCS5B01G465000 chr7B 80.663 181 28 5 522 696 604118798 604118977 2.630000e-27 134.0
40 TraesCS5B01G465000 chr3B 79.134 508 79 9 1 483 615908626 615908121 4.040000e-85 326.0
41 TraesCS5B01G465000 chr3B 91.912 136 11 0 1 136 489718641 489718776 1.540000e-44 191.0
42 TraesCS5B01G465000 chr6A 87.770 139 17 0 1 139 414262873 414263011 3.350000e-36 163.0
43 TraesCS5B01G465000 chr4A 86.232 138 18 1 1 138 537290378 537290514 9.390000e-32 148.0
44 TraesCS5B01G465000 chr4A 86.957 92 11 1 669 760 146707675 146707765 7.410000e-18 102.0
45 TraesCS5B01G465000 chr4A 94.286 35 2 0 487 521 146707501 146707535 2.000000e-03 54.7
46 TraesCS5B01G465000 chr4D 75.618 283 37 9 525 778 447991841 447992120 1.230000e-20 111.0
47 TraesCS5B01G465000 chrUn 88.158 76 8 1 669 744 381045352 381045278 5.770000e-14 89.8
48 TraesCS5B01G465000 chrUn 100.000 28 0 0 1196 1223 264230510 264230537 8.000000e-03 52.8
49 TraesCS5B01G465000 chr3A 92.063 63 4 1 669 731 69643360 69643299 2.080000e-13 87.9
50 TraesCS5B01G465000 chr6B 88.889 63 7 0 669 731 21032966 21032904 1.250000e-10 78.7
51 TraesCS5B01G465000 chr6B 88.889 63 7 0 669 731 21033847 21033785 1.250000e-10 78.7
52 TraesCS5B01G465000 chr2A 79.747 79 13 3 704 781 711635788 711635864 2.000000e-03 54.7


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 TraesCS5B01G465000 chr5B 639674655 639678844 4189 False 7738.00 7738 100.0000 1 4190 1 chr5B.!!$F1 4189
1 TraesCS5B01G465000 chr5B 639648943 639649621 678 True 929.00 929 91.5570 1001 1675 1 chr5B.!!$R1 674
2 TraesCS5B01G465000 chr5B 639620076 639621582 1506 True 593.50 684 82.6805 1671 3202 2 chr5B.!!$R3 1531
3 TraesCS5B01G465000 chr5A 636409602 636414888 5286 False 2621.00 4769 89.1385 847 4190 2 chr5A.!!$F1 3343
4 TraesCS5B01G465000 chr5A 636305949 636311401 5452 True 609.75 1376 84.7865 1001 3205 4 chr5A.!!$R2 2204
5 TraesCS5B01G465000 chr5D 509134458 509137921 3463 False 4747.00 4747 91.7580 793 4190 1 chr5D.!!$F1 3397
6 TraesCS5B01G465000 chr5D 509019452 509023215 3763 True 583.25 1400 86.6530 1001 3205 4 chr5D.!!$R1 2204
7 TraesCS5B01G465000 chr7D 88148025 88148564 539 False 503.00 503 83.6660 1210 1753 1 chr7D.!!$F2 543
8 TraesCS5B01G465000 chr7A 89833884 89835718 1834 False 402.50 518 85.3015 1210 3190 2 chr7A.!!$F1 1980
9 TraesCS5B01G465000 chr2D 572643747 572644248 501 True 411.00 411 82.1430 1 482 1 chr2D.!!$R2 481
10 TraesCS5B01G465000 chr3B 615908121 615908626 505 True 326.00 326 79.1340 1 483 1 chr3B.!!$R1 482

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
594 626 0.108472 GGCCTGAAAATTGAGCCAGC 60.108 55.0 0.00 0.00 43.32 4.85 F
964 2034 0.179020 CACAGCCACAGGTTCTTCCA 60.179 55.0 0.00 0.00 39.02 3.53 F
972 2042 0.535102 CAGGTTCTTCCACTGCCGTT 60.535 55.0 0.00 0.00 39.02 4.44 F
1812 4157 0.809636 CAACCTCGATACATGCGGCA 60.810 55.0 4.58 4.58 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 4823 0.036952 CGGCTTCTTCTTCTCCTGCA 60.037 55.0 0.0 0.0 0.0 4.41 R
2705 5247 1.939974 CGATCACCATGTTGTCCGAT 58.060 50.0 0.0 0.0 0.0 4.18 R
2864 5406 2.290896 CCTCAGGTATTCAGGTTTGGCA 60.291 50.0 0.0 0.0 0.0 4.92 R
3589 6266 0.687920 TTGGGGAAGCGATGTACACA 59.312 50.0 0.0 0.0 0.0 3.72 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
25 26 1.765657 GGCAGAGAGGAGGATGGCT 60.766 63.158 0.00 0.00 35.51 4.75
60 61 1.063183 AGAAAGGGAGAAGCAGCTGT 58.937 50.000 16.64 0.00 0.00 4.40
88 89 4.828925 GAGTGCTCCTGCCGCCTC 62.829 72.222 0.00 0.00 38.71 4.70
130 131 2.049185 AGCCGCAGATCTGAGTCGT 61.049 57.895 27.04 6.76 0.00 4.34
132 133 1.297967 CCGCAGATCTGAGTCGTCG 60.298 63.158 27.04 17.52 0.00 5.12
135 136 1.297967 CAGATCTGAGTCGTCGCCG 60.298 63.158 18.34 0.00 0.00 6.46
154 186 2.418910 CCACCGGTGCCAACAACAA 61.419 57.895 29.75 0.00 30.57 2.83
156 188 0.527385 CACCGGTGCCAACAACAAAG 60.527 55.000 24.02 0.00 30.57 2.77
157 189 1.067250 CCGGTGCCAACAACAAAGG 59.933 57.895 0.00 0.00 30.57 3.11
172 204 1.351017 CAAAGGAGGGCTTGTCCTACA 59.649 52.381 6.25 0.00 44.17 2.74
173 205 1.742308 AAGGAGGGCTTGTCCTACAA 58.258 50.000 6.25 0.00 44.17 2.41
185 217 4.383931 TGTCCTACAACTAGAGGTGAGT 57.616 45.455 0.53 0.00 34.20 3.41
186 218 4.079970 TGTCCTACAACTAGAGGTGAGTG 58.920 47.826 0.53 0.00 34.20 3.51
208 240 1.917568 GTAAATGGGGTGGTGAGGGTA 59.082 52.381 0.00 0.00 0.00 3.69
240 272 1.000896 CCCCACCTCGGCTGATTTT 60.001 57.895 0.00 0.00 0.00 1.82
247 279 0.464554 CTCGGCTGATTTTCCCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
249 281 1.453928 GGCTGATTTTCCCCTCCCG 60.454 63.158 0.00 0.00 0.00 5.14
303 335 2.290883 ACGTCGCGTCTTCGTTTTT 58.709 47.368 5.77 0.00 33.69 1.94
305 337 0.227735 CGTCGCGTCTTCGTTTTTCA 59.772 50.000 5.77 0.00 39.49 2.69
325 357 2.512515 CCACTTAGCCTGGCTCGC 60.513 66.667 27.16 0.00 40.44 5.03
384 416 1.165270 CTGGGGTGCTTTAAGTTCCG 58.835 55.000 0.00 0.00 0.00 4.30
388 420 0.948678 GGTGCTTTAAGTTCCGTGCA 59.051 50.000 0.00 0.00 0.00 4.57
397 429 1.738099 GTTCCGTGCAGATGCGAGT 60.738 57.895 0.00 0.00 45.83 4.18
424 456 2.336088 CTGCAGGCAACCAAACGG 59.664 61.111 5.57 0.00 37.17 4.44
429 461 1.152830 AGGCAACCAAACGGTCCAT 59.847 52.632 0.00 0.00 34.92 3.41
431 463 0.391228 GGCAACCAAACGGTCCATTT 59.609 50.000 0.00 0.00 34.92 2.32
435 467 3.801983 GCAACCAAACGGTCCATTTTCAT 60.802 43.478 0.00 0.00 34.92 2.57
437 469 2.560981 ACCAAACGGTCCATTTTCATCC 59.439 45.455 0.00 0.00 26.76 3.51
438 470 2.825532 CCAAACGGTCCATTTTCATCCT 59.174 45.455 0.00 0.00 0.00 3.24
440 472 1.463674 ACGGTCCATTTTCATCCTGC 58.536 50.000 0.00 0.00 0.00 4.85
441 473 1.271871 ACGGTCCATTTTCATCCTGCA 60.272 47.619 0.00 0.00 0.00 4.41
442 474 1.133025 CGGTCCATTTTCATCCTGCAC 59.867 52.381 0.00 0.00 0.00 4.57
446 478 0.179129 CATTTTCATCCTGCACGGGC 60.179 55.000 0.34 0.34 41.68 6.13
448 480 2.424842 TTTTCATCCTGCACGGGCCT 62.425 55.000 7.46 0.00 40.13 5.19
463 495 4.247781 CCTGGTTGGGCTATGCAG 57.752 61.111 0.00 0.00 0.00 4.41
475 507 1.000938 GCTATGCAGCCTACCAAATGC 60.001 52.381 0.00 0.00 42.37 3.56
476 508 1.265095 CTATGCAGCCTACCAAATGCG 59.735 52.381 0.00 0.00 41.58 4.73
478 510 2.800736 CAGCCTACCAAATGCGCC 59.199 61.111 4.18 0.00 0.00 6.53
480 512 2.440247 GCCTACCAAATGCGCCCT 60.440 61.111 4.18 0.00 0.00 5.19
483 515 0.180406 CCTACCAAATGCGCCCTAGT 59.820 55.000 4.18 0.00 0.00 2.57
484 516 1.414919 CCTACCAAATGCGCCCTAGTA 59.585 52.381 4.18 0.00 0.00 1.82
485 517 2.548067 CCTACCAAATGCGCCCTAGTAG 60.548 54.545 4.18 9.64 0.00 2.57
487 519 2.112998 ACCAAATGCGCCCTAGTAGTA 58.887 47.619 4.18 0.00 0.00 1.82
488 520 2.704065 ACCAAATGCGCCCTAGTAGTAT 59.296 45.455 4.18 0.00 0.00 2.12
489 521 3.899360 ACCAAATGCGCCCTAGTAGTATA 59.101 43.478 4.18 0.00 0.00 1.47
501 533 2.450609 GTAGTATACGTGGCCATGGG 57.549 55.000 28.37 14.30 0.00 4.00
541 573 4.476752 CCCGATCCGGCCCGAAAA 62.477 66.667 3.71 0.00 46.86 2.29
548 580 2.895372 CGGCCCGAAAATCCCGAG 60.895 66.667 0.00 0.00 43.20 4.63
549 581 3.209812 GGCCCGAAAATCCCGAGC 61.210 66.667 0.00 0.00 0.00 5.03
551 583 2.895372 CCCGAAAATCCCGAGCCG 60.895 66.667 0.00 0.00 0.00 5.52
553 585 1.883084 CCGAAAATCCCGAGCCGAG 60.883 63.158 0.00 0.00 0.00 4.63
554 586 2.526120 CGAAAATCCCGAGCCGAGC 61.526 63.158 0.00 0.00 0.00 5.03
555 587 1.153349 GAAAATCCCGAGCCGAGCT 60.153 57.895 0.00 0.00 43.88 4.09
558 590 2.303549 AAATCCCGAGCCGAGCTGAG 62.304 60.000 2.98 0.00 39.88 3.35
569 601 4.853050 AGCTGAGCCCGAGCATGC 62.853 66.667 10.51 10.51 43.56 4.06
573 605 2.976903 GAGCCCGAGCATGCCATC 60.977 66.667 15.66 5.36 43.56 3.51
588 620 1.473258 CCATCGGGCCTGAAAATTGA 58.527 50.000 20.61 0.00 0.00 2.57
589 621 1.406539 CCATCGGGCCTGAAAATTGAG 59.593 52.381 20.61 2.90 0.00 3.02
592 624 1.250154 CGGGCCTGAAAATTGAGCCA 61.250 55.000 5.28 0.00 45.72 4.75
593 625 0.533951 GGGCCTGAAAATTGAGCCAG 59.466 55.000 0.84 0.00 45.72 4.85
594 626 0.108472 GGCCTGAAAATTGAGCCAGC 60.108 55.000 0.00 0.00 43.32 4.85
595 627 0.893447 GCCTGAAAATTGAGCCAGCT 59.107 50.000 0.00 0.00 0.00 4.24
596 628 1.403780 GCCTGAAAATTGAGCCAGCTG 60.404 52.381 6.78 6.78 0.00 4.24
597 629 1.203994 CCTGAAAATTGAGCCAGCTGG 59.796 52.381 29.34 29.34 38.53 4.85
598 630 1.203994 CTGAAAATTGAGCCAGCTGGG 59.796 52.381 33.46 15.81 40.85 4.45
632 664 2.049248 CGGGCTTGCGCAAAACAT 60.049 55.556 25.01 0.00 38.10 2.71
634 666 1.006337 GGGCTTGCGCAAAACATGA 60.006 52.632 25.01 0.00 38.10 3.07
635 667 0.390209 GGGCTTGCGCAAAACATGAT 60.390 50.000 25.01 0.00 38.10 2.45
636 668 1.431496 GGCTTGCGCAAAACATGATT 58.569 45.000 25.01 0.00 38.10 2.57
638 670 2.223845 GGCTTGCGCAAAACATGATTTT 59.776 40.909 25.01 0.00 38.10 1.82
639 671 3.431572 GGCTTGCGCAAAACATGATTTTA 59.568 39.130 25.01 0.00 38.10 1.52
640 672 4.434593 GGCTTGCGCAAAACATGATTTTAG 60.435 41.667 25.01 8.42 38.10 1.85
642 674 2.992543 TGCGCAAAACATGATTTTAGCC 59.007 40.909 8.16 7.09 0.00 3.93
643 675 2.992543 GCGCAAAACATGATTTTAGCCA 59.007 40.909 0.30 0.00 0.00 4.75
644 676 3.618150 GCGCAAAACATGATTTTAGCCAT 59.382 39.130 0.30 0.00 0.00 4.40
669 701 3.795342 CCGTGCCGGGCTTTTACG 61.795 66.667 21.46 20.18 44.15 3.18
674 706 2.822701 CCGGGCTTTTACGGGCTC 60.823 66.667 0.00 0.00 46.08 4.70
675 707 3.192922 CGGGCTTTTACGGGCTCG 61.193 66.667 3.27 3.27 45.78 5.03
676 708 2.822701 GGGCTTTTACGGGCTCGG 60.823 66.667 12.42 0.00 41.39 4.63
677 709 2.822701 GGCTTTTACGGGCTCGGG 60.823 66.667 12.42 0.00 41.39 5.14
678 710 3.506096 GCTTTTACGGGCTCGGGC 61.506 66.667 12.42 0.00 41.39 6.13
690 722 2.156343 GCTCGGGCCTGATTTAGTAG 57.844 55.000 16.52 2.12 0.00 2.57
691 723 1.270358 GCTCGGGCCTGATTTAGTAGG 60.270 57.143 16.52 1.29 37.14 3.18
697 729 2.528041 CCTGATTTAGTAGGCCCGAC 57.472 55.000 0.00 0.00 0.00 4.79
731 763 3.579685 GCTCGAGCCTGGGTTTTC 58.420 61.111 27.22 0.00 34.31 2.29
732 764 1.302511 GCTCGAGCCTGGGTTTTCA 60.303 57.895 27.22 0.00 34.31 2.69
734 766 0.875059 CTCGAGCCTGGGTTTTCAAC 59.125 55.000 0.00 0.00 0.00 3.18
737 769 0.673985 GAGCCTGGGTTTTCAACACC 59.326 55.000 0.00 0.00 32.46 4.16
738 770 1.106944 AGCCTGGGTTTTCAACACCG 61.107 55.000 0.00 0.00 34.79 4.94
739 771 2.037871 CCTGGGTTTTCAACACCGG 58.962 57.895 0.00 0.00 34.79 5.28
741 773 2.082629 CTGGGTTTTCAACACCGGGC 62.083 60.000 6.32 0.00 34.79 6.13
742 774 1.830847 GGGTTTTCAACACCGGGCT 60.831 57.895 6.32 0.00 34.79 5.19
743 775 1.396607 GGGTTTTCAACACCGGGCTT 61.397 55.000 6.32 0.00 34.79 4.35
744 776 0.462375 GGTTTTCAACACCGGGCTTT 59.538 50.000 6.32 0.00 0.00 3.51
772 804 3.925090 GGCCCGGTCCGAGGTATG 61.925 72.222 14.39 0.00 0.00 2.39
773 805 4.603946 GCCCGGTCCGAGGTATGC 62.604 72.222 14.39 1.56 0.00 3.14
775 807 3.925090 CCGGTCCGAGGTATGCCC 61.925 72.222 14.39 0.00 34.57 5.36
777 809 2.822399 GGTCCGAGGTATGCCCAG 59.178 66.667 0.00 0.00 34.66 4.45
778 810 2.808206 GGTCCGAGGTATGCCCAGG 61.808 68.421 0.00 0.00 34.66 4.45
779 811 2.064581 GTCCGAGGTATGCCCAGGT 61.065 63.158 10.25 0.00 34.60 4.00
782 814 0.834612 CCGAGGTATGCCCAGGTAAA 59.165 55.000 0.00 0.00 34.66 2.01
783 815 1.210967 CCGAGGTATGCCCAGGTAAAA 59.789 52.381 0.00 0.00 34.66 1.52
784 816 2.285977 CGAGGTATGCCCAGGTAAAAC 58.714 52.381 0.00 0.00 34.66 2.43
786 818 3.133362 CGAGGTATGCCCAGGTAAAACTA 59.867 47.826 0.00 0.00 34.66 2.24
788 820 4.109320 AGGTATGCCCAGGTAAAACTAGT 58.891 43.478 0.00 0.00 34.66 2.57
791 823 7.077745 AGGTATGCCCAGGTAAAACTAGTATA 58.922 38.462 0.00 0.00 34.66 1.47
827 859 4.119136 GGATTGGTTGTTTGGTTTCACTG 58.881 43.478 0.00 0.00 0.00 3.66
838 870 2.102252 TGGTTTCACTGTTCCATTTGCC 59.898 45.455 0.00 0.00 0.00 4.52
844 876 1.202879 ACTGTTCCATTTGCCTCGGAA 60.203 47.619 0.00 0.00 36.46 4.30
869 1912 4.374702 CACGCGTTCTGCACCTGC 62.375 66.667 10.22 0.00 46.97 4.85
964 2034 0.179020 CACAGCCACAGGTTCTTCCA 60.179 55.000 0.00 0.00 39.02 3.53
972 2042 0.535102 CAGGTTCTTCCACTGCCGTT 60.535 55.000 0.00 0.00 39.02 4.44
1233 3504 2.726351 GGAGGAGGGGCAGTTCGAG 61.726 68.421 0.00 0.00 0.00 4.04
1528 3829 4.407365 CCCTGTAATCACCATTAATCCCC 58.593 47.826 0.00 0.00 0.00 4.81
1539 3840 6.011628 TCACCATTAATCCCCTCTCTTTCTTT 60.012 38.462 0.00 0.00 0.00 2.52
1542 3843 7.122048 CCATTAATCCCCTCTCTTTCTTTCTT 58.878 38.462 0.00 0.00 0.00 2.52
1543 3844 7.617329 CCATTAATCCCCTCTCTTTCTTTCTTT 59.383 37.037 0.00 0.00 0.00 2.52
1544 3845 8.681806 CATTAATCCCCTCTCTTTCTTTCTTTC 58.318 37.037 0.00 0.00 0.00 2.62
1548 3849 4.566697 CCCCTCTCTTTCTTTCTTTCTCCC 60.567 50.000 0.00 0.00 0.00 4.30
1555 3856 3.784701 TCTTTCTTTCTCCCTCGATCG 57.215 47.619 9.36 9.36 0.00 3.69
1558 3859 3.992260 TTCTTTCTCCCTCGATCGATC 57.008 47.619 19.78 15.68 0.00 3.69
1812 4157 0.809636 CAACCTCGATACATGCGGCA 60.810 55.000 4.58 4.58 0.00 5.69
1857 4227 2.639839 ACAGCTCACTTGATACCCTTGT 59.360 45.455 0.00 0.00 0.00 3.16
1998 4399 4.351938 CCGACACGGCCGAGTTCA 62.352 66.667 35.90 0.00 41.17 3.18
2024 4436 1.768275 TCACACTGTCACTGAATGGGT 59.232 47.619 0.00 0.00 0.00 4.51
2170 4589 3.709880 CTTCCGGTATGTCGCGCCA 62.710 63.158 0.00 0.00 0.00 5.69
2250 4715 2.079170 TTGGGCAGACACATTTTCCA 57.921 45.000 0.00 0.00 0.00 3.53
2251 4716 2.307496 TGGGCAGACACATTTTCCAT 57.693 45.000 0.00 0.00 0.00 3.41
2328 4808 4.494199 GGTTGTTCAGAAGTTGACAGTTCG 60.494 45.833 0.00 0.00 37.42 3.95
2330 4810 4.250464 TGTTCAGAAGTTGACAGTTCGTT 58.750 39.130 0.00 0.00 37.42 3.85
2332 4812 4.386867 TCAGAAGTTGACAGTTCGTTCT 57.613 40.909 0.00 0.00 37.42 3.01
2342 4823 4.216687 TGACAGTTCGTTCTTTTGGTTTGT 59.783 37.500 0.00 0.00 0.00 2.83
2359 4844 2.175878 TGTGCAGGAGAAGAAGAAGC 57.824 50.000 0.00 0.00 0.00 3.86
2360 4845 1.271054 TGTGCAGGAGAAGAAGAAGCC 60.271 52.381 0.00 0.00 0.00 4.35
2622 5130 1.165907 TCAGTCAGCAAGCAAACCCG 61.166 55.000 0.00 0.00 0.00 5.28
2705 5247 1.443025 CGTGTATGTGCCGACGTCA 60.443 57.895 17.16 0.00 0.00 4.35
2864 5406 5.809001 TGCAACATTCTAACTCTTCTCCAT 58.191 37.500 0.00 0.00 0.00 3.41
2885 5435 2.290896 TGCCAAACCTGAATACCTGAGG 60.291 50.000 0.00 0.00 0.00 3.86
2946 5497 3.451665 AGGTACTGGTCGCACGTT 58.548 55.556 0.00 0.00 37.18 3.99
3312 5989 8.027771 ACCGATAGTAGCTGTATATAAAAGCAC 58.972 37.037 16.89 13.19 39.47 4.40
3342 6019 3.007473 TCTCTTCAAACCAAAACCGGT 57.993 42.857 0.00 0.00 42.71 5.28
3367 6044 5.800296 TCCGATTTTCACTCAAATCCAGTA 58.200 37.500 1.52 0.00 39.20 2.74
3383 6060 9.467258 CAAATCCAGTACATAAATGCTAAATGG 57.533 33.333 0.00 0.00 0.00 3.16
3589 6266 6.006275 AGGGCAATACATCTTAATGTCAGT 57.994 37.500 0.00 0.00 42.59 3.41
3669 6407 1.005450 TCCTGGTAAAACTGGATGCCC 59.995 52.381 0.00 0.00 34.09 5.36
3824 6570 9.364989 CAGTTCCAGTGAATTTTTACAAAGAAA 57.635 29.630 0.00 0.00 31.98 2.52
3869 6615 2.512885 CGCAGCATTCATGTTCAGAAC 58.487 47.619 6.32 6.32 0.00 3.01
3895 6641 8.398665 CAATACAGCTTTCTGGGTAATTAAGAC 58.601 37.037 0.00 0.00 44.54 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.612676 TTCTTCTTCGACTCCGTCCA 58.387 50.000 0.00 0.00 37.05 4.02
138 139 1.671901 CCTTTGTTGTTGGCACCGGT 61.672 55.000 0.00 0.00 0.00 5.28
154 186 1.351350 GTTGTAGGACAAGCCCTCCTT 59.649 52.381 0.00 0.00 39.00 3.36
156 188 0.984995 AGTTGTAGGACAAGCCCTCC 59.015 55.000 0.00 0.00 39.00 4.30
157 189 3.097614 TCTAGTTGTAGGACAAGCCCTC 58.902 50.000 0.00 0.00 39.00 4.30
172 204 5.187967 CCCATTTACTCACTCACCTCTAGTT 59.812 44.000 0.00 0.00 0.00 2.24
173 205 4.712337 CCCATTTACTCACTCACCTCTAGT 59.288 45.833 0.00 0.00 0.00 2.57
185 217 1.633432 CCTCACCACCCCATTTACTCA 59.367 52.381 0.00 0.00 0.00 3.41
186 218 1.064685 CCCTCACCACCCCATTTACTC 60.065 57.143 0.00 0.00 0.00 2.59
208 240 2.123468 GGGGGTGGCGCCAAATAT 60.123 61.111 34.66 0.00 38.28 1.28
240 272 4.880426 GGAGATGGCGGGAGGGGA 62.880 72.222 0.00 0.00 0.00 4.81
287 319 1.644409 GTGAAAAACGAAGACGCGAC 58.356 50.000 15.93 6.86 43.96 5.19
288 320 0.578211 GGTGAAAAACGAAGACGCGA 59.422 50.000 15.93 0.00 43.96 5.87
303 335 2.602676 GCCAGGCTAAGTGGGGTGA 61.603 63.158 3.29 0.00 35.39 4.02
305 337 2.204151 AGCCAGGCTAAGTGGGGT 60.204 61.111 14.18 0.00 36.99 4.95
325 357 1.729149 GCTCGAATTTGCCGTTTCCAG 60.729 52.381 0.00 0.00 0.00 3.86
336 368 1.635663 CGCTGGGAACGCTCGAATTT 61.636 55.000 0.00 0.00 0.00 1.82
337 369 2.100631 CGCTGGGAACGCTCGAATT 61.101 57.895 0.00 0.00 0.00 2.17
384 416 1.079543 ACCTGACTCGCATCTGCAC 60.080 57.895 2.72 0.00 42.21 4.57
388 420 1.803943 GTCGACCTGACTCGCATCT 59.196 57.895 3.51 0.00 44.58 2.90
424 456 1.133025 CCGTGCAGGATGAAAATGGAC 59.867 52.381 8.24 0.00 45.00 4.02
429 461 1.976474 GGCCCGTGCAGGATGAAAA 60.976 57.895 8.24 0.00 45.00 2.29
431 463 3.329889 AGGCCCGTGCAGGATGAA 61.330 61.111 8.24 0.00 45.00 2.57
446 478 2.123428 GCTGCATAGCCCAACCAGG 61.123 63.158 0.00 0.00 44.33 4.45
457 489 1.308047 CGCATTTGGTAGGCTGCATA 58.692 50.000 4.64 0.00 34.29 3.14
458 490 2.008268 GCGCATTTGGTAGGCTGCAT 62.008 55.000 0.30 0.00 34.29 3.96
460 492 2.102946 GCGCATTTGGTAGGCTGC 59.897 61.111 0.30 0.00 0.00 5.25
462 494 1.632018 TAGGGCGCATTTGGTAGGCT 61.632 55.000 10.83 0.00 0.00 4.58
463 495 1.153046 TAGGGCGCATTTGGTAGGC 60.153 57.895 10.83 0.00 0.00 3.93
464 496 0.180406 ACTAGGGCGCATTTGGTAGG 59.820 55.000 10.83 0.00 0.00 3.18
466 498 2.112998 ACTACTAGGGCGCATTTGGTA 58.887 47.619 10.83 5.43 0.00 3.25
468 500 2.902705 TACTACTAGGGCGCATTTGG 57.097 50.000 10.83 0.00 0.00 3.28
470 502 3.571401 ACGTATACTACTAGGGCGCATTT 59.429 43.478 10.83 0.00 0.00 2.32
473 505 1.875514 CACGTATACTACTAGGGCGCA 59.124 52.381 10.83 0.00 0.00 6.09
474 506 1.198637 CCACGTATACTACTAGGGCGC 59.801 57.143 0.00 0.00 0.00 6.53
475 507 1.198637 GCCACGTATACTACTAGGGCG 59.801 57.143 0.56 0.00 30.92 6.13
476 508 1.543358 GGCCACGTATACTACTAGGGC 59.457 57.143 0.00 4.36 38.14 5.19
478 510 3.192844 CCATGGCCACGTATACTACTAGG 59.807 52.174 8.16 0.00 0.00 3.02
480 512 3.159472 CCCATGGCCACGTATACTACTA 58.841 50.000 8.16 0.00 0.00 1.82
483 515 0.682852 GCCCATGGCCACGTATACTA 59.317 55.000 8.16 0.00 44.06 1.82
484 516 1.450211 GCCCATGGCCACGTATACT 59.550 57.895 8.16 0.00 44.06 2.12
485 517 4.058797 GCCCATGGCCACGTATAC 57.941 61.111 8.16 0.00 44.06 1.47
512 544 3.432051 GATCGGGTCAGGCCGTCTG 62.432 68.421 0.00 0.00 44.68 3.51
526 558 2.251642 GGATTTTCGGGCCGGATCG 61.252 63.158 27.98 8.29 0.00 3.69
527 559 1.897137 GGGATTTTCGGGCCGGATC 60.897 63.158 27.98 23.91 0.00 3.36
529 561 4.476752 CGGGATTTTCGGGCCGGA 62.477 66.667 27.98 16.80 0.00 5.14
530 562 4.476752 TCGGGATTTTCGGGCCGG 62.477 66.667 27.98 7.20 0.00 6.13
531 563 2.895372 CTCGGGATTTTCGGGCCG 60.895 66.667 22.51 22.51 0.00 6.13
534 566 2.895372 CGGCTCGGGATTTTCGGG 60.895 66.667 0.00 0.00 0.00 5.14
535 567 1.883084 CTCGGCTCGGGATTTTCGG 60.883 63.158 0.00 0.00 0.00 4.30
536 568 2.526120 GCTCGGCTCGGGATTTTCG 61.526 63.158 0.00 0.00 0.00 3.46
537 569 1.153349 AGCTCGGCTCGGGATTTTC 60.153 57.895 0.00 0.00 30.62 2.29
538 570 1.450312 CAGCTCGGCTCGGGATTTT 60.450 57.895 0.00 0.00 36.40 1.82
541 573 3.222855 CTCAGCTCGGCTCGGGAT 61.223 66.667 0.00 0.00 36.40 3.85
551 583 2.588314 CATGCTCGGGCTCAGCTC 60.588 66.667 9.62 0.00 37.79 4.09
554 586 3.769369 ATGGCATGCTCGGGCTCAG 62.769 63.158 18.92 0.00 39.59 3.35
555 587 3.762429 GATGGCATGCTCGGGCTCA 62.762 63.158 18.92 5.25 39.59 4.26
569 601 1.406539 CTCAATTTTCAGGCCCGATGG 59.593 52.381 0.00 0.00 0.00 3.51
573 605 1.250154 TGGCTCAATTTTCAGGCCCG 61.250 55.000 0.00 0.00 41.84 6.13
576 608 0.893447 AGCTGGCTCAATTTTCAGGC 59.107 50.000 0.00 0.00 35.76 4.85
577 609 1.203994 CCAGCTGGCTCAATTTTCAGG 59.796 52.381 22.33 0.00 0.00 3.86
579 611 1.259609 CCCAGCTGGCTCAATTTTCA 58.740 50.000 28.39 0.00 0.00 2.69
619 651 4.434593 GGCTAAAATCATGTTTTGCGCAAG 60.435 41.667 23.68 11.49 39.26 4.01
620 652 3.431572 GGCTAAAATCATGTTTTGCGCAA 59.568 39.130 21.02 21.02 39.26 4.85
624 656 5.234972 GGCTATGGCTAAAATCATGTTTTGC 59.765 40.000 0.00 10.05 38.15 3.68
625 657 6.339730 TGGCTATGGCTAAAATCATGTTTTG 58.660 36.000 0.00 2.41 38.73 2.44
626 658 6.407299 CCTGGCTATGGCTAAAATCATGTTTT 60.407 38.462 0.00 9.78 38.73 2.43
632 664 2.586425 GCCTGGCTATGGCTAAAATCA 58.414 47.619 12.43 0.00 46.38 2.57
658 690 3.192922 CGAGCCCGTAAAAGCCCG 61.193 66.667 0.00 0.00 0.00 6.13
661 693 3.506096 GCCCGAGCCCGTAAAAGC 61.506 66.667 0.00 0.00 0.00 3.51
671 703 1.270358 CCTACTAAATCAGGCCCGAGC 60.270 57.143 0.00 0.00 38.76 5.03
672 704 2.821991 CCTACTAAATCAGGCCCGAG 57.178 55.000 0.00 0.00 0.00 4.63
678 710 1.269621 CGTCGGGCCTACTAAATCAGG 60.270 57.143 0.84 0.00 34.85 3.86
680 712 0.748450 CCGTCGGGCCTACTAAATCA 59.252 55.000 2.34 0.00 0.00 2.57
681 713 3.582743 CCGTCGGGCCTACTAAATC 57.417 57.895 2.34 0.00 0.00 2.17
716 748 3.015516 GTTGAAAACCCAGGCTCGA 57.984 52.632 0.00 0.00 42.21 4.04
755 787 3.925090 CATACCTCGGACCGGGCC 61.925 72.222 19.81 19.81 0.00 5.80
756 788 4.603946 GCATACCTCGGACCGGGC 62.604 72.222 15.25 0.21 0.00 6.13
757 789 3.925090 GGCATACCTCGGACCGGG 61.925 72.222 15.25 11.29 0.00 5.73
758 790 3.925090 GGGCATACCTCGGACCGG 61.925 72.222 15.25 0.00 35.85 5.28
760 792 2.808206 CCTGGGCATACCTCGGACC 61.808 68.421 0.00 0.00 41.11 4.46
761 793 0.757935 TACCTGGGCATACCTCGGAC 60.758 60.000 0.00 0.00 41.11 4.79
762 794 0.031917 TTACCTGGGCATACCTCGGA 60.032 55.000 0.00 0.00 41.11 4.55
763 795 0.834612 TTTACCTGGGCATACCTCGG 59.165 55.000 0.00 0.00 41.11 4.63
764 796 2.093128 AGTTTTACCTGGGCATACCTCG 60.093 50.000 0.00 0.00 41.11 4.63
765 797 3.646736 AGTTTTACCTGGGCATACCTC 57.353 47.619 0.00 0.00 41.11 3.85
767 799 4.498894 ACTAGTTTTACCTGGGCATACC 57.501 45.455 0.00 0.00 40.81 2.73
771 803 7.128077 ACTACTATACTAGTTTTACCTGGGCA 58.872 38.462 0.00 0.00 40.14 5.36
772 804 7.594351 ACTACTATACTAGTTTTACCTGGGC 57.406 40.000 0.00 0.00 40.14 5.36
806 838 4.754322 ACAGTGAAACCAAACAACCAATC 58.246 39.130 0.00 0.00 37.80 2.67
810 842 3.056465 TGGAACAGTGAAACCAAACAACC 60.056 43.478 0.00 0.00 37.80 3.77
838 870 2.805353 CGTGGAGTGCGTTCCGAG 60.805 66.667 2.29 0.00 40.27 4.63
869 1912 1.384989 ATCGCCACGTCTCTACCTGG 61.385 60.000 0.00 0.00 35.54 4.45
871 1914 1.948145 CTTATCGCCACGTCTCTACCT 59.052 52.381 0.00 0.00 0.00 3.08
944 2012 0.179018 GGAAGAACCTGTGGCTGTGT 60.179 55.000 0.00 0.00 35.41 3.72
989 2059 2.356313 GATCCATGGCGCGTCGAT 60.356 61.111 6.96 2.09 0.00 3.59
1233 3504 1.003718 GTACCACTGGTCCAGCCAC 60.004 63.158 19.40 7.78 43.61 5.01
1528 3829 5.047660 TCGAGGGAGAAAGAAAGAAAGAGAG 60.048 44.000 0.00 0.00 0.00 3.20
1539 3840 2.881513 CTGATCGATCGAGGGAGAAAGA 59.118 50.000 23.84 0.00 0.00 2.52
1542 3843 2.640316 TCTGATCGATCGAGGGAGAA 57.360 50.000 23.84 3.92 0.00 2.87
1543 3844 2.640316 TTCTGATCGATCGAGGGAGA 57.360 50.000 23.84 19.11 0.00 3.71
1544 3845 3.376540 GTTTTCTGATCGATCGAGGGAG 58.623 50.000 23.84 17.25 0.00 4.30
1548 3849 5.530519 TTTTGGTTTTCTGATCGATCGAG 57.469 39.130 23.84 17.05 0.00 4.04
1555 3856 7.160726 TCCATTTCCATTTTGGTTTTCTGATC 58.839 34.615 0.00 0.00 39.03 2.92
1558 3859 7.586747 CAATCCATTTCCATTTTGGTTTTCTG 58.413 34.615 0.00 0.00 39.03 3.02
1812 4157 1.210204 TTCTGCAATGGAGGGAGGCT 61.210 55.000 1.05 0.00 0.00 4.58
1857 4227 2.494471 CTCCACCAACACATCGTACCTA 59.506 50.000 0.00 0.00 0.00 3.08
1990 4391 2.733552 CAGTGTGAACTGATGAACTCGG 59.266 50.000 0.00 0.00 39.99 4.63
1996 4397 3.384467 TCAGTGACAGTGTGAACTGATGA 59.616 43.478 24.59 11.08 38.59 2.92
1997 4398 3.721035 TCAGTGACAGTGTGAACTGATG 58.279 45.455 24.59 9.44 38.59 3.07
1998 4399 4.406648 TTCAGTGACAGTGTGAACTGAT 57.593 40.909 27.06 1.25 40.94 2.90
2024 4436 5.895636 AGAACAACAACTGAATCAACACA 57.104 34.783 0.00 0.00 0.00 3.72
2170 4589 1.141881 CGAGCCGTAGAAGGTGCAT 59.858 57.895 0.00 0.00 0.00 3.96
2285 4750 2.289945 CCCCTGTTTGTTCTCCTCTGAG 60.290 54.545 0.00 0.00 40.17 3.35
2328 4808 3.130340 TCTCCTGCACAAACCAAAAGAAC 59.870 43.478 0.00 0.00 0.00 3.01
2330 4810 3.011566 TCTCCTGCACAAACCAAAAGA 57.988 42.857 0.00 0.00 0.00 2.52
2332 4812 3.360867 TCTTCTCCTGCACAAACCAAAA 58.639 40.909 0.00 0.00 0.00 2.44
2342 4823 0.036952 CGGCTTCTTCTTCTCCTGCA 60.037 55.000 0.00 0.00 0.00 4.41
2359 4844 3.197790 CATGAACTGAGGCGGCGG 61.198 66.667 9.78 0.29 0.00 6.13
2360 4845 3.869272 GCATGAACTGAGGCGGCG 61.869 66.667 0.51 0.51 0.00 6.46
2606 5114 2.050077 GCGGGTTTGCTTGCTGAC 60.050 61.111 0.00 0.00 0.00 3.51
2622 5130 2.751806 CCTGAAATGAGGGAAGAACAGC 59.248 50.000 0.00 0.00 0.00 4.40
2705 5247 1.939974 CGATCACCATGTTGTCCGAT 58.060 50.000 0.00 0.00 0.00 4.18
2864 5406 2.290896 CCTCAGGTATTCAGGTTTGGCA 60.291 50.000 0.00 0.00 0.00 4.92
2885 5435 3.634397 TCAGATGGGGTTCACTGAATC 57.366 47.619 0.00 0.00 36.63 2.52
3342 6019 5.534654 ACTGGATTTGAGTGAAAATCGGAAA 59.465 36.000 4.16 0.00 44.20 3.13
3367 6044 6.849085 TTGTCACCCATTTAGCATTTATGT 57.151 33.333 0.00 0.00 0.00 2.29
3509 6186 3.450457 ACCTGGATGTGCTTTTGAAAACA 59.550 39.130 0.00 0.00 0.00 2.83
3515 6192 7.489113 GTGAAATAATACCTGGATGTGCTTTTG 59.511 37.037 0.00 0.00 0.00 2.44
3516 6193 7.397192 AGTGAAATAATACCTGGATGTGCTTTT 59.603 33.333 0.00 0.00 0.00 2.27
3518 6195 6.426587 AGTGAAATAATACCTGGATGTGCTT 58.573 36.000 0.00 0.00 0.00 3.91
3529 6206 9.836076 GGTAGTTTTGTGAAGTGAAATAATACC 57.164 33.333 0.00 0.00 0.00 2.73
3589 6266 0.687920 TTGGGGAAGCGATGTACACA 59.312 50.000 0.00 0.00 0.00 3.72
3628 6307 5.654650 AGGAATTCAGTAACCAACAACACAA 59.345 36.000 7.93 0.00 0.00 3.33
3638 6317 6.072119 CCAGTTTTACCAGGAATTCAGTAACC 60.072 42.308 7.93 5.69 0.00 2.85
3669 6407 2.421424 CTGAATCCGCCTCCTCAAAAAG 59.579 50.000 0.00 0.00 0.00 2.27
3683 6421 6.479884 AGGCCATAGACATAATTCTGAATCC 58.520 40.000 5.01 0.00 0.00 3.01
3824 6570 6.461231 GGGTCGTCTGTACTTTGATAGCTAAT 60.461 42.308 0.00 0.00 0.00 1.73
3869 6615 8.398665 GTCTTAATTACCCAGAAAGCTGTATTG 58.601 37.037 0.00 0.00 40.63 1.90
3980 6726 3.003482 TGCATCAACTTTTTGCCAATTGC 59.997 39.130 0.00 0.00 41.77 3.56
3982 6728 4.883006 ACTTGCATCAACTTTTTGCCAATT 59.117 33.333 0.00 0.00 35.51 2.32


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

AutoCloner maintained by Alex Coulton.