Multiple sequence alignment - TraesCS6A01G168500

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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 TraesCS6A01G168500 chr6A 100.000 2561 0 0 1 2561 175559738 175562298 0.000000e+00 4730.0
1 TraesCS6A01G168500 chr6A 87.644 866 61 28 875 1702 175621805 175622662 0.000000e+00 965.0
2 TraesCS6A01G168500 chr6D 93.178 1290 48 11 787 2046 134676300 134677579 0.000000e+00 1858.0
3 TraesCS6A01G168500 chr6D 92.646 1183 59 7 886 2046 134241134 134242310 0.000000e+00 1677.0
4 TraesCS6A01G168500 chr6D 90.889 922 47 13 2 890 134235666 134236583 0.000000e+00 1203.0
5 TraesCS6A01G168500 chr6D 84.623 1008 87 40 750 1702 134279186 134280180 0.000000e+00 941.0
6 TraesCS6A01G168500 chr6D 86.159 867 79 29 864 1702 134682542 134683395 0.000000e+00 898.0
7 TraesCS6A01G168500 chr6D 92.990 485 19 5 1 470 134674070 134674554 0.000000e+00 693.0
8 TraesCS6A01G168500 chr6D 93.824 340 20 1 2047 2386 134242358 134242696 6.320000e-141 510.0
9 TraesCS6A01G168500 chr6D 93.559 295 18 1 2095 2389 134677693 134677986 3.030000e-119 438.0
10 TraesCS6A01G168500 chr6D 96.273 161 4 1 640 800 134675052 134675210 1.950000e-66 263.0
11 TraesCS6A01G168500 chr6D 93.023 172 12 0 2390 2561 80593233 80593404 4.230000e-63 252.0
12 TraesCS6A01G168500 chr6D 95.652 138 6 0 502 639 134674553 134674690 3.320000e-54 222.0
13 TraesCS6A01G168500 chr6B 89.663 832 66 14 900 1716 233010403 233011229 0.000000e+00 1042.0
14 TraesCS6A01G168500 chr6B 83.531 1178 102 49 766 1865 233013632 233014795 0.000000e+00 1016.0
15 TraesCS6A01G168500 chr6B 78.362 818 101 46 790 1561 233023505 233024292 6.460000e-126 460.0
16 TraesCS6A01G168500 chr1D 95.833 168 7 0 2389 2556 339342518 339342351 3.250000e-69 272.0
17 TraesCS6A01G168500 chr1D 94.118 170 10 0 2390 2559 131304622 131304453 2.530000e-65 259.0
18 TraesCS6A01G168500 chr5A 95.238 168 8 0 2390 2557 578848837 578848670 1.510000e-67 267.0
19 TraesCS6A01G168500 chr5A 94.578 166 9 0 2390 2555 29919295 29919130 9.090000e-65 257.0
20 TraesCS6A01G168500 chr4D 93.714 175 10 1 2385 2559 495635368 495635195 7.030000e-66 261.0
21 TraesCS6A01G168500 chr1A 94.578 166 9 0 2386 2551 45820037 45819872 9.090000e-65 257.0
22 TraesCS6A01G168500 chr3D 94.048 168 10 0 2389 2556 300145901 300146068 3.270000e-64 255.0
23 TraesCS6A01G168500 chr7A 93.529 170 11 0 2390 2559 497051785 497051616 1.180000e-63 254.0
24 TraesCS6A01G168500 chr2A 73.585 265 52 12 2121 2382 383594302 383594053 4.540000e-13 86.1


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 TraesCS6A01G168500 chr6A 175559738 175562298 2560 False 4730.0 4730 100.0000 1 2561 1 chr6A.!!$F1 2560
1 TraesCS6A01G168500 chr6A 175621805 175622662 857 False 965.0 965 87.6440 875 1702 1 chr6A.!!$F2 827
2 TraesCS6A01G168500 chr6D 134235666 134236583 917 False 1203.0 1203 90.8890 2 890 1 chr6D.!!$F2 888
3 TraesCS6A01G168500 chr6D 134241134 134242696 1562 False 1093.5 1677 93.2350 886 2386 2 chr6D.!!$F5 1500
4 TraesCS6A01G168500 chr6D 134279186 134280180 994 False 941.0 941 84.6230 750 1702 1 chr6D.!!$F3 952
5 TraesCS6A01G168500 chr6D 134682542 134683395 853 False 898.0 898 86.1590 864 1702 1 chr6D.!!$F4 838
6 TraesCS6A01G168500 chr6D 134674070 134677986 3916 False 694.8 1858 94.3304 1 2389 5 chr6D.!!$F6 2388
7 TraesCS6A01G168500 chr6B 233010403 233014795 4392 False 1029.0 1042 86.5970 766 1865 2 chr6B.!!$F2 1099
8 TraesCS6A01G168500 chr6B 233023505 233024292 787 False 460.0 460 78.3620 790 1561 1 chr6B.!!$F1 771

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
897 3830 0.252696 TCCTATGCTCACCACCCACT 60.253 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 5630 0.039035 TATTGGAGTTGTGGCCCACC 59.961 55.0 12.25 0.0 32.73 4.61 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
488 520 3.833645 CGCAATGCTGCCATGCCT 61.834 61.111 17.49 0.00 46.56 4.75
493 525 1.550130 AATGCTGCCATGCCTTTGCT 61.550 50.000 0.00 0.00 38.71 3.91
494 526 1.550130 ATGCTGCCATGCCTTTGCTT 61.550 50.000 0.00 0.00 38.71 3.91
499 531 0.389426 GCCATGCCTTTGCTTGTCAG 60.389 55.000 0.00 0.00 40.15 3.51
546 578 4.039703 CGGCATCTCATTGCTTTTGTATG 58.960 43.478 0.00 0.00 42.38 2.39
556 588 1.890573 GCTTTTGTATGCCTGTCCCCA 60.891 52.381 0.00 0.00 0.00 4.96
598 630 2.025321 TGGGTAGGAAATTGGAGCTTCC 60.025 50.000 0.00 0.00 41.32 3.46
829 3739 2.296752 TGCATGTTCACAATTGGACAGG 59.703 45.455 10.83 13.38 44.92 4.00
842 3752 1.276622 GGACAGGAAGCAAGGGACTA 58.723 55.000 0.00 0.00 38.49 2.59
881 3814 6.498651 TGTCTCCTTTTCTTATCACTTCTCCT 59.501 38.462 0.00 0.00 0.00 3.69
897 3830 0.252696 TCCTATGCTCACCACCCACT 60.253 55.000 0.00 0.00 0.00 4.00
930 3876 3.242739 CGCCACCATCCTTTTTAATCTCG 60.243 47.826 0.00 0.00 0.00 4.04
974 3932 7.793927 ACTCGAAAGAAAAATCTCACTTTCT 57.206 32.000 0.15 0.00 43.08 2.52
1368 4361 1.966451 CGGCGGCAAGAAGAACCTT 60.966 57.895 10.53 0.00 0.00 3.50
1667 4699 4.260139 GCCTAGGCCTAAGTCAATAGTC 57.740 50.000 24.19 0.00 34.56 2.59
1670 4702 5.740513 GCCTAGGCCTAAGTCAATAGTCTTG 60.741 48.000 24.19 0.00 34.56 3.02
1733 4786 0.394352 CTCCCGGTGGCAAAAGCTAT 60.394 55.000 0.00 0.00 0.00 2.97
1734 4787 0.039035 TCCCGGTGGCAAAAGCTATT 59.961 50.000 0.00 0.00 0.00 1.73
1760 4813 5.984926 TGAATGCCAAAAACTGATTCTTGAC 59.015 36.000 0.00 0.00 0.00 3.18
1807 4863 8.345565 TGGTATTTTGTTTATTTGCGCAAAATT 58.654 25.926 36.42 24.43 44.24 1.82
1942 5001 3.425525 GTCGTGATGTATGCAAGTATCCG 59.574 47.826 0.00 1.82 0.00 4.18
1964 5023 5.238432 CCGCAATATAATGGTGCACTTCTTA 59.762 40.000 17.98 11.99 38.19 2.10
2012 5071 9.405587 CTTACGGCATTCTTCTTTAAAATGAAA 57.594 29.630 1.79 0.00 33.22 2.69
2073 5179 6.371548 TGAAAAAGGAATCGATGACAACTAGG 59.628 38.462 0.00 0.00 0.00 3.02
2084 5190 5.636903 ATGACAACTAGGCATCCATAAGT 57.363 39.130 0.00 0.00 44.97 2.24
2206 5340 1.349627 GCCTGCATCATCGTCGTTG 59.650 57.895 0.00 0.00 0.00 4.10
2239 5373 3.607741 TCTTCCTCAATAGACGAGTCGT 58.392 45.455 20.02 20.02 45.10 4.34
2286 5420 7.778083 TGTATATGTACTTCATGTCCGAAACT 58.222 34.615 1.08 0.00 37.91 2.66
2295 5429 3.616821 TCATGTCCGAAACTATTGCTTCG 59.383 43.478 5.83 5.83 43.12 3.79
2392 5526 4.111016 CTGCGCGACGGACCTGTA 62.111 66.667 12.10 0.00 0.00 2.74
2393 5527 4.111016 TGCGCGACGGACCTGTAG 62.111 66.667 12.10 0.00 0.00 2.74
2394 5528 3.807538 GCGCGACGGACCTGTAGA 61.808 66.667 12.10 0.00 0.00 2.59
2395 5529 2.099831 CGCGACGGACCTGTAGAC 59.900 66.667 0.00 0.00 0.00 2.59
2396 5530 2.099831 GCGACGGACCTGTAGACG 59.900 66.667 0.00 0.00 0.00 4.18
2397 5531 2.393768 GCGACGGACCTGTAGACGA 61.394 63.158 0.00 0.00 0.00 4.20
2398 5532 1.714414 CGACGGACCTGTAGACGAG 59.286 63.158 0.00 0.00 0.00 4.18
2399 5533 0.738762 CGACGGACCTGTAGACGAGA 60.739 60.000 0.00 0.00 0.00 4.04
2400 5534 1.446907 GACGGACCTGTAGACGAGAA 58.553 55.000 0.00 0.00 0.00 2.87
2401 5535 1.808945 GACGGACCTGTAGACGAGAAA 59.191 52.381 0.00 0.00 0.00 2.52
2402 5536 1.811359 ACGGACCTGTAGACGAGAAAG 59.189 52.381 0.00 0.00 0.00 2.62
2403 5537 1.811359 CGGACCTGTAGACGAGAAAGT 59.189 52.381 0.00 0.00 0.00 2.66
2404 5538 2.228343 CGGACCTGTAGACGAGAAAGTT 59.772 50.000 0.00 0.00 0.00 2.66
2405 5539 3.305199 CGGACCTGTAGACGAGAAAGTTT 60.305 47.826 0.00 0.00 0.00 2.66
2406 5540 3.988517 GGACCTGTAGACGAGAAAGTTTG 59.011 47.826 0.00 0.00 0.00 2.93
2407 5541 3.391049 ACCTGTAGACGAGAAAGTTTGC 58.609 45.455 0.00 0.00 0.00 3.68
2408 5542 3.181469 ACCTGTAGACGAGAAAGTTTGCA 60.181 43.478 0.00 0.00 0.00 4.08
2409 5543 3.807622 CCTGTAGACGAGAAAGTTTGCAA 59.192 43.478 0.00 0.00 0.00 4.08
2410 5544 4.452455 CCTGTAGACGAGAAAGTTTGCAAT 59.548 41.667 0.00 0.00 0.00 3.56
2411 5545 5.637810 CCTGTAGACGAGAAAGTTTGCAATA 59.362 40.000 0.00 0.00 0.00 1.90
2412 5546 6.401153 CCTGTAGACGAGAAAGTTTGCAATAC 60.401 42.308 0.00 1.64 0.00 1.89
2413 5547 5.986741 TGTAGACGAGAAAGTTTGCAATACA 59.013 36.000 0.00 0.00 0.00 2.29
2414 5548 6.480651 TGTAGACGAGAAAGTTTGCAATACAA 59.519 34.615 0.00 0.00 36.13 2.41
2415 5549 6.560253 AGACGAGAAAGTTTGCAATACAAT 57.440 33.333 0.00 0.00 38.31 2.71
2416 5550 7.667043 AGACGAGAAAGTTTGCAATACAATA 57.333 32.000 0.00 0.00 38.31 1.90
2417 5551 8.094798 AGACGAGAAAGTTTGCAATACAATAA 57.905 30.769 0.00 0.00 38.31 1.40
2418 5552 8.564574 AGACGAGAAAGTTTGCAATACAATAAA 58.435 29.630 0.00 0.00 38.31 1.40
2419 5553 9.176181 GACGAGAAAGTTTGCAATACAATAAAA 57.824 29.630 0.00 0.00 38.31 1.52
2420 5554 9.180678 ACGAGAAAGTTTGCAATACAATAAAAG 57.819 29.630 0.00 0.00 38.31 2.27
2421 5555 9.180678 CGAGAAAGTTTGCAATACAATAAAAGT 57.819 29.630 0.00 0.00 38.31 2.66
2435 5569 7.790782 ACAATAAAAGTTGTATTGATGGGGT 57.209 32.000 25.99 5.85 40.35 4.95
2436 5570 7.610865 ACAATAAAAGTTGTATTGATGGGGTG 58.389 34.615 25.99 4.64 40.35 4.61
2437 5571 4.535526 AAAAGTTGTATTGATGGGGTGC 57.464 40.909 0.00 0.00 0.00 5.01
2438 5572 3.456380 AAGTTGTATTGATGGGGTGCT 57.544 42.857 0.00 0.00 0.00 4.40
2439 5573 2.726821 AGTTGTATTGATGGGGTGCTG 58.273 47.619 0.00 0.00 0.00 4.41
2440 5574 1.750778 GTTGTATTGATGGGGTGCTGG 59.249 52.381 0.00 0.00 0.00 4.85
2441 5575 0.998928 TGTATTGATGGGGTGCTGGT 59.001 50.000 0.00 0.00 0.00 4.00
2442 5576 1.340893 TGTATTGATGGGGTGCTGGTG 60.341 52.381 0.00 0.00 0.00 4.17
2443 5577 0.395586 TATTGATGGGGTGCTGGTGC 60.396 55.000 0.00 0.00 40.20 5.01
2459 5593 6.926313 TGCTGGTGCACGTATATATAATACA 58.074 36.000 11.45 0.00 45.31 2.29
2460 5594 7.379750 TGCTGGTGCACGTATATATAATACAA 58.620 34.615 11.45 0.00 45.31 2.41
2461 5595 7.873505 TGCTGGTGCACGTATATATAATACAAA 59.126 33.333 11.45 0.00 45.31 2.83
2462 5596 8.380644 GCTGGTGCACGTATATATAATACAAAG 58.619 37.037 11.45 0.00 39.41 2.77
2463 5597 8.766000 TGGTGCACGTATATATAATACAAAGG 57.234 34.615 11.45 0.00 0.00 3.11
2464 5598 7.820386 TGGTGCACGTATATATAATACAAAGGG 59.180 37.037 11.45 0.00 0.00 3.95
2465 5599 8.036575 GGTGCACGTATATATAATACAAAGGGA 58.963 37.037 11.45 0.00 0.00 4.20
2466 5600 9.084164 GTGCACGTATATATAATACAAAGGGAG 57.916 37.037 0.00 0.00 0.00 4.30
2467 5601 8.255206 TGCACGTATATATAATACAAAGGGAGG 58.745 37.037 0.00 0.00 0.00 4.30
2468 5602 7.224167 GCACGTATATATAATACAAAGGGAGGC 59.776 40.741 0.00 0.00 0.00 4.70
2469 5603 7.709613 CACGTATATATAATACAAAGGGAGGCC 59.290 40.741 0.00 0.00 0.00 5.19
2470 5604 7.622479 ACGTATATATAATACAAAGGGAGGCCT 59.378 37.037 3.86 3.86 0.00 5.19
2471 5605 8.142551 CGTATATATAATACAAAGGGAGGCCTC 58.857 40.741 25.59 25.59 0.00 4.70
2472 5606 9.214962 GTATATATAATACAAAGGGAGGCCTCT 57.785 37.037 31.36 13.79 0.00 3.69
2474 5608 9.975464 ATATATAATACAAAGGGAGGCCTCTAT 57.025 33.333 31.36 19.03 0.00 1.98
2475 5609 4.984146 AATACAAAGGGAGGCCTCTATC 57.016 45.455 31.36 20.30 0.00 2.08
2476 5610 2.577772 ACAAAGGGAGGCCTCTATCT 57.422 50.000 31.36 22.05 0.00 1.98
2477 5611 2.403561 ACAAAGGGAGGCCTCTATCTC 58.596 52.381 31.36 14.75 0.00 2.75
2478 5612 2.293184 ACAAAGGGAGGCCTCTATCTCA 60.293 50.000 31.36 0.00 0.00 3.27
2479 5613 2.774234 CAAAGGGAGGCCTCTATCTCAA 59.226 50.000 31.36 0.00 0.00 3.02
2480 5614 2.095604 AGGGAGGCCTCTATCTCAAC 57.904 55.000 31.36 12.50 0.00 3.18
2481 5615 1.578215 AGGGAGGCCTCTATCTCAACT 59.422 52.381 31.36 13.68 0.00 3.16
2482 5616 2.792370 AGGGAGGCCTCTATCTCAACTA 59.208 50.000 31.36 0.00 0.00 2.24
2483 5617 3.404425 AGGGAGGCCTCTATCTCAACTAT 59.596 47.826 31.36 3.65 0.00 2.12
2484 5618 4.608473 AGGGAGGCCTCTATCTCAACTATA 59.392 45.833 31.36 0.00 0.00 1.31
2485 5619 4.707934 GGGAGGCCTCTATCTCAACTATAC 59.292 50.000 31.36 9.84 0.00 1.47
2486 5620 5.326069 GGAGGCCTCTATCTCAACTATACA 58.674 45.833 31.36 0.00 0.00 2.29
2487 5621 5.775701 GGAGGCCTCTATCTCAACTATACAA 59.224 44.000 31.36 0.00 0.00 2.41
2488 5622 6.071616 GGAGGCCTCTATCTCAACTATACAAG 60.072 46.154 31.36 0.00 0.00 3.16
2489 5623 6.615617 AGGCCTCTATCTCAACTATACAAGA 58.384 40.000 0.00 0.00 0.00 3.02
2490 5624 6.492087 AGGCCTCTATCTCAACTATACAAGAC 59.508 42.308 0.00 0.00 0.00 3.01
2491 5625 6.492087 GGCCTCTATCTCAACTATACAAGACT 59.508 42.308 0.00 0.00 0.00 3.24
2492 5626 7.666388 GGCCTCTATCTCAACTATACAAGACTA 59.334 40.741 0.00 0.00 0.00 2.59
2493 5627 8.726988 GCCTCTATCTCAACTATACAAGACTAG 58.273 40.741 0.00 0.00 0.00 2.57
2494 5628 9.226606 CCTCTATCTCAACTATACAAGACTAGG 57.773 40.741 0.00 0.00 0.00 3.02
2497 5631 9.226606 CTATCTCAACTATACAAGACTAGGAGG 57.773 40.741 0.00 0.00 0.00 4.30
2498 5632 6.971340 TCTCAACTATACAAGACTAGGAGGT 58.029 40.000 0.00 0.00 0.00 3.85
2499 5633 6.829298 TCTCAACTATACAAGACTAGGAGGTG 59.171 42.308 0.00 0.00 0.00 4.00
2500 5634 5.892119 TCAACTATACAAGACTAGGAGGTGG 59.108 44.000 0.00 0.00 0.00 4.61
2501 5635 4.805744 ACTATACAAGACTAGGAGGTGGG 58.194 47.826 0.00 0.00 0.00 4.61
2502 5636 1.861982 TACAAGACTAGGAGGTGGGC 58.138 55.000 0.00 0.00 0.00 5.36
2503 5637 0.910088 ACAAGACTAGGAGGTGGGCC 60.910 60.000 0.00 0.00 0.00 5.80
2504 5638 0.909610 CAAGACTAGGAGGTGGGCCA 60.910 60.000 0.00 0.00 37.19 5.36
2505 5639 0.910088 AAGACTAGGAGGTGGGCCAC 60.910 60.000 28.69 28.69 37.19 5.01
2506 5640 1.612442 GACTAGGAGGTGGGCCACA 60.612 63.158 35.69 15.84 35.86 4.17
2507 5641 1.151899 ACTAGGAGGTGGGCCACAA 60.152 57.895 35.69 15.37 35.86 3.33
2508 5642 1.299976 CTAGGAGGTGGGCCACAAC 59.700 63.158 35.69 26.73 35.86 3.32
2512 5646 2.776526 AGGTGGGCCACAACTCCA 60.777 61.111 35.69 0.00 46.59 3.86
2513 5647 2.197324 GGTGGGCCACAACTCCAA 59.803 61.111 35.69 0.00 35.86 3.53
2514 5648 1.228862 GGTGGGCCACAACTCCAAT 60.229 57.895 35.69 0.00 35.86 3.16
2515 5649 0.039035 GGTGGGCCACAACTCCAATA 59.961 55.000 35.69 0.00 35.86 1.90
2516 5650 1.173913 GTGGGCCACAACTCCAATAC 58.826 55.000 31.26 0.00 34.08 1.89
2517 5651 0.774276 TGGGCCACAACTCCAATACA 59.226 50.000 0.00 0.00 0.00 2.29
2518 5652 1.173913 GGGCCACAACTCCAATACAC 58.826 55.000 4.39 0.00 0.00 2.90
2519 5653 0.802494 GGCCACAACTCCAATACACG 59.198 55.000 0.00 0.00 0.00 4.49
2520 5654 1.519408 GCCACAACTCCAATACACGT 58.481 50.000 0.00 0.00 0.00 4.49
2521 5655 1.196808 GCCACAACTCCAATACACGTG 59.803 52.381 15.48 15.48 0.00 4.49
2522 5656 1.196808 CCACAACTCCAATACACGTGC 59.803 52.381 17.22 0.00 0.00 5.34
2523 5657 1.870402 CACAACTCCAATACACGTGCA 59.130 47.619 17.22 2.06 0.00 4.57
2524 5658 2.289274 CACAACTCCAATACACGTGCAA 59.711 45.455 17.22 4.26 0.00 4.08
2525 5659 3.058293 CACAACTCCAATACACGTGCAAT 60.058 43.478 17.22 6.83 0.00 3.56
2526 5660 4.153296 CACAACTCCAATACACGTGCAATA 59.847 41.667 17.22 0.36 0.00 1.90
2527 5661 4.153475 ACAACTCCAATACACGTGCAATAC 59.847 41.667 17.22 0.00 0.00 1.89
2528 5662 3.932822 ACTCCAATACACGTGCAATACA 58.067 40.909 17.22 0.00 0.00 2.29
2529 5663 4.320023 ACTCCAATACACGTGCAATACAA 58.680 39.130 17.22 0.00 0.00 2.41
2530 5664 4.757657 ACTCCAATACACGTGCAATACAAA 59.242 37.500 17.22 0.00 0.00 2.83
2531 5665 5.239744 ACTCCAATACACGTGCAATACAAAA 59.760 36.000 17.22 0.00 0.00 2.44
2532 5666 5.453648 TCCAATACACGTGCAATACAAAAC 58.546 37.500 17.22 0.00 0.00 2.43
2533 5667 5.008712 TCCAATACACGTGCAATACAAAACA 59.991 36.000 17.22 0.00 0.00 2.83
2534 5668 5.116377 CCAATACACGTGCAATACAAAACAC 59.884 40.000 17.22 0.00 0.00 3.32
2535 5669 3.766676 ACACGTGCAATACAAAACACA 57.233 38.095 17.22 0.00 33.23 3.72
2536 5670 4.300189 ACACGTGCAATACAAAACACAT 57.700 36.364 17.22 0.00 33.23 3.21
2537 5671 5.425577 ACACGTGCAATACAAAACACATA 57.574 34.783 17.22 0.00 33.23 2.29
2538 5672 5.209240 ACACGTGCAATACAAAACACATAC 58.791 37.500 17.22 0.00 33.23 2.39
2539 5673 5.008217 ACACGTGCAATACAAAACACATACT 59.992 36.000 17.22 0.00 33.23 2.12
2540 5674 5.563751 CACGTGCAATACAAAACACATACTC 59.436 40.000 0.82 0.00 33.23 2.59
2541 5675 5.237561 ACGTGCAATACAAAACACATACTCA 59.762 36.000 0.00 0.00 33.23 3.41
2542 5676 6.139435 CGTGCAATACAAAACACATACTCAA 58.861 36.000 0.00 0.00 33.23 3.02
2543 5677 6.086241 CGTGCAATACAAAACACATACTCAAC 59.914 38.462 0.00 0.00 33.23 3.18
2544 5678 6.915300 GTGCAATACAAAACACATACTCAACA 59.085 34.615 0.00 0.00 33.23 3.33
2545 5679 6.915300 TGCAATACAAAACACATACTCAACAC 59.085 34.615 0.00 0.00 0.00 3.32
2546 5680 6.362283 GCAATACAAAACACATACTCAACACC 59.638 38.462 0.00 0.00 0.00 4.16
2547 5681 4.911514 ACAAAACACATACTCAACACCC 57.088 40.909 0.00 0.00 0.00 4.61
2548 5682 3.634910 ACAAAACACATACTCAACACCCC 59.365 43.478 0.00 0.00 0.00 4.95
2549 5683 2.579410 AACACATACTCAACACCCCC 57.421 50.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.182507 ACAAAGAGGTAGTTCCAACACATA 57.817 37.500 0.00 0.00 39.02 2.29
146 147 1.021390 CCGGACGCTTGCTCTTCAAT 61.021 55.000 0.00 0.00 33.57 2.57
373 405 2.125766 GACCCCCAGTGAACACCTCC 62.126 65.000 1.11 0.00 0.00 4.30
556 588 4.925054 CCATTTGCAAAACACGATTCTCAT 59.075 37.500 17.19 0.00 0.00 2.90
598 630 1.068125 CACACATCACATTGCAGTGGG 60.068 52.381 14.25 9.93 39.93 4.61
728 1123 3.300066 GTCGTAAGTGTCGAACTGCATAC 59.700 47.826 0.00 0.00 39.81 2.39
729 1124 3.189910 AGTCGTAAGTGTCGAACTGCATA 59.810 43.478 0.00 0.00 39.81 3.14
829 3739 2.563179 TGTCACTCTAGTCCCTTGCTTC 59.437 50.000 0.00 0.00 0.00 3.86
881 3814 1.656587 AGAAGTGGGTGGTGAGCATA 58.343 50.000 0.00 0.00 0.00 3.14
897 3830 7.490657 AAAGGATGGTGGCGTATATATAGAA 57.509 36.000 0.00 0.00 0.00 2.10
974 3932 1.937223 CTTTGCGGTTGTGTAGTGTGA 59.063 47.619 0.00 0.00 0.00 3.58
1584 4601 6.172630 AGGAACAAAAATCAAAAGCACTGTT 58.827 32.000 0.00 0.00 0.00 3.16
1656 4688 9.956720 CAAAAATCAGTTCAAGACTATTGACTT 57.043 29.630 0.00 0.00 36.65 3.01
1657 4689 9.125026 ACAAAAATCAGTTCAAGACTATTGACT 57.875 29.630 0.00 0.00 36.65 3.41
1667 4699 9.846248 CCCTAAATCTACAAAAATCAGTTCAAG 57.154 33.333 0.00 0.00 0.00 3.02
1670 4702 7.772166 CCCCCTAAATCTACAAAAATCAGTTC 58.228 38.462 0.00 0.00 0.00 3.01
1733 4786 8.366401 TCAAGAATCAGTTTTTGGCATTCATAA 58.634 29.630 0.00 0.00 32.06 1.90
1734 4787 7.814107 GTCAAGAATCAGTTTTTGGCATTCATA 59.186 33.333 0.00 0.00 34.99 2.15
1760 4813 6.349300 ACCATGCAGATTAGTAGGTAACAAG 58.651 40.000 0.00 0.00 41.41 3.16
1882 4941 3.270877 GAGTACCTCCGCATGTCAAAAT 58.729 45.455 0.00 0.00 0.00 1.82
1942 5001 7.965107 GCTATAAGAAGTGCACCATTATATTGC 59.035 37.037 14.63 14.66 36.76 3.56
1964 5023 3.366052 ACGGTTGGATTCTTTGGCTAT 57.634 42.857 0.00 0.00 0.00 2.97
2012 5071 2.290916 CGTGCAGTCCTACGATGACTAT 59.709 50.000 6.06 0.00 41.02 2.12
2084 5190 1.528129 TGGCGCATGTGTATTTGACA 58.472 45.000 10.83 0.00 34.94 3.58
2206 5340 2.771089 TGAGGAAGATTATGCGGATGC 58.229 47.619 0.00 0.00 43.20 3.91
2239 5373 1.921243 CACTATGTTGCGTCATCCGA 58.079 50.000 0.00 0.00 39.56 4.55
2286 5420 4.801330 TTGTCTCCTCTTCGAAGCAATA 57.199 40.909 20.56 2.05 0.00 1.90
2312 5446 5.414454 GTGTTTGGTGGAATGTCTATGCTAA 59.586 40.000 0.00 0.00 0.00 3.09
2318 5452 5.888724 TGAAAAGTGTTTGGTGGAATGTCTA 59.111 36.000 0.00 0.00 0.00 2.59
2321 5455 5.413309 TTGAAAAGTGTTTGGTGGAATGT 57.587 34.783 0.00 0.00 0.00 2.71
2366 5500 1.299089 CGTCGCGCAGGTATCATCA 60.299 57.895 8.75 0.00 0.00 3.07
2389 5523 5.986741 TGTATTGCAAACTTTCTCGTCTACA 59.013 36.000 1.71 0.00 0.00 2.74
2390 5524 6.462073 TGTATTGCAAACTTTCTCGTCTAC 57.538 37.500 1.71 0.00 0.00 2.59
2391 5525 7.667043 ATTGTATTGCAAACTTTCTCGTCTA 57.333 32.000 1.71 0.00 40.91 2.59
2392 5526 6.560253 ATTGTATTGCAAACTTTCTCGTCT 57.440 33.333 1.71 0.00 40.91 4.18
2393 5527 8.722342 TTTATTGTATTGCAAACTTTCTCGTC 57.278 30.769 1.71 0.00 40.91 4.20
2394 5528 9.180678 CTTTTATTGTATTGCAAACTTTCTCGT 57.819 29.630 1.71 0.00 40.91 4.18
2395 5529 9.180678 ACTTTTATTGTATTGCAAACTTTCTCG 57.819 29.630 1.71 0.00 40.91 4.04
2410 5544 8.744652 CACCCCATCAATACAACTTTTATTGTA 58.255 33.333 7.31 1.16 46.33 2.41
2411 5545 7.610865 CACCCCATCAATACAACTTTTATTGT 58.389 34.615 7.31 0.00 44.87 2.71
2412 5546 6.534793 GCACCCCATCAATACAACTTTTATTG 59.465 38.462 2.42 2.42 38.00 1.90
2413 5547 6.440328 AGCACCCCATCAATACAACTTTTATT 59.560 34.615 0.00 0.00 0.00 1.40
2414 5548 5.957774 AGCACCCCATCAATACAACTTTTAT 59.042 36.000 0.00 0.00 0.00 1.40
2415 5549 5.184864 CAGCACCCCATCAATACAACTTTTA 59.815 40.000 0.00 0.00 0.00 1.52
2416 5550 4.021192 CAGCACCCCATCAATACAACTTTT 60.021 41.667 0.00 0.00 0.00 2.27
2417 5551 3.511146 CAGCACCCCATCAATACAACTTT 59.489 43.478 0.00 0.00 0.00 2.66
2418 5552 3.091545 CAGCACCCCATCAATACAACTT 58.908 45.455 0.00 0.00 0.00 2.66
2419 5553 2.621407 CCAGCACCCCATCAATACAACT 60.621 50.000 0.00 0.00 0.00 3.16
2420 5554 1.750778 CCAGCACCCCATCAATACAAC 59.249 52.381 0.00 0.00 0.00 3.32
2421 5555 1.357420 ACCAGCACCCCATCAATACAA 59.643 47.619 0.00 0.00 0.00 2.41
2422 5556 0.998928 ACCAGCACCCCATCAATACA 59.001 50.000 0.00 0.00 0.00 2.29
2423 5557 1.392589 CACCAGCACCCCATCAATAC 58.607 55.000 0.00 0.00 0.00 1.89
2424 5558 0.395586 GCACCAGCACCCCATCAATA 60.396 55.000 0.00 0.00 41.58 1.90
2425 5559 1.683365 GCACCAGCACCCCATCAAT 60.683 57.895 0.00 0.00 41.58 2.57
2426 5560 2.283101 GCACCAGCACCCCATCAA 60.283 61.111 0.00 0.00 41.58 2.57
2436 5570 7.821595 TTGTATTATATATACGTGCACCAGC 57.178 36.000 12.15 0.00 42.57 4.85
2437 5571 8.869897 CCTTTGTATTATATATACGTGCACCAG 58.130 37.037 12.15 0.00 0.00 4.00
2438 5572 7.820386 CCCTTTGTATTATATATACGTGCACCA 59.180 37.037 12.15 0.00 0.00 4.17
2439 5573 8.036575 TCCCTTTGTATTATATATACGTGCACC 58.963 37.037 12.15 0.00 0.00 5.01
2440 5574 8.991243 TCCCTTTGTATTATATATACGTGCAC 57.009 34.615 6.82 6.82 0.00 4.57
2441 5575 8.255206 CCTCCCTTTGTATTATATATACGTGCA 58.745 37.037 0.00 0.00 0.00 4.57
2442 5576 7.224167 GCCTCCCTTTGTATTATATATACGTGC 59.776 40.741 0.00 0.00 0.00 5.34
2443 5577 7.709613 GGCCTCCCTTTGTATTATATATACGTG 59.290 40.741 0.00 0.00 0.00 4.49
2444 5578 7.622479 AGGCCTCCCTTTGTATTATATATACGT 59.378 37.037 0.00 0.00 38.74 3.57
2445 5579 8.019656 AGGCCTCCCTTTGTATTATATATACG 57.980 38.462 0.00 0.00 38.74 3.06
2446 5580 9.214962 AGAGGCCTCCCTTTGTATTATATATAC 57.785 37.037 29.54 0.00 43.12 1.47
2448 5582 9.975464 ATAGAGGCCTCCCTTTGTATTATATAT 57.025 33.333 29.54 11.84 43.12 0.86
2449 5583 9.435570 GATAGAGGCCTCCCTTTGTATTATATA 57.564 37.037 29.54 9.96 43.12 0.86
2450 5584 8.132285 AGATAGAGGCCTCCCTTTGTATTATAT 58.868 37.037 29.54 14.94 43.12 0.86
2451 5585 7.488205 AGATAGAGGCCTCCCTTTGTATTATA 58.512 38.462 29.54 10.62 43.12 0.98
2452 5586 6.335115 AGATAGAGGCCTCCCTTTGTATTAT 58.665 40.000 29.54 16.17 43.12 1.28
2453 5587 5.727630 AGATAGAGGCCTCCCTTTGTATTA 58.272 41.667 29.54 11.91 43.12 0.98
2454 5588 4.571951 AGATAGAGGCCTCCCTTTGTATT 58.428 43.478 29.54 9.89 43.12 1.89
2455 5589 4.164204 GAGATAGAGGCCTCCCTTTGTAT 58.836 47.826 29.54 18.34 43.12 2.29
2456 5590 3.052109 TGAGATAGAGGCCTCCCTTTGTA 60.052 47.826 29.54 14.18 43.12 2.41
2457 5591 2.293184 TGAGATAGAGGCCTCCCTTTGT 60.293 50.000 29.54 12.24 43.12 2.83
2458 5592 2.402564 TGAGATAGAGGCCTCCCTTTG 58.597 52.381 29.54 0.00 43.12 2.77
2459 5593 2.774809 GTTGAGATAGAGGCCTCCCTTT 59.225 50.000 29.54 13.43 43.12 3.11
2460 5594 2.022527 AGTTGAGATAGAGGCCTCCCTT 60.023 50.000 29.54 13.83 43.12 3.95
2461 5595 1.578215 AGTTGAGATAGAGGCCTCCCT 59.422 52.381 29.54 22.45 46.74 4.20
2462 5596 2.095604 AGTTGAGATAGAGGCCTCCC 57.904 55.000 29.54 18.12 0.00 4.30
2463 5597 5.326069 TGTATAGTTGAGATAGAGGCCTCC 58.674 45.833 29.54 14.29 0.00 4.30
2464 5598 6.717540 TCTTGTATAGTTGAGATAGAGGCCTC 59.282 42.308 26.22 26.22 0.00 4.70
2465 5599 6.492087 GTCTTGTATAGTTGAGATAGAGGCCT 59.508 42.308 3.86 3.86 0.00 5.19
2466 5600 6.492087 AGTCTTGTATAGTTGAGATAGAGGCC 59.508 42.308 0.00 0.00 0.00 5.19
2467 5601 7.519032 AGTCTTGTATAGTTGAGATAGAGGC 57.481 40.000 0.00 0.00 0.00 4.70
2468 5602 9.226606 CCTAGTCTTGTATAGTTGAGATAGAGG 57.773 40.741 0.00 0.00 0.00 3.69
2471 5605 9.226606 CCTCCTAGTCTTGTATAGTTGAGATAG 57.773 40.741 0.00 0.00 0.00 2.08
2472 5606 8.725256 ACCTCCTAGTCTTGTATAGTTGAGATA 58.275 37.037 0.00 0.00 0.00 1.98
2473 5607 7.504238 CACCTCCTAGTCTTGTATAGTTGAGAT 59.496 40.741 0.00 0.00 0.00 2.75
2474 5608 6.829298 CACCTCCTAGTCTTGTATAGTTGAGA 59.171 42.308 0.00 0.00 0.00 3.27
2475 5609 6.039941 CCACCTCCTAGTCTTGTATAGTTGAG 59.960 46.154 0.00 0.00 0.00 3.02
2476 5610 5.892119 CCACCTCCTAGTCTTGTATAGTTGA 59.108 44.000 0.00 0.00 0.00 3.18
2477 5611 5.069251 CCCACCTCCTAGTCTTGTATAGTTG 59.931 48.000 0.00 0.00 0.00 3.16
2478 5612 5.209659 CCCACCTCCTAGTCTTGTATAGTT 58.790 45.833 0.00 0.00 0.00 2.24
2479 5613 4.805744 CCCACCTCCTAGTCTTGTATAGT 58.194 47.826 0.00 0.00 0.00 2.12
2480 5614 3.574826 GCCCACCTCCTAGTCTTGTATAG 59.425 52.174 0.00 0.00 0.00 1.31
2481 5615 3.573695 GCCCACCTCCTAGTCTTGTATA 58.426 50.000 0.00 0.00 0.00 1.47
2482 5616 2.399580 GCCCACCTCCTAGTCTTGTAT 58.600 52.381 0.00 0.00 0.00 2.29
2483 5617 1.621622 GGCCCACCTCCTAGTCTTGTA 60.622 57.143 0.00 0.00 0.00 2.41
2484 5618 0.910088 GGCCCACCTCCTAGTCTTGT 60.910 60.000 0.00 0.00 0.00 3.16
2485 5619 0.909610 TGGCCCACCTCCTAGTCTTG 60.910 60.000 0.00 0.00 36.63 3.02
2486 5620 0.910088 GTGGCCCACCTCCTAGTCTT 60.910 60.000 1.17 0.00 36.63 3.01
2487 5621 1.306226 GTGGCCCACCTCCTAGTCT 60.306 63.158 1.17 0.00 36.63 3.24
2488 5622 1.198759 TTGTGGCCCACCTCCTAGTC 61.199 60.000 12.25 0.00 36.63 2.59
2489 5623 1.151899 TTGTGGCCCACCTCCTAGT 60.152 57.895 12.25 0.00 36.63 2.57
2490 5624 1.201429 AGTTGTGGCCCACCTCCTAG 61.201 60.000 12.25 0.00 36.63 3.02
2491 5625 1.151899 AGTTGTGGCCCACCTCCTA 60.152 57.895 12.25 0.00 36.63 2.94
2492 5626 2.450502 AGTTGTGGCCCACCTCCT 60.451 61.111 12.25 1.06 36.63 3.69
2493 5627 2.034221 GAGTTGTGGCCCACCTCC 59.966 66.667 12.25 0.00 36.63 4.30
2494 5628 2.034221 GGAGTTGTGGCCCACCTC 59.966 66.667 12.25 11.32 36.63 3.85
2495 5629 1.729267 ATTGGAGTTGTGGCCCACCT 61.729 55.000 12.25 1.20 36.63 4.00
2496 5630 0.039035 TATTGGAGTTGTGGCCCACC 59.961 55.000 12.25 0.00 32.73 4.61
2497 5631 1.173913 GTATTGGAGTTGTGGCCCAC 58.826 55.000 7.01 7.01 34.56 4.61
2498 5632 0.774276 TGTATTGGAGTTGTGGCCCA 59.226 50.000 0.00 0.00 0.00 5.36
2499 5633 1.173913 GTGTATTGGAGTTGTGGCCC 58.826 55.000 0.00 0.00 0.00 5.80
2500 5634 0.802494 CGTGTATTGGAGTTGTGGCC 59.198 55.000 0.00 0.00 0.00 5.36
2501 5635 1.196808 CACGTGTATTGGAGTTGTGGC 59.803 52.381 7.58 0.00 0.00 5.01
2502 5636 1.196808 GCACGTGTATTGGAGTTGTGG 59.803 52.381 18.38 0.00 0.00 4.17
2503 5637 1.870402 TGCACGTGTATTGGAGTTGTG 59.130 47.619 18.38 0.00 0.00 3.33
2504 5638 2.248280 TGCACGTGTATTGGAGTTGT 57.752 45.000 18.38 0.00 0.00 3.32
2505 5639 3.829886 ATTGCACGTGTATTGGAGTTG 57.170 42.857 18.38 0.00 0.00 3.16
2506 5640 4.320023 TGTATTGCACGTGTATTGGAGTT 58.680 39.130 18.38 0.00 0.00 3.01
2507 5641 3.932822 TGTATTGCACGTGTATTGGAGT 58.067 40.909 18.38 0.00 0.00 3.85
2508 5642 4.937696 TTGTATTGCACGTGTATTGGAG 57.062 40.909 18.38 0.00 0.00 3.86
2509 5643 5.008712 TGTTTTGTATTGCACGTGTATTGGA 59.991 36.000 18.38 0.00 0.00 3.53
2510 5644 5.116377 GTGTTTTGTATTGCACGTGTATTGG 59.884 40.000 18.38 0.00 0.00 3.16
2511 5645 5.683302 TGTGTTTTGTATTGCACGTGTATTG 59.317 36.000 18.38 0.00 34.86 1.90
2512 5646 5.822278 TGTGTTTTGTATTGCACGTGTATT 58.178 33.333 18.38 11.76 34.86 1.89
2513 5647 5.425577 TGTGTTTTGTATTGCACGTGTAT 57.574 34.783 18.38 13.28 34.86 2.29
2514 5648 4.877323 TGTGTTTTGTATTGCACGTGTA 57.123 36.364 18.38 10.46 34.86 2.90
2515 5649 3.766676 TGTGTTTTGTATTGCACGTGT 57.233 38.095 18.38 0.00 34.86 4.49
2516 5650 5.448438 AGTATGTGTTTTGTATTGCACGTG 58.552 37.500 12.28 12.28 34.86 4.49
2517 5651 5.237561 TGAGTATGTGTTTTGTATTGCACGT 59.762 36.000 0.00 0.00 34.86 4.49
2518 5652 5.684850 TGAGTATGTGTTTTGTATTGCACG 58.315 37.500 0.00 0.00 34.86 5.34
2519 5653 6.915300 TGTTGAGTATGTGTTTTGTATTGCAC 59.085 34.615 0.00 0.00 0.00 4.57
2520 5654 6.915300 GTGTTGAGTATGTGTTTTGTATTGCA 59.085 34.615 0.00 0.00 0.00 4.08
2521 5655 6.362283 GGTGTTGAGTATGTGTTTTGTATTGC 59.638 38.462 0.00 0.00 0.00 3.56
2522 5656 6.861055 GGGTGTTGAGTATGTGTTTTGTATTG 59.139 38.462 0.00 0.00 0.00 1.90
2523 5657 6.015772 GGGGTGTTGAGTATGTGTTTTGTATT 60.016 38.462 0.00 0.00 0.00 1.89
2524 5658 5.475564 GGGGTGTTGAGTATGTGTTTTGTAT 59.524 40.000 0.00 0.00 0.00 2.29
2525 5659 4.822896 GGGGTGTTGAGTATGTGTTTTGTA 59.177 41.667 0.00 0.00 0.00 2.41
2526 5660 3.634910 GGGGTGTTGAGTATGTGTTTTGT 59.365 43.478 0.00 0.00 0.00 2.83
2527 5661 3.005367 GGGGGTGTTGAGTATGTGTTTTG 59.995 47.826 0.00 0.00 0.00 2.44
2528 5662 3.227614 GGGGGTGTTGAGTATGTGTTTT 58.772 45.455 0.00 0.00 0.00 2.43
2529 5663 2.871453 GGGGGTGTTGAGTATGTGTTT 58.129 47.619 0.00 0.00 0.00 2.83
2530 5664 2.579410 GGGGGTGTTGAGTATGTGTT 57.421 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.