Multiple sequence alignment - TraesCS1A01G205300

Loading Multiple Alignment...

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 TraesCS1A01G205300 chr1A 100.000 5250 0 0 1 5250 367869805 367875054 0.000000e+00 9696
1 TraesCS1A01G205300 chr1B 95.635 2268 86 11 170 2434 396356437 396358694 0.000000e+00 3627
2 TraesCS1A01G205300 chr1B 92.133 2199 101 25 2525 4662 396358695 396360882 0.000000e+00 3037
3 TraesCS1A01G205300 chr1B 95.893 487 16 2 4767 5250 396361204 396361689 0.000000e+00 785
4 TraesCS1A01G205300 chr1D 97.061 1599 28 10 3664 5250 294741701 294743292 0.000000e+00 2675
5 TraesCS1A01G205300 chr1D 96.279 1317 35 9 72 1385 294738098 294739403 0.000000e+00 2148
6 TraesCS1A01G205300 chr1D 96.060 1142 28 7 2526 3665 294740484 294741610 0.000000e+00 1844
7 TraesCS1A01G205300 chr1D 94.972 1074 41 4 1369 2433 294739417 294740486 0.000000e+00 1672
8 TraesCS1A01G205300 chr4A 99.000 100 1 0 2432 2531 584930961 584931060 4.180000e-41 180
9 TraesCS1A01G205300 chr4A 96.117 103 4 0 2429 2531 650040981 650040879 9.040000e-38 169
10 TraesCS1A01G205300 chr5D 96.226 106 4 0 2432 2537 343630406 343630511 1.940000e-39 174
11 TraesCS1A01G205300 chr5B 97.030 101 3 0 2431 2531 635839276 635839176 2.510000e-38 171
12 TraesCS1A01G205300 chr5B 96.040 101 4 0 2431 2531 33626336 33626236 1.170000e-36 165
13 TraesCS1A01G205300 chr5B 95.192 104 5 0 2428 2531 223038240 223038343 1.170000e-36 165
14 TraesCS1A01G205300 chr3B 95.192 104 5 0 2428 2531 164060808 164060911 1.170000e-36 165
15 TraesCS1A01G205300 chr3B 94.340 106 5 1 2424 2529 99666449 99666553 1.510000e-35 161
16 TraesCS1A01G205300 chr7B 89.600 125 10 3 2421 2543 94256078 94256201 7.040000e-34 156


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 TraesCS1A01G205300 chr1A 367869805 367875054 5249 False 9696.00 9696 100.000000 1 5250 1 chr1A.!!$F1 5249
1 TraesCS1A01G205300 chr1B 396356437 396361689 5252 False 2483.00 3627 94.553667 170 5250 3 chr1B.!!$F1 5080
2 TraesCS1A01G205300 chr1D 294738098 294743292 5194 False 2084.75 2675 96.093000 72 5250 4 chr1D.!!$F1 5178

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
37 38 0.322546 CCAGAAGCGCCTTAGGGTTT 60.323 55.0 2.29 0.00 34.45 3.27 F
1006 1011 0.246086 GCGGAGATGAGGGATGCTAG 59.754 60.0 0.00 0.00 0.00 3.42 F
1200 1205 0.485543 TGGAGGACCACAGTCAGGTA 59.514 55.0 0.00 0.00 45.48 3.08 F
1613 1649 2.169832 TGTTCAGAGCAGTTGCCTAC 57.830 50.0 0.00 0.00 43.38 3.18 F
2754 2799 0.108329 GCCATGCAATTGCTTCTGCT 60.108 50.0 29.37 6.23 42.66 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1205 1.260538 TGCTCAGCGACCCAGATTCT 61.261 55.000 0.00 0.00 0.00 2.40 R
2070 2113 0.624254 TCTCTCGCCTAACCTCCTCA 59.376 55.000 0.00 0.00 0.00 3.86 R
2518 2562 1.072489 GCCTTGGCTAATACTCCCTCC 59.928 57.143 4.11 0.00 0.00 4.30 R
3468 3513 1.002792 GACCGGCAGAGAAACACAAAC 60.003 52.381 0.00 0.00 0.00 2.93 R
4695 5010 1.267806 ACAGAAAACCGATGCTGCAAG 59.732 47.619 6.36 3.78 31.74 4.01 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
17 18 4.496670 CAAACCCTAGAGTCGCCG 57.503 61.111 0.00 0.00 0.00 6.46
18 19 1.810030 CAAACCCTAGAGTCGCCGC 60.810 63.158 0.00 0.00 0.00 6.53
19 20 3.015312 AAACCCTAGAGTCGCCGCC 62.015 63.158 0.00 0.00 0.00 6.13
20 21 4.753662 ACCCTAGAGTCGCCGCCA 62.754 66.667 0.00 0.00 0.00 5.69
21 22 3.905678 CCCTAGAGTCGCCGCCAG 61.906 72.222 0.00 0.00 0.00 4.85
22 23 2.829003 CCTAGAGTCGCCGCCAGA 60.829 66.667 0.00 0.00 0.00 3.86
23 24 2.415608 CCTAGAGTCGCCGCCAGAA 61.416 63.158 0.00 0.00 0.00 3.02
24 25 1.064946 CTAGAGTCGCCGCCAGAAG 59.935 63.158 0.00 0.00 0.00 2.85
25 26 2.945398 CTAGAGTCGCCGCCAGAAGC 62.945 65.000 0.00 0.00 38.52 3.86
34 35 2.514824 GCCAGAAGCGCCTTAGGG 60.515 66.667 2.29 0.22 0.00 3.53
35 36 2.990479 CCAGAAGCGCCTTAGGGT 59.010 61.111 2.29 0.00 34.45 4.34
36 37 1.299976 CCAGAAGCGCCTTAGGGTT 59.700 57.895 2.29 0.00 34.45 4.11
37 38 0.322546 CCAGAAGCGCCTTAGGGTTT 60.323 55.000 2.29 0.00 34.45 3.27
38 39 1.087501 CAGAAGCGCCTTAGGGTTTC 58.912 55.000 2.29 4.49 43.61 2.78
39 40 0.391263 AGAAGCGCCTTAGGGTTTCG 60.391 55.000 2.29 0.00 46.44 3.46
40 41 0.390735 GAAGCGCCTTAGGGTTTCGA 60.391 55.000 2.29 0.00 36.65 3.71
41 42 0.672711 AAGCGCCTTAGGGTTTCGAC 60.673 55.000 2.29 0.00 34.45 4.20
42 43 2.450345 GCGCCTTAGGGTTTCGACG 61.450 63.158 0.00 0.00 34.45 5.12
43 44 1.213537 CGCCTTAGGGTTTCGACGA 59.786 57.895 0.00 0.00 34.45 4.20
44 45 0.388907 CGCCTTAGGGTTTCGACGAA 60.389 55.000 6.10 6.10 34.45 3.85
45 46 1.799544 GCCTTAGGGTTTCGACGAAA 58.200 50.000 18.66 18.66 34.45 3.46
46 47 2.145536 GCCTTAGGGTTTCGACGAAAA 58.854 47.619 23.59 6.47 33.14 2.29
47 48 2.549329 GCCTTAGGGTTTCGACGAAAAA 59.451 45.455 23.59 13.54 33.14 1.94
48 49 3.364664 GCCTTAGGGTTTCGACGAAAAAG 60.365 47.826 23.59 20.80 33.14 2.27
49 50 3.811497 CCTTAGGGTTTCGACGAAAAAGT 59.189 43.478 23.59 13.26 33.14 2.66
50 51 4.084171 CCTTAGGGTTTCGACGAAAAAGTC 60.084 45.833 23.59 11.68 33.14 3.01
59 60 1.411089 CGAAAAAGTCGGTCGAGCG 59.589 57.895 29.80 29.80 46.45 5.03
60 61 1.000233 CGAAAAAGTCGGTCGAGCGA 61.000 55.000 33.45 33.45 46.45 4.93
61 62 0.708918 GAAAAAGTCGGTCGAGCGAG 59.291 55.000 36.97 11.60 0.00 5.03
62 63 1.282930 AAAAAGTCGGTCGAGCGAGC 61.283 55.000 36.97 28.78 39.05 5.03
68 69 2.202623 GGTCGAGCGAGCGAACAT 60.203 61.111 9.99 0.00 46.68 2.71
69 70 1.063649 GGTCGAGCGAGCGAACATA 59.936 57.895 9.99 0.00 46.68 2.29
70 71 0.524816 GGTCGAGCGAGCGAACATAA 60.525 55.000 9.99 0.00 46.68 1.90
71 72 1.265568 GTCGAGCGAGCGAACATAAA 58.734 50.000 1.60 0.00 42.55 1.40
72 73 1.652124 GTCGAGCGAGCGAACATAAAA 59.348 47.619 1.60 0.00 42.55 1.52
73 74 2.091588 GTCGAGCGAGCGAACATAAAAA 59.908 45.455 1.60 0.00 42.55 1.94
98 99 3.578282 CCTTTTTCTTAACAGGTGCCCAT 59.422 43.478 0.00 0.00 0.00 4.00
106 107 6.905736 TCTTAACAGGTGCCCATATGAATAA 58.094 36.000 3.65 0.00 0.00 1.40
113 114 8.614814 ACAGGTGCCCATATGAATAAAGTATAT 58.385 33.333 3.65 0.00 0.00 0.86
133 134 2.343101 TGTACATGCGTTTGTAGAGGC 58.657 47.619 0.00 0.00 32.92 4.70
151 152 1.730593 GCGATCGTCAGTGTGTACGC 61.731 60.000 17.81 0.00 38.94 4.42
152 153 0.453782 CGATCGTCAGTGTGTACGCA 60.454 55.000 7.03 4.65 38.94 5.24
242 243 3.274095 AGATAAGAAAGGCAGCCAGAC 57.726 47.619 15.80 3.82 0.00 3.51
405 407 1.479709 TGCTTGCTAGTCCTCTCTCC 58.520 55.000 0.00 0.00 0.00 3.71
551 556 5.993106 AAGCGCATCTTATTTTAGTCTCC 57.007 39.130 11.47 0.00 32.10 3.71
588 593 2.107141 GCTTCGTCTGGATCCCGG 59.893 66.667 9.90 0.00 0.00 5.73
602 607 4.787280 CCGGAGAGGAGCCCACCT 62.787 72.222 0.00 0.00 45.00 4.00
603 608 2.685380 CGGAGAGGAGCCCACCTT 60.685 66.667 0.00 0.00 40.73 3.50
610 615 1.142688 AGGAGCCCACCTTGTTCCAT 61.143 55.000 0.00 0.00 36.86 3.41
773 778 1.873591 CTTGTTTGGTCCCTCGTCTTG 59.126 52.381 0.00 0.00 0.00 3.02
782 787 1.577328 CCCTCGTCTTGCAATGCGTT 61.577 55.000 18.02 0.00 0.00 4.84
872 877 3.854784 GCTCTTGATCTTGGTGTTTGTGC 60.855 47.826 0.00 0.00 0.00 4.57
873 878 3.554934 TCTTGATCTTGGTGTTTGTGCT 58.445 40.909 0.00 0.00 0.00 4.40
874 879 3.953612 TCTTGATCTTGGTGTTTGTGCTT 59.046 39.130 0.00 0.00 0.00 3.91
875 880 3.713858 TGATCTTGGTGTTTGTGCTTG 57.286 42.857 0.00 0.00 0.00 4.01
876 881 3.023119 TGATCTTGGTGTTTGTGCTTGT 58.977 40.909 0.00 0.00 0.00 3.16
877 882 2.937469 TCTTGGTGTTTGTGCTTGTG 57.063 45.000 0.00 0.00 0.00 3.33
939 944 1.341581 GGGAGAGGATATCGGGAGAGG 60.342 61.905 0.00 0.00 45.48 3.69
1006 1011 0.246086 GCGGAGATGAGGGATGCTAG 59.754 60.000 0.00 0.00 0.00 3.42
1008 1013 1.643310 GGAGATGAGGGATGCTAGCT 58.357 55.000 17.23 0.83 0.00 3.32
1200 1205 0.485543 TGGAGGACCACAGTCAGGTA 59.514 55.000 0.00 0.00 45.48 3.08
1206 1211 3.100671 GGACCACAGTCAGGTAGAATCT 58.899 50.000 0.00 0.00 45.48 2.40
1495 1531 6.449698 TGATTGTTCTCAGCCATTTTTCTTC 58.550 36.000 0.00 0.00 0.00 2.87
1547 1583 6.315642 CCTGCATTGCATAGGATATAGTTCTG 59.684 42.308 12.53 0.00 38.13 3.02
1552 1588 6.670695 TGCATAGGATATAGTTCTGCTTGA 57.329 37.500 0.00 0.00 0.00 3.02
1613 1649 2.169832 TGTTCAGAGCAGTTGCCTAC 57.830 50.000 0.00 0.00 43.38 3.18
1617 1653 2.771089 TCAGAGCAGTTGCCTACTTTG 58.229 47.619 0.00 0.00 43.38 2.77
1732 1775 4.322804 CGTTTACTCACCTTCACGTCATAC 59.677 45.833 0.00 0.00 0.00 2.39
1799 1842 6.547141 TCACATGATGAACTTCCTTTTTCAGT 59.453 34.615 0.00 0.00 35.25 3.41
1881 1924 2.622942 CGAGGAGGGATTTCTCTCTCTG 59.377 54.545 7.37 0.00 46.64 3.35
2070 2113 4.951715 TCAGCAGAACATAATGCATCCTTT 59.048 37.500 0.00 0.00 45.01 3.11
2270 2313 7.880160 ACTTTTCATTATAGCCATAACTGCA 57.120 32.000 0.00 0.00 29.44 4.41
2422 2466 5.854010 ATAATGCAAGAGTCCGAGTCTTA 57.146 39.130 16.53 4.81 35.80 2.10
2423 2467 4.537135 AATGCAAGAGTCCGAGTCTTAA 57.463 40.909 16.53 9.73 35.80 1.85
2434 2478 7.614974 AGAGTCCGAGTCTTAAAATTAGGTACT 59.385 37.037 0.00 0.00 46.37 2.73
2435 2479 7.770201 AGTCCGAGTCTTAAAATTAGGTACTC 58.230 38.462 0.00 0.00 41.75 2.59
2436 2480 7.614974 AGTCCGAGTCTTAAAATTAGGTACTCT 59.385 37.037 0.00 0.00 41.75 3.24
2437 2481 7.914871 GTCCGAGTCTTAAAATTAGGTACTCTC 59.085 40.741 0.00 0.00 41.75 3.20
2438 2482 7.833183 TCCGAGTCTTAAAATTAGGTACTCTCT 59.167 37.037 0.00 0.00 41.75 3.10
2439 2483 8.130469 CCGAGTCTTAAAATTAGGTACTCTCTC 58.870 40.741 0.00 0.00 41.75 3.20
2440 2484 8.130469 CGAGTCTTAAAATTAGGTACTCTCTCC 58.870 40.741 0.00 0.00 41.75 3.71
2441 2485 7.998580 AGTCTTAAAATTAGGTACTCTCTCCG 58.001 38.462 0.00 0.00 41.75 4.63
2442 2486 7.614974 AGTCTTAAAATTAGGTACTCTCTCCGT 59.385 37.037 0.00 0.00 41.75 4.69
2443 2487 8.249638 GTCTTAAAATTAGGTACTCTCTCCGTT 58.750 37.037 0.00 0.00 41.75 4.44
2444 2488 8.465201 TCTTAAAATTAGGTACTCTCTCCGTTC 58.535 37.037 0.00 0.00 41.75 3.95
2445 2489 5.595257 AAATTAGGTACTCTCTCCGTTCC 57.405 43.478 0.00 0.00 41.75 3.62
2446 2490 3.726557 TTAGGTACTCTCTCCGTTCCA 57.273 47.619 0.00 0.00 41.75 3.53
2447 2491 2.599408 AGGTACTCTCTCCGTTCCAA 57.401 50.000 0.00 0.00 0.00 3.53
2448 2492 2.885616 AGGTACTCTCTCCGTTCCAAA 58.114 47.619 0.00 0.00 0.00 3.28
2449 2493 3.236896 AGGTACTCTCTCCGTTCCAAAA 58.763 45.455 0.00 0.00 0.00 2.44
2450 2494 3.838903 AGGTACTCTCTCCGTTCCAAAAT 59.161 43.478 0.00 0.00 0.00 1.82
2451 2495 5.021458 AGGTACTCTCTCCGTTCCAAAATA 58.979 41.667 0.00 0.00 0.00 1.40
2452 2496 5.127356 AGGTACTCTCTCCGTTCCAAAATAG 59.873 44.000 0.00 0.00 0.00 1.73
2453 2497 5.126707 GGTACTCTCTCCGTTCCAAAATAGA 59.873 44.000 0.00 0.00 0.00 1.98
2454 2498 5.941555 ACTCTCTCCGTTCCAAAATAGAT 57.058 39.130 0.00 0.00 0.00 1.98
2455 2499 5.665459 ACTCTCTCCGTTCCAAAATAGATG 58.335 41.667 0.00 0.00 0.00 2.90
2456 2500 5.422331 ACTCTCTCCGTTCCAAAATAGATGA 59.578 40.000 0.00 0.00 0.00 2.92
2457 2501 5.661458 TCTCTCCGTTCCAAAATAGATGAC 58.339 41.667 0.00 0.00 0.00 3.06
2458 2502 5.422331 TCTCTCCGTTCCAAAATAGATGACT 59.578 40.000 0.00 0.00 0.00 3.41
2459 2503 5.661458 TCTCCGTTCCAAAATAGATGACTC 58.339 41.667 0.00 0.00 0.00 3.36
2460 2504 5.186992 TCTCCGTTCCAAAATAGATGACTCA 59.813 40.000 0.00 0.00 0.00 3.41
2461 2505 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2462 2506 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2463 2507 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2464 2508 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2465 2509 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2466 2510 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2467 2511 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2468 2512 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2469 2513 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2470 2514 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2504 2548 8.004087 ACTACAGTTAGTACAAAGTTGAGTCA 57.996 34.615 0.00 0.00 36.73 3.41
2505 2549 8.639761 ACTACAGTTAGTACAAAGTTGAGTCAT 58.360 33.333 0.00 0.00 36.73 3.06
2506 2550 7.948278 ACAGTTAGTACAAAGTTGAGTCATC 57.052 36.000 0.00 0.00 0.00 2.92
2507 2551 7.727181 ACAGTTAGTACAAAGTTGAGTCATCT 58.273 34.615 0.00 0.00 0.00 2.90
2508 2552 8.857098 ACAGTTAGTACAAAGTTGAGTCATCTA 58.143 33.333 4.14 0.00 0.00 1.98
2509 2553 9.862371 CAGTTAGTACAAAGTTGAGTCATCTAT 57.138 33.333 4.14 0.00 0.00 1.98
2514 2558 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2515 2559 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2516 2560 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2517 2561 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2518 2562 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2519 2563 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2520 2564 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2521 2565 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2522 2566 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2523 2567 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2537 2581 1.344763 CGGAGGGAGTATTAGCCAAGG 59.655 57.143 0.00 0.00 0.00 3.61
2579 2623 5.221682 TGTTGAATGCATTTCCCTTGATGTT 60.222 36.000 14.33 0.00 33.04 2.71
2642 2686 6.743575 AAAACAGATATGAGGTGTGCTAAC 57.256 37.500 0.00 0.00 0.00 2.34
2648 2692 2.183478 TGAGGTGTGCTAACCATGTG 57.817 50.000 10.48 0.00 43.20 3.21
2675 2719 3.609853 TGGTCATGTGCATTTCCTAGAC 58.390 45.455 0.00 0.00 0.00 2.59
2754 2799 0.108329 GCCATGCAATTGCTTCTGCT 60.108 50.000 29.37 6.23 42.66 4.24
2988 3033 4.101114 TCTGGGAGCATCTTAGTAACCAA 58.899 43.478 0.00 0.00 33.73 3.67
3032 3077 4.976731 CAGTAGTCCTCGTAATGTATGTGC 59.023 45.833 0.00 0.00 0.00 4.57
3104 3149 5.243507 TGCTAGTTCATGCATTCTTTTTCCA 59.756 36.000 0.00 0.00 33.94 3.53
3155 3200 8.610248 TTGTAGTAATTTCATCGTTCTTTGGA 57.390 30.769 0.00 0.00 0.00 3.53
3272 3317 9.120538 AGTTTTGATAACATGTAACAGTTCTGT 57.879 29.630 0.00 0.00 0.00 3.41
3332 3377 1.549203 AGATTTTGTTCGCCTGCCAT 58.451 45.000 0.00 0.00 0.00 4.40
3468 3513 5.221661 ACAACAGTGGTTTAGTCCCTAGAAG 60.222 44.000 0.00 0.00 34.21 2.85
3615 3677 0.675633 GTCTGCAAATGCCTGGTTGT 59.324 50.000 2.46 0.00 41.18 3.32
3716 3892 9.896645 TTAGATCTCTTAAACATCTGCATTCTT 57.103 29.630 0.00 0.00 0.00 2.52
3953 4131 6.968131 TCCTTCATTCATTTCGTAGAACAG 57.032 37.500 0.00 0.00 45.90 3.16
3959 4137 4.340894 TCATTTCGTAGAACAGCATTGC 57.659 40.909 0.00 0.00 45.90 3.56
4193 4375 0.679505 CCGTCCCACAGTTTCTCTGA 59.320 55.000 1.79 0.00 46.27 3.27
4295 4481 2.558359 CGAAGGCCAGAAAAGAAATGGT 59.442 45.455 5.01 0.00 36.43 3.55
4335 4521 0.033504 CAGCCACGGTCAAGTGTAGT 59.966 55.000 0.00 0.00 40.33 2.73
4620 4806 7.148869 CGATCTACAACGTTATTCTGTTGACAA 60.149 37.037 11.60 0.00 46.45 3.18
4695 5010 6.874288 AGCAAGCATGATAAACCTAAGATC 57.126 37.500 0.00 0.00 0.00 2.75
4725 5040 2.955660 TCGGTTTTCTGTTGCCAAGAAT 59.044 40.909 0.00 0.00 0.00 2.40
5172 5591 2.621000 GCTATGCCGAAAGACGCG 59.379 61.111 3.53 3.53 41.07 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.810030 GCGGCGACTCTAGGGTTTG 60.810 63.158 12.98 0.00 0.00 2.93
4 5 3.905678 CTGGCGGCGACTCTAGGG 61.906 72.222 16.45 0.00 0.00 3.53
6 7 1.064946 CTTCTGGCGGCGACTCTAG 59.935 63.158 16.45 2.50 0.00 2.43
7 8 3.064987 GCTTCTGGCGGCGACTCTA 62.065 63.158 16.45 0.00 0.00 2.43
8 9 4.443266 GCTTCTGGCGGCGACTCT 62.443 66.667 16.45 0.00 0.00 3.24
17 18 2.514824 CCCTAAGGCGCTTCTGGC 60.515 66.667 7.64 0.00 37.64 4.85
18 19 0.322546 AAACCCTAAGGCGCTTCTGG 60.323 55.000 7.64 5.51 36.11 3.86
19 20 1.087501 GAAACCCTAAGGCGCTTCTG 58.912 55.000 7.64 0.00 36.11 3.02
20 21 0.391263 CGAAACCCTAAGGCGCTTCT 60.391 55.000 7.64 0.00 36.11 2.85
21 22 0.390735 TCGAAACCCTAAGGCGCTTC 60.391 55.000 7.64 0.00 36.11 3.86
22 23 0.672711 GTCGAAACCCTAAGGCGCTT 60.673 55.000 7.64 0.00 36.11 4.68
23 24 1.079336 GTCGAAACCCTAAGGCGCT 60.079 57.895 7.64 0.00 36.11 5.92
24 25 2.450345 CGTCGAAACCCTAAGGCGC 61.450 63.158 0.00 0.00 36.11 6.53
25 26 0.388907 TTCGTCGAAACCCTAAGGCG 60.389 55.000 4.91 0.00 36.11 5.52
26 27 1.799544 TTTCGTCGAAACCCTAAGGC 58.200 50.000 16.22 0.00 36.11 4.35
27 28 3.811497 ACTTTTTCGTCGAAACCCTAAGG 59.189 43.478 23.59 12.95 40.04 2.69
28 29 5.015067 GACTTTTTCGTCGAAACCCTAAG 57.985 43.478 19.59 20.12 30.83 2.18
42 43 0.708918 CTCGCTCGACCGACTTTTTC 59.291 55.000 0.00 0.00 33.12 2.29
43 44 1.282930 GCTCGCTCGACCGACTTTTT 61.283 55.000 0.00 0.00 33.12 1.94
44 45 1.733399 GCTCGCTCGACCGACTTTT 60.733 57.895 0.00 0.00 33.12 2.27
45 46 2.126424 GCTCGCTCGACCGACTTT 60.126 61.111 0.00 0.00 33.12 2.66
46 47 4.462417 CGCTCGCTCGACCGACTT 62.462 66.667 0.00 0.00 33.12 3.01
48 49 4.456253 TTCGCTCGCTCGACCGAC 62.456 66.667 8.90 0.00 38.30 4.79
49 50 4.456253 GTTCGCTCGCTCGACCGA 62.456 66.667 2.39 2.39 38.30 4.69
50 51 2.642249 TATGTTCGCTCGCTCGACCG 62.642 60.000 0.00 0.00 38.30 4.79
51 52 0.524816 TTATGTTCGCTCGCTCGACC 60.525 55.000 0.00 0.00 38.30 4.79
52 53 1.265568 TTTATGTTCGCTCGCTCGAC 58.734 50.000 0.00 0.00 38.30 4.20
53 54 1.985334 TTTTATGTTCGCTCGCTCGA 58.015 45.000 0.00 0.00 36.60 4.04
54 55 2.780361 TTTTTATGTTCGCTCGCTCG 57.220 45.000 0.00 0.00 0.00 5.03
106 107 7.652105 CCTCTACAAACGCATGTACATATACTT 59.348 37.037 8.32 0.00 34.75 2.24
113 114 2.343101 GCCTCTACAAACGCATGTACA 58.657 47.619 0.00 0.00 34.75 2.90
118 119 1.571919 GATCGCCTCTACAAACGCAT 58.428 50.000 0.00 0.00 0.00 4.73
133 134 0.453782 TGCGTACACACTGACGATCG 60.454 55.000 14.88 14.88 41.60 3.69
151 152 6.748658 AGCATGATACAAATCAAACGTTCATG 59.251 34.615 0.00 8.16 45.12 3.07
152 153 6.855836 AGCATGATACAAATCAAACGTTCAT 58.144 32.000 0.00 0.00 45.12 2.57
222 223 2.573462 TGTCTGGCTGCCTTTCTTATCT 59.427 45.455 21.03 0.00 0.00 1.98
242 243 5.509498 TCCATTAATCTCTCCCCTGTTTTG 58.491 41.667 0.00 0.00 0.00 2.44
405 407 1.675415 GCTCCACAGCAAAGAGAGAGG 60.675 57.143 0.00 0.00 46.06 3.69
471 475 1.833787 AATTTTGCAGGCAGGCAGGG 61.834 55.000 4.10 0.00 45.88 4.45
496 501 4.856607 CGGTCTCCCTTCTCGCGC 62.857 72.222 0.00 0.00 0.00 6.86
588 593 0.035915 GAACAAGGTGGGCTCCTCTC 60.036 60.000 2.68 0.00 36.74 3.20
610 615 2.286365 AGCGGAAGATTGGGTTTTGA 57.714 45.000 0.00 0.00 0.00 2.69
773 778 0.109319 CCACACCCTAAACGCATTGC 60.109 55.000 0.00 0.00 0.00 3.56
782 787 1.071071 CCAAGAACGACCACACCCTAA 59.929 52.381 0.00 0.00 0.00 2.69
872 877 1.021202 TCGAAGCCAACCAACACAAG 58.979 50.000 0.00 0.00 0.00 3.16
873 878 1.336440 CATCGAAGCCAACCAACACAA 59.664 47.619 0.00 0.00 0.00 3.33
874 879 0.950836 CATCGAAGCCAACCAACACA 59.049 50.000 0.00 0.00 0.00 3.72
875 880 0.240945 CCATCGAAGCCAACCAACAC 59.759 55.000 0.00 0.00 0.00 3.32
876 881 1.523154 GCCATCGAAGCCAACCAACA 61.523 55.000 0.00 0.00 0.00 3.33
877 882 1.212751 GCCATCGAAGCCAACCAAC 59.787 57.895 0.00 0.00 0.00 3.77
939 944 2.246719 AAGCCATGTCTATTCGCCTC 57.753 50.000 0.00 0.00 0.00 4.70
1006 1011 1.869767 CAGGTAATCCATCGCAGAAGC 59.130 52.381 0.00 0.00 43.58 3.86
1008 1013 3.031013 TCTCAGGTAATCCATCGCAGAA 58.969 45.455 0.00 0.00 43.58 3.02
1200 1205 1.260538 TGCTCAGCGACCCAGATTCT 61.261 55.000 0.00 0.00 0.00 2.40
1206 1211 4.314440 GTGGTGCTCAGCGACCCA 62.314 66.667 13.72 7.05 31.92 4.51
1495 1531 9.182214 CATCCAATAAATATCTACTTCCATGGG 57.818 37.037 13.02 0.00 0.00 4.00
1534 1570 9.384764 GTTTTACTTCAAGCAGAACTATATCCT 57.615 33.333 0.00 0.00 31.61 3.24
1547 1583 7.027161 TGTTTGTTCTCTGTTTTACTTCAAGC 58.973 34.615 0.00 0.00 0.00 4.01
1552 1588 6.027749 CGCTTGTTTGTTCTCTGTTTTACTT 58.972 36.000 0.00 0.00 0.00 2.24
1558 1594 1.742831 TGCGCTTGTTTGTTCTCTGTT 59.257 42.857 9.73 0.00 0.00 3.16
1613 1649 8.765219 CAACCAAGGATCGAATATAGTACAAAG 58.235 37.037 0.00 0.00 0.00 2.77
1617 1653 9.490379 AAATCAACCAAGGATCGAATATAGTAC 57.510 33.333 0.00 0.00 0.00 2.73
1749 1792 5.297776 GGGAACTAATGGAGATTGACATGTG 59.702 44.000 1.15 0.00 0.00 3.21
1799 1842 4.202284 TGCACTTCTGCTCAGATGCATATA 60.202 41.667 18.76 2.91 44.09 0.86
1881 1924 2.936498 CACCGACCATTGATTACTGACC 59.064 50.000 0.00 0.00 0.00 4.02
2070 2113 0.624254 TCTCTCGCCTAACCTCCTCA 59.376 55.000 0.00 0.00 0.00 3.86
2270 2313 5.203528 AGCATAGGGACACAGCATTTAAAT 58.796 37.500 0.00 0.00 0.00 1.40
2288 2331 6.623549 GCAGCAACAATTCTAACAGAAGCATA 60.624 38.462 0.00 0.00 37.69 3.14
2409 2453 7.770201 AGTACCTAATTTTAAGACTCGGACTC 58.230 38.462 0.00 0.00 0.00 3.36
2422 2466 5.482878 TGGAACGGAGAGAGTACCTAATTTT 59.517 40.000 0.00 0.00 0.00 1.82
2423 2467 5.021458 TGGAACGGAGAGAGTACCTAATTT 58.979 41.667 0.00 0.00 0.00 1.82
2434 2478 5.422331 AGTCATCTATTTTGGAACGGAGAGA 59.578 40.000 0.00 0.00 0.00 3.10
2435 2479 5.665459 AGTCATCTATTTTGGAACGGAGAG 58.335 41.667 0.00 0.00 0.00 3.20
2436 2480 5.186992 TGAGTCATCTATTTTGGAACGGAGA 59.813 40.000 0.00 0.00 0.00 3.71
2437 2481 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2438 2482 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2439 2483 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2440 2484 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2441 2485 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2442 2486 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2443 2487 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2444 2488 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2478 2522 9.123902 TGACTCAACTTTGTACTAACTGTAGTA 57.876 33.333 0.00 0.00 41.06 1.82
2479 2523 8.004087 TGACTCAACTTTGTACTAACTGTAGT 57.996 34.615 0.00 0.00 43.27 2.73
2480 2524 9.130312 GATGACTCAACTTTGTACTAACTGTAG 57.870 37.037 0.00 0.00 0.00 2.74
2481 2525 8.857098 AGATGACTCAACTTTGTACTAACTGTA 58.143 33.333 0.00 0.00 0.00 2.74
2482 2526 7.727181 AGATGACTCAACTTTGTACTAACTGT 58.273 34.615 0.00 0.00 0.00 3.55
2483 2527 9.862371 ATAGATGACTCAACTTTGTACTAACTG 57.138 33.333 0.00 0.00 0.00 3.16
2488 2532 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2489 2533 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2490 2534 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2491 2535 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2492 2536 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2493 2537 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2494 2538 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2495 2539 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2496 2540 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2497 2541 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2498 2542 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2499 2543 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2500 2544 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2501 2545 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2502 2546 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2503 2547 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2504 2548 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2505 2549 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2506 2550 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2507 2551 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
2508 2552 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
2509 2553 4.624604 GCTAATACTCCCTCCGTTCCAAAA 60.625 45.833 0.00 0.00 0.00 2.44
2510 2554 3.118519 GCTAATACTCCCTCCGTTCCAAA 60.119 47.826 0.00 0.00 0.00 3.28
2511 2555 2.433239 GCTAATACTCCCTCCGTTCCAA 59.567 50.000 0.00 0.00 0.00 3.53
2512 2556 2.037144 GCTAATACTCCCTCCGTTCCA 58.963 52.381 0.00 0.00 0.00 3.53
2513 2557 1.343789 GGCTAATACTCCCTCCGTTCC 59.656 57.143 0.00 0.00 0.00 3.62
2514 2558 2.037144 TGGCTAATACTCCCTCCGTTC 58.963 52.381 0.00 0.00 0.00 3.95
2515 2559 2.170012 TGGCTAATACTCCCTCCGTT 57.830 50.000 0.00 0.00 0.00 4.44
2516 2560 2.040178 CTTGGCTAATACTCCCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
2517 2561 1.344763 CCTTGGCTAATACTCCCTCCG 59.655 57.143 0.00 0.00 0.00 4.63
2518 2562 1.072489 GCCTTGGCTAATACTCCCTCC 59.928 57.143 4.11 0.00 0.00 4.30
2519 2563 1.768870 TGCCTTGGCTAATACTCCCTC 59.231 52.381 13.18 0.00 0.00 4.30
2520 2564 1.893315 TGCCTTGGCTAATACTCCCT 58.107 50.000 13.18 0.00 0.00 4.20
2521 2565 2.729028 TTGCCTTGGCTAATACTCCC 57.271 50.000 13.18 0.00 0.00 4.30
2522 2566 4.519350 GGTATTTGCCTTGGCTAATACTCC 59.481 45.833 34.37 25.02 37.97 3.85
2523 2567 5.130350 TGGTATTTGCCTTGGCTAATACTC 58.870 41.667 34.37 28.44 37.97 2.59
2537 2581 6.135290 TCAACAGCTGAATATGGTATTTGC 57.865 37.500 23.35 0.00 0.00 3.68
2648 2692 4.053295 GGAAATGCACATGACCATATTGC 58.947 43.478 0.00 0.00 32.51 3.56
2675 2719 5.349817 AGACAACAGCAGATTAAGTGATTCG 59.650 40.000 0.00 0.00 0.00 3.34
3104 3149 7.023197 AGCAGAAATACGTACTTTGTTGTTT 57.977 32.000 0.00 0.00 0.00 2.83
3155 3200 5.707298 CCACTTACCTCAACAGAAACATCAT 59.293 40.000 0.00 0.00 0.00 2.45
3250 3295 9.772973 ACTTACAGAACTGTTACATGTTATCAA 57.227 29.630 12.66 0.00 41.83 2.57
3468 3513 1.002792 GACCGGCAGAGAAACACAAAC 60.003 52.381 0.00 0.00 0.00 2.93
3547 3592 1.200020 GCGAAGTGACATGAAAAGGGG 59.800 52.381 0.00 0.00 0.00 4.79
3615 3677 9.261180 CTACAAAATATCTCCTCAATAAGCGAA 57.739 33.333 0.00 0.00 0.00 4.70
3675 3851 4.781934 AGATCTAAAAATGGTTCCCTCGG 58.218 43.478 0.00 0.00 0.00 4.63
3701 3877 5.867716 GCTTCAATGAAGAATGCAGATGTTT 59.132 36.000 25.54 0.00 41.71 2.83
3716 3892 4.461431 AGCTCATTCACAATGCTTCAATGA 59.539 37.500 0.00 0.00 38.77 2.57
4295 4481 3.181462 TGCTGCTCTTCTTGTCTTCTTCA 60.181 43.478 0.00 0.00 0.00 3.02
4335 4521 1.495584 GAGAACGCACAGGAAACGCA 61.496 55.000 0.00 0.00 0.00 5.24
4369 4555 6.940867 AGTAACCAGGTTGAATCTAAAAGGTC 59.059 38.462 15.82 0.00 0.00 3.85
4620 4806 2.642427 TGTGCAAGTTCACATGTGACT 58.358 42.857 27.88 22.66 41.57 3.41
4695 5010 1.267806 ACAGAAAACCGATGCTGCAAG 59.732 47.619 6.36 3.78 31.74 4.01
4774 5185 9.676195 TGATGTTTCATTGCCATAAATTATACG 57.324 29.630 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.