Multiple sequence alignment - TraesCS6A01G210500

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 TraesCS6A01G210500 chr6A 100.000 2194 0 0 1 2194 381527372 381525179 0.000000e+00 4052.0
1 TraesCS6A01G210500 chr6A 100.000 1362 0 0 2598 3959 381524775 381523414 0.000000e+00 2516.0
2 TraesCS6A01G210500 chr6B 93.865 2119 102 13 98 2194 416102940 416100828 0.000000e+00 3168.0
3 TraesCS6A01G210500 chr6B 92.030 527 17 8 2598 3103 416100723 416100201 0.000000e+00 717.0
4 TraesCS6A01G210500 chr6B 83.651 630 68 20 3181 3786 416100067 416099449 9.610000e-156 560.0
5 TraesCS6A01G210500 chr6D 94.300 1649 72 8 565 2194 267730227 267728582 0.000000e+00 2505.0
6 TraesCS6A01G210500 chr6D 89.915 1418 84 25 2598 3959 267728477 267727063 0.000000e+00 1772.0
7 TraesCS6A01G210500 chr6D 91.636 275 19 3 98 369 267730496 267730223 1.040000e-100 377.0
8 TraesCS6A01G210500 chr1D 82.353 153 26 1 3807 3959 68197550 68197701 8.930000e-27 132.0
9 TraesCS6A01G210500 chr2B 81.333 150 28 0 3810 3959 212568774 212568625 5.370000e-24 122.0
10 TraesCS6A01G210500 chr4D 94.000 50 3 0 1376 1425 403182525 403182574 4.240000e-10 76.8
11 TraesCS6A01G210500 chr4D 78.899 109 14 8 1320 1425 494877439 494877541 9.180000e-07 65.8
12 TraesCS6A01G210500 chr4B 100.000 41 0 0 1385 1425 500053200 500053240 4.240000e-10 76.8
13 TraesCS6A01G210500 chr4B 89.796 49 3 2 1379 1426 634981586 634981633 1.190000e-05 62.1
14 TraesCS6A01G210500 chr4A 94.000 50 3 0 1376 1425 60730865 60730914 4.240000e-10 76.8
15 TraesCS6A01G210500 chr4A 94.000 50 3 0 1376 1425 60880338 60880387 4.240000e-10 76.8
16 TraesCS6A01G210500 chr5A 80.000 110 13 8 1320 1426 674576481 674576584 5.490000e-09 73.1


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 TraesCS6A01G210500 chr6A 381523414 381527372 3958 True 3284.000000 4052 100.000000 1 3959 2 chr6A.!!$R1 3958
1 TraesCS6A01G210500 chr6B 416099449 416102940 3491 True 1481.666667 3168 89.848667 98 3786 3 chr6B.!!$R1 3688
2 TraesCS6A01G210500 chr6D 267727063 267730496 3433 True 1551.333333 2505 91.950333 98 3959 3 chr6D.!!$R1 3861

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
311 312 0.031994 GTGCGAGCAAAACCCATTGT 59.968 50.000 0.0 0.0 32.80 2.71 F
378 381 0.531200 CGGGCGTAGGGGAGAATATC 59.469 60.000 0.0 0.0 0.00 1.63 F
848 854 1.261619 GGTCACAAGCACGACTCAAAG 59.738 52.381 0.0 0.0 32.57 2.77 F
1856 1879 1.267574 AAGATCGGGAGCCTGCAAGA 61.268 55.000 0.0 0.0 34.07 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1212 1.065928 CGCCCCAGTCGTAGATGTC 59.934 63.158 0.00 0.00 40.67 3.06 R
1438 1461 2.182791 CGCCGAGTGCATCTCAGT 59.817 61.111 14.09 0.00 42.88 3.41 R
2816 2839 2.282180 ACGGTGGTGCAATGGACC 60.282 61.111 17.42 17.42 0.00 4.46 R
3552 3676 0.164432 GGGTTTCTTACGGCGTTTCG 59.836 55.000 21.24 7.24 0.00 3.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.441312 AACTAAACTCGTTAAGAATCACCAAA 57.559 30.769 0.00 0.00 0.00 3.28
26 27 8.084590 ACTAAACTCGTTAAGAATCACCAAAG 57.915 34.615 0.00 0.00 0.00 2.77
27 28 7.929785 ACTAAACTCGTTAAGAATCACCAAAGA 59.070 33.333 0.00 0.00 0.00 2.52
28 29 7.562454 AAACTCGTTAAGAATCACCAAAGAA 57.438 32.000 0.00 0.00 0.00 2.52
29 30 6.541111 ACTCGTTAAGAATCACCAAAGAAC 57.459 37.500 0.00 0.00 0.00 3.01
30 31 5.176958 ACTCGTTAAGAATCACCAAAGAACG 59.823 40.000 0.00 0.00 39.67 3.95
31 32 5.291178 TCGTTAAGAATCACCAAAGAACGA 58.709 37.500 2.70 2.70 43.44 3.85
32 33 5.929992 TCGTTAAGAATCACCAAAGAACGAT 59.070 36.000 2.70 0.00 41.54 3.73
33 34 7.092079 TCGTTAAGAATCACCAAAGAACGATA 58.908 34.615 2.70 0.00 41.54 2.92
34 35 7.062605 TCGTTAAGAATCACCAAAGAACGATAC 59.937 37.037 2.70 0.00 41.54 2.24
35 36 5.779806 AAGAATCACCAAAGAACGATACG 57.220 39.130 0.00 0.00 0.00 3.06
36 37 3.617263 AGAATCACCAAAGAACGATACGC 59.383 43.478 0.00 0.00 0.00 4.42
37 38 1.717194 TCACCAAAGAACGATACGCC 58.283 50.000 0.00 0.00 0.00 5.68
38 39 0.368907 CACCAAAGAACGATACGCCG 59.631 55.000 0.00 0.00 0.00 6.46
39 40 0.244450 ACCAAAGAACGATACGCCGA 59.756 50.000 0.00 0.00 0.00 5.54
40 41 1.134907 ACCAAAGAACGATACGCCGAT 60.135 47.619 0.00 0.00 0.00 4.18
41 42 1.931172 CCAAAGAACGATACGCCGATT 59.069 47.619 0.00 0.00 0.00 3.34
42 43 2.350498 CCAAAGAACGATACGCCGATTT 59.650 45.455 0.00 0.00 0.00 2.17
43 44 3.181514 CCAAAGAACGATACGCCGATTTT 60.182 43.478 0.00 0.00 0.00 1.82
44 45 4.033129 CCAAAGAACGATACGCCGATTTTA 59.967 41.667 0.00 0.00 0.00 1.52
45 46 4.766969 AAGAACGATACGCCGATTTTAC 57.233 40.909 0.00 0.00 0.00 2.01
46 47 3.772932 AGAACGATACGCCGATTTTACA 58.227 40.909 0.00 0.00 0.00 2.41
47 48 4.175516 AGAACGATACGCCGATTTTACAA 58.824 39.130 0.00 0.00 0.00 2.41
48 49 4.807304 AGAACGATACGCCGATTTTACAAT 59.193 37.500 0.00 0.00 0.00 2.71
49 50 4.446857 ACGATACGCCGATTTTACAATG 57.553 40.909 0.00 0.00 0.00 2.82
50 51 3.866910 ACGATACGCCGATTTTACAATGT 59.133 39.130 0.00 0.00 0.00 2.71
51 52 5.042593 ACGATACGCCGATTTTACAATGTA 58.957 37.500 0.00 0.00 0.00 2.29
52 53 5.174398 ACGATACGCCGATTTTACAATGTAG 59.826 40.000 0.00 0.00 0.00 2.74
53 54 5.400188 CGATACGCCGATTTTACAATGTAGA 59.600 40.000 0.00 0.00 0.00 2.59
54 55 6.089016 CGATACGCCGATTTTACAATGTAGAT 59.911 38.462 0.00 0.00 0.00 1.98
55 56 5.403897 ACGCCGATTTTACAATGTAGATG 57.596 39.130 0.00 0.00 0.00 2.90
56 57 4.211389 CGCCGATTTTACAATGTAGATGC 58.789 43.478 0.00 0.00 0.00 3.91
57 58 4.537015 GCCGATTTTACAATGTAGATGCC 58.463 43.478 0.00 0.00 0.00 4.40
58 59 4.772434 CCGATTTTACAATGTAGATGCCG 58.228 43.478 0.00 0.00 0.00 5.69
59 60 4.319477 CCGATTTTACAATGTAGATGCCGG 60.319 45.833 0.00 0.00 0.00 6.13
60 61 4.509970 CGATTTTACAATGTAGATGCCGGA 59.490 41.667 5.05 0.00 0.00 5.14
61 62 5.179368 CGATTTTACAATGTAGATGCCGGAT 59.821 40.000 5.05 0.00 0.00 4.18
62 63 6.293407 CGATTTTACAATGTAGATGCCGGATT 60.293 38.462 5.05 0.00 0.00 3.01
63 64 6.767524 TTTTACAATGTAGATGCCGGATTT 57.232 33.333 5.05 0.00 0.00 2.17
64 65 6.767524 TTTACAATGTAGATGCCGGATTTT 57.232 33.333 5.05 0.00 0.00 1.82
65 66 6.767524 TTACAATGTAGATGCCGGATTTTT 57.232 33.333 5.05 0.00 0.00 1.94
66 67 5.248870 ACAATGTAGATGCCGGATTTTTC 57.751 39.130 5.05 0.00 0.00 2.29
67 68 4.097892 ACAATGTAGATGCCGGATTTTTCC 59.902 41.667 5.05 0.00 0.00 3.13
68 69 3.358111 TGTAGATGCCGGATTTTTCCA 57.642 42.857 5.05 0.00 0.00 3.53
69 70 3.691575 TGTAGATGCCGGATTTTTCCAA 58.308 40.909 5.05 0.00 0.00 3.53
70 71 3.442273 TGTAGATGCCGGATTTTTCCAAC 59.558 43.478 5.05 0.00 0.00 3.77
71 72 2.524306 AGATGCCGGATTTTTCCAACA 58.476 42.857 5.05 0.00 0.00 3.33
72 73 2.231235 AGATGCCGGATTTTTCCAACAC 59.769 45.455 5.05 0.00 0.00 3.32
73 74 0.676736 TGCCGGATTTTTCCAACACC 59.323 50.000 5.05 0.00 0.00 4.16
74 75 0.037697 GCCGGATTTTTCCAACACCC 60.038 55.000 5.05 0.00 0.00 4.61
75 76 1.333177 CCGGATTTTTCCAACACCCA 58.667 50.000 0.00 0.00 0.00 4.51
76 77 1.899142 CCGGATTTTTCCAACACCCAT 59.101 47.619 0.00 0.00 0.00 4.00
77 78 2.353605 CCGGATTTTTCCAACACCCATG 60.354 50.000 0.00 0.00 0.00 3.66
78 79 2.698803 GGATTTTTCCAACACCCATGC 58.301 47.619 0.00 0.00 0.00 4.06
79 80 2.038295 GGATTTTTCCAACACCCATGCA 59.962 45.455 0.00 0.00 0.00 3.96
80 81 3.495806 GGATTTTTCCAACACCCATGCAA 60.496 43.478 0.00 0.00 0.00 4.08
81 82 2.906691 TTTTCCAACACCCATGCAAG 57.093 45.000 0.00 0.00 0.00 4.01
82 83 1.047002 TTTCCAACACCCATGCAAGG 58.953 50.000 0.00 0.00 0.00 3.61
91 92 3.286404 CCATGCAAGGGAATCCACA 57.714 52.632 0.09 0.00 43.46 4.17
92 93 0.819582 CCATGCAAGGGAATCCACAC 59.180 55.000 0.09 0.00 43.46 3.82
93 94 0.819582 CATGCAAGGGAATCCACACC 59.180 55.000 0.09 0.00 34.83 4.16
94 95 0.680921 ATGCAAGGGAATCCACACCG 60.681 55.000 0.09 0.00 34.83 4.94
95 96 2.700773 GCAAGGGAATCCACACCGC 61.701 63.158 0.09 0.00 34.83 5.68
96 97 2.046285 CAAGGGAATCCACACCGCC 61.046 63.158 0.09 0.00 34.83 6.13
152 153 6.991938 TCATCCGGTTGAAGAAAAATTTCAT 58.008 32.000 12.87 0.00 39.61 2.57
199 200 4.202161 CCCGTGTAGTCATCAATTAGCTCT 60.202 45.833 0.00 0.00 0.00 4.09
269 270 2.529780 ACGGTTGTGACGGAAATACA 57.470 45.000 0.00 0.00 35.23 2.29
274 275 3.306166 GGTTGTGACGGAAATACAGATCG 59.694 47.826 0.00 0.00 0.00 3.69
277 278 5.006153 TGTGACGGAAATACAGATCGATT 57.994 39.130 0.00 0.00 0.00 3.34
311 312 0.031994 GTGCGAGCAAAACCCATTGT 59.968 50.000 0.00 0.00 32.80 2.71
312 313 1.268352 GTGCGAGCAAAACCCATTGTA 59.732 47.619 0.00 0.00 32.80 2.41
316 317 3.552068 GCGAGCAAAACCCATTGTAGTTT 60.552 43.478 0.00 0.00 37.80 2.66
320 321 6.173427 AGCAAAACCCATTGTAGTTTCAAT 57.827 33.333 3.39 0.00 35.19 2.57
369 372 3.615509 TTTCTTGGCGGGCGTAGGG 62.616 63.158 0.00 0.00 0.00 3.53
376 379 2.205152 GCGGGCGTAGGGGAGAATA 61.205 63.158 0.00 0.00 0.00 1.75
377 380 1.542187 GCGGGCGTAGGGGAGAATAT 61.542 60.000 0.00 0.00 0.00 1.28
378 381 0.531200 CGGGCGTAGGGGAGAATATC 59.469 60.000 0.00 0.00 0.00 1.63
390 393 3.833070 GGGAGAATATCAGGTGATACCGT 59.167 47.826 1.72 0.00 44.90 4.83
417 420 5.323382 TGTATGCTCCCATCATACCAATT 57.677 39.130 9.73 0.00 43.31 2.32
418 421 5.704354 TGTATGCTCCCATCATACCAATTT 58.296 37.500 9.73 0.00 43.31 1.82
421 424 4.608269 TGCTCCCATCATACCAATTTGAA 58.392 39.130 0.00 0.00 0.00 2.69
424 427 6.044682 GCTCCCATCATACCAATTTGAAAAG 58.955 40.000 0.00 0.00 0.00 2.27
427 430 6.154363 TCCCATCATACCAATTTGAAAAGGTC 59.846 38.462 8.42 0.00 35.62 3.85
492 496 6.481976 TGTTCACAACACATAAGTCTACAAGG 59.518 38.462 0.00 0.00 36.25 3.61
493 497 6.169557 TCACAACACATAAGTCTACAAGGT 57.830 37.500 0.00 0.00 0.00 3.50
495 499 6.041637 TCACAACACATAAGTCTACAAGGTCT 59.958 38.462 0.00 0.00 0.00 3.85
500 504 9.490379 AACACATAAGTCTACAAGGTCTAAAAG 57.510 33.333 0.00 0.00 0.00 2.27
517 521 9.118236 GGTCTAAAAGTTTCAGATCAAAATTCG 57.882 33.333 0.00 0.00 0.00 3.34
539 543 6.387465 TCGGAGTACACATAGAGAAACAAAG 58.613 40.000 0.00 0.00 0.00 2.77
562 566 6.899114 AGAAGACAAAACCGAATGTGAATAC 58.101 36.000 0.00 0.00 0.00 1.89
582 586 7.554835 TGAATACTGTAGGTTTTGACACTGTTT 59.445 33.333 0.00 0.00 0.00 2.83
597 603 7.806690 TGACACTGTTTATGCTTGTCTTTATC 58.193 34.615 0.00 0.00 37.94 1.75
604 610 7.172532 TGTTTATGCTTGTCTTTATCGACACTT 59.827 33.333 0.00 0.00 43.11 3.16
633 639 8.410030 TGTTGAATTTGTCTTTCATGTTTCTG 57.590 30.769 0.00 0.00 33.37 3.02
637 643 8.681806 TGAATTTGTCTTTCATGTTTCTGTACA 58.318 29.630 0.00 0.00 0.00 2.90
690 696 9.747898 TTTTAGGGATTGTAGACACATATGTTT 57.252 29.630 5.37 0.00 39.95 2.83
763 769 7.762588 TTTTTCCAAATTAGTATCACGGGAA 57.237 32.000 0.00 0.00 0.00 3.97
774 780 2.465860 TCACGGGAACATACAAGTGG 57.534 50.000 0.00 0.00 0.00 4.00
783 789 5.437060 GGAACATACAAGTGGTGGTATCAT 58.563 41.667 0.00 0.00 0.00 2.45
784 790 5.527582 GGAACATACAAGTGGTGGTATCATC 59.472 44.000 0.00 0.00 0.00 2.92
836 842 2.012937 TAAATACGGGCGGTCACAAG 57.987 50.000 0.00 0.00 0.00 3.16
842 848 3.712881 GGCGGTCACAAGCACGAC 61.713 66.667 0.00 0.00 34.54 4.34
848 854 1.261619 GGTCACAAGCACGACTCAAAG 59.738 52.381 0.00 0.00 32.57 2.77
891 897 2.031919 CACGCCCACACCTAAGCA 59.968 61.111 0.00 0.00 0.00 3.91
920 926 2.177977 CTCGATCGCACACTTCAGTAC 58.822 52.381 11.09 0.00 0.00 2.73
1189 1212 4.753877 TCTTCGCGCACCTCGACG 62.754 66.667 8.75 0.00 41.67 5.12
1343 1366 2.266279 CTTCTCCAACTACCCCAAGGA 58.734 52.381 0.00 0.00 36.73 3.36
1807 1830 4.452733 GGGAGTTCGCCGAGTGGG 62.453 72.222 0.00 0.00 39.58 4.61
1840 1863 4.742201 GGACCGAGCTGCGCAAGA 62.742 66.667 13.05 0.00 43.02 3.02
1845 1868 3.267860 GAGCTGCGCAAGATCGGG 61.268 66.667 13.05 0.00 43.02 5.14
1856 1879 1.267574 AAGATCGGGAGCCTGCAAGA 61.268 55.000 0.00 0.00 34.07 3.02
2685 2708 2.596452 CGTACACGCAGATGAAGACTT 58.404 47.619 0.00 0.00 0.00 3.01
2718 2741 3.263503 CTGGAGACGTTCGCGGTGA 62.264 63.158 6.13 0.00 46.45 4.02
2816 2839 3.388703 GAGGAGGGAGCAGCAGCAG 62.389 68.421 3.17 0.00 45.49 4.24
2869 2892 2.688507 TCAACTTTCAGTCCATCTCGC 58.311 47.619 0.00 0.00 0.00 5.03
2941 2976 6.997655 ACTTTCTTTTCCTGATTTTGGGATC 58.002 36.000 0.00 0.00 0.00 3.36
3025 3072 2.663826 ACAGATCTCTGAAGGTTCGC 57.336 50.000 13.94 0.00 46.59 4.70
3044 3091 1.338389 GCTTTCAACCATGCAGGCAAT 60.338 47.619 0.00 0.00 43.14 3.56
3127 3205 2.441164 TCTGCTCCTCTCTCCGCC 60.441 66.667 0.00 0.00 0.00 6.13
3136 3214 1.943116 CTCTCTCCGCCTCTGTGTGG 61.943 65.000 0.00 0.00 37.24 4.17
3146 3226 1.233019 CTCTGTGTGGTCCTTGCTTG 58.767 55.000 0.00 0.00 0.00 4.01
3176 3256 3.568686 GCGTCCACATGCGGTAAA 58.431 55.556 0.00 0.00 0.00 2.01
3179 3259 1.153353 CGTCCACATGCGGTAAAGTT 58.847 50.000 0.00 0.00 0.00 2.66
3227 3331 9.072294 GTTGTTATACATGAGTTTGGCAAATAC 57.928 33.333 16.74 13.15 0.00 1.89
3245 3349 9.382275 GGCAAATACTGTATTGATTTGGAATTT 57.618 29.630 13.42 0.00 39.75 1.82
3506 3630 6.903883 TTTTGCGCCAATTTTTACAAAGTA 57.096 29.167 4.18 0.00 0.00 2.24
3513 3637 7.529185 GCGCCAATTTTTACAAAGTAAATCAAC 59.471 33.333 0.00 0.00 0.00 3.18
3569 3693 2.650900 AACGAAACGCCGTAAGAAAC 57.349 45.000 0.00 0.00 42.54 2.78
3593 3717 6.053005 CCCTCGGATGCAAACTAACTTATTA 58.947 40.000 0.00 0.00 0.00 0.98
3594 3718 6.018180 CCCTCGGATGCAAACTAACTTATTAC 60.018 42.308 0.00 0.00 0.00 1.89
3614 3738 1.400629 CGCACCAAAGCTGAGACAATG 60.401 52.381 0.00 0.00 0.00 2.82
3643 3767 9.860898 AAAATGAGGCAATAACATCTTAGTTTC 57.139 29.630 0.00 0.00 33.07 2.78
3751 3881 5.119931 TCATTAAAATTGAGTGCGCAAGT 57.880 34.783 14.00 1.06 41.68 3.16
3755 3885 0.235665 AATTGAGTGCGCAAGTCACG 59.764 50.000 20.33 0.00 45.01 4.35
3833 3976 3.396260 GGCTTGTATGCCGGATAACTA 57.604 47.619 5.05 0.00 43.74 2.24
3839 3982 5.864418 TGTATGCCGGATAACTACTCTTT 57.136 39.130 5.05 0.00 0.00 2.52
3841 3984 5.361571 TGTATGCCGGATAACTACTCTTTGA 59.638 40.000 5.05 0.00 0.00 2.69
3849 3992 6.316390 CGGATAACTACTCTTTGAAAGCCATT 59.684 38.462 0.00 0.00 0.00 3.16
3851 3994 5.712152 AACTACTCTTTGAAAGCCATTGG 57.288 39.130 0.00 0.00 0.00 3.16
3856 3999 4.895297 ACTCTTTGAAAGCCATTGGAAGAA 59.105 37.500 6.95 0.00 0.00 2.52
3867 4010 3.564133 CCATTGGAAGAATGGTGGAGGAA 60.564 47.826 0.00 0.00 41.68 3.36
3882 4025 0.253347 AGGAAGAGATTGGGGGAGCA 60.253 55.000 0.00 0.00 0.00 4.26
3884 4027 0.915364 GAAGAGATTGGGGGAGCAGT 59.085 55.000 0.00 0.00 0.00 4.40
3888 4031 1.225704 GATTGGGGGAGCAGTGGAG 59.774 63.158 0.00 0.00 0.00 3.86
3907 4050 2.112297 GGTGTGGTTCTTGCCCGA 59.888 61.111 0.00 0.00 0.00 5.14
3924 4067 1.069378 CGACGTCTGCCCTCGTTTAC 61.069 60.000 14.70 0.00 40.39 2.01
3929 4072 2.159282 CGTCTGCCCTCGTTTACATAGT 60.159 50.000 0.00 0.00 0.00 2.12
3932 4075 1.296727 GCCCTCGTTTACATAGTGGC 58.703 55.000 0.00 0.00 0.00 5.01
3940 4083 0.683828 TTACATAGTGGCCGGACGGA 60.684 55.000 15.99 0.00 37.50 4.69
3951 4094 2.754658 GGACGGAAGGAGCTCGGA 60.755 66.667 7.83 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.441312 TTTGGTGATTCTTAACGAGTTTAGTT 57.559 30.769 0.00 0.00 35.75 2.24
1 2 7.929785 TCTTTGGTGATTCTTAACGAGTTTAGT 59.070 33.333 0.00 0.00 0.00 2.24
2 3 8.306680 TCTTTGGTGATTCTTAACGAGTTTAG 57.693 34.615 0.00 0.00 0.00 1.85
3 4 8.553696 GTTCTTTGGTGATTCTTAACGAGTTTA 58.446 33.333 0.00 0.00 0.00 2.01
4 5 7.415229 GTTCTTTGGTGATTCTTAACGAGTTT 58.585 34.615 0.00 0.00 0.00 2.66
5 6 6.292703 CGTTCTTTGGTGATTCTTAACGAGTT 60.293 38.462 0.00 0.00 40.48 3.01
6 7 5.176958 CGTTCTTTGGTGATTCTTAACGAGT 59.823 40.000 0.00 0.00 40.48 4.18
7 8 5.404366 TCGTTCTTTGGTGATTCTTAACGAG 59.596 40.000 0.00 0.00 41.51 4.18
8 9 5.291178 TCGTTCTTTGGTGATTCTTAACGA 58.709 37.500 0.00 0.00 43.38 3.85
9 10 5.585500 TCGTTCTTTGGTGATTCTTAACG 57.415 39.130 0.00 0.00 39.67 3.18
10 11 7.171434 CGTATCGTTCTTTGGTGATTCTTAAC 58.829 38.462 0.00 0.00 0.00 2.01
11 12 6.183360 GCGTATCGTTCTTTGGTGATTCTTAA 60.183 38.462 0.00 0.00 0.00 1.85
12 13 5.290158 GCGTATCGTTCTTTGGTGATTCTTA 59.710 40.000 0.00 0.00 0.00 2.10
13 14 4.092968 GCGTATCGTTCTTTGGTGATTCTT 59.907 41.667 0.00 0.00 0.00 2.52
14 15 3.617263 GCGTATCGTTCTTTGGTGATTCT 59.383 43.478 0.00 0.00 0.00 2.40
15 16 3.242316 GGCGTATCGTTCTTTGGTGATTC 60.242 47.826 0.00 0.00 0.00 2.52
16 17 2.676342 GGCGTATCGTTCTTTGGTGATT 59.324 45.455 0.00 0.00 0.00 2.57
17 18 2.277084 GGCGTATCGTTCTTTGGTGAT 58.723 47.619 0.00 0.00 0.00 3.06
18 19 1.717194 GGCGTATCGTTCTTTGGTGA 58.283 50.000 0.00 0.00 0.00 4.02
19 20 0.368907 CGGCGTATCGTTCTTTGGTG 59.631 55.000 0.00 0.00 0.00 4.17
20 21 0.244450 TCGGCGTATCGTTCTTTGGT 59.756 50.000 6.85 0.00 0.00 3.67
21 22 1.567504 ATCGGCGTATCGTTCTTTGG 58.432 50.000 6.85 0.00 0.00 3.28
22 23 3.651562 AAATCGGCGTATCGTTCTTTG 57.348 42.857 6.85 0.00 0.00 2.77
23 24 4.626604 TGTAAAATCGGCGTATCGTTCTTT 59.373 37.500 6.85 0.00 0.00 2.52
24 25 4.175516 TGTAAAATCGGCGTATCGTTCTT 58.824 39.130 6.85 0.00 0.00 2.52
25 26 3.772932 TGTAAAATCGGCGTATCGTTCT 58.227 40.909 6.85 0.00 0.00 3.01
26 27 4.503767 TTGTAAAATCGGCGTATCGTTC 57.496 40.909 6.85 0.00 0.00 3.95
27 28 4.330620 ACATTGTAAAATCGGCGTATCGTT 59.669 37.500 6.85 0.00 0.00 3.85
28 29 3.866910 ACATTGTAAAATCGGCGTATCGT 59.133 39.130 6.85 0.00 0.00 3.73
29 30 4.446857 ACATTGTAAAATCGGCGTATCG 57.553 40.909 6.85 0.00 0.00 2.92
30 31 6.758593 TCTACATTGTAAAATCGGCGTATC 57.241 37.500 6.85 0.00 0.00 2.24
31 32 6.347402 GCATCTACATTGTAAAATCGGCGTAT 60.347 38.462 6.85 0.00 0.00 3.06
32 33 5.050634 GCATCTACATTGTAAAATCGGCGTA 60.051 40.000 6.85 0.00 0.00 4.42
33 34 4.260620 GCATCTACATTGTAAAATCGGCGT 60.261 41.667 6.85 0.00 0.00 5.68
34 35 4.211389 GCATCTACATTGTAAAATCGGCG 58.789 43.478 0.00 0.00 0.00 6.46
35 36 4.537015 GGCATCTACATTGTAAAATCGGC 58.463 43.478 0.00 0.00 0.00 5.54
36 37 4.319477 CCGGCATCTACATTGTAAAATCGG 60.319 45.833 0.00 4.86 0.00 4.18
37 38 4.509970 TCCGGCATCTACATTGTAAAATCG 59.490 41.667 0.00 0.01 0.00 3.34
38 39 6.560253 ATCCGGCATCTACATTGTAAAATC 57.440 37.500 0.00 0.00 0.00 2.17
39 40 6.959639 AATCCGGCATCTACATTGTAAAAT 57.040 33.333 0.00 0.00 0.00 1.82
40 41 6.767524 AAATCCGGCATCTACATTGTAAAA 57.232 33.333 0.00 0.00 0.00 1.52
41 42 6.767524 AAAATCCGGCATCTACATTGTAAA 57.232 33.333 0.00 0.00 0.00 2.01
42 43 6.183360 GGAAAAATCCGGCATCTACATTGTAA 60.183 38.462 0.00 0.00 0.00 2.41
43 44 5.298276 GGAAAAATCCGGCATCTACATTGTA 59.702 40.000 0.00 0.00 0.00 2.41
44 45 4.097892 GGAAAAATCCGGCATCTACATTGT 59.902 41.667 0.00 0.00 0.00 2.71
45 46 4.097741 TGGAAAAATCCGGCATCTACATTG 59.902 41.667 0.00 0.00 0.00 2.82
46 47 4.277476 TGGAAAAATCCGGCATCTACATT 58.723 39.130 0.00 0.00 0.00 2.71
47 48 3.897239 TGGAAAAATCCGGCATCTACAT 58.103 40.909 0.00 0.00 0.00 2.29
48 49 3.358111 TGGAAAAATCCGGCATCTACA 57.642 42.857 0.00 0.00 0.00 2.74
49 50 3.442273 TGTTGGAAAAATCCGGCATCTAC 59.558 43.478 0.00 0.00 0.00 2.59
50 51 3.442273 GTGTTGGAAAAATCCGGCATCTA 59.558 43.478 0.00 0.00 0.00 1.98
51 52 2.231235 GTGTTGGAAAAATCCGGCATCT 59.769 45.455 0.00 0.00 0.00 2.90
52 53 2.606108 GTGTTGGAAAAATCCGGCATC 58.394 47.619 0.00 0.00 0.00 3.91
53 54 1.275010 GGTGTTGGAAAAATCCGGCAT 59.725 47.619 0.00 0.00 0.00 4.40
54 55 0.676736 GGTGTTGGAAAAATCCGGCA 59.323 50.000 0.00 0.00 0.00 5.69
55 56 0.037697 GGGTGTTGGAAAAATCCGGC 60.038 55.000 0.00 0.00 0.00 6.13
56 57 1.333177 TGGGTGTTGGAAAAATCCGG 58.667 50.000 0.00 0.00 0.00 5.14
57 58 2.930455 GCATGGGTGTTGGAAAAATCCG 60.930 50.000 0.00 0.00 0.00 4.18
58 59 2.038295 TGCATGGGTGTTGGAAAAATCC 59.962 45.455 0.00 0.00 0.00 3.01
59 60 3.399440 TGCATGGGTGTTGGAAAAATC 57.601 42.857 0.00 0.00 0.00 2.17
60 61 3.496515 CCTTGCATGGGTGTTGGAAAAAT 60.497 43.478 10.81 0.00 0.00 1.82
61 62 2.158842 CCTTGCATGGGTGTTGGAAAAA 60.159 45.455 10.81 0.00 0.00 1.94
62 63 1.415659 CCTTGCATGGGTGTTGGAAAA 59.584 47.619 10.81 0.00 0.00 2.29
63 64 1.047002 CCTTGCATGGGTGTTGGAAA 58.953 50.000 10.81 0.00 0.00 3.13
64 65 0.831288 CCCTTGCATGGGTGTTGGAA 60.831 55.000 26.14 0.00 42.25 3.53
65 66 1.228831 CCCTTGCATGGGTGTTGGA 60.229 57.895 26.14 0.00 42.25 3.53
66 67 3.379880 CCCTTGCATGGGTGTTGG 58.620 61.111 26.14 3.00 42.25 3.77
73 74 0.819582 GTGTGGATTCCCTTGCATGG 59.180 55.000 11.68 11.68 0.00 3.66
74 75 0.819582 GGTGTGGATTCCCTTGCATG 59.180 55.000 0.00 0.00 0.00 4.06
75 76 0.680921 CGGTGTGGATTCCCTTGCAT 60.681 55.000 0.00 0.00 0.00 3.96
76 77 1.303236 CGGTGTGGATTCCCTTGCA 60.303 57.895 0.00 0.00 0.00 4.08
77 78 2.700773 GCGGTGTGGATTCCCTTGC 61.701 63.158 0.00 0.00 0.00 4.01
78 79 2.046285 GGCGGTGTGGATTCCCTTG 61.046 63.158 0.00 0.00 0.00 3.61
79 80 2.355115 GGCGGTGTGGATTCCCTT 59.645 61.111 0.00 0.00 0.00 3.95
80 81 2.933287 TGGCGGTGTGGATTCCCT 60.933 61.111 0.00 0.00 0.00 4.20
81 82 2.438434 CTGGCGGTGTGGATTCCC 60.438 66.667 0.00 0.00 0.00 3.97
82 83 1.745489 GACTGGCGGTGTGGATTCC 60.745 63.158 2.25 0.00 0.00 3.01
83 84 1.003839 TGACTGGCGGTGTGGATTC 60.004 57.895 2.25 0.00 0.00 2.52
84 85 1.003355 CTGACTGGCGGTGTGGATT 60.003 57.895 2.25 0.00 0.00 3.01
85 86 1.267574 ATCTGACTGGCGGTGTGGAT 61.268 55.000 2.25 1.56 0.00 3.41
86 87 1.480212 AATCTGACTGGCGGTGTGGA 61.480 55.000 2.25 0.00 0.00 4.02
87 88 1.003355 AATCTGACTGGCGGTGTGG 60.003 57.895 2.25 0.00 0.00 4.17
88 89 0.320683 TGAATCTGACTGGCGGTGTG 60.321 55.000 2.25 0.00 0.00 3.82
89 90 0.396435 TTGAATCTGACTGGCGGTGT 59.604 50.000 2.25 0.00 0.00 4.16
90 91 1.081892 CTTGAATCTGACTGGCGGTG 58.918 55.000 2.25 0.00 0.00 4.94
91 92 0.687354 ACTTGAATCTGACTGGCGGT 59.313 50.000 0.00 0.00 0.00 5.68
92 93 1.081892 CACTTGAATCTGACTGGCGG 58.918 55.000 0.00 0.00 0.00 6.13
93 94 1.081892 CCACTTGAATCTGACTGGCG 58.918 55.000 0.00 0.00 0.00 5.69
94 95 2.479566 TCCACTTGAATCTGACTGGC 57.520 50.000 0.00 0.00 0.00 4.85
95 96 6.351711 TCAATATCCACTTGAATCTGACTGG 58.648 40.000 0.00 0.00 29.96 4.00
96 97 7.270779 TCTCAATATCCACTTGAATCTGACTG 58.729 38.462 0.00 0.00 32.53 3.51
130 131 6.991938 TCATGAAATTTTTCTTCAACCGGAT 58.008 32.000 9.46 0.00 36.43 4.18
152 153 4.401202 TGACTCGGATGTGCTAGTTATTCA 59.599 41.667 0.00 0.00 0.00 2.57
199 200 2.245159 CTCCACTGAGCAAAGTGTCA 57.755 50.000 15.26 3.73 45.08 3.58
269 270 6.256539 CACTGCTACACATTGTAAATCGATCT 59.743 38.462 0.00 0.00 31.67 2.75
274 275 4.092821 TCGCACTGCTACACATTGTAAATC 59.907 41.667 0.00 0.00 31.67 2.17
277 278 2.993220 CTCGCACTGCTACACATTGTAA 59.007 45.455 0.00 0.00 31.67 2.41
288 289 2.555547 GGGTTTTGCTCGCACTGCT 61.556 57.895 0.00 0.00 0.00 4.24
311 312 6.018751 GCTGCATATTCGAGACATTGAAACTA 60.019 38.462 0.00 0.00 32.46 2.24
312 313 5.220739 GCTGCATATTCGAGACATTGAAACT 60.221 40.000 0.00 0.00 32.46 2.66
316 317 2.796593 CGCTGCATATTCGAGACATTGA 59.203 45.455 0.00 0.00 0.00 2.57
320 321 0.744281 TCCGCTGCATATTCGAGACA 59.256 50.000 0.00 0.00 0.00 3.41
349 352 2.046700 TACGCCCGCCAAGAAAGG 60.047 61.111 0.00 0.00 0.00 3.11
351 354 2.046700 CCTACGCCCGCCAAGAAA 60.047 61.111 0.00 0.00 0.00 2.52
369 372 4.523173 TGACGGTATCACCTGATATTCTCC 59.477 45.833 0.00 0.00 39.03 3.71
390 393 4.202357 GGTATGATGGGAGCATACAAGTGA 60.202 45.833 12.60 0.00 46.16 3.41
418 421 9.712305 TCAAAACATTTAAACTTGACCTTTTCA 57.288 25.926 0.00 0.00 0.00 2.69
457 460 9.292846 CTTATGTGTTGTGAACATCCATAATTG 57.707 33.333 10.51 1.87 44.35 2.32
492 496 9.118236 CCGAATTTTGATCTGAAACTTTTAGAC 57.882 33.333 0.00 0.00 0.00 2.59
493 497 9.062524 TCCGAATTTTGATCTGAAACTTTTAGA 57.937 29.630 0.00 0.00 0.00 2.10
495 499 8.846211 ACTCCGAATTTTGATCTGAAACTTTTA 58.154 29.630 0.00 0.00 0.00 1.52
500 504 7.015877 GTGTACTCCGAATTTTGATCTGAAAC 58.984 38.462 0.00 0.00 0.00 2.78
517 521 8.088981 TCTTCTTTGTTTCTCTATGTGTACTCC 58.911 37.037 0.00 0.00 0.00 3.85
539 543 6.797033 CAGTATTCACATTCGGTTTTGTCTTC 59.203 38.462 0.00 0.00 0.00 2.87
562 566 6.017109 AGCATAAACAGTGTCAAAACCTACAG 60.017 38.462 0.00 0.00 0.00 2.74
597 603 8.560576 AAGACAAATTCAACATAAAAGTGTCG 57.439 30.769 0.00 0.00 0.00 4.35
763 769 5.425217 TCAGATGATACCACCACTTGTATGT 59.575 40.000 0.00 0.00 0.00 2.29
774 780 4.130118 GGGTGAACATCAGATGATACCAC 58.870 47.826 24.04 19.50 34.88 4.16
783 789 1.215382 CGCTCGGGTGAACATCAGA 59.785 57.895 0.00 0.00 0.00 3.27
784 790 1.078759 GACGCTCGGGTGAACATCAG 61.079 60.000 0.98 0.00 0.00 2.90
836 842 1.658095 GAGATGAGCTTTGAGTCGTGC 59.342 52.381 0.00 0.00 0.00 5.34
842 848 5.005203 GTGTACATTCGAGATGAGCTTTGAG 59.995 44.000 0.00 0.00 0.00 3.02
848 854 3.066369 TCGTGTACATTCGAGATGAGC 57.934 47.619 0.00 6.80 0.00 4.26
891 897 2.510238 GCGATCGAGCTTGCACCT 60.510 61.111 21.57 0.00 0.00 4.00
920 926 2.163412 ACGCTGCTAGAGAAGAGTGAAG 59.837 50.000 0.00 0.00 32.20 3.02
1189 1212 1.065928 CGCCCCAGTCGTAGATGTC 59.934 63.158 0.00 0.00 40.67 3.06
1312 1335 5.699915 GGTAGTTGGAGAAGTTGGTCTTAAC 59.300 44.000 0.00 0.00 36.40 2.01
1343 1366 3.217743 GCTCGCGGTAGTAGGGCT 61.218 66.667 6.13 0.00 0.00 5.19
1438 1461 2.182791 CGCCGAGTGCATCTCAGT 59.817 61.111 14.09 0.00 42.88 3.41
1840 1863 2.586792 GTCTTGCAGGCTCCCGAT 59.413 61.111 0.00 0.00 0.00 4.18
1845 1868 3.123620 CAGCGGTCTTGCAGGCTC 61.124 66.667 0.00 0.00 37.31 4.70
2012 2035 4.717629 CAAGGACGCGTGCCTCGA 62.718 66.667 27.74 0.00 42.86 4.04
2816 2839 2.282180 ACGGTGGTGCAATGGACC 60.282 61.111 17.42 17.42 0.00 4.46
2869 2892 1.408702 CAGTTTGTTTGGGTGGTCAGG 59.591 52.381 0.00 0.00 0.00 3.86
2915 2945 6.816136 TCCCAAAATCAGGAAAAGAAAGTTC 58.184 36.000 0.00 0.00 0.00 3.01
2918 2948 6.071952 TCGATCCCAAAATCAGGAAAAGAAAG 60.072 38.462 0.00 0.00 35.30 2.62
2922 2952 5.048083 TGTTCGATCCCAAAATCAGGAAAAG 60.048 40.000 0.00 0.00 35.30 2.27
2941 2976 1.530441 CCATCATTCTTGCGCTGTTCG 60.530 52.381 9.73 0.00 42.12 3.95
3025 3072 2.754946 ATTGCCTGCATGGTTGAAAG 57.245 45.000 0.00 0.00 38.35 2.62
3044 3091 2.977829 CGTCTCGAACGTCTTGATCAAA 59.022 45.455 9.88 0.00 46.42 2.69
3127 3205 1.233019 CAAGCAAGGACCACACAGAG 58.767 55.000 0.00 0.00 0.00 3.35
3146 3226 1.326548 GTGGACGCGATAATTGGTGAC 59.673 52.381 15.93 0.00 0.00 3.67
3171 3251 8.460831 TTAACGAGAAACGGTATAACTTTACC 57.539 34.615 0.00 0.00 43.84 2.85
3176 3256 9.807649 ACATATTTAACGAGAAACGGTATAACT 57.192 29.630 0.00 0.00 43.84 2.24
3179 3259 9.585099 ACAACATATTTAACGAGAAACGGTATA 57.415 29.630 0.00 0.00 43.84 1.47
3270 3374 1.227089 CTTCACCCCGAGCGATGAG 60.227 63.158 0.00 0.00 0.00 2.90
3339 3457 8.717821 CATTCTCTTTTGACTTCCAACGTAATA 58.282 33.333 0.00 0.00 33.85 0.98
3506 3630 7.703328 ACAAATAGTCACGTTCAAGTTGATTT 58.297 30.769 6.36 0.00 0.00 2.17
3513 3637 7.520119 TGCTATACAAATAGTCACGTTCAAG 57.480 36.000 0.00 0.00 37.90 3.02
3552 3676 0.164432 GGGTTTCTTACGGCGTTTCG 59.836 55.000 21.24 7.24 0.00 3.46
3569 3693 2.403252 AGTTAGTTTGCATCCGAGGG 57.597 50.000 0.00 0.00 0.00 4.30
3593 3717 0.463654 TTGTCTCAGCTTTGGTGCGT 60.464 50.000 0.00 0.00 38.13 5.24
3594 3718 0.877071 ATTGTCTCAGCTTTGGTGCG 59.123 50.000 0.00 0.00 38.13 5.34
3614 3738 8.462016 ACTAAGATGTTATTGCCTCATTTTCAC 58.538 33.333 0.00 0.00 0.00 3.18
3643 3767 9.269415 GTTATTTAGTTAGCAAATACACCAACG 57.731 33.333 0.00 0.00 29.75 4.10
3672 3796 4.893424 TGCTTTTTCTTAGTGTTCGCTT 57.107 36.364 0.00 0.00 0.00 4.68
3673 3797 4.893424 TTGCTTTTTCTTAGTGTTCGCT 57.107 36.364 0.00 0.00 0.00 4.93
3729 3853 5.119931 ACTTGCGCACTCAATTTTAATGA 57.880 34.783 11.12 0.00 0.00 2.57
3739 3869 1.215014 CTTCGTGACTTGCGCACTCA 61.215 55.000 11.12 11.68 34.18 3.41
3751 3881 3.126858 GCAATTCAATGCCTACTTCGTGA 59.873 43.478 0.00 0.00 40.49 4.35
3828 3971 6.539173 TCCAATGGCTTTCAAAGAGTAGTTA 58.461 36.000 0.00 0.00 0.00 2.24
3833 3976 4.473444 TCTTCCAATGGCTTTCAAAGAGT 58.527 39.130 0.00 0.00 0.00 3.24
3849 3992 2.573462 CTCTTCCTCCACCATTCTTCCA 59.427 50.000 0.00 0.00 0.00 3.53
3851 3994 4.769345 ATCTCTTCCTCCACCATTCTTC 57.231 45.455 0.00 0.00 0.00 2.87
3856 3999 1.849039 CCCAATCTCTTCCTCCACCAT 59.151 52.381 0.00 0.00 0.00 3.55
3867 4010 1.277580 CCACTGCTCCCCCAATCTCT 61.278 60.000 0.00 0.00 0.00 3.10
3882 4025 0.697854 AAGAACCACACCCCTCCACT 60.698 55.000 0.00 0.00 0.00 4.00
3884 4027 1.843421 CAAGAACCACACCCCTCCA 59.157 57.895 0.00 0.00 0.00 3.86
3888 4031 2.600470 GGGCAAGAACCACACCCC 60.600 66.667 0.00 0.00 34.23 4.95
3907 4050 0.606604 ATGTAAACGAGGGCAGACGT 59.393 50.000 0.00 0.00 44.57 4.34
3924 4067 1.227263 CTTCCGTCCGGCCACTATG 60.227 63.158 2.24 0.00 34.68 2.23
3932 4075 4.194720 CGAGCTCCTTCCGTCCGG 62.195 72.222 8.47 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.