Multiple sequence alignment - TraesCS1B01G295400

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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 TraesCS1B01G295400 chr1B 100.000 2803 0 0 1 2803 513482580 513479778 0.000000e+00 5177.0
1 TraesCS1B01G295400 chr1D 91.332 2169 113 29 451 2576 383178816 383176680 0.000000e+00 2894.0
2 TraesCS1B01G295400 chr1D 85.273 421 27 13 50 455 383251291 383250891 4.350000e-108 401.0
3 TraesCS1B01G295400 chr1A 89.101 2404 148 40 460 2803 482964938 482962589 0.000000e+00 2883.0
4 TraesCS1B01G295400 chr1A 85.219 433 27 12 38 455 482966253 482965843 7.230000e-111 411.0
5 TraesCS1B01G295400 chr1A 86.667 270 17 9 2283 2534 482962325 482962057 5.910000e-72 281.0
6 TraesCS1B01G295400 chr1A 98.462 65 1 0 2283 2347 482911439 482911375 6.340000e-22 115.0
7 TraesCS1B01G295400 chr3B 80.357 224 20 15 1156 1355 612799907 612800130 6.260000e-32 148.0
8 TraesCS1B01G295400 chr3A 80.176 227 18 15 1156 1355 604325763 604325989 8.090000e-31 145.0
9 TraesCS1B01G295400 chr3D 79.736 227 19 15 1156 1355 461951390 461951616 3.760000e-29 139.0
10 TraesCS1B01G295400 chr4D 76.650 197 38 4 1162 1354 351737265 351737457 4.940000e-18 102.0
11 TraesCS1B01G295400 chr5A 91.304 69 6 0 1286 1354 651588881 651588949 8.270000e-16 95.3
12 TraesCS1B01G295400 chr5A 91.304 69 6 0 1286 1354 651635828 651635896 8.270000e-16 95.3
13 TraesCS1B01G295400 chr5A 86.667 75 10 0 1157 1231 651755183 651755257 1.790000e-12 84.2
14 TraesCS1B01G295400 chr5D 89.855 69 7 0 1286 1354 525388793 525388861 3.850000e-14 89.8
15 TraesCS1B01G295400 chr5D 83.516 91 14 1 1142 1231 525086290 525086200 1.790000e-12 84.2
16 TraesCS1B01G295400 chr5D 86.667 75 10 0 1157 1231 525302716 525302790 1.790000e-12 84.2
17 TraesCS1B01G295400 chr5D 74.786 234 34 18 1143 1354 525119259 525119029 6.440000e-12 82.4
18 TraesCS1B01G295400 chr5B 83.516 91 14 1 1142 1231 659471575 659471485 1.790000e-12 84.2
19 TraesCS1B01G295400 chr5B 82.796 93 14 2 1139 1231 659463034 659462944 6.440000e-12 82.4
20 TraesCS1B01G295400 chr5B 85.526 76 11 0 1156 1231 659597166 659597091 2.310000e-11 80.5
21 TraesCS1B01G295400 chr6D 91.228 57 4 1 2114 2169 320698236 320698180 2.990000e-10 76.8
22 TraesCS1B01G295400 chr6B 91.228 57 4 1 2114 2169 502316238 502316294 2.990000e-10 76.8
23 TraesCS1B01G295400 chr6A 91.228 57 4 1 2114 2169 458212061 458212005 2.990000e-10 76.8
24 TraesCS1B01G295400 chr2D 89.831 59 5 1 2112 2169 46297775 46297717 1.080000e-09 75.0
25 TraesCS1B01G295400 chr2D 87.302 63 7 1 2112 2173 467062455 467062517 1.390000e-08 71.3
26 TraesCS1B01G295400 chr7B 86.567 67 5 3 2105 2169 505937479 505937415 1.390000e-08 71.3
27 TraesCS1B01G295400 chr7B 83.333 78 9 3 2101 2176 531614397 531614322 5.010000e-08 69.4


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 TraesCS1B01G295400 chr1B 513479778 513482580 2802 True 5177.000000 5177 100.000000 1 2803 1 chr1B.!!$R1 2802
1 TraesCS1B01G295400 chr1D 383176680 383178816 2136 True 2894.000000 2894 91.332000 451 2576 1 chr1D.!!$R1 2125
2 TraesCS1B01G295400 chr1A 482962057 482966253 4196 True 1191.666667 2883 86.995667 38 2803 3 chr1A.!!$R2 2765

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
512 1428 0.251742 CCCATGGGAAAGCAGTGGAA 60.252 55.0 28.27 0.0 37.5 3.53 F
766 1696 0.907704 TCCCCTACATGCCAGTCGTT 60.908 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 2694 0.591659 TCCAGACAGACACGAACTCG 59.408 55.0 0.0 0.0 46.33 4.18 R
2556 3543 0.248866 CGCTTTGTGTTGGTTGTCCC 60.249 55.0 0.0 0.0 0.00 4.46 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
24 25 7.120789 CAATACCAGAGTTTGCCAAAAATTC 57.879 36.000 0.00 0.00 0.00 2.17
25 26 4.751767 ACCAGAGTTTGCCAAAAATTCA 57.248 36.364 0.00 0.00 0.00 2.57
26 27 4.441792 ACCAGAGTTTGCCAAAAATTCAC 58.558 39.130 0.00 0.00 0.00 3.18
27 28 3.809279 CCAGAGTTTGCCAAAAATTCACC 59.191 43.478 0.00 0.00 0.00 4.02
28 29 4.443315 CCAGAGTTTGCCAAAAATTCACCT 60.443 41.667 0.00 0.00 0.00 4.00
29 30 5.118286 CAGAGTTTGCCAAAAATTCACCTT 58.882 37.500 0.00 0.00 0.00 3.50
30 31 5.006941 CAGAGTTTGCCAAAAATTCACCTTG 59.993 40.000 0.00 0.00 0.00 3.61
31 32 3.627123 AGTTTGCCAAAAATTCACCTTGC 59.373 39.130 0.00 0.00 0.00 4.01
32 33 2.996249 TGCCAAAAATTCACCTTGCA 57.004 40.000 0.00 0.00 0.00 4.08
33 34 2.836262 TGCCAAAAATTCACCTTGCAG 58.164 42.857 0.00 0.00 0.00 4.41
34 35 1.532437 GCCAAAAATTCACCTTGCAGC 59.468 47.619 0.00 0.00 0.00 5.25
35 36 2.807837 GCCAAAAATTCACCTTGCAGCT 60.808 45.455 0.00 0.00 0.00 4.24
36 37 3.554752 GCCAAAAATTCACCTTGCAGCTA 60.555 43.478 0.00 0.00 0.00 3.32
48 49 3.118629 CCTTGCAGCTATGAAGGTAGACA 60.119 47.826 8.73 0.00 33.00 3.41
61 62 1.002087 GGTAGACAGTTGTGACCAGGG 59.998 57.143 7.67 0.00 33.19 4.45
75 76 3.326006 TGACCAGGGAGCATATGAAGATC 59.674 47.826 6.97 0.00 0.00 2.75
76 77 2.641815 ACCAGGGAGCATATGAAGATCC 59.358 50.000 6.97 7.45 0.00 3.36
77 78 2.911636 CCAGGGAGCATATGAAGATCCT 59.088 50.000 6.97 2.56 0.00 3.24
78 79 3.307550 CCAGGGAGCATATGAAGATCCTG 60.308 52.174 6.97 13.72 39.94 3.86
79 80 2.911636 AGGGAGCATATGAAGATCCTGG 59.088 50.000 6.97 0.00 0.00 4.45
80 81 2.909006 GGGAGCATATGAAGATCCTGGA 59.091 50.000 6.97 0.00 0.00 3.86
81 82 3.522750 GGGAGCATATGAAGATCCTGGAT 59.477 47.826 9.42 9.42 0.00 3.41
82 83 4.383989 GGGAGCATATGAAGATCCTGGATC 60.384 50.000 25.90 25.90 39.17 3.36
83 84 4.431809 GAGCATATGAAGATCCTGGATCG 58.568 47.826 26.52 14.17 43.17 3.69
84 85 4.092279 AGCATATGAAGATCCTGGATCGA 58.908 43.478 26.52 16.91 43.17 3.59
87 88 2.827800 TGAAGATCCTGGATCGATGC 57.172 50.000 26.52 18.18 43.17 3.91
88 89 2.041701 TGAAGATCCTGGATCGATGCA 58.958 47.619 26.52 19.11 43.17 3.96
89 90 2.435437 TGAAGATCCTGGATCGATGCAA 59.565 45.455 26.52 7.42 43.17 4.08
90 91 2.835580 AGATCCTGGATCGATGCAAG 57.164 50.000 26.52 14.82 43.17 4.01
91 92 2.045524 AGATCCTGGATCGATGCAAGT 58.954 47.619 26.52 9.29 43.17 3.16
92 93 2.036992 AGATCCTGGATCGATGCAAGTC 59.963 50.000 26.52 16.74 43.17 3.01
103 104 4.102649 TCGATGCAAGTCATGTAACTACG 58.897 43.478 0.00 0.00 35.05 3.51
112 113 3.370061 GTCATGTAACTACGTTGCCTTCC 59.630 47.826 0.00 0.00 0.00 3.46
113 114 2.460757 TGTAACTACGTTGCCTTCCC 57.539 50.000 0.00 0.00 0.00 3.97
125 130 1.866853 GCCTTCCCTCCGCTTGTTTG 61.867 60.000 0.00 0.00 0.00 2.93
141 146 1.673920 GTTTGTTGAACTCGGAGGCAA 59.326 47.619 10.23 10.28 35.31 4.52
167 172 7.800155 TGCCTCGATCAATGTATTTTGATTA 57.200 32.000 1.60 0.00 44.35 1.75
170 175 9.979270 GCCTCGATCAATGTATTTTGATTATAG 57.021 33.333 1.60 1.19 44.35 1.31
203 208 1.187715 CGGTTAATTGCGCAAATCCG 58.812 50.000 28.81 28.80 0.00 4.18
234 239 1.444119 CCACAACCGTCCACACAAGG 61.444 60.000 0.00 0.00 0.00 3.61
267 280 1.600107 TGGTAACATCGGAGGCACC 59.400 57.895 6.99 6.99 46.17 5.01
286 299 3.986006 TCGGCCGACCTGACACAC 61.986 66.667 27.28 0.00 0.00 3.82
313 326 2.762535 AACCACACATACTTCCGAGG 57.237 50.000 0.00 0.00 0.00 4.63
314 327 1.640917 ACCACACATACTTCCGAGGT 58.359 50.000 0.00 0.00 0.00 3.85
315 328 2.811410 ACCACACATACTTCCGAGGTA 58.189 47.619 0.00 0.00 0.00 3.08
370 386 2.949106 GAGCGAGCAAGCAAGCAA 59.051 55.556 12.73 0.00 40.15 3.91
371 387 1.154263 GAGCGAGCAAGCAAGCAAG 60.154 57.895 12.73 0.00 40.15 4.01
372 388 2.804090 GCGAGCAAGCAAGCAAGC 60.804 61.111 3.19 4.16 36.85 4.01
373 389 2.640989 CGAGCAAGCAAGCAAGCA 59.359 55.556 10.52 0.00 36.85 3.91
374 390 1.008194 CGAGCAAGCAAGCAAGCAA 60.008 52.632 10.52 0.00 36.85 3.91
375 391 1.273455 CGAGCAAGCAAGCAAGCAAC 61.273 55.000 10.52 4.50 36.85 4.17
376 392 0.942884 GAGCAAGCAAGCAAGCAACC 60.943 55.000 10.52 0.00 36.85 3.77
377 393 1.227321 GCAAGCAAGCAAGCAACCA 60.227 52.632 3.19 0.00 36.85 3.67
378 394 1.493134 GCAAGCAAGCAAGCAACCAC 61.493 55.000 3.19 0.00 36.85 4.16
411 427 3.608662 GACCACCGTCCGACACCA 61.609 66.667 0.00 0.00 32.40 4.17
412 428 3.853597 GACCACCGTCCGACACCAC 62.854 68.421 0.00 0.00 32.40 4.16
413 429 3.612681 CCACCGTCCGACACCACT 61.613 66.667 0.00 0.00 0.00 4.00
414 430 2.049433 CACCGTCCGACACCACTC 60.049 66.667 0.00 0.00 0.00 3.51
415 431 2.520020 ACCGTCCGACACCACTCA 60.520 61.111 0.00 0.00 0.00 3.41
416 432 2.049433 CCGTCCGACACCACTCAC 60.049 66.667 0.00 0.00 0.00 3.51
417 433 2.049433 CGTCCGACACCACTCACC 60.049 66.667 0.00 0.00 0.00 4.02
439 455 3.198863 CGACAGTCACGCTTTAGTAGT 57.801 47.619 0.41 0.00 0.00 2.73
471 1387 2.801631 ATGCCACGCTAGCTCCTCC 61.802 63.158 13.93 0.00 0.00 4.30
507 1423 0.609131 ACGAACCCATGGGAAAGCAG 60.609 55.000 38.07 21.58 38.96 4.24
508 1424 0.609131 CGAACCCATGGGAAAGCAGT 60.609 55.000 38.07 10.26 38.96 4.40
510 1426 0.542702 AACCCATGGGAAAGCAGTGG 60.543 55.000 38.07 6.78 38.96 4.00
511 1427 1.383799 CCCATGGGAAAGCAGTGGA 59.616 57.895 28.27 0.00 37.50 4.02
512 1428 0.251742 CCCATGGGAAAGCAGTGGAA 60.252 55.000 28.27 0.00 37.50 3.53
513 1429 1.631405 CCATGGGAAAGCAGTGGAAA 58.369 50.000 2.85 0.00 31.59 3.13
514 1430 1.547372 CCATGGGAAAGCAGTGGAAAG 59.453 52.381 2.85 0.00 31.59 2.62
515 1431 2.517959 CATGGGAAAGCAGTGGAAAGA 58.482 47.619 0.00 0.00 0.00 2.52
532 1448 4.023963 GGAAAGAAAGAAAAGTCACTCCCG 60.024 45.833 0.00 0.00 0.00 5.14
539 1455 2.989055 AAAGTCACTCCCGGCACACG 62.989 60.000 0.00 0.00 43.80 4.49
542 1458 4.988598 CACTCCCGGCACACGCTT 62.989 66.667 0.00 0.00 42.52 4.68
577 1493 1.521906 CGTCGTCACCAAACCACCA 60.522 57.895 0.00 0.00 0.00 4.17
580 1496 1.525995 CGTCACCAAACCACCAGCT 60.526 57.895 0.00 0.00 0.00 4.24
588 1506 3.261390 ACCAAACCACCAGCTTATACGTA 59.739 43.478 0.00 0.00 0.00 3.57
766 1696 0.907704 TCCCCTACATGCCAGTCGTT 60.908 55.000 0.00 0.00 0.00 3.85
858 1789 5.821995 AGCTTAGCACAGTACTACTACTACC 59.178 44.000 7.07 0.00 31.46 3.18
865 1796 3.064545 CAGTACTACTACTACCACGTGCC 59.935 52.174 10.91 0.00 31.46 5.01
899 1834 4.629115 AAGGCAGCGCGTGTTTGC 62.629 61.111 8.43 16.05 37.11 3.68
971 1918 1.387756 CCGCGACGTTAAAAAGATCGT 59.612 47.619 8.23 0.00 39.21 3.73
977 1924 1.662122 CGTTAAAAAGATCGTCCGGGG 59.338 52.381 0.00 0.00 0.00 5.73
1006 1953 2.047274 CGCGGGACACCATGAAGT 60.047 61.111 0.00 0.00 36.13 3.01
1315 2265 4.116328 TCTGCGGGCTCGAGTTCG 62.116 66.667 12.03 18.00 39.00 3.95
1515 2465 3.691342 CCGCGTGTGGAGGAGGAA 61.691 66.667 4.92 0.00 37.92 3.36
1668 2618 3.921521 GGTGACGACCGAGGAGAT 58.078 61.111 0.00 0.00 30.61 2.75
1718 2676 1.185618 AACCTCCTCGTGTAGCTGCA 61.186 55.000 0.00 0.00 0.00 4.41
1719 2677 0.972983 ACCTCCTCGTGTAGCTGCAT 60.973 55.000 8.05 0.00 0.00 3.96
1721 2679 1.150567 CTCCTCGTGTAGCTGCATGC 61.151 60.000 18.23 11.82 43.29 4.06
1723 2681 2.509111 TCGTGTAGCTGCATGCCG 60.509 61.111 18.23 10.48 44.23 5.69
1736 2694 3.757248 ATGCCGGGCTGACGATTCC 62.757 63.158 21.46 0.00 35.47 3.01
2049 3011 3.755112 TCTCCGTTCCAACATGTAACA 57.245 42.857 0.00 0.00 0.00 2.41
2051 3013 4.250464 TCTCCGTTCCAACATGTAACATC 58.750 43.478 0.00 0.00 0.00 3.06
2052 3014 3.340034 TCCGTTCCAACATGTAACATCC 58.660 45.455 0.00 0.00 0.00 3.51
2053 3015 2.095213 CCGTTCCAACATGTAACATCCG 59.905 50.000 0.00 0.00 0.00 4.18
2054 3016 2.475519 CGTTCCAACATGTAACATCCGC 60.476 50.000 0.00 0.00 0.00 5.54
2059 3021 0.035534 ACATGTAACATCCGCCTGCA 60.036 50.000 0.00 0.00 0.00 4.41
2094 3056 5.200483 TGTTTGTCCCAGATGACTTCTTTT 58.800 37.500 0.00 0.00 36.21 2.27
2186 3148 8.839343 CATTGACTATGTATGGTGATTGCTTTA 58.161 33.333 0.00 0.00 0.00 1.85
2201 3163 9.614465 GTGATTGCTTTACGTAAAAAGAAAAAC 57.386 29.630 20.47 11.75 37.50 2.43
2423 3394 5.498393 ACTTCTCCACGTAGTAGAATCTGA 58.502 41.667 6.81 0.00 41.61 3.27
2435 3406 9.249457 CGTAGTAGAATCTGAAAATTCATAGCA 57.751 33.333 0.00 0.00 37.98 3.49
2442 3413 8.804912 AATCTGAAAATTCATAGCAGAAGAGT 57.195 30.769 0.00 0.00 38.87 3.24
2470 3441 6.867662 TTCTTCCAAGAAAACAGAGATGAC 57.132 37.500 0.00 0.00 41.75 3.06
2472 3443 6.356556 TCTTCCAAGAAAACAGAGATGACAA 58.643 36.000 0.00 0.00 30.73 3.18
2473 3444 6.828273 TCTTCCAAGAAAACAGAGATGACAAA 59.172 34.615 0.00 0.00 30.73 2.83
2474 3445 6.377327 TCCAAGAAAACAGAGATGACAAAC 57.623 37.500 0.00 0.00 0.00 2.93
2476 3447 5.973565 CCAAGAAAACAGAGATGACAAACAC 59.026 40.000 0.00 0.00 0.00 3.32
2477 3448 5.757850 AGAAAACAGAGATGACAAACACC 57.242 39.130 0.00 0.00 0.00 4.16
2478 3449 4.580580 AGAAAACAGAGATGACAAACACCC 59.419 41.667 0.00 0.00 0.00 4.61
2479 3450 2.568623 ACAGAGATGACAAACACCCC 57.431 50.000 0.00 0.00 0.00 4.95
2481 3452 1.352352 CAGAGATGACAAACACCCCCT 59.648 52.381 0.00 0.00 0.00 4.79
2483 3454 1.630878 GAGATGACAAACACCCCCTCT 59.369 52.381 0.00 0.00 0.00 3.69
2495 3482 0.676736 CCCCCTCTAGATCGTCTTGC 59.323 60.000 0.00 0.00 0.00 4.01
2498 3485 2.366916 CCCCTCTAGATCGTCTTGCAAT 59.633 50.000 0.00 0.00 0.00 3.56
2534 3521 9.976511 AACGATTTTATATTATGAGACGAAGGA 57.023 29.630 0.00 0.00 0.00 3.36
2552 3539 7.222161 ACGAAGGAAGTAGTTGAAAAGGTATT 58.778 34.615 0.00 0.00 0.00 1.89
2558 3545 9.557061 GGAAGTAGTTGAAAAGGTATTATAGGG 57.443 37.037 0.00 0.00 0.00 3.53
2562 3549 9.895138 GTAGTTGAAAAGGTATTATAGGGACAA 57.105 33.333 0.00 0.00 0.00 3.18
2563 3550 8.803397 AGTTGAAAAGGTATTATAGGGACAAC 57.197 34.615 0.00 0.00 34.84 3.32
2564 3551 7.832685 AGTTGAAAAGGTATTATAGGGACAACC 59.167 37.037 0.00 0.00 40.67 3.77
2565 3552 7.273457 TGAAAAGGTATTATAGGGACAACCA 57.727 36.000 0.00 0.00 43.89 3.67
2566 3553 7.700846 TGAAAAGGTATTATAGGGACAACCAA 58.299 34.615 0.00 0.00 43.89 3.67
2567 3554 7.612633 TGAAAAGGTATTATAGGGACAACCAAC 59.387 37.037 0.00 0.00 43.89 3.77
2568 3555 6.645884 AAGGTATTATAGGGACAACCAACA 57.354 37.500 0.00 0.00 43.89 3.33
2569 3556 5.997843 AGGTATTATAGGGACAACCAACAC 58.002 41.667 0.00 0.00 43.89 3.32
2570 3557 5.489637 AGGTATTATAGGGACAACCAACACA 59.510 40.000 0.00 0.00 43.89 3.72
2571 3558 6.012333 AGGTATTATAGGGACAACCAACACAA 60.012 38.462 0.00 0.00 43.89 3.33
2572 3559 6.660094 GGTATTATAGGGACAACCAACACAAA 59.340 38.462 0.00 0.00 43.89 2.83
2573 3560 6.834168 ATTATAGGGACAACCAACACAAAG 57.166 37.500 0.00 0.00 43.89 2.77
2574 3561 1.111277 AGGGACAACCAACACAAAGC 58.889 50.000 0.00 0.00 43.89 3.51
2591 3578 0.681564 AGCGGGACAACCAACACAAA 60.682 50.000 0.00 0.00 40.22 2.83
2612 3599 4.185467 AGCGTAATCCATAGATGAGCTG 57.815 45.455 0.00 0.00 36.53 4.24
2615 3602 4.082517 GCGTAATCCATAGATGAGCTGAGA 60.083 45.833 0.00 0.00 31.29 3.27
2616 3603 5.394005 GCGTAATCCATAGATGAGCTGAGAT 60.394 44.000 0.00 0.00 31.29 2.75
2650 3637 7.102346 TCCCGCATGAACAATAAATTTGAAAT 58.898 30.769 0.00 0.00 0.00 2.17
2652 3639 8.877779 CCCGCATGAACAATAAATTTGAAATAA 58.122 29.630 0.00 0.00 0.00 1.40
2674 3662 8.838649 ATAATAGACAAAAATACCAGGCCTTT 57.161 30.769 0.00 0.00 0.00 3.11
2737 3728 9.507329 TTTTGTCTAGAGCTACTCAAATTTCAT 57.493 29.630 0.00 0.00 32.06 2.57
2757 3748 5.374921 TCATTTGTCCCAAAACATTTGCAT 58.625 33.333 0.00 0.00 0.00 3.96
2758 3749 5.238868 TCATTTGTCCCAAAACATTTGCATG 59.761 36.000 0.00 0.00 36.34 4.06
2788 3780 1.072806 ACTTGAGCATCTTCAGTGCCA 59.927 47.619 0.00 0.00 43.50 4.92
2796 3788 3.858503 GCATCTTCAGTGCCAAAGGAAAC 60.859 47.826 0.00 0.00 36.61 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.705381 TGAATTTTTGGCAAACTCTGGTATTG 59.295 34.615 13.10 0.00 0.00 1.90
1 2 6.705825 GTGAATTTTTGGCAAACTCTGGTATT 59.294 34.615 13.10 4.26 0.00 1.89
2 3 6.223120 GTGAATTTTTGGCAAACTCTGGTAT 58.777 36.000 13.10 0.00 0.00 2.73
3 4 5.452636 GGTGAATTTTTGGCAAACTCTGGTA 60.453 40.000 13.10 0.00 0.00 3.25
4 5 4.441792 GTGAATTTTTGGCAAACTCTGGT 58.558 39.130 13.10 0.00 0.00 4.00
5 6 3.809279 GGTGAATTTTTGGCAAACTCTGG 59.191 43.478 13.10 0.00 0.00 3.86
6 7 4.696455 AGGTGAATTTTTGGCAAACTCTG 58.304 39.130 13.10 0.00 0.00 3.35
7 8 5.118286 CAAGGTGAATTTTTGGCAAACTCT 58.882 37.500 13.10 0.00 0.00 3.24
8 9 4.260743 GCAAGGTGAATTTTTGGCAAACTC 60.261 41.667 13.10 10.14 0.00 3.01
9 10 3.627123 GCAAGGTGAATTTTTGGCAAACT 59.373 39.130 13.10 1.49 0.00 2.66
10 11 3.376546 TGCAAGGTGAATTTTTGGCAAAC 59.623 39.130 13.10 1.52 0.00 2.93
11 12 3.614092 TGCAAGGTGAATTTTTGGCAAA 58.386 36.364 8.93 8.93 0.00 3.68
12 13 3.204526 CTGCAAGGTGAATTTTTGGCAA 58.795 40.909 0.00 0.00 0.00 4.52
13 14 2.836262 CTGCAAGGTGAATTTTTGGCA 58.164 42.857 0.00 0.00 0.00 4.92
14 15 1.532437 GCTGCAAGGTGAATTTTTGGC 59.468 47.619 0.00 0.00 0.00 4.52
26 27 3.118629 TGTCTACCTTCATAGCTGCAAGG 60.119 47.826 13.23 13.23 42.27 3.61
27 28 4.118410 CTGTCTACCTTCATAGCTGCAAG 58.882 47.826 1.02 0.00 0.00 4.01
28 29 3.515502 ACTGTCTACCTTCATAGCTGCAA 59.484 43.478 1.02 0.00 0.00 4.08
29 30 3.099905 ACTGTCTACCTTCATAGCTGCA 58.900 45.455 1.02 0.00 0.00 4.41
30 31 3.810310 ACTGTCTACCTTCATAGCTGC 57.190 47.619 0.00 0.00 0.00 5.25
31 32 4.867047 CACAACTGTCTACCTTCATAGCTG 59.133 45.833 0.00 0.00 0.00 4.24
32 33 4.772624 TCACAACTGTCTACCTTCATAGCT 59.227 41.667 0.00 0.00 0.00 3.32
33 34 4.865365 GTCACAACTGTCTACCTTCATAGC 59.135 45.833 0.00 0.00 0.00 2.97
34 35 5.047306 TGGTCACAACTGTCTACCTTCATAG 60.047 44.000 10.68 0.00 34.08 2.23
35 36 4.836175 TGGTCACAACTGTCTACCTTCATA 59.164 41.667 10.68 0.00 34.08 2.15
36 37 3.646162 TGGTCACAACTGTCTACCTTCAT 59.354 43.478 10.68 0.00 34.08 2.57
48 49 1.656587 TATGCTCCCTGGTCACAACT 58.343 50.000 0.00 0.00 0.00 3.16
61 62 4.159321 TCGATCCAGGATCTTCATATGCTC 59.841 45.833 24.57 0.00 36.96 4.26
75 76 1.871676 CATGACTTGCATCGATCCAGG 59.128 52.381 0.00 0.00 34.15 4.45
76 77 2.558378 ACATGACTTGCATCGATCCAG 58.442 47.619 0.00 0.00 34.15 3.86
77 78 2.696989 ACATGACTTGCATCGATCCA 57.303 45.000 0.00 0.00 34.15 3.41
78 79 4.122776 AGTTACATGACTTGCATCGATCC 58.877 43.478 0.00 0.00 34.15 3.36
79 80 5.108217 CGTAGTTACATGACTTGCATCGATC 60.108 44.000 0.00 0.00 34.15 3.69
80 81 4.740205 CGTAGTTACATGACTTGCATCGAT 59.260 41.667 0.00 0.00 34.15 3.59
81 82 4.102649 CGTAGTTACATGACTTGCATCGA 58.897 43.478 0.00 0.00 34.15 3.59
82 83 3.857665 ACGTAGTTACATGACTTGCATCG 59.142 43.478 0.00 0.00 37.78 3.84
103 104 2.034221 AAGCGGAGGGAAGGCAAC 59.966 61.111 0.00 0.00 0.00 4.17
112 113 1.676006 AGTTCAACAAACAAGCGGAGG 59.324 47.619 0.00 0.00 40.56 4.30
113 114 2.599848 CGAGTTCAACAAACAAGCGGAG 60.600 50.000 0.00 0.00 40.56 4.63
125 130 1.401539 GCAATTGCCTCCGAGTTCAAC 60.402 52.381 20.06 0.00 34.31 3.18
141 146 6.698008 TCAAAATACATTGATCGAGGCAAT 57.302 33.333 9.71 9.71 34.50 3.56
179 184 0.523966 TTGCGCAATTAACCGGGAAG 59.476 50.000 21.02 0.00 0.00 3.46
181 186 1.133407 GATTTGCGCAATTAACCGGGA 59.867 47.619 25.64 5.65 0.00 5.14
182 187 1.555477 GATTTGCGCAATTAACCGGG 58.445 50.000 25.64 0.00 0.00 5.73
234 239 4.780815 TGTTACCATGGAATCTCATGTCC 58.219 43.478 21.47 0.00 42.02 4.02
242 255 3.403038 CCTCCGATGTTACCATGGAATC 58.597 50.000 21.47 13.95 31.91 2.52
286 299 4.804139 GGAAGTATGTGTGGTTATCTGTCG 59.196 45.833 0.00 0.00 0.00 4.35
313 326 4.695455 ACCATGATGTTTGTGTGCTACTAC 59.305 41.667 0.00 0.00 0.00 2.73
314 327 4.905429 ACCATGATGTTTGTGTGCTACTA 58.095 39.130 0.00 0.00 0.00 1.82
315 328 3.753272 GACCATGATGTTTGTGTGCTACT 59.247 43.478 0.00 0.00 0.00 2.57
376 392 3.041940 GTCGGTGGCCAAGTCGTG 61.042 66.667 7.24 0.00 0.00 4.35
377 393 4.657824 CGTCGGTGGCCAAGTCGT 62.658 66.667 7.24 0.00 0.00 4.34
378 394 4.351938 TCGTCGGTGGCCAAGTCG 62.352 66.667 7.24 14.75 0.00 4.18
411 427 2.335369 GTGACTGTCGCGGTGAGT 59.665 61.111 6.13 5.71 0.00 3.41
412 428 2.801162 CGTGACTGTCGCGGTGAG 60.801 66.667 30.14 7.25 45.61 3.51
437 453 3.687698 GTGGCATGGTTAACGAACATACT 59.312 43.478 0.00 0.00 37.29 2.12
438 454 3.484557 CGTGGCATGGTTAACGAACATAC 60.485 47.826 0.00 0.00 38.27 2.39
439 455 2.673862 CGTGGCATGGTTAACGAACATA 59.326 45.455 0.00 0.00 38.27 2.29
483 1399 0.250989 TTCCCATGGGTTCGTTCACC 60.251 55.000 30.28 0.00 36.47 4.02
507 1423 5.221067 GGGAGTGACTTTTCTTTCTTTCCAC 60.221 44.000 0.00 0.00 0.00 4.02
508 1424 4.887655 GGGAGTGACTTTTCTTTCTTTCCA 59.112 41.667 0.00 0.00 0.00 3.53
510 1426 4.023963 CCGGGAGTGACTTTTCTTTCTTTC 60.024 45.833 0.00 0.00 0.00 2.62
511 1427 3.883489 CCGGGAGTGACTTTTCTTTCTTT 59.117 43.478 0.00 0.00 0.00 2.52
512 1428 3.477530 CCGGGAGTGACTTTTCTTTCTT 58.522 45.455 0.00 0.00 0.00 2.52
513 1429 2.810767 GCCGGGAGTGACTTTTCTTTCT 60.811 50.000 2.18 0.00 0.00 2.52
514 1430 1.535896 GCCGGGAGTGACTTTTCTTTC 59.464 52.381 2.18 0.00 0.00 2.62
515 1431 1.133915 TGCCGGGAGTGACTTTTCTTT 60.134 47.619 2.18 0.00 0.00 2.52
532 1448 2.128853 TTAGCAAGCAAGCGTGTGCC 62.129 55.000 10.77 0.00 46.14 5.01
539 1455 2.350197 CGCCAGATATTAGCAAGCAAGC 60.350 50.000 0.00 0.00 0.00 4.01
540 1456 2.874701 ACGCCAGATATTAGCAAGCAAG 59.125 45.455 0.00 0.00 0.00 4.01
541 1457 2.872245 GACGCCAGATATTAGCAAGCAA 59.128 45.455 0.00 0.00 0.00 3.91
542 1458 2.483876 GACGCCAGATATTAGCAAGCA 58.516 47.619 0.00 0.00 0.00 3.91
577 1493 1.008079 GCCCGCGTACGTATAAGCT 60.008 57.895 17.90 0.00 37.70 3.74
580 1496 1.359833 CAGGCCCGCGTACGTATAA 59.640 57.895 17.90 0.00 37.70 0.98
736 1658 3.759581 CATGTAGGGGATGGGATCTTTG 58.240 50.000 0.00 0.00 0.00 2.77
926 1861 1.007238 CTTCTCCTCTCTGGGTGGGTA 59.993 57.143 0.00 0.00 36.20 3.69
929 1864 1.621672 GGCTTCTCCTCTCTGGGTGG 61.622 65.000 0.00 0.00 36.20 4.61
930 1865 0.906756 TGGCTTCTCCTCTCTGGGTG 60.907 60.000 0.00 0.00 36.20 4.61
1350 2300 2.195567 TGGCTCAACCTGCTTGTGC 61.196 57.895 3.39 3.39 45.05 4.57
1498 2448 3.649277 CTTCCTCCTCCACACGCGG 62.649 68.421 12.47 1.27 0.00 6.46
1668 2618 4.287781 TCTGACGCGGCGGAACAA 62.288 61.111 24.09 0.00 0.00 2.83
1718 2676 2.203070 GAATCGTCAGCCCGGCAT 60.203 61.111 13.15 0.00 0.00 4.40
1719 2677 4.467084 GGAATCGTCAGCCCGGCA 62.467 66.667 13.15 0.00 0.00 5.69
1721 2679 3.774959 CTCGGAATCGTCAGCCCGG 62.775 68.421 0.00 0.00 42.03 5.73
1723 2681 0.806492 GAACTCGGAATCGTCAGCCC 60.806 60.000 0.00 0.00 37.69 5.19
1736 2694 0.591659 TCCAGACAGACACGAACTCG 59.408 55.000 0.00 0.00 46.33 4.18
1836 2794 5.362263 GCAATAGCCATGGAACATGAAAAT 58.638 37.500 18.40 0.00 37.87 1.82
1864 2826 5.978919 ACTGACTAGATTCTAGACGTACTCG 59.021 44.000 24.24 10.53 43.34 4.18
1866 2828 7.069085 AGAGACTGACTAGATTCTAGACGTACT 59.931 40.741 24.24 16.89 0.00 2.73
1988 2950 2.970324 GCTCGTTGTCGGCACCAA 60.970 61.111 0.00 0.00 37.69 3.67
1989 2951 3.529341 ATGCTCGTTGTCGGCACCA 62.529 57.895 0.00 0.00 42.38 4.17
2053 3015 1.303309 CATGGTAGTTAGCTGCAGGC 58.697 55.000 17.12 7.98 42.19 4.85
2054 3016 2.698855 ACATGGTAGTTAGCTGCAGG 57.301 50.000 17.12 0.00 0.00 4.85
2059 3021 3.329520 TGGGACAAACATGGTAGTTAGCT 59.670 43.478 0.00 0.00 31.92 3.32
2160 3122 6.872628 AGCAATCACCATACATAGTCAATG 57.127 37.500 0.00 0.00 41.74 2.82
2173 3135 6.621316 TCTTTTTACGTAAAGCAATCACCA 57.379 33.333 19.31 0.41 35.56 4.17
2178 3140 8.705048 TGGTTTTTCTTTTTACGTAAAGCAAT 57.295 26.923 19.31 0.00 35.56 3.56
2186 3148 9.240159 GATGTTACATGGTTTTTCTTTTTACGT 57.760 29.630 1.24 0.00 0.00 3.57
2201 3163 2.238942 TAGCTGCGGATGTTACATGG 57.761 50.000 1.24 0.00 0.00 3.66
2335 3302 3.415212 AGCTGCTTTGCTTCATTACAGA 58.585 40.909 0.00 0.00 40.93 3.41
2462 3433 1.630878 GAGGGGGTGTTTGTCATCTCT 59.369 52.381 0.00 0.00 0.00 3.10
2464 3435 1.747444 AGAGGGGGTGTTTGTCATCT 58.253 50.000 0.00 0.00 0.00 2.90
2465 3436 2.838202 TCTAGAGGGGGTGTTTGTCATC 59.162 50.000 0.00 0.00 0.00 2.92
2467 3438 2.409064 TCTAGAGGGGGTGTTTGTCA 57.591 50.000 0.00 0.00 0.00 3.58
2470 3441 1.831736 ACGATCTAGAGGGGGTGTTTG 59.168 52.381 0.00 0.00 0.00 2.93
2472 3443 1.288335 AGACGATCTAGAGGGGGTGTT 59.712 52.381 0.00 0.00 0.00 3.32
2473 3444 0.927767 AGACGATCTAGAGGGGGTGT 59.072 55.000 0.00 0.00 0.00 4.16
2474 3445 1.683917 CAAGACGATCTAGAGGGGGTG 59.316 57.143 0.00 0.00 0.00 4.61
2476 3447 0.676736 GCAAGACGATCTAGAGGGGG 59.323 60.000 0.00 0.00 0.00 5.40
2477 3448 1.403814 TGCAAGACGATCTAGAGGGG 58.596 55.000 0.00 0.00 0.00 4.79
2478 3449 3.742433 ATTGCAAGACGATCTAGAGGG 57.258 47.619 4.94 0.00 0.00 4.30
2479 3450 4.022416 AGCTATTGCAAGACGATCTAGAGG 60.022 45.833 4.94 0.00 42.74 3.69
2481 3452 5.284864 CAAGCTATTGCAAGACGATCTAGA 58.715 41.667 4.94 0.00 42.74 2.43
2552 3539 4.076394 GCTTTGTGTTGGTTGTCCCTATA 58.924 43.478 0.00 0.00 0.00 1.31
2556 3543 0.248866 CGCTTTGTGTTGGTTGTCCC 60.249 55.000 0.00 0.00 0.00 4.46
2557 3544 0.248866 CCGCTTTGTGTTGGTTGTCC 60.249 55.000 0.00 0.00 0.00 4.02
2558 3545 0.248866 CCCGCTTTGTGTTGGTTGTC 60.249 55.000 0.00 0.00 0.00 3.18
2559 3546 0.681564 TCCCGCTTTGTGTTGGTTGT 60.682 50.000 0.00 0.00 0.00 3.32
2560 3547 0.248866 GTCCCGCTTTGTGTTGGTTG 60.249 55.000 0.00 0.00 0.00 3.77
2562 3549 0.681564 TTGTCCCGCTTTGTGTTGGT 60.682 50.000 0.00 0.00 0.00 3.67
2563 3550 0.248866 GTTGTCCCGCTTTGTGTTGG 60.249 55.000 0.00 0.00 0.00 3.77
2564 3551 0.248866 GGTTGTCCCGCTTTGTGTTG 60.249 55.000 0.00 0.00 0.00 3.33
2565 3552 0.681564 TGGTTGTCCCGCTTTGTGTT 60.682 50.000 0.00 0.00 35.15 3.32
2566 3553 0.681564 TTGGTTGTCCCGCTTTGTGT 60.682 50.000 0.00 0.00 35.15 3.72
2567 3554 0.248866 GTTGGTTGTCCCGCTTTGTG 60.249 55.000 0.00 0.00 35.15 3.33
2568 3555 0.681564 TGTTGGTTGTCCCGCTTTGT 60.682 50.000 0.00 0.00 35.15 2.83
2569 3556 0.248866 GTGTTGGTTGTCCCGCTTTG 60.249 55.000 0.00 0.00 35.15 2.77
2570 3557 0.681564 TGTGTTGGTTGTCCCGCTTT 60.682 50.000 0.00 0.00 35.15 3.51
2571 3558 0.681564 TTGTGTTGGTTGTCCCGCTT 60.682 50.000 0.00 0.00 35.15 4.68
2572 3559 0.681564 TTTGTGTTGGTTGTCCCGCT 60.682 50.000 0.00 0.00 35.15 5.52
2573 3560 0.248866 CTTTGTGTTGGTTGTCCCGC 60.249 55.000 0.00 0.00 35.15 6.13
2574 3561 0.248866 GCTTTGTGTTGGTTGTCCCG 60.249 55.000 0.00 0.00 35.15 5.14
2591 3578 3.829026 TCAGCTCATCTATGGATTACGCT 59.171 43.478 0.00 0.00 31.04 5.07
2612 3599 3.256879 TCATGCGGGAGTAGATGAATCTC 59.743 47.826 0.00 0.00 38.32 2.75
2615 3602 3.134623 TGTTCATGCGGGAGTAGATGAAT 59.865 43.478 0.00 0.00 35.82 2.57
2616 3603 2.499693 TGTTCATGCGGGAGTAGATGAA 59.500 45.455 0.00 0.00 33.08 2.57
2650 3637 9.756571 TTAAAGGCCTGGTATTTTTGTCTATTA 57.243 29.630 5.69 0.00 0.00 0.98
2652 3639 8.658840 TTTAAAGGCCTGGTATTTTTGTCTAT 57.341 30.769 5.69 0.00 0.00 1.98
2758 3749 0.393537 ATGCTCAAGTGTGCTAGGGC 60.394 55.000 6.87 0.00 35.73 5.19
2771 3763 2.156917 CTTTGGCACTGAAGATGCTCA 58.843 47.619 0.00 0.00 42.93 4.26
2774 3766 1.538047 TCCTTTGGCACTGAAGATGC 58.462 50.000 0.00 0.00 42.62 3.91


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

AutoCloner maintained by Alex Coulton.