Multiple sequence alignment - TraesCS5A01G326000

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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 TraesCS5A01G326000 chr5A 100.000 3260 0 0 1 3260 536677328 536674069 0.000000e+00 6021.0
1 TraesCS5A01G326000 chr5A 85.921 2692 305 25 412 3068 536656852 536654200 0.000000e+00 2804.0
2 TraesCS5A01G326000 chr5A 79.384 1819 319 39 850 2632 536796688 536798486 0.000000e+00 1230.0
3 TraesCS5A01G326000 chr5A 81.210 1554 259 21 847 2396 536852974 536854498 0.000000e+00 1221.0
4 TraesCS5A01G326000 chr5A 79.830 1646 282 29 1015 2627 536869675 536871303 0.000000e+00 1155.0
5 TraesCS5A01G326000 chr5A 76.000 150 32 4 237 384 382073059 382073206 1.250000e-09 75.0
6 TraesCS5A01G326000 chr5B 95.162 2687 108 9 436 3115 510728294 510725623 0.000000e+00 4222.0
7 TraesCS5A01G326000 chr5B 79.454 1869 320 42 804 2632 510887134 510888978 0.000000e+00 1266.0
8 TraesCS5A01G326000 chr5B 79.777 1790 320 28 868 2632 511026528 511028300 0.000000e+00 1262.0
9 TraesCS5A01G326000 chr5B 95.973 149 4 1 3112 3260 393717043 393717189 1.170000e-59 241.0
10 TraesCS5A01G326000 chr5D 86.496 2229 284 10 412 2634 423229566 423227349 0.000000e+00 2433.0
11 TraesCS5A01G326000 chr5D 79.389 1897 314 52 782 2632 423317394 423319259 0.000000e+00 1266.0
12 TraesCS5A01G326000 chr5D 90.435 345 21 12 51 392 423230015 423229680 8.300000e-121 444.0
13 TraesCS5A01G326000 chr5D 81.407 398 65 9 2654 3048 423222156 423221765 1.890000e-82 316.0
14 TraesCS5A01G326000 chr5D 81.667 120 17 5 295 411 513645938 513646055 9.630000e-16 95.3
15 TraesCS5A01G326000 chr5D 80.851 94 16 2 237 329 288550315 288550407 4.510000e-09 73.1
16 TraesCS5A01G326000 chr4A 97.931 145 1 2 3116 3260 374219550 374219408 1.940000e-62 250.0
17 TraesCS5A01G326000 chr4A 97.260 146 2 2 3115 3260 165515846 165515989 2.510000e-61 246.0
18 TraesCS5A01G326000 chr2A 97.279 147 2 2 3115 3260 126453911 126453766 6.980000e-62 248.0
19 TraesCS5A01G326000 chr3B 97.241 145 4 0 3116 3260 656450725 656450581 2.510000e-61 246.0
20 TraesCS5A01G326000 chr7D 97.241 145 3 1 3116 3260 197264805 197264662 9.040000e-61 244.0
21 TraesCS5A01G326000 chr7D 79.375 160 27 5 254 410 541380881 541380725 1.240000e-19 108.0
22 TraesCS5A01G326000 chr4D 96.599 147 3 2 3114 3260 19501302 19501158 3.250000e-60 243.0
23 TraesCS5A01G326000 chr2B 96.599 147 3 2 3115 3260 212880235 212880090 3.250000e-60 243.0
24 TraesCS5A01G326000 chr6A 94.839 155 6 2 3107 3260 31258564 31258411 1.170000e-59 241.0
25 TraesCS5A01G326000 chr3A 80.000 175 28 7 242 412 8796891 8797062 4.420000e-24 122.0
26 TraesCS5A01G326000 chr4B 78.344 157 28 6 240 392 521734982 521734828 2.680000e-16 97.1
27 TraesCS5A01G326000 chrUn 81.731 104 15 3 240 342 320357055 320357155 2.080000e-12 84.2
28 TraesCS5A01G326000 chr6B 81.731 104 15 3 240 342 19906127 19906227 2.080000e-12 84.2


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 TraesCS5A01G326000 chr5A 536674069 536677328 3259 True 6021.0 6021 100.0000 1 3260 1 chr5A.!!$R2 3259
1 TraesCS5A01G326000 chr5A 536654200 536656852 2652 True 2804.0 2804 85.9210 412 3068 1 chr5A.!!$R1 2656
2 TraesCS5A01G326000 chr5A 536796688 536798486 1798 False 1230.0 1230 79.3840 850 2632 1 chr5A.!!$F2 1782
3 TraesCS5A01G326000 chr5A 536852974 536854498 1524 False 1221.0 1221 81.2100 847 2396 1 chr5A.!!$F3 1549
4 TraesCS5A01G326000 chr5A 536869675 536871303 1628 False 1155.0 1155 79.8300 1015 2627 1 chr5A.!!$F4 1612
5 TraesCS5A01G326000 chr5B 510725623 510728294 2671 True 4222.0 4222 95.1620 436 3115 1 chr5B.!!$R1 2679
6 TraesCS5A01G326000 chr5B 510887134 510888978 1844 False 1266.0 1266 79.4540 804 2632 1 chr5B.!!$F2 1828
7 TraesCS5A01G326000 chr5B 511026528 511028300 1772 False 1262.0 1262 79.7770 868 2632 1 chr5B.!!$F3 1764
8 TraesCS5A01G326000 chr5D 423227349 423230015 2666 True 1438.5 2433 88.4655 51 2634 2 chr5D.!!$R2 2583
9 TraesCS5A01G326000 chr5D 423317394 423319259 1865 False 1266.0 1266 79.3890 782 2632 1 chr5D.!!$F2 1850

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
21 22 0.174389 TTTGTTGGCTTTGCTTGCGA 59.826 45.0 0.00 0.0 0.00 5.10 F
1293 1410 0.179065 GGATACCAAGCACCGGGTAC 60.179 60.0 6.32 0.0 42.12 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1576 0.535335 GTCGGCAAGGTGATGGTAGA 59.465 55.0 0.0 0.0 0.0 2.59 R
3143 3353 0.106669 GTTGCCTATTCACCCTCCCC 60.107 60.0 0.0 0.0 0.0 4.81 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
19 20 1.938625 TCTTTGTTGGCTTTGCTTGC 58.061 45.000 0.00 0.00 0.00 4.01
20 21 0.578211 CTTTGTTGGCTTTGCTTGCG 59.422 50.000 0.00 0.00 0.00 4.85
21 22 0.174389 TTTGTTGGCTTTGCTTGCGA 59.826 45.000 0.00 0.00 0.00 5.10
22 23 0.248990 TTGTTGGCTTTGCTTGCGAG 60.249 50.000 0.00 0.00 0.00 5.03
23 24 1.372128 GTTGGCTTTGCTTGCGAGG 60.372 57.895 2.37 0.00 0.00 4.63
24 25 1.827789 TTGGCTTTGCTTGCGAGGT 60.828 52.632 2.37 0.00 0.00 3.85
25 26 0.536233 TTGGCTTTGCTTGCGAGGTA 60.536 50.000 2.37 0.00 0.00 3.08
26 27 1.234615 TGGCTTTGCTTGCGAGGTAC 61.235 55.000 2.37 0.00 0.00 3.34
28 29 0.875059 GCTTTGCTTGCGAGGTACTT 59.125 50.000 2.37 0.00 41.55 2.24
29 30 1.135944 GCTTTGCTTGCGAGGTACTTC 60.136 52.381 2.37 0.00 41.55 3.01
30 31 1.464997 CTTTGCTTGCGAGGTACTTCC 59.535 52.381 2.37 0.00 41.55 3.46
47 48 8.832735 AGGTACTTCCTATGTAAAGAAATTGGA 58.167 33.333 0.00 0.00 46.10 3.53
48 49 9.457436 GGTACTTCCTATGTAAAGAAATTGGAA 57.543 33.333 0.00 0.00 35.99 3.53
67 68 2.503895 AAATAGTGCCAGCTGCTTCT 57.496 45.000 8.66 8.01 42.00 2.85
91 92 8.999431 TCTCATTTCTTCAACCAGTAATTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
108 109 7.793948 AATTGTACTAAGTGGTCTTCTAGGT 57.206 36.000 0.00 0.00 35.36 3.08
112 113 8.517062 TGTACTAAGTGGTCTTCTAGGTAATC 57.483 38.462 0.00 0.00 35.36 1.75
133 134 9.022884 GTAATCCCTCTTTCCTAATAGTACGAT 57.977 37.037 0.00 0.00 0.00 3.73
135 136 7.992754 TCCCTCTTTCCTAATAGTACGATAC 57.007 40.000 0.00 0.00 0.00 2.24
136 137 6.652481 TCCCTCTTTCCTAATAGTACGATACG 59.348 42.308 0.00 0.00 0.00 3.06
137 138 6.652481 CCCTCTTTCCTAATAGTACGATACGA 59.348 42.308 0.00 0.00 0.00 3.43
152 153 3.606384 CGATACGAGTTCGAGTACCATGG 60.606 52.174 11.19 11.19 43.02 3.66
164 165 3.456277 GAGTACCATGGACCAGGATCTTT 59.544 47.826 21.47 0.00 0.00 2.52
249 251 0.554792 AGCGCTAGGGGTCTAAGGTA 59.445 55.000 8.99 0.00 0.00 3.08
252 254 2.595238 CGCTAGGGGTCTAAGGTATGT 58.405 52.381 0.00 0.00 0.00 2.29
264 266 1.755179 AGGTATGTTGACATGGCAGC 58.245 50.000 8.73 8.73 37.15 5.25
285 287 1.679153 CACATGGCCGTATTTTACCCC 59.321 52.381 0.00 0.00 0.00 4.95
292 294 2.424601 GCCGTATTTTACCCCCTCAAAC 59.575 50.000 0.00 0.00 0.00 2.93
293 295 3.688235 CCGTATTTTACCCCCTCAAACA 58.312 45.455 0.00 0.00 0.00 2.83
295 297 4.329392 CGTATTTTACCCCCTCAAACAGT 58.671 43.478 0.00 0.00 0.00 3.55
299 301 5.346181 TTTTACCCCCTCAAACAGTTTTG 57.654 39.130 0.00 0.00 43.17 2.44
300 302 1.119684 ACCCCCTCAAACAGTTTTGC 58.880 50.000 0.00 0.00 41.78 3.68
343 346 8.259049 ACGAGTTTATGGTTTAAATTGATCGA 57.741 30.769 0.00 0.00 0.00 3.59
350 353 9.929722 TTATGGTTTAAATTGATCGATTCTTCG 57.070 29.630 8.68 0.00 46.87 3.79
354 357 8.392612 GGTTTAAATTGATCGATTCTTCGGTTA 58.607 33.333 8.68 0.00 45.53 2.85
376 379 1.062525 GGCCTAAAGCGTGCAATCG 59.937 57.895 0.00 0.00 45.17 3.34
378 381 1.644786 GCCTAAAGCGTGCAATCGGT 61.645 55.000 0.00 0.00 43.29 4.69
392 395 4.704540 TGCAATCGGTTTGAGTTAATGGAT 59.295 37.500 3.06 0.00 37.53 3.41
393 396 5.883115 TGCAATCGGTTTGAGTTAATGGATA 59.117 36.000 3.06 0.00 37.53 2.59
394 397 6.375736 TGCAATCGGTTTGAGTTAATGGATAA 59.624 34.615 3.06 0.00 37.53 1.75
397 400 9.236691 CAATCGGTTTGAGTTAATGGATAAATG 57.763 33.333 0.00 0.00 37.53 2.32
398 401 8.746052 ATCGGTTTGAGTTAATGGATAAATGA 57.254 30.769 0.00 0.00 0.00 2.57
400 403 7.608376 TCGGTTTGAGTTAATGGATAAATGACA 59.392 33.333 0.00 0.00 0.00 3.58
411 414 8.585471 AATGGATAAATGACACATTTCACTCT 57.415 30.769 12.02 0.00 0.00 3.24
412 415 8.585471 ATGGATAAATGACACATTTCACTCTT 57.415 30.769 12.02 0.00 0.00 2.85
419 516 4.202451 TGACACATTTCACTCTTGGGATGA 60.202 41.667 0.00 0.00 0.00 2.92
424 521 4.371624 TTTCACTCTTGGGATGACACAT 57.628 40.909 0.00 0.00 0.00 3.21
426 523 2.094026 TCACTCTTGGGATGACACATCG 60.094 50.000 0.00 0.00 0.00 3.84
432 529 1.224592 GGATGACACATCGGGGCTT 59.775 57.895 0.00 0.00 0.00 4.35
440 537 0.327924 ACATCGGGGCTTGTTCATGA 59.672 50.000 0.00 0.00 0.00 3.07
503 600 1.681538 TGAGAGTAGGCGATGGAGAC 58.318 55.000 0.00 0.00 0.00 3.36
568 665 2.365582 GTCAATGCGGGAGGTGTTATT 58.634 47.619 0.00 0.00 0.00 1.40
583 680 4.443034 GGTGTTATTGCCTTATCGGAGAGT 60.443 45.833 0.00 0.00 43.63 3.24
606 704 1.668628 GCGCGACAAAATTGAATGGGT 60.669 47.619 12.10 0.00 0.00 4.51
630 728 5.757886 TGTTTTGGAATCTCATCAAACGAC 58.242 37.500 0.00 0.00 31.21 4.34
635 733 4.151689 TGGAATCTCATCAAACGACGAAAC 59.848 41.667 0.00 0.00 0.00 2.78
671 769 2.476619 AGATTTAAGCGAATCGATGGCG 59.523 45.455 6.91 14.47 40.22 5.69
701 799 3.691609 GGTCTGACAAATGACTTCCATCC 59.308 47.826 10.38 0.00 33.53 3.51
762 860 1.253100 TTGGGAAATTCGGGAGTTGC 58.747 50.000 0.00 0.00 0.00 4.17
843 947 1.889105 CCATCGATTCACCGCCAGG 60.889 63.158 0.00 0.00 45.13 4.45
931 1043 1.379977 TCCTTCGTCTCCTCCGCAT 60.380 57.895 0.00 0.00 0.00 4.73
966 1078 2.923121 ACCCATCATTGATCTGGTTCG 58.077 47.619 10.32 0.00 0.00 3.95
1005 1122 0.812549 TACTTACCGCAGCGATGTCA 59.187 50.000 18.75 0.00 0.00 3.58
1212 1329 1.599606 CGCTCCTCGCCATAGCCTAT 61.600 60.000 0.00 0.00 34.57 2.57
1229 1346 3.589988 CCTATTGCGATGATAGTGGGAC 58.410 50.000 0.00 0.00 0.00 4.46
1256 1373 4.562394 CGGCGTTGCAATTTCAGATATTTT 59.438 37.500 0.59 0.00 0.00 1.82
1293 1410 0.179065 GGATACCAAGCACCGGGTAC 60.179 60.000 6.32 0.00 42.12 3.34
1305 1422 3.587923 CACCGGGTACGAAATTGTTCTA 58.412 45.455 6.32 0.00 44.60 2.10
1390 1516 4.630785 GCGCGCGGCTAGATCTCA 62.631 66.667 33.06 0.00 39.11 3.27
1421 1547 3.709587 ACTGGATTTTCTACTCTCGGGA 58.290 45.455 0.00 0.00 0.00 5.14
1423 1549 4.342665 ACTGGATTTTCTACTCTCGGGATC 59.657 45.833 0.00 0.00 0.00 3.36
1450 1576 2.534396 TTGAACCCGGCCACTGGAT 61.534 57.895 2.24 0.00 0.00 3.41
1503 1629 2.754552 GGAATTGGTGCATGAGCTACAA 59.245 45.455 0.00 0.00 42.74 2.41
1548 1674 1.482955 CAAAGTCGAGTCGTGTGCG 59.517 57.895 13.12 0.00 39.92 5.34
1695 1821 2.491086 CCCTCCGTCCCATATCTGTACT 60.491 54.545 0.00 0.00 0.00 2.73
2142 2271 4.348020 AGGTATCCTTGGTAGTGGAGAA 57.652 45.455 0.00 0.00 35.63 2.87
2189 2318 7.177878 AGTTATGATCCAAGAAATGACACCTT 58.822 34.615 0.00 0.00 0.00 3.50
2349 2497 3.119137 TCAGTGAGACAATGTACCGATGG 60.119 47.826 0.00 0.00 31.07 3.51
2350 2498 3.096852 AGTGAGACAATGTACCGATGGA 58.903 45.455 0.00 0.00 0.00 3.41
2351 2499 3.706594 AGTGAGACAATGTACCGATGGAT 59.293 43.478 0.00 0.00 0.00 3.41
2352 2500 3.804325 GTGAGACAATGTACCGATGGATG 59.196 47.826 0.00 0.00 0.00 3.51
2353 2501 3.450817 TGAGACAATGTACCGATGGATGT 59.549 43.478 0.00 0.00 0.00 3.06
2354 2502 4.081142 TGAGACAATGTACCGATGGATGTT 60.081 41.667 0.00 0.00 0.00 2.71
2355 2503 4.442706 AGACAATGTACCGATGGATGTTC 58.557 43.478 0.00 0.00 0.00 3.18
2356 2504 3.541632 ACAATGTACCGATGGATGTTCC 58.458 45.455 0.00 0.00 36.96 3.62
2357 2505 2.526304 ATGTACCGATGGATGTTCCG 57.474 50.000 0.00 0.00 40.17 4.30
2358 2506 1.476477 TGTACCGATGGATGTTCCGA 58.524 50.000 0.00 0.00 40.17 4.55
2359 2507 2.036387 TGTACCGATGGATGTTCCGAT 58.964 47.619 0.00 0.00 40.17 4.18
2360 2508 2.223947 TGTACCGATGGATGTTCCGATG 60.224 50.000 0.00 0.00 40.17 3.84
2365 2513 3.187227 CCGATGGATGTTCCGATGAAATC 59.813 47.826 0.00 0.00 40.17 2.17
2727 2935 5.167845 GTTCCTTCACAGTTGCTTGAAAAA 58.832 37.500 0.00 0.00 31.41 1.94
2728 2936 4.743493 TCCTTCACAGTTGCTTGAAAAAC 58.257 39.130 0.00 0.00 31.41 2.43
2729 2937 3.547468 CCTTCACAGTTGCTTGAAAAACG 59.453 43.478 0.00 0.00 31.41 3.60
2732 2940 4.799678 TCACAGTTGCTTGAAAAACGAAA 58.200 34.783 0.00 0.00 0.00 3.46
2733 2941 4.619336 TCACAGTTGCTTGAAAAACGAAAC 59.381 37.500 0.00 0.00 0.00 2.78
2735 2943 4.621034 ACAGTTGCTTGAAAAACGAAACAG 59.379 37.500 0.00 0.00 0.00 3.16
2838 3047 9.218440 CTTTTGCCACCATTATTTTACTGAATT 57.782 29.630 0.00 0.00 0.00 2.17
2952 3162 2.016318 TGAGCGGCTGTTATTGAATGG 58.984 47.619 7.50 0.00 0.00 3.16
3039 3249 5.047021 CAGAACCCTAGTCTCAAGATCAACA 60.047 44.000 0.00 0.00 0.00 3.33
3047 3257 8.037758 CCTAGTCTCAAGATCAACATTTACTGT 58.962 37.037 0.00 0.00 40.84 3.55
3070 3280 9.764363 CTGTACAAATAGGATGCTTATGTAGAA 57.236 33.333 0.00 0.00 0.00 2.10
3125 3335 8.229811 TGTCTTTAACATGTTCTGAAATGATCG 58.770 33.333 15.85 0.00 31.20 3.69
3126 3336 8.443160 GTCTTTAACATGTTCTGAAATGATCGA 58.557 33.333 15.85 1.33 0.00 3.59
3127 3337 9.166173 TCTTTAACATGTTCTGAAATGATCGAT 57.834 29.630 15.85 0.00 0.00 3.59
3131 3341 7.430992 ACATGTTCTGAAATGATCGATATGG 57.569 36.000 0.00 0.00 0.00 2.74
3132 3342 6.994496 ACATGTTCTGAAATGATCGATATGGT 59.006 34.615 0.00 0.00 0.00 3.55
3133 3343 7.500227 ACATGTTCTGAAATGATCGATATGGTT 59.500 33.333 0.00 0.00 0.00 3.67
3134 3344 7.250445 TGTTCTGAAATGATCGATATGGTTG 57.750 36.000 0.00 0.00 0.00 3.77
3135 3345 7.047271 TGTTCTGAAATGATCGATATGGTTGA 58.953 34.615 0.00 0.00 0.00 3.18
3136 3346 7.011389 TGTTCTGAAATGATCGATATGGTTGAC 59.989 37.037 0.00 0.00 0.00 3.18
3137 3347 6.820335 TCTGAAATGATCGATATGGTTGACT 58.180 36.000 0.00 0.00 0.00 3.41
3138 3348 7.951591 TCTGAAATGATCGATATGGTTGACTA 58.048 34.615 0.00 0.00 0.00 2.59
3139 3349 8.084684 TCTGAAATGATCGATATGGTTGACTAG 58.915 37.037 0.00 0.00 0.00 2.57
3140 3350 7.951591 TGAAATGATCGATATGGTTGACTAGA 58.048 34.615 0.00 0.00 0.00 2.43
3141 3351 8.084684 TGAAATGATCGATATGGTTGACTAGAG 58.915 37.037 0.00 0.00 0.00 2.43
3142 3352 5.966742 TGATCGATATGGTTGACTAGAGG 57.033 43.478 0.00 0.00 0.00 3.69
3143 3353 4.767409 TGATCGATATGGTTGACTAGAGGG 59.233 45.833 0.00 0.00 0.00 4.30
3144 3354 3.497332 TCGATATGGTTGACTAGAGGGG 58.503 50.000 0.00 0.00 0.00 4.79
3145 3355 2.563179 CGATATGGTTGACTAGAGGGGG 59.437 54.545 0.00 0.00 0.00 5.40
3159 3369 3.251891 GGGGGAGGGTGAATAGGC 58.748 66.667 0.00 0.00 0.00 3.93
3160 3370 1.696314 GGGGGAGGGTGAATAGGCA 60.696 63.158 0.00 0.00 0.00 4.75
3161 3371 1.286305 GGGGGAGGGTGAATAGGCAA 61.286 60.000 0.00 0.00 0.00 4.52
3162 3372 0.106669 GGGGAGGGTGAATAGGCAAC 60.107 60.000 0.00 0.00 0.00 4.17
3206 3416 9.823647 TTCTTTACCAAATTAAACTTTGCATCA 57.176 25.926 0.00 0.00 35.28 3.07
3207 3417 9.823647 TCTTTACCAAATTAAACTTTGCATCAA 57.176 25.926 0.00 0.00 35.28 2.57
3219 3429 5.695851 CTTTGCATCAAAGTAGGTTGTCT 57.304 39.130 10.28 0.00 43.85 3.41
3220 3430 6.801539 CTTTGCATCAAAGTAGGTTGTCTA 57.198 37.500 10.28 0.00 43.85 2.59
3221 3431 6.801539 TTTGCATCAAAGTAGGTTGTCTAG 57.198 37.500 0.00 0.00 0.00 2.43
3222 3432 5.738619 TGCATCAAAGTAGGTTGTCTAGA 57.261 39.130 0.00 0.00 0.00 2.43
3223 3433 6.299805 TGCATCAAAGTAGGTTGTCTAGAT 57.700 37.500 0.00 0.00 0.00 1.98
3224 3434 7.418337 TGCATCAAAGTAGGTTGTCTAGATA 57.582 36.000 0.00 0.00 0.00 1.98
3225 3435 8.023021 TGCATCAAAGTAGGTTGTCTAGATAT 57.977 34.615 0.00 0.00 0.00 1.63
3226 3436 7.928167 TGCATCAAAGTAGGTTGTCTAGATATG 59.072 37.037 0.00 0.00 0.00 1.78
3227 3437 7.095439 GCATCAAAGTAGGTTGTCTAGATATGC 60.095 40.741 0.00 0.00 0.00 3.14
3228 3438 7.418337 TCAAAGTAGGTTGTCTAGATATGCA 57.582 36.000 0.00 0.00 0.00 3.96
3229 3439 7.847096 TCAAAGTAGGTTGTCTAGATATGCAA 58.153 34.615 0.00 0.00 0.00 4.08
3230 3440 7.764443 TCAAAGTAGGTTGTCTAGATATGCAAC 59.236 37.037 13.07 13.07 40.08 4.17
3231 3441 7.425224 AAGTAGGTTGTCTAGATATGCAACT 57.575 36.000 18.23 7.55 40.49 3.16
3232 3442 8.534954 AAGTAGGTTGTCTAGATATGCAACTA 57.465 34.615 18.23 9.66 40.49 2.24
3233 3443 8.172352 AGTAGGTTGTCTAGATATGCAACTAG 57.828 38.462 18.23 15.26 40.49 2.57
3234 3444 6.412362 AGGTTGTCTAGATATGCAACTAGG 57.588 41.667 18.23 7.22 40.49 3.02
3235 3445 5.900123 AGGTTGTCTAGATATGCAACTAGGT 59.100 40.000 18.23 0.00 40.49 3.08
3236 3446 5.986135 GGTTGTCTAGATATGCAACTAGGTG 59.014 44.000 18.23 2.45 40.49 4.00
3237 3447 6.183360 GGTTGTCTAGATATGCAACTAGGTGA 60.183 42.308 13.29 0.00 40.49 4.02
3238 3448 6.641169 TGTCTAGATATGCAACTAGGTGAG 57.359 41.667 13.29 0.00 37.34 3.51
3239 3449 5.010112 TGTCTAGATATGCAACTAGGTGAGC 59.990 44.000 13.29 0.00 37.34 4.26
3240 3450 5.010112 GTCTAGATATGCAACTAGGTGAGCA 59.990 44.000 13.29 3.07 41.73 4.26
3241 3451 4.760530 AGATATGCAACTAGGTGAGCAA 57.239 40.909 13.29 0.00 40.76 3.91
3242 3452 4.446371 AGATATGCAACTAGGTGAGCAAC 58.554 43.478 13.29 0.00 40.76 4.17
3254 3464 3.743521 GGTGAGCAACCTATATGATGCA 58.256 45.455 11.71 0.00 46.55 3.96
3255 3465 4.136796 GGTGAGCAACCTATATGATGCAA 58.863 43.478 11.71 0.00 46.55 4.08
3256 3466 4.023707 GGTGAGCAACCTATATGATGCAAC 60.024 45.833 11.71 9.22 46.55 4.17
3257 3467 4.576053 GTGAGCAACCTATATGATGCAACA 59.424 41.667 11.71 0.00 41.18 3.33
3258 3468 5.066375 GTGAGCAACCTATATGATGCAACAA 59.934 40.000 11.71 0.00 41.18 2.83
3259 3469 5.066375 TGAGCAACCTATATGATGCAACAAC 59.934 40.000 11.71 0.00 41.18 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.802136 CGCAAGCAAAGCCAACAAAGA 60.802 47.619 0.00 0.00 0.00 2.52
1 2 0.578211 CGCAAGCAAAGCCAACAAAG 59.422 50.000 0.00 0.00 0.00 2.77
6 7 0.536233 TACCTCGCAAGCAAAGCCAA 60.536 50.000 0.00 0.00 37.18 4.52
7 8 1.072332 TACCTCGCAAGCAAAGCCA 59.928 52.632 0.00 0.00 37.18 4.75
8 9 0.955919 AGTACCTCGCAAGCAAAGCC 60.956 55.000 0.00 0.00 37.18 4.35
9 10 0.875059 AAGTACCTCGCAAGCAAAGC 59.125 50.000 0.00 0.00 37.18 3.51
10 11 1.464997 GGAAGTACCTCGCAAGCAAAG 59.535 52.381 0.00 0.00 35.41 2.77
11 12 1.519408 GGAAGTACCTCGCAAGCAAA 58.481 50.000 0.00 0.00 35.41 3.68
12 13 3.226884 GGAAGTACCTCGCAAGCAA 57.773 52.632 0.00 0.00 35.41 3.91
22 23 9.457436 TTCCAATTTCTTTACATAGGAAGTACC 57.543 33.333 0.00 0.00 39.35 3.34
32 33 8.592809 TGGCACTATTTTCCAATTTCTTTACAT 58.407 29.630 0.00 0.00 0.00 2.29
33 34 7.957002 TGGCACTATTTTCCAATTTCTTTACA 58.043 30.769 0.00 0.00 0.00 2.41
34 35 7.063426 GCTGGCACTATTTTCCAATTTCTTTAC 59.937 37.037 0.00 0.00 0.00 2.01
35 36 7.039082 AGCTGGCACTATTTTCCAATTTCTTTA 60.039 33.333 0.00 0.00 0.00 1.85
36 37 5.934043 GCTGGCACTATTTTCCAATTTCTTT 59.066 36.000 0.00 0.00 0.00 2.52
37 38 5.246883 AGCTGGCACTATTTTCCAATTTCTT 59.753 36.000 0.00 0.00 0.00 2.52
38 39 4.774200 AGCTGGCACTATTTTCCAATTTCT 59.226 37.500 0.00 0.00 0.00 2.52
39 40 4.866486 CAGCTGGCACTATTTTCCAATTTC 59.134 41.667 5.57 0.00 0.00 2.17
40 41 4.824289 CAGCTGGCACTATTTTCCAATTT 58.176 39.130 5.57 0.00 0.00 1.82
41 42 3.368739 GCAGCTGGCACTATTTTCCAATT 60.369 43.478 17.12 0.00 43.97 2.32
42 43 2.167075 GCAGCTGGCACTATTTTCCAAT 59.833 45.455 17.12 0.00 43.97 3.16
43 44 1.545582 GCAGCTGGCACTATTTTCCAA 59.454 47.619 17.12 0.00 43.97 3.53
44 45 1.176527 GCAGCTGGCACTATTTTCCA 58.823 50.000 17.12 0.00 43.97 3.53
55 56 1.461559 AGAAATGAGAAGCAGCTGGC 58.538 50.000 17.12 7.98 45.30 4.85
56 57 3.079578 TGAAGAAATGAGAAGCAGCTGG 58.920 45.455 17.12 0.00 0.00 4.85
67 68 8.918202 AGTACAATTACTGGTTGAAGAAATGA 57.082 30.769 0.00 0.00 37.15 2.57
91 92 6.408107 GGGATTACCTAGAAGACCACTTAG 57.592 45.833 0.00 0.00 34.58 2.18
112 113 6.652481 TCGTATCGTACTATTAGGAAAGAGGG 59.348 42.308 0.00 0.00 0.00 4.30
133 134 2.679837 GTCCATGGTACTCGAACTCGTA 59.320 50.000 12.58 0.00 40.80 3.43
134 135 1.471684 GTCCATGGTACTCGAACTCGT 59.528 52.381 12.58 0.00 40.80 4.18
135 136 1.202268 GGTCCATGGTACTCGAACTCG 60.202 57.143 12.58 0.00 41.45 4.18
136 137 1.822990 TGGTCCATGGTACTCGAACTC 59.177 52.381 12.58 0.00 0.00 3.01
137 138 1.825474 CTGGTCCATGGTACTCGAACT 59.175 52.381 12.58 0.00 0.00 3.01
249 251 0.540133 TGTGGCTGCCATGTCAACAT 60.540 50.000 26.22 0.00 35.28 2.71
252 254 1.252215 CCATGTGGCTGCCATGTCAA 61.252 55.000 26.22 8.91 38.39 3.18
264 266 1.679153 GGGTAAAATACGGCCATGTGG 59.321 52.381 2.24 0.00 38.53 4.17
271 273 2.423446 TTGAGGGGGTAAAATACGGC 57.577 50.000 0.00 0.00 0.00 5.68
276 278 5.686387 GCAAAACTGTTTGAGGGGGTAAAAT 60.686 40.000 6.53 0.00 45.99 1.82
281 283 1.119684 GCAAAACTGTTTGAGGGGGT 58.880 50.000 6.53 0.00 45.99 4.95
285 287 6.279882 TCAAATAAGGCAAAACTGTTTGAGG 58.720 36.000 6.53 1.41 45.99 3.86
343 346 4.563140 TTAGGCCAAGTAACCGAAGAAT 57.437 40.909 5.01 0.00 0.00 2.40
348 351 1.673626 CGCTTTAGGCCAAGTAACCGA 60.674 52.381 5.01 0.00 37.74 4.69
349 352 0.725117 CGCTTTAGGCCAAGTAACCG 59.275 55.000 5.01 0.00 37.74 4.44
350 353 1.467342 CACGCTTTAGGCCAAGTAACC 59.533 52.381 5.01 0.00 37.74 2.85
354 357 0.821711 TTGCACGCTTTAGGCCAAGT 60.822 50.000 5.01 0.00 37.74 3.16
376 379 8.519526 TGTGTCATTTATCCATTAACTCAAACC 58.480 33.333 0.00 0.00 0.00 3.27
392 395 6.303054 TCCCAAGAGTGAAATGTGTCATTTA 58.697 36.000 7.54 0.00 0.00 1.40
393 396 5.139727 TCCCAAGAGTGAAATGTGTCATTT 58.860 37.500 7.32 7.32 0.00 2.32
394 397 4.728772 TCCCAAGAGTGAAATGTGTCATT 58.271 39.130 0.00 0.00 0.00 2.57
397 400 4.154918 GTCATCCCAAGAGTGAAATGTGTC 59.845 45.833 0.00 0.00 0.00 3.67
398 401 4.074970 GTCATCCCAAGAGTGAAATGTGT 58.925 43.478 0.00 0.00 0.00 3.72
400 403 4.074970 GTGTCATCCCAAGAGTGAAATGT 58.925 43.478 0.00 0.00 0.00 2.71
404 407 3.617288 CGATGTGTCATCCCAAGAGTGAA 60.617 47.826 4.48 0.00 0.00 3.18
405 408 2.094026 CGATGTGTCATCCCAAGAGTGA 60.094 50.000 4.48 0.00 0.00 3.41
407 410 1.208052 CCGATGTGTCATCCCAAGAGT 59.792 52.381 4.48 0.00 0.00 3.24
409 412 0.541392 CCCGATGTGTCATCCCAAGA 59.459 55.000 4.48 0.00 0.00 3.02
410 413 0.464373 CCCCGATGTGTCATCCCAAG 60.464 60.000 4.48 0.00 0.00 3.61
411 414 1.607071 CCCCGATGTGTCATCCCAA 59.393 57.895 4.48 0.00 0.00 4.12
412 415 3.042733 GCCCCGATGTGTCATCCCA 62.043 63.158 4.48 0.00 0.00 4.37
419 516 0.038166 ATGAACAAGCCCCGATGTGT 59.962 50.000 0.00 0.00 0.00 3.72
424 521 0.617935 TCATCATGAACAAGCCCCGA 59.382 50.000 0.00 0.00 0.00 5.14
426 523 2.686915 CTCTTCATCATGAACAAGCCCC 59.313 50.000 0.00 0.00 32.21 5.80
432 529 3.840078 TCCTCACCTCTTCATCATGAACA 59.160 43.478 0.00 0.00 32.21 3.18
440 537 1.901085 GCCGTCCTCACCTCTTCAT 59.099 57.895 0.00 0.00 0.00 2.57
503 600 4.271816 CCCCATCGCTCGTCCTCG 62.272 72.222 0.00 0.00 38.55 4.63
568 665 1.269723 CGCATACTCTCCGATAAGGCA 59.730 52.381 0.00 0.00 40.77 4.75
583 680 3.433709 CCATTCAATTTTGTCGCGCATA 58.566 40.909 8.75 0.00 0.00 3.14
606 704 6.205784 GTCGTTTGATGAGATTCCAAAACAA 58.794 36.000 0.00 0.00 32.44 2.83
630 728 1.227734 ACGGTCAAGGGTGGTTTCG 60.228 57.895 0.00 0.00 0.00 3.46
635 733 0.324943 AATCTCACGGTCAAGGGTGG 59.675 55.000 0.00 0.00 34.93 4.61
671 769 1.237285 ATTTGTCAGACCAGCCGCAC 61.237 55.000 0.00 0.00 0.00 5.34
701 799 4.502558 GAAACACTTTACAACAGACGTCG 58.497 43.478 10.46 7.86 0.00 5.12
762 860 0.652592 GGATCGATGCAAAGTGTCCG 59.347 55.000 12.54 0.00 0.00 4.79
843 947 1.078143 ATGTCAGAGGGGAAAGCGC 60.078 57.895 0.00 0.00 0.00 5.92
931 1043 1.748732 TGGGTTCAGATGGGGTTGTA 58.251 50.000 0.00 0.00 0.00 2.41
1140 1257 2.338500 GTGATGAAGAGTGGGTCGAAC 58.662 52.381 0.00 0.00 0.00 3.95
1212 1329 1.199615 TGGTCCCACTATCATCGCAA 58.800 50.000 0.00 0.00 0.00 4.85
1229 1346 0.596083 TGAAATTGCAACGCCGTTGG 60.596 50.000 28.94 12.68 42.99 3.77
1242 1359 6.256321 GCACATTGCCGAAAATATCTGAAATT 59.744 34.615 0.00 0.00 37.42 1.82
1256 1373 2.679934 CGCTTCAGCACATTGCCGA 61.680 57.895 0.00 0.00 46.52 5.54
1305 1422 1.215647 GCCCGATGACTCGTTCACT 59.784 57.895 0.00 0.00 43.49 3.41
1375 1501 0.732196 CAGATGAGATCTAGCCGCGC 60.732 60.000 0.00 0.00 37.58 6.86
1390 1516 6.479884 AGTAGAAAATCCAGTTGAAGCAGAT 58.520 36.000 0.00 0.00 0.00 2.90
1450 1576 0.535335 GTCGGCAAGGTGATGGTAGA 59.465 55.000 0.00 0.00 0.00 2.59
1503 1629 3.308473 GCCACTCTTTTATTCCCTCCACT 60.308 47.826 0.00 0.00 0.00 4.00
1548 1674 1.066071 GTAGAGGAGACCTGCCCAAAC 60.066 57.143 0.00 0.00 31.76 2.93
1695 1821 1.749063 ACACATCTTATCTCGCGACCA 59.251 47.619 3.71 0.00 0.00 4.02
2142 2271 1.134280 CGCAGAAATCCATCTCCTGGT 60.134 52.381 0.00 0.00 46.08 4.00
2151 2280 4.816385 GGATCATAACTTCGCAGAAATCCA 59.184 41.667 0.00 0.00 45.90 3.41
2189 2318 6.707290 TCTCCCAATTCTAACGAATCAAGAA 58.293 36.000 0.00 0.00 38.89 2.52
2357 2505 5.296813 AGGCACAAAAGTACGATTTCATC 57.703 39.130 0.00 0.00 0.00 2.92
2358 2506 5.240623 TGAAGGCACAAAAGTACGATTTCAT 59.759 36.000 0.00 0.00 0.00 2.57
2359 2507 4.576873 TGAAGGCACAAAAGTACGATTTCA 59.423 37.500 0.00 0.00 0.00 2.69
2360 2508 5.103290 TGAAGGCACAAAAGTACGATTTC 57.897 39.130 0.00 0.00 0.00 2.17
2365 2513 4.287238 ACTTTGAAGGCACAAAAGTACG 57.713 40.909 8.97 2.36 38.90 3.67
2727 2935 1.595794 CACAAAGTACCGCTGTTTCGT 59.404 47.619 0.00 0.00 0.00 3.85
2728 2936 1.595794 ACACAAAGTACCGCTGTTTCG 59.404 47.619 0.00 0.00 0.00 3.46
2729 2937 4.124594 GTACACAAAGTACCGCTGTTTC 57.875 45.455 0.00 0.00 45.94 2.78
2973 3183 4.785346 AATTGCCACATCCAGAGAGTAT 57.215 40.909 0.00 0.00 0.00 2.12
3078 3288 5.754782 ACATCCACCTAAATGCAGATGTAA 58.245 37.500 11.06 0.00 41.75 2.41
3111 3321 7.225538 AGTCAACCATATCGATCATTTCAGAAC 59.774 37.037 0.00 0.00 0.00 3.01
3115 3325 7.951591 TCTAGTCAACCATATCGATCATTTCA 58.048 34.615 0.00 0.00 0.00 2.69
3116 3326 7.543868 CCTCTAGTCAACCATATCGATCATTTC 59.456 40.741 0.00 0.00 0.00 2.17
3117 3327 7.382110 CCTCTAGTCAACCATATCGATCATTT 58.618 38.462 0.00 0.00 0.00 2.32
3118 3328 6.071108 CCCTCTAGTCAACCATATCGATCATT 60.071 42.308 0.00 0.00 0.00 2.57
3119 3329 5.420421 CCCTCTAGTCAACCATATCGATCAT 59.580 44.000 0.00 0.00 0.00 2.45
3120 3330 4.767409 CCCTCTAGTCAACCATATCGATCA 59.233 45.833 0.00 0.00 0.00 2.92
3121 3331 4.158764 CCCCTCTAGTCAACCATATCGATC 59.841 50.000 0.00 0.00 0.00 3.69
3122 3332 4.090090 CCCCTCTAGTCAACCATATCGAT 58.910 47.826 2.16 2.16 0.00 3.59
3123 3333 3.497332 CCCCTCTAGTCAACCATATCGA 58.503 50.000 0.00 0.00 0.00 3.59
3124 3334 2.563179 CCCCCTCTAGTCAACCATATCG 59.437 54.545 0.00 0.00 0.00 2.92
3142 3352 1.286305 TTGCCTATTCACCCTCCCCC 61.286 60.000 0.00 0.00 0.00 5.40
3143 3353 0.106669 GTTGCCTATTCACCCTCCCC 60.107 60.000 0.00 0.00 0.00 4.81
3144 3354 0.919710 AGTTGCCTATTCACCCTCCC 59.080 55.000 0.00 0.00 0.00 4.30
3145 3355 3.054655 TGTTAGTTGCCTATTCACCCTCC 60.055 47.826 0.00 0.00 0.00 4.30
3146 3356 4.216411 TGTTAGTTGCCTATTCACCCTC 57.784 45.455 0.00 0.00 0.00 4.30
3147 3357 4.650972 TTGTTAGTTGCCTATTCACCCT 57.349 40.909 0.00 0.00 0.00 4.34
3148 3358 5.914898 AATTGTTAGTTGCCTATTCACCC 57.085 39.130 0.00 0.00 0.00 4.61
3149 3359 9.699703 TTAAAAATTGTTAGTTGCCTATTCACC 57.300 29.630 0.00 0.00 0.00 4.02
3180 3390 9.823647 TGATGCAAAGTTTAATTTGGTAAAGAA 57.176 25.926 0.00 0.00 39.94 2.52
3181 3391 9.823647 TTGATGCAAAGTTTAATTTGGTAAAGA 57.176 25.926 0.00 0.00 39.94 2.52
3198 3408 6.530120 TCTAGACAACCTACTTTGATGCAAA 58.470 36.000 0.00 0.00 0.00 3.68
3199 3409 6.109156 TCTAGACAACCTACTTTGATGCAA 57.891 37.500 0.00 0.00 0.00 4.08
3200 3410 5.738619 TCTAGACAACCTACTTTGATGCA 57.261 39.130 0.00 0.00 0.00 3.96
3201 3411 7.095439 GCATATCTAGACAACCTACTTTGATGC 60.095 40.741 0.00 0.00 0.00 3.91
3202 3412 7.928167 TGCATATCTAGACAACCTACTTTGATG 59.072 37.037 0.00 0.00 0.00 3.07
3203 3413 8.023021 TGCATATCTAGACAACCTACTTTGAT 57.977 34.615 0.00 0.00 0.00 2.57
3204 3414 7.418337 TGCATATCTAGACAACCTACTTTGA 57.582 36.000 0.00 0.00 0.00 2.69
3205 3415 7.766278 AGTTGCATATCTAGACAACCTACTTTG 59.234 37.037 16.29 0.00 42.61 2.77
3206 3416 7.852263 AGTTGCATATCTAGACAACCTACTTT 58.148 34.615 16.29 0.03 42.61 2.66
3207 3417 7.425224 AGTTGCATATCTAGACAACCTACTT 57.575 36.000 16.29 0.58 42.61 2.24
3208 3418 7.231722 CCTAGTTGCATATCTAGACAACCTACT 59.768 40.741 16.29 10.57 42.61 2.57
3209 3419 7.014422 ACCTAGTTGCATATCTAGACAACCTAC 59.986 40.741 16.29 5.11 42.61 3.18
3210 3420 7.014326 CACCTAGTTGCATATCTAGACAACCTA 59.986 40.741 16.29 9.74 42.61 3.08
3211 3421 5.900123 ACCTAGTTGCATATCTAGACAACCT 59.100 40.000 16.29 9.28 42.61 3.50
3212 3422 5.986135 CACCTAGTTGCATATCTAGACAACC 59.014 44.000 16.29 3.97 42.61 3.77
3213 3423 6.806751 TCACCTAGTTGCATATCTAGACAAC 58.193 40.000 13.43 13.43 42.08 3.32
3214 3424 6.461648 GCTCACCTAGTTGCATATCTAGACAA 60.462 42.308 17.11 0.00 36.66 3.18
3215 3425 5.010112 GCTCACCTAGTTGCATATCTAGACA 59.990 44.000 17.11 0.00 36.66 3.41
3216 3426 5.010112 TGCTCACCTAGTTGCATATCTAGAC 59.990 44.000 17.11 0.00 36.66 2.59
3217 3427 5.140454 TGCTCACCTAGTTGCATATCTAGA 58.860 41.667 17.11 0.00 36.66 2.43
3218 3428 5.459536 TGCTCACCTAGTTGCATATCTAG 57.540 43.478 11.63 11.63 34.98 2.43
3219 3429 5.453339 GGTTGCTCACCTAGTTGCATATCTA 60.453 44.000 0.00 0.00 43.29 1.98
3220 3430 4.446371 GTTGCTCACCTAGTTGCATATCT 58.554 43.478 0.00 0.00 35.27 1.98
3221 3431 3.561725 GGTTGCTCACCTAGTTGCATATC 59.438 47.826 0.00 0.00 43.29 1.63
3222 3432 3.545703 GGTTGCTCACCTAGTTGCATAT 58.454 45.455 0.00 0.00 43.29 1.78
3223 3433 2.985896 GGTTGCTCACCTAGTTGCATA 58.014 47.619 0.00 0.00 43.29 3.14
3224 3434 1.826385 GGTTGCTCACCTAGTTGCAT 58.174 50.000 0.00 0.00 43.29 3.96
3225 3435 3.322514 GGTTGCTCACCTAGTTGCA 57.677 52.632 0.00 0.00 43.29 4.08
3234 3444 4.576053 TGTTGCATCATATAGGTTGCTCAC 59.424 41.667 18.26 15.10 36.10 3.51
3235 3445 4.779696 TGTTGCATCATATAGGTTGCTCA 58.220 39.130 18.26 14.57 36.10 4.26
3236 3446 5.514279 GTTGTTGCATCATATAGGTTGCTC 58.486 41.667 18.26 12.75 36.10 4.26
3237 3447 5.505173 GTTGTTGCATCATATAGGTTGCT 57.495 39.130 18.26 0.00 36.10 3.91


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

AutoCloner maintained by Alex Coulton.