Multiple sequence alignment - TraesCS4D01G031800

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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 TraesCS4D01G031800 chr4D 100.000 2675 0 0 1 2675 14850339 14853013 0.000000e+00 4940.0
1 TraesCS4D01G031800 chr4D 87.942 1584 138 29 794 2335 14862582 14864154 0.000000e+00 1818.0
2 TraesCS4D01G031800 chr4D 86.751 1668 162 30 731 2362 14914333 14915977 0.000000e+00 1801.0
3 TraesCS4D01G031800 chr4D 88.132 1247 114 21 716 1933 14857609 14858850 0.000000e+00 1452.0
4 TraesCS4D01G031800 chr4D 83.592 902 121 19 794 1688 14517461 14518342 0.000000e+00 821.0
5 TraesCS4D01G031800 chr4D 87.739 628 62 11 1720 2343 14896157 14896773 0.000000e+00 719.0
6 TraesCS4D01G031800 chr4D 86.626 658 68 15 1709 2362 14433508 14432867 0.000000e+00 710.0
7 TraesCS4D01G031800 chr4D 90.574 244 10 5 470 709 14914125 14914359 7.190000e-81 311.0
8 TraesCS4D01G031800 chr4D 84.639 319 32 12 2027 2343 14458738 14458435 4.330000e-78 302.0
9 TraesCS4D01G031800 chr4D 94.565 184 6 2 533 715 14460186 14460006 5.640000e-72 281.0
10 TraesCS4D01G031800 chr4D 92.414 145 7 4 1 143 14857240 14857382 1.260000e-48 204.0
11 TraesCS4D01G031800 chr4D 93.333 90 5 1 887 975 14557404 14557315 6.010000e-27 132.0
12 TraesCS4D01G031800 chr4D 86.777 121 9 6 882 998 14514237 14514354 7.770000e-26 128.0
13 TraesCS4D01G031800 chr4A 90.718 1993 155 20 300 2277 586700597 586698620 0.000000e+00 2628.0
14 TraesCS4D01G031800 chr4A 90.356 1659 129 19 300 1944 456456612 456454971 0.000000e+00 2148.0
15 TraesCS4D01G031800 chr4A 85.621 1690 164 38 716 2362 586683039 586681386 0.000000e+00 1701.0
16 TraesCS4D01G031800 chr4A 92.532 308 15 6 1 302 456456947 456456642 4.090000e-118 435.0
17 TraesCS4D01G031800 chr4A 86.735 294 24 7 2069 2362 456420488 456420210 2.000000e-81 313.0
18 TraesCS4D01G031800 chr4A 93.269 208 12 2 96 302 586700833 586700627 3.350000e-79 305.0
19 TraesCS4D01G031800 chr4A 95.699 186 8 0 533 718 586683172 586682987 1.560000e-77 300.0
20 TraesCS4D01G031800 chr4A 95.213 188 7 1 533 718 456437579 456437392 2.010000e-76 296.0
21 TraesCS4D01G031800 chr4A 90.148 203 14 2 519 715 456450419 456450217 2.640000e-65 259.0
22 TraesCS4D01G031800 chr4A 91.429 105 3 4 1 100 586706004 586705901 3.590000e-29 139.0
23 TraesCS4D01G031800 chr4B 87.402 1651 161 27 736 2353 24759151 24760787 0.000000e+00 1853.0
24 TraesCS4D01G031800 chr4B 84.638 1686 186 35 716 2362 24745483 24747134 0.000000e+00 1611.0
25 TraesCS4D01G031800 chr4B 85.445 1168 136 23 881 2021 24690641 24689481 0.000000e+00 1184.0
26 TraesCS4D01G031800 chr4B 96.591 176 5 1 535 709 24741226 24741401 9.370000e-75 291.0
27 TraesCS4D01G031800 chr3B 84.798 1684 184 36 716 2362 452717238 452715590 0.000000e+00 1626.0
28 TraesCS4D01G031800 chr3B 94.652 187 9 1 533 718 452728490 452728676 3.370000e-74 289.0
29 TraesCS4D01G031800 chr3D 97.436 273 7 0 2403 2675 110223884 110223612 1.450000e-127 466.0
30 TraesCS4D01G031800 chr3D 100.000 36 0 0 2364 2399 234451109 234451074 1.720000e-07 67.6
31 TraesCS4D01G031800 chr1D 96.751 277 9 0 2399 2675 437505114 437505390 1.880000e-126 462.0
32 TraesCS4D01G031800 chr6D 96.403 278 9 1 2398 2675 379010399 379010675 8.730000e-125 457.0
33 TraesCS4D01G031800 chr6D 95.699 279 12 0 2397 2675 68692456 68692178 1.460000e-122 449.0
34 TraesCS4D01G031800 chrUn 96.029 277 11 0 2399 2675 70418013 70418289 4.060000e-123 451.0
35 TraesCS4D01G031800 chr2D 96.029 277 11 0 2399 2675 108631138 108631414 4.060000e-123 451.0
36 TraesCS4D01G031800 chr2D 95.683 278 12 0 2398 2675 46166328 46166605 5.250000e-122 448.0
37 TraesCS4D01G031800 chr2D 95.620 274 12 0 2402 2675 401443877 401444150 8.790000e-120 440.0
38 TraesCS4D01G031800 chr7D 96.337 273 10 0 2403 2675 626213513 626213241 1.460000e-122 449.0
39 TraesCS4D01G031800 chr5D 97.619 42 1 0 2358 2399 418686057 418686098 3.690000e-09 73.1
40 TraesCS4D01G031800 chr5A 100.000 36 0 0 2364 2399 616809064 616809099 1.720000e-07 67.6
41 TraesCS4D01G031800 chr7B 94.737 38 2 0 307 344 479780531 479780494 2.880000e-05 60.2
42 TraesCS4D01G031800 chr3A 97.059 34 1 0 2364 2397 607966919 607966886 1.030000e-04 58.4


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 TraesCS4D01G031800 chr4D 14850339 14853013 2674 False 4940.0 4940 100.0000 1 2675 1 chr4D.!!$F1 2674
1 TraesCS4D01G031800 chr4D 14857240 14864154 6914 False 1158.0 1818 89.4960 1 2335 3 chr4D.!!$F4 2334
2 TraesCS4D01G031800 chr4D 14914125 14915977 1852 False 1056.0 1801 88.6625 470 2362 2 chr4D.!!$F5 1892
3 TraesCS4D01G031800 chr4D 14896157 14896773 616 False 719.0 719 87.7390 1720 2343 1 chr4D.!!$F2 623
4 TraesCS4D01G031800 chr4D 14432867 14433508 641 True 710.0 710 86.6260 1709 2362 1 chr4D.!!$R1 653
5 TraesCS4D01G031800 chr4D 14514237 14518342 4105 False 474.5 821 85.1845 794 1688 2 chr4D.!!$F3 894
6 TraesCS4D01G031800 chr4D 14458435 14460186 1751 True 291.5 302 89.6020 533 2343 2 chr4D.!!$R3 1810
7 TraesCS4D01G031800 chr4A 586698620 586700833 2213 True 1466.5 2628 91.9935 96 2277 2 chr4A.!!$R7 2181
8 TraesCS4D01G031800 chr4A 456454971 456456947 1976 True 1291.5 2148 91.4440 1 1944 2 chr4A.!!$R5 1943
9 TraesCS4D01G031800 chr4A 586681386 586683172 1786 True 1000.5 1701 90.6600 533 2362 2 chr4A.!!$R6 1829
10 TraesCS4D01G031800 chr4B 24759151 24760787 1636 False 1853.0 1853 87.4020 736 2353 1 chr4B.!!$F3 1617
11 TraesCS4D01G031800 chr4B 24745483 24747134 1651 False 1611.0 1611 84.6380 716 2362 1 chr4B.!!$F2 1646
12 TraesCS4D01G031800 chr4B 24689481 24690641 1160 True 1184.0 1184 85.4450 881 2021 1 chr4B.!!$R1 1140
13 TraesCS4D01G031800 chr3B 452715590 452717238 1648 True 1626.0 1626 84.7980 716 2362 1 chr3B.!!$R1 1646

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
130 135 0.179137 TGACGATCCACTAGCTTGCG 60.179 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 7331 0.396435 TTCAAGACCGCTCACCATGT 59.604 50.0 0.0 0.0 0.0 3.21 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
37 42 0.933097 GACCATCATGCTACACGCTG 59.067 55.000 0.00 0.00 40.11 5.18
121 126 2.109126 GGCTGCCTTGACGATCCAC 61.109 63.158 12.43 0.00 0.00 4.02
130 135 0.179137 TGACGATCCACTAGCTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
182 187 1.375523 GTCGTCCAAGCCCAACGAT 60.376 57.895 0.00 0.00 45.88 3.73
186 191 1.653151 GTCCAAGCCCAACGATAGAC 58.347 55.000 0.00 0.00 41.38 2.59
216 222 2.429250 TGGATACAGCCGATCGAGAAAA 59.571 45.455 18.66 0.00 46.17 2.29
257 263 7.094805 ACGTGTATGTACTTGCAGAATGAAATT 60.095 33.333 0.00 0.00 39.69 1.82
297 303 1.752683 TCGCTGAGAAGTACTCCCTC 58.247 55.000 14.83 14.83 44.34 4.30
312 350 4.607239 ACTCCCTCCGTAGTGATCTAAAA 58.393 43.478 0.00 0.00 0.00 1.52
316 354 4.500035 CCCTCCGTAGTGATCTAAAAGCTC 60.500 50.000 0.00 0.00 0.00 4.09
320 358 6.793349 TCCGTAGTGATCTAAAAGCTCTTAC 58.207 40.000 0.00 0.00 0.00 2.34
334 372 5.000012 AGCTCTTACATTAGTTCACGGAG 58.000 43.478 0.00 0.00 0.00 4.63
370 409 2.311124 GCTAAACCAGCGACAGGTAT 57.689 50.000 0.00 0.00 41.37 2.73
374 413 4.448060 GCTAAACCAGCGACAGGTATTATC 59.552 45.833 0.00 0.00 41.37 1.75
433 472 4.778534 CAGCATAATGGTGGATGGATTC 57.221 45.455 0.00 0.00 41.77 2.52
458 497 0.523072 CACATCAACGGAGCAAAGGG 59.477 55.000 0.00 0.00 0.00 3.95
468 507 4.511838 GCAAAGGGCTTGGTGGTA 57.488 55.556 0.00 0.00 40.25 3.25
491 530 2.165167 AGACACTGGCATTTCACCATG 58.835 47.619 0.00 0.00 36.36 3.66
516 555 1.000896 CCGGCCCCTGAACTTGATT 60.001 57.895 0.00 0.00 0.00 2.57
525 564 4.349342 CCCCTGAACTTGATTAGCCTAGAT 59.651 45.833 0.00 0.00 0.00 1.98
682 735 1.779061 TTGACTCTGACCTTGCCCCC 61.779 60.000 0.00 0.00 0.00 5.40
683 736 2.121963 ACTCTGACCTTGCCCCCA 60.122 61.111 0.00 0.00 0.00 4.96
706 759 6.238676 CCATCTCCATTTTCATCACAAGCTAG 60.239 42.308 0.00 0.00 0.00 3.42
977 1092 5.343593 CACACTCTCGATCAACAAACTCTAC 59.656 44.000 0.00 0.00 0.00 2.59
1131 6441 2.430367 GGCAAGGTGGTCTCGGTT 59.570 61.111 0.00 0.00 0.00 4.44
1312 6624 2.740826 GCGTGGACTTTGCGCCTA 60.741 61.111 4.18 0.00 44.67 3.93
1392 6705 1.272147 GGTGAGCTCCTTGTGGGAATT 60.272 52.381 12.15 0.00 44.58 2.17
1418 6731 2.885861 CCTCGACTCCGGGAACAG 59.114 66.667 0.00 0.00 38.95 3.16
1419 6732 1.677966 CCTCGACTCCGGGAACAGA 60.678 63.158 0.00 0.00 38.95 3.41
1464 6777 1.419381 GAGAGACCTTCCTCATCCCC 58.581 60.000 0.00 0.00 35.68 4.81
1467 6780 1.689582 GACCTTCCTCATCCCCCGT 60.690 63.158 0.00 0.00 0.00 5.28
1584 6897 1.118838 CTCTCTTCGGCTCCAATCCT 58.881 55.000 0.00 0.00 0.00 3.24
1587 6900 0.325671 TCTTCGGCTCCAATCCTCCT 60.326 55.000 0.00 0.00 0.00 3.69
1590 6903 2.103153 TCGGCTCCAATCCTCCTATT 57.897 50.000 0.00 0.00 0.00 1.73
1620 6933 4.069232 CTCACCAAGGCGCTCCGA 62.069 66.667 7.64 0.00 37.47 4.55
1707 7023 6.008960 AGCCTTCCCTGAAATGATCAATATC 58.991 40.000 0.00 0.00 37.67 1.63
1755 7075 9.230932 GCAAGATTTAATAATTCTCAGCAGAAC 57.769 33.333 12.92 0.00 41.64 3.01
1763 7083 7.783090 ATAATTCTCAGCAGAACACATGTAG 57.217 36.000 0.00 0.00 41.64 2.74
1772 7092 4.612259 GCAGAACACATGTAGTCAAGCTTG 60.612 45.833 20.81 20.81 0.00 4.01
1775 7095 2.371841 ACACATGTAGTCAAGCTTGGGA 59.628 45.455 25.73 5.08 0.00 4.37
1781 7101 6.891908 ACATGTAGTCAAGCTTGGGATTAATT 59.108 34.615 25.73 5.30 0.00 1.40
1783 7103 7.156876 TGTAGTCAAGCTTGGGATTAATTTG 57.843 36.000 25.73 0.00 0.00 2.32
1801 7127 9.664332 ATTAATTTGGCATGCAGTTGTAATAAA 57.336 25.926 21.36 6.43 0.00 1.40
1883 7230 9.789029 GTACTACTTTTTATTGTCGTCTTTGTC 57.211 33.333 0.00 0.00 0.00 3.18
1893 7241 3.563808 TGTCGTCTTTGTCCTTTCATTGG 59.436 43.478 0.00 0.00 0.00 3.16
1934 7286 7.132213 AGCATTTTCGTATATTTGTCCGATTG 58.868 34.615 0.00 0.00 0.00 2.67
1944 7298 9.601217 GTATATTTGTCCGATTGCCTTCTATAT 57.399 33.333 0.00 0.00 0.00 0.86
1951 7305 6.260050 GTCCGATTGCCTTCTATATGTCAAAA 59.740 38.462 0.00 0.00 0.00 2.44
1952 7306 6.260050 TCCGATTGCCTTCTATATGTCAAAAC 59.740 38.462 0.00 0.00 0.00 2.43
1955 7309 7.588854 CGATTGCCTTCTATATGTCAAAACATG 59.411 37.037 1.40 0.00 45.72 3.21
1957 7311 7.087409 TGCCTTCTATATGTCAAAACATGTG 57.913 36.000 0.00 0.00 45.72 3.21
1958 7312 5.973565 GCCTTCTATATGTCAAAACATGTGC 59.026 40.000 0.00 0.00 45.72 4.57
1989 7347 2.880879 CGACGACATGGTGAGCGG 60.881 66.667 0.00 0.00 0.00 5.52
1997 7355 1.081892 CATGGTGAGCGGTCTTGAAG 58.918 55.000 16.64 0.00 0.00 3.02
2000 7358 0.318762 GGTGAGCGGTCTTGAAGTCT 59.681 55.000 16.64 0.00 0.00 3.24
2032 7390 4.946784 ATGCTCTGAAAATTACGTGGAC 57.053 40.909 0.00 0.00 0.00 4.02
2057 7415 7.439056 ACACATTGTCAGAATTCAAAATGTTCC 59.561 33.333 17.93 1.53 36.40 3.62
2058 7416 7.438757 CACATTGTCAGAATTCAAAATGTTCCA 59.561 33.333 17.93 3.39 36.40 3.53
2059 7417 8.152246 ACATTGTCAGAATTCAAAATGTTCCAT 58.848 29.630 8.44 0.00 35.33 3.41
2060 7418 7.949903 TTGTCAGAATTCAAAATGTTCCATG 57.050 32.000 8.44 0.00 0.00 3.66
2173 7547 5.810587 GTCCGTTGTTGCTTAGAGATTCATA 59.189 40.000 0.00 0.00 0.00 2.15
2184 7570 9.383519 TGCTTAGAGATTCATACTACTTTTTGG 57.616 33.333 0.00 0.00 0.00 3.28
2301 7709 5.391736 CGCTTAGTTATATGGTAGACCTCCG 60.392 48.000 0.00 0.00 36.82 4.63
2312 7875 2.607750 ACCTCCGTGCTCACCCAT 60.608 61.111 0.00 0.00 0.00 4.00
2338 9516 2.593026 GGGGATTGTGTTGTTCAAGGA 58.407 47.619 0.00 0.00 0.00 3.36
2366 9643 4.584874 TCTCGGCCATGACTATTTTTCAA 58.415 39.130 2.24 0.00 0.00 2.69
2367 9644 5.007034 TCTCGGCCATGACTATTTTTCAAA 58.993 37.500 2.24 0.00 0.00 2.69
2368 9645 5.123820 TCTCGGCCATGACTATTTTTCAAAG 59.876 40.000 2.24 0.00 0.00 2.77
2369 9646 4.764823 TCGGCCATGACTATTTTTCAAAGT 59.235 37.500 2.24 0.00 0.00 2.66
2370 9647 5.242838 TCGGCCATGACTATTTTTCAAAGTT 59.757 36.000 2.24 0.00 0.00 2.66
2371 9648 5.572896 CGGCCATGACTATTTTTCAAAGTTC 59.427 40.000 2.24 0.00 0.00 3.01
2373 9650 6.454795 GCCATGACTATTTTTCAAAGTTCCA 58.545 36.000 0.00 0.00 0.00 3.53
2374 9651 6.366061 GCCATGACTATTTTTCAAAGTTCCAC 59.634 38.462 0.00 0.00 0.00 4.02
2376 9653 6.067263 TGACTATTTTTCAAAGTTCCACGG 57.933 37.500 0.00 0.00 0.00 4.94
2377 9654 5.823570 TGACTATTTTTCAAAGTTCCACGGA 59.176 36.000 0.00 0.00 0.00 4.69
2378 9655 6.319152 TGACTATTTTTCAAAGTTCCACGGAA 59.681 34.615 0.00 0.00 0.00 4.30
2379 9656 7.102847 ACTATTTTTCAAAGTTCCACGGAAA 57.897 32.000 0.00 0.00 35.75 3.13
2380 9657 7.200455 ACTATTTTTCAAAGTTCCACGGAAAG 58.800 34.615 0.00 0.00 35.75 2.62
2382 9659 2.045561 TCAAAGTTCCACGGAAAGCA 57.954 45.000 0.00 0.00 35.75 3.91
2383 9660 1.946768 TCAAAGTTCCACGGAAAGCAG 59.053 47.619 0.00 0.00 35.75 4.24
2386 9663 2.922740 AGTTCCACGGAAAGCAGTAA 57.077 45.000 0.00 0.00 35.75 2.24
2387 9664 3.202829 AGTTCCACGGAAAGCAGTAAA 57.797 42.857 0.00 0.00 35.75 2.01
2389 9666 3.564225 AGTTCCACGGAAAGCAGTAAAAG 59.436 43.478 0.00 0.00 35.75 2.27
2390 9667 3.202829 TCCACGGAAAGCAGTAAAAGT 57.797 42.857 0.00 0.00 0.00 2.66
2391 9668 3.547746 TCCACGGAAAGCAGTAAAAGTT 58.452 40.909 0.00 0.00 0.00 2.66
2392 9669 3.314080 TCCACGGAAAGCAGTAAAAGTTG 59.686 43.478 0.00 0.00 0.00 3.16
2395 9672 3.564225 ACGGAAAGCAGTAAAAGTTGGAG 59.436 43.478 0.00 0.00 0.00 3.86
2396 9673 3.609409 CGGAAAGCAGTAAAAGTTGGAGC 60.609 47.826 0.00 0.00 0.00 4.70
2397 9674 3.305403 GGAAAGCAGTAAAAGTTGGAGCC 60.305 47.826 0.00 0.00 0.00 4.70
2398 9675 2.656947 AGCAGTAAAAGTTGGAGCCA 57.343 45.000 0.00 0.00 0.00 4.75
2399 9676 2.944129 AGCAGTAAAAGTTGGAGCCAA 58.056 42.857 0.00 0.00 0.00 4.52
2448 9725 2.818274 GTGAAACCCTAGCCGCCG 60.818 66.667 0.00 0.00 0.00 6.46
2449 9726 4.770874 TGAAACCCTAGCCGCCGC 62.771 66.667 0.00 0.00 0.00 6.53
2465 9742 3.658422 GCCCCCGTTTCCCCTCTT 61.658 66.667 0.00 0.00 0.00 2.85
2466 9743 2.675371 CCCCCGTTTCCCCTCTTC 59.325 66.667 0.00 0.00 0.00 2.87
2467 9744 1.923909 CCCCCGTTTCCCCTCTTCT 60.924 63.158 0.00 0.00 0.00 2.85
2468 9745 1.602771 CCCCGTTTCCCCTCTTCTC 59.397 63.158 0.00 0.00 0.00 2.87
2469 9746 1.602771 CCCGTTTCCCCTCTTCTCC 59.397 63.158 0.00 0.00 0.00 3.71
2471 9748 0.912486 CCGTTTCCCCTCTTCTCCAT 59.088 55.000 0.00 0.00 0.00 3.41
2472 9749 1.134371 CCGTTTCCCCTCTTCTCCATC 60.134 57.143 0.00 0.00 0.00 3.51
2473 9750 1.134371 CGTTTCCCCTCTTCTCCATCC 60.134 57.143 0.00 0.00 0.00 3.51
2474 9751 1.916181 GTTTCCCCTCTTCTCCATCCA 59.084 52.381 0.00 0.00 0.00 3.41
2475 9752 1.584724 TTCCCCTCTTCTCCATCCAC 58.415 55.000 0.00 0.00 0.00 4.02
2476 9753 0.326618 TCCCCTCTTCTCCATCCACC 60.327 60.000 0.00 0.00 0.00 4.61
2478 9755 1.348775 CCCTCTTCTCCATCCACCCC 61.349 65.000 0.00 0.00 0.00 4.95
2479 9756 1.690219 CCTCTTCTCCATCCACCCCG 61.690 65.000 0.00 0.00 0.00 5.73
2480 9757 2.190578 CTTCTCCATCCACCCCGC 59.809 66.667 0.00 0.00 0.00 6.13
2481 9758 2.285368 TTCTCCATCCACCCCGCT 60.285 61.111 0.00 0.00 0.00 5.52
2482 9759 2.599645 CTTCTCCATCCACCCCGCTG 62.600 65.000 0.00 0.00 0.00 5.18
2483 9760 4.864334 CTCCATCCACCCCGCTGC 62.864 72.222 0.00 0.00 0.00 5.25
2507 9784 2.220479 GGAGGAAACCGACGGATAAG 57.780 55.000 23.38 0.00 0.00 1.73
2508 9785 1.202498 GGAGGAAACCGACGGATAAGG 60.202 57.143 23.38 0.00 0.00 2.69
2509 9786 0.177373 AGGAAACCGACGGATAAGGC 59.823 55.000 23.38 3.25 0.00 4.35
2517 9794 2.279918 CGGATAAGGCCCGTTCGG 60.280 66.667 0.00 4.08 41.91 4.30
2518 9795 2.905681 GGATAAGGCCCGTTCGGT 59.094 61.111 0.00 0.00 0.00 4.69
2519 9796 1.523032 GGATAAGGCCCGTTCGGTG 60.523 63.158 0.00 3.35 0.00 4.94
2520 9797 1.523032 GATAAGGCCCGTTCGGTGG 60.523 63.158 0.00 0.00 0.00 4.61
2521 9798 1.963464 GATAAGGCCCGTTCGGTGGA 61.963 60.000 0.00 0.00 0.00 4.02
2522 9799 1.342672 ATAAGGCCCGTTCGGTGGAT 61.343 55.000 0.00 0.00 0.00 3.41
2523 9800 2.246761 TAAGGCCCGTTCGGTGGATG 62.247 60.000 0.00 0.00 0.00 3.51
2528 9805 4.752879 CGTTCGGTGGATGGCGGT 62.753 66.667 0.00 0.00 0.00 5.68
2529 9806 3.124921 GTTCGGTGGATGGCGGTG 61.125 66.667 0.00 0.00 0.00 4.94
2530 9807 4.402528 TTCGGTGGATGGCGGTGG 62.403 66.667 0.00 0.00 0.00 4.61
2547 9824 3.894947 GCGGGCTCTCGTCCTCTC 61.895 72.222 0.00 0.00 30.74 3.20
2548 9825 3.213402 CGGGCTCTCGTCCTCTCC 61.213 72.222 0.00 0.00 30.74 3.71
2549 9826 2.277404 GGGCTCTCGTCCTCTCCT 59.723 66.667 0.00 0.00 30.13 3.69
2550 9827 2.124693 GGGCTCTCGTCCTCTCCTG 61.125 68.421 0.00 0.00 30.13 3.86
2551 9828 2.781158 GGCTCTCGTCCTCTCCTGC 61.781 68.421 0.00 0.00 0.00 4.85
2552 9829 2.781158 GCTCTCGTCCTCTCCTGCC 61.781 68.421 0.00 0.00 0.00 4.85
2553 9830 2.438614 TCTCGTCCTCTCCTGCCG 60.439 66.667 0.00 0.00 0.00 5.69
2554 9831 2.438614 CTCGTCCTCTCCTGCCGA 60.439 66.667 0.00 0.00 0.00 5.54
2555 9832 2.438614 TCGTCCTCTCCTGCCGAG 60.439 66.667 0.00 0.00 40.30 4.63
2557 9834 3.151022 GTCCTCTCCTGCCGAGGG 61.151 72.222 6.27 0.57 46.43 4.30
2560 9837 3.151022 CTCTCCTGCCGAGGGGAC 61.151 72.222 0.00 0.00 44.84 4.46
2624 9901 4.286320 CGGAGCTCGGAATCGGGG 62.286 72.222 15.82 0.00 37.35 5.73
2641 9918 2.563427 GCGGCAGCCTCAACTTTC 59.437 61.111 10.54 0.00 37.42 2.62
2642 9919 1.968540 GCGGCAGCCTCAACTTTCT 60.969 57.895 10.54 0.00 37.42 2.52
2643 9920 1.871772 CGGCAGCCTCAACTTTCTG 59.128 57.895 10.54 0.00 0.00 3.02
2644 9921 1.580845 CGGCAGCCTCAACTTTCTGG 61.581 60.000 10.54 0.00 0.00 3.86
2645 9922 0.538287 GGCAGCCTCAACTTTCTGGT 60.538 55.000 3.29 0.00 0.00 4.00
2646 9923 0.595095 GCAGCCTCAACTTTCTGGTG 59.405 55.000 0.00 0.00 33.88 4.17
2647 9924 1.242076 CAGCCTCAACTTTCTGGTGG 58.758 55.000 0.00 0.00 33.29 4.61
2648 9925 0.846693 AGCCTCAACTTTCTGGTGGT 59.153 50.000 0.00 0.00 33.29 4.16
2650 9927 1.609208 CCTCAACTTTCTGGTGGTGG 58.391 55.000 0.00 0.00 33.29 4.61
2651 9928 0.954452 CTCAACTTTCTGGTGGTGGC 59.046 55.000 0.00 0.00 33.29 5.01
2652 9929 0.550914 TCAACTTTCTGGTGGTGGCT 59.449 50.000 0.00 0.00 33.29 4.75
2654 9931 1.067516 CAACTTTCTGGTGGTGGCTTG 59.932 52.381 0.00 0.00 0.00 4.01
2655 9932 0.468029 ACTTTCTGGTGGTGGCTTGG 60.468 55.000 0.00 0.00 0.00 3.61
2656 9933 1.809567 CTTTCTGGTGGTGGCTTGGC 61.810 60.000 0.00 0.00 0.00 4.52
2657 9934 2.296945 TTTCTGGTGGTGGCTTGGCT 62.297 55.000 0.00 0.00 0.00 4.75
2658 9935 2.981914 TTCTGGTGGTGGCTTGGCTG 62.982 60.000 0.00 0.00 0.00 4.85
2659 9936 4.601794 TGGTGGTGGCTTGGCTGG 62.602 66.667 0.00 0.00 0.00 4.85
2660 9937 4.284550 GGTGGTGGCTTGGCTGGA 62.285 66.667 0.00 0.00 0.00 3.86
2662 9939 4.666253 TGGTGGCTTGGCTGGAGC 62.666 66.667 0.00 0.00 39.41 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.343782 TGATGGTCAGAGATGGGAGCT 60.344 52.381 0.00 0.00 32.93 4.09
6 7 1.126488 TGATGGTCAGAGATGGGAGC 58.874 55.000 0.00 0.00 0.00 4.70
7 8 2.550423 GCATGATGGTCAGAGATGGGAG 60.550 54.545 0.00 0.00 0.00 4.30
45 50 0.898320 CTGAAGGGACGTCTCCATGT 59.102 55.000 12.98 3.02 38.52 3.21
121 126 2.742372 AACCGTGCCGCAAGCTAG 60.742 61.111 0.00 0.00 44.23 3.42
130 135 2.267426 GCCATTAATTTCAACCGTGCC 58.733 47.619 0.00 0.00 0.00 5.01
160 165 4.680237 TGGGCTTGGACGACTGCG 62.680 66.667 0.00 0.00 44.79 5.18
182 187 4.523083 GCTGTATCCACCCATTTTGTCTA 58.477 43.478 0.00 0.00 0.00 2.59
186 191 1.405105 CGGCTGTATCCACCCATTTTG 59.595 52.381 0.00 0.00 0.00 2.44
206 212 9.010366 GTAGGTTAATTTTGCATTTTCTCGATC 57.990 33.333 0.00 0.00 0.00 3.69
216 222 7.385778 ACATACACGTAGGTTAATTTTGCAT 57.614 32.000 0.00 0.00 0.00 3.96
263 269 1.160329 AGCGAATAAGCGACCATGGC 61.160 55.000 13.04 3.65 43.00 4.40
276 282 2.691011 GAGGGAGTACTTCTCAGCGAAT 59.309 50.000 17.18 0.00 44.40 3.34
297 303 6.561614 TGTAAGAGCTTTTAGATCACTACGG 58.438 40.000 0.00 0.00 31.99 4.02
312 350 4.142138 CCTCCGTGAACTAATGTAAGAGCT 60.142 45.833 0.00 0.00 0.00 4.09
316 354 4.159879 ACTCCCTCCGTGAACTAATGTAAG 59.840 45.833 0.00 0.00 0.00 2.34
320 358 3.700038 AGTACTCCCTCCGTGAACTAATG 59.300 47.826 0.00 0.00 0.00 1.90
325 363 3.087781 AGTTAGTACTCCCTCCGTGAAC 58.912 50.000 0.00 0.00 0.00 3.18
328 366 3.257624 ACAAAGTTAGTACTCCCTCCGTG 59.742 47.826 0.00 0.00 31.99 4.94
334 372 5.410746 GGTTTAGCACAAAGTTAGTACTCCC 59.589 44.000 0.00 0.00 31.99 4.30
428 467 4.129380 TCCGTTGATGTGATGATGAATCC 58.871 43.478 0.00 0.00 34.00 3.01
430 469 3.562973 GCTCCGTTGATGTGATGATGAAT 59.437 43.478 0.00 0.00 0.00 2.57
431 470 2.938451 GCTCCGTTGATGTGATGATGAA 59.062 45.455 0.00 0.00 0.00 2.57
432 471 2.093553 TGCTCCGTTGATGTGATGATGA 60.094 45.455 0.00 0.00 0.00 2.92
433 472 2.282407 TGCTCCGTTGATGTGATGATG 58.718 47.619 0.00 0.00 0.00 3.07
458 497 2.417719 CAGTGTCTTCTACCACCAAGC 58.582 52.381 0.00 0.00 31.88 4.01
468 507 2.158623 TGGTGAAATGCCAGTGTCTTCT 60.159 45.455 0.00 0.00 0.00 2.85
516 555 7.237471 TCAATCATATGGGTTTCATCTAGGCTA 59.763 37.037 2.13 0.00 37.30 3.93
525 564 5.097742 ACTCGTCAATCATATGGGTTTCA 57.902 39.130 2.13 0.00 0.00 2.69
682 735 5.578005 AGCTTGTGATGAAAATGGAGATG 57.422 39.130 0.00 0.00 0.00 2.90
683 736 5.298777 GCTAGCTTGTGATGAAAATGGAGAT 59.701 40.000 7.70 0.00 0.00 2.75
706 759 1.439644 GGTCAGAGTCGGGATGAGC 59.560 63.158 0.00 0.00 34.69 4.26
775 846 7.595311 TGAGGCAGCGTTTATTATACATATG 57.405 36.000 0.00 0.00 0.00 1.78
782 854 4.199310 ACACATGAGGCAGCGTTTATTAT 58.801 39.130 0.00 0.00 0.00 1.28
791 863 1.135199 CAAATGGACACATGAGGCAGC 60.135 52.381 0.00 0.00 37.40 5.25
870 972 5.007385 CCTTTATATAGGGGATCGGTTCG 57.993 47.826 1.41 0.00 0.00 3.95
977 1092 2.031682 GCTTGCTATGCAACTAATCGGG 60.032 50.000 0.45 0.00 43.99 5.14
1121 6431 2.208619 TGCCCGTTAACCGAGACCA 61.209 57.895 0.00 0.00 39.56 4.02
1392 6705 3.134792 GAGTCGAGGCTGCCGAGA 61.135 66.667 13.96 13.76 36.66 4.04
1418 6731 1.187087 CACCACCCTGGAGTAGAGTC 58.813 60.000 0.00 0.00 40.96 3.36
1419 6732 0.905337 GCACCACCCTGGAGTAGAGT 60.905 60.000 0.00 0.00 40.96 3.24
1452 6765 2.911143 CCACGGGGGATGAGGAAG 59.089 66.667 0.00 0.00 40.01 3.46
1464 6777 2.360350 AAGTGCATGAGGCCACGG 60.360 61.111 5.01 0.00 43.89 4.94
1467 6780 1.001764 CTGGAAGTGCATGAGGCCA 60.002 57.895 5.01 0.00 43.89 5.36
1707 7023 9.188588 CTTGCTACCATGCATAAATTGAATTAG 57.811 33.333 0.00 0.00 42.96 1.73
1726 7044 9.875675 CTGCTGAGAATTATTAAATCTTGCTAC 57.124 33.333 15.20 0.00 0.00 3.58
1755 7075 3.057969 TCCCAAGCTTGACTACATGTG 57.942 47.619 28.05 7.28 0.00 3.21
1763 7083 4.183865 GCCAAATTAATCCCAAGCTTGAC 58.816 43.478 28.05 0.00 0.00 3.18
1772 7092 3.825143 ACTGCATGCCAAATTAATCCC 57.175 42.857 16.68 0.00 0.00 3.85
1775 7095 9.664332 TTTATTACAACTGCATGCCAAATTAAT 57.336 25.926 16.68 14.12 0.00 1.40
1781 7101 7.157347 TCAATTTTATTACAACTGCATGCCAA 58.843 30.769 16.68 0.00 0.00 4.52
1783 7103 7.593875 TTCAATTTTATTACAACTGCATGCC 57.406 32.000 16.68 0.00 0.00 4.40
1801 7127 6.079712 ACCCTGAGGCTAACTTATTCAATT 57.920 37.500 0.00 0.00 36.11 2.32
1821 7147 2.579410 TGGTTCTGAAGGCTAAACCC 57.421 50.000 14.62 1.23 40.37 4.11
1934 7286 5.973565 GCACATGTTTTGACATATAGAAGGC 59.026 40.000 0.00 0.00 0.00 4.35
1944 7298 5.287274 CGTAAACTTTGCACATGTTTTGACA 59.713 36.000 13.63 0.00 35.77 3.58
1951 7305 3.545228 CGTGACGTAAACTTTGCACATGT 60.545 43.478 0.00 0.00 0.00 3.21
1952 7306 2.964123 CGTGACGTAAACTTTGCACATG 59.036 45.455 0.00 0.00 0.00 3.21
1954 7308 2.029486 GTCGTGACGTAAACTTTGCACA 59.971 45.455 4.40 0.00 0.00 4.57
1955 7309 2.621587 GTCGTGACGTAAACTTTGCAC 58.378 47.619 4.40 0.00 0.00 4.57
1977 7331 0.396435 TTCAAGACCGCTCACCATGT 59.604 50.000 0.00 0.00 0.00 3.21
2018 7376 5.753744 TGACAATGTGTCCACGTAATTTTC 58.246 37.500 5.96 0.00 46.40 2.29
2032 7390 7.438757 TGGAACATTTTGAATTCTGACAATGTG 59.561 33.333 17.90 6.88 0.00 3.21
2057 7415 3.977427 AGATTGCTACAATGCATGCATG 58.023 40.909 32.79 25.94 42.96 4.06
2058 7416 3.005472 GGAGATTGCTACAATGCATGCAT 59.995 43.478 27.46 27.46 42.96 3.96
2059 7417 2.359848 GGAGATTGCTACAATGCATGCA 59.640 45.455 25.04 25.04 42.96 3.96
2060 7418 2.359848 TGGAGATTGCTACAATGCATGC 59.640 45.455 11.82 11.82 42.96 4.06
2108 7476 5.473504 GGATATTCCGTGCATGGTAGAAAAT 59.526 40.000 24.24 17.38 0.00 1.82
2338 9516 0.616111 AGTCATGGCCGAGAGAACCT 60.616 55.000 0.00 0.00 0.00 3.50
2366 9643 2.922740 TACTGCTTTCCGTGGAACTT 57.077 45.000 0.00 0.00 33.41 2.66
2367 9644 2.922740 TTACTGCTTTCCGTGGAACT 57.077 45.000 0.00 0.00 33.41 3.01
2368 9645 3.314357 ACTTTTACTGCTTTCCGTGGAAC 59.686 43.478 0.00 0.00 33.41 3.62
2369 9646 3.547746 ACTTTTACTGCTTTCCGTGGAA 58.452 40.909 0.00 0.00 0.00 3.53
2370 9647 3.202829 ACTTTTACTGCTTTCCGTGGA 57.797 42.857 0.00 0.00 0.00 4.02
2371 9648 3.550030 CCAACTTTTACTGCTTTCCGTGG 60.550 47.826 0.00 0.00 0.00 4.94
2373 9650 3.547746 TCCAACTTTTACTGCTTTCCGT 58.452 40.909 0.00 0.00 0.00 4.69
2374 9651 3.609409 GCTCCAACTTTTACTGCTTTCCG 60.609 47.826 0.00 0.00 0.00 4.30
2376 9653 3.317993 TGGCTCCAACTTTTACTGCTTTC 59.682 43.478 0.00 0.00 0.00 2.62
2377 9654 3.295973 TGGCTCCAACTTTTACTGCTTT 58.704 40.909 0.00 0.00 0.00 3.51
2378 9655 2.944129 TGGCTCCAACTTTTACTGCTT 58.056 42.857 0.00 0.00 0.00 3.91
2379 9656 2.656947 TGGCTCCAACTTTTACTGCT 57.343 45.000 0.00 0.00 0.00 4.24
2432 9709 4.770874 GCGGCGGCTAGGGTTTCA 62.771 66.667 9.78 0.00 35.83 2.69
2448 9725 3.640257 GAAGAGGGGAAACGGGGGC 62.640 68.421 0.00 0.00 0.00 5.80
2449 9726 1.911702 GAGAAGAGGGGAAACGGGGG 61.912 65.000 0.00 0.00 0.00 5.40
2451 9728 1.198759 TGGAGAAGAGGGGAAACGGG 61.199 60.000 0.00 0.00 0.00 5.28
2452 9729 0.912486 ATGGAGAAGAGGGGAAACGG 59.088 55.000 0.00 0.00 0.00 4.44
2454 9731 1.916181 TGGATGGAGAAGAGGGGAAAC 59.084 52.381 0.00 0.00 0.00 2.78
2455 9732 1.916181 GTGGATGGAGAAGAGGGGAAA 59.084 52.381 0.00 0.00 0.00 3.13
2456 9733 1.584724 GTGGATGGAGAAGAGGGGAA 58.415 55.000 0.00 0.00 0.00 3.97
2457 9734 0.326618 GGTGGATGGAGAAGAGGGGA 60.327 60.000 0.00 0.00 0.00 4.81
2459 9736 1.348775 GGGGTGGATGGAGAAGAGGG 61.349 65.000 0.00 0.00 0.00 4.30
2461 9738 1.826024 CGGGGTGGATGGAGAAGAG 59.174 63.158 0.00 0.00 0.00 2.85
2462 9739 2.367202 GCGGGGTGGATGGAGAAGA 61.367 63.158 0.00 0.00 0.00 2.87
2463 9740 2.190578 GCGGGGTGGATGGAGAAG 59.809 66.667 0.00 0.00 0.00 2.85
2464 9741 2.285368 AGCGGGGTGGATGGAGAA 60.285 61.111 0.00 0.00 0.00 2.87
2465 9742 3.083349 CAGCGGGGTGGATGGAGA 61.083 66.667 0.00 0.00 0.00 3.71
2466 9743 4.864334 GCAGCGGGGTGGATGGAG 62.864 72.222 0.00 0.00 0.00 3.86
2488 9765 1.202498 CCTTATCCGTCGGTTTCCTCC 60.202 57.143 11.88 0.00 0.00 4.30
2489 9766 1.805495 GCCTTATCCGTCGGTTTCCTC 60.805 57.143 11.88 0.00 0.00 3.71
2490 9767 0.177373 GCCTTATCCGTCGGTTTCCT 59.823 55.000 11.88 0.00 0.00 3.36
2492 9769 0.812811 GGGCCTTATCCGTCGGTTTC 60.813 60.000 11.88 0.00 0.00 2.78
2493 9770 1.222661 GGGCCTTATCCGTCGGTTT 59.777 57.895 11.88 2.89 0.00 3.27
2495 9772 3.534056 CGGGCCTTATCCGTCGGT 61.534 66.667 11.88 1.23 42.33 4.69
2501 9778 1.523032 CACCGAACGGGCCTTATCC 60.523 63.158 17.44 0.00 40.62 2.59
2503 9780 1.342672 ATCCACCGAACGGGCCTTAT 61.343 55.000 17.44 1.44 40.62 1.73
2505 9782 3.327404 ATCCACCGAACGGGCCTT 61.327 61.111 17.44 0.00 40.62 4.35
2506 9783 4.096003 CATCCACCGAACGGGCCT 62.096 66.667 17.44 0.00 40.62 5.19
2512 9789 3.124921 CACCGCCATCCACCGAAC 61.125 66.667 0.00 0.00 0.00 3.95
2513 9790 4.402528 CCACCGCCATCCACCGAA 62.403 66.667 0.00 0.00 0.00 4.30
2530 9807 3.894947 GAGAGGACGAGAGCCCGC 61.895 72.222 0.00 0.00 39.40 6.13
2531 9808 3.213402 GGAGAGGACGAGAGCCCG 61.213 72.222 0.00 0.00 39.40 6.13
2532 9809 2.124693 CAGGAGAGGACGAGAGCCC 61.125 68.421 0.00 0.00 0.00 5.19
2533 9810 2.781158 GCAGGAGAGGACGAGAGCC 61.781 68.421 0.00 0.00 0.00 4.70
2534 9811 2.781158 GGCAGGAGAGGACGAGAGC 61.781 68.421 0.00 0.00 0.00 4.09
2535 9812 2.477176 CGGCAGGAGAGGACGAGAG 61.477 68.421 0.00 0.00 0.00 3.20
2536 9813 2.438614 CGGCAGGAGAGGACGAGA 60.439 66.667 0.00 0.00 0.00 4.04
2537 9814 2.438614 TCGGCAGGAGAGGACGAG 60.439 66.667 0.00 0.00 0.00 4.18
2538 9815 2.438614 CTCGGCAGGAGAGGACGA 60.439 66.667 0.00 0.00 46.23 4.20
2543 9820 3.151022 GTCCCCTCGGCAGGAGAG 61.151 72.222 5.65 0.00 46.23 3.20
2544 9821 4.779733 GGTCCCCTCGGCAGGAGA 62.780 72.222 5.65 0.00 46.23 3.71
2545 9822 4.787280 AGGTCCCCTCGGCAGGAG 62.787 72.222 4.77 0.00 43.65 3.69
2546 9823 4.779733 GAGGTCCCCTCGGCAGGA 62.780 72.222 4.77 0.00 43.65 3.86
2602 9879 3.832720 GATTCCGAGCTCCGCCGAG 62.833 68.421 8.47 0.00 39.33 4.63
2603 9880 3.900892 GATTCCGAGCTCCGCCGA 61.901 66.667 8.47 0.00 36.84 5.54
2605 9882 4.951963 CCGATTCCGAGCTCCGCC 62.952 72.222 8.47 0.00 38.22 6.13
2606 9883 4.951963 CCCGATTCCGAGCTCCGC 62.952 72.222 8.47 0.00 38.22 5.54
2607 9884 4.286320 CCCCGATTCCGAGCTCCG 62.286 72.222 8.47 5.19 38.22 4.63
2608 9885 4.610714 GCCCCGATTCCGAGCTCC 62.611 72.222 8.47 0.00 38.22 4.70
2609 9886 4.951963 CGCCCCGATTCCGAGCTC 62.952 72.222 2.73 2.73 38.22 4.09
2624 9901 1.968540 AGAAAGTTGAGGCTGCCGC 60.969 57.895 16.00 16.00 0.00 6.53
2635 9912 1.402787 CAAGCCACCACCAGAAAGTT 58.597 50.000 0.00 0.00 0.00 2.66
2639 9916 2.203480 GCCAAGCCACCACCAGAA 60.203 61.111 0.00 0.00 0.00 3.02
2640 9917 3.177884 AGCCAAGCCACCACCAGA 61.178 61.111 0.00 0.00 0.00 3.86
2641 9918 2.987547 CAGCCAAGCCACCACCAG 60.988 66.667 0.00 0.00 0.00 4.00
2642 9919 4.601794 CCAGCCAAGCCACCACCA 62.602 66.667 0.00 0.00 0.00 4.17
2643 9920 4.284550 TCCAGCCAAGCCACCACC 62.285 66.667 0.00 0.00 0.00 4.61
2644 9921 2.674380 CTCCAGCCAAGCCACCAC 60.674 66.667 0.00 0.00 0.00 4.16
2645 9922 4.666253 GCTCCAGCCAAGCCACCA 62.666 66.667 0.00 0.00 33.53 4.17


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

AutoCloner maintained by Alex Coulton.