Multiple sequence alignment - TraesCS6D01G081400

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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 TraesCS6D01G081400 chr6D 100.000 2472 0 0 1 2472 46872759 46875230 0.000000e+00 4566.0
1 TraesCS6D01G081400 chr6D 79.749 479 30 31 1530 1989 54835757 54835327 4.020000e-73 285.0
2 TraesCS6D01G081400 chr6D 77.256 554 40 45 1530 2038 54897262 54896750 1.900000e-61 246.0
3 TraesCS6D01G081400 chr6D 91.333 150 8 2 2144 2293 54896602 54896458 1.500000e-47 200.0
4 TraesCS6D01G081400 chr6D 90.164 122 9 3 1987 2107 54835294 54835175 3.290000e-34 156.0
5 TraesCS6D01G081400 chr6D 90.625 64 5 1 1976 2038 54854639 54854576 1.580000e-12 84.2
6 TraesCS6D01G081400 chr6D 92.727 55 3 1 2126 2180 54854471 54854418 7.330000e-11 78.7
7 TraesCS6D01G081400 chr6D 93.182 44 2 1 2362 2404 54896492 54896449 2.050000e-06 63.9
8 TraesCS6D01G081400 chr6A 89.879 1156 72 27 394 1535 60504816 60505940 0.000000e+00 1445.0
9 TraesCS6D01G081400 chr6A 87.476 527 20 19 1659 2167 60529938 60530436 1.280000e-157 566.0
10 TraesCS6D01G081400 chr6A 87.387 333 20 4 1 316 60501455 60501782 1.810000e-96 363.0
11 TraesCS6D01G081400 chr6A 81.435 474 34 22 1530 1989 60558114 60558547 3.050000e-89 339.0
12 TraesCS6D01G081400 chr6A 94.764 191 10 0 2172 2362 60530952 60531142 5.170000e-77 298.0
13 TraesCS6D01G081400 chr6A 91.509 106 8 1 1530 1634 60529844 60529949 7.130000e-31 145.0
14 TraesCS6D01G081400 chr6A 84.337 166 6 7 2113 2278 60538739 60538884 7.130000e-31 145.0
15 TraesCS6D01G081400 chr6A 94.253 87 5 0 314 400 60502839 60502925 1.540000e-27 134.0
16 TraesCS6D01G081400 chr6A 100.000 57 0 0 2416 2472 60531139 60531195 3.360000e-19 106.0
17 TraesCS6D01G081400 chr6A 97.222 36 1 0 2125 2160 46630093 46630128 7.380000e-06 62.1
18 TraesCS6D01G081400 chr6B 87.697 951 51 22 623 1535 116112834 116113756 0.000000e+00 1048.0
19 TraesCS6D01G081400 chr6B 84.728 753 45 38 1601 2318 116114085 116114802 0.000000e+00 689.0
20 TraesCS6D01G081400 chr6B 82.821 553 57 17 5 535 116112295 116112831 6.230000e-126 460.0
21 TraesCS6D01G081400 chr6B 93.529 170 8 3 2113 2281 116140456 116140623 1.470000e-62 250.0
22 TraesCS6D01G081400 chr6B 79.330 358 28 17 1530 1875 116200050 116200373 2.490000e-50 209.0
23 TraesCS6D01G081400 chr6B 82.500 200 20 11 1987 2180 116281342 116281532 7.070000e-36 161.0
24 TraesCS6D01G081400 chr6B 83.212 137 17 3 123 256 707944887 707945020 1.200000e-23 121.0
25 TraesCS6D01G081400 chr6B 81.457 151 15 10 1799 1941 116188550 116188695 7.230000e-21 111.0
26 TraesCS6D01G081400 chr6B 96.667 60 2 0 2048 2107 116140355 116140414 1.560000e-17 100.0
27 TraesCS6D01G081400 chr6B 94.545 55 2 1 2126 2180 116188932 116188985 1.580000e-12 84.2
28 TraesCS6D01G081400 chr3B 79.121 273 33 7 7 258 50152739 50153008 1.520000e-37 167.0
29 TraesCS6D01G081400 chr3B 81.818 165 24 3 95 256 151219359 151219198 1.540000e-27 134.0
30 TraesCS6D01G081400 chr3B 79.394 165 27 5 95 256 421611031 421610871 2.600000e-20 110.0
31 TraesCS6D01G081400 chr4D 78.358 268 38 4 7 254 4821960 4821693 3.290000e-34 156.0
32 TraesCS6D01G081400 chr7B 77.574 272 41 7 7 258 117792193 117792464 1.980000e-31 147.0
33 TraesCS6D01G081400 chr7B 78.363 171 26 3 39 198 221792944 221793114 1.560000e-17 100.0
34 TraesCS6D01G081400 chr4A 83.448 145 20 2 116 256 740204098 740203954 5.550000e-27 132.0
35 TraesCS6D01G081400 chr2D 76.953 256 36 19 36 280 562343579 562343336 9.280000e-25 124.0
36 TraesCS6D01G081400 chr2B 75.502 249 35 13 31 256 75687412 75687167 5.630000e-17 99.0
37 TraesCS6D01G081400 chr7A 93.333 60 3 1 37 95 149307768 149307827 1.220000e-13 87.9
38 TraesCS6D01G081400 chr7A 81.081 111 16 3 1 111 37853001 37853106 1.580000e-12 84.2
39 TraesCS6D01G081400 chrUn 100.000 36 0 0 2125 2160 27580057 27580092 1.590000e-07 67.6


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 TraesCS6D01G081400 chr6D 46872759 46875230 2471 False 4566.000000 4566 100.000000 1 2472 1 chr6D.!!$F1 2471
1 TraesCS6D01G081400 chr6D 54835175 54835757 582 True 220.500000 285 84.956500 1530 2107 2 chr6D.!!$R1 577
2 TraesCS6D01G081400 chr6A 60501455 60505940 4485 False 647.333333 1445 90.506333 1 1535 3 chr6A.!!$F4 1534
3 TraesCS6D01G081400 chr6A 60529844 60531195 1351 False 278.750000 566 93.437250 1530 2472 4 chr6A.!!$F5 942
4 TraesCS6D01G081400 chr6B 116112295 116114802 2507 False 732.333333 1048 85.082000 5 2318 3 chr6B.!!$F4 2313

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
529 3510 0.106217 CCTCTCCTCCACCCTCTCTC 60.106 65.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 6333 0.031857 CCTCATTTTTGTGTGCCGCA 59.968 50.0 0.0 0.0 0.0 5.69 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 5.295540 CCCAGTGCTAGCTTAGAGAAAAATC 59.704 44.000 17.23 0.00 0.00 2.17
27 28 6.597280 CCAGTGCTAGCTTAGAGAAAAATCTT 59.403 38.462 17.23 0.00 0.00 2.40
205 225 6.970484 AGTGTCCACAAACTTTAATGATCAC 58.030 36.000 0.00 0.00 0.00 3.06
208 228 6.077838 GTCCACAAACTTTAATGATCACGAC 58.922 40.000 0.00 0.00 0.00 4.34
224 246 7.981142 TGATCACGACCTTTAAAAATATCCAC 58.019 34.615 0.00 0.00 0.00 4.02
327 1408 7.284820 TGGCTACCTTTTACTACTCTGTTTTT 58.715 34.615 0.00 0.00 0.00 1.94
328 1409 7.443272 TGGCTACCTTTTACTACTCTGTTTTTC 59.557 37.037 0.00 0.00 0.00 2.29
424 3404 2.048127 GTCACACCGAGCCACCTC 60.048 66.667 0.00 0.00 34.66 3.85
425 3405 2.523168 TCACACCGAGCCACCTCA 60.523 61.111 0.00 0.00 38.00 3.86
426 3406 2.047844 CACACCGAGCCACCTCAG 60.048 66.667 0.00 0.00 38.00 3.35
427 3407 4.008933 ACACCGAGCCACCTCAGC 62.009 66.667 0.00 0.00 38.00 4.26
473 3454 2.738480 CGGTTGGACCAACGGAGA 59.262 61.111 31.16 0.00 44.36 3.71
524 3505 2.360980 CGTCCTCTCCTCCACCCT 59.639 66.667 0.00 0.00 0.00 4.34
525 3506 1.755008 CGTCCTCTCCTCCACCCTC 60.755 68.421 0.00 0.00 0.00 4.30
526 3507 1.700985 GTCCTCTCCTCCACCCTCT 59.299 63.158 0.00 0.00 0.00 3.69
527 3508 0.396556 GTCCTCTCCTCCACCCTCTC 60.397 65.000 0.00 0.00 0.00 3.20
529 3510 0.106217 CCTCTCCTCCACCCTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
530 3511 0.926293 CTCTCCTCCACCCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
531 3512 0.923358 TCTCCTCCACCCTCTCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
532 3513 0.926293 CTCCTCCACCCTCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
533 3514 0.923358 TCCTCCACCCTCTCTCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
534 3515 0.926293 CCTCCACCCTCTCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
535 3516 1.133792 CCTCCACCCTCTCTCTCTCTC 60.134 61.905 0.00 0.00 0.00 3.20
536 3517 1.846439 CTCCACCCTCTCTCTCTCTCT 59.154 57.143 0.00 0.00 0.00 3.10
550 3531 2.437281 CTCTCTCTCTCTCTCTCTGCCT 59.563 54.545 0.00 0.00 0.00 4.75
560 3541 0.814457 CTCTCTGCCTTGACTACGCT 59.186 55.000 0.00 0.00 0.00 5.07
575 3556 4.057428 GCTGACGACGGCCTGAGT 62.057 66.667 7.51 0.00 42.05 3.41
599 3580 4.021925 GGGACCTCGCTTGTGGCT 62.022 66.667 0.00 0.00 39.13 4.75
688 3675 0.806868 AGCTGCATGGTGTCGATTTG 59.193 50.000 1.02 0.00 0.00 2.32
690 3677 0.452987 CTGCATGGTGTCGATTTGGG 59.547 55.000 0.00 0.00 0.00 4.12
716 3706 5.626543 CGAATCTTGATTTGTGTCTTTGTGG 59.373 40.000 0.00 0.00 0.00 4.17
775 3765 2.035155 ATCTGCAAGCTGGCTGCA 59.965 55.556 15.68 13.06 45.94 4.41
817 3807 1.673665 GCTGGTGAGGAAGGCTGTG 60.674 63.158 0.00 0.00 0.00 3.66
818 3808 1.002868 CTGGTGAGGAAGGCTGTGG 60.003 63.158 0.00 0.00 0.00 4.17
965 3955 1.300697 GGAAGAACTGCACCGTCGT 60.301 57.895 0.00 0.00 0.00 4.34
980 3970 0.802607 GTCGTCTCCATCCTGTTCGC 60.803 60.000 0.00 0.00 0.00 4.70
990 3980 1.154093 CCTGTTCGCGCTCTCGTAA 60.154 57.895 5.56 0.00 38.14 3.18
991 3981 0.731514 CCTGTTCGCGCTCTCGTAAA 60.732 55.000 5.56 0.00 38.14 2.01
992 3982 0.362512 CTGTTCGCGCTCTCGTAAAC 59.637 55.000 5.56 0.00 38.14 2.01
996 3986 0.455633 TCGCGCTCTCGTAAACTTCC 60.456 55.000 5.56 0.00 38.14 3.46
999 3989 1.411493 CGCTCTCGTAAACTTCCGGC 61.411 60.000 0.00 0.00 0.00 6.13
1020 4010 1.485124 TGATCGCCCTGCTTCTCTTA 58.515 50.000 0.00 0.00 0.00 2.10
1313 4337 3.769844 TGGATTTCGAGAGGCTTCTTACT 59.230 43.478 0.00 0.00 32.53 2.24
1316 4340 6.070995 TGGATTTCGAGAGGCTTCTTACTTAA 60.071 38.462 0.00 0.00 32.53 1.85
1352 4376 0.108756 GTTGTGCTCGGTCCTACTCC 60.109 60.000 0.00 0.00 0.00 3.85
1371 4395 0.318275 CTCGCCCTCTTCTACATCGC 60.318 60.000 0.00 0.00 0.00 4.58
1378 4402 0.179100 TCTTCTACATCGCTGCTGCC 60.179 55.000 10.24 0.00 35.36 4.85
1398 4422 0.033228 GTGGCGATCTGGAGGATGAG 59.967 60.000 0.00 0.00 34.33 2.90
1448 4472 2.942804 TCAGGATGAGTCTCAGGCTAG 58.057 52.381 8.82 0.00 42.56 3.42
1450 4474 0.313672 GGATGAGTCTCAGGCTAGCG 59.686 60.000 9.00 0.00 0.00 4.26
1451 4475 1.313772 GATGAGTCTCAGGCTAGCGA 58.686 55.000 9.00 0.00 0.00 4.93
1452 4476 1.001815 GATGAGTCTCAGGCTAGCGAC 60.002 57.143 9.00 10.36 0.00 5.19
1453 4477 0.034960 TGAGTCTCAGGCTAGCGACT 60.035 55.000 19.11 19.11 39.27 4.18
1589 4908 1.203994 TCTTGGAACAGCTAGCCGTAC 59.796 52.381 12.13 4.95 42.39 3.67
1607 4930 2.099633 ACGTTTGAATCGTGTTGTGC 57.900 45.000 0.00 0.00 40.07 4.57
1660 4995 1.131638 CCTGCTGACCATAGGCCTTA 58.868 55.000 12.58 0.00 0.00 2.69
1662 4997 2.107204 CCTGCTGACCATAGGCCTTAAT 59.893 50.000 12.58 0.00 0.00 1.40
1663 4998 3.435601 CCTGCTGACCATAGGCCTTAATT 60.436 47.826 12.58 0.00 0.00 1.40
1664 4999 4.210331 CTGCTGACCATAGGCCTTAATTT 58.790 43.478 12.58 0.00 0.00 1.82
1665 5000 4.207165 TGCTGACCATAGGCCTTAATTTC 58.793 43.478 12.58 2.01 0.00 2.17
1666 5001 4.207165 GCTGACCATAGGCCTTAATTTCA 58.793 43.478 12.58 7.09 0.00 2.69
1678 5024 5.985530 GGCCTTAATTTCATCATTTACTGGC 59.014 40.000 0.00 0.00 0.00 4.85
1708 5054 1.095600 GGAAGAATTTCGAGGTGGCC 58.904 55.000 0.00 0.00 33.98 5.36
1739 5089 7.857456 AGATGATGGAGATCGAGTACTACTAT 58.143 38.462 0.00 0.00 0.00 2.12
1740 5090 8.983789 AGATGATGGAGATCGAGTACTACTATA 58.016 37.037 0.00 0.00 0.00 1.31
1741 5091 8.951787 ATGATGGAGATCGAGTACTACTATAC 57.048 38.462 0.00 0.00 0.00 1.47
1782 5132 5.017490 TGCTTCTGTTTCCTAGCTACTACT 58.983 41.667 0.00 0.00 34.77 2.57
1783 5133 6.095160 GTGCTTCTGTTTCCTAGCTACTACTA 59.905 42.308 0.00 0.00 34.77 1.82
1784 5134 6.095160 TGCTTCTGTTTCCTAGCTACTACTAC 59.905 42.308 0.00 0.00 34.77 2.73
1785 5135 6.674694 TTCTGTTTCCTAGCTACTACTACG 57.325 41.667 0.00 0.00 0.00 3.51
1786 5136 5.121811 TCTGTTTCCTAGCTACTACTACGG 58.878 45.833 0.00 0.00 0.00 4.02
1787 5137 4.848357 TGTTTCCTAGCTACTACTACGGT 58.152 43.478 0.00 0.00 0.00 4.83
1788 5138 5.989477 TGTTTCCTAGCTACTACTACGGTA 58.011 41.667 0.00 0.00 0.00 4.02
1789 5139 5.817816 TGTTTCCTAGCTACTACTACGGTAC 59.182 44.000 0.00 0.00 0.00 3.34
1790 5140 5.878406 TTCCTAGCTACTACTACGGTACT 57.122 43.478 0.00 0.00 0.00 2.73
1791 5141 6.978674 TTCCTAGCTACTACTACGGTACTA 57.021 41.667 0.00 0.00 0.00 1.82
1792 5142 6.334102 TCCTAGCTACTACTACGGTACTAC 57.666 45.833 0.00 0.00 0.00 2.73
1793 5143 5.244178 TCCTAGCTACTACTACGGTACTACC 59.756 48.000 0.00 0.00 34.05 3.18
1797 5147 9.179909 CTAGCTACTACTACGGTACTACCTATA 57.820 40.741 3.68 0.00 35.66 1.31
1857 5207 3.117994 CGATCGTGTGATGCGTAGTTATG 59.882 47.826 7.03 0.00 34.09 1.90
1858 5208 3.497297 TCGTGTGATGCGTAGTTATGT 57.503 42.857 0.00 0.00 0.00 2.29
1859 5209 4.619437 TCGTGTGATGCGTAGTTATGTA 57.381 40.909 0.00 0.00 0.00 2.29
1860 5210 4.594136 TCGTGTGATGCGTAGTTATGTAG 58.406 43.478 0.00 0.00 0.00 2.74
1941 5296 6.477253 TGTCACTATGGCTGTTTGGTTAATA 58.523 36.000 0.00 0.00 0.00 0.98
1942 5297 6.943146 TGTCACTATGGCTGTTTGGTTAATAA 59.057 34.615 0.00 0.00 0.00 1.40
1943 5298 7.613801 TGTCACTATGGCTGTTTGGTTAATAAT 59.386 33.333 0.00 0.00 0.00 1.28
2053 5441 5.895636 TCATTGCTGATTTGTATCCGTTT 57.104 34.783 0.00 0.00 0.00 3.60
2220 6166 1.007011 CAGCGTCGATCGAATTGTCAC 60.007 52.381 21.31 5.01 42.86 3.67
2281 6231 7.926674 TCTCAGATGAAGCACAATTTTCATA 57.073 32.000 3.62 0.00 42.43 2.15
2284 6234 6.038356 CAGATGAAGCACAATTTTCATACCC 58.962 40.000 3.62 0.00 42.43 3.69
2293 6243 5.465056 CACAATTTTCATACCCCACACAAAC 59.535 40.000 0.00 0.00 0.00 2.93
2361 6311 8.549338 AGTAGTTATTTGCTTCAAGTAGTTCC 57.451 34.615 0.00 0.00 0.00 3.62
2362 6312 8.376270 AGTAGTTATTTGCTTCAAGTAGTTCCT 58.624 33.333 0.00 0.00 0.00 3.36
2363 6313 7.674471 AGTTATTTGCTTCAAGTAGTTCCTC 57.326 36.000 0.00 0.00 0.00 3.71
2364 6314 7.224297 AGTTATTTGCTTCAAGTAGTTCCTCA 58.776 34.615 0.00 0.00 0.00 3.86
2365 6315 7.389053 AGTTATTTGCTTCAAGTAGTTCCTCAG 59.611 37.037 0.00 0.00 0.00 3.35
2366 6316 4.955811 TTGCTTCAAGTAGTTCCTCAGA 57.044 40.909 0.00 0.00 0.00 3.27
2367 6317 5.489792 TTGCTTCAAGTAGTTCCTCAGAT 57.510 39.130 0.00 0.00 0.00 2.90
2368 6318 4.825422 TGCTTCAAGTAGTTCCTCAGATG 58.175 43.478 0.00 0.00 0.00 2.90
2369 6319 4.528206 TGCTTCAAGTAGTTCCTCAGATGA 59.472 41.667 0.00 0.00 0.00 2.92
2370 6320 5.012046 TGCTTCAAGTAGTTCCTCAGATGAA 59.988 40.000 0.00 0.00 0.00 2.57
2371 6321 5.580297 GCTTCAAGTAGTTCCTCAGATGAAG 59.420 44.000 7.60 7.60 43.20 3.02
2372 6322 5.078411 TCAAGTAGTTCCTCAGATGAAGC 57.922 43.478 0.00 0.00 0.00 3.86
2373 6323 4.528206 TCAAGTAGTTCCTCAGATGAAGCA 59.472 41.667 0.00 0.00 0.00 3.91
2374 6324 4.464069 AGTAGTTCCTCAGATGAAGCAC 57.536 45.455 0.00 0.00 0.00 4.40
2375 6325 3.834813 AGTAGTTCCTCAGATGAAGCACA 59.165 43.478 0.00 0.00 0.00 4.57
2376 6326 3.777106 AGTTCCTCAGATGAAGCACAA 57.223 42.857 0.00 0.00 0.00 3.33
2377 6327 4.298103 AGTTCCTCAGATGAAGCACAAT 57.702 40.909 0.00 0.00 0.00 2.71
2378 6328 4.660168 AGTTCCTCAGATGAAGCACAATT 58.340 39.130 0.00 0.00 0.00 2.32
2379 6329 5.075493 AGTTCCTCAGATGAAGCACAATTT 58.925 37.500 0.00 0.00 0.00 1.82
2380 6330 5.537674 AGTTCCTCAGATGAAGCACAATTTT 59.462 36.000 0.00 0.00 0.00 1.82
2381 6331 5.633830 TCCTCAGATGAAGCACAATTTTC 57.366 39.130 0.00 0.00 0.00 2.29
2382 6332 5.072055 TCCTCAGATGAAGCACAATTTTCA 58.928 37.500 0.00 0.00 37.68 2.69
2383 6333 5.713389 TCCTCAGATGAAGCACAATTTTCAT 59.287 36.000 3.31 3.31 44.39 2.57
2384 6334 5.805486 CCTCAGATGAAGCACAATTTTCATG 59.195 40.000 7.63 0.00 42.43 3.07
2385 6335 5.165676 TCAGATGAAGCACAATTTTCATGC 58.834 37.500 7.63 1.12 42.43 4.06
2386 6336 4.031314 CAGATGAAGCACAATTTTCATGCG 59.969 41.667 7.63 0.00 42.43 4.73
2387 6337 2.674954 TGAAGCACAATTTTCATGCGG 58.325 42.857 0.00 0.00 44.25 5.69
2388 6338 1.391144 GAAGCACAATTTTCATGCGGC 59.609 47.619 0.00 0.00 44.25 6.53
2389 6339 0.317799 AGCACAATTTTCATGCGGCA 59.682 45.000 4.58 4.58 44.25 5.69
2390 6340 0.439600 GCACAATTTTCATGCGGCAC 59.560 50.000 4.03 0.00 0.00 5.01
2391 6341 1.780806 CACAATTTTCATGCGGCACA 58.219 45.000 4.03 0.00 0.00 4.57
2392 6342 1.456544 CACAATTTTCATGCGGCACAC 59.543 47.619 4.03 0.00 0.00 3.82
2393 6343 1.068281 ACAATTTTCATGCGGCACACA 59.932 42.857 4.03 0.00 0.00 3.72
2394 6344 2.133553 CAATTTTCATGCGGCACACAA 58.866 42.857 4.03 0.00 0.00 3.33
2395 6345 2.522836 ATTTTCATGCGGCACACAAA 57.477 40.000 4.03 4.76 0.00 2.83
2396 6346 2.299993 TTTTCATGCGGCACACAAAA 57.700 40.000 4.03 8.06 0.00 2.44
2397 6347 2.299993 TTTCATGCGGCACACAAAAA 57.700 40.000 4.03 0.00 0.00 1.94
2398 6348 2.522836 TTCATGCGGCACACAAAAAT 57.477 40.000 4.03 0.00 0.00 1.82
2399 6349 1.780806 TCATGCGGCACACAAAAATG 58.219 45.000 4.03 0.00 0.00 2.32
2400 6350 1.339291 TCATGCGGCACACAAAAATGA 59.661 42.857 4.03 0.00 0.00 2.57
2401 6351 1.722464 CATGCGGCACACAAAAATGAG 59.278 47.619 4.03 0.00 0.00 2.90
2402 6352 0.031857 TGCGGCACACAAAAATGAGG 59.968 50.000 0.00 0.00 0.00 3.86
2403 6353 0.313672 GCGGCACACAAAAATGAGGA 59.686 50.000 0.00 0.00 0.00 3.71
2404 6354 1.269517 GCGGCACACAAAAATGAGGAA 60.270 47.619 0.00 0.00 0.00 3.36
2405 6355 2.801342 GCGGCACACAAAAATGAGGAAA 60.801 45.455 0.00 0.00 0.00 3.13
2406 6356 3.452474 CGGCACACAAAAATGAGGAAAA 58.548 40.909 0.00 0.00 0.00 2.29
2407 6357 4.057432 CGGCACACAAAAATGAGGAAAAT 58.943 39.130 0.00 0.00 0.00 1.82
2408 6358 4.511082 CGGCACACAAAAATGAGGAAAATT 59.489 37.500 0.00 0.00 0.00 1.82
2409 6359 5.007528 CGGCACACAAAAATGAGGAAAATTT 59.992 36.000 0.00 0.00 0.00 1.82
2410 6360 6.429624 GGCACACAAAAATGAGGAAAATTTC 58.570 36.000 0.00 0.00 0.00 2.17
2411 6361 6.038050 GGCACACAAAAATGAGGAAAATTTCA 59.962 34.615 8.09 0.00 0.00 2.69
2412 6362 7.414984 GGCACACAAAAATGAGGAAAATTTCAA 60.415 33.333 8.09 0.00 0.00 2.69
2413 6363 7.641020 GCACACAAAAATGAGGAAAATTTCAAG 59.359 33.333 8.09 0.00 0.00 3.02
2414 6364 7.641020 CACACAAAAATGAGGAAAATTTCAAGC 59.359 33.333 8.09 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 9.859427 ATGAATATGTTTTCAATTCACGAATGT 57.141 25.926 0.00 0.00 38.98 2.71
199 219 7.201574 CGTGGATATTTTTAAAGGTCGTGATCA 60.202 37.037 0.00 0.00 0.00 2.92
289 311 4.060038 AGGTAGCCATCGTGAATAACAG 57.940 45.455 0.00 0.00 0.00 3.16
327 1408 0.469892 TGAGTGGTCTGGCTGTGAGA 60.470 55.000 0.00 0.00 0.00 3.27
328 1409 0.320247 GTGAGTGGTCTGGCTGTGAG 60.320 60.000 0.00 0.00 0.00 3.51
389 1472 1.227853 CTGGGGTATTACGGCCTGC 60.228 63.158 0.00 0.00 0.00 4.85
424 3404 1.961277 GTGAAGTGACCGGTGGCTG 60.961 63.158 14.63 0.00 0.00 4.85
425 3405 2.100879 GAGTGAAGTGACCGGTGGCT 62.101 60.000 14.63 6.78 0.00 4.75
426 3406 1.668151 GAGTGAAGTGACCGGTGGC 60.668 63.158 14.63 3.90 0.00 5.01
427 3407 1.004918 GGAGTGAAGTGACCGGTGG 60.005 63.158 14.63 0.00 0.00 4.61
434 3414 2.564504 CTCTGGATGTGGAGTGAAGTGA 59.435 50.000 0.00 0.00 0.00 3.41
509 3490 0.553862 AGAGAGGGTGGAGGAGAGGA 60.554 60.000 0.00 0.00 0.00 3.71
524 3505 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
525 3506 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
526 3507 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
527 3508 3.494048 GGCAGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
529 3510 2.437281 AGGCAGAGAGAGAGAGAGAGAG 59.563 54.545 0.00 0.00 0.00 3.20
530 3511 2.481441 AGGCAGAGAGAGAGAGAGAGA 58.519 52.381 0.00 0.00 0.00 3.10
531 3512 2.947652 CAAGGCAGAGAGAGAGAGAGAG 59.052 54.545 0.00 0.00 0.00 3.20
532 3513 2.575735 TCAAGGCAGAGAGAGAGAGAGA 59.424 50.000 0.00 0.00 0.00 3.10
533 3514 2.684881 GTCAAGGCAGAGAGAGAGAGAG 59.315 54.545 0.00 0.00 0.00 3.20
534 3515 2.308570 AGTCAAGGCAGAGAGAGAGAGA 59.691 50.000 0.00 0.00 0.00 3.10
535 3516 2.726821 AGTCAAGGCAGAGAGAGAGAG 58.273 52.381 0.00 0.00 0.00 3.20
536 3517 2.897271 AGTCAAGGCAGAGAGAGAGA 57.103 50.000 0.00 0.00 0.00 3.10
550 3531 1.208358 CCGTCGTCAGCGTAGTCAA 59.792 57.895 0.00 0.00 39.49 3.18
560 3541 2.910479 ACACTCAGGCCGTCGTCA 60.910 61.111 0.00 0.00 0.00 4.35
613 3594 3.818787 GCAATCAGGCCTGCACCG 61.819 66.667 28.91 16.35 38.48 4.94
654 3635 2.583593 GCTACAAGCGAGCTCCCG 60.584 66.667 8.47 0.00 36.96 5.14
688 3675 4.003648 AGACACAAATCAAGATTCGACCC 58.996 43.478 0.00 0.00 0.00 4.46
690 3677 6.358030 CACAAAGACACAAATCAAGATTCGAC 59.642 38.462 0.00 0.00 0.00 4.20
716 3706 0.723981 GTGCCTGAAACAGATCGAGC 59.276 55.000 0.00 0.00 32.44 5.03
965 3955 2.184322 GCGCGAACAGGATGGAGA 59.816 61.111 12.10 0.00 43.62 3.71
980 3970 1.411493 GCCGGAAGTTTACGAGAGCG 61.411 60.000 5.05 0.00 44.79 5.03
990 3980 1.819632 GGCGATCATGCCGGAAGTT 60.820 57.895 5.05 0.00 46.75 2.66
991 3981 2.203070 GGCGATCATGCCGGAAGT 60.203 61.111 5.05 0.00 46.75 3.01
999 3989 0.106335 AGAGAAGCAGGGCGATCATG 59.894 55.000 0.00 0.00 0.00 3.07
1080 4070 2.396955 CGGCGACTGAGGAGTACGT 61.397 63.158 0.00 0.00 30.16 3.57
1081 4071 2.403987 CGGCGACTGAGGAGTACG 59.596 66.667 0.00 0.00 30.16 3.67
1082 4072 2.102553 GCGGCGACTGAGGAGTAC 59.897 66.667 12.98 0.00 30.16 2.73
1083 4073 3.138798 GGCGGCGACTGAGGAGTA 61.139 66.667 12.98 0.00 30.16 2.59
1313 4337 2.164663 CAGCCGCGACGCAGATTAA 61.165 57.895 21.35 0.00 0.00 1.40
1352 4376 0.318275 GCGATGTAGAAGAGGGCGAG 60.318 60.000 0.00 0.00 0.00 5.03
1371 4395 4.827087 AGATCGCCACGGCAGCAG 62.827 66.667 9.11 0.00 42.06 4.24
1378 4402 1.300465 CATCCTCCAGATCGCCACG 60.300 63.158 0.00 0.00 30.59 4.94
1398 4422 1.975363 GATGCTGCGCTGTTGAGGAC 61.975 60.000 16.05 0.00 0.00 3.85
1446 4470 0.108992 CGCCACCTTGTTAGTCGCTA 60.109 55.000 0.00 0.00 0.00 4.26
1448 4472 2.388232 CCGCCACCTTGTTAGTCGC 61.388 63.158 0.00 0.00 0.00 5.19
1450 4474 0.320697 ACTCCGCCACCTTGTTAGTC 59.679 55.000 0.00 0.00 0.00 2.59
1451 4475 1.549170 CTACTCCGCCACCTTGTTAGT 59.451 52.381 0.00 0.00 0.00 2.24
1452 4476 1.739371 GCTACTCCGCCACCTTGTTAG 60.739 57.143 0.00 0.00 0.00 2.34
1453 4477 0.248289 GCTACTCCGCCACCTTGTTA 59.752 55.000 0.00 0.00 0.00 2.41
1473 4497 1.816835 TGAGTACGTAGGTGAAGCTGG 59.183 52.381 0.00 0.00 0.00 4.85
1589 4908 1.034293 CGCACAACACGATTCAAACG 58.966 50.000 0.00 0.00 0.00 3.60
1660 4995 5.025453 ACCTGGCCAGTAAATGATGAAATT 58.975 37.500 30.63 0.00 0.00 1.82
1662 4997 3.763360 CACCTGGCCAGTAAATGATGAAA 59.237 43.478 30.63 0.00 0.00 2.69
1663 4998 3.355378 CACCTGGCCAGTAAATGATGAA 58.645 45.455 30.63 0.00 0.00 2.57
1664 4999 2.945440 GCACCTGGCCAGTAAATGATGA 60.945 50.000 30.63 0.00 36.11 2.92
1665 5000 1.406539 GCACCTGGCCAGTAAATGATG 59.593 52.381 30.63 15.25 36.11 3.07
1666 5001 1.005805 TGCACCTGGCCAGTAAATGAT 59.994 47.619 30.63 4.74 43.89 2.45
1678 5024 1.915141 AATTCTTCCTGTGCACCTGG 58.085 50.000 15.69 16.46 0.00 4.45
1708 5054 2.030451 TCGATCTCCATCATCTTCTGCG 60.030 50.000 0.00 0.00 0.00 5.18
1739 5089 3.353557 CACTCCTGCACTGGTAGTAGTA 58.646 50.000 0.00 0.00 25.45 1.82
1740 5090 2.171840 CACTCCTGCACTGGTAGTAGT 58.828 52.381 0.00 0.00 0.00 2.73
1741 5091 1.134965 GCACTCCTGCACTGGTAGTAG 60.135 57.143 0.00 0.00 43.62 2.57
1782 5132 8.324306 AGAGCAACATATATAGGTAGTACCGTA 58.676 37.037 13.76 11.12 44.90 4.02
1783 5133 7.173722 AGAGCAACATATATAGGTAGTACCGT 58.826 38.462 13.76 9.29 44.90 4.83
1784 5134 7.627298 AGAGCAACATATATAGGTAGTACCG 57.373 40.000 13.76 0.32 44.90 4.02
1785 5135 8.804204 ACAAGAGCAACATATATAGGTAGTACC 58.196 37.037 11.73 11.73 38.99 3.34
1786 5136 9.627395 CACAAGAGCAACATATATAGGTAGTAC 57.373 37.037 0.00 0.00 0.00 2.73
1787 5137 9.582648 TCACAAGAGCAACATATATAGGTAGTA 57.417 33.333 0.00 0.00 0.00 1.82
1788 5138 8.478775 TCACAAGAGCAACATATATAGGTAGT 57.521 34.615 0.00 0.00 0.00 2.73
1789 5139 9.197694 GTTCACAAGAGCAACATATATAGGTAG 57.802 37.037 0.00 0.00 0.00 3.18
1790 5140 8.700973 TGTTCACAAGAGCAACATATATAGGTA 58.299 33.333 0.00 0.00 31.64 3.08
1791 5141 7.564793 TGTTCACAAGAGCAACATATATAGGT 58.435 34.615 0.00 0.00 31.64 3.08
1792 5142 8.437360 TTGTTCACAAGAGCAACATATATAGG 57.563 34.615 0.00 0.00 39.60 2.57
1797 5147 9.013229 TCTTAATTGTTCACAAGAGCAACATAT 57.987 29.630 0.00 0.00 45.71 1.78
1875 5225 7.968956 CGAATCAAGCTTACTGAGACTAAGTTA 59.031 37.037 0.00 0.00 0.00 2.24
1876 5226 6.809196 CGAATCAAGCTTACTGAGACTAAGTT 59.191 38.462 0.00 0.00 0.00 2.66
1877 5227 6.151312 TCGAATCAAGCTTACTGAGACTAAGT 59.849 38.462 0.00 0.00 0.00 2.24
1879 5229 6.510879 TCGAATCAAGCTTACTGAGACTAA 57.489 37.500 0.00 0.00 0.00 2.24
1880 5230 6.499172 CATCGAATCAAGCTTACTGAGACTA 58.501 40.000 0.00 0.00 0.00 2.59
1881 5231 5.347342 CATCGAATCAAGCTTACTGAGACT 58.653 41.667 0.00 0.00 0.00 3.24
1882 5232 4.026145 GCATCGAATCAAGCTTACTGAGAC 60.026 45.833 0.00 0.00 0.00 3.36
1941 5296 3.775316 AGGTCCGGTTCAGACTTCATATT 59.225 43.478 0.00 0.00 34.56 1.28
1942 5297 3.375699 AGGTCCGGTTCAGACTTCATAT 58.624 45.455 0.00 0.00 34.56 1.78
1943 5298 2.758979 GAGGTCCGGTTCAGACTTCATA 59.241 50.000 0.00 0.00 39.45 2.15
2034 5422 3.823873 ACCAAACGGATACAAATCAGCAA 59.176 39.130 0.00 0.00 33.41 3.91
2053 5441 2.490115 CGCCCAGCAAAGTAATTAACCA 59.510 45.455 0.00 0.00 0.00 3.67
2169 5606 1.584175 GCACATGCATCTCTCTCTGG 58.416 55.000 0.00 0.00 41.59 3.86
2220 6166 1.302383 TGCAAATTGTAGGGGACGCG 61.302 55.000 3.53 3.53 0.00 6.01
2246 6196 2.951726 TCATCTGAGAAGCAACACTCG 58.048 47.619 0.00 0.00 36.11 4.18
2281 6231 0.253610 TTCTCACGTTTGTGTGGGGT 59.746 50.000 0.00 0.00 46.49 4.95
2358 6308 5.535783 TGAAAATTGTGCTTCATCTGAGGAA 59.464 36.000 4.56 4.56 0.00 3.36
2359 6309 5.072055 TGAAAATTGTGCTTCATCTGAGGA 58.928 37.500 0.00 0.00 0.00 3.71
2360 6310 5.381174 TGAAAATTGTGCTTCATCTGAGG 57.619 39.130 0.00 0.00 0.00 3.86
2361 6311 5.288712 GCATGAAAATTGTGCTTCATCTGAG 59.711 40.000 0.00 0.00 39.66 3.35
2362 6312 5.165676 GCATGAAAATTGTGCTTCATCTGA 58.834 37.500 0.00 0.00 39.66 3.27
2363 6313 4.031314 CGCATGAAAATTGTGCTTCATCTG 59.969 41.667 0.00 0.00 39.66 2.90
2364 6314 4.171005 CGCATGAAAATTGTGCTTCATCT 58.829 39.130 0.00 0.00 39.66 2.90
2365 6315 3.305094 CCGCATGAAAATTGTGCTTCATC 59.695 43.478 0.00 0.00 39.66 2.92
2366 6316 3.255725 CCGCATGAAAATTGTGCTTCAT 58.744 40.909 0.00 0.00 41.80 2.57
2367 6317 2.674954 CCGCATGAAAATTGTGCTTCA 58.325 42.857 0.00 0.00 36.74 3.02
2368 6318 1.391144 GCCGCATGAAAATTGTGCTTC 59.609 47.619 0.00 0.00 36.74 3.86
2369 6319 1.270199 TGCCGCATGAAAATTGTGCTT 60.270 42.857 0.00 0.00 36.74 3.91
2370 6320 0.317799 TGCCGCATGAAAATTGTGCT 59.682 45.000 0.00 0.00 36.74 4.40
2371 6321 0.439600 GTGCCGCATGAAAATTGTGC 59.560 50.000 0.00 0.00 35.59 4.57
2372 6322 1.456544 GTGTGCCGCATGAAAATTGTG 59.543 47.619 0.00 0.00 0.00 3.33
2373 6323 1.068281 TGTGTGCCGCATGAAAATTGT 59.932 42.857 0.00 0.00 0.00 2.71
2374 6324 1.780806 TGTGTGCCGCATGAAAATTG 58.219 45.000 0.00 0.00 0.00 2.32
2375 6325 2.522836 TTGTGTGCCGCATGAAAATT 57.477 40.000 0.00 0.00 0.00 1.82
2376 6326 2.522836 TTTGTGTGCCGCATGAAAAT 57.477 40.000 0.00 0.00 0.00 1.82
2377 6327 2.299993 TTTTGTGTGCCGCATGAAAA 57.700 40.000 0.00 0.00 0.00 2.29
2378 6328 2.299993 TTTTTGTGTGCCGCATGAAA 57.700 40.000 0.00 0.00 0.00 2.69
2379 6329 2.133553 CATTTTTGTGTGCCGCATGAA 58.866 42.857 0.00 0.00 0.00 2.57
2380 6330 1.339291 TCATTTTTGTGTGCCGCATGA 59.661 42.857 0.00 0.00 0.00 3.07
2381 6331 1.722464 CTCATTTTTGTGTGCCGCATG 59.278 47.619 0.00 0.00 0.00 4.06
2382 6332 1.337074 CCTCATTTTTGTGTGCCGCAT 60.337 47.619 0.00 0.00 0.00 4.73
2383 6333 0.031857 CCTCATTTTTGTGTGCCGCA 59.968 50.000 0.00 0.00 0.00 5.69
2384 6334 0.313672 TCCTCATTTTTGTGTGCCGC 59.686 50.000 0.00 0.00 0.00 6.53
2385 6335 2.791383 TTCCTCATTTTTGTGTGCCG 57.209 45.000 0.00 0.00 0.00 5.69
2386 6336 6.038050 TGAAATTTTCCTCATTTTTGTGTGCC 59.962 34.615 6.68 0.00 0.00 5.01
2387 6337 7.014092 TGAAATTTTCCTCATTTTTGTGTGC 57.986 32.000 6.68 0.00 0.00 4.57
2388 6338 7.641020 GCTTGAAATTTTCCTCATTTTTGTGTG 59.359 33.333 6.68 0.00 0.00 3.82
2389 6339 7.336427 TGCTTGAAATTTTCCTCATTTTTGTGT 59.664 29.630 6.68 0.00 0.00 3.72
2390 6340 7.695820 TGCTTGAAATTTTCCTCATTTTTGTG 58.304 30.769 6.68 0.00 0.00 3.33
2391 6341 7.862512 TGCTTGAAATTTTCCTCATTTTTGT 57.137 28.000 6.68 0.00 0.00 2.83
2392 6342 8.019094 GGATGCTTGAAATTTTCCTCATTTTTG 58.981 33.333 6.68 0.00 0.00 2.44
2393 6343 7.720515 TGGATGCTTGAAATTTTCCTCATTTTT 59.279 29.630 6.68 0.00 0.00 1.94
2394 6344 7.225725 TGGATGCTTGAAATTTTCCTCATTTT 58.774 30.769 6.68 0.00 0.00 1.82
2395 6345 6.771573 TGGATGCTTGAAATTTTCCTCATTT 58.228 32.000 6.68 0.00 0.00 2.32
2396 6346 6.363167 TGGATGCTTGAAATTTTCCTCATT 57.637 33.333 6.68 0.00 0.00 2.57
2397 6347 6.555463 ATGGATGCTTGAAATTTTCCTCAT 57.445 33.333 6.68 7.02 0.00 2.90
2398 6348 6.014413 TCAATGGATGCTTGAAATTTTCCTCA 60.014 34.615 6.68 2.85 29.96 3.86
2399 6349 6.400568 TCAATGGATGCTTGAAATTTTCCTC 58.599 36.000 6.68 0.00 29.96 3.71
2400 6350 6.363167 TCAATGGATGCTTGAAATTTTCCT 57.637 33.333 6.68 0.00 29.96 3.36
2401 6351 7.201670 GGAATCAATGGATGCTTGAAATTTTCC 60.202 37.037 6.68 10.60 36.30 3.13
2402 6352 7.334921 TGGAATCAATGGATGCTTGAAATTTTC 59.665 33.333 2.05 2.05 36.30 2.29
2403 6353 7.169591 TGGAATCAATGGATGCTTGAAATTTT 58.830 30.769 0.00 0.00 36.30 1.82
2404 6354 6.713276 TGGAATCAATGGATGCTTGAAATTT 58.287 32.000 0.00 0.00 36.30 1.82
2405 6355 6.302535 TGGAATCAATGGATGCTTGAAATT 57.697 33.333 3.92 0.00 36.30 1.82
2406 6356 5.943349 TGGAATCAATGGATGCTTGAAAT 57.057 34.783 3.92 0.00 36.30 2.17
2407 6357 5.188163 ACATGGAATCAATGGATGCTTGAAA 59.812 36.000 2.30 0.00 36.30 2.69
2408 6358 4.712829 ACATGGAATCAATGGATGCTTGAA 59.287 37.500 2.30 0.00 36.30 2.69
2409 6359 4.283337 ACATGGAATCAATGGATGCTTGA 58.717 39.130 2.30 2.61 37.06 3.02
2410 6360 4.665833 ACATGGAATCAATGGATGCTTG 57.334 40.909 2.30 0.00 32.92 4.01
2411 6361 4.276678 CGTACATGGAATCAATGGATGCTT 59.723 41.667 2.30 0.00 32.92 3.91
2412 6362 3.817084 CGTACATGGAATCAATGGATGCT 59.183 43.478 2.30 0.00 32.92 3.79
2413 6363 3.610114 GCGTACATGGAATCAATGGATGC 60.610 47.826 11.02 11.02 34.47 3.91
2414 6364 3.817084 AGCGTACATGGAATCAATGGATG 59.183 43.478 2.30 0.00 32.92 3.51


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

AutoCloner maintained by Alex Coulton.