Multiple sequence alignment - TraesCS7D01G236800

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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 TraesCS7D01G236800 chr7D 100.000 5396 0 0 1 5396 199827736 199833131 0.000000e+00 9965
1 TraesCS7D01G236800 chr7B 92.276 3418 179 44 733 4084 164944912 164948310 0.000000e+00 4771
2 TraesCS7D01G236800 chr7B 89.595 740 70 5 1 734 97508463 97507725 0.000000e+00 933
3 TraesCS7D01G236800 chr7B 91.679 661 42 7 4745 5396 164950584 164951240 0.000000e+00 904
4 TraesCS7D01G236800 chr7B 93.333 495 30 3 4084 4578 164949930 164950421 0.000000e+00 728
5 TraesCS7D01G236800 chr7A 94.139 2491 77 27 1720 4171 211794492 211796952 0.000000e+00 3727
6 TraesCS7D01G236800 chr7A 91.034 948 60 19 733 1666 211793569 211794505 0.000000e+00 1256
7 TraesCS7D01G236800 chr7A 89.474 741 70 6 1 734 34324430 34325169 0.000000e+00 929
8 TraesCS7D01G236800 chr7A 91.745 424 26 7 4161 4578 211796973 211797393 1.010000e-161 580
9 TraesCS7D01G236800 chr7A 87.914 513 34 9 4894 5396 211798363 211798857 3.620000e-161 579
10 TraesCS7D01G236800 chr2B 94.737 741 34 2 1 736 639028912 639028172 0.000000e+00 1147
11 TraesCS7D01G236800 chr2B 94.437 737 36 2 1 732 639038164 639037428 0.000000e+00 1129
12 TraesCS7D01G236800 chr4D 94.309 738 33 3 1 733 470437041 470437774 0.000000e+00 1122
13 TraesCS7D01G236800 chr6B 90.148 741 65 5 1 734 96234777 96235516 0.000000e+00 957
14 TraesCS7D01G236800 chr6B 89.024 738 75 4 1 733 33719424 33718688 0.000000e+00 909
15 TraesCS7D01G236800 chr1B 89.023 747 75 5 1 742 372225502 372224758 0.000000e+00 918
16 TraesCS7D01G236800 chr5B 89.175 739 75 3 1 734 638603505 638604243 0.000000e+00 917


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 TraesCS7D01G236800 chr7D 199827736 199833131 5395 False 9965.000000 9965 100.000000 1 5396 1 chr7D.!!$F1 5395
1 TraesCS7D01G236800 chr7B 164944912 164951240 6328 False 2134.333333 4771 92.429333 733 5396 3 chr7B.!!$F1 4663
2 TraesCS7D01G236800 chr7B 97507725 97508463 738 True 933.000000 933 89.595000 1 734 1 chr7B.!!$R1 733
3 TraesCS7D01G236800 chr7A 211793569 211798857 5288 False 1535.500000 3727 91.208000 733 5396 4 chr7A.!!$F2 4663
4 TraesCS7D01G236800 chr7A 34324430 34325169 739 False 929.000000 929 89.474000 1 734 1 chr7A.!!$F1 733
5 TraesCS7D01G236800 chr2B 639028172 639028912 740 True 1147.000000 1147 94.737000 1 736 1 chr2B.!!$R1 735
6 TraesCS7D01G236800 chr2B 639037428 639038164 736 True 1129.000000 1129 94.437000 1 732 1 chr2B.!!$R2 731
7 TraesCS7D01G236800 chr4D 470437041 470437774 733 False 1122.000000 1122 94.309000 1 733 1 chr4D.!!$F1 732
8 TraesCS7D01G236800 chr6B 96234777 96235516 739 False 957.000000 957 90.148000 1 734 1 chr6B.!!$F1 733
9 TraesCS7D01G236800 chr6B 33718688 33719424 736 True 909.000000 909 89.024000 1 733 1 chr6B.!!$R1 732
10 TraesCS7D01G236800 chr1B 372224758 372225502 744 True 918.000000 918 89.023000 1 742 1 chr1B.!!$R1 741
11 TraesCS7D01G236800 chr5B 638603505 638604243 738 False 917.000000 917 89.175000 1 734 1 chr5B.!!$F1 733

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
170 172 0.100682 CGAAGACCTAGCGCTGCTTA 59.899 55.000 22.90 0.0 40.44 3.09 F
659 665 0.325765 GGACTCCACCCCTAGCTTCT 60.326 60.000 0.00 0.0 0.00 2.85 F
1374 1386 0.179100 ATGTCGAGTGGAATGAGCCG 60.179 55.000 0.00 0.0 0.00 5.52 F
1535 1566 0.251916 CTTGGCCGTGGTCATCCTTA 59.748 55.000 0.00 0.0 34.23 2.69 F
1538 1569 1.283613 TGGCCGTGGTCATCCTTAAAT 59.716 47.619 0.00 0.0 34.23 1.40 F
2100 2133 1.304381 GGGCTTGCCTCCAATGTCA 60.304 57.895 11.71 0.0 0.00 3.58 F
2474 2508 1.852157 ATTGTCATCACTGGCCCCGT 61.852 55.000 0.00 0.0 0.00 5.28 F
3054 3138 2.054799 TGGCTTAGAGGTTCACCACTT 58.945 47.619 0.91 0.0 38.01 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 1375 0.179111 GTCATCGACGGCTCATTCCA 60.179 55.000 0.00 0.0 0.00 3.53 R
2293 2326 0.034089 AAGGATCGAGGCAAAAGGGG 60.034 55.000 0.00 0.0 0.00 4.79 R
2734 2818 2.414994 ATGCTGCTGTCACATTAGCT 57.585 45.000 12.95 0.0 40.52 3.32 R
3364 3448 2.889170 TTAGGCATACAGGGCAAACA 57.111 45.000 0.00 0.0 35.46 2.83 R
3766 3856 4.941263 TGGTGGTTATGTGCTACAAGAATC 59.059 41.667 0.00 0.0 0.00 2.52 R
4082 4176 4.346127 TGCATCAGCTATACAGAGGTCATT 59.654 41.667 0.00 0.0 42.74 2.57 R
4386 6133 0.391130 TGGTGCGCTATCAGGTTGAC 60.391 55.000 9.73 0.0 0.00 3.18 R
5270 7690 0.037303 ATATTGGCATCGCAGGGGAG 59.963 55.000 0.00 0.0 0.00 4.30 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
96 98 2.095059 GCAATCTGGATGTCCACAACAC 60.095 50.000 0.00 0.00 41.75 3.32
170 172 0.100682 CGAAGACCTAGCGCTGCTTA 59.899 55.000 22.90 0.00 40.44 3.09
280 282 4.321156 GCAATACAGTTTGATGCTGGTTCA 60.321 41.667 0.00 0.00 38.22 3.18
427 433 1.251251 AGCTTCGAGGCTTTTTGCAT 58.749 45.000 17.38 0.00 45.15 3.96
477 483 3.496160 GCAGTAAACCTCTGGAACCTTGA 60.496 47.826 0.00 0.00 33.98 3.02
550 556 5.278218 GCTCTCTGCTAGCTTTTTGTCTTTT 60.278 40.000 17.23 0.00 37.01 2.27
617 623 0.389296 TGCTAAGCGTGCATGTACGT 60.389 50.000 31.88 18.93 45.36 3.57
659 665 0.325765 GGACTCCACCCCTAGCTTCT 60.326 60.000 0.00 0.00 0.00 2.85
696 706 2.751436 TGCCCAGCGAATGCCTTC 60.751 61.111 0.00 0.00 44.31 3.46
712 722 7.414540 CGAATGCCTTCACTTAATAAAGCTCTT 60.415 37.037 2.57 0.00 36.05 2.85
723 733 7.945109 ACTTAATAAAGCTCTTTGAAGTTCCCT 59.055 33.333 0.00 0.00 36.05 4.20
1017 1028 1.616921 CATGATGGGGAGCAGGGTT 59.383 57.895 0.00 0.00 0.00 4.11
1123 1134 1.687297 CCCCGCTCCTTCTAGGGTTC 61.687 65.000 0.00 0.00 42.26 3.62
1167 1178 4.787280 CGCCACCTCCCTCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1300 1312 0.884704 GCTTGCGTGGTTCCTCTTGA 60.885 55.000 0.00 0.00 0.00 3.02
1304 1316 3.627395 TGCGTGGTTCCTCTTGATTAT 57.373 42.857 0.00 0.00 0.00 1.28
1317 1329 6.016860 TCCTCTTGATTATGCCATCATTTTCG 60.017 38.462 0.00 0.00 33.07 3.46
1334 1346 2.277373 GAGGCGCGTGAGTCGTAG 60.277 66.667 7.63 0.00 42.13 3.51
1336 1348 2.177531 GGCGCGTGAGTCGTAGAA 59.822 61.111 8.43 0.00 39.69 2.10
1337 1349 2.150837 GGCGCGTGAGTCGTAGAAC 61.151 63.158 8.43 0.00 39.69 3.01
1344 1356 4.088923 CGCGTGAGTCGTAGAACAATTTTA 59.911 41.667 0.00 0.00 39.69 1.52
1345 1357 5.303485 GCGTGAGTCGTAGAACAATTTTAC 58.697 41.667 0.00 0.00 39.69 2.01
1372 1384 1.590238 CGAATGTCGAGTGGAATGAGC 59.410 52.381 0.00 0.00 43.74 4.26
1373 1385 1.936547 GAATGTCGAGTGGAATGAGCC 59.063 52.381 0.00 0.00 0.00 4.70
1374 1386 0.179100 ATGTCGAGTGGAATGAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
1375 1387 1.215647 GTCGAGTGGAATGAGCCGT 59.784 57.895 0.00 0.00 0.00 5.68
1376 1388 0.802607 GTCGAGTGGAATGAGCCGTC 60.803 60.000 0.00 0.00 0.00 4.79
1377 1389 1.874019 CGAGTGGAATGAGCCGTCG 60.874 63.158 0.00 0.00 32.81 5.12
1378 1390 1.511305 GAGTGGAATGAGCCGTCGA 59.489 57.895 0.00 0.00 0.00 4.20
1394 1406 2.094258 CGTCGATGACCATTTTGTGAGG 59.906 50.000 0.00 0.00 0.00 3.86
1395 1407 3.334691 GTCGATGACCATTTTGTGAGGA 58.665 45.455 0.00 0.00 0.00 3.71
1396 1408 3.372206 GTCGATGACCATTTTGTGAGGAG 59.628 47.826 0.00 0.00 0.00 3.69
1397 1409 3.260632 TCGATGACCATTTTGTGAGGAGA 59.739 43.478 0.00 0.00 0.00 3.71
1399 1411 3.855255 TGACCATTTTGTGAGGAGACA 57.145 42.857 0.00 0.00 0.00 3.41
1400 1412 4.371624 TGACCATTTTGTGAGGAGACAT 57.628 40.909 0.00 0.00 0.00 3.06
1402 1414 5.875224 TGACCATTTTGTGAGGAGACATTA 58.125 37.500 0.00 0.00 0.00 1.90
1403 1415 5.939883 TGACCATTTTGTGAGGAGACATTAG 59.060 40.000 0.00 0.00 0.00 1.73
1437 1461 8.593679 TTCTATGTGAGACATTCTGGTTTAGAA 58.406 33.333 0.00 0.00 40.94 2.10
1469 1493 8.707839 CAATTTTATTACGTTGCAGTGGAAAAT 58.292 29.630 0.00 0.00 0.00 1.82
1506 1530 7.118680 TGCTGTAATAAACTTGTAGTTGTAGCC 59.881 37.037 0.00 0.00 38.66 3.93
1519 1550 3.701040 AGTTGTAGCCCCAATAATGCTTG 59.299 43.478 0.00 0.00 36.57 4.01
1531 1562 1.315257 AATGCTTGGCCGTGGTCATC 61.315 55.000 0.00 0.00 0.00 2.92
1535 1566 0.251916 CTTGGCCGTGGTCATCCTTA 59.748 55.000 0.00 0.00 34.23 2.69
1538 1569 1.283613 TGGCCGTGGTCATCCTTAAAT 59.716 47.619 0.00 0.00 34.23 1.40
1656 1689 3.202818 TGGATATGTTGATGCCAAGGAGT 59.797 43.478 0.00 0.00 32.06 3.85
1658 1691 2.885135 ATGTTGATGCCAAGGAGTGA 57.115 45.000 0.00 0.00 32.06 3.41
1673 1706 6.201517 CAAGGAGTGACACTTGTTTTATGTG 58.798 40.000 10.01 0.00 39.30 3.21
1679 1712 6.321181 AGTGACACTTGTTTTATGTGTGGAAT 59.679 34.615 1.07 0.00 44.78 3.01
1680 1713 6.417635 GTGACACTTGTTTTATGTGTGGAATG 59.582 38.462 2.63 0.00 44.78 2.67
1705 1738 9.777297 TGCATGCTCTAACTATACAATCAATTA 57.223 29.630 20.33 0.00 0.00 1.40
1796 1829 9.030301 GTTACAAAATGCTACACTTGTTGAAAT 57.970 29.630 3.15 0.00 34.08 2.17
1805 1838 7.870445 TGCTACACTTGTTGAAATTAATTTCCC 59.130 33.333 29.31 22.05 44.16 3.97
1837 1870 3.184541 GGTGCTTCATTTGCATCATGTC 58.815 45.455 6.35 0.21 42.69 3.06
1885 1918 5.661458 GGAAAATGTCTACTACTGCAGCTA 58.339 41.667 15.27 4.75 0.00 3.32
2055 2088 2.967397 CTCACACGTTCGGGGCTA 59.033 61.111 0.00 0.00 0.00 3.93
2100 2133 1.304381 GGGCTTGCCTCCAATGTCA 60.304 57.895 11.71 0.00 0.00 3.58
2286 2319 3.181490 CGTTGGTGCTAGTGCTACAGATA 60.181 47.826 0.00 0.00 40.48 1.98
2293 2326 3.670991 GCTAGTGCTACAGATATTCACGC 59.329 47.826 0.00 0.00 36.03 5.34
2295 2328 2.135933 GTGCTACAGATATTCACGCCC 58.864 52.381 0.00 0.00 0.00 6.13
2306 2339 3.737172 CACGCCCCTTTTGCCTCG 61.737 66.667 0.00 0.00 0.00 4.63
2337 2370 3.782656 AATCCCCTTGTCAGTTTACGT 57.217 42.857 0.00 0.00 0.00 3.57
2474 2508 1.852157 ATTGTCATCACTGGCCCCGT 61.852 55.000 0.00 0.00 0.00 5.28
2513 2547 9.731819 GTGAGATCACGTTCTAACTTGATAATA 57.268 33.333 13.02 2.78 44.70 0.98
2610 2652 8.483758 TGTTCCAGTTACTCTTTTAGAGAACTT 58.516 33.333 10.50 0.00 45.07 2.66
2631 2673 9.556030 GAACTTTGATATGGTTTTGCTAGTTAC 57.444 33.333 0.00 0.00 0.00 2.50
2677 2747 9.859427 CATTTTGTAGGAAGAAAGCATTATTGA 57.141 29.630 0.00 0.00 0.00 2.57
2734 2818 4.127171 CTCTTTTCTCCTTCCACGTTTCA 58.873 43.478 0.00 0.00 0.00 2.69
2885 2969 4.503741 TGCTGTTCCTTTTGCATACTTC 57.496 40.909 0.00 0.00 0.00 3.01
3000 3084 4.104102 TGGTGAAAAGTGGTCTTGAGGTAT 59.896 41.667 0.00 0.00 33.79 2.73
3009 3093 8.788325 AAGTGGTCTTGAGGTATTAATACAAC 57.212 34.615 23.59 17.09 32.27 3.32
3054 3138 2.054799 TGGCTTAGAGGTTCACCACTT 58.945 47.619 0.91 0.00 38.01 3.16
3101 3185 4.095483 GCATCTGAGTATGTTGAACCAAGG 59.905 45.833 0.00 0.00 0.00 3.61
3364 3448 9.323985 CTCTCATAAAAACTATGCTTAGCTTCT 57.676 33.333 5.60 0.00 0.00 2.85
3701 3790 9.582431 TTTTATATTAATCGATAGCTCCTTCGG 57.418 33.333 0.00 0.00 36.08 4.30
3766 3856 2.638480 TTCTTGGGACCAGTTCACTG 57.362 50.000 0.00 0.00 43.40 3.66
3831 3921 4.681744 ACTTGTTGCAGGTTAACATGTTG 58.318 39.130 21.42 5.70 41.01 3.33
3995 4089 6.109156 TGCTCTTCAGGTATAGTTCACAAA 57.891 37.500 0.00 0.00 0.00 2.83
4068 4162 5.164620 TCCATGCAGTTCTGACTCATAAA 57.835 39.130 3.84 0.00 32.54 1.40
4104 5819 4.533919 ATGACCTCTGTATAGCTGATGC 57.466 45.455 0.00 0.00 40.05 3.91
4116 5831 7.967178 TGTATAGCTGATGCATGATTTTATCG 58.033 34.615 2.46 0.00 42.74 2.92
4386 6133 2.095869 GTCACTTGCATCTGCTGTGAAG 60.096 50.000 22.73 12.95 46.88 3.02
4398 6145 3.930336 TGCTGTGAAGTCAACCTGATAG 58.070 45.455 0.00 0.00 0.00 2.08
4400 6147 2.926200 CTGTGAAGTCAACCTGATAGCG 59.074 50.000 0.00 0.00 0.00 4.26
4402 6149 1.275010 TGAAGTCAACCTGATAGCGCA 59.725 47.619 11.47 0.00 0.00 6.09
4407 6154 1.065491 TCAACCTGATAGCGCACCATT 60.065 47.619 11.47 0.00 0.00 3.16
4415 6162 4.450976 TGATAGCGCACCATTAATCAGTT 58.549 39.130 11.47 0.00 0.00 3.16
4428 6175 9.860650 ACCATTAATCAGTTACAATGGCTATTA 57.139 29.630 11.18 0.00 0.00 0.98
4465 6212 2.210144 TAACATGCACTGGCCCCCTC 62.210 60.000 0.00 0.00 40.13 4.30
4476 6223 1.241990 GGCCCCCTCGTTTCTTTGAC 61.242 60.000 0.00 0.00 0.00 3.18
4492 6239 9.516314 GTTTCTTTGACTGCTAAAGTATTTGTT 57.484 29.630 0.00 0.00 40.07 2.83
4529 6276 2.603075 TGGGTAAAGGCTGCTTCATT 57.397 45.000 0.00 0.00 0.00 2.57
4548 6298 2.715737 TGTTTTCTGGCGCCAAATAC 57.284 45.000 32.09 26.81 0.00 1.89
4578 6328 6.794534 ACCCTTCTGAAAGTTCCTTTGATAT 58.205 36.000 0.00 0.00 33.49 1.63
4581 6331 8.844244 CCCTTCTGAAAGTTCCTTTGATATATG 58.156 37.037 0.00 0.00 33.49 1.78
4599 6738 8.752187 TGATATATGAGTAGTATTGCATGCAGA 58.248 33.333 21.50 12.42 0.00 4.26
4609 6748 4.585955 ATTGCATGCAGAATCTCATTCC 57.414 40.909 21.50 0.00 40.13 3.01
4621 6760 2.035626 CATTCCGGGGGTGCTGTT 59.964 61.111 0.00 0.00 0.00 3.16
4658 6797 6.125327 TCTGATAGATCTTGTCTGTCGAAC 57.875 41.667 0.00 0.00 45.24 3.95
4659 6798 5.883115 TCTGATAGATCTTGTCTGTCGAACT 59.117 40.000 0.00 0.00 45.24 3.01
4661 6800 7.553044 TCTGATAGATCTTGTCTGTCGAACTTA 59.447 37.037 0.00 0.00 45.24 2.24
4662 6801 7.473366 TGATAGATCTTGTCTGTCGAACTTAC 58.527 38.462 0.00 0.00 45.24 2.34
4663 6802 5.968528 AGATCTTGTCTGTCGAACTTACT 57.031 39.130 0.00 0.00 35.31 2.24
4664 6803 5.945155 AGATCTTGTCTGTCGAACTTACTC 58.055 41.667 0.00 0.00 35.31 2.59
4675 6815 5.163824 TGTCGAACTTACTCTGTATGTACCG 60.164 44.000 0.00 0.00 0.00 4.02
4694 6834 0.601046 GAAAGGCTGCCAAGGTTTGC 60.601 55.000 22.65 0.01 0.00 3.68
4735 6884 7.602644 TGTATAAGTAACTTCCAAGAACTGCTG 59.397 37.037 0.00 0.00 0.00 4.41
4738 6887 4.999950 AGTAACTTCCAAGAACTGCTGATG 59.000 41.667 0.00 0.00 0.00 3.07
4740 6889 1.471684 CTTCCAAGAACTGCTGATGGC 59.528 52.381 0.00 0.00 42.22 4.40
4745 6894 3.984193 GAACTGCTGATGGCCCGCT 62.984 63.158 0.00 0.00 40.92 5.52
4749 6898 2.030262 GCTGATGGCCCGCTCTAG 59.970 66.667 0.00 0.00 34.27 2.43
4754 6903 2.037772 CTGATGGCCCGCTCTAGTTATT 59.962 50.000 0.00 0.00 0.00 1.40
4790 6939 8.178964 GCTTGTTATGTTTTGATCAACGGTATA 58.821 33.333 7.89 2.63 0.00 1.47
4801 6950 3.956233 TCAACGGTATAGCATGTACGTC 58.044 45.455 0.00 0.00 0.00 4.34
4807 6956 5.471116 ACGGTATAGCATGTACGTCTTCATA 59.529 40.000 0.00 0.00 0.00 2.15
4820 6969 3.123621 CGTCTTCATACACCTGAAAGTGC 59.876 47.826 0.00 0.00 41.67 4.40
4838 6987 1.878070 CACATTCTGCATGCGTGGT 59.122 52.632 14.09 3.85 36.14 4.16
4839 6988 1.085893 CACATTCTGCATGCGTGGTA 58.914 50.000 14.09 0.09 36.14 3.25
4864 7013 5.494390 ACCCCATCGTTTTACTTAGAAGT 57.506 39.130 0.00 0.00 42.91 3.01
4889 7045 7.851822 AGTAACAGTTTTATGTTGCGATTTG 57.148 32.000 2.48 0.00 46.50 2.32
4891 7047 6.509317 AACAGTTTTATGTTGCGATTTGTG 57.491 33.333 0.00 0.00 41.76 3.33
4892 7048 4.981674 ACAGTTTTATGTTGCGATTTGTGG 59.018 37.500 0.00 0.00 0.00 4.17
4921 7333 3.643792 AGGTGCTACTGAGATGGGAATAC 59.356 47.826 0.00 0.00 0.00 1.89
4928 7340 5.983333 ACTGAGATGGGAATACAAGGAAT 57.017 39.130 0.00 0.00 0.00 3.01
4938 7350 8.073467 TGGGAATACAAGGAATTTTGGATAAC 57.927 34.615 0.00 0.00 30.31 1.89
4961 7373 7.961326 ACCTGTTCCTGATTATAGCAAAATT 57.039 32.000 0.00 0.00 0.00 1.82
4986 7398 3.902881 TGTGTTCCAAACATGCCTTTT 57.097 38.095 0.00 0.00 44.35 2.27
5016 7428 1.069090 TGTTGTCGGACAGGTCTGC 59.931 57.895 11.14 0.47 35.96 4.26
5097 7510 8.657387 TTCATAAACAATGGGAGTGGATTTAA 57.343 30.769 0.00 0.00 36.15 1.52
5100 7513 3.981212 ACAATGGGAGTGGATTTAAGGG 58.019 45.455 0.00 0.00 0.00 3.95
5167 7587 5.667539 TCTCTAAAGTCTGAACCCATCTG 57.332 43.478 0.00 0.00 0.00 2.90
5299 7719 3.964875 GCCAATATGCCACCGCCG 61.965 66.667 0.00 0.00 0.00 6.46
5328 7748 1.403647 GCTGCACACGTACACTATCCA 60.404 52.381 0.00 0.00 0.00 3.41
5331 7751 2.758423 TGCACACGTACACTATCCATCT 59.242 45.455 0.00 0.00 0.00 2.90
5332 7752 3.949113 TGCACACGTACACTATCCATCTA 59.051 43.478 0.00 0.00 0.00 1.98
5333 7753 4.036380 TGCACACGTACACTATCCATCTAG 59.964 45.833 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 0.878523 TTCTTGGTCGTGCGTCCTTG 60.879 55.000 9.02 2.94 0.00 3.61
170 172 2.635915 TGAAACTCTGACGGGGTATGTT 59.364 45.455 0.00 0.00 0.00 2.71
280 282 1.618447 AACACCCCCTAATCCGGCT 60.618 57.895 0.00 0.00 0.00 5.52
427 433 0.396435 AGTCGGATTCCAGTTGCACA 59.604 50.000 3.09 0.00 0.00 4.57
550 556 9.151471 GCGGCTCTTATTACATGAGAAATATTA 57.849 33.333 0.00 0.00 31.50 0.98
617 623 2.878406 GCCAGCTTTCAGTCACAGTAAA 59.122 45.455 0.00 0.00 0.00 2.01
659 665 2.752358 CAGGAGGCTGCTGACCAA 59.248 61.111 29.69 0.00 38.14 3.67
696 706 8.023706 GGGAACTTCAAAGAGCTTTATTAAGTG 58.976 37.037 13.56 0.00 33.46 3.16
770 780 9.003112 CATTGTACACATTCGATCATCTTTTTC 57.997 33.333 0.00 0.00 0.00 2.29
772 782 8.267620 TCATTGTACACATTCGATCATCTTTT 57.732 30.769 0.00 0.00 0.00 2.27
776 786 5.333645 GGCTCATTGTACACATTCGATCATC 60.334 44.000 0.00 0.00 0.00 2.92
890 901 4.994201 GCGCTGGTCACGTCGTGA 62.994 66.667 23.70 23.70 40.50 4.35
1053 1064 1.300233 GATCGTCATCAGGGCGGAC 60.300 63.158 0.00 0.00 0.00 4.79
1114 1125 0.822532 GAGCCGGATCGAACCCTAGA 60.823 60.000 5.05 0.00 0.00 2.43
1164 1175 3.407967 GATTGCGGGGGTGGAGGA 61.408 66.667 0.00 0.00 0.00 3.71
1300 1312 3.058016 CGCCTCGAAAATGATGGCATAAT 60.058 43.478 0.00 0.00 43.38 1.28
1304 1316 1.992233 GCGCCTCGAAAATGATGGCA 61.992 55.000 9.87 0.00 43.38 4.92
1317 1329 2.249557 TTCTACGACTCACGCGCCTC 62.250 60.000 5.73 0.00 46.94 4.70
1334 1346 8.515473 CGACATTCGAATCATGTAAAATTGTTC 58.485 33.333 7.92 0.00 43.74 3.18
1336 1348 7.747888 TCGACATTCGAATCATGTAAAATTGT 58.252 30.769 7.92 0.00 46.90 2.71
1363 1375 0.179111 GTCATCGACGGCTCATTCCA 60.179 55.000 0.00 0.00 0.00 3.53
1364 1376 0.876342 GGTCATCGACGGCTCATTCC 60.876 60.000 0.00 0.00 32.65 3.01
1365 1377 0.179111 TGGTCATCGACGGCTCATTC 60.179 55.000 0.00 0.00 32.65 2.67
1366 1378 0.465705 ATGGTCATCGACGGCTCATT 59.534 50.000 0.00 0.00 32.65 2.57
1367 1379 0.465705 AATGGTCATCGACGGCTCAT 59.534 50.000 0.00 0.00 32.65 2.90
1369 1381 1.062587 CAAAATGGTCATCGACGGCTC 59.937 52.381 0.00 0.00 32.65 4.70
1370 1382 1.086696 CAAAATGGTCATCGACGGCT 58.913 50.000 0.00 0.00 32.65 5.52
1372 1384 2.073056 TCACAAAATGGTCATCGACGG 58.927 47.619 0.00 0.00 32.65 4.79
1373 1385 2.094258 CCTCACAAAATGGTCATCGACG 59.906 50.000 0.00 0.00 32.65 5.12
1374 1386 3.334691 TCCTCACAAAATGGTCATCGAC 58.665 45.455 0.00 0.00 0.00 4.20
1375 1387 3.260632 TCTCCTCACAAAATGGTCATCGA 59.739 43.478 0.00 0.00 0.00 3.59
1376 1388 3.372206 GTCTCCTCACAAAATGGTCATCG 59.628 47.826 0.00 0.00 0.00 3.84
1377 1389 4.326826 TGTCTCCTCACAAAATGGTCATC 58.673 43.478 0.00 0.00 0.00 2.92
1378 1390 4.371624 TGTCTCCTCACAAAATGGTCAT 57.628 40.909 0.00 0.00 0.00 3.06
1397 1409 6.321435 TCTCACATAGAATCCGACACTAATGT 59.679 38.462 0.00 0.00 43.71 2.71
1399 1411 6.321435 TGTCTCACATAGAATCCGACACTAAT 59.679 38.462 0.00 0.00 35.47 1.73
1400 1412 5.650703 TGTCTCACATAGAATCCGACACTAA 59.349 40.000 0.00 0.00 35.47 2.24
1402 1414 4.017126 TGTCTCACATAGAATCCGACACT 58.983 43.478 0.00 0.00 35.47 3.55
1403 1415 4.371855 TGTCTCACATAGAATCCGACAC 57.628 45.455 0.00 0.00 35.47 3.67
1411 1435 8.134202 TCTAAACCAGAATGTCTCACATAGAA 57.866 34.615 0.00 0.00 37.97 2.10
1445 1469 7.148656 GCATTTTCCACTGCAACGTAATAAAAT 60.149 33.333 0.00 0.00 38.28 1.82
1448 1472 5.048364 AGCATTTTCCACTGCAACGTAATAA 60.048 36.000 0.00 0.00 40.88 1.40
1449 1473 4.457603 AGCATTTTCCACTGCAACGTAATA 59.542 37.500 0.00 0.00 40.88 0.98
1459 1483 5.067413 AGCAATCAGATAGCATTTTCCACTG 59.933 40.000 0.00 0.00 0.00 3.66
1469 1493 8.615211 CAAGTTTATTACAGCAATCAGATAGCA 58.385 33.333 0.00 0.00 0.00 3.49
1519 1550 2.052782 ATTTAAGGATGACCACGGCC 57.947 50.000 0.00 0.00 38.94 6.13
1547 1578 6.343716 AGTAGCATGTGATATTCCTCTGAG 57.656 41.667 0.00 0.00 0.00 3.35
1656 1689 6.502652 CATTCCACACATAAAACAAGTGTCA 58.497 36.000 0.00 0.00 44.02 3.58
1658 1691 5.163468 TGCATTCCACACATAAAACAAGTGT 60.163 36.000 0.00 0.00 46.54 3.55
1673 1706 5.991606 TGTATAGTTAGAGCATGCATTCCAC 59.008 40.000 21.98 9.54 0.00 4.02
1679 1712 8.681486 AATTGATTGTATAGTTAGAGCATGCA 57.319 30.769 21.98 0.00 0.00 3.96
1718 1751 6.159988 GTGATGAGCTACATAGTGTATTCCC 58.840 44.000 0.00 0.00 39.56 3.97
1796 1829 7.740805 AGCACCAGTAAATTTTGGGAAATTAA 58.259 30.769 12.48 0.00 42.97 1.40
1805 1838 6.018098 TGCAAATGAAGCACCAGTAAATTTTG 60.018 34.615 0.00 0.00 37.02 2.44
1837 1870 2.496871 TGCATTGGCCCATAAAACTCTG 59.503 45.455 0.00 0.00 40.13 3.35
1885 1918 5.863397 CGTTTGCCATATTTGAATTCAGTGT 59.137 36.000 8.41 1.75 0.00 3.55
2055 2088 4.248859 CGAACTTCCAGTCAGTCATTGAT 58.751 43.478 0.00 0.00 38.29 2.57
2100 2133 3.176924 TCCAGTAGCCACTCTTCTTCT 57.823 47.619 0.00 0.00 30.46 2.85
2260 2293 0.389948 AGCACTAGCACCAACGCTAC 60.390 55.000 0.00 0.00 45.49 3.58
2286 2319 1.228862 AGGCAAAAGGGGCGTGAAT 60.229 52.632 0.00 0.00 38.57 2.57
2293 2326 0.034089 AAGGATCGAGGCAAAAGGGG 60.034 55.000 0.00 0.00 0.00 4.79
2295 2328 3.343617 TGTTAAGGATCGAGGCAAAAGG 58.656 45.455 0.00 0.00 0.00 3.11
2306 2339 5.261216 TGACAAGGGGATTTGTTAAGGATC 58.739 41.667 0.00 0.00 41.15 3.36
2337 2370 6.759272 AGCTGTAAACACTTGTTCTCAGATA 58.241 36.000 20.71 0.00 39.07 1.98
2440 2474 9.685276 AGTGATGACAATTAATCAATCCTTACA 57.315 29.630 0.00 0.00 34.70 2.41
2474 2508 4.507710 GTGATCTCACAGGCATGTTCTAA 58.492 43.478 0.00 0.00 45.75 2.10
2513 2547 7.880195 CCTTCATATAGGCTGCTAGTGTTAAAT 59.120 37.037 0.00 0.00 0.00 1.40
2610 2652 6.092944 CCACGTAACTAGCAAAACCATATCAA 59.907 38.462 0.00 0.00 0.00 2.57
2646 2688 5.221224 TGCTTTCTTCCTACAAAATGTGTGG 60.221 40.000 0.00 0.00 41.89 4.17
2734 2818 2.414994 ATGCTGCTGTCACATTAGCT 57.585 45.000 12.95 0.00 40.52 3.32
2885 2969 3.498082 GGTAACATAGCCTTTTGCAACG 58.502 45.455 0.00 0.00 44.83 4.10
3009 3093 3.660865 ACTTACTAGTTCAACAAGGGCG 58.339 45.455 0.00 0.00 0.00 6.13
3068 3152 4.904251 ACATACTCAGATGCTGGTTCCTAT 59.096 41.667 0.00 0.00 31.51 2.57
3364 3448 2.889170 TTAGGCATACAGGGCAAACA 57.111 45.000 0.00 0.00 35.46 2.83
3766 3856 4.941263 TGGTGGTTATGTGCTACAAGAATC 59.059 41.667 0.00 0.00 0.00 2.52
3995 4089 8.992073 GTCAACAAAAGAGCCAAATAAATCAAT 58.008 29.630 0.00 0.00 0.00 2.57
4003 4097 5.524646 CACAATGTCAACAAAAGAGCCAAAT 59.475 36.000 0.00 0.00 0.00 2.32
4075 4169 8.540388 TCAGCTATACAGAGGTCATTAAGTTTT 58.460 33.333 0.00 0.00 0.00 2.43
4079 4173 6.589523 GCATCAGCTATACAGAGGTCATTAAG 59.410 42.308 0.00 0.00 37.91 1.85
4080 4174 6.041979 TGCATCAGCTATACAGAGGTCATTAA 59.958 38.462 0.00 0.00 42.74 1.40
4082 4176 4.346127 TGCATCAGCTATACAGAGGTCATT 59.654 41.667 0.00 0.00 42.74 2.57
4116 5831 4.506758 AGGTTTGGCATATTGTTTGATGC 58.493 39.130 0.00 0.00 46.31 3.91
4386 6133 0.391130 TGGTGCGCTATCAGGTTGAC 60.391 55.000 9.73 0.00 0.00 3.18
4398 6145 4.349663 TTGTAACTGATTAATGGTGCGC 57.650 40.909 0.00 0.00 0.00 6.09
4465 6212 7.855904 ACAAATACTTTAGCAGTCAAAGAAACG 59.144 33.333 2.07 0.00 36.88 3.60
4516 6263 3.243975 CCAGAAAACAATGAAGCAGCCTT 60.244 43.478 0.00 0.00 0.00 4.35
4529 6276 2.235016 AGTATTTGGCGCCAGAAAACA 58.765 42.857 30.75 11.29 0.00 2.83
4548 6298 5.377478 AGGAACTTTCAGAAGGGTTTGTAG 58.623 41.667 0.00 0.00 37.19 2.74
4578 6328 7.674120 AGATTCTGCATGCAATACTACTCATA 58.326 34.615 22.88 0.00 0.00 2.15
4581 6331 5.987953 TGAGATTCTGCATGCAATACTACTC 59.012 40.000 22.88 21.86 0.00 2.59
4583 6333 6.798315 ATGAGATTCTGCATGCAATACTAC 57.202 37.500 22.88 12.36 0.00 2.73
4584 6334 6.429078 GGAATGAGATTCTGCATGCAATACTA 59.571 38.462 22.88 5.62 39.24 1.82
4586 6336 5.458891 GGAATGAGATTCTGCATGCAATAC 58.541 41.667 22.88 12.96 39.24 1.89
4588 6338 3.004419 CGGAATGAGATTCTGCATGCAAT 59.996 43.478 22.88 13.51 38.67 3.56
4599 6738 1.227383 GCACCCCCGGAATGAGATT 59.773 57.895 0.73 0.00 0.00 2.40
4609 6748 1.106944 ACTTTTGAACAGCACCCCCG 61.107 55.000 0.00 0.00 0.00 5.73
4621 6760 5.213891 TCTATCAGAGCACACACTTTTGA 57.786 39.130 0.00 0.00 0.00 2.69
4658 6797 5.041940 GCCTTTCGGTACATACAGAGTAAG 58.958 45.833 0.00 0.00 32.30 2.34
4659 6798 4.708421 AGCCTTTCGGTACATACAGAGTAA 59.292 41.667 0.00 0.00 32.30 2.24
4661 6800 3.097614 AGCCTTTCGGTACATACAGAGT 58.902 45.455 0.00 0.00 32.30 3.24
4662 6801 3.448686 CAGCCTTTCGGTACATACAGAG 58.551 50.000 0.00 0.00 32.30 3.35
4663 6802 2.418197 GCAGCCTTTCGGTACATACAGA 60.418 50.000 0.00 0.00 0.00 3.41
4664 6803 1.933853 GCAGCCTTTCGGTACATACAG 59.066 52.381 0.00 0.00 0.00 2.74
4675 6815 0.601046 GCAAACCTTGGCAGCCTTTC 60.601 55.000 14.15 0.00 0.00 2.62
4716 6865 4.154918 CCATCAGCAGTTCTTGGAAGTTAC 59.845 45.833 0.00 0.00 0.00 2.50
4720 6869 1.471684 GCCATCAGCAGTTCTTGGAAG 59.528 52.381 0.00 0.00 42.97 3.46
4722 6871 0.322816 GGCCATCAGCAGTTCTTGGA 60.323 55.000 0.00 0.00 46.50 3.53
4730 6879 2.712325 CTAGAGCGGGCCATCAGCAG 62.712 65.000 4.39 0.00 46.50 4.24
4735 6884 2.300437 AGAATAACTAGAGCGGGCCATC 59.700 50.000 4.39 0.00 0.00 3.51
4738 6887 1.687123 TGAGAATAACTAGAGCGGGCC 59.313 52.381 0.00 0.00 0.00 5.80
4740 6889 4.038042 TCACATGAGAATAACTAGAGCGGG 59.962 45.833 0.00 0.00 0.00 6.13
4745 6894 7.175347 ACAAGCTCACATGAGAATAACTAGA 57.825 36.000 13.15 0.00 44.74 2.43
4749 6898 7.978982 ACATAACAAGCTCACATGAGAATAAC 58.021 34.615 13.15 0.00 44.74 1.89
4754 6903 6.486320 TCAAAACATAACAAGCTCACATGAGA 59.514 34.615 13.15 0.00 44.74 3.27
4790 6939 3.447586 AGGTGTATGAAGACGTACATGCT 59.552 43.478 14.74 0.00 45.98 3.79
4801 6950 3.814842 TGTGCACTTTCAGGTGTATGAAG 59.185 43.478 19.41 0.00 40.16 3.02
4807 6956 2.620115 CAGAATGTGCACTTTCAGGTGT 59.380 45.455 34.00 18.55 39.21 4.16
4838 6987 7.397192 ACTTCTAAGTAAAACGATGGGGTACTA 59.603 37.037 0.00 0.00 37.52 1.82
4839 6988 6.212187 ACTTCTAAGTAAAACGATGGGGTACT 59.788 38.462 0.00 0.00 37.52 2.73
4864 7013 8.561212 ACAAATCGCAACATAAAACTGTTACTA 58.439 29.630 0.00 0.00 37.25 1.82
4889 7045 2.017049 CAGTAGCACCTTAATGGCCAC 58.983 52.381 8.16 0.00 40.22 5.01
4891 7047 2.170607 TCTCAGTAGCACCTTAATGGCC 59.829 50.000 0.00 0.00 40.22 5.36
4892 7048 3.543680 TCTCAGTAGCACCTTAATGGC 57.456 47.619 0.00 0.00 40.22 4.40
4921 7333 6.211384 AGGAACAGGTTATCCAAAATTCCTTG 59.789 38.462 9.49 0.00 38.49 3.61
4928 7340 9.627123 CTATAATCAGGAACAGGTTATCCAAAA 57.373 33.333 0.00 0.00 38.23 2.44
4938 7350 7.428826 GGAATTTTGCTATAATCAGGAACAGG 58.571 38.462 0.00 0.00 0.00 4.00
4961 7373 1.686052 GCATGTTTGGAACACAAGGGA 59.314 47.619 0.00 0.00 45.50 4.20
4986 7398 4.936411 TGTCCGACAACACTTTTAACTTCA 59.064 37.500 0.00 0.00 0.00 3.02
5016 7428 3.108144 CAACCTTTGTTGCTTGACTTCG 58.892 45.455 0.00 0.00 44.86 3.79
5041 7453 2.436417 ACATTTCCATTGTCCTCACGG 58.564 47.619 0.00 0.00 0.00 4.94
5097 7510 0.476771 CCACAACCAACTACCACCCT 59.523 55.000 0.00 0.00 0.00 4.34
5100 7513 1.394618 TTGCCACAACCAACTACCAC 58.605 50.000 0.00 0.00 0.00 4.16
5136 7550 4.763073 TCAGACTTTAGAGATCCGACGTA 58.237 43.478 0.00 0.00 0.00 3.57
5167 7587 0.106521 GCTCTCTGCTTCCATCTCCC 59.893 60.000 0.00 0.00 38.95 4.30
5270 7690 0.037303 ATATTGGCATCGCAGGGGAG 59.963 55.000 0.00 0.00 0.00 4.30
5299 7719 2.434359 GTGTGCAGCCCCTACGAC 60.434 66.667 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.