Multiple sequence alignment - TraesCS3B01G126800

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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 TraesCS3B01G126800 chr3B 100.000 3026 0 0 1 3026 103723709 103720684 0.000000e+00 5589.0
1 TraesCS3B01G126800 chr3B 89.326 178 18 1 2844 3020 103239674 103239497 3.930000e-54 222.0
2 TraesCS3B01G126800 chr3B 85.714 119 17 0 1245 1363 519777996 519777878 3.170000e-25 126.0
3 TraesCS3B01G126800 chr3B 83.217 143 16 8 1000 1138 478323394 478323256 1.140000e-24 124.0
4 TraesCS3B01G126800 chr3A 86.969 1742 120 54 806 2496 72898122 72896437 0.000000e+00 1860.0
5 TraesCS3B01G126800 chr3A 86.854 852 37 27 1 814 72899110 72898296 0.000000e+00 883.0
6 TraesCS3B01G126800 chr3A 87.524 529 39 15 2520 3026 72896441 72895918 1.210000e-163 586.0
7 TraesCS3B01G126800 chr3A 86.957 115 15 0 1245 1359 514612170 514612056 2.450000e-26 130.0
8 TraesCS3B01G126800 chr3A 85.542 83 10 2 1477 1558 514611935 514611854 5.380000e-13 86.1
9 TraesCS3B01G126800 chr3D 92.148 866 32 14 1246 2084 63460739 63459883 0.000000e+00 1190.0
10 TraesCS3B01G126800 chr3D 85.227 880 62 27 2166 3026 63459861 63459031 0.000000e+00 843.0
11 TraesCS3B01G126800 chr3D 89.213 686 24 12 508 1175 63461425 63460772 0.000000e+00 811.0
12 TraesCS3B01G126800 chr3D 84.440 482 28 9 35 505 63461936 63461491 5.990000e-117 431.0
13 TraesCS3B01G126800 chr3D 93.868 212 11 1 966 1175 63467845 63467634 4.870000e-83 318.0
14 TraesCS3B01G126800 chr3D 86.555 119 16 0 1245 1363 395065177 395065059 6.810000e-27 132.0
15 TraesCS3B01G126800 chr5B 76.702 382 59 26 1001 1376 391144731 391145088 5.150000e-43 185.0
16 TraesCS3B01G126800 chr5A 75.192 391 67 27 1001 1376 436089151 436089526 1.120000e-34 158.0
17 TraesCS3B01G126800 chr5A 85.542 83 10 2 1477 1558 451389468 451389549 5.380000e-13 86.1
18 TraesCS3B01G126800 chr5D 93.878 98 6 0 1242 1339 334255461 334255558 6.760000e-32 148.0
19 TraesCS3B01G126800 chr5D 85.542 83 10 2 1477 1558 350953950 350954031 5.380000e-13 86.1
20 TraesCS3B01G126800 chr6B 94.366 71 4 0 997 1067 652631348 652631278 3.190000e-20 110.0
21 TraesCS3B01G126800 chr6B 80.508 118 16 6 999 1114 477689272 477689384 1.930000e-12 84.2
22 TraesCS3B01G126800 chr6A 94.366 71 4 0 997 1067 578887723 578887653 3.190000e-20 110.0
23 TraesCS3B01G126800 chr6A 80.508 118 16 6 999 1114 446520785 446520897 1.930000e-12 84.2
24 TraesCS3B01G126800 chr2D 90.361 83 8 0 1476 1558 424015076 424014994 3.190000e-20 110.0
25 TraesCS3B01G126800 chr2B 90.361 83 8 0 1476 1558 498310556 498310474 3.190000e-20 110.0
26 TraesCS3B01G126800 chr2A 90.361 83 8 0 1476 1558 564218838 564218920 3.190000e-20 110.0
27 TraesCS3B01G126800 chr1D 83.810 105 17 0 1245 1349 344606291 344606395 1.920000e-17 100.0
28 TraesCS3B01G126800 chrUn 82.353 102 15 2 1459 1558 232286108 232286008 5.380000e-13 86.1
29 TraesCS3B01G126800 chr6D 80.508 118 16 6 999 1114 309718608 309718720 1.930000e-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 TraesCS3B01G126800 chr3B 103720684 103723709 3025 True 5589.000000 5589 100.000000 1 3026 1 chr3B.!!$R2 3025
1 TraesCS3B01G126800 chr3A 72895918 72899110 3192 True 1109.666667 1860 87.115667 1 3026 3 chr3A.!!$R1 3025
2 TraesCS3B01G126800 chr3D 63459031 63461936 2905 True 818.750000 1190 87.757000 35 3026 4 chr3D.!!$R3 2991

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
360 371 0.107312 ACAGAGCTGCATGGTGGATC 60.107 55.0 1.02 0.0 0.0 3.36 F
366 377 0.107508 CTGCATGGTGGATCTTCGGT 60.108 55.0 0.00 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1736 0.240945 CACGAAAAGGATGCCGCTTT 59.759 50.0 0.0 0.0 0.00 3.51 R
2205 2557 0.324923 ACATGGGCATGGAAGCATGT 60.325 50.0 0.0 0.0 42.91 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
24 25 2.680339 GAGGAAAGCCCATCTTCTTTCG 59.320 50.000 8.15 0.00 45.44 3.46
56 57 0.468226 TCCACGACTGGCCCATATTC 59.532 55.000 0.00 0.00 37.49 1.75
78 79 1.073199 CCTTCGTGCCCTTTCCTGT 59.927 57.895 0.00 0.00 0.00 4.00
147 148 4.342665 TGCTACTTTTTCCGTTTTGGGATT 59.657 37.500 0.00 0.00 38.76 3.01
218 219 1.331756 GAGTGCGCCTTAATCATGGTG 59.668 52.381 4.18 0.00 36.95 4.17
219 220 1.065491 AGTGCGCCTTAATCATGGTGA 60.065 47.619 4.18 0.00 36.02 4.02
220 221 1.064060 GTGCGCCTTAATCATGGTGAC 59.936 52.381 4.18 0.00 36.02 3.67
263 264 4.338539 GAGGGCGACGTCGTGTGT 62.339 66.667 35.48 19.78 42.22 3.72
264 265 3.836176 GAGGGCGACGTCGTGTGTT 62.836 63.158 35.48 18.70 42.22 3.32
265 266 3.698463 GGGCGACGTCGTGTGTTG 61.698 66.667 35.48 9.81 42.22 3.33
266 267 3.698463 GGCGACGTCGTGTGTTGG 61.698 66.667 35.48 9.06 42.22 3.77
267 268 2.958016 GCGACGTCGTGTGTTGGT 60.958 61.111 35.48 0.00 42.22 3.67
268 269 2.917901 CGACGTCGTGTGTTGGTG 59.082 61.111 29.08 0.00 34.11 4.17
269 270 1.874915 CGACGTCGTGTGTTGGTGT 60.875 57.895 29.08 0.00 34.11 4.16
328 329 4.708177 CCAAGGAGATATCGGTGACAAAT 58.292 43.478 0.00 0.00 0.00 2.32
329 330 4.752101 CCAAGGAGATATCGGTGACAAATC 59.248 45.833 0.00 0.00 0.00 2.17
339 340 3.250762 TCGGTGACAAATCAAGCAAGAAG 59.749 43.478 0.00 0.00 36.31 2.85
360 371 0.107312 ACAGAGCTGCATGGTGGATC 60.107 55.000 1.02 0.00 0.00 3.36
366 377 0.107508 CTGCATGGTGGATCTTCGGT 60.108 55.000 0.00 0.00 0.00 4.69
525 608 6.863126 CACCACAAAATAGGCAGTAAAAAGAG 59.137 38.462 0.00 0.00 0.00 2.85
527 610 5.863935 CACAAAATAGGCAGTAAAAAGAGGC 59.136 40.000 0.00 0.00 0.00 4.70
553 638 3.904717 TGCCAGGAACAAAAAGGAAGTA 58.095 40.909 0.00 0.00 0.00 2.24
554 639 3.888930 TGCCAGGAACAAAAAGGAAGTAG 59.111 43.478 0.00 0.00 0.00 2.57
557 642 5.621193 CCAGGAACAAAAAGGAAGTAGAGA 58.379 41.667 0.00 0.00 0.00 3.10
563 653 8.775527 GGAACAAAAAGGAAGTAGAGAAGTAAG 58.224 37.037 0.00 0.00 0.00 2.34
597 687 3.896888 TGCCAGGAGAATCAACAATGTTT 59.103 39.130 0.00 0.00 36.25 2.83
632 722 2.738314 CAATGTTCTCTGCGTGTGATGA 59.262 45.455 0.00 0.00 0.00 2.92
637 733 0.799917 CTCTGCGTGTGATGAGACCG 60.800 60.000 0.00 0.00 0.00 4.79
659 755 2.989253 GGCCCGTGACCCAAAAGG 60.989 66.667 0.00 0.00 43.78 3.11
660 756 3.680786 GCCCGTGACCCAAAAGGC 61.681 66.667 0.00 0.00 40.58 4.35
668 764 1.343478 TGACCCAAAAGGCCAAAAGGA 60.343 47.619 5.01 0.00 40.58 3.36
717 813 2.158784 AGCAGCAGAGAATCAAGGATCC 60.159 50.000 2.48 2.48 37.82 3.36
779 880 0.681564 GCCCCTCTCTCTTCTCGACA 60.682 60.000 0.00 0.00 0.00 4.35
853 1136 1.891060 GCGGTGTTCTGCTCTGTTCG 61.891 60.000 0.00 0.00 42.20 3.95
859 1142 2.049156 CTGCTCTGTTCGCCGACA 60.049 61.111 0.00 0.00 0.00 4.35
1127 1423 2.750657 GCTGGATCACCCTCCCCAG 61.751 68.421 0.00 0.00 46.67 4.45
1142 1438 2.620112 CCAGCAAAGCCGGTGAGTG 61.620 63.158 1.90 0.00 36.48 3.51
1143 1439 1.893808 CAGCAAAGCCGGTGAGTGT 60.894 57.895 1.90 0.00 36.48 3.55
1154 1470 1.529244 GTGAGTGTGCTGCCCCTTT 60.529 57.895 0.00 0.00 0.00 3.11
1159 1475 1.153524 TGTGCTGCCCCTTTCATGT 59.846 52.632 0.00 0.00 0.00 3.21
1163 1479 1.002134 CTGCCCCTTTCATGTCCGT 60.002 57.895 0.00 0.00 0.00 4.69
1175 1491 3.723348 GTCCGTCCGTGCCTTTGC 61.723 66.667 0.00 0.00 38.26 3.68
1178 1494 2.978010 CGTCCGTGCCTTTGCCTT 60.978 61.111 0.00 0.00 36.33 4.35
1179 1495 2.551912 CGTCCGTGCCTTTGCCTTT 61.552 57.895 0.00 0.00 36.33 3.11
1180 1496 1.007387 GTCCGTGCCTTTGCCTTTG 60.007 57.895 0.00 0.00 36.33 2.77
1181 1497 2.356194 CCGTGCCTTTGCCTTTGC 60.356 61.111 0.00 0.00 36.33 3.68
1182 1498 2.730094 CGTGCCTTTGCCTTTGCT 59.270 55.556 0.00 0.00 38.71 3.91
1183 1499 1.372128 CGTGCCTTTGCCTTTGCTC 60.372 57.895 0.00 0.00 38.71 4.26
1184 1500 1.372128 GTGCCTTTGCCTTTGCTCG 60.372 57.895 0.00 0.00 38.71 5.03
1185 1501 1.528076 TGCCTTTGCCTTTGCTCGA 60.528 52.632 0.00 0.00 38.71 4.04
1186 1502 1.081175 GCCTTTGCCTTTGCTCGAC 60.081 57.895 0.00 0.00 38.71 4.20
1187 1503 1.207593 CCTTTGCCTTTGCTCGACG 59.792 57.895 0.00 0.00 38.71 5.12
1188 1504 1.441016 CTTTGCCTTTGCTCGACGC 60.441 57.895 0.00 0.58 38.71 5.19
1189 1505 3.235292 TTTGCCTTTGCTCGACGCG 62.235 57.895 3.53 3.53 43.27 6.01
1190 1506 4.961511 TGCCTTTGCTCGACGCGT 62.962 61.111 13.85 13.85 43.27 6.01
1191 1507 4.430423 GCCTTTGCTCGACGCGTG 62.430 66.667 20.70 9.70 43.27 5.34
1192 1508 3.777925 CCTTTGCTCGACGCGTGG 61.778 66.667 20.70 17.88 43.27 4.94
1193 1509 4.430423 CTTTGCTCGACGCGTGGC 62.430 66.667 20.70 18.71 43.27 5.01
1213 1529 4.253273 GCGCGCGTGTTCTCGATC 62.253 66.667 32.35 6.30 0.00 3.69
1215 1531 2.576053 GCGCGTGTTCTCGATCGA 60.576 61.111 18.32 18.32 0.00 3.59
1217 1533 1.857023 GCGCGTGTTCTCGATCGATC 61.857 60.000 19.78 15.68 0.00 3.69
1232 1548 5.990745 GATCGATCGATGATCTTTGTCTC 57.009 43.478 33.86 12.80 39.30 3.36
1233 1549 3.878245 TCGATCGATGATCTTTGTCTCG 58.122 45.455 15.15 0.00 36.96 4.04
1234 1550 2.976509 CGATCGATGATCTTTGTCTCGG 59.023 50.000 10.26 0.00 36.96 4.63
1235 1551 2.871182 TCGATGATCTTTGTCTCGGG 57.129 50.000 0.00 0.00 0.00 5.14
1236 1552 2.100197 TCGATGATCTTTGTCTCGGGT 58.900 47.619 0.00 0.00 0.00 5.28
1237 1553 2.159240 TCGATGATCTTTGTCTCGGGTG 60.159 50.000 0.00 0.00 0.00 4.61
1238 1554 2.555199 GATGATCTTTGTCTCGGGTGG 58.445 52.381 0.00 0.00 0.00 4.61
1239 1555 0.613260 TGATCTTTGTCTCGGGTGGG 59.387 55.000 0.00 0.00 0.00 4.61
1240 1556 0.613777 GATCTTTGTCTCGGGTGGGT 59.386 55.000 0.00 0.00 0.00 4.51
1241 1557 0.324943 ATCTTTGTCTCGGGTGGGTG 59.675 55.000 0.00 0.00 0.00 4.61
1244 1560 2.951475 TTTGTCTCGGGTGGGTGTGC 62.951 60.000 0.00 0.00 0.00 4.57
1397 1721 5.468409 GCAAGTAAGCACTCTTCTCTTTCTT 59.532 40.000 0.00 0.00 32.29 2.52
1412 1736 2.125552 CTTGATCACCAGGCGCGA 60.126 61.111 12.10 0.00 0.00 5.87
1459 1783 1.638467 GCATGACCGATCAAGACGC 59.362 57.895 0.00 0.00 38.69 5.19
1491 1830 1.391933 ATCGCAGGTGGTCGCTGATA 61.392 55.000 0.00 0.00 0.00 2.15
1598 1937 4.101448 CTTCTCCACCGCCCCCTG 62.101 72.222 0.00 0.00 0.00 4.45
1626 1965 2.892425 CCGTCCTTCATGCCGCTC 60.892 66.667 0.00 0.00 0.00 5.03
1908 2247 4.308458 TCCAACTGGTCGGCGGTG 62.308 66.667 7.21 0.00 36.34 4.94
2005 2344 2.421811 GGCTTCTACTACCCTCTCGACT 60.422 54.545 0.00 0.00 0.00 4.18
2011 2350 0.178533 CTACCCTCTCGACTCGACCT 59.821 60.000 0.00 0.00 0.00 3.85
2036 2375 5.177696 TGTCACTAGTGTAGATCGATCGATG 59.822 44.000 33.86 18.83 34.60 3.84
2037 2376 5.177881 GTCACTAGTGTAGATCGATCGATGT 59.822 44.000 33.86 30.68 34.60 3.06
2038 2377 5.177696 TCACTAGTGTAGATCGATCGATGTG 59.822 44.000 33.86 27.91 34.60 3.21
2041 2380 3.877508 AGTGTAGATCGATCGATGTGTGA 59.122 43.478 33.86 13.40 34.60 3.58
2042 2381 3.969352 GTGTAGATCGATCGATGTGTGAC 59.031 47.826 33.86 23.58 34.60 3.67
2043 2382 2.391322 AGATCGATCGATGTGTGACG 57.609 50.000 33.86 0.00 34.60 4.35
2045 2384 1.002792 GATCGATCGATGTGTGACGGA 60.003 52.381 33.86 0.75 34.60 4.69
2048 2395 1.472276 GATCGATGTGTGACGGACGC 61.472 60.000 0.54 0.00 35.45 5.19
2084 2431 3.173599 GACCGATCGATCAAACGTGTTA 58.826 45.455 24.40 0.00 34.70 2.41
2085 2432 3.777478 ACCGATCGATCAAACGTGTTAT 58.223 40.909 24.40 0.00 34.70 1.89
2086 2433 3.795101 ACCGATCGATCAAACGTGTTATC 59.205 43.478 24.40 0.00 34.70 1.75
2087 2434 3.181774 CCGATCGATCAAACGTGTTATCC 59.818 47.826 24.40 0.00 34.70 2.59
2088 2435 3.181774 CGATCGATCAAACGTGTTATCCC 59.818 47.826 24.40 0.00 34.70 3.85
2092 2443 3.682858 CGATCAAACGTGTTATCCCAAGT 59.317 43.478 0.00 0.00 0.00 3.16
2095 2446 5.217978 TCAAACGTGTTATCCCAAGTACT 57.782 39.130 0.00 0.00 0.00 2.73
2102 2453 5.521544 GTGTTATCCCAAGTACTCGATCTC 58.478 45.833 0.00 0.00 0.00 2.75
2109 2460 3.551863 CCAAGTACTCGATCTCCATGAGC 60.552 52.174 0.00 0.00 32.98 4.26
2128 2479 4.830912 GAGCAAATTCAGATACAAGCTCG 58.169 43.478 0.00 0.00 38.00 5.03
2138 2489 2.741486 TACAAGCTCGGGTTGCCACC 62.741 60.000 13.44 0.00 43.71 4.61
2156 2507 3.771577 ACCTGAAAAGGTGATCTTCGT 57.228 42.857 0.00 0.00 41.33 3.85
2158 2509 5.422214 ACCTGAAAAGGTGATCTTCGTAT 57.578 39.130 0.00 0.00 41.33 3.06
2160 2511 4.034510 CCTGAAAAGGTGATCTTCGTATGC 59.965 45.833 0.00 0.00 33.94 3.14
2169 2520 4.631813 GTGATCTTCGTATGCTTGGAAACT 59.368 41.667 0.00 0.00 0.00 2.66
2198 2550 5.375773 TGTGGTTCTTGAATCTTGATCACA 58.624 37.500 0.00 0.00 0.00 3.58
2205 2557 8.820933 GTTCTTGAATCTTGATCACATCGATTA 58.179 33.333 0.00 0.00 33.17 1.75
2218 2571 9.875729 GATCACATCGATTACATGCTTCCATGC 62.876 44.444 0.00 0.00 42.68 4.06
2227 2580 1.350071 TGCTTCCATGCCCATGTTTT 58.650 45.000 7.42 0.00 37.11 2.43
2228 2581 1.002201 TGCTTCCATGCCCATGTTTTG 59.998 47.619 7.42 0.00 37.11 2.44
2229 2582 1.002315 GCTTCCATGCCCATGTTTTGT 59.998 47.619 7.42 0.00 37.11 2.83
2230 2583 2.932187 GCTTCCATGCCCATGTTTTGTC 60.932 50.000 7.42 0.00 37.11 3.18
2231 2584 2.307496 TCCATGCCCATGTTTTGTCT 57.693 45.000 7.42 0.00 37.11 3.41
2232 2585 2.607499 TCCATGCCCATGTTTTGTCTT 58.393 42.857 7.42 0.00 37.11 3.01
2233 2586 2.562298 TCCATGCCCATGTTTTGTCTTC 59.438 45.455 7.42 0.00 37.11 2.87
2256 2609 6.054941 TCTCAAGTGTATGCAGTTCTTTGAA 58.945 36.000 0.28 0.00 36.20 2.69
2271 2624 6.313658 AGTTCTTTGAACAGAAATTTTGTGCC 59.686 34.615 12.16 0.39 34.50 5.01
2272 2625 4.803088 TCTTTGAACAGAAATTTTGTGCCG 59.197 37.500 6.21 0.00 0.00 5.69
2273 2626 2.468831 TGAACAGAAATTTTGTGCCGC 58.531 42.857 6.21 0.00 0.00 6.53
2276 2629 4.202060 TGAACAGAAATTTTGTGCCGCTAA 60.202 37.500 6.21 0.00 0.00 3.09
2277 2630 4.519540 ACAGAAATTTTGTGCCGCTAAT 57.480 36.364 6.21 0.00 0.00 1.73
2279 2632 3.859386 CAGAAATTTTGTGCCGCTAATCC 59.141 43.478 0.00 0.00 0.00 3.01
2280 2633 3.763897 AGAAATTTTGTGCCGCTAATCCT 59.236 39.130 0.00 0.00 0.00 3.24
2281 2634 3.508744 AATTTTGTGCCGCTAATCCTG 57.491 42.857 0.00 0.00 0.00 3.86
2282 2635 2.192664 TTTTGTGCCGCTAATCCTGA 57.807 45.000 0.00 0.00 0.00 3.86
2283 2636 2.418368 TTTGTGCCGCTAATCCTGAT 57.582 45.000 0.00 0.00 0.00 2.90
2287 2640 2.092968 TGTGCCGCTAATCCTGATCTTT 60.093 45.455 0.00 0.00 0.00 2.52
2304 2657 7.331440 CCTGATCTTTTCCTAGATGATCAATCG 59.669 40.741 0.00 0.00 41.62 3.34
2305 2658 6.648310 TGATCTTTTCCTAGATGATCAATCGC 59.352 38.462 0.00 0.00 40.01 4.58
2306 2659 4.984785 TCTTTTCCTAGATGATCAATCGCG 59.015 41.667 0.00 0.00 40.54 5.87
2308 2661 0.987715 CCTAGATGATCAATCGCGCG 59.012 55.000 26.76 26.76 40.54 6.86
2310 2663 1.337110 TAGATGATCAATCGCGCGCG 61.337 55.000 44.84 44.84 40.54 6.86
2456 2827 0.107508 CTTCCGTCCCTGCATGATGT 60.108 55.000 0.00 0.00 0.00 3.06
2489 2869 4.309950 GGTCGGTCGCCAAGTGGT 62.310 66.667 0.00 0.00 37.57 4.16
2494 2874 1.514087 GGTCGCCAAGTGGTCGATA 59.486 57.895 16.20 0.00 42.38 2.92
2497 2877 0.892755 TCGCCAAGTGGTCGATAAGT 59.107 50.000 11.23 0.00 38.26 2.24
2499 2879 2.492881 TCGCCAAGTGGTCGATAAGTAA 59.507 45.455 11.23 0.00 38.26 2.24
2510 2890 5.049267 TGGTCGATAAGTAACACCAAAAAGC 60.049 40.000 0.00 0.00 34.10 3.51
2520 2900 1.962807 CACCAAAAAGCAGTCCATGGA 59.037 47.619 11.44 11.44 0.00 3.41
2547 2927 0.460459 GGTAAAGCCGGAGAGACAGC 60.460 60.000 5.05 0.00 0.00 4.40
2637 3017 5.604565 CTTGTGTGATGATAGAGGCACATA 58.395 41.667 0.00 0.00 42.45 2.29
2735 3123 6.370166 GGTCTATATTATCCTTGCTTGACTGC 59.630 42.308 0.00 0.00 0.00 4.40
2743 3131 1.952296 CTTGCTTGACTGCCAGAAACT 59.048 47.619 0.00 0.00 0.00 2.66
2744 3132 1.311859 TGCTTGACTGCCAGAAACTG 58.688 50.000 0.00 0.00 0.00 3.16
2790 3179 5.537674 TGGAGGTAGTACGATCCTTTTATCC 59.462 44.000 18.81 5.59 32.79 2.59
2840 3238 6.004574 AGATGATGATGATGGATCAAAGTGG 58.995 40.000 0.00 0.00 44.50 4.00
2859 3257 1.588082 CCTGGCATGAACAGCAACC 59.412 57.895 11.20 0.00 34.65 3.77
2860 3258 1.180456 CCTGGCATGAACAGCAACCA 61.180 55.000 11.20 0.00 35.96 3.67
2862 3260 0.388659 TGGCATGAACAGCAACCAAC 59.611 50.000 0.00 0.00 34.81 3.77
2868 3266 0.237498 GAACAGCAACCAACGTAGGC 59.763 55.000 0.00 0.00 0.00 3.93
2943 3342 1.072678 CGATGCTCATCCCTGCCAT 59.927 57.895 4.45 0.00 34.40 4.40
2991 3391 2.828877 TCGAAAGCGAAACAGAAAGGA 58.171 42.857 0.00 0.00 44.78 3.36
2995 3395 4.495844 CGAAAGCGAAACAGAAAGGAAAGT 60.496 41.667 0.00 0.00 40.82 2.66
3011 3411 4.773117 GTCGACGTGGACGGAGCC 62.773 72.222 15.08 0.00 44.95 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 2.884997 AATCGCCATGCCCGTGCTTA 62.885 55.000 0.00 0.00 38.71 3.09
228 229 1.620323 CTCACACACTCTCACCCATGA 59.380 52.381 0.00 0.00 0.00 3.07
229 230 1.338484 CCTCACACACTCTCACCCATG 60.338 57.143 0.00 0.00 0.00 3.66
230 231 0.979665 CCTCACACACTCTCACCCAT 59.020 55.000 0.00 0.00 0.00 4.00
231 232 1.121407 CCCTCACACACTCTCACCCA 61.121 60.000 0.00 0.00 0.00 4.51
232 233 1.674057 CCCTCACACACTCTCACCC 59.326 63.158 0.00 0.00 0.00 4.61
233 234 1.004440 GCCCTCACACACTCTCACC 60.004 63.158 0.00 0.00 0.00 4.02
234 235 1.373497 CGCCCTCACACACTCTCAC 60.373 63.158 0.00 0.00 0.00 3.51
259 260 0.877743 CACACACACACACCAACACA 59.122 50.000 0.00 0.00 0.00 3.72
260 261 0.878416 ACACACACACACACCAACAC 59.122 50.000 0.00 0.00 0.00 3.32
261 262 0.877743 CACACACACACACACCAACA 59.122 50.000 0.00 0.00 0.00 3.33
262 263 0.878416 ACACACACACACACACCAAC 59.122 50.000 0.00 0.00 0.00 3.77
263 264 0.877743 CACACACACACACACACCAA 59.122 50.000 0.00 0.00 0.00 3.67
264 265 0.250510 ACACACACACACACACACCA 60.251 50.000 0.00 0.00 0.00 4.17
265 266 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
266 267 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
267 268 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
268 269 1.152510 TGACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
269 270 3.614399 TGACACACACACACACACA 57.386 47.368 0.00 0.00 0.00 3.72
328 329 3.136763 CAGCTCTGTTCTTCTTGCTTGA 58.863 45.455 0.00 0.00 0.00 3.02
329 330 2.350580 GCAGCTCTGTTCTTCTTGCTTG 60.351 50.000 0.00 0.00 0.00 4.01
339 340 0.321919 TCCACCATGCAGCTCTGTTC 60.322 55.000 0.00 0.00 0.00 3.18
360 371 2.032799 TGCTTTTGTTACTGCACCGAAG 59.967 45.455 0.00 0.00 0.00 3.79
416 427 3.244491 GCACTGAAGATCCCTCTGCATAT 60.244 47.826 0.00 0.00 36.42 1.78
527 610 3.132925 CCTTTTTGTTCCTGGCATGTTG 58.867 45.455 0.00 0.00 0.00 3.33
553 638 5.411053 GCAGATGCTGTTTTCTTACTTCTCT 59.589 40.000 0.00 0.00 38.21 3.10
554 639 5.391416 GGCAGATGCTGTTTTCTTACTTCTC 60.391 44.000 4.59 0.00 41.70 2.87
557 642 4.144297 TGGCAGATGCTGTTTTCTTACTT 58.856 39.130 4.59 0.00 41.70 2.24
563 653 1.471684 CTCCTGGCAGATGCTGTTTTC 59.528 52.381 17.94 0.00 41.70 2.29
597 687 0.318869 ACATTGTACGCGACCGAACA 60.319 50.000 15.93 5.99 38.29 3.18
653 749 2.695147 ACAGTCTCCTTTTGGCCTTTTG 59.305 45.455 3.32 0.00 40.12 2.44
654 750 2.695147 CACAGTCTCCTTTTGGCCTTTT 59.305 45.455 3.32 0.00 40.12 2.27
655 751 2.091885 TCACAGTCTCCTTTTGGCCTTT 60.092 45.455 3.32 0.00 40.12 3.11
656 752 1.494721 TCACAGTCTCCTTTTGGCCTT 59.505 47.619 3.32 0.00 40.12 4.35
657 753 1.140312 TCACAGTCTCCTTTTGGCCT 58.860 50.000 3.32 0.00 40.12 5.19
658 754 1.981256 TTCACAGTCTCCTTTTGGCC 58.019 50.000 0.00 0.00 40.12 5.36
659 755 3.214328 TCTTTCACAGTCTCCTTTTGGC 58.786 45.455 0.00 0.00 40.12 4.52
660 756 4.708177 TCTCTTTCACAGTCTCCTTTTGG 58.292 43.478 0.00 0.00 42.21 3.28
668 764 4.698575 GGTTGTTCTCTCTTTCACAGTCT 58.301 43.478 0.00 0.00 0.00 3.24
717 813 1.291906 GGGCGTGGTTTCCCATTTG 59.708 57.895 0.00 0.00 44.35 2.32
836 1119 1.569479 GGCGAACAGAGCAGAACACC 61.569 60.000 0.00 0.00 36.08 4.16
859 1142 3.841758 GTATCGACCCCGCCCGTT 61.842 66.667 0.00 0.00 35.37 4.44
1127 1423 2.639286 CACACTCACCGGCTTTGC 59.361 61.111 0.00 0.00 0.00 3.68
1142 1438 1.598701 GGACATGAAAGGGGCAGCAC 61.599 60.000 0.00 0.00 0.00 4.40
1143 1439 1.304381 GGACATGAAAGGGGCAGCA 60.304 57.895 0.00 0.00 0.00 4.41
1154 1470 2.107041 AAAGGCACGGACGGACATGA 62.107 55.000 0.00 0.00 0.00 3.07
1163 1479 2.855514 GCAAAGGCAAAGGCACGGA 61.856 57.895 0.00 0.00 43.71 4.69
1196 1512 4.253273 GATCGAGAACACGCGCGC 62.253 66.667 32.58 23.91 0.00 6.86
1197 1513 3.949348 CGATCGAGAACACGCGCG 61.949 66.667 30.96 30.96 0.00 6.86
1198 1514 1.857023 GATCGATCGAGAACACGCGC 61.857 60.000 23.84 0.00 0.00 6.86
1199 1515 2.117338 GATCGATCGAGAACACGCG 58.883 57.895 23.84 3.53 0.00 6.01
1213 1529 2.976509 CCGAGACAAAGATCATCGATCG 59.023 50.000 9.36 9.36 43.17 3.69
1215 1531 2.695666 ACCCGAGACAAAGATCATCGAT 59.304 45.455 0.00 0.00 35.47 3.59
1217 1533 2.196749 CACCCGAGACAAAGATCATCG 58.803 52.381 0.00 0.00 0.00 3.84
1218 1534 2.555199 CCACCCGAGACAAAGATCATC 58.445 52.381 0.00 0.00 0.00 2.92
1219 1535 1.210478 CCCACCCGAGACAAAGATCAT 59.790 52.381 0.00 0.00 0.00 2.45
1225 1541 1.147376 CACACCCACCCGAGACAAA 59.853 57.895 0.00 0.00 0.00 2.83
1228 1544 3.883744 CTGCACACCCACCCGAGAC 62.884 68.421 0.00 0.00 0.00 3.36
1230 1546 4.704833 CCTGCACACCCACCCGAG 62.705 72.222 0.00 0.00 0.00 4.63
1235 1551 3.790416 TTCAGCCCTGCACACCCAC 62.790 63.158 0.00 0.00 0.00 4.61
1236 1552 3.496309 CTTCAGCCCTGCACACCCA 62.496 63.158 0.00 0.00 0.00 4.51
1237 1553 2.674380 CTTCAGCCCTGCACACCC 60.674 66.667 0.00 0.00 0.00 4.61
1238 1554 1.673665 CTCTTCAGCCCTGCACACC 60.674 63.158 0.00 0.00 0.00 4.16
1239 1555 1.673665 CCTCTTCAGCCCTGCACAC 60.674 63.158 0.00 0.00 0.00 3.82
1240 1556 2.149383 ACCTCTTCAGCCCTGCACA 61.149 57.895 0.00 0.00 0.00 4.57
1241 1557 1.673665 CACCTCTTCAGCCCTGCAC 60.674 63.158 0.00 0.00 0.00 4.57
1244 1560 2.435586 CGCACCTCTTCAGCCCTG 60.436 66.667 0.00 0.00 0.00 4.45
1251 1567 2.394563 GCTCTTGCCGCACCTCTTC 61.395 63.158 0.00 0.00 0.00 2.87
1329 1645 1.799933 AGATGATGGTGTCCTCCTCC 58.200 55.000 0.00 0.00 0.00 4.30
1368 1684 0.322008 AGAGTGCTTACTTGCTGCCC 60.322 55.000 0.00 0.00 0.00 5.36
1397 1721 1.741401 CTTTCGCGCCTGGTGATCA 60.741 57.895 12.29 0.00 34.56 2.92
1412 1736 0.240945 CACGAAAAGGATGCCGCTTT 59.759 50.000 0.00 0.00 0.00 3.51
1602 1941 2.363795 ATGAAGGACGGGGAGCGA 60.364 61.111 0.00 0.00 0.00 4.93
1968 2307 3.382832 CCGCCGAGGAACTGGTCT 61.383 66.667 0.00 0.00 41.55 3.85
2005 2344 4.011966 TCTACACTAGTGACAAGGTCGA 57.988 45.455 29.30 4.56 34.95 4.20
2011 2350 5.114081 TCGATCGATCTACACTAGTGACAA 58.886 41.667 29.30 13.24 0.00 3.18
2084 2431 3.314307 TGGAGATCGAGTACTTGGGAT 57.686 47.619 10.33 7.41 0.00 3.85
2085 2432 2.820728 TGGAGATCGAGTACTTGGGA 57.179 50.000 10.33 2.72 0.00 4.37
2086 2433 2.959030 TCATGGAGATCGAGTACTTGGG 59.041 50.000 10.33 0.00 0.00 4.12
2087 2434 3.551863 GCTCATGGAGATCGAGTACTTGG 60.552 52.174 10.33 0.00 0.00 3.61
2088 2435 3.067320 TGCTCATGGAGATCGAGTACTTG 59.933 47.826 3.44 3.44 0.00 3.16
2092 2443 4.944619 ATTTGCTCATGGAGATCGAGTA 57.055 40.909 0.00 0.00 0.00 2.59
2095 2446 4.124970 CTGAATTTGCTCATGGAGATCGA 58.875 43.478 0.00 0.00 0.00 3.59
2102 2453 5.067413 AGCTTGTATCTGAATTTGCTCATGG 59.933 40.000 0.00 0.00 0.00 3.66
2109 2460 3.941483 ACCCGAGCTTGTATCTGAATTTG 59.059 43.478 0.00 0.00 0.00 2.32
2138 2489 4.872691 AGCATACGAAGATCACCTTTTCAG 59.127 41.667 0.00 0.00 34.68 3.02
2142 2493 3.941483 CCAAGCATACGAAGATCACCTTT 59.059 43.478 0.00 0.00 34.68 3.11
2156 2507 5.304101 ACCACATTTCAAGTTTCCAAGCATA 59.696 36.000 0.00 0.00 0.00 3.14
2158 2509 3.450457 ACCACATTTCAAGTTTCCAAGCA 59.550 39.130 0.00 0.00 0.00 3.91
2160 2511 5.906073 AGAACCACATTTCAAGTTTCCAAG 58.094 37.500 0.00 0.00 0.00 3.61
2169 2520 7.345422 TCAAGATTCAAGAACCACATTTCAA 57.655 32.000 0.00 0.00 0.00 2.69
2198 2550 2.816087 GGCATGGAAGCATGTAATCGAT 59.184 45.455 0.00 0.00 35.16 3.59
2205 2557 0.324923 ACATGGGCATGGAAGCATGT 60.325 50.000 0.00 0.00 42.91 3.21
2218 2571 4.339247 ACACTTGAGAAGACAAAACATGGG 59.661 41.667 0.00 0.00 0.00 4.00
2222 2575 5.588246 TGCATACACTTGAGAAGACAAAACA 59.412 36.000 0.00 0.00 0.00 2.83
2227 2580 4.607293 ACTGCATACACTTGAGAAGACA 57.393 40.909 0.00 0.00 0.00 3.41
2228 2581 5.233988 AGAACTGCATACACTTGAGAAGAC 58.766 41.667 0.00 0.00 0.00 3.01
2229 2582 5.474578 AGAACTGCATACACTTGAGAAGA 57.525 39.130 0.00 0.00 0.00 2.87
2230 2583 6.203530 TCAAAGAACTGCATACACTTGAGAAG 59.796 38.462 0.00 0.00 0.00 2.85
2231 2584 6.054941 TCAAAGAACTGCATACACTTGAGAA 58.945 36.000 0.00 0.00 0.00 2.87
2232 2585 5.610398 TCAAAGAACTGCATACACTTGAGA 58.390 37.500 0.00 0.00 0.00 3.27
2233 2586 5.929697 TCAAAGAACTGCATACACTTGAG 57.070 39.130 0.00 0.00 0.00 3.02
2256 2609 4.485163 GATTAGCGGCACAAAATTTCTGT 58.515 39.130 1.45 0.00 0.00 3.41
2271 2624 6.090483 TCTAGGAAAAGATCAGGATTAGCG 57.910 41.667 0.00 0.00 0.00 4.26
2272 2625 7.675062 TCATCTAGGAAAAGATCAGGATTAGC 58.325 38.462 0.00 0.00 33.87 3.09
2273 2626 9.874205 GATCATCTAGGAAAAGATCAGGATTAG 57.126 37.037 0.00 0.00 33.87 1.73
2276 2629 7.868792 TGATCATCTAGGAAAAGATCAGGAT 57.131 36.000 0.00 0.00 39.89 3.24
2277 2630 7.681259 TTGATCATCTAGGAAAAGATCAGGA 57.319 36.000 0.00 0.00 43.93 3.86
2279 2632 7.148606 GCGATTGATCATCTAGGAAAAGATCAG 60.149 40.741 0.00 0.00 43.93 2.90
2280 2633 6.648310 GCGATTGATCATCTAGGAAAAGATCA 59.352 38.462 0.00 0.00 42.19 2.92
2281 2634 6.183360 CGCGATTGATCATCTAGGAAAAGATC 60.183 42.308 0.00 0.00 33.87 2.75
2282 2635 5.636965 CGCGATTGATCATCTAGGAAAAGAT 59.363 40.000 0.00 0.00 36.64 2.40
2283 2636 4.984785 CGCGATTGATCATCTAGGAAAAGA 59.015 41.667 0.00 0.00 0.00 2.52
2287 2640 2.677199 GCGCGATTGATCATCTAGGAA 58.323 47.619 12.10 0.00 0.00 3.36
2312 2665 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
2314 2667 0.451383 ACATGTGTGTGTGTGTGTGC 59.549 50.000 0.00 0.00 37.14 4.57
2401 2772 2.098770 GGTCATGGCTCATCTTCTTTGC 59.901 50.000 0.00 0.00 0.00 3.68
2477 2848 1.278238 CTTATCGACCACTTGGCGAC 58.722 55.000 14.31 0.00 42.88 5.19
2478 2849 0.892755 ACTTATCGACCACTTGGCGA 59.107 50.000 14.36 14.36 43.68 5.54
2489 2869 5.761234 ACTGCTTTTTGGTGTTACTTATCGA 59.239 36.000 0.00 0.00 0.00 3.59
2494 2874 4.020543 TGGACTGCTTTTTGGTGTTACTT 58.979 39.130 0.00 0.00 0.00 2.24
2497 2877 3.320541 CCATGGACTGCTTTTTGGTGTTA 59.679 43.478 5.56 0.00 0.00 2.41
2499 2879 1.688197 CCATGGACTGCTTTTTGGTGT 59.312 47.619 5.56 0.00 0.00 4.16
2661 3047 1.061131 CGCGACCTGTCATCAATCAAC 59.939 52.381 0.00 0.00 0.00 3.18
2743 3131 2.088423 GGATGTACCGCAAATTGTCCA 58.912 47.619 0.00 0.00 0.00 4.02
2744 3132 2.088423 TGGATGTACCGCAAATTGTCC 58.912 47.619 0.00 0.00 42.61 4.02
2753 3141 0.180406 ACCTCCAATGGATGTACCGC 59.820 55.000 8.47 0.00 42.61 5.68
2755 3143 4.261909 CGTACTACCTCCAATGGATGTACC 60.262 50.000 12.44 4.47 36.75 3.34
2790 3179 4.450419 CAGCCCTTCTAATTATCTTCTGCG 59.550 45.833 0.00 0.00 0.00 5.18
2840 3238 1.080298 GTTGCTGTTCATGCCAGGC 60.080 57.895 3.66 3.66 0.00 4.85
2943 3342 0.874175 CGACACGACAAGAACTGGCA 60.874 55.000 0.00 0.00 28.94 4.92
2964 3363 0.179248 GTTTCGCTTTCGAGCTTCCG 60.179 55.000 0.00 0.00 46.34 4.30
2979 3378 3.554731 ACGTCGACTTTCCTTTCTGTTTC 59.445 43.478 14.70 0.00 0.00 2.78
2989 3389 1.731969 CCGTCCACGTCGACTTTCC 60.732 63.158 14.70 0.00 37.74 3.13
2991 3391 1.285023 CTCCGTCCACGTCGACTTT 59.715 57.895 14.70 0.00 37.74 2.66


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

AutoCloner maintained by Alex Coulton.