Multiple sequence alignment - TraesCS7D01G418900

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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 TraesCS7D01G418900 chr7D 100.000 2729 0 0 1 2729 538585239 538587967 0.000000e+00 5040.0
1 TraesCS7D01G418900 chr7D 84.232 1725 182 61 403 2077 538141440 538139756 0.000000e+00 1596.0
2 TraesCS7D01G418900 chr7D 85.357 1359 141 41 753 2077 538661827 538663161 0.000000e+00 1354.0
3 TraesCS7D01G418900 chr7D 84.127 1386 146 40 745 2105 538594537 538595873 0.000000e+00 1273.0
4 TraesCS7D01G418900 chr7D 84.078 1388 150 37 753 2105 538602418 538603769 0.000000e+00 1273.0
5 TraesCS7D01G418900 chr7D 89.326 965 80 13 1134 2077 538333165 538332203 0.000000e+00 1190.0
6 TraesCS7D01G418900 chr7D 85.780 1090 117 17 997 2074 538212130 538211067 0.000000e+00 1120.0
7 TraesCS7D01G418900 chr7D 85.948 854 49 23 301 1095 538333997 538333156 0.000000e+00 846.0
8 TraesCS7D01G418900 chr7D 77.836 573 81 33 399 949 538240497 538239949 2.040000e-81 313.0
9 TraesCS7D01G418900 chr7D 99.346 153 1 0 2360 2512 538596294 538596446 7.440000e-71 278.0
10 TraesCS7D01G418900 chr7D 89.506 162 8 5 2360 2512 538604943 538605104 2.140000e-46 196.0
11 TraesCS7D01G418900 chr7D 98.077 52 1 0 2257 2308 538596171 538596222 1.040000e-14 91.6
12 TraesCS7D01G418900 chr7B 86.449 1808 143 49 333 2077 580970994 580969226 0.000000e+00 1888.0
13 TraesCS7D01G418900 chr7B 84.764 1608 155 40 749 2322 581313550 581315101 0.000000e+00 1530.0
14 TraesCS7D01G418900 chr7B 83.382 1715 193 50 399 2072 580886269 580884606 0.000000e+00 1504.0
15 TraesCS7D01G418900 chr7B 86.863 1355 130 30 745 2077 581333190 581334518 0.000000e+00 1472.0
16 TraesCS7D01G418900 chr7B 89.296 355 15 7 358 710 581306580 581306913 9.030000e-115 424.0
17 TraesCS7D01G418900 chr7B 83.333 282 20 8 67 347 581305074 581305329 4.540000e-58 235.0
18 TraesCS7D01G418900 chr7B 90.741 162 6 5 2360 2512 581315181 581315342 9.900000e-50 207.0
19 TraesCS7D01G418900 chr7A 85.827 1524 138 56 584 2077 619167382 619165907 0.000000e+00 1546.0
20 TraesCS7D01G418900 chr7A 89.772 1183 78 21 400 1567 619634623 619633469 0.000000e+00 1474.0
21 TraesCS7D01G418900 chr7A 89.772 1183 78 21 400 1567 619906575 619907729 0.000000e+00 1474.0
22 TraesCS7D01G418900 chr7A 85.725 1345 139 35 758 2077 620171357 620172673 0.000000e+00 1371.0
23 TraesCS7D01G418900 chr7A 85.524 1354 148 31 745 2077 620201246 620202572 0.000000e+00 1371.0
24 TraesCS7D01G418900 chr7A 84.645 1029 107 33 584 1577 619577095 619576083 0.000000e+00 977.0
25 TraesCS7D01G418900 chr7A 91.039 491 42 1 1617 2105 619907740 619908230 0.000000e+00 662.0
26 TraesCS7D01G418900 chr7A 92.130 432 33 1 1647 2078 619576033 619575603 2.320000e-170 608.0
27 TraesCS7D01G418900 chr7A 92.593 162 3 1 2360 2512 619908503 619908664 9.830000e-55 224.0
28 TraesCS7D01G418900 chr7A 88.889 162 18 0 2513 2674 730603085 730603246 1.660000e-47 200.0
29 TraesCS7D01G418900 chr7A 98.276 58 1 0 2360 2417 620197883 620197940 4.810000e-18 102.0
30 TraesCS7D01G418900 chr6A 89.506 162 17 0 2513 2674 503245897 503245736 3.560000e-49 206.0
31 TraesCS7D01G418900 chr6A 88.889 162 18 0 2513 2674 615711037 615711198 1.660000e-47 200.0
32 TraesCS7D01G418900 chr1A 89.506 162 17 0 2513 2674 329013773 329013934 3.560000e-49 206.0
33 TraesCS7D01G418900 chr3A 90.728 151 14 0 2521 2671 653920765 653920915 4.610000e-48 202.0
34 TraesCS7D01G418900 chr6D 88.344 163 18 1 2513 2674 254904020 254904182 7.710000e-46 195.0
35 TraesCS7D01G418900 chr4D 88.679 159 18 0 2513 2671 100317692 100317850 7.710000e-46 195.0
36 TraesCS7D01G418900 chr2A 88.272 162 19 0 2513 2674 575349187 575349026 7.710000e-46 195.0
37 TraesCS7D01G418900 chr2A 88.272 162 19 0 2513 2674 608600891 608601052 7.710000e-46 195.0


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 TraesCS7D01G418900 chr7D 538585239 538587967 2728 False 5040.000000 5040 100.000000 1 2729 1 chr7D.!!$F1 2728
1 TraesCS7D01G418900 chr7D 538139756 538141440 1684 True 1596.000000 1596 84.232000 403 2077 1 chr7D.!!$R1 1674
2 TraesCS7D01G418900 chr7D 538661827 538663161 1334 False 1354.000000 1354 85.357000 753 2077 1 chr7D.!!$F2 1324
3 TraesCS7D01G418900 chr7D 538211067 538212130 1063 True 1120.000000 1120 85.780000 997 2074 1 chr7D.!!$R2 1077
4 TraesCS7D01G418900 chr7D 538332203 538333997 1794 True 1018.000000 1190 87.637000 301 2077 2 chr7D.!!$R4 1776
5 TraesCS7D01G418900 chr7D 538602418 538605104 2686 False 734.500000 1273 86.792000 753 2512 2 chr7D.!!$F4 1759
6 TraesCS7D01G418900 chr7D 538594537 538596446 1909 False 547.533333 1273 93.850000 745 2512 3 chr7D.!!$F3 1767
7 TraesCS7D01G418900 chr7D 538239949 538240497 548 True 313.000000 313 77.836000 399 949 1 chr7D.!!$R3 550
8 TraesCS7D01G418900 chr7B 580969226 580970994 1768 True 1888.000000 1888 86.449000 333 2077 1 chr7B.!!$R2 1744
9 TraesCS7D01G418900 chr7B 580884606 580886269 1663 True 1504.000000 1504 83.382000 399 2072 1 chr7B.!!$R1 1673
10 TraesCS7D01G418900 chr7B 581333190 581334518 1328 False 1472.000000 1472 86.863000 745 2077 1 chr7B.!!$F1 1332
11 TraesCS7D01G418900 chr7B 581313550 581315342 1792 False 868.500000 1530 87.752500 749 2512 2 chr7B.!!$F3 1763
12 TraesCS7D01G418900 chr7B 581305074 581306913 1839 False 329.500000 424 86.314500 67 710 2 chr7B.!!$F2 643
13 TraesCS7D01G418900 chr7A 619165907 619167382 1475 True 1546.000000 1546 85.827000 584 2077 1 chr7A.!!$R1 1493
14 TraesCS7D01G418900 chr7A 619633469 619634623 1154 True 1474.000000 1474 89.772000 400 1567 1 chr7A.!!$R2 1167
15 TraesCS7D01G418900 chr7A 620171357 620172673 1316 False 1371.000000 1371 85.725000 758 2077 1 chr7A.!!$F1 1319
16 TraesCS7D01G418900 chr7A 619575603 619577095 1492 True 792.500000 977 88.387500 584 2078 2 chr7A.!!$R3 1494
17 TraesCS7D01G418900 chr7A 619906575 619908664 2089 False 786.666667 1474 91.134667 400 2512 3 chr7A.!!$F3 2112
18 TraesCS7D01G418900 chr7A 620197883 620202572 4689 False 736.500000 1371 91.900000 745 2417 2 chr7A.!!$F4 1672

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
229 230 0.536460 GAGAGGAGCGACTAGGGAGG 60.536 65.0 0.0 0.0 0.0 4.30 F
1086 3793 0.664761 TCGACAAGGAGTTCGACGTT 59.335 50.0 0.0 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 4233 0.252057 TGTGGGATCGAACCAGAGGA 60.252 55.000 14.28 0.00 39.00 3.71 R
2310 6097 1.133853 TGTGGCTATATGCATGCACCA 60.134 47.619 25.37 22.12 45.15 4.17 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
17 18 3.142393 CCTCCGAATCTGGCCGAT 58.858 61.111 0.00 0.60 0.00 4.18
18 19 1.447643 CCTCCGAATCTGGCCGATT 59.552 57.895 18.63 18.63 44.87 3.34
32 33 2.582959 CGATTCGGACTGCTACTGC 58.417 57.895 0.00 0.00 40.20 4.40
34 35 0.872021 GATTCGGACTGCTACTGCCG 60.872 60.000 0.00 0.00 44.83 5.69
35 36 2.907897 ATTCGGACTGCTACTGCCGC 62.908 60.000 0.00 0.00 43.26 6.53
54 55 3.793144 GCCAGCGAACCTGCGAAG 61.793 66.667 0.00 0.00 40.36 3.79
177 178 2.513897 GAGGAATCCCCGTTGCCG 60.514 66.667 0.00 0.00 40.87 5.69
223 224 2.895865 CGGCGAGAGGAGCGACTA 60.896 66.667 0.00 0.00 33.81 2.59
224 225 2.887889 CGGCGAGAGGAGCGACTAG 61.888 68.421 0.00 0.00 33.81 2.57
225 226 2.548295 GGCGAGAGGAGCGACTAGG 61.548 68.421 0.00 0.00 33.04 3.02
226 227 2.548295 GCGAGAGGAGCGACTAGGG 61.548 68.421 0.00 0.00 0.00 3.53
228 229 0.882927 CGAGAGGAGCGACTAGGGAG 60.883 65.000 0.00 0.00 0.00 4.30
229 230 0.536460 GAGAGGAGCGACTAGGGAGG 60.536 65.000 0.00 0.00 0.00 4.30
230 231 1.529713 GAGGAGCGACTAGGGAGGG 60.530 68.421 0.00 0.00 0.00 4.30
231 232 2.522193 GGAGCGACTAGGGAGGGG 60.522 72.222 0.00 0.00 0.00 4.79
232 233 2.601868 GAGCGACTAGGGAGGGGA 59.398 66.667 0.00 0.00 0.00 4.81
233 234 1.076192 GAGCGACTAGGGAGGGGAA 60.076 63.158 0.00 0.00 0.00 3.97
234 235 1.075896 AGCGACTAGGGAGGGGAAG 60.076 63.158 0.00 0.00 0.00 3.46
266 267 2.160205 GCCTTCTAAGTTGACCCAACC 58.840 52.381 6.24 0.00 44.49 3.77
273 275 7.255486 CCTTCTAAGTTGACCCAACCTTTTTAG 60.255 40.741 6.24 7.79 44.49 1.85
284 286 6.491062 ACCCAACCTTTTTAGTAATAAAGCGT 59.509 34.615 0.00 7.92 31.54 5.07
285 287 7.025365 CCCAACCTTTTTAGTAATAAAGCGTC 58.975 38.462 0.00 0.00 31.54 5.19
367 1609 0.761187 TTGTCTCAACCAGAGCTGCT 59.239 50.000 0.00 0.00 44.35 4.24
414 1659 2.778299 TGTGAATCTAACACACCAGGC 58.222 47.619 0.00 0.00 42.20 4.85
506 1753 5.845103 TCTTGTTCATGCATCATGTGTTTT 58.155 33.333 0.00 0.00 41.98 2.43
509 1756 5.224135 TGTTCATGCATCATGTGTTTTCTG 58.776 37.500 0.00 0.00 41.98 3.02
514 1762 6.878389 TCATGCATCATGTGTTTTCTGTACTA 59.122 34.615 0.00 0.00 41.98 1.82
530 1778 5.479027 TCTGTACTACTGTACTGCCATTTGA 59.521 40.000 7.67 0.00 46.70 2.69
655 1953 2.042464 TCGATGCTTAATGCCCTCTCT 58.958 47.619 0.00 0.00 42.00 3.10
712 2016 0.736325 AGTCGGGCGTCTCATTTTCG 60.736 55.000 0.00 0.00 0.00 3.46
738 2046 3.123621 AGAAAATTGTTCGCTACTCGCTG 59.876 43.478 0.00 0.00 38.27 5.18
754 3388 1.215647 CTGCAGTACCGTCCTGTCC 59.784 63.158 5.25 0.00 32.41 4.02
806 3441 2.298158 AATACACCGGAGCTGGCGAG 62.298 60.000 9.46 0.00 0.00 5.03
873 3528 6.021030 ACGCTTATCTCCAAACCCCTATATA 58.979 40.000 0.00 0.00 0.00 0.86
1013 3714 4.783621 ACGCATGGCTCGCATGGT 62.784 61.111 0.00 0.00 0.00 3.55
1046 3753 1.930100 CGATCCTGCTCGCATGTTC 59.070 57.895 0.00 0.00 0.00 3.18
1056 3763 2.644418 GCATGTTCTGCCGTTGCA 59.356 55.556 0.00 0.00 45.66 4.08
1086 3793 0.664761 TCGACAAGGAGTTCGACGTT 59.335 50.000 0.00 0.00 0.00 3.99
1230 3937 4.421479 CTCAAGCTCGTCGCCGGT 62.421 66.667 1.90 0.00 40.39 5.28
1233 3940 1.518572 CAAGCTCGTCGCCGGTAAT 60.519 57.895 1.90 0.00 40.39 1.89
1309 4033 2.309528 TTTCGGTCTTGATCGGATGG 57.690 50.000 3.37 0.00 0.00 3.51
1317 4041 0.742990 TTGATCGGATGGCACGGTTC 60.743 55.000 0.00 0.00 0.00 3.62
1318 4042 2.202878 ATCGGATGGCACGGTTCG 60.203 61.111 0.00 0.00 0.00 3.95
1410 4161 1.503818 TTCGAGTTCCTTGGCAACGC 61.504 55.000 0.00 0.00 42.51 4.84
1435 4186 2.187946 GAGCCCTACACGCTGCAT 59.812 61.111 0.00 0.00 36.48 3.96
1501 4252 0.252057 TCCTCTGGTTCGATCCCACA 60.252 55.000 10.02 0.00 0.00 4.17
1550 4301 5.775513 CTGGAACCCAAAGCACATCATGC 62.776 52.174 0.00 0.00 43.99 4.06
1614 4376 0.532862 AACGCCGGCCATCTATTCAG 60.533 55.000 23.46 4.79 0.00 3.02
1615 4377 2.320587 CGCCGGCCATCTATTCAGC 61.321 63.158 23.46 0.00 0.00 4.26
1619 4381 1.224075 CGGCCATCTATTCAGCACAG 58.776 55.000 2.24 0.00 0.00 3.66
1622 4384 2.224719 GGCCATCTATTCAGCACAGGAT 60.225 50.000 0.00 0.00 0.00 3.24
1726 4513 0.253327 GATCGCCTTCCCCAAGAACT 59.747 55.000 0.00 0.00 0.00 3.01
1942 4738 2.522638 GCGGCCGAAGATTGGTACG 61.523 63.158 33.48 0.00 33.92 3.67
2021 4817 2.165641 TGATCTACAACTACTGCACGGG 59.834 50.000 0.00 0.00 0.00 5.28
2112 4968 2.094854 AGACGACCGGAGATGTGTAAAC 60.095 50.000 9.46 0.00 0.00 2.01
2179 5049 5.235616 CGCCCAACTCGTGTGTAATATATTT 59.764 40.000 2.68 0.00 0.00 1.40
2187 5057 7.506261 ACTCGTGTGTAATATATTTCCTCCTCT 59.494 37.037 2.68 0.00 0.00 3.69
2188 5058 8.929260 TCGTGTGTAATATATTTCCTCCTCTA 57.071 34.615 2.68 0.00 0.00 2.43
2189 5059 9.011095 TCGTGTGTAATATATTTCCTCCTCTAG 57.989 37.037 2.68 0.00 0.00 2.43
2190 5060 8.794553 CGTGTGTAATATATTTCCTCCTCTAGT 58.205 37.037 2.68 0.00 0.00 2.57
2192 5062 9.310449 TGTGTAATATATTTCCTCCTCTAGTCC 57.690 37.037 2.68 0.00 0.00 3.85
2193 5063 9.536510 GTGTAATATATTTCCTCCTCTAGTCCT 57.463 37.037 2.68 0.00 0.00 3.85
2194 5064 9.756571 TGTAATATATTTCCTCCTCTAGTCCTC 57.243 37.037 2.68 0.00 0.00 3.71
2209 5897 1.200716 GTCCTCGTACGTTCATCACCA 59.799 52.381 16.05 0.00 0.00 4.17
2217 5905 4.496840 CGTACGTTCATCACCAGTATGCTA 60.497 45.833 7.22 0.00 31.97 3.49
2233 5921 3.087370 TGCTACTCTCTGCTCACCTTA 57.913 47.619 0.00 0.00 0.00 2.69
2234 5922 3.636679 TGCTACTCTCTGCTCACCTTAT 58.363 45.455 0.00 0.00 0.00 1.73
2235 5923 4.793201 TGCTACTCTCTGCTCACCTTATA 58.207 43.478 0.00 0.00 0.00 0.98
2238 5926 5.278266 GCTACTCTCTGCTCACCTTATACAG 60.278 48.000 0.00 0.00 0.00 2.74
2310 6097 3.627395 TTCTGCTTCGTCCATTGGTAT 57.373 42.857 1.86 0.00 0.00 2.73
2320 6107 1.112950 CCATTGGTATGGTGCATGCA 58.887 50.000 18.46 18.46 45.34 3.96
2321 6108 1.689813 CCATTGGTATGGTGCATGCAT 59.310 47.619 25.64 10.90 45.34 3.96
2512 6355 4.672542 CGTTCGAAATTGATCAGGTTGCAT 60.673 41.667 0.00 0.00 0.00 3.96
2513 6356 5.447144 CGTTCGAAATTGATCAGGTTGCATA 60.447 40.000 0.00 0.00 0.00 3.14
2514 6357 6.498304 GTTCGAAATTGATCAGGTTGCATAT 58.502 36.000 0.00 0.00 0.00 1.78
2515 6358 6.063640 TCGAAATTGATCAGGTTGCATATG 57.936 37.500 0.00 0.00 0.00 1.78
2516 6359 4.678287 CGAAATTGATCAGGTTGCATATGC 59.322 41.667 21.09 21.09 42.50 3.14
2517 6360 4.595762 AATTGATCAGGTTGCATATGCC 57.404 40.909 24.54 10.19 41.18 4.40
2518 6361 2.732844 TGATCAGGTTGCATATGCCA 57.267 45.000 24.54 11.61 41.18 4.92
2519 6362 2.300433 TGATCAGGTTGCATATGCCAC 58.700 47.619 24.54 22.52 41.18 5.01
2530 6373 7.642071 GTTGCATATGCCACCAAATTAATAG 57.358 36.000 24.54 0.00 41.18 1.73
2531 6374 5.782047 TGCATATGCCACCAAATTAATAGC 58.218 37.500 24.54 0.00 41.18 2.97
2532 6375 5.303845 TGCATATGCCACCAAATTAATAGCA 59.696 36.000 24.54 0.00 41.18 3.49
2533 6376 6.014413 TGCATATGCCACCAAATTAATAGCAT 60.014 34.615 24.54 0.00 41.89 3.79
2534 6377 6.875195 GCATATGCCACCAAATTAATAGCATT 59.125 34.615 17.26 0.00 39.89 3.56
2535 6378 8.034215 GCATATGCCACCAAATTAATAGCATTA 58.966 33.333 17.26 0.00 39.89 1.90
2536 6379 9.577110 CATATGCCACCAAATTAATAGCATTAG 57.423 33.333 0.00 0.00 39.89 1.73
2537 6380 7.838079 ATGCCACCAAATTAATAGCATTAGA 57.162 32.000 0.00 0.00 36.10 2.10
2538 6381 7.838079 TGCCACCAAATTAATAGCATTAGAT 57.162 32.000 0.00 0.00 0.00 1.98
2539 6382 8.248904 TGCCACCAAATTAATAGCATTAGATT 57.751 30.769 0.00 0.00 0.00 2.40
2540 6383 8.359642 TGCCACCAAATTAATAGCATTAGATTC 58.640 33.333 0.00 0.00 0.00 2.52
2541 6384 8.359642 GCCACCAAATTAATAGCATTAGATTCA 58.640 33.333 0.00 0.00 0.00 2.57
2579 6422 8.821147 TTTTCATCATATGCCTATTTGATTGC 57.179 30.769 0.00 0.00 34.18 3.56
2580 6423 7.527568 TTCATCATATGCCTATTTGATTGCA 57.472 32.000 0.00 0.00 34.18 4.08
2581 6424 6.916440 TCATCATATGCCTATTTGATTGCAC 58.084 36.000 0.00 0.00 34.18 4.57
2582 6425 6.490721 TCATCATATGCCTATTTGATTGCACA 59.509 34.615 0.00 0.00 34.18 4.57
2583 6426 6.712179 TCATATGCCTATTTGATTGCACAA 57.288 33.333 0.00 0.00 36.41 3.33
2584 6427 7.110043 TCATATGCCTATTTGATTGCACAAA 57.890 32.000 5.09 5.09 42.58 2.83
2585 6428 6.979817 TCATATGCCTATTTGATTGCACAAAC 59.020 34.615 4.76 0.00 41.49 2.93
2586 6429 4.597404 TGCCTATTTGATTGCACAAACA 57.403 36.364 4.76 0.00 41.49 2.83
2587 6430 5.149973 TGCCTATTTGATTGCACAAACAT 57.850 34.783 4.76 0.00 41.49 2.71
2588 6431 5.549347 TGCCTATTTGATTGCACAAACATT 58.451 33.333 4.76 0.00 41.49 2.71
2589 6432 6.695429 TGCCTATTTGATTGCACAAACATTA 58.305 32.000 4.76 0.00 41.49 1.90
2590 6433 7.157347 TGCCTATTTGATTGCACAAACATTAA 58.843 30.769 4.76 0.00 41.49 1.40
2591 6434 7.823310 TGCCTATTTGATTGCACAAACATTAAT 59.177 29.630 4.76 0.00 41.49 1.40
2592 6435 9.311916 GCCTATTTGATTGCACAAACATTAATA 57.688 29.630 4.76 0.00 41.49 0.98
2667 6510 7.803279 AAGTTGGAAGTACACTCTTTTAAGG 57.197 36.000 0.00 0.00 0.00 2.69
2668 6511 7.133133 AGTTGGAAGTACACTCTTTTAAGGA 57.867 36.000 0.00 0.00 0.00 3.36
2669 6512 6.990939 AGTTGGAAGTACACTCTTTTAAGGAC 59.009 38.462 0.00 0.00 0.00 3.85
2670 6513 5.535333 TGGAAGTACACTCTTTTAAGGACG 58.465 41.667 0.00 0.00 0.00 4.79
2671 6514 4.928020 GGAAGTACACTCTTTTAAGGACGG 59.072 45.833 0.00 0.00 0.00 4.79
2672 6515 5.279156 GGAAGTACACTCTTTTAAGGACGGA 60.279 44.000 0.00 0.00 0.00 4.69
2673 6516 5.388408 AGTACACTCTTTTAAGGACGGAG 57.612 43.478 0.00 0.00 0.00 4.63
2674 6517 5.075493 AGTACACTCTTTTAAGGACGGAGA 58.925 41.667 0.00 0.00 0.00 3.71
2675 6518 4.950205 ACACTCTTTTAAGGACGGAGAA 57.050 40.909 0.00 0.00 0.00 2.87
2676 6519 5.286267 ACACTCTTTTAAGGACGGAGAAA 57.714 39.130 0.00 0.00 0.00 2.52
2677 6520 5.677567 ACACTCTTTTAAGGACGGAGAAAA 58.322 37.500 0.00 0.00 0.00 2.29
2678 6521 6.117488 ACACTCTTTTAAGGACGGAGAAAAA 58.883 36.000 0.00 0.00 0.00 1.94
2703 6546 8.647143 AAAAGAAATTCAACACCAGTAATGTG 57.353 30.769 0.00 0.00 39.63 3.21
2704 6547 7.581213 AAGAAATTCAACACCAGTAATGTGA 57.419 32.000 0.00 0.00 37.18 3.58
2705 6548 7.581213 AGAAATTCAACACCAGTAATGTGAA 57.419 32.000 0.00 0.00 37.18 3.18
2706 6549 8.181904 AGAAATTCAACACCAGTAATGTGAAT 57.818 30.769 0.00 2.07 37.18 2.57
2707 6550 9.295825 AGAAATTCAACACCAGTAATGTGAATA 57.704 29.630 7.04 0.00 37.18 1.75
2708 6551 9.906660 GAAATTCAACACCAGTAATGTGAATAA 57.093 29.630 7.04 0.00 37.18 1.40
2709 6552 9.691362 AAATTCAACACCAGTAATGTGAATAAC 57.309 29.630 7.04 0.00 37.18 1.89
2710 6553 6.474819 TCAACACCAGTAATGTGAATAACG 57.525 37.500 0.00 0.00 37.18 3.18
2711 6554 6.224584 TCAACACCAGTAATGTGAATAACGA 58.775 36.000 0.00 0.00 37.18 3.85
2712 6555 6.146510 TCAACACCAGTAATGTGAATAACGAC 59.853 38.462 0.00 0.00 37.18 4.34
2713 6556 5.543714 ACACCAGTAATGTGAATAACGACA 58.456 37.500 0.00 0.00 37.18 4.35
2714 6557 5.992829 ACACCAGTAATGTGAATAACGACAA 59.007 36.000 0.00 0.00 37.18 3.18
2715 6558 6.147164 ACACCAGTAATGTGAATAACGACAAG 59.853 38.462 0.00 0.00 37.18 3.16
2716 6559 6.367695 CACCAGTAATGTGAATAACGACAAGA 59.632 38.462 0.00 0.00 35.74 3.02
2717 6560 6.367969 ACCAGTAATGTGAATAACGACAAGAC 59.632 38.462 0.00 0.00 0.00 3.01
2718 6561 6.367695 CCAGTAATGTGAATAACGACAAGACA 59.632 38.462 0.00 0.00 0.00 3.41
2719 6562 7.064609 CCAGTAATGTGAATAACGACAAGACAT 59.935 37.037 0.00 0.00 0.00 3.06
2720 6563 7.899841 CAGTAATGTGAATAACGACAAGACATG 59.100 37.037 0.00 0.00 0.00 3.21
2721 6564 7.817478 AGTAATGTGAATAACGACAAGACATGA 59.183 33.333 0.00 0.00 0.00 3.07
2722 6565 7.433708 AATGTGAATAACGACAAGACATGAA 57.566 32.000 0.00 0.00 0.00 2.57
2723 6566 7.615582 ATGTGAATAACGACAAGACATGAAT 57.384 32.000 0.00 0.00 0.00 2.57
2724 6567 8.716646 ATGTGAATAACGACAAGACATGAATA 57.283 30.769 0.00 0.00 0.00 1.75
2725 6568 8.716646 TGTGAATAACGACAAGACATGAATAT 57.283 30.769 0.00 0.00 0.00 1.28
2726 6569 9.161629 TGTGAATAACGACAAGACATGAATATT 57.838 29.630 0.00 0.00 0.00 1.28
2727 6570 9.425893 GTGAATAACGACAAGACATGAATATTG 57.574 33.333 0.00 1.13 0.00 1.90
2728 6571 9.161629 TGAATAACGACAAGACATGAATATTGT 57.838 29.630 0.00 4.54 38.53 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.872021 GCAGTAGCAGTCCGAATCGG 60.872 60.000 16.75 16.75 44.39 4.18
14 15 0.872021 GGCAGTAGCAGTCCGAATCG 60.872 60.000 0.00 0.00 44.61 3.34
16 17 1.141881 CGGCAGTAGCAGTCCGAAT 59.858 57.895 0.00 0.00 44.23 3.34
17 18 2.571757 CGGCAGTAGCAGTCCGAA 59.428 61.111 0.00 0.00 44.23 4.30
18 19 4.129737 GCGGCAGTAGCAGTCCGA 62.130 66.667 3.51 0.00 44.23 4.55
38 39 3.793144 GCTTCGCAGGTTCGCTGG 61.793 66.667 0.00 0.00 0.00 4.85
43 44 3.056328 GGTGGGCTTCGCAGGTTC 61.056 66.667 0.00 0.00 0.00 3.62
137 138 2.978010 CAGTTCGGTGGCGGCTTT 60.978 61.111 11.43 0.00 0.00 3.51
212 213 1.529713 CCCTCCCTAGTCGCTCCTC 60.530 68.421 0.00 0.00 0.00 3.71
213 214 2.604152 CCCTCCCTAGTCGCTCCT 59.396 66.667 0.00 0.00 0.00 3.69
214 215 2.522193 CCCCTCCCTAGTCGCTCC 60.522 72.222 0.00 0.00 0.00 4.70
215 216 1.076192 TTCCCCTCCCTAGTCGCTC 60.076 63.158 0.00 0.00 0.00 5.03
216 217 1.075896 CTTCCCCTCCCTAGTCGCT 60.076 63.158 0.00 0.00 0.00 4.93
217 218 2.134933 CCTTCCCCTCCCTAGTCGC 61.135 68.421 0.00 0.00 0.00 5.19
218 219 1.457831 CCCTTCCCCTCCCTAGTCG 60.458 68.421 0.00 0.00 0.00 4.18
219 220 1.074395 CCCCTTCCCCTCCCTAGTC 60.074 68.421 0.00 0.00 0.00 2.59
220 221 2.658404 CCCCCTTCCCCTCCCTAGT 61.658 68.421 0.00 0.00 0.00 2.57
221 222 2.290745 CCCCCTTCCCCTCCCTAG 59.709 72.222 0.00 0.00 0.00 3.02
223 224 4.371231 CACCCCCTTCCCCTCCCT 62.371 72.222 0.00 0.00 0.00 4.20
226 227 3.653122 TAGCCACCCCCTTCCCCTC 62.653 68.421 0.00 0.00 0.00 4.30
228 229 3.097162 CTAGCCACCCCCTTCCCC 61.097 72.222 0.00 0.00 0.00 4.81
229 230 3.097162 CCTAGCCACCCCCTTCCC 61.097 72.222 0.00 0.00 0.00 3.97
230 231 3.810188 GCCTAGCCACCCCCTTCC 61.810 72.222 0.00 0.00 0.00 3.46
297 299 9.656040 CTTCTCAGAGCTATCATTGCTATTTAT 57.344 33.333 0.00 0.00 41.30 1.40
298 300 8.646004 ACTTCTCAGAGCTATCATTGCTATTTA 58.354 33.333 0.00 0.00 41.30 1.40
299 301 7.507829 ACTTCTCAGAGCTATCATTGCTATTT 58.492 34.615 0.00 0.00 41.30 1.40
322 324 7.180051 ACTCAAAATGGATAGAAGTCTCTGACT 59.820 37.037 0.00 0.00 45.64 3.41
414 1659 1.913317 TCTCGAAGCGTGTGATGATG 58.087 50.000 0.00 0.00 0.00 3.07
514 1762 6.952773 TTTTTACTCAAATGGCAGTACAGT 57.047 33.333 0.00 0.00 0.00 3.55
538 1786 8.959548 TCTGTATATGCAGATGATTTTGTGTTT 58.040 29.630 18.36 0.00 40.23 2.83
539 1787 8.510243 TCTGTATATGCAGATGATTTTGTGTT 57.490 30.769 18.36 0.00 40.23 3.32
655 1953 1.454201 CAGAGGCTCTCACGTACAGA 58.546 55.000 15.60 0.00 32.06 3.41
712 2016 5.484958 CGAGTAGCGAACAATTTTCTGATC 58.515 41.667 0.00 0.00 44.57 2.92
738 2046 2.577593 GGGACAGGACGGTACTGC 59.422 66.667 20.21 12.45 39.55 4.40
754 3388 1.457455 GCCAGAGGAGAGGAGAGGG 60.457 68.421 0.00 0.00 0.00 4.30
806 3441 2.028337 GGCGAATCGGAGAGGAGC 59.972 66.667 4.35 0.00 43.63 4.70
873 3528 4.653888 CGGGGCGTGAGGGGTTTT 62.654 66.667 0.00 0.00 0.00 2.43
1056 3763 1.517257 CTTGTCGAAGCTCGCCGAT 60.517 57.895 8.66 0.00 40.21 4.18
1230 3937 4.085204 ACGGTGCCGGCGGAATTA 62.085 61.111 33.44 9.52 44.69 1.40
1309 4033 1.226030 ACCAAGTTAGCGAACCGTGC 61.226 55.000 6.04 0.00 36.08 5.34
1317 4041 1.069500 CCAAACCGAACCAAGTTAGCG 60.069 52.381 0.00 0.00 0.00 4.26
1318 4042 1.951602 ACCAAACCGAACCAAGTTAGC 59.048 47.619 0.00 0.00 0.00 3.09
1482 4233 0.252057 TGTGGGATCGAACCAGAGGA 60.252 55.000 14.28 0.00 39.00 3.71
1501 4252 2.036862 GGAGTAGGTGTGGAAGTCGTTT 59.963 50.000 0.00 0.00 0.00 3.60
1550 4301 0.652592 GACGGCGATCAATCCACTTG 59.347 55.000 16.62 0.00 36.09 3.16
1555 4306 3.338676 GGCGACGGCGATCAATCC 61.339 66.667 18.90 0.00 41.24 3.01
1614 4376 2.175878 AGTCACTGAACATCCTGTGC 57.824 50.000 0.00 0.00 36.39 4.57
1615 4377 6.808008 AAATTAGTCACTGAACATCCTGTG 57.192 37.500 0.00 0.00 37.35 3.66
1619 4381 7.875971 ACAAGAAAATTAGTCACTGAACATCC 58.124 34.615 0.00 0.00 0.00 3.51
1639 4418 4.081406 ACCATGAAGCTGCATTTACAAGA 58.919 39.130 3.72 0.00 0.00 3.02
1785 4572 1.736645 CCAATCCGTCTTGACGCGT 60.737 57.895 13.85 13.85 0.00 6.01
2049 4845 1.815421 CTACATGGTGCACTCGGCC 60.815 63.158 17.98 0.00 43.89 6.13
2123 4993 2.091541 ACATGAACTGGGCGTAAATGG 58.908 47.619 0.00 0.00 0.00 3.16
2179 5049 1.411977 CGTACGAGGACTAGAGGAGGA 59.588 57.143 10.44 0.00 0.00 3.71
2187 5057 2.679837 GGTGATGAACGTACGAGGACTA 59.320 50.000 24.41 0.94 0.00 2.59
2188 5058 1.471684 GGTGATGAACGTACGAGGACT 59.528 52.381 24.41 1.88 0.00 3.85
2189 5059 1.200716 TGGTGATGAACGTACGAGGAC 59.799 52.381 24.41 10.15 0.00 3.85
2190 5060 1.471287 CTGGTGATGAACGTACGAGGA 59.529 52.381 24.41 4.73 0.00 3.71
2191 5061 1.201647 ACTGGTGATGAACGTACGAGG 59.798 52.381 24.41 0.00 0.00 4.63
2192 5062 2.631418 ACTGGTGATGAACGTACGAG 57.369 50.000 24.41 7.79 0.00 4.18
2193 5063 3.732774 GCATACTGGTGATGAACGTACGA 60.733 47.826 24.41 0.00 0.00 3.43
2194 5064 2.534349 GCATACTGGTGATGAACGTACG 59.466 50.000 15.01 15.01 0.00 3.67
2217 5905 4.861196 TCTGTATAAGGTGAGCAGAGAGT 58.139 43.478 0.00 0.00 33.05 3.24
2233 5921 5.411669 GGAACCGAATGTTTCAGTTCTGTAT 59.588 40.000 13.23 0.00 43.35 2.29
2234 5922 4.753107 GGAACCGAATGTTTCAGTTCTGTA 59.247 41.667 13.23 0.00 43.35 2.74
2235 5923 3.564225 GGAACCGAATGTTTCAGTTCTGT 59.436 43.478 13.23 0.00 43.35 3.41
2238 5926 3.606153 CGTGGAACCGAATGTTTCAGTTC 60.606 47.826 7.50 7.50 43.23 3.01
2310 6097 1.133853 TGTGGCTATATGCATGCACCA 60.134 47.619 25.37 22.12 45.15 4.17
2320 6107 2.547218 CGGCGTTTAGGTGTGGCTATAT 60.547 50.000 0.00 0.00 0.00 0.86
2321 6108 1.202440 CGGCGTTTAGGTGTGGCTATA 60.202 52.381 0.00 0.00 0.00 1.31
2512 6355 8.932434 TCTAATGCTATTAATTTGGTGGCATA 57.068 30.769 0.00 0.00 37.85 3.14
2513 6356 7.838079 TCTAATGCTATTAATTTGGTGGCAT 57.162 32.000 0.00 0.00 40.04 4.40
2514 6357 7.838079 ATCTAATGCTATTAATTTGGTGGCA 57.162 32.000 0.00 0.00 0.00 4.92
2515 6358 8.359642 TGAATCTAATGCTATTAATTTGGTGGC 58.640 33.333 0.00 0.00 0.00 5.01
2553 6396 9.431887 GCAATCAAATAGGCATATGATGAAAAT 57.568 29.630 6.97 0.53 33.06 1.82
2554 6397 8.422566 TGCAATCAAATAGGCATATGATGAAAA 58.577 29.630 6.97 0.00 33.06 2.29
2555 6398 7.868922 GTGCAATCAAATAGGCATATGATGAAA 59.131 33.333 6.97 0.00 38.68 2.69
2556 6399 7.014422 TGTGCAATCAAATAGGCATATGATGAA 59.986 33.333 6.97 0.00 38.68 2.57
2557 6400 6.490721 TGTGCAATCAAATAGGCATATGATGA 59.509 34.615 6.97 8.89 38.68 2.92
2558 6401 6.683715 TGTGCAATCAAATAGGCATATGATG 58.316 36.000 6.97 0.00 38.68 3.07
2559 6402 6.904463 TGTGCAATCAAATAGGCATATGAT 57.096 33.333 6.97 0.00 38.68 2.45
2560 6403 6.712179 TTGTGCAATCAAATAGGCATATGA 57.288 33.333 6.97 0.00 38.68 2.15
2561 6404 6.757478 TGTTTGTGCAATCAAATAGGCATATG 59.243 34.615 5.85 0.00 39.09 1.78
2562 6405 6.876155 TGTTTGTGCAATCAAATAGGCATAT 58.124 32.000 5.85 0.00 39.09 1.78
2563 6406 6.278172 TGTTTGTGCAATCAAATAGGCATA 57.722 33.333 5.85 0.00 39.09 3.14
2564 6407 5.149973 TGTTTGTGCAATCAAATAGGCAT 57.850 34.783 5.85 0.00 39.09 4.40
2565 6408 4.597404 TGTTTGTGCAATCAAATAGGCA 57.403 36.364 5.85 0.00 39.09 4.75
2566 6409 7.593875 TTAATGTTTGTGCAATCAAATAGGC 57.406 32.000 5.85 0.00 39.09 3.93
2641 6484 9.333724 CCTTAAAAGAGTGTACTTCCAACTTTA 57.666 33.333 0.00 0.00 0.00 1.85
2642 6485 8.050930 TCCTTAAAAGAGTGTACTTCCAACTTT 58.949 33.333 0.00 0.00 0.00 2.66
2643 6486 7.498239 GTCCTTAAAAGAGTGTACTTCCAACTT 59.502 37.037 0.00 0.00 0.00 2.66
2644 6487 6.990939 GTCCTTAAAAGAGTGTACTTCCAACT 59.009 38.462 0.00 0.00 0.00 3.16
2645 6488 6.073927 CGTCCTTAAAAGAGTGTACTTCCAAC 60.074 42.308 0.00 0.00 0.00 3.77
2646 6489 5.987347 CGTCCTTAAAAGAGTGTACTTCCAA 59.013 40.000 0.00 0.00 0.00 3.53
2647 6490 5.510179 CCGTCCTTAAAAGAGTGTACTTCCA 60.510 44.000 0.00 0.00 0.00 3.53
2648 6491 4.928020 CCGTCCTTAAAAGAGTGTACTTCC 59.072 45.833 0.00 0.00 0.00 3.46
2649 6492 5.776744 TCCGTCCTTAAAAGAGTGTACTTC 58.223 41.667 0.00 0.00 0.00 3.01
2650 6493 5.537674 TCTCCGTCCTTAAAAGAGTGTACTT 59.462 40.000 0.00 0.00 0.00 2.24
2651 6494 5.075493 TCTCCGTCCTTAAAAGAGTGTACT 58.925 41.667 0.00 0.00 0.00 2.73
2652 6495 5.382618 TCTCCGTCCTTAAAAGAGTGTAC 57.617 43.478 0.00 0.00 0.00 2.90
2653 6496 6.409524 TTTCTCCGTCCTTAAAAGAGTGTA 57.590 37.500 0.00 0.00 0.00 2.90
2654 6497 4.950205 TTCTCCGTCCTTAAAAGAGTGT 57.050 40.909 0.00 0.00 0.00 3.55
2655 6498 6.613755 TTTTTCTCCGTCCTTAAAAGAGTG 57.386 37.500 0.00 0.00 0.00 3.51
2677 6520 9.097257 CACATTACTGGTGTTGAATTTCTTTTT 57.903 29.630 0.00 0.00 0.00 1.94
2678 6521 8.474025 TCACATTACTGGTGTTGAATTTCTTTT 58.526 29.630 0.00 0.00 37.52 2.27
2679 6522 8.006298 TCACATTACTGGTGTTGAATTTCTTT 57.994 30.769 0.00 0.00 37.52 2.52
2680 6523 7.581213 TCACATTACTGGTGTTGAATTTCTT 57.419 32.000 0.00 0.00 37.52 2.52
2681 6524 7.581213 TTCACATTACTGGTGTTGAATTTCT 57.419 32.000 0.00 0.00 37.52 2.52
2682 6525 9.906660 TTATTCACATTACTGGTGTTGAATTTC 57.093 29.630 0.00 0.00 37.52 2.17
2683 6526 9.691362 GTTATTCACATTACTGGTGTTGAATTT 57.309 29.630 0.00 0.00 37.52 1.82
2684 6527 8.020819 CGTTATTCACATTACTGGTGTTGAATT 58.979 33.333 0.00 0.00 37.52 2.17
2685 6528 7.389330 TCGTTATTCACATTACTGGTGTTGAAT 59.611 33.333 0.00 0.00 37.52 2.57
2686 6529 6.706716 TCGTTATTCACATTACTGGTGTTGAA 59.293 34.615 0.00 0.00 37.52 2.69
2687 6530 6.146510 GTCGTTATTCACATTACTGGTGTTGA 59.853 38.462 0.00 0.00 37.52 3.18
2688 6531 6.073494 TGTCGTTATTCACATTACTGGTGTTG 60.073 38.462 0.00 0.00 37.52 3.33
2689 6532 5.992829 TGTCGTTATTCACATTACTGGTGTT 59.007 36.000 0.00 0.00 37.52 3.32
2690 6533 5.543714 TGTCGTTATTCACATTACTGGTGT 58.456 37.500 0.00 0.00 37.52 4.16
2691 6534 6.367695 TCTTGTCGTTATTCACATTACTGGTG 59.632 38.462 0.00 0.00 37.60 4.17
2692 6535 6.367969 GTCTTGTCGTTATTCACATTACTGGT 59.632 38.462 0.00 0.00 0.00 4.00
2693 6536 6.367695 TGTCTTGTCGTTATTCACATTACTGG 59.632 38.462 0.00 0.00 0.00 4.00
2694 6537 7.346208 TGTCTTGTCGTTATTCACATTACTG 57.654 36.000 0.00 0.00 0.00 2.74
2695 6538 7.817478 TCATGTCTTGTCGTTATTCACATTACT 59.183 33.333 0.00 0.00 0.00 2.24
2696 6539 7.959733 TCATGTCTTGTCGTTATTCACATTAC 58.040 34.615 0.00 0.00 0.00 1.89
2697 6540 8.541133 TTCATGTCTTGTCGTTATTCACATTA 57.459 30.769 0.00 0.00 0.00 1.90
2698 6541 7.433708 TTCATGTCTTGTCGTTATTCACATT 57.566 32.000 0.00 0.00 0.00 2.71
2699 6542 7.615582 ATTCATGTCTTGTCGTTATTCACAT 57.384 32.000 0.00 0.00 0.00 3.21
2700 6543 8.716646 ATATTCATGTCTTGTCGTTATTCACA 57.283 30.769 0.00 0.00 0.00 3.58
2701 6544 9.425893 CAATATTCATGTCTTGTCGTTATTCAC 57.574 33.333 0.00 0.00 0.00 3.18
2702 6545 9.161629 ACAATATTCATGTCTTGTCGTTATTCA 57.838 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.