Multiple sequence alignment - TraesCS5D01G526400

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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 TraesCS5D01G526400 chr5D 100.000 4471 0 0 1 4471 544288298 544283828 0.000000e+00 8257
1 TraesCS5D01G526400 chr5D 84.495 1722 202 34 1780 3480 543858939 543857262 0.000000e+00 1640
2 TraesCS5D01G526400 chr5D 83.654 1609 210 23 2185 3766 543840021 543838439 0.000000e+00 1465
3 TraesCS5D01G526400 chr5D 80.593 742 113 19 1467 2191 543841332 543840605 1.090000e-150 544
4 TraesCS5D01G526400 chr5D 83.468 248 29 7 1488 1726 543859187 543858943 2.090000e-53 220
5 TraesCS5D01G526400 chr4A 98.708 1858 21 3 2058 3914 624982274 624984129 0.000000e+00 3295
6 TraesCS5D01G526400 chr4A 90.655 1466 82 32 1 1423 624976102 624977555 0.000000e+00 1897
7 TraesCS5D01G526400 chr4A 83.569 2051 271 36 1467 3475 625247518 625249544 0.000000e+00 1860
8 TraesCS5D01G526400 chr4A 86.240 1439 159 23 2074 3504 625176736 625178143 0.000000e+00 1524
9 TraesCS5D01G526400 chr4A 92.409 606 32 5 1465 2066 624977640 624978235 0.000000e+00 852
10 TraesCS5D01G526400 chr4A 93.217 516 19 4 3945 4459 624985316 624985816 0.000000e+00 745
11 TraesCS5D01G526400 chr4A 83.898 236 30 5 1496 1726 625176170 625176402 7.530000e-53 219
12 TraesCS5D01G526400 chr5B 82.872 2131 302 30 1647 3745 685993367 685991268 0.000000e+00 1855
13 TraesCS5D01G526400 chr5B 83.540 1774 224 42 1949 3676 685951466 685949715 0.000000e+00 1596
14 TraesCS5D01G526400 chr5B 83.961 1727 199 47 1780 3477 686051305 686049628 0.000000e+00 1583
15 TraesCS5D01G526400 chr5B 83.020 1755 224 46 1782 3504 686212506 686210794 0.000000e+00 1522
16 TraesCS5D01G526400 chr5B 84.948 1455 178 19 2048 3475 685648698 685650138 0.000000e+00 1435
17 TraesCS5D01G526400 chr3B 79.779 1993 295 58 1784 3735 2987393 2989318 0.000000e+00 1349
18 TraesCS5D01G526400 chr6B 85.061 743 95 11 2172 2910 703833789 703833059 0.000000e+00 743


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 TraesCS5D01G526400 chr5D 544283828 544288298 4470 True 8257.0 8257 100.0000 1 4471 1 chr5D.!!$R1 4470
1 TraesCS5D01G526400 chr5D 543838439 543841332 2893 True 1004.5 1465 82.1235 1467 3766 2 chr5D.!!$R2 2299
2 TraesCS5D01G526400 chr5D 543857262 543859187 1925 True 930.0 1640 83.9815 1488 3480 2 chr5D.!!$R3 1992
3 TraesCS5D01G526400 chr4A 624982274 624985816 3542 False 2020.0 3295 95.9625 2058 4459 2 chr4A.!!$F3 2401
4 TraesCS5D01G526400 chr4A 625247518 625249544 2026 False 1860.0 1860 83.5690 1467 3475 1 chr4A.!!$F1 2008
5 TraesCS5D01G526400 chr4A 624976102 624978235 2133 False 1374.5 1897 91.5320 1 2066 2 chr4A.!!$F2 2065
6 TraesCS5D01G526400 chr4A 625176170 625178143 1973 False 871.5 1524 85.0690 1496 3504 2 chr4A.!!$F4 2008
7 TraesCS5D01G526400 chr5B 685991268 685993367 2099 True 1855.0 1855 82.8720 1647 3745 1 chr5B.!!$R2 2098
8 TraesCS5D01G526400 chr5B 685949715 685951466 1751 True 1596.0 1596 83.5400 1949 3676 1 chr5B.!!$R1 1727
9 TraesCS5D01G526400 chr5B 686049628 686051305 1677 True 1583.0 1583 83.9610 1780 3477 1 chr5B.!!$R3 1697
10 TraesCS5D01G526400 chr5B 686210794 686212506 1712 True 1522.0 1522 83.0200 1782 3504 1 chr5B.!!$R4 1722
11 TraesCS5D01G526400 chr5B 685648698 685650138 1440 False 1435.0 1435 84.9480 2048 3475 1 chr5B.!!$F1 1427
12 TraesCS5D01G526400 chr3B 2987393 2989318 1925 False 1349.0 1349 79.7790 1784 3735 1 chr3B.!!$F1 1951
13 TraesCS5D01G526400 chr6B 703833059 703833789 730 True 743.0 743 85.0610 2172 2910 1 chr6B.!!$R1 738

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
998 1014 0.872388 AAAAAGTAGTGCTTCGCCCG 59.128 50.0 0.00 0.0 36.17 6.13 F
1921 2134 0.107897 AACGGGAGCATCGTATTGCA 60.108 50.0 9.65 0.0 45.23 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 3158 0.396974 AGGTAGAGGCTGAGGCTGAG 60.397 60.000 15.18 0.0 38.98 3.35 R
3780 4694 1.398390 GACATTGATCCAAGGTGACGC 59.602 52.381 1.59 0.0 38.49 5.19 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
28 29 4.250464 CACCCATTGATACGTACAACTGT 58.750 43.478 0.00 1.23 0.00 3.55
56 57 6.530019 AGAAAATTTACCCATCATGGACAC 57.470 37.500 4.75 0.00 40.96 3.67
68 69 2.043248 GGACACGGAGAGCCCCTA 60.043 66.667 0.00 0.00 0.00 3.53
83 84 2.833582 CTAAGAGGCCCTCGCGGA 60.834 66.667 6.13 0.00 35.36 5.54
84 85 2.363276 TAAGAGGCCCTCGCGGAA 60.363 61.111 6.13 0.00 35.36 4.30
157 162 8.442632 TCTCAAATGCTCATATAGGACAAAAG 57.557 34.615 0.00 0.00 0.00 2.27
408 414 8.893727 AGGTTCTATAAAAATCATGTGTACAGC 58.106 33.333 0.00 0.00 0.00 4.40
432 438 3.493176 GCAAGAATGGTTGGCTTCAAGTT 60.493 43.478 0.00 0.00 0.00 2.66
436 442 6.670695 AGAATGGTTGGCTTCAAGTTTATT 57.329 33.333 0.00 0.00 0.00 1.40
449 455 7.360946 GCTTCAAGTTTATTCGTTAGTGGTCAT 60.361 37.037 0.00 0.00 0.00 3.06
500 506 1.001378 GAGCAACATGACACCACAACC 60.001 52.381 0.00 0.00 0.00 3.77
506 512 1.608590 CATGACACCACAACCACCTTC 59.391 52.381 0.00 0.00 0.00 3.46
532 538 2.021722 TGTTTCCACAGAGTTGCGC 58.978 52.632 0.00 0.00 0.00 6.09
539 545 4.680237 CAGAGTTGCGCCGACCCA 62.680 66.667 4.18 0.00 0.00 4.51
552 558 1.067974 CCGACCCAAGGAACAAAAACC 59.932 52.381 0.00 0.00 0.00 3.27
580 586 7.603784 AGAACTTTTTAAAATGCATAGCAAGGG 59.396 33.333 12.41 0.00 43.62 3.95
600 606 4.723789 AGGGATCATACAAGGAAGTGACAT 59.276 41.667 0.00 0.00 0.00 3.06
624 630 3.234730 CTAGGCTAGGGTGGCGGG 61.235 72.222 13.92 0.00 37.59 6.13
641 647 1.482553 CGGGGAGGATATGGTAGTGGT 60.483 57.143 0.00 0.00 0.00 4.16
649 655 1.669049 TATGGTAGTGGTCACCGGCG 61.669 60.000 0.00 0.00 39.04 6.46
652 658 3.376078 TAGTGGTCACCGGCGGAC 61.376 66.667 35.78 21.52 34.52 4.79
670 676 2.996621 GGACAACAACGAGGAAGATGAG 59.003 50.000 0.00 0.00 0.00 2.90
676 682 2.675348 CAACGAGGAAGATGAGGCTTTC 59.325 50.000 0.00 0.00 0.00 2.62
697 703 8.144478 GCTTTCTAATTTTCCTTCTTTTGAGGT 58.856 33.333 0.00 0.00 0.00 3.85
713 719 2.147150 GAGGTCCTTCTTTGTGACTGC 58.853 52.381 0.00 0.00 0.00 4.40
813 828 6.331369 TCTTTAATTGTTTCCTGCCTCTTG 57.669 37.500 0.00 0.00 0.00 3.02
819 834 4.385358 TGTTTCCTGCCTCTTGTTTTTC 57.615 40.909 0.00 0.00 0.00 2.29
833 848 8.064814 CCTCTTGTTTTTCTAGAAGAGTTTTCG 58.935 37.037 13.36 0.54 39.81 3.46
897 912 2.106511 TCTTTTGTCTGCAGGCTAAGGT 59.893 45.455 20.86 0.00 0.00 3.50
998 1014 0.872388 AAAAAGTAGTGCTTCGCCCG 59.128 50.000 0.00 0.00 36.17 6.13
1091 1107 0.527385 GCAGACGCCACTCTCATCTC 60.527 60.000 0.00 0.00 0.00 2.75
1129 1145 1.478916 CCTCTCCCCGTCTCTCTTTTC 59.521 57.143 0.00 0.00 0.00 2.29
1134 1150 2.563179 TCCCCGTCTCTCTTTTCTCTTG 59.437 50.000 0.00 0.00 0.00 3.02
1155 1171 2.684881 GCACATCTTGATTAGGGTGGTG 59.315 50.000 0.00 0.00 33.15 4.17
1170 1186 3.442273 GGGTGGTGCATCGAAATTAGAAA 59.558 43.478 0.00 0.00 0.00 2.52
1171 1187 4.097892 GGGTGGTGCATCGAAATTAGAAAT 59.902 41.667 0.00 0.00 0.00 2.17
1172 1188 5.394115 GGGTGGTGCATCGAAATTAGAAATT 60.394 40.000 0.00 0.00 0.00 1.82
1173 1189 6.183360 GGGTGGTGCATCGAAATTAGAAATTA 60.183 38.462 0.00 0.00 0.00 1.40
1175 1191 6.912591 GTGGTGCATCGAAATTAGAAATTAGG 59.087 38.462 0.00 0.00 0.00 2.69
1178 1216 7.132863 GTGCATCGAAATTAGAAATTAGGGTC 58.867 38.462 0.00 0.00 0.00 4.46
1182 1220 8.552034 CATCGAAATTAGAAATTAGGGTCAGTC 58.448 37.037 0.00 0.00 0.00 3.51
1186 1224 9.396022 GAAATTAGAAATTAGGGTCAGTCATCA 57.604 33.333 0.00 0.00 0.00 3.07
1192 1230 0.463204 AGGGTCAGTCATCATGCTCG 59.537 55.000 0.00 0.00 0.00 5.03
1193 1231 1.156645 GGGTCAGTCATCATGCTCGC 61.157 60.000 0.00 0.00 0.00 5.03
1194 1232 0.179089 GGTCAGTCATCATGCTCGCT 60.179 55.000 0.00 0.00 0.00 4.93
1195 1233 0.928922 GTCAGTCATCATGCTCGCTG 59.071 55.000 0.00 0.00 0.00 5.18
1197 1235 0.461516 CAGTCATCATGCTCGCTGGT 60.462 55.000 0.00 0.00 0.00 4.00
1203 1241 0.245266 TCATGCTCGCTGGTTTCGTA 59.755 50.000 0.00 0.00 0.00 3.43
1204 1242 0.647410 CATGCTCGCTGGTTTCGTAG 59.353 55.000 0.00 0.00 0.00 3.51
1205 1243 0.246635 ATGCTCGCTGGTTTCGTAGT 59.753 50.000 0.00 0.00 0.00 2.73
1209 1250 1.986378 CTCGCTGGTTTCGTAGTGAAG 59.014 52.381 0.00 0.00 37.99 3.02
1216 1257 5.280654 TGGTTTCGTAGTGAAGTTTAGGT 57.719 39.130 0.00 0.00 37.99 3.08
1228 1269 7.722363 AGTGAAGTTTAGGTTATTTTTGTGGG 58.278 34.615 0.00 0.00 0.00 4.61
1242 1283 6.752285 TTTTTGTGGGTTAGTAGAGGTAGT 57.248 37.500 0.00 0.00 0.00 2.73
1246 1287 6.144845 TGTGGGTTAGTAGAGGTAGTTAGT 57.855 41.667 0.00 0.00 0.00 2.24
1319 1360 2.507058 CCTGAATCTGGATCTCCACCAA 59.493 50.000 0.00 0.00 42.01 3.67
1342 1383 0.669625 GTCTACAAGGTGTGTCGGCC 60.670 60.000 0.00 0.00 41.98 6.13
1352 1393 1.206371 GTGTGTCGGCCTGGTACTATT 59.794 52.381 0.00 0.00 0.00 1.73
1360 1401 4.058817 CGGCCTGGTACTATTCTGATTTC 58.941 47.826 0.00 0.00 0.00 2.17
1361 1402 4.202264 CGGCCTGGTACTATTCTGATTTCT 60.202 45.833 0.00 0.00 0.00 2.52
1364 1405 5.008118 GCCTGGTACTATTCTGATTTCTTGC 59.992 44.000 0.00 0.00 0.00 4.01
1365 1406 5.235186 CCTGGTACTATTCTGATTTCTTGCG 59.765 44.000 0.00 0.00 0.00 4.85
1369 1410 6.961554 GGTACTATTCTGATTTCTTGCGTTTG 59.038 38.462 0.00 0.00 0.00 2.93
1370 1411 6.560253 ACTATTCTGATTTCTTGCGTTTGT 57.440 33.333 0.00 0.00 0.00 2.83
1371 1412 7.667043 ACTATTCTGATTTCTTGCGTTTGTA 57.333 32.000 0.00 0.00 0.00 2.41
1372 1413 7.519002 ACTATTCTGATTTCTTGCGTTTGTAC 58.481 34.615 0.00 0.00 0.00 2.90
1373 1414 6.560253 ATTCTGATTTCTTGCGTTTGTACT 57.440 33.333 0.00 0.00 0.00 2.73
1375 1416 7.485418 TTCTGATTTCTTGCGTTTGTACTAA 57.515 32.000 0.00 0.00 0.00 2.24
1376 1417 6.884187 TCTGATTTCTTGCGTTTGTACTAAC 58.116 36.000 9.78 9.78 0.00 2.34
1378 1419 7.011576 TCTGATTTCTTGCGTTTGTACTAACAA 59.988 33.333 18.14 6.88 43.85 2.83
1412 1455 5.401531 AGCAAGTTCACTCGGATTAGTTA 57.598 39.130 0.00 0.00 0.00 2.24
1414 1457 6.407202 AGCAAGTTCACTCGGATTAGTTATT 58.593 36.000 0.00 0.00 0.00 1.40
1415 1458 7.553334 AGCAAGTTCACTCGGATTAGTTATTA 58.447 34.615 0.00 0.00 0.00 0.98
1440 1510 7.731556 ATAACTTCATTACAACGTAGACGAC 57.268 36.000 9.41 0.00 43.02 4.34
1447 1517 8.201554 TCATTACAACGTAGACGACTATTACT 57.798 34.615 9.41 0.00 43.02 2.24
1448 1518 9.313118 TCATTACAACGTAGACGACTATTACTA 57.687 33.333 9.41 0.00 43.02 1.82
1449 1519 9.920826 CATTACAACGTAGACGACTATTACTAA 57.079 33.333 9.41 0.00 43.02 2.24
1452 1522 8.886816 ACAACGTAGACGACTATTACTAAAAG 57.113 34.615 9.41 0.00 43.02 2.27
1516 1602 4.322080 AGTCATGAACTGAAACTCGACA 57.678 40.909 0.00 0.00 36.65 4.35
1550 1636 9.473007 TGATTTGATGGATACTTTTATGGTGAA 57.527 29.630 0.00 0.00 37.61 3.18
1709 1807 6.114187 TCCAAAGTAGAATCAGCAAAGAGA 57.886 37.500 0.00 0.00 0.00 3.10
1716 1814 5.075858 AGAATCAGCAAAGAGAGTCTCTG 57.924 43.478 23.33 13.60 40.28 3.35
1767 1867 2.409870 GCGCTTGGGTTGGATCCAG 61.410 63.158 15.53 3.09 35.48 3.86
1772 1872 2.357154 GCTTGGGTTGGATCCAGTGTAT 60.357 50.000 15.53 0.00 35.48 2.29
1773 1873 3.118038 GCTTGGGTTGGATCCAGTGTATA 60.118 47.826 15.53 0.00 35.48 1.47
1774 1874 4.446311 GCTTGGGTTGGATCCAGTGTATAT 60.446 45.833 15.53 0.00 35.48 0.86
1775 1875 4.705110 TGGGTTGGATCCAGTGTATATG 57.295 45.455 15.53 0.00 0.00 1.78
1776 1876 3.394274 TGGGTTGGATCCAGTGTATATGG 59.606 47.826 15.53 0.00 39.33 2.74
1777 1877 3.394606 GGGTTGGATCCAGTGTATATGGT 59.605 47.826 15.53 0.00 39.01 3.55
1778 1878 4.389374 GGTTGGATCCAGTGTATATGGTG 58.611 47.826 15.53 0.00 39.01 4.17
1818 1926 2.019984 GGTCTTTCTCATGGTCATGGC 58.980 52.381 10.61 0.00 39.24 4.40
1831 1939 4.147701 ATGGCGCTGCTATGAACC 57.852 55.556 7.64 0.00 0.00 3.62
1833 1941 0.394216 ATGGCGCTGCTATGAACCAA 60.394 50.000 7.64 0.00 0.00 3.67
1853 1961 7.944729 ACCAAGCTTACATCTGTTTAATGAT 57.055 32.000 0.00 0.00 0.00 2.45
1914 2127 1.676529 TCTAGAAGAACGGGAGCATCG 59.323 52.381 0.00 0.00 34.37 3.84
1921 2134 0.107897 AACGGGAGCATCGTATTGCA 60.108 50.000 9.65 0.00 45.23 4.08
2145 2391 2.586425 CCAGTTGACACTCCCATTTGT 58.414 47.619 0.00 0.00 0.00 2.83
2309 3158 0.741221 CTAAGAACACCTGCCTCGCC 60.741 60.000 0.00 0.00 0.00 5.54
3772 4686 7.845800 AGGTATAACTTGGGTACTATGTTGGTA 59.154 37.037 0.00 0.00 37.69 3.25
3780 4694 8.851541 TTGGGTACTATGTTGGTACTTTAAAG 57.148 34.615 13.76 13.76 39.36 1.85
3805 4719 5.278463 CGTCACCTTGGATCAATGTCTTTTT 60.278 40.000 0.00 0.00 0.00 1.94
3935 6018 4.761235 ACTCACTGTGCAAATGATCTTG 57.239 40.909 2.12 0.00 0.00 3.02
3936 6019 4.139786 ACTCACTGTGCAAATGATCTTGT 58.860 39.130 2.12 0.00 0.00 3.16
3937 6020 4.023450 ACTCACTGTGCAAATGATCTTGTG 60.023 41.667 2.12 0.00 0.00 3.33
3938 6021 2.984471 CACTGTGCAAATGATCTTGTGC 59.016 45.455 15.24 15.24 37.51 4.57
3939 6022 2.889045 ACTGTGCAAATGATCTTGTGCT 59.111 40.909 20.91 2.14 37.87 4.40
3940 6023 3.319972 ACTGTGCAAATGATCTTGTGCTT 59.680 39.130 20.91 4.32 37.87 3.91
3941 6024 3.904571 TGTGCAAATGATCTTGTGCTTC 58.095 40.909 20.91 15.08 37.87 3.86
3942 6025 3.248266 GTGCAAATGATCTTGTGCTTCC 58.752 45.455 20.91 8.46 37.87 3.46
3943 6026 2.095110 TGCAAATGATCTTGTGCTTCCG 60.095 45.455 20.91 0.00 37.87 4.30
3944 6027 2.095059 GCAAATGATCTTGTGCTTCCGT 60.095 45.455 14.92 0.00 34.13 4.69
3945 6028 3.751621 CAAATGATCTTGTGCTTCCGTC 58.248 45.455 0.00 0.00 0.00 4.79
3946 6029 3.340814 AATGATCTTGTGCTTCCGTCT 57.659 42.857 0.00 0.00 0.00 4.18
3947 6030 2.839486 TGATCTTGTGCTTCCGTCTT 57.161 45.000 0.00 0.00 0.00 3.01
3993 6076 1.852895 GCCTCGTCGTGTATTTGCTAG 59.147 52.381 0.00 0.00 0.00 3.42
4007 6090 2.691409 TGCTAGGCAGTGGTAATCAC 57.309 50.000 0.00 0.00 46.39 3.06
4036 6119 3.257127 ACACTCTACTCTGCTCCAGTTTC 59.743 47.826 0.00 0.00 32.61 2.78
4072 6156 8.940952 GCAGTTTAAGATTGTACTCAAATCTCT 58.059 33.333 7.23 0.00 37.11 3.10
4175 6259 7.935210 TGGATCGTCAGTATACTATTCACAGTA 59.065 37.037 4.74 0.00 35.54 2.74
4176 6260 8.444715 GGATCGTCAGTATACTATTCACAGTAG 58.555 40.741 4.74 0.00 34.59 2.57
4177 6261 8.905660 ATCGTCAGTATACTATTCACAGTAGT 57.094 34.615 4.74 0.00 34.59 2.73
4178 6262 9.993454 ATCGTCAGTATACTATTCACAGTAGTA 57.007 33.333 4.74 0.00 38.57 1.82
4179 6263 9.473640 TCGTCAGTATACTATTCACAGTAGTAG 57.526 37.037 4.74 0.00 37.87 2.57
4180 6264 9.258826 CGTCAGTATACTATTCACAGTAGTAGT 57.741 37.037 4.74 0.00 37.87 2.73
4187 6271 7.762588 ACTATTCACAGTAGTAGTTCACAGT 57.237 36.000 0.00 0.00 30.91 3.55
4204 6288 7.282224 AGTTCACAGTTCACATAGTTTAGCAAA 59.718 33.333 0.00 0.00 0.00 3.68
4246 6330 1.522668 TTGCTGCAGTGACATGGTAC 58.477 50.000 16.64 0.00 0.00 3.34
4254 6338 3.067106 CAGTGACATGGTACTTCACACC 58.933 50.000 13.89 0.00 41.83 4.16
4272 6356 3.005554 CACCTCACATAGTTCAGCAAGG 58.994 50.000 0.00 0.00 0.00 3.61
4281 6365 6.091441 CACATAGTTCAGCAAGGAAAGAGTAC 59.909 42.308 0.00 0.00 0.00 2.73
4352 6436 2.279741 TGTAGTTCCATTCGAGCATGC 58.720 47.619 10.51 10.51 0.00 4.06
4390 6474 5.010617 TCCATTTCATCATCCATGCATGAAG 59.989 40.000 28.31 16.13 36.36 3.02
4416 6500 5.500234 CTTTGGGTCCTCAACATTATCAGA 58.500 41.667 0.00 0.00 0.00 3.27
4417 6501 4.760530 TGGGTCCTCAACATTATCAGAG 57.239 45.455 0.00 0.00 0.00 3.35
4418 6502 3.118261 TGGGTCCTCAACATTATCAGAGC 60.118 47.826 0.00 0.00 0.00 4.09
4423 6507 3.390639 CCTCAACATTATCAGAGCCCTCT 59.609 47.826 0.00 0.00 41.37 3.69
4442 6526 2.945008 TCTTGCAACTCCAAGAACACAG 59.055 45.455 0.00 0.00 45.88 3.66
4459 6543 5.762825 ACACAGGCAAGCATAGATTAATG 57.237 39.130 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.013898 TCCATGATGGGTAAATTTTCTTGCAA 60.014 34.615 12.26 0.00 38.32 4.08
56 57 2.503382 GCCTCTTAGGGGCTCTCCG 61.503 68.421 17.19 0.00 45.57 4.63
105 106 5.398603 TTTTGTTGTGTGAACCATGAAGT 57.601 34.783 0.00 0.00 0.00 3.01
292 297 1.811965 CATGGGTTGTCATCGAGCAAA 59.188 47.619 0.00 0.00 0.00 3.68
295 300 1.718757 GGCATGGGTTGTCATCGAGC 61.719 60.000 0.00 0.00 0.00 5.03
326 332 2.464459 CCGCTCGCCAGCCTTAAAG 61.464 63.158 0.00 0.00 43.56 1.85
364 370 7.528298 AGAACCTTCTACATGGTCGACCAAC 62.528 48.000 39.04 12.47 42.09 3.77
368 374 3.870633 AGAACCTTCTACATGGTCGAC 57.129 47.619 7.13 7.13 35.34 4.20
408 414 1.614903 TGAAGCCAACCATTCTTGCAG 59.385 47.619 0.00 0.00 0.00 4.41
500 506 1.801178 GGAAACAGAAGCGAGAAGGTG 59.199 52.381 0.00 0.00 0.00 4.00
506 512 2.064762 CTCTGTGGAAACAGAAGCGAG 58.935 52.381 9.64 0.00 44.98 5.03
532 538 1.067974 GGTTTTTGTTCCTTGGGTCGG 59.932 52.381 0.00 0.00 0.00 4.79
580 586 4.747108 CCGATGTCACTTCCTTGTATGATC 59.253 45.833 0.00 0.00 0.00 2.92
600 606 2.123425 CCCTAGCCTAGGTGCCGA 60.123 66.667 16.54 0.00 44.73 5.54
618 624 0.544357 CTACCATATCCTCCCCGCCA 60.544 60.000 0.00 0.00 0.00 5.69
624 630 2.633481 GGTGACCACTACCATATCCTCC 59.367 54.545 0.00 0.00 38.12 4.30
641 647 2.589442 GTTGTTGTCCGCCGGTGA 60.589 61.111 18.79 3.77 0.00 4.02
649 655 2.996621 CTCATCTTCCTCGTTGTTGTCC 59.003 50.000 0.00 0.00 0.00 4.02
652 658 1.734465 GCCTCATCTTCCTCGTTGTTG 59.266 52.381 0.00 0.00 0.00 3.33
670 676 7.600375 CCTCAAAAGAAGGAAAATTAGAAAGCC 59.400 37.037 0.00 0.00 35.83 4.35
676 682 7.767250 AGGACCTCAAAAGAAGGAAAATTAG 57.233 36.000 0.00 0.00 37.35 1.73
697 703 0.468226 ACCGCAGTCACAAAGAAGGA 59.532 50.000 0.00 0.00 0.00 3.36
791 804 6.089249 ACAAGAGGCAGGAAACAATTAAAG 57.911 37.500 0.00 0.00 0.00 1.85
813 828 5.238868 AGGCCGAAAACTCTTCTAGAAAAAC 59.761 40.000 6.63 0.00 0.00 2.43
819 834 3.878160 AGAGGCCGAAAACTCTTCTAG 57.122 47.619 0.00 0.00 41.05 2.43
833 848 9.614792 TTTCTTTCTTACAGATTATAAGAGGCC 57.385 33.333 0.00 0.00 39.28 5.19
897 912 2.407562 TGATGGCTTGGCTAGTATGGA 58.592 47.619 0.00 0.00 0.00 3.41
933 948 1.151810 TTGCCACTCCCCTTCTCCT 60.152 57.895 0.00 0.00 0.00 3.69
934 949 1.002011 GTTGCCACTCCCCTTCTCC 60.002 63.158 0.00 0.00 0.00 3.71
938 953 2.084930 ACCAGTTGCCACTCCCCTT 61.085 57.895 0.00 0.00 0.00 3.95
1091 1107 2.348998 GTGAGGGTGCAGACCTGG 59.651 66.667 14.30 0.00 42.66 4.45
1129 1145 4.334759 CACCCTAATCAAGATGTGCAAGAG 59.665 45.833 0.00 0.00 0.00 2.85
1134 1150 2.684881 CACCACCCTAATCAAGATGTGC 59.315 50.000 0.00 0.00 0.00 4.57
1155 1171 7.012421 ACTGACCCTAATTTCTAATTTCGATGC 59.988 37.037 0.00 0.00 0.00 3.91
1170 1186 3.244009 CGAGCATGATGACTGACCCTAAT 60.244 47.826 0.00 0.00 0.00 1.73
1171 1187 2.101415 CGAGCATGATGACTGACCCTAA 59.899 50.000 0.00 0.00 0.00 2.69
1172 1188 1.683385 CGAGCATGATGACTGACCCTA 59.317 52.381 0.00 0.00 0.00 3.53
1173 1189 0.463204 CGAGCATGATGACTGACCCT 59.537 55.000 0.00 0.00 0.00 4.34
1175 1191 0.179089 AGCGAGCATGATGACTGACC 60.179 55.000 0.00 0.00 0.00 4.02
1178 1216 0.461516 ACCAGCGAGCATGATGACTG 60.462 55.000 0.00 0.00 0.00 3.51
1182 1220 0.027194 CGAAACCAGCGAGCATGATG 59.973 55.000 0.00 0.00 0.00 3.07
1186 1224 0.246635 ACTACGAAACCAGCGAGCAT 59.753 50.000 0.00 0.00 0.00 3.79
1192 1230 4.151867 CCTAAACTTCACTACGAAACCAGC 59.848 45.833 0.00 0.00 31.71 4.85
1193 1231 5.295152 ACCTAAACTTCACTACGAAACCAG 58.705 41.667 0.00 0.00 31.71 4.00
1194 1232 5.280654 ACCTAAACTTCACTACGAAACCA 57.719 39.130 0.00 0.00 31.71 3.67
1195 1233 7.895975 ATAACCTAAACTTCACTACGAAACC 57.104 36.000 0.00 0.00 31.71 3.27
1203 1241 7.343574 ACCCACAAAAATAACCTAAACTTCACT 59.656 33.333 0.00 0.00 0.00 3.41
1204 1242 7.494211 ACCCACAAAAATAACCTAAACTTCAC 58.506 34.615 0.00 0.00 0.00 3.18
1205 1243 7.663043 ACCCACAAAAATAACCTAAACTTCA 57.337 32.000 0.00 0.00 0.00 3.02
1216 1257 8.883302 ACTACCTCTACTAACCCACAAAAATAA 58.117 33.333 0.00 0.00 0.00 1.40
1228 1269 8.517062 TCCATGAACTAACTACCTCTACTAAC 57.483 38.462 0.00 0.00 0.00 2.34
1242 1283 9.056005 CGAAATAGATCCAAATCCATGAACTAA 57.944 33.333 0.00 0.00 31.78 2.24
1246 1287 8.210946 ACTACGAAATAGATCCAAATCCATGAA 58.789 33.333 0.00 0.00 34.65 2.57
1339 1380 5.297569 AGAAATCAGAATAGTACCAGGCC 57.702 43.478 0.00 0.00 0.00 5.19
1342 1383 5.812642 ACGCAAGAAATCAGAATAGTACCAG 59.187 40.000 0.00 0.00 43.62 4.00
1352 1393 6.480651 TGTTAGTACAAACGCAAGAAATCAGA 59.519 34.615 0.00 0.00 43.62 3.27
1370 1411 9.899661 ACTTGCTCCATATTACATTTGTTAGTA 57.100 29.630 0.00 0.00 0.00 1.82
1371 1412 8.807948 ACTTGCTCCATATTACATTTGTTAGT 57.192 30.769 0.00 0.00 0.00 2.24
1372 1413 9.722056 GAACTTGCTCCATATTACATTTGTTAG 57.278 33.333 0.00 0.00 0.00 2.34
1373 1414 9.237187 TGAACTTGCTCCATATTACATTTGTTA 57.763 29.630 0.00 0.00 0.00 2.41
1375 1416 7.394359 AGTGAACTTGCTCCATATTACATTTGT 59.606 33.333 0.00 0.00 0.00 2.83
1376 1417 7.765307 AGTGAACTTGCTCCATATTACATTTG 58.235 34.615 0.00 0.00 0.00 2.32
1378 1419 6.258727 CGAGTGAACTTGCTCCATATTACATT 59.741 38.462 0.00 0.00 0.00 2.71
1379 1420 5.755375 CGAGTGAACTTGCTCCATATTACAT 59.245 40.000 0.00 0.00 0.00 2.29
1391 1434 6.663944 AATAACTAATCCGAGTGAACTTGC 57.336 37.500 0.00 0.00 0.00 4.01
1414 1457 9.277565 GTCGTCTACGTTGTAATGAAGTTATTA 57.722 33.333 0.00 0.00 40.80 0.98
1415 1458 8.025445 AGTCGTCTACGTTGTAATGAAGTTATT 58.975 33.333 0.00 0.00 40.80 1.40
1423 1466 9.920826 TTAGTAATAGTCGTCTACGTTGTAATG 57.079 33.333 0.00 0.00 40.80 1.90
1429 1499 8.268850 TCCTTTTAGTAATAGTCGTCTACGTT 57.731 34.615 0.00 0.00 40.80 3.99
1447 1517 7.014201 GGCAGCAGCAAAAAGTTATCCTTTTA 61.014 38.462 2.65 0.00 45.77 1.52
1448 1518 6.255885 GGCAGCAGCAAAAAGTTATCCTTTT 61.256 40.000 2.65 0.00 45.05 2.27
1449 1519 4.309933 GCAGCAGCAAAAAGTTATCCTTT 58.690 39.130 0.00 0.00 42.15 3.11
1450 1520 3.306294 GGCAGCAGCAAAAAGTTATCCTT 60.306 43.478 2.65 0.00 44.61 3.36
1451 1521 2.232208 GGCAGCAGCAAAAAGTTATCCT 59.768 45.455 2.65 0.00 44.61 3.24
1452 1522 2.232208 AGGCAGCAGCAAAAAGTTATCC 59.768 45.455 2.65 0.00 44.61 2.59
1457 1527 1.113788 TCAAGGCAGCAGCAAAAAGT 58.886 45.000 2.65 0.00 44.61 2.66
1465 1535 1.170919 AGCACAGTTCAAGGCAGCAG 61.171 55.000 0.00 0.00 0.00 4.24
1767 1867 6.817184 ACAAGAGACCATACACCATATACAC 58.183 40.000 0.00 0.00 0.00 2.90
1772 1872 7.490657 AACTAACAAGAGACCATACACCATA 57.509 36.000 0.00 0.00 0.00 2.74
1773 1873 6.374417 AACTAACAAGAGACCATACACCAT 57.626 37.500 0.00 0.00 0.00 3.55
1774 1874 5.818678 AACTAACAAGAGACCATACACCA 57.181 39.130 0.00 0.00 0.00 4.17
1775 1875 5.411669 CCAAACTAACAAGAGACCATACACC 59.588 44.000 0.00 0.00 0.00 4.16
1776 1876 5.995897 ACCAAACTAACAAGAGACCATACAC 59.004 40.000 0.00 0.00 0.00 2.90
1777 1877 6.042781 AGACCAAACTAACAAGAGACCATACA 59.957 38.462 0.00 0.00 0.00 2.29
1778 1878 6.465084 AGACCAAACTAACAAGAGACCATAC 58.535 40.000 0.00 0.00 0.00 2.39
1818 1926 1.089920 AAGCTTGGTTCATAGCAGCG 58.910 50.000 0.00 0.00 39.85 5.18
1831 1939 9.499585 CTTGATCATTAAACAGATGTAAGCTTG 57.500 33.333 9.86 0.00 0.00 4.01
1833 1941 8.671921 CACTTGATCATTAAACAGATGTAAGCT 58.328 33.333 0.00 0.00 0.00 3.74
1853 1961 9.500785 TCATTTACTTATGTGTGATTCACTTGA 57.499 29.630 17.26 2.43 46.27 3.02
1904 2117 0.530650 AGTGCAATACGATGCTCCCG 60.531 55.000 12.30 0.00 46.54 5.14
1921 2134 6.640907 GTGATGATTTTCCTTAACGCAAAAGT 59.359 34.615 0.00 0.00 0.00 2.66
2066 2302 8.573885 CGAGAACAACCTACACCTTGATATATA 58.426 37.037 0.00 0.00 0.00 0.86
2145 2391 8.898761 TGAGCAAGTTTTAACTGAACAATAAGA 58.101 29.630 0.00 0.00 39.66 2.10
2309 3158 0.396974 AGGTAGAGGCTGAGGCTGAG 60.397 60.000 15.18 0.00 38.98 3.35
3772 4686 3.202829 TCCAAGGTGACGCTTTAAAGT 57.797 42.857 16.38 0.00 0.00 2.66
3780 4694 1.398390 GACATTGATCCAAGGTGACGC 59.602 52.381 1.59 0.00 38.49 5.19
3935 6018 1.339727 ACCCCAATAAGACGGAAGCAC 60.340 52.381 0.00 0.00 0.00 4.40
3936 6019 0.988832 ACCCCAATAAGACGGAAGCA 59.011 50.000 0.00 0.00 0.00 3.91
3937 6020 2.124277 AACCCCAATAAGACGGAAGC 57.876 50.000 0.00 0.00 0.00 3.86
3938 6021 3.689649 CAGAAACCCCAATAAGACGGAAG 59.310 47.826 0.00 0.00 0.00 3.46
3939 6022 3.073356 ACAGAAACCCCAATAAGACGGAA 59.927 43.478 0.00 0.00 0.00 4.30
3940 6023 2.640826 ACAGAAACCCCAATAAGACGGA 59.359 45.455 0.00 0.00 0.00 4.69
3941 6024 3.007635 GACAGAAACCCCAATAAGACGG 58.992 50.000 0.00 0.00 0.00 4.79
3942 6025 3.939066 AGACAGAAACCCCAATAAGACG 58.061 45.455 0.00 0.00 0.00 4.18
3943 6026 6.183360 GCATAAGACAGAAACCCCAATAAGAC 60.183 42.308 0.00 0.00 0.00 3.01
3944 6027 5.885912 GCATAAGACAGAAACCCCAATAAGA 59.114 40.000 0.00 0.00 0.00 2.10
3945 6028 5.888161 AGCATAAGACAGAAACCCCAATAAG 59.112 40.000 0.00 0.00 0.00 1.73
3946 6029 5.826643 AGCATAAGACAGAAACCCCAATAA 58.173 37.500 0.00 0.00 0.00 1.40
3947 6030 5.450818 AGCATAAGACAGAAACCCCAATA 57.549 39.130 0.00 0.00 0.00 1.90
3993 6076 3.058224 GTGTTTCTGTGATTACCACTGCC 60.058 47.826 0.00 0.00 45.86 4.85
4007 6090 4.233789 GAGCAGAGTAGAGTGTGTTTCTG 58.766 47.826 0.00 0.00 36.13 3.02
4095 6179 9.906660 CAAAAACAGCCTAAATTACATACTGAA 57.093 29.630 0.00 0.00 0.00 3.02
4175 6259 7.599245 GCTAAACTATGTGAACTGTGAACTACT 59.401 37.037 0.00 0.00 0.00 2.57
4176 6260 7.384115 TGCTAAACTATGTGAACTGTGAACTAC 59.616 37.037 0.00 0.00 0.00 2.73
4177 6261 7.438564 TGCTAAACTATGTGAACTGTGAACTA 58.561 34.615 0.00 0.00 0.00 2.24
4178 6262 6.288294 TGCTAAACTATGTGAACTGTGAACT 58.712 36.000 0.00 0.00 0.00 3.01
4179 6263 6.539649 TGCTAAACTATGTGAACTGTGAAC 57.460 37.500 0.00 0.00 0.00 3.18
4180 6264 7.497579 TCTTTGCTAAACTATGTGAACTGTGAA 59.502 33.333 0.00 0.00 0.00 3.18
4181 6265 6.989759 TCTTTGCTAAACTATGTGAACTGTGA 59.010 34.615 0.00 0.00 0.00 3.58
4182 6266 7.189693 TCTTTGCTAAACTATGTGAACTGTG 57.810 36.000 0.00 0.00 0.00 3.66
4183 6267 7.801716 TTCTTTGCTAAACTATGTGAACTGT 57.198 32.000 0.00 0.00 0.00 3.55
4184 6268 9.683069 ATTTTCTTTGCTAAACTATGTGAACTG 57.317 29.630 0.00 0.00 0.00 3.16
4204 6288 7.360101 GCAATCGGACGTGCTTATATATTTTCT 60.360 37.037 5.27 0.00 37.78 2.52
4222 6306 0.036105 ATGTCACTGCAGCAATCGGA 60.036 50.000 15.27 0.00 0.00 4.55
4246 6330 3.681897 GCTGAACTATGTGAGGTGTGAAG 59.318 47.826 0.00 0.00 0.00 3.02
4254 6338 5.240891 TCTTTCCTTGCTGAACTATGTGAG 58.759 41.667 0.00 0.00 0.00 3.51
4272 6356 6.648725 AATACTTGCATCGTGTACTCTTTC 57.351 37.500 0.00 0.00 0.00 2.62
4281 6365 6.991485 AAAGTTTGAAATACTTGCATCGTG 57.009 33.333 0.00 0.00 36.06 4.35
4328 6412 4.106029 TGCTCGAATGGAACTACAGTAC 57.894 45.455 0.00 0.00 0.00 2.73
4331 6415 2.286294 GCATGCTCGAATGGAACTACAG 59.714 50.000 11.37 0.00 0.00 2.74
4352 6436 3.068448 TGAAATGGATGAATGAATGCGGG 59.932 43.478 0.00 0.00 0.00 6.13
4390 6474 2.586648 ATGTTGAGGACCCAAAGGAC 57.413 50.000 0.00 0.00 36.73 3.85
4416 6500 0.251077 CTTGGAGTTGCAAGAGGGCT 60.251 55.000 0.00 0.00 34.04 5.19
4417 6501 0.250901 TCTTGGAGTTGCAAGAGGGC 60.251 55.000 11.40 0.00 33.07 5.19
4418 6502 1.882623 GTTCTTGGAGTTGCAAGAGGG 59.117 52.381 14.34 0.00 38.48 4.30
4423 6507 2.023673 CCTGTGTTCTTGGAGTTGCAA 58.976 47.619 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.