Multiple sequence alignment - TraesCS1A01G409300

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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 TraesCS1A01G409300 chr1A 100.000 2888 0 0 1 2888 570879229 570876342 0.000000e+00 5334
1 TraesCS1A01G409300 chr1A 84.388 1422 178 24 242 1637 570862635 570861232 0.000000e+00 1356
2 TraesCS1A01G409300 chr1A 84.196 1101 152 15 1640 2727 570861328 570860237 0.000000e+00 1050
3 TraesCS1A01G409300 chr1B 90.186 1671 122 23 1 1636 661123240 661121577 0.000000e+00 2139
4 TraesCS1A01G409300 chr1B 90.136 1328 95 17 341 1637 661055566 661054244 0.000000e+00 1694
5 TraesCS1A01G409300 chr1B 90.763 1245 91 6 1640 2879 661121672 661120447 0.000000e+00 1640
6 TraesCS1A01G409300 chr1B 90.112 1254 97 7 1640 2888 660879930 660878699 0.000000e+00 1604
7 TraesCS1A01G409300 chr1B 85.151 1421 173 18 245 1641 660684647 660683241 0.000000e+00 1421
8 TraesCS1A01G409300 chr1B 88.900 964 80 15 697 1636 660880795 660879835 0.000000e+00 1162
9 TraesCS1A01G409300 chr1B 85.828 1009 114 13 654 1637 660997309 660996305 0.000000e+00 1044
10 TraesCS1A01G409300 chr1B 85.487 1006 117 9 654 1637 660950480 660949482 0.000000e+00 1022
11 TraesCS1A01G409300 chr1B 83.514 1104 161 20 1643 2732 660683341 660682245 0.000000e+00 1011
12 TraesCS1A01G409300 chr1B 83.303 1102 162 14 1640 2730 660914100 660913010 0.000000e+00 996
13 TraesCS1A01G409300 chr1B 82.805 1105 164 21 1643 2732 660963275 660962182 0.000000e+00 965
14 TraesCS1A01G409300 chr1B 82.656 1107 167 19 1640 2730 661054346 661053249 0.000000e+00 957
15 TraesCS1A01G409300 chr1B 82.550 1106 174 14 1640 2732 660949581 660948482 0.000000e+00 955
16 TraesCS1A01G409300 chr1B 81.544 1192 178 20 479 1641 660530442 660529264 0.000000e+00 944
17 TraesCS1A01G409300 chr1B 81.541 1181 176 23 493 1641 660964345 660963175 0.000000e+00 935
18 TraesCS1A01G409300 chr1B 81.182 1201 179 31 478 1641 660746639 660745449 0.000000e+00 922
19 TraesCS1A01G409300 chr1B 88.259 758 74 7 1640 2386 660640080 660639327 0.000000e+00 893
20 TraesCS1A01G409300 chr1B 82.218 1046 158 9 611 1637 660723362 660722326 0.000000e+00 876
21 TraesCS1A01G409300 chr1B 95.279 233 9 2 242 473 660723644 660723413 4.550000e-98 368
22 TraesCS1A01G409300 chr1B 79.418 447 75 11 2432 2875 660744718 660744286 1.680000e-77 300
23 TraesCS1A01G409300 chr1B 83.810 315 49 2 2426 2739 660995578 660995265 6.050000e-77 298
24 TraesCS1A01G409300 chr1B 82.555 321 53 3 2421 2739 660721582 660721263 2.190000e-71 279
25 TraesCS1A01G409300 chr1B 93.750 112 7 0 242 353 661059632 661059521 4.950000e-38 169
26 TraesCS1A01G409300 chr1D 84.305 1287 170 19 374 1636 475178735 475177457 0.000000e+00 1229
27 TraesCS1A01G409300 chr1D 82.545 1100 172 14 1643 2730 475177552 475176461 0.000000e+00 950
28 TraesCS1A01G409300 chr1D 84.635 768 96 12 1640 2391 475195256 475194495 0.000000e+00 745
29 TraesCS1A01G409300 chr1D 83.492 315 50 2 2426 2739 475194427 475194114 2.810000e-75 292


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 TraesCS1A01G409300 chr1A 570876342 570879229 2887 True 5334.000000 5334 100.000000 1 2888 1 chr1A.!!$R1 2887
1 TraesCS1A01G409300 chr1A 570860237 570862635 2398 True 1203.000000 1356 84.292000 242 2727 2 chr1A.!!$R2 2485
2 TraesCS1A01G409300 chr1B 661120447 661123240 2793 True 1889.500000 2139 90.474500 1 2879 2 chr1B.!!$R12 2878
3 TraesCS1A01G409300 chr1B 660878699 660880795 2096 True 1383.000000 1604 89.506000 697 2888 2 chr1B.!!$R7 2191
4 TraesCS1A01G409300 chr1B 660682245 660684647 2402 True 1216.000000 1421 84.332500 245 2732 2 chr1B.!!$R4 2487
5 TraesCS1A01G409300 chr1B 660913010 660914100 1090 True 996.000000 996 83.303000 1640 2730 1 chr1B.!!$R3 1090
6 TraesCS1A01G409300 chr1B 660948482 660950480 1998 True 988.500000 1022 84.018500 654 2732 2 chr1B.!!$R8 2078
7 TraesCS1A01G409300 chr1B 660962182 660964345 2163 True 950.000000 965 82.173000 493 2732 2 chr1B.!!$R9 2239
8 TraesCS1A01G409300 chr1B 660529264 660530442 1178 True 944.000000 944 81.544000 479 1641 1 chr1B.!!$R1 1162
9 TraesCS1A01G409300 chr1B 661053249 661059632 6383 True 940.000000 1694 88.847333 242 2730 3 chr1B.!!$R11 2488
10 TraesCS1A01G409300 chr1B 660639327 660640080 753 True 893.000000 893 88.259000 1640 2386 1 chr1B.!!$R2 746
11 TraesCS1A01G409300 chr1B 660995265 660997309 2044 True 671.000000 1044 84.819000 654 2739 2 chr1B.!!$R10 2085
12 TraesCS1A01G409300 chr1B 660744286 660746639 2353 True 611.000000 922 80.300000 478 2875 2 chr1B.!!$R6 2397
13 TraesCS1A01G409300 chr1B 660721263 660723644 2381 True 507.666667 876 86.684000 242 2739 3 chr1B.!!$R5 2497
14 TraesCS1A01G409300 chr1D 475176461 475178735 2274 True 1089.500000 1229 83.425000 374 2730 2 chr1D.!!$R1 2356
15 TraesCS1A01G409300 chr1D 475194114 475195256 1142 True 518.500000 745 84.063500 1640 2739 2 chr1D.!!$R2 1099

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
227 237 0.036010 GGCTGTGTGAGGTAGTGCAT 60.036 55.000 0.0 0.0 0.0 3.96 F
228 238 1.081892 GCTGTGTGAGGTAGTGCATG 58.918 55.000 0.0 0.0 0.0 4.06 F
1529 5544 1.068127 CAAAGAGCATAATGGGGCAGC 59.932 52.381 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 5093 0.320697 AGCGAAGGACCAGTACCAAC 59.679 55.000 0.0 0.0 0.00 3.77 R
1604 5619 0.667993 CGGCAAAGCAGGAAAGTCAA 59.332 50.000 0.0 0.0 0.00 3.18 R
2601 6715 1.073923 GGAAGACTCCAAAGCCTCCAA 59.926 52.381 0.0 0.0 41.96 3.53 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
41 42 5.661056 TCAATTCCAGACTACAGTACCAG 57.339 43.478 0.00 0.00 0.00 4.00
48 57 3.741344 CAGACTACAGTACCAGCAAACAC 59.259 47.826 0.00 0.00 0.00 3.32
55 64 2.700897 AGTACCAGCAAACACAGTCTCT 59.299 45.455 0.00 0.00 0.00 3.10
59 68 3.243907 ACCAGCAAACACAGTCTCTACTC 60.244 47.826 0.00 0.00 31.97 2.59
82 91 5.779771 TCTTGAAATACTTCATTTTGCCCCT 59.220 36.000 0.00 0.00 41.22 4.79
84 93 7.453126 TCTTGAAATACTTCATTTTGCCCCTAA 59.547 33.333 0.00 0.00 41.22 2.69
87 96 2.536066 ACTTCATTTTGCCCCTAACCC 58.464 47.619 0.00 0.00 0.00 4.11
88 97 2.158234 ACTTCATTTTGCCCCTAACCCA 60.158 45.455 0.00 0.00 0.00 4.51
89 98 2.230130 TCATTTTGCCCCTAACCCAG 57.770 50.000 0.00 0.00 0.00 4.45
90 99 1.194218 CATTTTGCCCCTAACCCAGG 58.806 55.000 0.00 0.00 45.07 4.45
95 104 4.109675 CCCCTAACCCAGGCCACG 62.110 72.222 5.01 0.00 43.98 4.94
118 127 2.755103 CCATTTAAGGCAACCTGACTCC 59.245 50.000 0.00 0.00 31.94 3.85
129 138 4.578928 GCAACCTGACTCCTTTTAGACAAA 59.421 41.667 0.00 0.00 0.00 2.83
130 139 5.067283 GCAACCTGACTCCTTTTAGACAAAA 59.933 40.000 0.00 0.00 32.73 2.44
131 140 6.405397 GCAACCTGACTCCTTTTAGACAAAAA 60.405 38.462 0.00 0.00 33.33 1.94
172 181 4.692155 GCATCATGGTGATACAATCGATCA 59.308 41.667 11.02 0.00 34.28 2.92
181 190 7.011389 TGGTGATACAATCGATCAGAATTCAAC 59.989 37.037 8.44 1.53 34.02 3.18
215 225 2.158755 AGCTTTGTCTAGTTGGCTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
216 226 2.031682 GCTTTGTCTAGTTGGCTGTGTG 60.032 50.000 0.00 0.00 0.00 3.82
217 227 3.466836 CTTTGTCTAGTTGGCTGTGTGA 58.533 45.455 0.00 0.00 0.00 3.58
218 228 2.820059 TGTCTAGTTGGCTGTGTGAG 57.180 50.000 0.00 0.00 0.00 3.51
219 229 1.344438 TGTCTAGTTGGCTGTGTGAGG 59.656 52.381 0.00 0.00 0.00 3.86
220 230 1.344763 GTCTAGTTGGCTGTGTGAGGT 59.655 52.381 0.00 0.00 0.00 3.85
221 231 2.561419 GTCTAGTTGGCTGTGTGAGGTA 59.439 50.000 0.00 0.00 0.00 3.08
225 235 0.250295 TTGGCTGTGTGAGGTAGTGC 60.250 55.000 0.00 0.00 0.00 4.40
226 236 1.371183 GGCTGTGTGAGGTAGTGCA 59.629 57.895 0.00 0.00 0.00 4.57
227 237 0.036010 GGCTGTGTGAGGTAGTGCAT 60.036 55.000 0.00 0.00 0.00 3.96
228 238 1.081892 GCTGTGTGAGGTAGTGCATG 58.918 55.000 0.00 0.00 0.00 4.06
229 239 1.609061 GCTGTGTGAGGTAGTGCATGT 60.609 52.381 0.00 0.00 0.00 3.21
563 4546 9.787435 ATACTTTAGTTTTCACTTACCATGACA 57.213 29.630 0.00 0.00 34.06 3.58
573 4556 4.397103 CACTTACCATGACAATGCAGTGAT 59.603 41.667 22.73 4.96 37.18 3.06
796 4792 2.097825 GTCAAGGCAGCATTTCCTGAT 58.902 47.619 0.00 0.00 34.77 2.90
901 4897 6.078664 ACCCTATCAAATGGTACCTCTAGAG 58.921 44.000 14.36 13.18 0.00 2.43
1078 5093 1.472376 GGGAGAGACTGCAAGATTCCG 60.472 57.143 0.00 0.00 37.43 4.30
1446 5461 7.862512 TGAAGAGAATTTTGCCATTGTTTTT 57.137 28.000 0.00 0.00 0.00 1.94
1476 5491 5.123820 CCGTATCTGCAATTCTTTTCCAAGA 59.876 40.000 0.00 0.00 37.24 3.02
1491 5506 3.834610 TCCAAGAAAGATTCGTCGTCTC 58.165 45.455 0.00 0.00 34.02 3.36
1503 5518 1.203928 GTCGTCTCTCCATGCAATCG 58.796 55.000 0.00 0.00 0.00 3.34
1505 5520 1.683385 TCGTCTCTCCATGCAATCGAT 59.317 47.619 0.00 0.00 0.00 3.59
1529 5544 1.068127 CAAAGAGCATAATGGGGCAGC 59.932 52.381 0.00 0.00 0.00 5.25
1547 5562 2.611292 CAGCCTATGCAGTTACAGAAGC 59.389 50.000 0.00 0.00 41.13 3.86
1548 5563 1.943340 GCCTATGCAGTTACAGAAGCC 59.057 52.381 0.00 0.00 37.47 4.35
1549 5564 2.680805 GCCTATGCAGTTACAGAAGCCA 60.681 50.000 0.00 0.00 37.47 4.75
1550 5565 3.609853 CCTATGCAGTTACAGAAGCCAA 58.390 45.455 0.00 0.00 0.00 4.52
1551 5566 3.624861 CCTATGCAGTTACAGAAGCCAAG 59.375 47.826 0.00 0.00 0.00 3.61
1552 5567 2.638480 TGCAGTTACAGAAGCCAAGT 57.362 45.000 0.00 0.00 0.00 3.16
1553 5568 2.930950 TGCAGTTACAGAAGCCAAGTT 58.069 42.857 0.00 0.00 0.00 2.66
1554 5569 4.079980 TGCAGTTACAGAAGCCAAGTTA 57.920 40.909 0.00 0.00 0.00 2.24
1555 5570 3.813166 TGCAGTTACAGAAGCCAAGTTAC 59.187 43.478 0.00 0.00 0.00 2.50
1556 5571 3.813166 GCAGTTACAGAAGCCAAGTTACA 59.187 43.478 0.00 0.00 0.00 2.41
1557 5572 4.455877 GCAGTTACAGAAGCCAAGTTACAT 59.544 41.667 0.00 0.00 0.00 2.29
1558 5573 5.390991 GCAGTTACAGAAGCCAAGTTACATC 60.391 44.000 0.00 0.00 0.00 3.06
1559 5574 5.934625 CAGTTACAGAAGCCAAGTTACATCT 59.065 40.000 0.00 0.00 0.00 2.90
1560 5575 6.428159 CAGTTACAGAAGCCAAGTTACATCTT 59.572 38.462 0.00 0.00 0.00 2.40
1561 5576 6.651225 AGTTACAGAAGCCAAGTTACATCTTC 59.349 38.462 0.00 0.00 34.84 2.87
1562 5577 3.997021 ACAGAAGCCAAGTTACATCTTCG 59.003 43.478 0.00 0.00 38.44 3.79
1563 5578 3.003480 AGAAGCCAAGTTACATCTTCGC 58.997 45.455 0.00 0.00 38.44 4.70
1564 5579 2.770164 AGCCAAGTTACATCTTCGCT 57.230 45.000 0.00 0.00 37.14 4.93
1565 5580 2.622436 AGCCAAGTTACATCTTCGCTC 58.378 47.619 0.00 0.00 37.32 5.03
1566 5581 2.028112 AGCCAAGTTACATCTTCGCTCA 60.028 45.455 0.00 0.00 37.32 4.26
1567 5582 2.939103 GCCAAGTTACATCTTCGCTCAT 59.061 45.455 0.00 0.00 30.97 2.90
1568 5583 3.375299 GCCAAGTTACATCTTCGCTCATT 59.625 43.478 0.00 0.00 30.97 2.57
1569 5584 4.728882 GCCAAGTTACATCTTCGCTCATTG 60.729 45.833 0.00 0.00 30.97 2.82
1570 5585 4.631377 CCAAGTTACATCTTCGCTCATTGA 59.369 41.667 0.00 0.00 0.00 2.57
1571 5586 5.446473 CCAAGTTACATCTTCGCTCATTGAC 60.446 44.000 0.00 0.00 0.00 3.18
1572 5587 5.078411 AGTTACATCTTCGCTCATTGACT 57.922 39.130 0.00 0.00 0.00 3.41
1573 5588 6.208988 AGTTACATCTTCGCTCATTGACTA 57.791 37.500 0.00 0.00 0.00 2.59
1574 5589 6.810911 AGTTACATCTTCGCTCATTGACTAT 58.189 36.000 0.00 0.00 0.00 2.12
1575 5590 6.699204 AGTTACATCTTCGCTCATTGACTATG 59.301 38.462 0.00 0.00 35.45 2.23
1576 5591 5.016051 ACATCTTCGCTCATTGACTATGT 57.984 39.130 0.00 0.00 35.64 2.29
1577 5592 5.423015 ACATCTTCGCTCATTGACTATGTT 58.577 37.500 0.00 0.00 35.64 2.71
1578 5593 5.877012 ACATCTTCGCTCATTGACTATGTTT 59.123 36.000 0.00 0.00 35.64 2.83
1579 5594 6.372659 ACATCTTCGCTCATTGACTATGTTTT 59.627 34.615 0.00 0.00 35.64 2.43
1580 5595 6.169419 TCTTCGCTCATTGACTATGTTTTG 57.831 37.500 0.00 0.00 35.64 2.44
1581 5596 4.944962 TCGCTCATTGACTATGTTTTGG 57.055 40.909 0.00 0.00 35.64 3.28
1582 5597 3.689161 TCGCTCATTGACTATGTTTTGGG 59.311 43.478 0.00 0.00 35.64 4.12
1583 5598 3.689161 CGCTCATTGACTATGTTTTGGGA 59.311 43.478 0.00 0.00 35.64 4.37
1584 5599 4.155826 CGCTCATTGACTATGTTTTGGGAA 59.844 41.667 0.00 0.00 35.64 3.97
1585 5600 5.644644 GCTCATTGACTATGTTTTGGGAAG 58.355 41.667 0.00 0.00 35.64 3.46
1586 5601 5.183904 GCTCATTGACTATGTTTTGGGAAGT 59.816 40.000 0.00 0.00 35.64 3.01
1587 5602 6.294731 GCTCATTGACTATGTTTTGGGAAGTT 60.295 38.462 0.00 0.00 35.64 2.66
1588 5603 7.214467 TCATTGACTATGTTTTGGGAAGTTC 57.786 36.000 0.00 0.00 35.64 3.01
1589 5604 6.775142 TCATTGACTATGTTTTGGGAAGTTCA 59.225 34.615 5.01 0.00 35.64 3.18
1590 5605 6.633500 TTGACTATGTTTTGGGAAGTTCAG 57.367 37.500 5.01 0.00 0.00 3.02
1591 5606 5.935945 TGACTATGTTTTGGGAAGTTCAGA 58.064 37.500 5.01 0.00 0.00 3.27
1592 5607 6.542821 TGACTATGTTTTGGGAAGTTCAGAT 58.457 36.000 5.01 0.00 0.00 2.90
1593 5608 7.685481 TGACTATGTTTTGGGAAGTTCAGATA 58.315 34.615 5.01 0.00 0.00 1.98
1594 5609 7.606456 TGACTATGTTTTGGGAAGTTCAGATAC 59.394 37.037 5.01 0.00 0.00 2.24
1595 5610 6.884836 ACTATGTTTTGGGAAGTTCAGATACC 59.115 38.462 5.01 0.00 0.00 2.73
1596 5611 5.319043 TGTTTTGGGAAGTTCAGATACCT 57.681 39.130 5.01 0.00 0.00 3.08
1597 5612 5.701224 TGTTTTGGGAAGTTCAGATACCTT 58.299 37.500 5.01 0.00 0.00 3.50
1598 5613 6.843752 TGTTTTGGGAAGTTCAGATACCTTA 58.156 36.000 5.01 0.00 0.00 2.69
1599 5614 7.466804 TGTTTTGGGAAGTTCAGATACCTTAT 58.533 34.615 5.01 0.00 0.00 1.73
1600 5615 8.607713 TGTTTTGGGAAGTTCAGATACCTTATA 58.392 33.333 5.01 0.00 0.00 0.98
1601 5616 9.628500 GTTTTGGGAAGTTCAGATACCTTATAT 57.372 33.333 5.01 0.00 0.00 0.86
1603 5618 9.627123 TTTGGGAAGTTCAGATACCTTATATTG 57.373 33.333 5.01 0.00 0.00 1.90
1604 5619 8.331931 TGGGAAGTTCAGATACCTTATATTGT 57.668 34.615 5.01 0.00 0.00 2.71
1605 5620 8.778059 TGGGAAGTTCAGATACCTTATATTGTT 58.222 33.333 5.01 0.00 0.00 2.83
1606 5621 9.057089 GGGAAGTTCAGATACCTTATATTGTTG 57.943 37.037 5.01 0.00 0.00 3.33
1607 5622 9.832445 GGAAGTTCAGATACCTTATATTGTTGA 57.168 33.333 5.01 0.00 0.00 3.18
1613 5628 9.832445 TCAGATACCTTATATTGTTGACTTTCC 57.168 33.333 0.00 0.00 0.00 3.13
1614 5629 9.838339 CAGATACCTTATATTGTTGACTTTCCT 57.162 33.333 0.00 0.00 0.00 3.36
1615 5630 9.838339 AGATACCTTATATTGTTGACTTTCCTG 57.162 33.333 0.00 0.00 0.00 3.86
1616 5631 6.759497 ACCTTATATTGTTGACTTTCCTGC 57.241 37.500 0.00 0.00 0.00 4.85
1617 5632 6.485171 ACCTTATATTGTTGACTTTCCTGCT 58.515 36.000 0.00 0.00 0.00 4.24
1618 5633 6.948309 ACCTTATATTGTTGACTTTCCTGCTT 59.052 34.615 0.00 0.00 0.00 3.91
1619 5634 7.451566 ACCTTATATTGTTGACTTTCCTGCTTT 59.548 33.333 0.00 0.00 0.00 3.51
1620 5635 7.756722 CCTTATATTGTTGACTTTCCTGCTTTG 59.243 37.037 0.00 0.00 0.00 2.77
1621 5636 2.869233 TGTTGACTTTCCTGCTTTGC 57.131 45.000 0.00 0.00 0.00 3.68
1622 5637 1.408702 TGTTGACTTTCCTGCTTTGCC 59.591 47.619 0.00 0.00 0.00 4.52
1623 5638 0.667993 TTGACTTTCCTGCTTTGCCG 59.332 50.000 0.00 0.00 0.00 5.69
1624 5639 1.172180 TGACTTTCCTGCTTTGCCGG 61.172 55.000 0.00 0.00 34.20 6.13
1625 5640 1.152756 ACTTTCCTGCTTTGCCGGT 60.153 52.632 1.90 0.00 34.54 5.28
1626 5641 1.286880 CTTTCCTGCTTTGCCGGTG 59.713 57.895 1.90 0.00 34.54 4.94
1627 5642 1.454847 TTTCCTGCTTTGCCGGTGT 60.455 52.632 1.90 0.00 34.54 4.16
1628 5643 1.040339 TTTCCTGCTTTGCCGGTGTT 61.040 50.000 1.90 0.00 34.54 3.32
1629 5644 1.733402 TTCCTGCTTTGCCGGTGTTG 61.733 55.000 1.90 0.00 34.54 3.33
1630 5645 2.336088 CTGCTTTGCCGGTGTTGG 59.664 61.111 1.90 0.00 0.00 3.77
1631 5646 2.124109 TGCTTTGCCGGTGTTGGA 60.124 55.556 1.90 0.00 0.00 3.53
1632 5647 1.526575 CTGCTTTGCCGGTGTTGGAT 61.527 55.000 1.90 0.00 0.00 3.41
1633 5648 1.212751 GCTTTGCCGGTGTTGGATC 59.787 57.895 1.90 0.00 0.00 3.36
1634 5649 1.244019 GCTTTGCCGGTGTTGGATCT 61.244 55.000 1.90 0.00 0.00 2.75
1635 5650 1.247567 CTTTGCCGGTGTTGGATCTT 58.752 50.000 1.90 0.00 0.00 2.40
1636 5651 0.958091 TTTGCCGGTGTTGGATCTTG 59.042 50.000 1.90 0.00 0.00 3.02
1637 5652 0.893270 TTGCCGGTGTTGGATCTTGG 60.893 55.000 1.90 0.00 0.00 3.61
1638 5653 2.700773 GCCGGTGTTGGATCTTGGC 61.701 63.158 1.90 0.00 0.00 4.52
1805 5832 1.001974 ACGTCAGCTGAGGTATTTGCA 59.998 47.619 34.24 0.00 40.84 4.08
1806 5833 1.394917 CGTCAGCTGAGGTATTTGCAC 59.605 52.381 24.86 6.53 0.00 4.57
1841 5868 5.091261 ACAATTACTGAGCTTCCTAGTGG 57.909 43.478 0.00 0.00 0.00 4.00
1843 5870 5.105146 ACAATTACTGAGCTTCCTAGTGGAG 60.105 44.000 0.00 0.00 44.24 3.86
1903 5938 7.508636 TGAGAGGCTGATATTCACTTCTAAGAT 59.491 37.037 0.00 0.00 0.00 2.40
2007 6054 1.617536 TCTGCAGGCCTTGGAGGAT 60.618 57.895 15.13 0.00 44.66 3.24
2053 6100 2.636830 CAGTGAGATTTGCGGAGGAAT 58.363 47.619 0.00 0.00 37.93 3.01
2080 6127 0.033366 GTCGGGCAAATGCAACCTTT 59.967 50.000 7.80 0.00 44.36 3.11
2122 6175 0.100682 GATAGCCGAGCGTCTGTTCA 59.899 55.000 0.00 0.00 0.00 3.18
2136 6189 2.086869 CTGTTCAGTAACCCATGCTGG 58.913 52.381 0.00 0.00 41.62 4.85
2147 6200 0.181350 CCATGCTGGACCTACCCTTC 59.819 60.000 0.00 0.00 40.96 3.46
2168 6221 6.405278 TTCCCTCCAAGTTCTTGAAATTTC 57.595 37.500 11.41 11.41 0.00 2.17
2370 6448 4.724399 TGGATTCAAACTGCTAAAGGTGA 58.276 39.130 0.00 0.00 0.00 4.02
2485 6599 2.125912 CCGACAGCTCCGTCTTGG 60.126 66.667 3.02 0.00 40.09 3.61
2601 6715 3.715097 GAGCAGCTCCAGGCAGGT 61.715 66.667 11.84 0.00 44.79 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.621991 TCAAGAGTAGAGACTGTGTTTGC 58.378 43.478 0.00 0.00 35.45 3.68
48 57 9.868277 AATGAAGTATTTCAAGAGTAGAGACTG 57.132 33.333 4.64 0.00 45.82 3.51
55 64 7.093945 GGGGCAAAATGAAGTATTTCAAGAGTA 60.094 37.037 4.64 0.00 45.82 2.59
59 68 6.041423 AGGGGCAAAATGAAGTATTTCAAG 57.959 37.500 4.64 0.00 45.82 3.02
90 99 2.494445 GCCTTAAATGGCCGTGGC 59.506 61.111 8.20 8.20 46.82 5.01
103 112 2.755952 AAAAGGAGTCAGGTTGCCTT 57.244 45.000 0.00 0.00 42.27 4.35
132 141 9.537852 ACCATGATGCCATGTTTAGAATATATT 57.462 29.630 0.00 0.00 46.68 1.28
133 142 8.963725 CACCATGATGCCATGTTTAGAATATAT 58.036 33.333 0.00 0.00 46.68 0.86
135 144 7.005902 TCACCATGATGCCATGTTTAGAATAT 58.994 34.615 0.00 0.00 46.68 1.28
136 145 6.363882 TCACCATGATGCCATGTTTAGAATA 58.636 36.000 0.00 0.00 46.68 1.75
137 146 5.202765 TCACCATGATGCCATGTTTAGAAT 58.797 37.500 0.00 0.00 46.68 2.40
165 174 4.151335 GCTATGCGTTGAATTCTGATCGAT 59.849 41.667 7.05 0.00 0.00 3.59
172 181 2.292267 CCCTGCTATGCGTTGAATTCT 58.708 47.619 7.05 0.00 0.00 2.40
181 190 2.117156 AAAGCTGCCCTGCTATGCG 61.117 57.895 0.00 0.00 43.24 4.73
225 235 1.067060 CCCTGCTCATTCATGCACATG 59.933 52.381 4.18 4.18 40.09 3.21
226 236 1.399714 CCCTGCTCATTCATGCACAT 58.600 50.000 0.00 0.00 35.20 3.21
227 237 1.317431 GCCCTGCTCATTCATGCACA 61.317 55.000 0.00 0.00 35.20 4.57
228 238 1.436336 GCCCTGCTCATTCATGCAC 59.564 57.895 0.00 0.00 35.20 4.57
229 239 2.116533 CGCCCTGCTCATTCATGCA 61.117 57.895 0.00 0.00 37.63 3.96
544 4527 5.301551 TGCATTGTCATGGTAAGTGAAAACT 59.698 36.000 0.00 0.00 0.00 2.66
901 4897 3.686726 ACAACTTTCGAGAAGCATCATCC 59.313 43.478 7.10 0.00 0.00 3.51
1078 5093 0.320697 AGCGAAGGACCAGTACCAAC 59.679 55.000 0.00 0.00 0.00 3.77
1213 5228 9.185192 CCATTTCAGTTCTTTACACTTGATTTC 57.815 33.333 0.00 0.00 0.00 2.17
1446 5461 4.085357 AGAATTGCAGATACGGCCATTA 57.915 40.909 2.24 0.00 28.05 1.90
1452 5467 4.963276 TGGAAAAGAATTGCAGATACGG 57.037 40.909 0.00 0.00 0.00 4.02
1458 5473 7.148853 CGAATCTTTCTTGGAAAAGAATTGCAG 60.149 37.037 3.45 0.00 45.62 4.41
1476 5491 3.775202 CATGGAGAGACGACGAATCTTT 58.225 45.455 0.00 0.00 0.00 2.52
1491 5506 1.026584 TGCCAATCGATTGCATGGAG 58.973 50.000 28.90 16.77 36.48 3.86
1503 5518 3.243975 CCCCATTATGCTCTTTGCCAATC 60.244 47.826 0.00 0.00 42.00 2.67
1505 5520 2.109774 CCCCATTATGCTCTTTGCCAA 58.890 47.619 0.00 0.00 42.00 4.52
1529 5544 3.266510 TGGCTTCTGTAACTGCATAGG 57.733 47.619 0.00 0.00 0.00 2.57
1543 5558 3.391227 GCGAAGATGTAACTTGGCTTC 57.609 47.619 0.00 0.00 44.18 3.86
1546 5561 2.346803 TGAGCGAAGATGTAACTTGGC 58.653 47.619 0.00 0.00 46.54 4.52
1547 5562 4.631377 TCAATGAGCGAAGATGTAACTTGG 59.369 41.667 0.00 0.00 0.00 3.61
1548 5563 5.349817 AGTCAATGAGCGAAGATGTAACTTG 59.650 40.000 0.00 0.00 0.00 3.16
1549 5564 5.482908 AGTCAATGAGCGAAGATGTAACTT 58.517 37.500 0.00 0.00 0.00 2.66
1550 5565 5.078411 AGTCAATGAGCGAAGATGTAACT 57.922 39.130 0.00 0.00 0.00 2.24
1551 5566 6.477033 ACATAGTCAATGAGCGAAGATGTAAC 59.523 38.462 0.00 0.00 39.07 2.50
1552 5567 6.573434 ACATAGTCAATGAGCGAAGATGTAA 58.427 36.000 0.00 0.00 39.07 2.41
1553 5568 6.149129 ACATAGTCAATGAGCGAAGATGTA 57.851 37.500 0.00 0.00 39.07 2.29
1554 5569 5.016051 ACATAGTCAATGAGCGAAGATGT 57.984 39.130 0.00 0.00 39.07 3.06
1555 5570 5.980698 AACATAGTCAATGAGCGAAGATG 57.019 39.130 0.00 0.00 39.07 2.90
1556 5571 6.183360 CCAAAACATAGTCAATGAGCGAAGAT 60.183 38.462 0.00 0.00 39.07 2.40
1557 5572 5.122239 CCAAAACATAGTCAATGAGCGAAGA 59.878 40.000 0.00 0.00 39.07 2.87
1558 5573 5.327091 CCAAAACATAGTCAATGAGCGAAG 58.673 41.667 0.00 0.00 39.07 3.79
1559 5574 4.155826 CCCAAAACATAGTCAATGAGCGAA 59.844 41.667 0.00 0.00 39.07 4.70
1560 5575 3.689161 CCCAAAACATAGTCAATGAGCGA 59.311 43.478 0.00 0.00 39.07 4.93
1561 5576 3.689161 TCCCAAAACATAGTCAATGAGCG 59.311 43.478 0.00 0.00 39.07 5.03
1562 5577 5.183904 ACTTCCCAAAACATAGTCAATGAGC 59.816 40.000 0.00 0.00 39.07 4.26
1563 5578 6.824305 ACTTCCCAAAACATAGTCAATGAG 57.176 37.500 0.00 0.00 39.07 2.90
1564 5579 6.775142 TGAACTTCCCAAAACATAGTCAATGA 59.225 34.615 0.00 0.00 39.07 2.57
1565 5580 6.980593 TGAACTTCCCAAAACATAGTCAATG 58.019 36.000 0.00 0.00 41.74 2.82
1566 5581 7.004086 TCTGAACTTCCCAAAACATAGTCAAT 58.996 34.615 0.00 0.00 0.00 2.57
1567 5582 6.361433 TCTGAACTTCCCAAAACATAGTCAA 58.639 36.000 0.00 0.00 0.00 3.18
1568 5583 5.935945 TCTGAACTTCCCAAAACATAGTCA 58.064 37.500 0.00 0.00 0.00 3.41
1569 5584 7.065923 GGTATCTGAACTTCCCAAAACATAGTC 59.934 40.741 0.00 0.00 0.00 2.59
1570 5585 6.884836 GGTATCTGAACTTCCCAAAACATAGT 59.115 38.462 0.00 0.00 0.00 2.12
1571 5586 7.112779 AGGTATCTGAACTTCCCAAAACATAG 58.887 38.462 0.00 0.00 0.00 2.23
1572 5587 7.027874 AGGTATCTGAACTTCCCAAAACATA 57.972 36.000 0.00 0.00 0.00 2.29
1573 5588 5.892348 AGGTATCTGAACTTCCCAAAACAT 58.108 37.500 0.00 0.00 0.00 2.71
1574 5589 5.319043 AGGTATCTGAACTTCCCAAAACA 57.681 39.130 0.00 0.00 0.00 2.83
1575 5590 7.939784 ATAAGGTATCTGAACTTCCCAAAAC 57.060 36.000 0.00 0.00 0.00 2.43
1577 5592 9.627123 CAATATAAGGTATCTGAACTTCCCAAA 57.373 33.333 0.00 0.00 0.00 3.28
1578 5593 8.778059 ACAATATAAGGTATCTGAACTTCCCAA 58.222 33.333 0.00 0.00 0.00 4.12
1579 5594 8.331931 ACAATATAAGGTATCTGAACTTCCCA 57.668 34.615 0.00 0.00 0.00 4.37
1580 5595 9.057089 CAACAATATAAGGTATCTGAACTTCCC 57.943 37.037 0.00 0.00 0.00 3.97
1581 5596 9.832445 TCAACAATATAAGGTATCTGAACTTCC 57.168 33.333 0.00 0.00 0.00 3.46
1587 5602 9.832445 GGAAAGTCAACAATATAAGGTATCTGA 57.168 33.333 0.00 0.00 0.00 3.27
1588 5603 9.838339 AGGAAAGTCAACAATATAAGGTATCTG 57.162 33.333 0.00 0.00 0.00 2.90
1589 5604 9.838339 CAGGAAAGTCAACAATATAAGGTATCT 57.162 33.333 0.00 0.00 0.00 1.98
1590 5605 8.560374 GCAGGAAAGTCAACAATATAAGGTATC 58.440 37.037 0.00 0.00 0.00 2.24
1591 5606 8.275040 AGCAGGAAAGTCAACAATATAAGGTAT 58.725 33.333 0.00 0.00 0.00 2.73
1592 5607 7.630082 AGCAGGAAAGTCAACAATATAAGGTA 58.370 34.615 0.00 0.00 0.00 3.08
1593 5608 6.485171 AGCAGGAAAGTCAACAATATAAGGT 58.515 36.000 0.00 0.00 0.00 3.50
1594 5609 7.396540 AAGCAGGAAAGTCAACAATATAAGG 57.603 36.000 0.00 0.00 0.00 2.69
1595 5610 7.274250 GCAAAGCAGGAAAGTCAACAATATAAG 59.726 37.037 0.00 0.00 0.00 1.73
1596 5611 7.090173 GCAAAGCAGGAAAGTCAACAATATAA 58.910 34.615 0.00 0.00 0.00 0.98
1597 5612 6.350110 GGCAAAGCAGGAAAGTCAACAATATA 60.350 38.462 0.00 0.00 0.00 0.86
1598 5613 5.473039 GCAAAGCAGGAAAGTCAACAATAT 58.527 37.500 0.00 0.00 0.00 1.28
1599 5614 4.261994 GGCAAAGCAGGAAAGTCAACAATA 60.262 41.667 0.00 0.00 0.00 1.90
1600 5615 3.493176 GGCAAAGCAGGAAAGTCAACAAT 60.493 43.478 0.00 0.00 0.00 2.71
1601 5616 2.159114 GGCAAAGCAGGAAAGTCAACAA 60.159 45.455 0.00 0.00 0.00 2.83
1602 5617 1.408702 GGCAAAGCAGGAAAGTCAACA 59.591 47.619 0.00 0.00 0.00 3.33
1603 5618 1.600413 CGGCAAAGCAGGAAAGTCAAC 60.600 52.381 0.00 0.00 0.00 3.18
1604 5619 0.667993 CGGCAAAGCAGGAAAGTCAA 59.332 50.000 0.00 0.00 0.00 3.18
1605 5620 1.172180 CCGGCAAAGCAGGAAAGTCA 61.172 55.000 1.79 0.00 46.43 3.41
1606 5621 1.172812 ACCGGCAAAGCAGGAAAGTC 61.173 55.000 14.91 0.00 46.43 3.01
1607 5622 1.152756 ACCGGCAAAGCAGGAAAGT 60.153 52.632 14.91 0.00 46.43 2.66
1608 5623 1.286880 CACCGGCAAAGCAGGAAAG 59.713 57.895 14.91 1.19 46.43 2.62
1609 5624 1.040339 AACACCGGCAAAGCAGGAAA 61.040 50.000 14.91 0.00 46.43 3.13
1610 5625 1.454847 AACACCGGCAAAGCAGGAA 60.455 52.632 14.91 0.00 46.43 3.36
1611 5626 2.192861 CAACACCGGCAAAGCAGGA 61.193 57.895 14.91 0.00 46.43 3.86
1613 5628 1.526575 ATCCAACACCGGCAAAGCAG 61.527 55.000 0.00 0.00 0.00 4.24
1614 5629 1.523154 GATCCAACACCGGCAAAGCA 61.523 55.000 0.00 0.00 0.00 3.91
1615 5630 1.212751 GATCCAACACCGGCAAAGC 59.787 57.895 0.00 0.00 0.00 3.51
1616 5631 1.068333 CAAGATCCAACACCGGCAAAG 60.068 52.381 0.00 0.00 0.00 2.77
1617 5632 0.958091 CAAGATCCAACACCGGCAAA 59.042 50.000 0.00 0.00 0.00 3.68
1618 5633 0.893270 CCAAGATCCAACACCGGCAA 60.893 55.000 0.00 0.00 0.00 4.52
1619 5634 1.303236 CCAAGATCCAACACCGGCA 60.303 57.895 0.00 0.00 0.00 5.69
1620 5635 2.700773 GCCAAGATCCAACACCGGC 61.701 63.158 0.00 0.00 0.00 6.13
1621 5636 2.398554 CGCCAAGATCCAACACCGG 61.399 63.158 0.00 0.00 0.00 5.28
1622 5637 0.953471 TTCGCCAAGATCCAACACCG 60.953 55.000 0.00 0.00 0.00 4.94
1623 5638 1.068541 GTTTCGCCAAGATCCAACACC 60.069 52.381 0.00 0.00 0.00 4.16
1624 5639 1.068541 GGTTTCGCCAAGATCCAACAC 60.069 52.381 0.00 0.00 37.17 3.32
1625 5640 1.243902 GGTTTCGCCAAGATCCAACA 58.756 50.000 0.00 0.00 37.17 3.33
1626 5641 1.243902 TGGTTTCGCCAAGATCCAAC 58.756 50.000 0.00 0.00 45.94 3.77
1627 5642 3.735704 TGGTTTCGCCAAGATCCAA 57.264 47.368 0.00 0.00 45.94 3.53
1636 5651 3.485216 CGAACATGTATCTTGGTTTCGCC 60.485 47.826 0.00 0.00 37.90 5.54
1637 5652 3.670203 CGAACATGTATCTTGGTTTCGC 58.330 45.455 0.00 0.00 0.00 4.70
1638 5653 3.370978 AGCGAACATGTATCTTGGTTTCG 59.629 43.478 0.00 2.31 0.00 3.46
1805 5832 5.767665 TCAGTAATTGTACCACTGCAAATGT 59.232 36.000 8.40 0.00 39.60 2.71
1806 5833 6.252967 TCAGTAATTGTACCACTGCAAATG 57.747 37.500 8.40 0.00 39.60 2.32
1820 5847 5.105146 ACTCCACTAGGAAGCTCAGTAATTG 60.105 44.000 0.00 0.00 45.19 2.32
1841 5868 1.669115 TGCTGCAGCTTTCCGACTC 60.669 57.895 36.61 6.97 42.66 3.36
1843 5870 1.510480 AAGTGCTGCAGCTTTCCGAC 61.510 55.000 36.61 25.35 42.66 4.79
1887 5914 8.844244 GTTGATGGCAATCTTAGAAGTGAATAT 58.156 33.333 2.00 0.00 36.22 1.28
2007 6054 6.427150 GTCGTCAGTTTTCTTGAAGCATAAA 58.573 36.000 0.00 0.00 0.00 1.40
2053 6100 2.822561 TGCATTTGCCCGACTCATTTAA 59.177 40.909 0.00 0.00 41.18 1.52
2080 6127 3.104512 CTCCACCAGTACCAAGATACCA 58.895 50.000 0.00 0.00 0.00 3.25
2136 6189 1.205055 CTTGGAGGGAAGGGTAGGTC 58.795 60.000 0.00 0.00 0.00 3.85
2147 6200 4.798574 CGAAATTTCAAGAACTTGGAGGG 58.201 43.478 17.99 0.00 40.78 4.30
2168 6221 2.892852 ACCATTTCCATTCCATATGGCG 59.107 45.455 17.58 7.69 39.46 5.69
2370 6448 6.341316 AGACTGACGTATATTTGAACTGCAT 58.659 36.000 0.00 0.00 0.00 3.96
2576 6690 1.405256 CCTGGAGCTGCTCTGTAACAG 60.405 57.143 27.09 22.80 36.96 3.16
2601 6715 1.073923 GGAAGACTCCAAAGCCTCCAA 59.926 52.381 0.00 0.00 41.96 3.53


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

AutoCloner maintained by Alex Coulton.