Multiple sequence alignment - TraesCS2B01G110000

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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 TraesCS2B01G110000 chr2B 100.000 2473 0 0 1 2473 71316992 71314520 0.000000e+00 4567.0
1 TraesCS2B01G110000 chr2B 84.189 740 76 10 771 1497 71367796 71367085 0.000000e+00 680.0
2 TraesCS2B01G110000 chr2B 87.629 388 38 3 1900 2278 71339133 71338747 2.260000e-120 442.0
3 TraesCS2B01G110000 chr2B 91.667 168 8 2 1 166 71371008 71370845 6.880000e-56 228.0
4 TraesCS2B01G110000 chr2B 87.568 185 19 2 1502 1686 741890408 741890228 6.930000e-51 211.0
5 TraesCS2B01G110000 chr2B 87.778 180 19 3 1511 1689 758149919 758150096 8.960000e-50 207.0
6 TraesCS2B01G110000 chr2B 86.813 182 20 2 1509 1690 741890222 741890045 1.500000e-47 200.0
7 TraesCS2B01G110000 chr2B 83.092 207 16 5 1687 1893 71348523 71348336 1.180000e-38 171.0
8 TraesCS2B01G110000 chr2B 100.000 30 0 0 482 511 768367809 768367780 3.440000e-04 56.5
9 TraesCS2B01G110000 chr2A 93.033 1507 80 12 1 1501 48406838 48405351 0.000000e+00 2178.0
10 TraesCS2B01G110000 chr2A 85.155 741 78 14 771 1497 48456965 48456243 0.000000e+00 730.0
11 TraesCS2B01G110000 chr2A 90.582 361 23 3 2124 2473 48402674 48402314 3.720000e-128 468.0
12 TraesCS2B01G110000 chr2A 89.846 325 17 8 1810 2129 48403123 48402810 1.070000e-108 403.0
13 TraesCS2B01G110000 chr2A 94.792 96 4 1 680 774 48457292 48457197 5.510000e-32 148.0
14 TraesCS2B01G110000 chr2D 86.059 746 73 11 771 1502 44600292 44599564 0.000000e+00 773.0
15 TraesCS2B01G110000 chr2D 87.457 582 53 9 1901 2473 44521325 44520755 0.000000e+00 652.0
16 TraesCS2B01G110000 chr2D 87.113 582 54 10 1901 2473 44530826 44530257 7.460000e-180 640.0
17 TraesCS2B01G110000 chr2D 90.870 471 24 8 2018 2473 44489196 44488730 4.520000e-172 614.0
18 TraesCS2B01G110000 chr2D 85.603 257 13 12 522 774 44600761 44600525 5.280000e-62 248.0
19 TraesCS2B01G110000 chr2D 96.262 107 4 0 1 107 44517497 44517391 2.530000e-40 176.0
20 TraesCS2B01G110000 chr2D 87.333 150 11 4 167 308 110844341 110844192 5.470000e-37 165.0
21 TraesCS2B01G110000 chr2D 100.000 29 0 0 490 518 126986086 126986058 1.000000e-03 54.7
22 TraesCS2B01G110000 chrUn 87.457 582 53 9 1901 2473 370354666 370354096 0.000000e+00 652.0
23 TraesCS2B01G110000 chrUn 86.747 332 27 10 2150 2473 399660940 399660618 1.090000e-93 353.0
24 TraesCS2B01G110000 chrUn 96.262 107 4 0 1 107 320620590 320620484 2.530000e-40 176.0
25 TraesCS2B01G110000 chrUn 96.262 107 4 0 1 107 378270131 378270237 2.530000e-40 176.0
26 TraesCS2B01G110000 chrUn 96.262 107 4 0 1 107 447954783 447954677 2.530000e-40 176.0
27 TraesCS2B01G110000 chrUn 95.327 107 5 0 1 107 374250973 374250867 1.180000e-38 171.0
28 TraesCS2B01G110000 chr1B 85.062 482 48 10 1995 2460 179581685 179581212 1.040000e-128 470.0
29 TraesCS2B01G110000 chr7A 87.368 190 18 3 1501 1689 120999031 120998847 1.930000e-51 213.0
30 TraesCS2B01G110000 chr7A 88.732 142 13 3 168 308 676361434 676361573 1.180000e-38 171.0
31 TraesCS2B01G110000 chr1D 87.027 185 19 4 1502 1686 373113726 373113905 1.160000e-48 204.0
32 TraesCS2B01G110000 chr1D 86.014 143 19 1 167 308 121770690 121770832 4.260000e-33 152.0
33 TraesCS2B01G110000 chr1D 94.737 38 2 0 482 519 400119908 400119945 2.660000e-05 60.2
34 TraesCS2B01G110000 chr5B 87.931 174 18 2 1509 1682 49563578 49563748 4.170000e-48 202.0
35 TraesCS2B01G110000 chr5B 86.413 184 18 4 1509 1691 35248201 35248024 6.980000e-46 195.0
36 TraesCS2B01G110000 chr5B 85.106 141 17 3 169 308 375380148 375380011 9.220000e-30 141.0
37 TraesCS2B01G110000 chr4A 86.631 187 18 5 1501 1687 648145404 648145583 1.500000e-47 200.0
38 TraesCS2B01G110000 chr4A 87.333 150 13 6 165 308 319821324 319821473 1.520000e-37 167.0
39 TraesCS2B01G110000 chr4D 87.079 178 20 3 1509 1686 30512962 30513136 5.390000e-47 198.0
40 TraesCS2B01G110000 chr7D 88.966 145 10 6 167 308 117242056 117242197 9.090000e-40 174.0
41 TraesCS2B01G110000 chr3B 87.586 145 16 2 164 307 446747920 446748063 1.520000e-37 167.0
42 TraesCS2B01G110000 chr6D 85.811 148 15 4 167 308 388209746 388209893 4.260000e-33 152.0
43 TraesCS2B01G110000 chr6D 97.297 37 1 0 482 518 97587452 97587416 2.050000e-06 63.9


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 TraesCS2B01G110000 chr2B 71314520 71316992 2472 True 4567.000000 4567 100.000000 1 2473 1 chr2B.!!$R1 2472
1 TraesCS2B01G110000 chr2B 71367085 71371008 3923 True 454.000000 680 87.928000 1 1497 2 chr2B.!!$R5 1496
2 TraesCS2B01G110000 chr2A 48402314 48406838 4524 True 1016.333333 2178 91.153667 1 2473 3 chr2A.!!$R1 2472
3 TraesCS2B01G110000 chr2A 48456243 48457292 1049 True 439.000000 730 89.973500 680 1497 2 chr2A.!!$R2 817
4 TraesCS2B01G110000 chr2D 44530257 44530826 569 True 640.000000 640 87.113000 1901 2473 1 chr2D.!!$R2 572
5 TraesCS2B01G110000 chr2D 44599564 44600761 1197 True 510.500000 773 85.831000 522 1502 2 chr2D.!!$R6 980
6 TraesCS2B01G110000 chr2D 44517391 44521325 3934 True 414.000000 652 91.859500 1 2473 2 chr2D.!!$R5 2472
7 TraesCS2B01G110000 chrUn 370354096 370354666 570 True 652.000000 652 87.457000 1901 2473 1 chrUn.!!$R2 572

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
622 2595 0.293433 GAAAAACGTGTGTGCGCAAC 59.707 50.0 14.0 13.7 34.88 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 4363 0.179145 CGTGGGTCGCTTTCTCGTAT 60.179 55.0 0.0 0.0 0.0 3.06 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
83 86 4.083003 GGCACATCCAAATACGAGAAACAA 60.083 41.667 0.00 0.00 34.01 2.83
178 181 9.562226 AGATATAAATATTAGGTGTGGCTAGGT 57.438 33.333 0.00 0.00 0.00 3.08
234 237 5.997129 TCAAGTGACATAACATGCAAGAGAA 59.003 36.000 0.00 0.00 0.00 2.87
280 283 9.598517 TTTTGGCATGGATCTTAATGTAAAATC 57.401 29.630 0.00 0.00 0.00 2.17
378 386 6.014840 TCCAAACCTAAGAGACACGAAATAGT 60.015 38.462 0.00 0.00 0.00 2.12
476 486 8.947115 GCTCACACTATAGGAAAAACATACTTT 58.053 33.333 4.43 0.00 0.00 2.66
485 495 5.238650 AGGAAAAACATACTTTCTGTGTCCG 59.761 40.000 0.00 0.00 33.99 4.79
612 2585 7.416022 ACGTAGAGATATCCTAGAAAAACGTG 58.584 38.462 12.62 0.00 0.00 4.49
622 2595 0.293433 GAAAAACGTGTGTGCGCAAC 59.707 50.000 14.00 13.70 34.88 4.17
662 2635 7.356089 TGTTGGGTATTAGTACTAGATGTGG 57.644 40.000 2.23 0.00 0.00 4.17
744 2718 8.355169 CCACATTTAAGGATGGAGATTGTTATG 58.645 37.037 0.00 0.00 33.80 1.90
937 3585 5.357596 ACGATAGGGCTAGCTAGCTTTATAC 59.642 44.000 37.42 23.07 44.29 1.47
1084 3759 1.202568 TGATCATCACGGTGGCTGATC 60.203 52.381 28.52 28.52 42.70 2.92
1355 4032 3.618997 GCTTCTTCCCCTTCATAACGACA 60.619 47.826 0.00 0.00 0.00 4.35
1382 4059 0.533755 GCACCAAGCACTGTCTCAGT 60.534 55.000 0.00 0.00 46.51 3.41
1440 4117 2.481276 GGTGACAAACAAACTCAAGCCC 60.481 50.000 0.00 0.00 0.00 5.19
1447 4124 6.468543 ACAAACAAACTCAAGCCCTTTTTAA 58.531 32.000 0.00 0.00 0.00 1.52
1504 4181 2.969821 TGGCACAATACAAGAAGGGT 57.030 45.000 0.00 0.00 31.92 4.34
1505 4182 3.237268 TGGCACAATACAAGAAGGGTT 57.763 42.857 0.00 0.00 31.92 4.11
1506 4183 3.571590 TGGCACAATACAAGAAGGGTTT 58.428 40.909 0.00 0.00 31.92 3.27
1507 4184 4.730966 TGGCACAATACAAGAAGGGTTTA 58.269 39.130 0.00 0.00 31.92 2.01
1508 4185 5.329399 TGGCACAATACAAGAAGGGTTTAT 58.671 37.500 0.00 0.00 31.92 1.40
1509 4186 5.417580 TGGCACAATACAAGAAGGGTTTATC 59.582 40.000 0.00 0.00 31.92 1.75
1510 4187 5.652452 GGCACAATACAAGAAGGGTTTATCT 59.348 40.000 0.00 0.00 0.00 1.98
1511 4188 6.826741 GGCACAATACAAGAAGGGTTTATCTA 59.173 38.462 0.00 0.00 0.00 1.98
1512 4189 7.012421 GGCACAATACAAGAAGGGTTTATCTAG 59.988 40.741 0.00 0.00 0.00 2.43
1513 4190 7.012421 GCACAATACAAGAAGGGTTTATCTAGG 59.988 40.741 0.00 0.00 0.00 3.02
1514 4191 7.499232 CACAATACAAGAAGGGTTTATCTAGGG 59.501 40.741 0.00 0.00 0.00 3.53
1515 4192 4.505324 ACAAGAAGGGTTTATCTAGGGC 57.495 45.455 0.00 0.00 0.00 5.19
1516 4193 3.850173 ACAAGAAGGGTTTATCTAGGGCA 59.150 43.478 0.00 0.00 0.00 5.36
1517 4194 4.200092 CAAGAAGGGTTTATCTAGGGCAC 58.800 47.826 0.00 0.00 0.00 5.01
1518 4195 3.460825 AGAAGGGTTTATCTAGGGCACA 58.539 45.455 0.00 0.00 0.00 4.57
1519 4196 4.047883 AGAAGGGTTTATCTAGGGCACAT 58.952 43.478 0.00 0.00 0.00 3.21
1520 4197 4.103311 AGAAGGGTTTATCTAGGGCACATC 59.897 45.833 0.00 0.00 0.00 3.06
1521 4198 3.669949 AGGGTTTATCTAGGGCACATCT 58.330 45.455 0.00 0.00 0.00 2.90
1522 4199 4.827789 AGGGTTTATCTAGGGCACATCTA 58.172 43.478 0.00 0.00 0.00 1.98
1523 4200 4.841246 AGGGTTTATCTAGGGCACATCTAG 59.159 45.833 0.00 0.00 36.46 2.43
1524 4201 4.838986 GGGTTTATCTAGGGCACATCTAGA 59.161 45.833 0.00 0.00 44.78 2.43
1559 4236 4.913335 TGTCATATCTAACCTGACGTCC 57.087 45.455 14.12 0.00 41.69 4.79
1560 4237 4.274978 TGTCATATCTAACCTGACGTCCA 58.725 43.478 14.12 0.01 41.69 4.02
1561 4238 4.097437 TGTCATATCTAACCTGACGTCCAC 59.903 45.833 14.12 0.00 41.69 4.02
1562 4239 4.338682 GTCATATCTAACCTGACGTCCACT 59.661 45.833 14.12 0.00 30.97 4.00
1563 4240 5.530171 GTCATATCTAACCTGACGTCCACTA 59.470 44.000 14.12 0.00 30.97 2.74
1564 4241 6.207025 GTCATATCTAACCTGACGTCCACTAT 59.793 42.308 14.12 0.00 30.97 2.12
1565 4242 4.920640 ATCTAACCTGACGTCCACTATG 57.079 45.455 14.12 0.00 0.00 2.23
1566 4243 3.693807 TCTAACCTGACGTCCACTATGT 58.306 45.455 14.12 0.00 0.00 2.29
1567 4244 4.084287 TCTAACCTGACGTCCACTATGTT 58.916 43.478 14.12 9.40 0.00 2.71
1568 4245 3.764237 AACCTGACGTCCACTATGTTT 57.236 42.857 14.12 0.00 0.00 2.83
1569 4246 3.040147 ACCTGACGTCCACTATGTTTG 57.960 47.619 14.12 0.00 0.00 2.93
1570 4247 2.367567 ACCTGACGTCCACTATGTTTGT 59.632 45.455 14.12 0.00 0.00 2.83
1571 4248 2.736721 CCTGACGTCCACTATGTTTGTG 59.263 50.000 14.12 0.00 35.39 3.33
1622 4299 4.653806 TTTTTGGTTTCTTGTTGTTGCG 57.346 36.364 0.00 0.00 0.00 4.85
1623 4300 3.305398 TTTGGTTTCTTGTTGTTGCGT 57.695 38.095 0.00 0.00 0.00 5.24
1624 4301 3.305398 TTGGTTTCTTGTTGTTGCGTT 57.695 38.095 0.00 0.00 0.00 4.84
1625 4302 4.436242 TTGGTTTCTTGTTGTTGCGTTA 57.564 36.364 0.00 0.00 0.00 3.18
1626 4303 4.640789 TGGTTTCTTGTTGTTGCGTTAT 57.359 36.364 0.00 0.00 0.00 1.89
1627 4304 5.000012 TGGTTTCTTGTTGTTGCGTTATT 58.000 34.783 0.00 0.00 0.00 1.40
1628 4305 5.411781 TGGTTTCTTGTTGTTGCGTTATTT 58.588 33.333 0.00 0.00 0.00 1.40
1629 4306 6.561614 TGGTTTCTTGTTGTTGCGTTATTTA 58.438 32.000 0.00 0.00 0.00 1.40
1630 4307 7.203910 TGGTTTCTTGTTGTTGCGTTATTTAT 58.796 30.769 0.00 0.00 0.00 1.40
1631 4308 7.168302 TGGTTTCTTGTTGTTGCGTTATTTATG 59.832 33.333 0.00 0.00 0.00 1.90
1632 4309 7.358848 GGTTTCTTGTTGTTGCGTTATTTATGG 60.359 37.037 0.00 0.00 0.00 2.74
1633 4310 5.704888 TCTTGTTGTTGCGTTATTTATGGG 58.295 37.500 0.00 0.00 0.00 4.00
1634 4311 5.473846 TCTTGTTGTTGCGTTATTTATGGGA 59.526 36.000 0.00 0.00 0.00 4.37
1635 4312 5.303747 TGTTGTTGCGTTATTTATGGGAG 57.696 39.130 0.00 0.00 0.00 4.30
1636 4313 4.762765 TGTTGTTGCGTTATTTATGGGAGT 59.237 37.500 0.00 0.00 0.00 3.85
1637 4314 5.241949 TGTTGTTGCGTTATTTATGGGAGTT 59.758 36.000 0.00 0.00 0.00 3.01
1638 4315 5.968528 TGTTGCGTTATTTATGGGAGTTT 57.031 34.783 0.00 0.00 0.00 2.66
1639 4316 7.040617 TGTTGTTGCGTTATTTATGGGAGTTTA 60.041 33.333 0.00 0.00 0.00 2.01
1640 4317 7.079182 TGTTGCGTTATTTATGGGAGTTTAG 57.921 36.000 0.00 0.00 0.00 1.85
1641 4318 6.879993 TGTTGCGTTATTTATGGGAGTTTAGA 59.120 34.615 0.00 0.00 0.00 2.10
1642 4319 7.554835 TGTTGCGTTATTTATGGGAGTTTAGAT 59.445 33.333 0.00 0.00 0.00 1.98
1643 4320 7.490962 TGCGTTATTTATGGGAGTTTAGATG 57.509 36.000 0.00 0.00 0.00 2.90
1644 4321 7.051623 TGCGTTATTTATGGGAGTTTAGATGT 58.948 34.615 0.00 0.00 0.00 3.06
1645 4322 7.011950 TGCGTTATTTATGGGAGTTTAGATGTG 59.988 37.037 0.00 0.00 0.00 3.21
1646 4323 7.225931 GCGTTATTTATGGGAGTTTAGATGTGA 59.774 37.037 0.00 0.00 0.00 3.58
1647 4324 8.548721 CGTTATTTATGGGAGTTTAGATGTGAC 58.451 37.037 0.00 0.00 0.00 3.67
1648 4325 9.391006 GTTATTTATGGGAGTTTAGATGTGACA 57.609 33.333 0.00 0.00 0.00 3.58
1650 4327 7.864108 TTTATGGGAGTTTAGATGTGACATG 57.136 36.000 1.23 0.00 0.00 3.21
1651 4328 3.609853 TGGGAGTTTAGATGTGACATGC 58.390 45.455 1.23 0.00 0.00 4.06
1652 4329 3.264193 TGGGAGTTTAGATGTGACATGCT 59.736 43.478 1.23 2.84 0.00 3.79
1653 4330 4.263462 TGGGAGTTTAGATGTGACATGCTT 60.263 41.667 1.23 0.00 0.00 3.91
1654 4331 5.045942 TGGGAGTTTAGATGTGACATGCTTA 60.046 40.000 1.23 0.00 0.00 3.09
1655 4332 5.880332 GGGAGTTTAGATGTGACATGCTTAA 59.120 40.000 1.23 0.00 0.00 1.85
1656 4333 6.374333 GGGAGTTTAGATGTGACATGCTTAAA 59.626 38.462 1.23 2.91 0.00 1.52
1657 4334 7.094377 GGGAGTTTAGATGTGACATGCTTAAAA 60.094 37.037 1.23 0.00 0.00 1.52
1658 4335 8.296713 GGAGTTTAGATGTGACATGCTTAAAAA 58.703 33.333 1.23 0.00 0.00 1.94
1691 4368 8.771920 AATGTGAATTAGACAAACTGATACGA 57.228 30.769 0.00 0.00 0.00 3.43
1692 4369 7.812309 TGTGAATTAGACAAACTGATACGAG 57.188 36.000 0.00 0.00 0.00 4.18
1693 4370 7.599171 TGTGAATTAGACAAACTGATACGAGA 58.401 34.615 0.00 0.00 0.00 4.04
1694 4371 8.085909 TGTGAATTAGACAAACTGATACGAGAA 58.914 33.333 0.00 0.00 0.00 2.87
1734 4411 1.474498 CGGTTGACCTTGCCCCTATAC 60.474 57.143 0.00 0.00 0.00 1.47
1735 4412 1.562475 GGTTGACCTTGCCCCTATACA 59.438 52.381 0.00 0.00 0.00 2.29
1737 4414 3.393278 GGTTGACCTTGCCCCTATACATA 59.607 47.826 0.00 0.00 0.00 2.29
1738 4415 4.042934 GGTTGACCTTGCCCCTATACATAT 59.957 45.833 0.00 0.00 0.00 1.78
1739 4416 5.249852 GGTTGACCTTGCCCCTATACATATA 59.750 44.000 0.00 0.00 0.00 0.86
1740 4417 6.069615 GGTTGACCTTGCCCCTATACATATAT 60.070 42.308 0.00 0.00 0.00 0.86
1741 4418 6.560003 TGACCTTGCCCCTATACATATATG 57.440 41.667 11.29 11.29 0.00 1.78
1742 4419 5.428457 TGACCTTGCCCCTATACATATATGG 59.572 44.000 16.96 0.00 0.00 2.74
1743 4420 4.166144 ACCTTGCCCCTATACATATATGGC 59.834 45.833 16.96 9.05 36.91 4.40
1744 4421 4.446311 CCTTGCCCCTATACATATATGGCC 60.446 50.000 16.96 0.00 36.18 5.36
1745 4422 3.741955 TGCCCCTATACATATATGGCCA 58.258 45.455 8.56 8.56 36.18 5.36
1746 4423 4.315115 TGCCCCTATACATATATGGCCAT 58.685 43.478 24.45 24.45 36.18 4.40
1747 4424 4.104579 TGCCCCTATACATATATGGCCATG 59.895 45.833 29.04 15.73 36.18 3.66
1784 4461 1.208535 TCCATGTTAAGTGGCCTACCG 59.791 52.381 3.32 0.00 39.70 4.02
1788 4465 1.338389 TGTTAAGTGGCCTACCGAAGC 60.338 52.381 3.32 0.00 39.70 3.86
1796 4473 1.080093 CCTACCGAAGCGCAGTCAA 60.080 57.895 11.47 0.00 0.00 3.18
1847 6645 5.560724 TGAGAGGTAGATTTTTCACCAAGG 58.439 41.667 0.00 0.00 34.62 3.61
1856 6654 5.424252 AGATTTTTCACCAAGGATGCATCAT 59.576 36.000 27.25 18.99 0.00 2.45
1860 6658 3.483421 TCACCAAGGATGCATCATCATC 58.517 45.455 27.25 10.19 42.13 2.92
1861 6659 3.117813 TCACCAAGGATGCATCATCATCA 60.118 43.478 27.25 2.73 43.44 3.07
1862 6660 3.826729 CACCAAGGATGCATCATCATCAT 59.173 43.478 27.25 2.66 43.44 2.45
1990 6788 3.490439 TGGAGTGCACTTTGATCTGAA 57.510 42.857 22.65 0.00 0.00 3.02
1993 6791 2.485814 GAGTGCACTTTGATCTGAACCC 59.514 50.000 22.65 0.00 0.00 4.11
2009 6807 3.803082 CCGTGATTGCAGGTGCGG 61.803 66.667 7.29 7.29 45.83 5.69
2010 6808 4.465512 CGTGATTGCAGGTGCGGC 62.466 66.667 0.00 0.00 45.83 6.53
2051 6849 5.942236 GGCAAGGCATATGAGATTTCAGATA 59.058 40.000 6.97 0.00 33.65 1.98
2053 6851 6.128063 GCAAGGCATATGAGATTTCAGATACC 60.128 42.308 6.97 2.53 38.30 2.73
2065 6868 2.190578 GATACCTGCCTTGCCGCT 59.809 61.111 0.00 0.00 0.00 5.52
2099 6903 0.173708 CTCCCCGGAGAAAAGAGACG 59.826 60.000 0.73 0.00 44.53 4.18
2130 7075 6.657836 TTTACATCGCTTTAACTTAGGCTC 57.342 37.500 0.00 0.00 0.00 4.70
2145 7091 2.094724 CTCGCGCACGCTTTTCTC 59.905 61.111 13.70 0.00 39.84 2.87
2146 7092 2.657757 CTCGCGCACGCTTTTCTCA 61.658 57.895 13.70 0.00 39.84 3.27
2148 7094 2.497628 GCGCACGCTTTTCTCACG 60.498 61.111 7.96 0.00 38.26 4.35
2223 7177 1.694133 ATGCCAGGCTCTAGCTGGTC 61.694 60.000 14.15 8.66 39.71 4.02
2243 7197 3.709633 TGCACGGCCAGATCAGCT 61.710 61.111 2.24 0.00 0.00 4.24
2278 7232 3.055458 TCAGGTCCGATGCTTCATGTTTA 60.055 43.478 0.08 0.00 0.00 2.01
2301 7255 4.787551 TGTTTGGGTTTCAGAGAGCTTAA 58.212 39.130 0.00 0.00 0.00 1.85
2374 7328 5.120674 GCATCTTGTTTGAAAATTACAGCCC 59.879 40.000 0.00 0.00 0.00 5.19
2389 7343 0.960364 AGCCCGAGAAACGTACGGTA 60.960 55.000 21.06 0.00 44.34 4.02
2421 7375 2.731976 CGTCTGGCTTGAAAGTAGACAC 59.268 50.000 19.86 5.22 39.81 3.67
2429 7383 6.014584 TGGCTTGAAAGTAGACACTGATCTTA 60.015 38.462 0.00 0.00 34.36 2.10
2430 7384 7.044798 GGCTTGAAAGTAGACACTGATCTTAT 58.955 38.462 0.00 0.00 34.36 1.73
2431 7385 7.550906 GGCTTGAAAGTAGACACTGATCTTATT 59.449 37.037 0.00 0.00 34.36 1.40
2432 7386 8.386606 GCTTGAAAGTAGACACTGATCTTATTG 58.613 37.037 0.00 0.00 34.36 1.90
2433 7387 9.645059 CTTGAAAGTAGACACTGATCTTATTGA 57.355 33.333 0.00 0.00 34.36 2.57
2434 7388 9.996554 TTGAAAGTAGACACTGATCTTATTGAA 57.003 29.630 0.00 0.00 34.36 2.69
2435 7389 9.996554 TGAAAGTAGACACTGATCTTATTGAAA 57.003 29.630 0.00 0.00 34.36 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 170 0.171455 CGACTGAGACCTAGCCACAC 59.829 60.000 0.00 0.00 0.00 3.82
209 212 5.409520 TCTCTTGCATGTTATGTCACTTGAC 59.590 40.000 2.19 2.19 44.97 3.18
211 214 5.868043 TCTCTTGCATGTTATGTCACTTG 57.132 39.130 0.00 0.00 0.00 3.16
292 295 6.268825 TCAGTTGCTAAGTCTTAGTCGATT 57.731 37.500 18.72 7.25 35.66 3.34
295 299 8.635877 ATTTATCAGTTGCTAAGTCTTAGTCG 57.364 34.615 18.72 5.79 35.66 4.18
342 350 9.026121 GTCTCTTAGGTTTGGATGCTATATCTA 57.974 37.037 0.00 0.00 0.00 1.98
358 366 7.176340 ACAACTACTATTTCGTGTCTCTTAGGT 59.824 37.037 0.00 0.00 0.00 3.08
612 2585 0.867746 TCAGAAGATGTTGCGCACAC 59.132 50.000 11.12 12.73 38.61 3.82
657 2630 1.401761 TTGTCAAAGCACAGCCACAT 58.598 45.000 0.00 0.00 0.00 3.21
658 2631 1.134753 CTTTGTCAAAGCACAGCCACA 59.865 47.619 12.26 0.00 0.00 4.17
659 2632 1.134946 ACTTTGTCAAAGCACAGCCAC 59.865 47.619 22.58 0.00 42.27 5.01
661 2634 2.159254 TCAACTTTGTCAAAGCACAGCC 60.159 45.455 22.58 0.00 42.27 4.85
662 2635 3.149436 TCAACTTTGTCAAAGCACAGC 57.851 42.857 22.58 0.00 42.27 4.40
744 2718 3.498777 GTCTAGGTCTTCAAAGGTGCAAC 59.501 47.826 0.00 0.00 0.00 4.17
805 3453 9.393249 ACAATTAGTTGTCATAAATCAACGTTG 57.607 29.630 22.35 22.35 45.14 4.10
937 3585 5.366186 CCTCCTCATATTCCCTATCCAGATG 59.634 48.000 0.00 0.00 0.00 2.90
956 3604 0.193574 TCTGTTTGGGGTCTCCTCCT 59.806 55.000 0.00 0.00 36.20 3.69
1084 3759 4.473520 AGGGATGTCCTTGGCGCG 62.474 66.667 0.00 0.00 45.47 6.86
1279 3956 2.774799 GGCTTATTGCAGGTGCCGG 61.775 63.158 0.00 0.00 45.15 6.13
1412 4089 3.161866 AGTTTGTTTGTCACCCTTGTGT 58.838 40.909 0.00 0.00 43.26 3.72
1440 4117 8.925700 GGTCATAAAGCCACATTCTTTAAAAAG 58.074 33.333 0.00 0.00 38.86 2.27
1447 4124 6.211184 TCAATTGGTCATAAAGCCACATTCTT 59.789 34.615 5.42 0.00 34.02 2.52
1501 4178 4.838986 TCTAGATGTGCCCTAGATAAACCC 59.161 45.833 0.00 0.00 38.08 4.11
1502 4179 6.402222 CATCTAGATGTGCCCTAGATAAACC 58.598 44.000 22.42 0.00 46.55 3.27
1533 4210 8.088981 GGACGTCAGGTTAGATATGACATAATT 58.911 37.037 18.91 0.00 42.76 1.40
1534 4211 7.232737 TGGACGTCAGGTTAGATATGACATAAT 59.767 37.037 18.91 0.00 42.76 1.28
1535 4212 6.548251 TGGACGTCAGGTTAGATATGACATAA 59.452 38.462 18.91 0.00 42.76 1.90
1536 4213 6.016527 GTGGACGTCAGGTTAGATATGACATA 60.017 42.308 18.91 0.00 42.76 2.29
1537 4214 4.893524 TGGACGTCAGGTTAGATATGACAT 59.106 41.667 18.91 0.00 42.76 3.06
1538 4215 4.097437 GTGGACGTCAGGTTAGATATGACA 59.903 45.833 18.91 0.00 42.76 3.58
1539 4216 4.338682 AGTGGACGTCAGGTTAGATATGAC 59.661 45.833 18.91 0.00 39.93 3.06
1540 4217 4.533815 AGTGGACGTCAGGTTAGATATGA 58.466 43.478 18.91 0.00 0.00 2.15
1541 4218 4.920640 AGTGGACGTCAGGTTAGATATG 57.079 45.455 18.91 0.00 0.00 1.78
1542 4219 6.069331 ACATAGTGGACGTCAGGTTAGATAT 58.931 40.000 18.91 1.26 0.00 1.63
1543 4220 5.443283 ACATAGTGGACGTCAGGTTAGATA 58.557 41.667 18.91 0.00 0.00 1.98
1544 4221 4.279145 ACATAGTGGACGTCAGGTTAGAT 58.721 43.478 18.91 0.00 0.00 1.98
1545 4222 3.693807 ACATAGTGGACGTCAGGTTAGA 58.306 45.455 18.91 0.00 0.00 2.10
1546 4223 4.451629 AACATAGTGGACGTCAGGTTAG 57.548 45.455 18.91 5.34 0.00 2.34
1547 4224 4.039488 ACAAACATAGTGGACGTCAGGTTA 59.961 41.667 18.91 4.43 0.00 2.85
1548 4225 3.181458 ACAAACATAGTGGACGTCAGGTT 60.181 43.478 18.91 7.85 0.00 3.50
1549 4226 2.367567 ACAAACATAGTGGACGTCAGGT 59.632 45.455 18.91 0.98 0.00 4.00
1550 4227 2.736721 CACAAACATAGTGGACGTCAGG 59.263 50.000 18.91 0.25 33.43 3.86
1601 4278 4.058817 ACGCAACAACAAGAAACCAAAAA 58.941 34.783 0.00 0.00 0.00 1.94
1602 4279 3.654414 ACGCAACAACAAGAAACCAAAA 58.346 36.364 0.00 0.00 0.00 2.44
1603 4280 3.305398 ACGCAACAACAAGAAACCAAA 57.695 38.095 0.00 0.00 0.00 3.28
1604 4281 3.305398 AACGCAACAACAAGAAACCAA 57.695 38.095 0.00 0.00 0.00 3.67
1605 4282 4.640789 ATAACGCAACAACAAGAAACCA 57.359 36.364 0.00 0.00 0.00 3.67
1606 4283 5.959652 AAATAACGCAACAACAAGAAACC 57.040 34.783 0.00 0.00 0.00 3.27
1607 4284 7.358848 CCCATAAATAACGCAACAACAAGAAAC 60.359 37.037 0.00 0.00 0.00 2.78
1608 4285 6.642950 CCCATAAATAACGCAACAACAAGAAA 59.357 34.615 0.00 0.00 0.00 2.52
1609 4286 6.016192 TCCCATAAATAACGCAACAACAAGAA 60.016 34.615 0.00 0.00 0.00 2.52
1610 4287 5.473846 TCCCATAAATAACGCAACAACAAGA 59.526 36.000 0.00 0.00 0.00 3.02
1611 4288 5.704888 TCCCATAAATAACGCAACAACAAG 58.295 37.500 0.00 0.00 0.00 3.16
1612 4289 5.241949 ACTCCCATAAATAACGCAACAACAA 59.758 36.000 0.00 0.00 0.00 2.83
1613 4290 4.762765 ACTCCCATAAATAACGCAACAACA 59.237 37.500 0.00 0.00 0.00 3.33
1614 4291 5.305139 ACTCCCATAAATAACGCAACAAC 57.695 39.130 0.00 0.00 0.00 3.32
1615 4292 5.968528 AACTCCCATAAATAACGCAACAA 57.031 34.783 0.00 0.00 0.00 2.83
1616 4293 5.968528 AAACTCCCATAAATAACGCAACA 57.031 34.783 0.00 0.00 0.00 3.33
1617 4294 7.311364 TCTAAACTCCCATAAATAACGCAAC 57.689 36.000 0.00 0.00 0.00 4.17
1618 4295 7.554835 ACATCTAAACTCCCATAAATAACGCAA 59.445 33.333 0.00 0.00 0.00 4.85
1619 4296 7.011950 CACATCTAAACTCCCATAAATAACGCA 59.988 37.037 0.00 0.00 0.00 5.24
1620 4297 7.225931 TCACATCTAAACTCCCATAAATAACGC 59.774 37.037 0.00 0.00 0.00 4.84
1621 4298 8.548721 GTCACATCTAAACTCCCATAAATAACG 58.451 37.037 0.00 0.00 0.00 3.18
1622 4299 9.391006 TGTCACATCTAAACTCCCATAAATAAC 57.609 33.333 0.00 0.00 0.00 1.89
1624 4301 9.559732 CATGTCACATCTAAACTCCCATAAATA 57.440 33.333 0.00 0.00 0.00 1.40
1625 4302 7.013655 GCATGTCACATCTAAACTCCCATAAAT 59.986 37.037 0.00 0.00 0.00 1.40
1626 4303 6.318648 GCATGTCACATCTAAACTCCCATAAA 59.681 38.462 0.00 0.00 0.00 1.40
1627 4304 5.822519 GCATGTCACATCTAAACTCCCATAA 59.177 40.000 0.00 0.00 0.00 1.90
1628 4305 5.130975 AGCATGTCACATCTAAACTCCCATA 59.869 40.000 0.00 0.00 0.00 2.74
1629 4306 4.080129 AGCATGTCACATCTAAACTCCCAT 60.080 41.667 0.00 0.00 0.00 4.00
1630 4307 3.264193 AGCATGTCACATCTAAACTCCCA 59.736 43.478 0.00 0.00 0.00 4.37
1631 4308 3.878778 AGCATGTCACATCTAAACTCCC 58.121 45.455 0.00 0.00 0.00 4.30
1632 4309 6.985188 TTAAGCATGTCACATCTAAACTCC 57.015 37.500 0.00 0.00 0.00 3.85
1665 4342 9.214957 TCGTATCAGTTTGTCTAATTCACATTT 57.785 29.630 0.00 0.00 0.00 2.32
1666 4343 8.771920 TCGTATCAGTTTGTCTAATTCACATT 57.228 30.769 0.00 0.00 0.00 2.71
1667 4344 8.251026 TCTCGTATCAGTTTGTCTAATTCACAT 58.749 33.333 0.00 0.00 0.00 3.21
1668 4345 7.599171 TCTCGTATCAGTTTGTCTAATTCACA 58.401 34.615 0.00 0.00 0.00 3.58
1669 4346 8.462143 TTCTCGTATCAGTTTGTCTAATTCAC 57.538 34.615 0.00 0.00 0.00 3.18
1670 4347 9.140286 CTTTCTCGTATCAGTTTGTCTAATTCA 57.860 33.333 0.00 0.00 0.00 2.57
1671 4348 8.111224 GCTTTCTCGTATCAGTTTGTCTAATTC 58.889 37.037 0.00 0.00 0.00 2.17
1672 4349 7.201444 CGCTTTCTCGTATCAGTTTGTCTAATT 60.201 37.037 0.00 0.00 0.00 1.40
1673 4350 6.253727 CGCTTTCTCGTATCAGTTTGTCTAAT 59.746 38.462 0.00 0.00 0.00 1.73
1674 4351 5.571741 CGCTTTCTCGTATCAGTTTGTCTAA 59.428 40.000 0.00 0.00 0.00 2.10
1675 4352 5.093457 CGCTTTCTCGTATCAGTTTGTCTA 58.907 41.667 0.00 0.00 0.00 2.59
1676 4353 3.921021 CGCTTTCTCGTATCAGTTTGTCT 59.079 43.478 0.00 0.00 0.00 3.41
1677 4354 3.918591 TCGCTTTCTCGTATCAGTTTGTC 59.081 43.478 0.00 0.00 0.00 3.18
1678 4355 3.673809 GTCGCTTTCTCGTATCAGTTTGT 59.326 43.478 0.00 0.00 0.00 2.83
1679 4356 3.060895 GGTCGCTTTCTCGTATCAGTTTG 59.939 47.826 0.00 0.00 0.00 2.93
1680 4357 3.251571 GGTCGCTTTCTCGTATCAGTTT 58.748 45.455 0.00 0.00 0.00 2.66
1681 4358 2.416972 GGGTCGCTTTCTCGTATCAGTT 60.417 50.000 0.00 0.00 0.00 3.16
1682 4359 1.134560 GGGTCGCTTTCTCGTATCAGT 59.865 52.381 0.00 0.00 0.00 3.41
1683 4360 1.134367 TGGGTCGCTTTCTCGTATCAG 59.866 52.381 0.00 0.00 0.00 2.90
1684 4361 1.135199 GTGGGTCGCTTTCTCGTATCA 60.135 52.381 0.00 0.00 0.00 2.15
1685 4362 1.557651 GTGGGTCGCTTTCTCGTATC 58.442 55.000 0.00 0.00 0.00 2.24
1686 4363 0.179145 CGTGGGTCGCTTTCTCGTAT 60.179 55.000 0.00 0.00 0.00 3.06
1687 4364 1.210931 CGTGGGTCGCTTTCTCGTA 59.789 57.895 0.00 0.00 0.00 3.43
1688 4365 2.049433 CGTGGGTCGCTTTCTCGT 60.049 61.111 0.00 0.00 0.00 4.18
1689 4366 2.809601 CCGTGGGTCGCTTTCTCG 60.810 66.667 0.00 0.00 38.35 4.04
1690 4367 2.434359 CCCGTGGGTCGCTTTCTC 60.434 66.667 0.00 0.00 38.35 2.87
1691 4368 4.016706 CCCCGTGGGTCGCTTTCT 62.017 66.667 3.83 0.00 38.25 2.52
1712 4389 4.660938 GGGGCAAGGTCAACCGCT 62.661 66.667 0.00 0.00 42.08 5.52
1744 4421 3.068590 GGAATGTCCCTAAACCATGCATG 59.931 47.826 20.19 20.19 0.00 4.06
1745 4422 3.299503 GGAATGTCCCTAAACCATGCAT 58.700 45.455 0.00 0.00 0.00 3.96
1746 4423 2.042297 TGGAATGTCCCTAAACCATGCA 59.958 45.455 0.00 0.00 35.03 3.96
1747 4424 2.733956 TGGAATGTCCCTAAACCATGC 58.266 47.619 0.00 0.00 35.03 4.06
1784 4461 4.864916 TGAAATAGATTGACTGCGCTTC 57.135 40.909 9.73 5.72 0.00 3.86
1788 4465 8.081208 AGTTATGATGAAATAGATTGACTGCG 57.919 34.615 0.00 0.00 0.00 5.18
1825 6623 5.805728 TCCTTGGTGAAAAATCTACCTCTC 58.194 41.667 0.00 0.00 35.51 3.20
1830 6628 5.643379 TGCATCCTTGGTGAAAAATCTAC 57.357 39.130 0.00 0.00 0.00 2.59
1839 6637 3.117813 TGATGATGATGCATCCTTGGTGA 60.118 43.478 23.67 3.58 43.10 4.02
1847 6645 5.483811 AGAGAGTGATGATGATGATGCATC 58.516 41.667 20.14 20.14 43.84 3.91
1856 6654 3.010420 ACGAACGAGAGAGTGATGATGA 58.990 45.455 0.14 0.00 0.00 2.92
1993 6791 4.465512 GCCGCACCTGCAATCACG 62.466 66.667 0.00 0.00 42.21 4.35
2051 6849 2.045926 CTTAGCGGCAAGGCAGGT 60.046 61.111 1.45 0.00 38.14 4.00
2081 6884 1.255667 CCGTCTCTTTTCTCCGGGGA 61.256 60.000 0.00 0.00 35.11 4.81
2084 6887 1.218316 CCCCGTCTCTTTTCTCCGG 59.782 63.158 0.00 0.00 38.39 5.14
2085 6888 1.218316 CCCCCGTCTCTTTTCTCCG 59.782 63.158 0.00 0.00 0.00 4.63
2099 6903 2.052782 AAGCGATGTAAATCACCCCC 57.947 50.000 0.00 0.00 0.00 5.40
2145 7091 2.789917 GCTGCATGAGCTTCCGTG 59.210 61.111 0.00 0.00 45.21 4.94
2146 7092 2.816958 CGCTGCATGAGCTTCCGT 60.817 61.111 13.06 0.00 46.64 4.69
2148 7094 3.109612 CTGCGCTGCATGAGCTTCC 62.110 63.158 9.73 4.84 46.64 3.46
2243 7197 2.715046 GGACCTGATGCAAGATCAACA 58.285 47.619 0.00 0.00 0.00 3.33
2278 7232 3.515602 AGCTCTCTGAAACCCAAACAT 57.484 42.857 0.00 0.00 0.00 2.71
2301 7255 6.438259 CAGAATGTGAGAAGCAGATCAAAT 57.562 37.500 0.00 0.00 28.89 2.32
2374 7328 1.194495 GGCATACCGTACGTTTCTCG 58.806 55.000 15.21 0.00 46.00 4.04
2421 7375 4.201990 GCTGGGCTGTTTCAATAAGATCAG 60.202 45.833 0.00 0.00 34.13 2.90
2429 7383 1.904287 TTACGCTGGGCTGTTTCAAT 58.096 45.000 0.00 0.00 0.00 2.57
2430 7384 1.681538 TTTACGCTGGGCTGTTTCAA 58.318 45.000 0.00 0.00 0.00 2.69
2431 7385 1.681538 TTTTACGCTGGGCTGTTTCA 58.318 45.000 0.00 0.00 0.00 2.69
2432 7386 2.227865 TCATTTTACGCTGGGCTGTTTC 59.772 45.455 0.00 0.00 0.00 2.78
2433 7387 2.030274 GTCATTTTACGCTGGGCTGTTT 60.030 45.455 0.00 0.00 0.00 2.83
2434 7388 1.539827 GTCATTTTACGCTGGGCTGTT 59.460 47.619 0.00 0.00 0.00 3.16
2435 7389 1.165270 GTCATTTTACGCTGGGCTGT 58.835 50.000 0.00 0.00 0.00 4.40
2436 7390 1.131126 CTGTCATTTTACGCTGGGCTG 59.869 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.