Multiple sequence alignment - TraesCS7D01G107700

Loading Multiple Alignment...

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 TraesCS7D01G107700 chr7D 100.000 4720 0 0 1 4720 64730406 64735125 0.000000e+00 8717.0
1 TraesCS7D01G107700 chr7D 88.000 75 3 2 4070 4138 64704241 64704167 3.030000e-12 84.2
2 TraesCS7D01G107700 chr7B 96.676 2226 54 7 1853 4068 6370600 6372815 0.000000e+00 3683.0
3 TraesCS7D01G107700 chr7B 94.428 1651 57 13 1 1629 6368905 6370542 0.000000e+00 2507.0
4 TraesCS7D01G107700 chr7B 97.549 204 5 0 4517 4720 6373285 6373488 2.700000e-92 350.0
5 TraesCS7D01G107700 chr7B 96.154 130 5 0 4358 4487 6372815 6372944 3.700000e-51 213.0
6 TraesCS7D01G107700 chr7B 82.524 103 12 6 4350 4451 6234149 6234052 8.420000e-13 86.1
7 TraesCS7D01G107700 chr7B 97.872 47 1 0 1748 1794 6370547 6370593 1.090000e-11 82.4
8 TraesCS7D01G107700 chr7B 86.667 75 3 3 4070 4138 6234678 6234605 5.060000e-10 76.8
9 TraesCS7D01G107700 chr7A 97.368 1786 33 4 2032 3804 68887670 68889454 0.000000e+00 3025.0
10 TraesCS7D01G107700 chr7A 90.634 1452 54 19 1 1444 68884284 68885661 0.000000e+00 1853.0
11 TraesCS7D01G107700 chr7A 96.528 288 10 0 1746 2033 68887289 68887576 1.190000e-130 477.0
12 TraesCS7D01G107700 chr7A 96.679 271 9 0 3852 4122 68889451 68889721 7.200000e-123 451.0
13 TraesCS7D01G107700 chr7A 93.066 274 4 5 4155 4414 68890435 68890707 2.060000e-103 387.0
14 TraesCS7D01G107700 chr7A 97.487 199 5 0 4522 4720 68900194 68900392 1.630000e-89 340.0
15 TraesCS7D01G107700 chr7A 98.160 163 3 0 1470 1632 68887128 68887290 7.730000e-73 285.0
16 TraesCS7D01G107700 chr7A 86.624 157 16 5 1631 1785 626943973 626944126 8.120000e-38 169.0
17 TraesCS7D01G107700 chr7A 87.209 86 5 1 4442 4521 68890700 68890785 5.030000e-15 93.5
18 TraesCS7D01G107700 chr7A 88.000 75 3 3 4070 4138 68880657 68880583 3.030000e-12 84.2
19 TraesCS7D01G107700 chr7A 100.000 30 0 0 4350 4379 68880127 68880098 6.600000e-04 56.5
20 TraesCS7D01G107700 chr4B 90.882 1985 123 23 1833 3768 673191027 673189052 0.000000e+00 2610.0
21 TraesCS7D01G107700 chr4B 79.829 937 80 51 279 1126 673193104 673192188 2.450000e-162 582.0
22 TraesCS7D01G107700 chr4B 95.283 106 2 1 1746 1848 673191328 673191223 1.050000e-36 165.0
23 TraesCS7D01G107700 chr2D 92.984 1354 74 9 2008 3351 614871715 614873057 0.000000e+00 1954.0
24 TraesCS7D01G107700 chr2D 85.526 608 59 9 1 602 614867553 614868137 4.040000e-170 608.0
25 TraesCS7D01G107700 chr2D 84.950 598 29 23 594 1160 614868570 614869137 2.480000e-152 549.0
26 TraesCS7D01G107700 chr2D 93.030 330 23 0 3423 3752 614875292 614875621 2.550000e-132 483.0
27 TraesCS7D01G107700 chr2D 90.217 276 19 2 1746 2013 614871262 614871537 2.090000e-93 353.0
28 TraesCS7D01G107700 chr2D 93.431 137 5 4 1620 1752 381869753 381869617 2.880000e-47 200.0
29 TraesCS7D01G107700 chr2D 87.826 115 7 3 1517 1629 614871151 614871260 1.380000e-25 128.0
30 TraesCS7D01G107700 chr2D 79.259 135 17 7 4281 4407 614848398 614848267 3.030000e-12 84.2
31 TraesCS7D01G107700 chr4A 86.141 1306 121 26 2422 3695 628330554 628329277 0.000000e+00 1354.0
32 TraesCS7D01G107700 chr4A 97.521 121 3 0 1628 1748 702148912 702148792 1.720000e-49 207.0
33 TraesCS7D01G107700 chr4A 95.349 129 4 2 1623 1750 658949239 658949112 2.230000e-48 204.0
34 TraesCS7D01G107700 chr4A 92.105 76 3 1 1520 1592 628332921 628332846 2.320000e-18 104.0
35 TraesCS7D01G107700 chr5B 88.298 940 81 12 2422 3352 682700496 682699577 0.000000e+00 1099.0
36 TraesCS7D01G107700 chr5B 86.792 318 35 2 3378 3695 682699412 682699102 9.720000e-92 348.0
37 TraesCS7D01G107700 chr5B 83.764 271 24 14 863 1123 535284562 535284822 6.100000e-59 239.0
38 TraesCS7D01G107700 chr5B 87.629 97 8 1 1389 1485 682703153 682703061 4.990000e-20 110.0
39 TraesCS7D01G107700 chr5D 87.979 940 84 12 2422 3352 540288857 540287938 0.000000e+00 1083.0
40 TraesCS7D01G107700 chr5D 87.975 316 31 2 3380 3695 540287712 540287404 2.680000e-97 366.0
41 TraesCS7D01G107700 chr5D 99.145 117 1 0 1631 1747 74721881 74721997 1.330000e-50 211.0
42 TraesCS7D01G107700 chr5D 85.124 121 12 2 998 1118 540290145 540290031 8.300000e-23 119.0
43 TraesCS7D01G107700 chr5A 90.505 653 41 10 2483 3123 707643607 707644250 0.000000e+00 843.0
44 TraesCS7D01G107700 chr5A 82.286 175 11 3 3397 3566 707644633 707644792 2.960000e-27 134.0
45 TraesCS7D01G107700 chr5A 90.385 52 5 0 2142 2193 622432175 622432226 8.480000e-08 69.4
46 TraesCS7D01G107700 chr5A 88.462 52 6 0 2142 2193 622425313 622425364 3.940000e-06 63.9
47 TraesCS7D01G107700 chrUn 88.366 404 36 4 2463 2855 99838357 99838760 4.270000e-130 475.0
48 TraesCS7D01G107700 chr2B 94.479 163 9 0 3423 3585 749287792 749287954 7.840000e-63 252.0
49 TraesCS7D01G107700 chr2B 97.521 121 3 0 1630 1750 52463335 52463215 1.720000e-49 207.0
50 TraesCS7D01G107700 chr2B 93.600 125 8 0 3585 3709 749300741 749300865 2.240000e-43 187.0
51 TraesCS7D01G107700 chr2B 97.222 108 3 0 2878 2985 749306151 749306258 2.900000e-42 183.0
52 TraesCS7D01G107700 chr2B 79.259 135 17 7 4281 4407 749233896 749233765 3.030000e-12 84.2
53 TraesCS7D01G107700 chr3B 83.150 273 27 14 863 1126 830562882 830562620 1.020000e-56 231.0
54 TraesCS7D01G107700 chr3B 97.521 121 2 1 1627 1747 637086448 637086329 6.190000e-49 206.0
55 TraesCS7D01G107700 chr3B 91.667 144 11 1 1622 1764 556520657 556520800 1.040000e-46 198.0
56 TraesCS7D01G107700 chr3B 87.903 124 14 1 1647 1770 4488202 4488324 1.370000e-30 145.0
57 TraesCS7D01G107700 chr3B 91.228 57 5 0 482 538 778413136 778413192 1.410000e-10 78.7
58 TraesCS7D01G107700 chr6B 95.312 128 6 0 1626 1753 563489226 563489353 2.230000e-48 204.0
59 TraesCS7D01G107700 chr1B 95.349 129 3 2 1631 1759 67115767 67115892 8.010000e-48 202.0
60 TraesCS7D01G107700 chr1B 85.000 160 10 9 863 1014 77961846 77961693 2.940000e-32 150.0


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 TraesCS7D01G107700 chr7D 64730406 64735125 4719 False 8717.000000 8717 100.000000 1 4720 1 chr7D.!!$F1 4719
1 TraesCS7D01G107700 chr7B 6368905 6373488 4583 False 1367.080000 3683 96.535800 1 4720 5 chr7B.!!$F1 4719
2 TraesCS7D01G107700 chr7A 68884284 68890785 6501 False 938.785714 3025 94.234857 1 4521 7 chr7A.!!$F3 4520
3 TraesCS7D01G107700 chr4B 673189052 673193104 4052 True 1119.000000 2610 88.664667 279 3768 3 chr4B.!!$R1 3489
4 TraesCS7D01G107700 chr2D 614867553 614875621 8068 False 679.166667 1954 89.088833 1 3752 6 chr2D.!!$F1 3751
5 TraesCS7D01G107700 chr4A 628329277 628332921 3644 True 729.000000 1354 89.123000 1520 3695 2 chr4A.!!$R3 2175
6 TraesCS7D01G107700 chr5B 682699102 682703153 4051 True 519.000000 1099 87.573000 1389 3695 3 chr5B.!!$R1 2306
7 TraesCS7D01G107700 chr5D 540287404 540290145 2741 True 522.666667 1083 87.026000 998 3695 3 chr5D.!!$R1 2697
8 TraesCS7D01G107700 chr5A 707643607 707644792 1185 False 488.500000 843 86.395500 2483 3566 2 chr5A.!!$F3 1083


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
213 223 0.307760 CAAACCTTCGAGTGCCACAC 59.692 55.0 0.00 0.0 34.10 3.82 F
1649 5448 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
1652 5451 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
1746 5545 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 5432 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
2550 9285 2.692557 AGCAGATATGCTGTCGTTCTCT 59.307 45.455 15.33 0.00 46.62 3.10 R
3675 12984 1.961277 GTGTGGAGGTGCGGAACTG 60.961 63.158 0.00 0.00 0.00 3.16 R
3769 13082 2.028930 GGGAATACTGAGCATACCGAGG 60.029 54.545 0.00 0.00 0.00 4.63 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
33 34 0.669619 TTCGCTACCGACACTTGTGA 59.330 50.000 7.83 0.00 44.30 3.58
137 145 2.288213 TGTCTTCACTCGCATCTTCGTT 60.288 45.455 0.00 0.00 0.00 3.85
213 223 0.307760 CAAACCTTCGAGTGCCACAC 59.692 55.000 0.00 0.00 34.10 3.82
241 251 0.655733 CACTCGTCGTGCAAACCTTT 59.344 50.000 0.00 0.00 36.72 3.11
242 252 1.862201 CACTCGTCGTGCAAACCTTTA 59.138 47.619 0.00 0.00 36.72 1.85
292 302 1.004628 TGAGGACAACATGACCCATGG 59.995 52.381 4.14 4.14 45.16 3.66
306 316 0.452987 CCATGGTGCAAACCTCATCG 59.547 55.000 2.57 0.00 0.00 3.84
605 1104 2.283966 CCACCCACTCGACCTCCT 60.284 66.667 0.00 0.00 0.00 3.69
651 1157 1.952367 GCAGGCTGCATCTAGTTTGGT 60.952 52.381 33.33 0.00 44.26 3.67
653 1159 1.065126 AGGCTGCATCTAGTTTGGTCC 60.065 52.381 0.50 0.00 0.00 4.46
853 1383 2.892784 AATCCGCTGTTCCTAGCTAC 57.107 50.000 0.00 0.00 41.51 3.58
855 1385 1.390565 TCCGCTGTTCCTAGCTACTC 58.609 55.000 0.00 0.00 41.51 2.59
856 1386 1.103803 CCGCTGTTCCTAGCTACTCA 58.896 55.000 0.00 0.00 41.51 3.41
980 1537 5.163488 TGACCAGTAACGAACGAATCCATAT 60.163 40.000 0.14 0.00 0.00 1.78
1276 3469 8.972127 TGATTCCAAATATATGAACCGGAAAAA 58.028 29.630 9.46 0.00 34.90 1.94
1277 3470 9.244799 GATTCCAAATATATGAACCGGAAAAAC 57.755 33.333 9.46 0.00 34.90 2.43
1278 3471 7.948034 TCCAAATATATGAACCGGAAAAACT 57.052 32.000 9.46 0.00 0.00 2.66
1321 3518 5.064558 TGGTTATTGTTTGACTTCGCCTTA 58.935 37.500 0.00 0.00 0.00 2.69
1400 3601 2.158534 ACACAGTTTGTATTCCTGGCCA 60.159 45.455 4.71 4.71 36.32 5.36
1485 5128 0.958091 TTGGTGCAAAGGTGGATTCG 59.042 50.000 0.00 0.00 0.00 3.34
1632 5431 5.238583 ACTGCAGGTCAGACAATTTACTAC 58.761 41.667 19.93 0.00 45.72 2.73
1633 5432 5.012148 ACTGCAGGTCAGACAATTTACTACT 59.988 40.000 19.93 0.00 45.72 2.57
1634 5433 5.479306 TGCAGGTCAGACAATTTACTACTC 58.521 41.667 2.17 0.00 0.00 2.59
1635 5434 4.870991 GCAGGTCAGACAATTTACTACTCC 59.129 45.833 2.17 0.00 0.00 3.85
1636 5435 5.420409 CAGGTCAGACAATTTACTACTCCC 58.580 45.833 2.17 0.00 0.00 4.30
1637 5436 5.187967 CAGGTCAGACAATTTACTACTCCCT 59.812 44.000 2.17 0.00 0.00 4.20
1638 5437 5.422650 AGGTCAGACAATTTACTACTCCCTC 59.577 44.000 2.17 0.00 0.00 4.30
1639 5438 5.395435 GGTCAGACAATTTACTACTCCCTCC 60.395 48.000 2.17 0.00 0.00 4.30
1640 5439 4.401519 TCAGACAATTTACTACTCCCTCCG 59.598 45.833 0.00 0.00 0.00 4.63
1641 5440 4.159879 CAGACAATTTACTACTCCCTCCGT 59.840 45.833 0.00 0.00 0.00 4.69
1642 5441 4.401837 AGACAATTTACTACTCCCTCCGTC 59.598 45.833 0.00 0.00 0.00 4.79
1643 5442 3.450096 ACAATTTACTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
1644 5443 1.755179 TTTACTACTCCCTCCGTCCG 58.245 55.000 0.00 0.00 0.00 4.79
1645 5444 0.107017 TTACTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
1646 5445 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
1647 5446 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
1648 5447 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
1649 5448 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1650 5449 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1651 5450 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1652 5451 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1653 5452 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1654 5453 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1655 5454 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1656 5455 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1657 5456 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1658 5457 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
1659 5458 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
1660 5459 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
1661 5460 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
1662 5461 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
1663 5462 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
1664 5463 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
1665 5464 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
1666 5465 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
1667 5466 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
1668 5467 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
1669 5468 6.990349 GGAAATACTTGTCGGAGAAATGGATA 59.010 38.462 0.00 0.00 39.69 2.59
1670 5469 7.497909 GGAAATACTTGTCGGAGAAATGGATAA 59.502 37.037 0.00 0.00 39.69 1.75
1671 5470 8.801882 AAATACTTGTCGGAGAAATGGATAAA 57.198 30.769 0.00 0.00 39.69 1.40
1672 5471 8.980481 AATACTTGTCGGAGAAATGGATAAAT 57.020 30.769 0.00 0.00 39.69 1.40
1675 5474 8.383318 ACTTGTCGGAGAAATGGATAAATATG 57.617 34.615 0.00 0.00 39.69 1.78
1676 5475 7.445402 ACTTGTCGGAGAAATGGATAAATATGG 59.555 37.037 0.00 0.00 39.69 2.74
1677 5476 7.073457 TGTCGGAGAAATGGATAAATATGGA 57.927 36.000 0.00 0.00 39.69 3.41
1678 5477 7.689299 TGTCGGAGAAATGGATAAATATGGAT 58.311 34.615 0.00 0.00 39.69 3.41
1679 5478 7.607607 TGTCGGAGAAATGGATAAATATGGATG 59.392 37.037 0.00 0.00 39.69 3.51
1680 5479 7.607991 GTCGGAGAAATGGATAAATATGGATGT 59.392 37.037 0.00 0.00 39.69 3.06
1681 5480 8.821817 TCGGAGAAATGGATAAATATGGATGTA 58.178 33.333 0.00 0.00 0.00 2.29
1682 5481 9.618890 CGGAGAAATGGATAAATATGGATGTAT 57.381 33.333 0.00 0.00 0.00 2.29
1719 5518 6.865834 ACATCTAGATACATCCATTCCTCC 57.134 41.667 4.54 0.00 0.00 4.30
1720 5519 5.420421 ACATCTAGATACATCCATTCCTCCG 59.580 44.000 4.54 0.00 0.00 4.63
1721 5520 5.256806 TCTAGATACATCCATTCCTCCGA 57.743 43.478 0.00 0.00 0.00 4.55
1722 5521 5.010933 TCTAGATACATCCATTCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
1723 5522 3.576861 AGATACATCCATTCCTCCGACA 58.423 45.455 0.00 0.00 0.00 4.35
1724 5523 3.967326 AGATACATCCATTCCTCCGACAA 59.033 43.478 0.00 0.00 0.00 3.18
1725 5524 2.698855 ACATCCATTCCTCCGACAAG 57.301 50.000 0.00 0.00 0.00 3.16
1726 5525 1.909302 ACATCCATTCCTCCGACAAGT 59.091 47.619 0.00 0.00 0.00 3.16
1727 5526 3.104512 ACATCCATTCCTCCGACAAGTA 58.895 45.455 0.00 0.00 0.00 2.24
1728 5527 3.711704 ACATCCATTCCTCCGACAAGTAT 59.288 43.478 0.00 0.00 0.00 2.12
1729 5528 4.164221 ACATCCATTCCTCCGACAAGTATT 59.836 41.667 0.00 0.00 0.00 1.89
1730 5529 4.837093 TCCATTCCTCCGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
1731 5530 4.766375 TCCATTCCTCCGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
1732 5531 3.877508 CCATTCCTCCGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
1733 5532 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
1734 5533 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
1735 5534 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
1736 5535 2.537401 CTCCGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 43.47 4.79
1737 5536 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
1738 5537 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
1739 5538 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
1740 5539 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1741 5540 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1742 5541 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1743 5542 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1744 5543 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1745 5544 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1746 5545 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1787 5589 5.659079 ACTAGCTAGAGGTTAGATGCAACTT 59.341 40.000 27.45 0.00 33.72 2.66
1879 5911 9.439500 TTGGTAGTGGTTGTTACTATATGTTTC 57.561 33.333 0.00 0.00 33.60 2.78
1889 5921 8.138365 TGTTACTATATGTTTCATCCTTTCGC 57.862 34.615 0.00 0.00 0.00 4.70
1893 5925 3.915437 ATGTTTCATCCTTTCGCGTTT 57.085 38.095 5.77 0.00 0.00 3.60
1951 5983 6.857964 CGTGCTGACTTGACTGAAATTATTTT 59.142 34.615 0.00 0.00 0.00 1.82
1988 6020 6.804783 GCTATAATGGTTGTTGGTTGTTACAC 59.195 38.462 0.00 0.00 0.00 2.90
2176 6494 9.434420 AATGTGGGTTATATGTCACAAAAATTG 57.566 29.630 0.00 0.00 42.35 2.32
2197 6515 6.825944 TTGAACCATTGAATTTGTATCCGA 57.174 33.333 0.00 0.00 0.00 4.55
2287 7143 2.032550 GCAGTTGCTGTGCATATACTGG 59.967 50.000 18.41 6.52 42.00 4.00
2550 9285 0.179001 TCAGTCACTGTCAGTCCCGA 60.179 55.000 4.28 0.00 32.61 5.14
2688 9423 1.523032 GGAACGGCGATTAGGTGGG 60.523 63.158 16.62 0.00 0.00 4.61
3081 9847 2.209064 CTTGGGCATGCTGCTGTCAC 62.209 60.000 18.92 0.00 44.28 3.67
3297 10086 5.861787 CGTCACAACACACATCTTGTATCTA 59.138 40.000 0.00 0.00 35.67 1.98
3322 10111 1.736126 TCTACGAGCTTGACTACGGTG 59.264 52.381 8.31 0.00 0.00 4.94
3390 10698 7.595875 CAGTTGCACAAACAGATTAATTCATGA 59.404 33.333 0.00 0.00 41.61 3.07
3675 12984 5.066893 TGGAGCTTCATTAAAGATGATGCAC 59.933 40.000 21.31 16.91 45.76 4.57
3769 13082 2.604462 CTCAAGGCAACACAAGCAAAAC 59.396 45.455 0.00 0.00 41.41 2.43
3782 13095 1.003118 AGCAAAACCTCGGTATGCTCA 59.997 47.619 18.29 0.00 43.29 4.26
3808 13121 2.189833 CTGGGTTCGATCAGGACGA 58.810 57.895 0.00 0.00 37.99 4.20
3819 13132 3.060940 CGATCAGGACGACAAATCATTCG 60.061 47.826 0.00 0.00 41.14 3.34
3856 13169 2.057137 TTTGGTCTGCAAACTCAGCT 57.943 45.000 0.00 0.00 34.19 4.24
3860 13173 1.803555 GGTCTGCAAACTCAGCTTCTC 59.196 52.381 0.00 0.00 34.19 2.87
4132 13993 6.206829 ACTGGCAAAAAGGTAGTATTTGAGTC 59.793 38.462 1.95 0.00 36.41 3.36
4196 14190 7.437748 CACACACCATTTTTATTAAGGGAACA 58.562 34.615 0.00 0.00 33.34 3.18
4239 14233 5.182380 TCCAATTATTCAAACTTCCACGGAC 59.818 40.000 0.00 0.00 0.00 4.79
4276 14271 6.758416 TGTCTTCTATGATTCTGATTTCCACG 59.242 38.462 0.00 0.00 0.00 4.94
4359 14367 8.652810 TTCCTTTTATAACCACGATAACTAGC 57.347 34.615 0.00 0.00 0.00 3.42
4398 14406 3.550437 AACAGTGACAAGAGCTGAGTT 57.450 42.857 0.00 0.00 34.60 3.01
4439 14447 2.680841 TGCACCGCCAAAACATAGTATC 59.319 45.455 0.00 0.00 0.00 2.24
4591 14910 1.038681 TGCTAGCACCATGCCCATTG 61.039 55.000 14.93 0.00 46.52 2.82
4592 14911 1.737816 CTAGCACCATGCCCATTGC 59.262 57.895 0.00 0.00 46.52 3.56
4617 14936 5.385198 TGGTGTTAAGGATGAAGCTTTTCT 58.615 37.500 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 145 0.034186 CAACATGCCCTCCTTAGCCA 60.034 55.000 0.00 0.00 0.00 4.75
170 178 3.417101 ACCGGTCATTTGCAACATAAGA 58.583 40.909 0.00 0.00 0.00 2.10
241 251 4.957481 CCAAATGGATCACGTTGTGCGTA 61.957 47.826 0.00 0.00 45.23 4.42
251 261 5.253330 TCAGAGGTTTACCAAATGGATCAC 58.747 41.667 6.42 0.00 38.89 3.06
292 302 2.083774 TCCAATCGATGAGGTTTGCAC 58.916 47.619 14.72 0.00 0.00 4.57
306 316 2.170166 TGTGCTTGGTCCAATCCAATC 58.830 47.619 4.34 0.00 44.94 2.67
439 463 6.156083 ACAACCCCTCAAAAAGAAATTCAAGA 59.844 34.615 0.00 0.00 0.00 3.02
499 532 0.550914 AGGCTGGAAACACAAGTCCA 59.449 50.000 0.00 0.00 41.72 4.02
853 1383 1.585668 CAGAAACGCATACGAGCTGAG 59.414 52.381 0.00 0.00 43.93 3.35
855 1385 0.025513 GCAGAAACGCATACGAGCTG 59.974 55.000 0.00 0.00 43.93 4.24
856 1386 0.108615 AGCAGAAACGCATACGAGCT 60.109 50.000 0.00 0.00 43.93 4.09
1129 1704 4.155709 ACAGGAGATGAGTCAAGAAGTGA 58.844 43.478 0.00 0.00 0.00 3.41
1130 1705 4.533919 ACAGGAGATGAGTCAAGAAGTG 57.466 45.455 0.00 0.00 0.00 3.16
1276 3469 2.188817 GTTAGATCCAGGGTGTCCAGT 58.811 52.381 0.00 0.00 34.83 4.00
1277 3470 2.187958 TGTTAGATCCAGGGTGTCCAG 58.812 52.381 0.00 0.00 34.83 3.86
1278 3471 2.335681 TGTTAGATCCAGGGTGTCCA 57.664 50.000 0.00 0.00 34.83 4.02
1280 3473 2.505819 ACCATGTTAGATCCAGGGTGTC 59.494 50.000 6.06 0.00 44.67 3.67
1281 3474 2.562296 ACCATGTTAGATCCAGGGTGT 58.438 47.619 6.06 0.00 44.67 4.16
1282 3475 3.652057 AACCATGTTAGATCCAGGGTG 57.348 47.619 7.43 0.00 45.56 4.61
1286 3479 8.184192 GTCAAACAATAACCATGTTAGATCCAG 58.816 37.037 0.00 0.00 39.98 3.86
1384 3585 3.153919 TCTGTTGGCCAGGAATACAAAC 58.846 45.455 5.11 0.00 41.83 2.93
1400 3601 8.859090 TGAAACTTGATTAATTGTCCATCTGTT 58.141 29.630 0.00 0.00 0.00 3.16
1485 5128 3.013921 TCATCTGTCGGCCAATTTAACC 58.986 45.455 2.24 0.00 0.00 2.85
1632 5431 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1633 5432 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1634 5433 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1635 5434 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1636 5435 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1637 5436 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
1638 5437 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
1639 5438 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
1640 5439 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
1641 5440 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
1642 5441 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
1643 5442 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
1644 5443 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
1645 5444 6.927294 ATCCATTTCTCCGACAAGTATTTC 57.073 37.500 0.00 0.00 0.00 2.17
1646 5445 8.801882 TTTATCCATTTCTCCGACAAGTATTT 57.198 30.769 0.00 0.00 0.00 1.40
1647 5446 8.980481 ATTTATCCATTTCTCCGACAAGTATT 57.020 30.769 0.00 0.00 0.00 1.89
1649 5448 9.489084 CATATTTATCCATTTCTCCGACAAGTA 57.511 33.333 0.00 0.00 0.00 2.24
1650 5449 7.445402 CCATATTTATCCATTTCTCCGACAAGT 59.555 37.037 0.00 0.00 0.00 3.16
1651 5450 7.661437 TCCATATTTATCCATTTCTCCGACAAG 59.339 37.037 0.00 0.00 0.00 3.16
1652 5451 7.513856 TCCATATTTATCCATTTCTCCGACAA 58.486 34.615 0.00 0.00 0.00 3.18
1653 5452 7.073457 TCCATATTTATCCATTTCTCCGACA 57.927 36.000 0.00 0.00 0.00 4.35
1654 5453 7.607991 ACATCCATATTTATCCATTTCTCCGAC 59.392 37.037 0.00 0.00 0.00 4.79
1655 5454 7.689299 ACATCCATATTTATCCATTTCTCCGA 58.311 34.615 0.00 0.00 0.00 4.55
1656 5455 7.928307 ACATCCATATTTATCCATTTCTCCG 57.072 36.000 0.00 0.00 0.00 4.63
1693 5492 8.986991 GGAGGAATGGATGTATCTAGATGTATT 58.013 37.037 15.79 6.57 0.00 1.89
1694 5493 7.286546 CGGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
1695 5494 6.603599 CGGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
1696 5495 5.420421 CGGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
1697 5496 5.654209 TCGGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
1698 5497 5.654650 GTCGGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 0.00 1.98
1699 5498 5.010933 GTCGGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
1700 5499 4.767409 TGTCGGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 0.00 2.43
1701 5500 4.736473 TGTCGGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 0.00 1.98
1702 5501 3.576861 TGTCGGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 0.00 1.98
1703 5502 4.202264 ACTTGTCGGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 0.00 2.24
1704 5503 3.711704 ACTTGTCGGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 0.00 2.29
1705 5504 3.104512 ACTTGTCGGAGGAATGGATGTA 58.895 45.455 0.00 0.00 0.00 2.29
1706 5505 1.909302 ACTTGTCGGAGGAATGGATGT 59.091 47.619 0.00 0.00 0.00 3.06
1707 5506 2.698855 ACTTGTCGGAGGAATGGATG 57.301 50.000 0.00 0.00 0.00 3.51
1708 5507 5.368989 GAAATACTTGTCGGAGGAATGGAT 58.631 41.667 0.00 0.00 0.00 3.41
1709 5508 4.383770 GGAAATACTTGTCGGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
1710 5509 3.877508 GGAAATACTTGTCGGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
1711 5510 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
1712 5511 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
1713 5512 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
1714 5513 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
1715 5514 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
1716 5515 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
1717 5516 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
1718 5517 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
1719 5518 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1720 5519 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1721 5520 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1722 5521 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1723 5522 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1724 5523 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1725 5524 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1726 5525 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1727 5526 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1728 5527 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
1729 5528 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
1730 5529 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
1731 5530 1.202855 TCTAATACTCCCTCCGTCCGG 60.203 57.143 0.00 0.00 0.00 5.14
1732 5531 2.267174 TCTAATACTCCCTCCGTCCG 57.733 55.000 0.00 0.00 0.00 4.79
1733 5532 4.150359 TGAATCTAATACTCCCTCCGTCC 58.850 47.826 0.00 0.00 0.00 4.79
1734 5533 5.071370 TCTGAATCTAATACTCCCTCCGTC 58.929 45.833 0.00 0.00 0.00 4.79
1735 5534 5.063017 TCTGAATCTAATACTCCCTCCGT 57.937 43.478 0.00 0.00 0.00 4.69
1736 5535 4.461081 CCTCTGAATCTAATACTCCCTCCG 59.539 50.000 0.00 0.00 0.00 4.63
1737 5536 5.646215 TCCTCTGAATCTAATACTCCCTCC 58.354 45.833 0.00 0.00 0.00 4.30
1738 5537 5.185056 GCTCCTCTGAATCTAATACTCCCTC 59.815 48.000 0.00 0.00 0.00 4.30
1739 5538 5.083821 GCTCCTCTGAATCTAATACTCCCT 58.916 45.833 0.00 0.00 0.00 4.20
1740 5539 4.835615 TGCTCCTCTGAATCTAATACTCCC 59.164 45.833 0.00 0.00 0.00 4.30
1741 5540 5.538433 AGTGCTCCTCTGAATCTAATACTCC 59.462 44.000 0.00 0.00 0.00 3.85
1742 5541 6.648879 AGTGCTCCTCTGAATCTAATACTC 57.351 41.667 0.00 0.00 0.00 2.59
1743 5542 6.208599 GCTAGTGCTCCTCTGAATCTAATACT 59.791 42.308 0.00 0.00 36.03 2.12
1744 5543 6.386654 GCTAGTGCTCCTCTGAATCTAATAC 58.613 44.000 0.00 0.00 36.03 1.89
1745 5544 6.582677 GCTAGTGCTCCTCTGAATCTAATA 57.417 41.667 0.00 0.00 36.03 0.98
1746 5545 5.467035 GCTAGTGCTCCTCTGAATCTAAT 57.533 43.478 0.00 0.00 36.03 1.73
1787 5589 4.280819 AGGTGCGGTAGTATAGTAACCAA 58.719 43.478 8.31 0.00 32.55 3.67
1859 5891 8.732746 AGGATGAAACATATAGTAACAACCAC 57.267 34.615 0.00 0.00 33.83 4.16
1879 5911 3.747099 ATGAAGAAACGCGAAAGGATG 57.253 42.857 15.93 0.00 0.00 3.51
1889 5921 9.265938 CATACTGTATTTCACAATGAAGAAACG 57.734 33.333 0.00 0.00 37.70 3.60
2162 6480 8.680039 ATTCAATGGTTCAATTTTTGTGACAT 57.320 26.923 0.00 0.00 0.00 3.06
2176 6494 8.527567 TTTTTCGGATACAAATTCAATGGTTC 57.472 30.769 0.00 0.00 0.00 3.62
2287 7143 5.064834 GTCACAATAGTTAGCTAAAGGTGGC 59.935 44.000 7.99 9.83 32.42 5.01
2550 9285 2.692557 AGCAGATATGCTGTCGTTCTCT 59.307 45.455 15.33 0.00 46.62 3.10
2688 9423 3.681897 CGTGATATTGAATAGGGCTCAGC 59.318 47.826 0.00 0.00 0.00 4.26
2698 9433 4.039124 GGGCCATTTTCCGTGATATTGAAT 59.961 41.667 4.39 0.00 0.00 2.57
3103 9874 8.258007 ACAAAATGAAGAATGAATGATGCTGAT 58.742 29.630 0.00 0.00 0.00 2.90
3297 10086 4.474113 CGTAGTCAAGCTCGTAGAAGTTT 58.526 43.478 0.00 0.00 34.09 2.66
3322 10111 6.798986 ACTCTAGGAGATGCAAAAGGAACTTC 60.799 42.308 0.00 0.00 39.78 3.01
3390 10698 5.530171 CAGGCATATAAACACAGAAGATGCT 59.470 40.000 0.00 0.00 38.56 3.79
3675 12984 1.961277 GTGTGGAGGTGCGGAACTG 60.961 63.158 0.00 0.00 0.00 3.16
3769 13082 2.028930 GGGAATACTGAGCATACCGAGG 60.029 54.545 0.00 0.00 0.00 4.63
3782 13095 2.700897 CTGATCGAACCCAGGGAATACT 59.299 50.000 14.54 0.00 0.00 2.12
3808 13121 3.888930 ACACCCAAAGACGAATGATTTGT 59.111 39.130 0.00 0.00 33.13 2.83
3819 13132 1.385528 AAACCGTGACACCCAAAGAC 58.614 50.000 0.00 0.00 0.00 3.01
3856 13169 0.885879 TAGAGCCGCAGAAACGAGAA 59.114 50.000 0.00 0.00 34.06 2.87
3860 13173 3.389206 GCTAGAGCCGCAGAAACG 58.611 61.111 0.00 0.00 34.31 3.60
3883 13196 7.824289 TCCTCATATCGATCAAAACAAAAGTCT 59.176 33.333 0.00 0.00 0.00 3.24
4104 13417 7.430441 TCAAATACTACCTTTTTGCCAGTTTC 58.570 34.615 0.00 0.00 31.88 2.78
4132 13993 2.224621 ACCAACTGTCATGAACTGGGAG 60.225 50.000 14.67 1.77 0.00 4.30
4196 14190 4.599041 TGGAGCTAATGTGTAGCCATTTT 58.401 39.130 1.81 0.00 41.25 1.82
4276 14271 7.193377 AGGAAATTGCAATTTTGTGAATGAC 57.807 32.000 32.09 18.47 38.64 3.06
4317 14322 9.777297 ATAAAAGGAAAACAATTATGTGCTGTT 57.223 25.926 0.00 0.00 40.46 3.16
4359 14367 6.843676 CTGTTTTCAGTTCATTCGCTAATG 57.156 37.500 4.61 4.61 41.78 1.90
4398 14406 3.156293 CAACATTGTGATGAGTTGGGGA 58.844 45.455 0.00 0.00 38.09 4.81
4591 14910 3.019564 AGCTTCATCCTTAACACCATGC 58.980 45.455 0.00 0.00 0.00 4.06
4592 14911 5.649782 AAAGCTTCATCCTTAACACCATG 57.350 39.130 0.00 0.00 0.00 3.66
4617 14936 3.415212 CCAAACCTCTCTCAAAGCATGA 58.585 45.455 0.00 0.00 36.38 3.07
4675 14994 1.086696 CGTGTCCCATTACCAGCTTG 58.913 55.000 0.00 0.00 0.00 4.01



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

AutoCloner maintained by Alex Coulton.