Multiple sequence alignment - TraesCS7A01G053500

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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 TraesCS7A01G053500 chr7A 100.000 3113 0 0 1 3113 25956694 25959806 0.000000e+00 5749.0
1 TraesCS7A01G053500 chr7A 84.984 626 58 11 1 601 25941520 25942134 1.240000e-168 603.0
2 TraesCS7A01G053500 chr7A 90.265 226 20 1 877 1102 25942375 25942598 8.440000e-76 294.0
3 TraesCS7A01G053500 chr4A 96.171 1149 35 8 1574 2717 708465799 708464655 0.000000e+00 1869.0
4 TraesCS7A01G053500 chr4A 94.424 807 32 5 1 802 708467140 708466342 0.000000e+00 1229.0
5 TraesCS7A01G053500 chr4A 93.478 552 30 4 852 1398 708466357 708465807 0.000000e+00 815.0
6 TraesCS7A01G053500 chr4A 90.380 395 38 0 2719 3113 708463112 708462718 1.280000e-143 520.0
7 TraesCS7A01G053500 chr4A 86.087 345 43 4 759 1102 708540892 708540552 1.760000e-97 366.0
8 TraesCS7A01G053500 chr4A 85.572 201 25 2 154 350 708542175 708541975 1.130000e-49 207.0
9 TraesCS7A01G053500 chr4A 91.216 148 10 3 1429 1573 38842401 38842254 6.810000e-47 198.0
10 TraesCS7A01G053500 chr4A 81.818 187 14 6 1 167 708543758 708543572 4.190000e-29 139.0
11 TraesCS7A01G053500 chr7D 95.913 1150 37 9 1574 2717 25131623 25132768 0.000000e+00 1855.0
12 TraesCS7A01G053500 chr7D 84.629 1132 118 22 1 1102 25056869 25057974 0.000000e+00 1075.0
13 TraesCS7A01G053500 chr7D 95.156 640 31 0 759 1398 25130976 25131615 0.000000e+00 1011.0
14 TraesCS7A01G053500 chr7D 95.463 551 17 2 3 552 25130012 25130555 0.000000e+00 872.0
15 TraesCS7A01G053500 chr7D 88.131 396 37 4 2718 3113 25134324 25134709 2.190000e-126 462.0
16 TraesCS7A01G053500 chr7D 89.130 138 5 6 633 761 25130579 25130715 2.480000e-36 163.0
17 TraesCS7A01G053500 chr7B 93.151 146 9 1 1429 1573 712770987 712770842 2.430000e-51 213.0
18 TraesCS7A01G053500 chr2B 93.197 147 6 4 1429 1573 800554482 800554626 2.430000e-51 213.0
19 TraesCS7A01G053500 chr2B 92.517 147 10 1 1429 1574 165254154 165254008 3.150000e-50 209.0
20 TraesCS7A01G053500 chr2B 91.216 148 8 4 1429 1573 636487512 636487367 2.450000e-46 196.0
21 TraesCS7A01G053500 chr6B 92.517 147 7 4 1429 1573 55694074 55694218 1.130000e-49 207.0
22 TraesCS7A01G053500 chr6B 81.513 119 20 2 2964 3081 65148194 65148311 2.560000e-16 97.1
23 TraesCS7A01G053500 chr5B 90.385 156 14 1 1420 1574 239275063 239275218 1.460000e-48 204.0
24 TraesCS7A01G053500 chr3B 91.156 147 9 4 1429 1573 561669025 561669169 2.450000e-46 196.0
25 TraesCS7A01G053500 chrUn 80.628 191 35 2 2915 3104 88125995 88125806 2.500000e-31 147.0
26 TraesCS7A01G053500 chrUn 80.628 191 35 2 2915 3104 88662884 88662695 2.500000e-31 147.0
27 TraesCS7A01G053500 chrUn 77.489 231 45 7 2880 3105 8147985 8148213 7.000000e-27 132.0
28 TraesCS7A01G053500 chr5D 82.667 150 23 3 2966 3113 531899238 531899090 2.520000e-26 130.0
29 TraesCS7A01G053500 chr5D 82.895 152 17 6 1425 1573 501340327 501340182 9.060000e-26 128.0
30 TraesCS7A01G053500 chr4D 74.487 341 61 22 2782 3113 309497712 309497389 1.170000e-24 124.0
31 TraesCS7A01G053500 chr2D 80.745 161 28 3 2946 3105 471425572 471425414 4.220000e-24 122.0
32 TraesCS7A01G053500 chr3D 84.034 119 17 2 2964 3081 56682477 56682594 2.540000e-21 113.0


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 TraesCS7A01G053500 chr7A 25956694 25959806 3112 False 5749.000000 5749 100.000000 1 3113 1 chr7A.!!$F1 3112
1 TraesCS7A01G053500 chr7A 25941520 25942598 1078 False 448.500000 603 87.624500 1 1102 2 chr7A.!!$F2 1101
2 TraesCS7A01G053500 chr4A 708462718 708467140 4422 True 1108.250000 1869 93.613250 1 3113 4 chr4A.!!$R2 3112
3 TraesCS7A01G053500 chr4A 708540552 708543758 3206 True 237.333333 366 84.492333 1 1102 3 chr4A.!!$R3 1101
4 TraesCS7A01G053500 chr7D 25056869 25057974 1105 False 1075.000000 1075 84.629000 1 1102 1 chr7D.!!$F1 1101
5 TraesCS7A01G053500 chr7D 25130012 25134709 4697 False 872.600000 1855 92.758600 3 3113 5 chr7D.!!$F2 3110

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
840 3331 0.034574 AATGCCGGACTACATTGCCA 60.035 50.0 5.05 0.0 35.24 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2831 7031 0.033228 CCCGAGCTAGCCAAGATCTG 59.967 60.0 12.13 0.0 38.54 2.9 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
126 160 5.804944 AACCACATCCACATCAATGAAAA 57.195 34.783 0.00 0.00 0.00 2.29
134 168 6.083098 TCCACATCAATGAAAACGTTCAAT 57.917 33.333 0.00 0.00 46.66 2.57
159 1603 2.486966 GCATTTCTGCGTGCTCCC 59.513 61.111 0.00 0.00 38.92 4.30
170 1614 0.249868 CGTGCTCCCTGTCTTTGTGA 60.250 55.000 0.00 0.00 0.00 3.58
210 1657 7.067615 AGCGTCAACGATAGAATATATGAGGAT 59.932 37.037 6.75 0.00 43.02 3.24
260 1707 7.507829 ACAATGAATTGGTTTTCTTGATCCAA 58.492 30.769 7.87 0.00 41.96 3.53
350 2535 8.110860 ACCAATGGTCTAAATAGTTTCACTTG 57.889 34.615 0.00 0.00 0.00 3.16
351 2536 7.942341 ACCAATGGTCTAAATAGTTTCACTTGA 59.058 33.333 0.00 0.00 0.00 3.02
352 2537 8.960591 CCAATGGTCTAAATAGTTTCACTTGAT 58.039 33.333 0.00 0.00 0.00 2.57
476 2673 4.569943 AGTGAGAGTATTTGCACGTGAAT 58.430 39.130 22.23 13.59 36.43 2.57
687 2906 1.032657 CCGGAGTCATCACGAGAGGT 61.033 60.000 0.00 0.00 0.00 3.85
815 3306 3.737559 AGGACCATGTGGCTAAATCAA 57.262 42.857 0.00 0.00 39.32 2.57
838 3329 3.304659 CCATAAATGCCGGACTACATTGC 60.305 47.826 5.05 0.00 36.64 3.56
840 3331 0.034574 AATGCCGGACTACATTGCCA 60.035 50.000 5.05 0.00 35.24 4.92
883 3507 3.274586 CGAGGCGTGGCATCCATG 61.275 66.667 10.68 0.82 42.95 3.66
887 3511 1.526686 GGCGTGGCATCCATGATCA 60.527 57.895 9.12 0.00 42.73 2.92
1014 3641 3.385193 TTGAAGATGTCGACAAGCAGA 57.615 42.857 24.13 4.03 0.00 4.26
1032 3659 3.601356 CAGAAAGCAATGTTCTATCGCG 58.399 45.455 0.00 0.00 33.53 5.87
1110 3738 1.528129 AGCAAGCCTCTTAAGTGCAC 58.472 50.000 9.40 9.40 37.68 4.57
1255 3886 4.020751 TGAAGCTACATCATCTAGGCATCC 60.021 45.833 0.00 0.00 0.00 3.51
1371 4002 1.220206 CCGTGAGCTGATCTGCCTT 59.780 57.895 19.74 3.54 0.00 4.35
1398 4029 7.396540 AGATTTAAATCTGTACCAGCCAAAG 57.603 36.000 26.26 0.00 43.81 2.77
1399 4030 6.948309 AGATTTAAATCTGTACCAGCCAAAGT 59.052 34.615 26.26 0.49 43.81 2.66
1401 4032 7.681939 TTTAAATCTGTACCAGCCAAAGTAG 57.318 36.000 0.00 0.00 0.00 2.57
1402 4033 4.910458 AATCTGTACCAGCCAAAGTAGT 57.090 40.909 0.00 0.00 0.00 2.73
1403 4034 6.368779 AAATCTGTACCAGCCAAAGTAGTA 57.631 37.500 0.00 0.00 0.00 1.82
1404 4035 6.561519 AATCTGTACCAGCCAAAGTAGTAT 57.438 37.500 0.00 0.00 0.00 2.12
1405 4036 7.670605 AATCTGTACCAGCCAAAGTAGTATA 57.329 36.000 0.00 0.00 0.00 1.47
1406 4037 7.857404 ATCTGTACCAGCCAAAGTAGTATAT 57.143 36.000 0.00 0.00 0.00 0.86
1407 4038 7.050970 TCTGTACCAGCCAAAGTAGTATATG 57.949 40.000 0.00 0.00 0.00 1.78
1408 4039 6.610020 TCTGTACCAGCCAAAGTAGTATATGT 59.390 38.462 0.00 0.00 0.00 2.29
1409 4040 7.781219 TCTGTACCAGCCAAAGTAGTATATGTA 59.219 37.037 0.00 0.00 0.00 2.29
1410 4041 7.719483 TGTACCAGCCAAAGTAGTATATGTAC 58.281 38.462 0.00 0.00 0.00 2.90
1411 4042 6.170846 ACCAGCCAAAGTAGTATATGTACC 57.829 41.667 0.00 0.00 0.00 3.34
1412 4043 5.903589 ACCAGCCAAAGTAGTATATGTACCT 59.096 40.000 0.00 0.00 0.00 3.08
1413 4044 6.041751 ACCAGCCAAAGTAGTATATGTACCTC 59.958 42.308 0.00 0.00 0.00 3.85
1414 4045 6.150318 CAGCCAAAGTAGTATATGTACCTCG 58.850 44.000 0.00 0.00 0.00 4.63
1415 4046 4.922103 GCCAAAGTAGTATATGTACCTCGC 59.078 45.833 0.00 0.00 0.00 5.03
1416 4047 5.508489 GCCAAAGTAGTATATGTACCTCGCA 60.508 44.000 0.00 0.00 0.00 5.10
1417 4048 6.150318 CCAAAGTAGTATATGTACCTCGCAG 58.850 44.000 0.00 0.00 0.00 5.18
1418 4049 6.016527 CCAAAGTAGTATATGTACCTCGCAGA 60.017 42.308 0.00 0.00 0.00 4.26
1419 4050 7.309255 CCAAAGTAGTATATGTACCTCGCAGAT 60.309 40.741 0.00 0.00 33.89 2.90
1420 4051 7.762588 AAGTAGTATATGTACCTCGCAGATT 57.237 36.000 0.00 0.00 33.89 2.40
1421 4052 7.762588 AGTAGTATATGTACCTCGCAGATTT 57.237 36.000 0.00 0.00 33.89 2.17
1422 4053 7.818642 AGTAGTATATGTACCTCGCAGATTTC 58.181 38.462 0.00 0.00 33.89 2.17
1423 4054 6.650427 AGTATATGTACCTCGCAGATTTCA 57.350 37.500 0.00 0.00 33.89 2.69
1424 4055 6.448006 AGTATATGTACCTCGCAGATTTCAC 58.552 40.000 0.00 0.00 33.89 3.18
1425 4056 3.610040 ATGTACCTCGCAGATTTCACA 57.390 42.857 0.00 0.00 33.89 3.58
1426 4057 2.683968 TGTACCTCGCAGATTTCACAC 58.316 47.619 0.00 0.00 33.89 3.82
1427 4058 2.036604 TGTACCTCGCAGATTTCACACA 59.963 45.455 0.00 0.00 33.89 3.72
1428 4059 2.479566 ACCTCGCAGATTTCACACAT 57.520 45.000 0.00 0.00 33.89 3.21
1429 4060 2.783135 ACCTCGCAGATTTCACACATT 58.217 42.857 0.00 0.00 33.89 2.71
1430 4061 2.744202 ACCTCGCAGATTTCACACATTC 59.256 45.455 0.00 0.00 33.89 2.67
1431 4062 2.096496 CCTCGCAGATTTCACACATTCC 59.904 50.000 0.00 0.00 33.89 3.01
1432 4063 3.005554 CTCGCAGATTTCACACATTCCT 58.994 45.455 0.00 0.00 33.89 3.36
1433 4064 2.743664 TCGCAGATTTCACACATTCCTG 59.256 45.455 0.00 0.00 0.00 3.86
1434 4065 2.485426 CGCAGATTTCACACATTCCTGT 59.515 45.455 0.00 0.00 35.44 4.00
1435 4066 3.058016 CGCAGATTTCACACATTCCTGTT 60.058 43.478 0.00 0.00 31.62 3.16
1436 4067 4.557296 CGCAGATTTCACACATTCCTGTTT 60.557 41.667 0.00 0.00 31.62 2.83
1437 4068 5.334802 CGCAGATTTCACACATTCCTGTTTA 60.335 40.000 0.00 0.00 31.62 2.01
1438 4069 6.088824 GCAGATTTCACACATTCCTGTTTAG 58.911 40.000 0.00 0.00 31.62 1.85
1439 4070 6.615088 CAGATTTCACACATTCCTGTTTAGG 58.385 40.000 0.00 0.00 46.06 2.69
1440 4071 4.846779 TTTCACACATTCCTGTTTAGGC 57.153 40.909 0.00 0.00 44.22 3.93
1441 4072 3.788227 TCACACATTCCTGTTTAGGCT 57.212 42.857 0.00 0.00 44.22 4.58
1442 4073 4.098914 TCACACATTCCTGTTTAGGCTT 57.901 40.909 0.00 0.00 44.22 4.35
1443 4074 3.820467 TCACACATTCCTGTTTAGGCTTG 59.180 43.478 0.00 0.00 44.22 4.01
1444 4075 3.057315 CACACATTCCTGTTTAGGCTTGG 60.057 47.826 0.00 0.00 44.22 3.61
1445 4076 3.157087 CACATTCCTGTTTAGGCTTGGT 58.843 45.455 0.00 0.00 44.22 3.67
1446 4077 3.057315 CACATTCCTGTTTAGGCTTGGTG 60.057 47.826 0.00 0.00 44.22 4.17
1447 4078 2.286365 TTCCTGTTTAGGCTTGGTGG 57.714 50.000 0.00 0.00 44.22 4.61
1448 4079 1.145571 TCCTGTTTAGGCTTGGTGGT 58.854 50.000 0.00 0.00 44.22 4.16
1449 4080 1.202879 TCCTGTTTAGGCTTGGTGGTG 60.203 52.381 0.00 0.00 44.22 4.17
1450 4081 1.247567 CTGTTTAGGCTTGGTGGTGG 58.752 55.000 0.00 0.00 0.00 4.61
1451 4082 0.825840 TGTTTAGGCTTGGTGGTGGC 60.826 55.000 0.00 0.00 0.00 5.01
1452 4083 1.228737 TTTAGGCTTGGTGGTGGCC 60.229 57.895 0.00 0.00 45.57 5.36
1456 4087 4.982701 GCTTGGTGGTGGCCTGCT 62.983 66.667 3.32 0.00 0.00 4.24
1457 4088 2.987547 CTTGGTGGTGGCCTGCTG 60.988 66.667 3.32 0.00 0.00 4.41
1461 4092 4.962836 GTGGTGGCCTGCTGCACT 62.963 66.667 3.32 0.00 43.89 4.40
1462 4093 4.208403 TGGTGGCCTGCTGCACTT 62.208 61.111 3.32 0.00 43.89 3.16
1463 4094 3.677648 GGTGGCCTGCTGCACTTG 61.678 66.667 3.32 0.00 43.89 3.16
1464 4095 4.353437 GTGGCCTGCTGCACTTGC 62.353 66.667 3.32 1.59 43.89 4.01
1465 4096 4.591399 TGGCCTGCTGCACTTGCT 62.591 61.111 3.32 0.00 43.89 3.91
1466 4097 4.052229 GGCCTGCTGCACTTGCTG 62.052 66.667 0.00 3.16 43.89 4.41
1467 4098 3.292936 GCCTGCTGCACTTGCTGT 61.293 61.111 0.00 0.00 42.66 4.40
1475 4106 4.695231 CACTTGCTGTGCTGCGCC 62.695 66.667 11.12 0.00 40.06 6.53
1486 4117 4.954970 CTGCGCCCACACCACCTT 62.955 66.667 4.18 0.00 0.00 3.50
1487 4118 4.947147 TGCGCCCACACCACCTTC 62.947 66.667 4.18 0.00 0.00 3.46
1488 4119 4.947147 GCGCCCACACCACCTTCA 62.947 66.667 0.00 0.00 0.00 3.02
1489 4120 2.034066 CGCCCACACCACCTTCAT 59.966 61.111 0.00 0.00 0.00 2.57
1490 4121 2.334946 CGCCCACACCACCTTCATG 61.335 63.158 0.00 0.00 0.00 3.07
1491 4122 1.228552 GCCCACACCACCTTCATGT 60.229 57.895 0.00 0.00 0.00 3.21
1492 4123 0.037590 GCCCACACCACCTTCATGTA 59.962 55.000 0.00 0.00 0.00 2.29
1493 4124 1.546773 GCCCACACCACCTTCATGTAA 60.547 52.381 0.00 0.00 0.00 2.41
1494 4125 2.883888 GCCCACACCACCTTCATGTAAT 60.884 50.000 0.00 0.00 0.00 1.89
1495 4126 3.623703 GCCCACACCACCTTCATGTAATA 60.624 47.826 0.00 0.00 0.00 0.98
1496 4127 4.792068 CCCACACCACCTTCATGTAATAT 58.208 43.478 0.00 0.00 0.00 1.28
1497 4128 4.580167 CCCACACCACCTTCATGTAATATG 59.420 45.833 0.00 0.00 0.00 1.78
1498 4129 5.436175 CCACACCACCTTCATGTAATATGA 58.564 41.667 0.00 0.00 0.00 2.15
1499 4130 5.296780 CCACACCACCTTCATGTAATATGAC 59.703 44.000 0.00 0.00 0.00 3.06
1500 4131 6.115446 CACACCACCTTCATGTAATATGACT 58.885 40.000 0.00 0.00 0.00 3.41
1501 4132 7.272244 CACACCACCTTCATGTAATATGACTA 58.728 38.462 0.00 0.00 0.00 2.59
1502 4133 7.224753 CACACCACCTTCATGTAATATGACTAC 59.775 40.741 0.00 0.00 0.00 2.73
1503 4134 7.125811 ACACCACCTTCATGTAATATGACTACT 59.874 37.037 0.00 0.00 0.00 2.57
1504 4135 7.439356 CACCACCTTCATGTAATATGACTACTG 59.561 40.741 0.00 0.00 0.00 2.74
1505 4136 7.125811 ACCACCTTCATGTAATATGACTACTGT 59.874 37.037 0.00 0.00 0.00 3.55
1506 4137 7.653713 CCACCTTCATGTAATATGACTACTGTC 59.346 40.741 0.00 0.00 43.20 3.51
1517 4148 3.329929 GACTACTGTCATCCGGGTTTT 57.670 47.619 0.00 0.00 42.48 2.43
1518 4149 3.671716 GACTACTGTCATCCGGGTTTTT 58.328 45.455 0.00 0.00 42.48 1.94
1519 4150 3.408634 ACTACTGTCATCCGGGTTTTTG 58.591 45.455 0.00 0.00 0.00 2.44
1520 4151 0.958822 ACTGTCATCCGGGTTTTTGC 59.041 50.000 0.00 0.00 0.00 3.68
1521 4152 0.243636 CTGTCATCCGGGTTTTTGCC 59.756 55.000 0.00 0.00 0.00 4.52
1522 4153 1.182385 TGTCATCCGGGTTTTTGCCC 61.182 55.000 0.00 0.00 45.21 5.36
1523 4154 1.608046 TCATCCGGGTTTTTGCCCC 60.608 57.895 0.00 0.00 45.91 5.80
1529 4160 2.696566 GGGTTTTTGCCCCGTTTTG 58.303 52.632 0.00 0.00 42.89 2.44
1530 4161 0.178301 GGGTTTTTGCCCCGTTTTGA 59.822 50.000 0.00 0.00 42.89 2.69
1531 4162 1.407025 GGGTTTTTGCCCCGTTTTGAA 60.407 47.619 0.00 0.00 42.89 2.69
1532 4163 2.566913 GGTTTTTGCCCCGTTTTGAAT 58.433 42.857 0.00 0.00 0.00 2.57
1533 4164 2.289274 GGTTTTTGCCCCGTTTTGAATG 59.711 45.455 0.00 0.00 0.00 2.67
1534 4165 1.587547 TTTTGCCCCGTTTTGAATGC 58.412 45.000 0.00 0.00 0.00 3.56
1535 4166 0.465705 TTTGCCCCGTTTTGAATGCA 59.534 45.000 0.00 0.00 0.00 3.96
1536 4167 0.683973 TTGCCCCGTTTTGAATGCAT 59.316 45.000 0.00 0.00 0.00 3.96
1537 4168 1.550327 TGCCCCGTTTTGAATGCATA 58.450 45.000 0.00 0.00 0.00 3.14
1538 4169 1.895798 TGCCCCGTTTTGAATGCATAA 59.104 42.857 0.00 0.00 0.00 1.90
1539 4170 2.094286 TGCCCCGTTTTGAATGCATAAG 60.094 45.455 0.00 0.00 0.00 1.73
1540 4171 2.738321 GCCCCGTTTTGAATGCATAAGG 60.738 50.000 0.00 0.00 0.00 2.69
1541 4172 2.495669 CCCCGTTTTGAATGCATAAGGT 59.504 45.455 0.00 0.00 0.00 3.50
1542 4173 3.697045 CCCCGTTTTGAATGCATAAGGTA 59.303 43.478 0.00 0.00 0.00 3.08
1543 4174 4.202010 CCCCGTTTTGAATGCATAAGGTAG 60.202 45.833 0.00 0.00 0.00 3.18
1544 4175 4.638421 CCCGTTTTGAATGCATAAGGTAGA 59.362 41.667 0.00 0.00 0.00 2.59
1545 4176 5.299279 CCCGTTTTGAATGCATAAGGTAGAT 59.701 40.000 0.00 0.00 0.00 1.98
1546 4177 6.430451 CCGTTTTGAATGCATAAGGTAGATC 58.570 40.000 0.00 0.00 0.00 2.75
1547 4178 6.038161 CCGTTTTGAATGCATAAGGTAGATCA 59.962 38.462 0.00 0.00 0.00 2.92
1548 4179 7.255242 CCGTTTTGAATGCATAAGGTAGATCAT 60.255 37.037 0.00 0.00 0.00 2.45
1549 4180 7.588854 CGTTTTGAATGCATAAGGTAGATCATG 59.411 37.037 0.00 0.00 0.00 3.07
1550 4181 8.623903 GTTTTGAATGCATAAGGTAGATCATGA 58.376 33.333 0.00 0.00 0.00 3.07
1551 4182 8.929260 TTTGAATGCATAAGGTAGATCATGAT 57.071 30.769 8.25 8.25 0.00 2.45
1552 4183 8.557592 TTGAATGCATAAGGTAGATCATGATC 57.442 34.615 25.42 25.42 38.09 2.92
1554 4185 9.039165 TGAATGCATAAGGTAGATCATGATCTA 57.961 33.333 32.49 32.49 45.69 1.98
1735 4366 5.007682 AGTTGGCCGTGAACATACTTAAAT 58.992 37.500 7.15 0.00 0.00 1.40
1819 4452 8.032451 TCAAAAGTAAGTTCCAAAAAGGTCTTG 58.968 33.333 0.00 0.00 39.02 3.02
1824 4460 8.033038 AGTAAGTTCCAAAAAGGTCTTGTTTTC 58.967 33.333 0.00 0.00 39.02 2.29
1826 4462 7.004555 AGTTCCAAAAAGGTCTTGTTTTCTT 57.995 32.000 0.00 0.00 39.02 2.52
1896 4533 4.331992 CACTACCGAGAAGATCAACGTAGA 59.668 45.833 0.00 0.00 0.00 2.59
1897 4534 5.007823 CACTACCGAGAAGATCAACGTAGAT 59.992 44.000 0.00 0.00 0.00 1.98
1898 4535 4.985538 ACCGAGAAGATCAACGTAGATT 57.014 40.909 0.00 0.00 0.00 2.40
1899 4536 5.326200 ACCGAGAAGATCAACGTAGATTT 57.674 39.130 0.00 0.00 0.00 2.17
1938 4575 7.015098 TCACAAGGTTGGTTGATCAACATAATT 59.985 33.333 33.42 20.17 46.29 1.40
1939 4576 7.329226 CACAAGGTTGGTTGATCAACATAATTC 59.671 37.037 33.42 22.49 46.29 2.17
2055 4692 3.565307 TGAGGTGAAGCTGGAAAATTGT 58.435 40.909 0.00 0.00 0.00 2.71
2091 4728 6.627395 TCGTTGGGTTATATTGCCTTATTG 57.373 37.500 0.00 0.00 0.00 1.90
2235 4872 5.927281 TGGTGACCAGTATTTCCTAGTAC 57.073 43.478 0.00 0.00 0.00 2.73
2246 4883 8.368126 CAGTATTTCCTAGTACAAACGTTTACG 58.632 37.037 14.20 4.95 46.33 3.18
2502 5139 5.689514 GCAAATTTAATTGGTTGGTTTTGGC 59.310 36.000 0.00 0.00 0.00 4.52
2574 5212 3.047796 CGGTTACTCGGTTTCCATATCG 58.952 50.000 0.00 0.00 0.00 2.92
2717 5355 0.760189 ATGTTTGGTTGCCTGCACCT 60.760 50.000 10.59 0.00 0.00 4.00
2721 6921 0.476338 TTGGTTGCCTGCACCTCTTA 59.524 50.000 10.59 0.00 0.00 2.10
2743 6943 2.033448 GTTGTCCATCCCGGCACA 59.967 61.111 0.00 0.00 33.14 4.57
2755 6955 0.389817 CCGGCACATCTTCGACTTCA 60.390 55.000 0.00 0.00 0.00 3.02
2765 6965 3.639538 TCTTCGACTTCAGTGCACTAAC 58.360 45.455 21.20 8.27 0.00 2.34
2831 7031 1.815003 CTTGAATCTGTGTTGCCCTCC 59.185 52.381 0.00 0.00 0.00 4.30
2871 7071 1.873270 CTCCGGTCACCGTCACATCA 61.873 60.000 16.87 0.00 46.80 3.07
2909 7109 2.495409 CCGCAGTGCCCCGTCTATA 61.495 63.158 10.11 0.00 0.00 1.31
2910 7110 1.440060 CGCAGTGCCCCGTCTATAA 59.560 57.895 10.11 0.00 0.00 0.98
2917 7117 1.664306 CCCCGTCTATAACTCCGCC 59.336 63.158 0.00 0.00 0.00 6.13
2929 7129 3.976701 CTCCGCCGCTCCATTGGTT 62.977 63.158 1.86 0.00 0.00 3.67
2968 7168 3.411517 CCCTCTTCCATGGCGGGT 61.412 66.667 6.96 0.00 34.36 5.28
2983 7183 1.920835 GGGTGTGGCTCCTCTTCCT 60.921 63.158 0.00 0.00 0.00 3.36
2984 7184 0.617820 GGGTGTGGCTCCTCTTCCTA 60.618 60.000 0.00 0.00 0.00 2.94
2989 7189 1.840635 GTGGCTCCTCTTCCTATGGTT 59.159 52.381 0.00 0.00 0.00 3.67
3026 7226 2.166254 GCCTGAGTTCCTCTTCTCTGAG 59.834 54.545 0.00 0.00 33.53 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 160 7.189512 GCAGAAATGCTCTAATTATTGAACGT 58.810 34.615 0.00 0.00 31.12 3.99
134 168 4.536364 GCACGCAGAAATGCTCTAATTA 57.464 40.909 0.00 0.00 38.84 1.40
146 180 1.758440 AAGACAGGGAGCACGCAGAA 61.758 55.000 0.36 0.00 0.00 3.02
151 185 0.249868 TCACAAAGACAGGGAGCACG 60.250 55.000 0.00 0.00 0.00 5.34
159 1603 4.980434 CCAAAAAGCTGATCACAAAGACAG 59.020 41.667 0.00 0.00 0.00 3.51
170 1614 2.229792 TGACGCTTCCAAAAAGCTGAT 58.770 42.857 8.03 0.00 40.94 2.90
210 1657 1.208844 TCAGAAATAACCCCCGGGCA 61.209 55.000 17.73 0.00 39.32 5.36
260 1707 2.764010 GGTTCTTGTTTGTTTGGGTCCT 59.236 45.455 0.00 0.00 0.00 3.85
390 2575 7.852971 ATGTTCTTGGCCATAAAATCATTTG 57.147 32.000 6.09 0.00 0.00 2.32
687 2906 1.110518 TCGGTGCTGTGGTGTACTCA 61.111 55.000 0.00 0.00 0.00 3.41
815 3306 3.857157 ATGTAGTCCGGCATTTATGGT 57.143 42.857 0.00 0.00 0.00 3.55
883 3507 7.440523 ACTTTTACACAGAAGTCCAATGATC 57.559 36.000 0.00 0.00 30.64 2.92
887 3511 9.574516 AGATTAACTTTTACACAGAAGTCCAAT 57.425 29.630 0.00 0.00 35.17 3.16
972 3597 8.627208 TCAAAATCAGAGCTCAAAAGAAGTAT 57.373 30.769 17.77 0.00 0.00 2.12
973 3598 8.450578 TTCAAAATCAGAGCTCAAAAGAAGTA 57.549 30.769 17.77 0.00 0.00 2.24
1014 3641 2.095853 CACCGCGATAGAACATTGCTTT 59.904 45.455 8.23 0.00 39.76 3.51
1032 3659 1.871772 CACTAGCAGCAGCAACACC 59.128 57.895 3.17 0.00 45.49 4.16
1151 3779 3.250040 GCTACACAACGAAACATGGTTCT 59.750 43.478 20.81 5.84 0.00 3.01
1398 4029 7.537991 GTGAAATCTGCGAGGTACATATACTAC 59.462 40.741 0.00 0.00 0.00 2.73
1399 4030 7.229907 TGTGAAATCTGCGAGGTACATATACTA 59.770 37.037 0.00 0.00 0.00 1.82
1401 4032 6.144080 GTGTGAAATCTGCGAGGTACATATAC 59.856 42.308 0.00 0.00 0.00 1.47
1402 4033 6.183360 TGTGTGAAATCTGCGAGGTACATATA 60.183 38.462 0.00 0.00 0.00 0.86
1403 4034 5.050490 GTGTGAAATCTGCGAGGTACATAT 58.950 41.667 0.00 0.00 0.00 1.78
1404 4035 4.081917 TGTGTGAAATCTGCGAGGTACATA 60.082 41.667 0.00 0.00 0.00 2.29
1405 4036 3.262420 GTGTGAAATCTGCGAGGTACAT 58.738 45.455 0.00 0.00 0.00 2.29
1406 4037 2.036604 TGTGTGAAATCTGCGAGGTACA 59.963 45.455 0.00 0.00 0.00 2.90
1407 4038 2.683968 TGTGTGAAATCTGCGAGGTAC 58.316 47.619 0.00 0.00 0.00 3.34
1408 4039 3.610040 ATGTGTGAAATCTGCGAGGTA 57.390 42.857 0.00 0.00 0.00 3.08
1409 4040 2.479566 ATGTGTGAAATCTGCGAGGT 57.520 45.000 0.00 0.00 0.00 3.85
1410 4041 2.096496 GGAATGTGTGAAATCTGCGAGG 59.904 50.000 0.00 0.00 0.00 4.63
1411 4042 3.005554 AGGAATGTGTGAAATCTGCGAG 58.994 45.455 0.00 0.00 0.00 5.03
1412 4043 2.743664 CAGGAATGTGTGAAATCTGCGA 59.256 45.455 0.00 0.00 0.00 5.10
1413 4044 2.485426 ACAGGAATGTGTGAAATCTGCG 59.515 45.455 0.00 0.00 0.00 5.18
1414 4045 4.510038 AACAGGAATGTGTGAAATCTGC 57.490 40.909 0.00 0.00 0.00 4.26
1415 4046 6.615088 CCTAAACAGGAATGTGTGAAATCTG 58.385 40.000 0.00 0.00 0.00 2.90
1416 4047 5.183904 GCCTAAACAGGAATGTGTGAAATCT 59.816 40.000 0.00 0.00 0.00 2.40
1417 4048 5.183904 AGCCTAAACAGGAATGTGTGAAATC 59.816 40.000 0.00 0.00 0.00 2.17
1418 4049 5.079643 AGCCTAAACAGGAATGTGTGAAAT 58.920 37.500 0.00 0.00 0.00 2.17
1419 4050 4.469657 AGCCTAAACAGGAATGTGTGAAA 58.530 39.130 0.00 0.00 0.00 2.69
1420 4051 4.098914 AGCCTAAACAGGAATGTGTGAA 57.901 40.909 0.00 0.00 0.00 3.18
1421 4052 3.788227 AGCCTAAACAGGAATGTGTGA 57.212 42.857 0.00 0.00 0.00 3.58
1422 4053 3.057315 CCAAGCCTAAACAGGAATGTGTG 60.057 47.826 0.00 0.00 0.00 3.82
1423 4054 3.157087 CCAAGCCTAAACAGGAATGTGT 58.843 45.455 0.00 0.00 0.00 3.72
1424 4055 3.057315 CACCAAGCCTAAACAGGAATGTG 60.057 47.826 0.00 0.00 0.00 3.21
1425 4056 3.157087 CACCAAGCCTAAACAGGAATGT 58.843 45.455 0.00 0.00 0.00 2.71
1426 4057 2.493278 CCACCAAGCCTAAACAGGAATG 59.507 50.000 0.00 0.00 0.00 2.67
1427 4058 2.110011 ACCACCAAGCCTAAACAGGAAT 59.890 45.455 0.00 0.00 0.00 3.01
1428 4059 1.497286 ACCACCAAGCCTAAACAGGAA 59.503 47.619 0.00 0.00 0.00 3.36
1429 4060 1.145571 ACCACCAAGCCTAAACAGGA 58.854 50.000 0.00 0.00 0.00 3.86
1430 4061 1.247567 CACCACCAAGCCTAAACAGG 58.752 55.000 0.00 0.00 0.00 4.00
1431 4062 1.247567 CCACCACCAAGCCTAAACAG 58.752 55.000 0.00 0.00 0.00 3.16
1432 4063 0.825840 GCCACCACCAAGCCTAAACA 60.826 55.000 0.00 0.00 0.00 2.83
1433 4064 1.532604 GGCCACCACCAAGCCTAAAC 61.533 60.000 0.00 0.00 43.62 2.01
1434 4065 1.228737 GGCCACCACCAAGCCTAAA 60.229 57.895 0.00 0.00 43.62 1.85
1435 4066 2.438795 GGCCACCACCAAGCCTAA 59.561 61.111 0.00 0.00 43.62 2.69
1439 4070 4.982701 AGCAGGCCACCACCAAGC 62.983 66.667 5.01 0.00 34.33 4.01
1440 4071 2.987547 CAGCAGGCCACCACCAAG 60.988 66.667 5.01 0.00 0.00 3.61
1444 4075 4.962836 AGTGCAGCAGGCCACCAC 62.963 66.667 5.01 4.28 43.89 4.16
1445 4076 4.208403 AAGTGCAGCAGGCCACCA 62.208 61.111 5.01 0.00 43.89 4.17
1446 4077 3.677648 CAAGTGCAGCAGGCCACC 61.678 66.667 5.01 0.00 43.89 4.61
1447 4078 4.353437 GCAAGTGCAGCAGGCCAC 62.353 66.667 5.01 0.00 43.89 5.01
1448 4079 4.591399 AGCAAGTGCAGCAGGCCA 62.591 61.111 5.01 0.00 45.16 5.36
1449 4080 4.052229 CAGCAAGTGCAGCAGGCC 62.052 66.667 6.00 0.00 45.16 5.19
1450 4081 3.292936 ACAGCAAGTGCAGCAGGC 61.293 61.111 6.00 0.00 45.16 4.85
1451 4082 2.643272 CACAGCAAGTGCAGCAGG 59.357 61.111 6.00 0.00 45.16 4.85
1469 4100 4.954970 AAGGTGGTGTGGGCGCAG 62.955 66.667 10.83 0.00 0.00 5.18
1470 4101 4.947147 GAAGGTGGTGTGGGCGCA 62.947 66.667 10.83 0.00 0.00 6.09
1471 4102 4.947147 TGAAGGTGGTGTGGGCGC 62.947 66.667 0.00 0.00 0.00 6.53
1472 4103 2.034066 ATGAAGGTGGTGTGGGCG 59.966 61.111 0.00 0.00 0.00 6.13
1473 4104 0.037590 TACATGAAGGTGGTGTGGGC 59.962 55.000 0.00 0.00 0.00 5.36
1474 4105 2.577606 TTACATGAAGGTGGTGTGGG 57.422 50.000 0.00 0.00 0.00 4.61
1475 4106 5.296780 GTCATATTACATGAAGGTGGTGTGG 59.703 44.000 0.00 0.00 0.00 4.17
1476 4107 6.115446 AGTCATATTACATGAAGGTGGTGTG 58.885 40.000 0.00 0.00 0.00 3.82
1477 4108 6.313519 AGTCATATTACATGAAGGTGGTGT 57.686 37.500 0.00 0.00 0.00 4.16
1478 4109 7.439356 CAGTAGTCATATTACATGAAGGTGGTG 59.561 40.741 0.00 0.00 0.00 4.17
1479 4110 7.125811 ACAGTAGTCATATTACATGAAGGTGGT 59.874 37.037 0.00 0.00 0.00 4.16
1480 4111 7.500992 ACAGTAGTCATATTACATGAAGGTGG 58.499 38.462 0.00 0.00 0.00 4.61
1481 4112 8.581057 GACAGTAGTCATATTACATGAAGGTG 57.419 38.462 0.00 0.00 44.34 4.00
1497 4128 3.329929 AAAACCCGGATGACAGTAGTC 57.670 47.619 0.73 0.00 45.19 2.59
1498 4129 3.408634 CAAAAACCCGGATGACAGTAGT 58.591 45.455 0.73 0.00 0.00 2.73
1499 4130 2.161609 GCAAAAACCCGGATGACAGTAG 59.838 50.000 0.73 0.00 0.00 2.57
1500 4131 2.156098 GCAAAAACCCGGATGACAGTA 58.844 47.619 0.73 0.00 0.00 2.74
1501 4132 0.958822 GCAAAAACCCGGATGACAGT 59.041 50.000 0.73 0.00 0.00 3.55
1502 4133 0.243636 GGCAAAAACCCGGATGACAG 59.756 55.000 0.73 0.00 0.00 3.51
1503 4134 1.182385 GGGCAAAAACCCGGATGACA 61.182 55.000 0.73 0.00 40.98 3.58
1504 4135 1.589630 GGGCAAAAACCCGGATGAC 59.410 57.895 0.73 0.00 40.98 3.06
1505 4136 4.105388 GGGCAAAAACCCGGATGA 57.895 55.556 0.73 0.00 40.98 2.92
1512 4143 2.025589 TTCAAAACGGGGCAAAAACC 57.974 45.000 0.00 0.00 0.00 3.27
1513 4144 2.286713 GCATTCAAAACGGGGCAAAAAC 60.287 45.455 0.00 0.00 0.00 2.43
1514 4145 1.943340 GCATTCAAAACGGGGCAAAAA 59.057 42.857 0.00 0.00 0.00 1.94
1515 4146 1.134401 TGCATTCAAAACGGGGCAAAA 60.134 42.857 0.00 0.00 0.00 2.44
1516 4147 0.465705 TGCATTCAAAACGGGGCAAA 59.534 45.000 0.00 0.00 0.00 3.68
1517 4148 0.683973 ATGCATTCAAAACGGGGCAA 59.316 45.000 0.00 0.00 34.64 4.52
1518 4149 1.550327 TATGCATTCAAAACGGGGCA 58.450 45.000 3.54 0.00 35.54 5.36
1519 4150 2.539476 CTTATGCATTCAAAACGGGGC 58.461 47.619 3.54 0.00 0.00 5.80
1520 4151 2.495669 ACCTTATGCATTCAAAACGGGG 59.504 45.455 3.54 0.00 0.00 5.73
1521 4152 3.866883 ACCTTATGCATTCAAAACGGG 57.133 42.857 3.54 0.00 0.00 5.28
1522 4153 5.811399 TCTACCTTATGCATTCAAAACGG 57.189 39.130 3.54 0.00 0.00 4.44
1523 4154 7.015226 TGATCTACCTTATGCATTCAAAACG 57.985 36.000 3.54 0.00 0.00 3.60
1524 4155 8.623903 TCATGATCTACCTTATGCATTCAAAAC 58.376 33.333 3.54 0.00 0.00 2.43
1525 4156 8.750515 TCATGATCTACCTTATGCATTCAAAA 57.249 30.769 3.54 0.00 0.00 2.44
1526 4157 8.929260 ATCATGATCTACCTTATGCATTCAAA 57.071 30.769 3.54 0.00 0.00 2.69
1527 4158 8.380867 AGATCATGATCTACCTTATGCATTCAA 58.619 33.333 32.26 0.00 45.69 2.69
1528 4159 7.914859 AGATCATGATCTACCTTATGCATTCA 58.085 34.615 32.26 0.00 45.69 2.57
1568 4199 7.558807 GGCCAGGGTTTACATATACTACTTTTT 59.441 37.037 0.00 0.00 0.00 1.94
1569 4200 7.058525 GGCCAGGGTTTACATATACTACTTTT 58.941 38.462 0.00 0.00 0.00 2.27
1570 4201 6.410041 GGGCCAGGGTTTACATATACTACTTT 60.410 42.308 4.39 0.00 0.00 2.66
1571 4202 5.072736 GGGCCAGGGTTTACATATACTACTT 59.927 44.000 4.39 0.00 0.00 2.24
1572 4203 4.596212 GGGCCAGGGTTTACATATACTACT 59.404 45.833 4.39 0.00 0.00 2.57
1819 4452 5.066505 TCTGGAGAAGCTGAACAAAGAAAAC 59.933 40.000 0.00 0.00 0.00 2.43
1824 4460 3.470709 TGTCTGGAGAAGCTGAACAAAG 58.529 45.455 0.00 0.00 0.00 2.77
1826 4462 3.118261 AGTTGTCTGGAGAAGCTGAACAA 60.118 43.478 0.00 0.00 0.00 2.83
2055 4692 1.236616 CCAACGAAGCAGCATCCACA 61.237 55.000 0.00 0.00 0.00 4.17
2170 4807 1.626321 TCCGTCAAAATGCACCCTAGA 59.374 47.619 0.00 0.00 0.00 2.43
2246 4883 4.512944 CACATGCATTAGTGTCCCATAGAC 59.487 45.833 8.62 0.00 46.51 2.59
2328 4965 2.169832 TGTAGTTGCTGCTGAAGACC 57.830 50.000 0.00 0.00 0.00 3.85
2502 5139 9.878599 AATAAAGTGAAATTCGTGTAGAACTTG 57.121 29.630 0.00 0.00 42.39 3.16
2574 5212 1.434622 CCAGTCGCTGATGTGGATGC 61.435 60.000 8.20 0.00 32.44 3.91
2639 5277 3.938963 CGGTAATACAACAGCTGGTCAAT 59.061 43.478 19.93 3.91 0.00 2.57
2743 6943 4.238514 GTTAGTGCACTGAAGTCGAAGAT 58.761 43.478 29.57 0.17 40.67 2.40
2755 6955 2.185004 AGCATTTCCGTTAGTGCACT 57.815 45.000 25.12 25.12 39.94 4.40
2765 6965 0.370273 CCGAACTCGAAGCATTTCCG 59.630 55.000 0.00 0.00 43.02 4.30
2831 7031 0.033228 CCCGAGCTAGCCAAGATCTG 59.967 60.000 12.13 0.00 38.54 2.90
2858 7058 2.654289 CGGGTGATGTGACGGTGA 59.346 61.111 0.00 0.00 0.00 4.02
2893 7093 0.464452 AGTTATAGACGGGGCACTGC 59.536 55.000 0.00 0.00 0.00 4.40
2909 7109 2.436646 CAATGGAGCGGCGGAGTT 60.437 61.111 9.78 0.00 0.00 3.01
2910 7110 4.473520 CCAATGGAGCGGCGGAGT 62.474 66.667 9.78 0.00 0.00 3.85
2917 7117 2.176546 CGCACAACCAATGGAGCG 59.823 61.111 6.16 12.19 46.10 5.03
2941 7141 3.155167 GAAGAGGGACCGGGCGAT 61.155 66.667 6.32 0.00 0.00 4.58
2968 7168 1.273838 ACCATAGGAAGAGGAGCCACA 60.274 52.381 0.00 0.00 0.00 4.17
2977 7177 3.907474 TCAGAACCACAACCATAGGAAGA 59.093 43.478 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.