Multiple sequence alignment - TraesCS6D01G022600

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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 TraesCS6D01G022600 chr6D 100.000 2570 0 0 1 2570 8759542 8756973 0.000000e+00 4747.0
1 TraesCS6D01G022600 chr6D 88.470 1379 119 16 536 1889 8744032 8742669 0.000000e+00 1629.0
2 TraesCS6D01G022600 chr6D 88.550 1179 102 18 726 1889 8733143 8731983 0.000000e+00 1399.0
3 TraesCS6D01G022600 chr6D 93.182 132 7 2 35 165 8744282 8744152 2.610000e-45 193.0
4 TraesCS6D01G022600 chr6A 86.156 2102 179 45 536 2558 9116011 9118079 0.000000e+00 2167.0
5 TraesCS6D01G022600 chr6A 86.108 2102 180 45 536 2558 9128024 9130092 0.000000e+00 2161.0
6 TraesCS6D01G022600 chr6A 86.061 2102 181 45 536 2558 9113009 9115077 0.000000e+00 2156.0
7 TraesCS6D01G022600 chr6A 86.061 2102 181 45 536 2558 9125021 9127089 0.000000e+00 2156.0
8 TraesCS6D01G022600 chr6A 86.013 2102 182 47 536 2558 9097989 9100057 0.000000e+00 2150.0
9 TraesCS6D01G022600 chr6A 86.013 2102 182 45 536 2558 9103996 9106064 0.000000e+00 2150.0
10 TraesCS6D01G022600 chr6A 86.013 2102 182 45 536 2558 9107000 9109068 0.000000e+00 2150.0
11 TraesCS6D01G022600 chr6A 85.966 2102 183 45 536 2558 9119014 9121082 0.000000e+00 2145.0
12 TraesCS6D01G022600 chr6A 85.966 2102 183 42 536 2558 9122018 9124086 0.000000e+00 2145.0
13 TraesCS6D01G022600 chr6A 85.884 2104 183 48 536 2558 9110004 9112074 0.000000e+00 2135.0
14 TraesCS6D01G022600 chr6A 85.823 2102 185 46 536 2558 9100993 9103060 0.000000e+00 2126.0
15 TraesCS6D01G022600 chr6A 86.645 1565 147 33 536 2067 9069877 9071412 0.000000e+00 1676.0
16 TraesCS6D01G022600 chr6A 82.010 2040 219 73 536 2460 9134028 9136034 0.000000e+00 1598.0
17 TraesCS6D01G022600 chr6A 87.773 1235 107 13 614 1824 9053913 9055127 0.000000e+00 1404.0
18 TraesCS6D01G022600 chr6A 82.435 1150 108 41 1466 2558 9181788 9182900 0.000000e+00 918.0
19 TraesCS6D01G022600 chr6A 90.705 312 20 5 167 470 9069566 9069876 8.560000e-110 407.0
20 TraesCS6D01G022600 chr6A 82.766 441 45 17 35 464 9097566 9097986 5.230000e-97 364.0
21 TraesCS6D01G022600 chr6A 94.318 176 9 1 167 342 9142616 9142790 4.220000e-68 268.0
22 TraesCS6D01G022600 chr6A 93.431 137 7 2 31 165 9069471 9069607 4.340000e-48 202.0
23 TraesCS6D01G022600 chr6A 89.076 119 13 0 346 464 9100872 9100990 5.730000e-32 148.0
24 TraesCS6D01G022600 chr6A 89.076 119 13 0 346 464 9103875 9103993 5.730000e-32 148.0
25 TraesCS6D01G022600 chr6A 89.076 119 13 0 346 464 9106879 9106997 5.730000e-32 148.0
26 TraesCS6D01G022600 chr6A 89.076 119 13 0 346 464 9109883 9110001 5.730000e-32 148.0
27 TraesCS6D01G022600 chr6A 89.076 119 13 0 346 464 9112888 9113006 5.730000e-32 148.0
28 TraesCS6D01G022600 chr6A 92.308 91 5 2 35 124 9103771 9103860 7.460000e-26 128.0
29 TraesCS6D01G022600 chr6A 92.308 91 5 2 35 124 9106775 9106864 7.460000e-26 128.0
30 TraesCS6D01G022600 chr6A 92.308 91 5 2 35 124 9109779 9109868 7.460000e-26 128.0
31 TraesCS6D01G022600 chr6A 92.308 91 5 2 35 124 9112785 9112874 7.460000e-26 128.0
32 TraesCS6D01G022600 chr6A 92.308 91 5 2 35 124 9115788 9115877 7.460000e-26 128.0
33 TraesCS6D01G022600 chr6A 95.890 73 3 0 191 263 9053685 9053757 4.490000e-23 119.0
34 TraesCS6D01G022600 chr6B 88.003 1417 115 20 406 1786 15885822 15884425 0.000000e+00 1624.0
35 TraesCS6D01G022600 chr6B 92.523 214 12 2 167 376 15886035 15885822 1.160000e-78 303.0
36 TraesCS6D01G022600 chr6B 93.684 95 6 0 169 263 15929154 15929060 2.670000e-30 143.0
37 TraesCS6D01G022600 chrUn 88.550 1179 102 18 726 1889 355457792 355456632 0.000000e+00 1399.0
38 TraesCS6D01G022600 chrUn 89.872 938 68 10 536 1456 396628438 396629365 0.000000e+00 1181.0
39 TraesCS6D01G022600 chrUn 89.076 119 13 0 346 464 396628317 396628435 5.730000e-32 148.0
40 TraesCS6D01G022600 chrUn 89.076 119 13 0 346 464 433112299 433112181 5.730000e-32 148.0
41 TraesCS6D01G022600 chrUn 92.308 91 5 2 35 124 396628213 396628302 7.460000e-26 128.0
42 TraesCS6D01G022600 chrUn 92.308 91 5 2 35 124 433112402 433112313 7.460000e-26 128.0
43 TraesCS6D01G022600 chr1D 77.619 210 29 9 1699 1893 247298932 247299138 7.520000e-21 111.0
44 TraesCS6D01G022600 chr4B 83.333 66 6 3 479 541 17498331 17498268 3.570000e-04 56.5
45 TraesCS6D01G022600 chr1B 100.000 30 0 0 514 543 550460412 550460383 3.570000e-04 56.5
46 TraesCS6D01G022600 chr1A 96.875 32 1 0 511 542 30196347 30196378 1.000000e-03 54.7
47 TraesCS6D01G022600 chr1A 100.000 28 0 0 514 541 487303501 487303474 5.000000e-03 52.8
48 TraesCS6D01G022600 chr5B 100.000 28 0 0 514 541 709828429 709828402 5.000000e-03 52.8
49 TraesCS6D01G022600 chr2A 100.000 28 0 0 514 541 1525955 1525982 5.000000e-03 52.8


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 TraesCS6D01G022600 chr6D 8756973 8759542 2569 True 4747.000000 4747 100.000000 1 2570 1 chr6D.!!$R2 2569
1 TraesCS6D01G022600 chr6D 8731983 8733143 1160 True 1399.000000 1399 88.550000 726 1889 1 chr6D.!!$R1 1163
2 TraesCS6D01G022600 chr6D 8742669 8744282 1613 True 911.000000 1629 90.826000 35 1889 2 chr6D.!!$R3 1854
3 TraesCS6D01G022600 chr6A 9097566 9136034 38468 False 1173.173913 2167 87.728696 35 2558 23 chr6A.!!$F5 2523
4 TraesCS6D01G022600 chr6A 9181788 9182900 1112 False 918.000000 918 82.435000 1466 2558 1 chr6A.!!$F2 1092
5 TraesCS6D01G022600 chr6A 9069471 9071412 1941 False 761.666667 1676 90.260333 31 2067 3 chr6A.!!$F4 2036
6 TraesCS6D01G022600 chr6A 9053685 9055127 1442 False 761.500000 1404 91.831500 191 1824 2 chr6A.!!$F3 1633
7 TraesCS6D01G022600 chr6B 15884425 15886035 1610 True 963.500000 1624 90.263000 167 1786 2 chr6B.!!$R2 1619
8 TraesCS6D01G022600 chrUn 355456632 355457792 1160 True 1399.000000 1399 88.550000 726 1889 1 chrUn.!!$R1 1163
9 TraesCS6D01G022600 chrUn 396628213 396629365 1152 False 485.666667 1181 90.418667 35 1456 3 chrUn.!!$F1 1421

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
378 445 0.956633 ACCTGCACGAACTAGACGAA 59.043 50.0 17.34 5.45 34.7 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 37763 0.520404 GACGCTAGACCGACAAGTGA 59.48 55.0 0.0 0.0 0.0 3.41 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
118 148 4.603131 AGTCCCACGTAACTATAAGGTGA 58.397 43.478 0.00 0.00 0.00 4.02
123 153 7.981225 GTCCCACGTAACTATAAGGTGAAAATA 59.019 37.037 0.00 0.00 0.00 1.40
124 154 8.538701 TCCCACGTAACTATAAGGTGAAAATAA 58.461 33.333 0.00 0.00 0.00 1.40
125 155 9.165035 CCCACGTAACTATAAGGTGAAAATAAA 57.835 33.333 0.00 0.00 0.00 1.40
146 176 9.623350 AATAAAAATGGCAAAAATATGTGTTGC 57.377 25.926 8.90 8.90 45.48 4.17
151 181 4.551056 GCAAAAATATGTGTTGCACGAG 57.449 40.909 11.44 0.00 45.51 4.18
152 182 3.181541 GCAAAAATATGTGTTGCACGAGC 60.182 43.478 11.44 0.00 45.51 5.03
162 192 2.558313 GCACGAGCAAGGAACTGC 59.442 61.111 0.00 0.00 40.86 4.40
163 193 2.253758 GCACGAGCAAGGAACTGCA 61.254 57.895 0.00 0.00 40.86 4.41
164 194 1.571460 CACGAGCAAGGAACTGCAC 59.429 57.895 0.00 0.00 40.86 4.57
165 195 1.956170 ACGAGCAAGGAACTGCACG 60.956 57.895 12.65 12.65 45.32 5.34
174 204 1.613437 AGGAACTGCACGAAAAATGGG 59.387 47.619 0.00 0.00 37.18 4.00
319 375 2.095466 TGCACATACGTGGCTTTTTAGC 60.095 45.455 0.00 0.00 43.81 3.09
378 445 0.956633 ACCTGCACGAACTAGACGAA 59.043 50.000 17.34 5.45 34.70 3.85
390 457 7.266335 CACGAACTAGACGAAATTAGCAAAAAG 59.734 37.037 17.34 0.00 34.70 2.27
400 467 6.562086 CGAAATTAGCAAAAAGGAAACAGTGC 60.562 38.462 0.00 0.00 0.00 4.40
430 497 4.745125 TCGAGCTGTGCTATACTATTTTGC 59.255 41.667 0.00 0.00 39.88 3.68
483 550 8.962912 TTAATATACTTACTCCCTTAGTCCCC 57.037 38.462 0.00 0.00 39.80 4.81
488 555 6.618836 ACTTACTCCCTTAGTCCCCTAATA 57.381 41.667 0.00 0.00 39.80 0.98
496 563 6.023603 CCCTTAGTCCCCTAATATAAGAGCA 58.976 44.000 0.00 0.00 32.82 4.26
505 572 7.444183 TCCCCTAATATAAGAGCATTTTTGACG 59.556 37.037 0.00 0.00 0.00 4.35
506 573 7.308589 CCCCTAATATAAGAGCATTTTTGACGG 60.309 40.741 0.00 0.00 0.00 4.79
509 592 7.865706 AATATAAGAGCATTTTTGACGGACT 57.134 32.000 0.00 0.00 0.00 3.85
512 595 3.070018 AGAGCATTTTTGACGGACTCTG 58.930 45.455 0.00 0.00 32.06 3.35
523 606 9.878667 TTTTTGACGGACTCTGTTATATTATGA 57.121 29.630 0.00 0.00 0.00 2.15
547 630 6.612741 AGACGGAGGGAGTATTTATCTAACT 58.387 40.000 0.00 0.00 0.00 2.24
595 678 2.073816 GATGGTGTTAGTCGTGGTTGG 58.926 52.381 0.00 0.00 0.00 3.77
711 807 3.162666 TCCGTGTAATCCTGTCTCTGTT 58.837 45.455 0.00 0.00 0.00 3.16
713 809 4.768448 TCCGTGTAATCCTGTCTCTGTTTA 59.232 41.667 0.00 0.00 0.00 2.01
753 6868 6.477033 ACACGATATATATACGTCCGACCTAC 59.523 42.308 13.70 0.00 38.18 3.18
754 6869 6.699204 CACGATATATATACGTCCGACCTACT 59.301 42.308 13.70 0.00 38.18 2.57
755 6870 7.862873 CACGATATATATACGTCCGACCTACTA 59.137 40.741 13.70 0.00 38.18 1.82
808 6923 1.802960 CAGTGCCATGTCTGAACTCAC 59.197 52.381 4.47 0.00 34.02 3.51
886 22019 6.393990 CAGAAGCACTGTATAAAGTCAGACT 58.606 40.000 0.00 0.00 41.30 3.24
897 22030 1.631405 AGTCAGACTCTGCAGCTCTT 58.369 50.000 9.47 0.00 0.00 2.85
931 22064 3.916172 CACAATCAATCGAGGCAAACAAG 59.084 43.478 0.00 0.00 0.00 3.16
976 22114 4.455190 AGAAGTAGACGAGCGTTAGAGTTT 59.545 41.667 0.00 0.00 0.00 2.66
977 22115 5.641209 AGAAGTAGACGAGCGTTAGAGTTTA 59.359 40.000 0.00 0.00 0.00 2.01
978 22116 6.315891 AGAAGTAGACGAGCGTTAGAGTTTAT 59.684 38.462 0.00 0.00 0.00 1.40
979 22117 6.434018 AGTAGACGAGCGTTAGAGTTTATT 57.566 37.500 0.00 0.00 0.00 1.40
1008 22146 2.466846 TCAGTAGCTAAGATGGCCACA 58.533 47.619 8.16 0.00 0.00 4.17
1065 22203 3.706373 GCGCTCTCCACCTCCCAA 61.706 66.667 0.00 0.00 0.00 4.12
1347 25489 0.843309 TCTCCACTGGCTGGTTCAAA 59.157 50.000 0.00 0.00 41.52 2.69
1449 25591 3.999051 GTCTATGGCTGCGACGAC 58.001 61.111 0.00 0.00 0.00 4.34
1516 25658 3.443045 CTGCGGTGTGGAATGCCC 61.443 66.667 0.00 0.00 0.00 5.36
1575 25717 3.750130 CCTGGTCTGATGAGTGAGTTTTG 59.250 47.826 0.00 0.00 0.00 2.44
1578 25720 5.436175 TGGTCTGATGAGTGAGTTTTGAAA 58.564 37.500 0.00 0.00 0.00 2.69
1579 25721 5.885352 TGGTCTGATGAGTGAGTTTTGAAAA 59.115 36.000 0.00 0.00 0.00 2.29
1580 25722 6.376864 TGGTCTGATGAGTGAGTTTTGAAAAA 59.623 34.615 0.00 0.00 0.00 1.94
1610 37763 3.009473 AGGTGAGTGCAGGTTGTTGATAT 59.991 43.478 0.00 0.00 0.00 1.63
1623 37781 4.801330 TGTTGATATCACTTGTCGGTCT 57.199 40.909 4.48 0.00 0.00 3.85
1626 37784 4.569761 TGATATCACTTGTCGGTCTAGC 57.430 45.455 0.00 0.00 0.00 3.42
1639 37797 3.497262 TCGGTCTAGCGTCATGTGTATAG 59.503 47.826 1.14 0.00 0.00 1.31
1643 37801 5.206299 GTCTAGCGTCATGTGTATAGTGTC 58.794 45.833 0.00 0.00 0.00 3.67
1644 37802 5.007823 GTCTAGCGTCATGTGTATAGTGTCT 59.992 44.000 0.00 0.00 0.00 3.41
1646 37804 2.535984 GCGTCATGTGTATAGTGTCTGC 59.464 50.000 0.00 0.00 0.00 4.26
1652 37810 5.639082 TCATGTGTATAGTGTCTGCTTGTTG 59.361 40.000 0.00 0.00 0.00 3.33
1663 37821 2.968574 TCTGCTTGTTGGAGAGAAGTCT 59.031 45.455 0.00 0.00 38.24 3.24
1723 37881 4.628766 CAGATTCTGTATATGATGCCGTGG 59.371 45.833 5.46 0.00 0.00 4.94
1724 37882 3.401033 TTCTGTATATGATGCCGTGGG 57.599 47.619 0.00 0.00 0.00 4.61
1730 37888 5.000591 TGTATATGATGCCGTGGGTTTATG 58.999 41.667 0.00 0.00 0.00 1.90
1778 37936 2.860735 GCACCTATGAGATGTTCGTGTC 59.139 50.000 0.00 0.00 0.00 3.67
1797 37963 4.568760 GTGTCTGCTCTTCAAGGCTATAAC 59.431 45.833 0.00 0.00 0.00 1.89
1817 37983 2.289072 ACAGTGAGTAGTGTGGTGCATC 60.289 50.000 0.00 0.00 38.99 3.91
1877 38047 7.630082 TGTATACTCATTTTCAAGGGTAGCTT 58.370 34.615 4.17 0.00 0.00 3.74
1889 38059 9.796180 TTTCAAGGGTAGCTTAACAAGTATAAA 57.204 29.630 0.00 0.00 0.00 1.40
1971 38173 5.363101 TCTCTAATTCTACGGAGCGTTCTA 58.637 41.667 0.00 0.00 41.54 2.10
2021 38233 3.123620 GCAGCGCAGGAAGAGTGG 61.124 66.667 11.47 0.00 0.00 4.00
2022 38234 2.659016 CAGCGCAGGAAGAGTGGA 59.341 61.111 11.47 0.00 0.00 4.02
2030 38242 1.345741 CAGGAAGAGTGGAAGTGCTCA 59.654 52.381 0.00 0.00 34.39 4.26
2035 38247 3.777106 AGAGTGGAAGTGCTCAATGAA 57.223 42.857 0.00 0.00 34.39 2.57
2058 38270 6.759497 AGCAGATTTAACTCCCATAACAAC 57.241 37.500 0.00 0.00 0.00 3.32
2124 38354 3.255642 TGGCAAAAGCATGAGGAACTAAC 59.744 43.478 0.00 0.00 41.55 2.34
2126 38356 4.479619 GCAAAAGCATGAGGAACTAACAG 58.520 43.478 0.00 0.00 41.55 3.16
2136 38366 4.530553 TGAGGAACTAACAGTCCATGCTTA 59.469 41.667 0.00 0.00 41.55 3.09
2220 38452 2.232756 TGTTACAAGCGCTCAACTCA 57.767 45.000 12.06 5.36 0.00 3.41
2236 38489 1.562942 ACTCAGGCATGATGATGGTGT 59.437 47.619 0.00 0.00 34.12 4.16
2269 38522 4.340263 GAAAATTGATAACCTCGAACCGC 58.660 43.478 0.00 0.00 0.00 5.68
2274 38527 5.518848 TTGATAACCTCGAACCGCTAATA 57.481 39.130 0.00 0.00 0.00 0.98
2278 38531 3.433513 ACCTCGAACCGCTAATAAGTC 57.566 47.619 0.00 0.00 0.00 3.01
2282 38535 4.421948 CTCGAACCGCTAATAAGTCAGTT 58.578 43.478 0.00 0.00 0.00 3.16
2288 38541 2.284417 CGCTAATAAGTCAGTTTCGGCC 59.716 50.000 0.00 0.00 0.00 6.13
2289 38542 3.267483 GCTAATAAGTCAGTTTCGGCCA 58.733 45.455 2.24 0.00 0.00 5.36
2298 38551 4.636206 AGTCAGTTTCGGCCAATATCTTTC 59.364 41.667 2.24 0.00 0.00 2.62
2299 38552 4.636206 GTCAGTTTCGGCCAATATCTTTCT 59.364 41.667 2.24 0.00 0.00 2.52
2332 38586 8.575565 TTACATAGTTATCTCAGAAATGTCGC 57.424 34.615 0.00 0.00 0.00 5.19
2333 38587 6.810911 ACATAGTTATCTCAGAAATGTCGCT 58.189 36.000 0.00 0.00 0.00 4.93
2335 38589 8.414003 ACATAGTTATCTCAGAAATGTCGCTTA 58.586 33.333 0.00 0.00 0.00 3.09
2336 38590 9.249457 CATAGTTATCTCAGAAATGTCGCTTAA 57.751 33.333 0.00 0.00 0.00 1.85
2337 38591 7.527084 AGTTATCTCAGAAATGTCGCTTAAC 57.473 36.000 0.00 0.00 0.00 2.01
2338 38592 6.535508 AGTTATCTCAGAAATGTCGCTTAACC 59.464 38.462 0.00 0.00 0.00 2.85
2339 38593 3.596214 TCTCAGAAATGTCGCTTAACCC 58.404 45.455 0.00 0.00 0.00 4.11
2358 38612 1.137872 CCTTCGAAGAGTATGCTGCCT 59.862 52.381 26.61 0.00 38.43 4.75
2371 38625 3.541996 TGCTGCCTGAGATAATTTCGA 57.458 42.857 0.00 0.00 0.00 3.71
2376 38630 4.832248 TGCCTGAGATAATTTCGACAACT 58.168 39.130 0.00 0.00 0.00 3.16
2422 38677 7.491048 GGTGCATGATTACGGAAATTATTTTGT 59.509 33.333 0.00 0.00 0.00 2.83
2447 38702 9.204570 GTTGGCATACGAGTATTATCATACTTT 57.795 33.333 1.17 0.00 44.94 2.66
2480 38735 9.771534 CAAAAATATAAGGGAAGTTTGGTCAAA 57.228 29.630 0.00 0.00 0.00 2.69
2484 38739 2.666317 AGGGAAGTTTGGTCAAAGTGG 58.334 47.619 4.74 0.00 34.45 4.00
2487 38742 2.481276 GGAAGTTTGGTCAAAGTGGTGC 60.481 50.000 4.74 0.00 34.45 5.01
2501 38756 2.101249 AGTGGTGCCAAATTGTTGTGAG 59.899 45.455 0.00 0.00 32.40 3.51
2506 38761 3.316308 GTGCCAAATTGTTGTGAGAGACT 59.684 43.478 0.00 0.00 32.40 3.24
2507 38762 3.316029 TGCCAAATTGTTGTGAGAGACTG 59.684 43.478 0.00 0.00 32.40 3.51
2509 38764 3.567164 CCAAATTGTTGTGAGAGACTGCT 59.433 43.478 0.00 0.00 32.40 4.24
2510 38765 4.320057 CCAAATTGTTGTGAGAGACTGCTC 60.320 45.833 0.00 0.00 35.81 4.26
2518 38773 7.386059 TGTTGTGAGAGACTGCTCAATATAAA 58.614 34.615 0.00 0.00 45.69 1.40
2522 38777 9.702494 TGTGAGAGACTGCTCAATATAAATATG 57.298 33.333 0.00 0.00 45.69 1.78
2545 38801 8.904099 ATGTATACTAAACCACATAGCTTTCC 57.096 34.615 4.17 0.00 30.04 3.13
2558 38814 8.689972 CCACATAGCTTTCCTATTTTCTCAAAT 58.310 33.333 0.00 0.00 34.49 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.183368 TGCCACATGTTATTTATTCTTCACATA 57.817 29.630 0.00 0.00 0.00 2.29
22 23 8.065473 TGCCACATGTTATTTATTCTTCACAT 57.935 30.769 0.00 0.00 0.00 3.21
23 24 7.459795 TGCCACATGTTATTTATTCTTCACA 57.540 32.000 0.00 0.00 0.00 3.58
24 25 8.931385 AATGCCACATGTTATTTATTCTTCAC 57.069 30.769 0.00 0.00 0.00 3.18
25 26 9.941325 AAAATGCCACATGTTATTTATTCTTCA 57.059 25.926 0.00 0.00 0.00 3.02
31 32 9.462174 CGATGTAAAATGCCACATGTTATTTAT 57.538 29.630 0.00 0.00 35.55 1.40
32 33 7.918033 CCGATGTAAAATGCCACATGTTATTTA 59.082 33.333 0.00 0.00 35.55 1.40
33 34 6.756074 CCGATGTAAAATGCCACATGTTATTT 59.244 34.615 0.00 1.13 35.55 1.40
34 35 6.127479 ACCGATGTAAAATGCCACATGTTATT 60.127 34.615 0.00 0.00 35.55 1.40
35 36 5.359576 ACCGATGTAAAATGCCACATGTTAT 59.640 36.000 0.00 0.00 35.55 1.89
36 37 4.702612 ACCGATGTAAAATGCCACATGTTA 59.297 37.500 0.00 0.00 35.55 2.41
37 38 3.509575 ACCGATGTAAAATGCCACATGTT 59.490 39.130 0.00 0.00 35.55 2.71
38 39 3.088532 ACCGATGTAAAATGCCACATGT 58.911 40.909 0.00 0.00 35.55 3.21
39 40 3.437428 CACCGATGTAAAATGCCACATG 58.563 45.455 0.00 0.00 35.55 3.21
123 153 6.916932 GTGCAACACATATTTTTGCCATTTTT 59.083 30.769 9.23 0.00 44.14 1.94
124 154 6.437094 GTGCAACACATATTTTTGCCATTTT 58.563 32.000 9.23 0.00 44.14 1.82
125 155 5.333952 CGTGCAACACATATTTTTGCCATTT 60.334 36.000 9.23 0.00 44.14 2.32
126 156 4.152045 CGTGCAACACATATTTTTGCCATT 59.848 37.500 9.23 0.00 44.14 3.16
127 157 3.679025 CGTGCAACACATATTTTTGCCAT 59.321 39.130 9.23 0.00 44.14 4.40
128 158 3.055591 CGTGCAACACATATTTTTGCCA 58.944 40.909 9.23 0.00 44.14 4.92
129 159 3.312828 TCGTGCAACACATATTTTTGCC 58.687 40.909 9.23 2.60 44.14 4.52
130 160 3.181541 GCTCGTGCAACACATATTTTTGC 60.182 43.478 4.26 5.95 44.84 3.68
131 161 4.551056 GCTCGTGCAACACATATTTTTG 57.449 40.909 4.26 0.00 39.41 2.44
145 175 2.253758 TGCAGTTCCTTGCTCGTGC 61.254 57.895 1.71 1.71 44.38 5.34
146 176 1.571460 GTGCAGTTCCTTGCTCGTG 59.429 57.895 0.00 0.00 44.38 4.35
147 177 4.049393 GTGCAGTTCCTTGCTCGT 57.951 55.556 0.00 0.00 44.38 4.18
149 179 0.944386 TTTCGTGCAGTTCCTTGCTC 59.056 50.000 0.00 0.00 44.38 4.26
150 180 1.388547 TTTTCGTGCAGTTCCTTGCT 58.611 45.000 0.00 0.00 44.38 3.91
151 181 2.202295 TTTTTCGTGCAGTTCCTTGC 57.798 45.000 0.00 0.00 44.33 4.01
152 182 3.052036 CCATTTTTCGTGCAGTTCCTTG 58.948 45.455 0.00 0.00 0.00 3.61
153 183 2.035832 CCCATTTTTCGTGCAGTTCCTT 59.964 45.455 0.00 0.00 0.00 3.36
154 184 1.613437 CCCATTTTTCGTGCAGTTCCT 59.387 47.619 0.00 0.00 0.00 3.36
155 185 1.611491 TCCCATTTTTCGTGCAGTTCC 59.389 47.619 0.00 0.00 0.00 3.62
156 186 3.363341 TTCCCATTTTTCGTGCAGTTC 57.637 42.857 0.00 0.00 0.00 3.01
157 187 3.810310 TTTCCCATTTTTCGTGCAGTT 57.190 38.095 0.00 0.00 0.00 3.16
158 188 3.810310 TTTTCCCATTTTTCGTGCAGT 57.190 38.095 0.00 0.00 0.00 4.40
159 189 6.368516 ACATATTTTTCCCATTTTTCGTGCAG 59.631 34.615 0.00 0.00 0.00 4.41
160 190 6.146837 CACATATTTTTCCCATTTTTCGTGCA 59.853 34.615 0.00 0.00 0.00 4.57
161 191 6.147000 ACACATATTTTTCCCATTTTTCGTGC 59.853 34.615 0.00 0.00 0.00 5.34
162 192 7.650834 ACACATATTTTTCCCATTTTTCGTG 57.349 32.000 0.00 0.00 0.00 4.35
163 193 7.307692 GCAACACATATTTTTCCCATTTTTCGT 60.308 33.333 0.00 0.00 0.00 3.85
164 194 7.014702 GCAACACATATTTTTCCCATTTTTCG 58.985 34.615 0.00 0.00 0.00 3.46
165 195 7.802720 GTGCAACACATATTTTTCCCATTTTTC 59.197 33.333 0.00 0.00 36.32 2.29
174 204 4.908966 GCTGGTGCAACACATATTTTTC 57.091 40.909 0.00 0.00 39.98 2.29
264 294 3.823873 TGCGTTCTTGAAAATGGTACCAT 59.176 39.130 22.23 22.23 38.46 3.55
319 375 1.074566 AGGCTTCTTCCCTTGTCCTTG 59.925 52.381 0.00 0.00 0.00 3.61
378 445 5.056480 GGCACTGTTTCCTTTTTGCTAATT 58.944 37.500 0.00 0.00 0.00 1.40
400 467 2.302199 TAGCACAGCTCGATGCCAGG 62.302 60.000 9.89 0.00 43.12 4.45
476 543 9.793259 CAAAAATGCTCTTATATTAGGGGACTA 57.207 33.333 0.00 0.00 43.67 2.59
478 545 8.568794 GTCAAAAATGCTCTTATATTAGGGGAC 58.431 37.037 0.00 0.00 0.00 4.46
480 547 7.308589 CCGTCAAAAATGCTCTTATATTAGGGG 60.309 40.741 0.00 0.00 0.00 4.79
483 550 9.046296 AGTCCGTCAAAAATGCTCTTATATTAG 57.954 33.333 0.00 0.00 0.00 1.73
488 555 5.352569 CAGAGTCCGTCAAAAATGCTCTTAT 59.647 40.000 0.00 0.00 30.47 1.73
505 572 7.362229 CCTCCGTCTCATAATATAACAGAGTCC 60.362 44.444 0.00 0.00 0.00 3.85
506 573 7.362229 CCCTCCGTCTCATAATATAACAGAGTC 60.362 44.444 0.00 0.00 0.00 3.36
509 592 6.549242 TCCCTCCGTCTCATAATATAACAGA 58.451 40.000 0.00 0.00 0.00 3.41
512 595 6.837471 ACTCCCTCCGTCTCATAATATAAC 57.163 41.667 0.00 0.00 0.00 1.89
522 605 6.716173 AGTTAGATAAATACTCCCTCCGTCTC 59.284 42.308 0.00 0.00 0.00 3.36
523 606 6.612741 AGTTAGATAAATACTCCCTCCGTCT 58.387 40.000 0.00 0.00 0.00 4.18
571 654 2.832129 ACCACGACTAACACCATCTGAT 59.168 45.455 0.00 0.00 0.00 2.90
595 678 1.461127 CACACTTCTTAGCGGTGCTTC 59.539 52.381 0.00 0.00 40.44 3.86
639 732 8.456471 TCAAAGAACTGAATGAATTGATAGCAG 58.544 33.333 6.26 6.26 0.00 4.24
711 807 3.835978 TCGTGTCTCCTTGGGAAAGATAA 59.164 43.478 0.00 0.00 0.00 1.75
713 809 2.257207 TCGTGTCTCCTTGGGAAAGAT 58.743 47.619 0.00 0.00 0.00 2.40
782 6897 2.436646 GACATGGCACTGGTCCGG 60.437 66.667 0.00 0.00 0.00 5.14
808 6923 1.462616 TCTCCACGGCAAATCATTGG 58.537 50.000 0.00 0.00 37.02 3.16
872 22002 5.004922 AGCTGCAGAGTCTGACTTTATAC 57.995 43.478 24.55 3.83 32.44 1.47
886 22019 2.158827 TGTGTGGTTAAAGAGCTGCAGA 60.159 45.455 20.43 0.00 0.00 4.26
897 22030 5.297029 TCGATTGATTGTGTTGTGTGGTTAA 59.703 36.000 0.00 0.00 0.00 2.01
931 22064 1.079503 GTTGCTGCTACAGTACTGGC 58.920 55.000 26.12 20.14 33.43 4.85
976 22114 7.640597 TCTTAGCTACTGAACAGTGCTAATA 57.359 36.000 28.63 24.02 45.42 0.98
977 22115 6.531503 TCTTAGCTACTGAACAGTGCTAAT 57.468 37.500 28.63 15.70 45.42 1.73
978 22116 5.977489 TCTTAGCTACTGAACAGTGCTAA 57.023 39.130 27.75 27.75 45.00 3.09
979 22117 5.163509 CCATCTTAGCTACTGAACAGTGCTA 60.164 44.000 22.15 22.15 41.95 3.49
1230 25372 3.722147 GAAGCTGTTGAGAGTCAAGACA 58.278 45.455 2.72 0.00 37.00 3.41
1239 25381 1.273606 CCCTTCTCGAAGCTGTTGAGA 59.726 52.381 8.33 8.33 37.11 3.27
1287 25429 1.133598 TCACTATGGTAGGCGTTGTCG 59.866 52.381 0.00 0.00 40.37 4.35
1305 25447 1.476891 GCGACTACCATCTCCTTGTCA 59.523 52.381 0.00 0.00 0.00 3.58
1347 25489 3.679738 CCGCAACGGGCCATGTTT 61.680 61.111 4.39 0.00 44.15 2.83
1449 25591 1.445582 GGGCTCGTAGTTGTGGTCG 60.446 63.158 0.00 0.00 0.00 4.79
1578 25720 7.015195 ACAACCTGCACTCACCTTATTTATTTT 59.985 33.333 0.00 0.00 0.00 1.82
1579 25721 6.493458 ACAACCTGCACTCACCTTATTTATTT 59.507 34.615 0.00 0.00 0.00 1.40
1580 25722 6.010219 ACAACCTGCACTCACCTTATTTATT 58.990 36.000 0.00 0.00 0.00 1.40
1581 25723 5.570320 ACAACCTGCACTCACCTTATTTAT 58.430 37.500 0.00 0.00 0.00 1.40
1582 25724 4.980573 ACAACCTGCACTCACCTTATTTA 58.019 39.130 0.00 0.00 0.00 1.40
1595 37748 4.397420 ACAAGTGATATCAACAACCTGCA 58.603 39.130 7.07 0.00 0.00 4.41
1610 37763 0.520404 GACGCTAGACCGACAAGTGA 59.480 55.000 0.00 0.00 0.00 3.41
1623 37781 4.497507 GCAGACACTATACACATGACGCTA 60.498 45.833 0.00 0.00 0.00 4.26
1626 37784 4.033990 AGCAGACACTATACACATGACG 57.966 45.455 0.00 0.00 0.00 4.35
1639 37797 2.533266 TCTCTCCAACAAGCAGACAC 57.467 50.000 0.00 0.00 0.00 3.67
1643 37801 3.399440 AGACTTCTCTCCAACAAGCAG 57.601 47.619 0.00 0.00 0.00 4.24
1644 37802 3.898123 ACTAGACTTCTCTCCAACAAGCA 59.102 43.478 0.00 0.00 0.00 3.91
1646 37804 5.461032 ACACTAGACTTCTCTCCAACAAG 57.539 43.478 0.00 0.00 0.00 3.16
1652 37810 7.040961 GGATATGTGTACACTAGACTTCTCTCC 60.041 44.444 25.60 12.34 0.00 3.71
1663 37821 9.543783 CGCTCTATATAGGATATGTGTACACTA 57.456 37.037 25.60 15.59 0.00 2.74
1683 37841 2.124403 GACCGACCTCCCGCTCTA 60.124 66.667 0.00 0.00 0.00 2.43
1685 37843 3.827898 CTGACCGACCTCCCGCTC 61.828 72.222 0.00 0.00 0.00 5.03
1698 37856 5.347093 CACGGCATCATATACAGAATCTGAC 59.653 44.000 18.20 0.00 35.18 3.51
1730 37888 4.399303 ACCATAGGCTGCACTGTTTATTTC 59.601 41.667 0.50 0.00 0.00 2.17
1762 37920 3.696548 AGAGCAGACACGAACATCTCATA 59.303 43.478 0.00 0.00 0.00 2.15
1778 37936 4.569966 CACTGTTATAGCCTTGAAGAGCAG 59.430 45.833 8.07 1.84 0.00 4.24
1797 37963 2.289010 TGATGCACCACACTACTCACTG 60.289 50.000 0.00 0.00 0.00 3.66
1817 37983 3.058224 GTCTTGTCCGTTCCCAATTCTTG 60.058 47.826 0.00 0.00 0.00 3.02
1831 37997 2.147150 GCTTTCTCAGGTGTCTTGTCC 58.853 52.381 0.00 0.00 0.00 4.02
1832 37998 2.805099 CAGCTTTCTCAGGTGTCTTGTC 59.195 50.000 0.00 0.00 44.77 3.18
1889 38059 5.916318 TGCTCTGTGGAATTTGACAATTTT 58.084 33.333 0.00 0.00 32.35 1.82
1897 38067 2.421424 GGTAGCTGCTCTGTGGAATTTG 59.579 50.000 4.91 0.00 0.00 2.32
1907 38088 1.974236 ACTGTCTTTGGTAGCTGCTCT 59.026 47.619 4.91 0.00 0.00 4.09
1949 38147 4.555348 AGAACGCTCCGTAGAATTAGAG 57.445 45.455 0.00 0.00 39.99 2.43
2030 38242 7.615365 TGTTATGGGAGTTAAATCTGCTTCATT 59.385 33.333 2.56 0.00 0.00 2.57
2035 38247 6.485171 AGTTGTTATGGGAGTTAAATCTGCT 58.515 36.000 2.56 0.00 0.00 4.24
2058 38270 5.404366 CCATTTGTTGATTGCTTTGAGTGAG 59.596 40.000 0.00 0.00 0.00 3.51
2124 38354 4.913335 AAGCATCAATAAGCATGGACTG 57.087 40.909 0.00 0.00 0.00 3.51
2126 38356 6.742109 ACATTAAGCATCAATAAGCATGGAC 58.258 36.000 0.00 0.00 0.00 4.02
2136 38366 9.013229 TGACTTACTGAAACATTAAGCATCAAT 57.987 29.630 0.00 0.00 32.31 2.57
2220 38452 2.125233 AGAGACACCATCATCATGCCT 58.875 47.619 0.00 0.00 0.00 4.75
2236 38489 6.940298 AGGTTATCAATTTTCGGAACAAGAGA 59.060 34.615 0.00 0.00 0.00 3.10
2269 38522 7.657761 AGATATTGGCCGAAACTGACTTATTAG 59.342 37.037 0.00 0.00 0.00 1.73
2274 38527 4.222124 AGATATTGGCCGAAACTGACTT 57.778 40.909 0.00 0.00 0.00 3.01
2278 38531 6.677781 TTAGAAAGATATTGGCCGAAACTG 57.322 37.500 0.00 0.00 0.00 3.16
2282 38535 8.974060 AACTAATTAGAAAGATATTGGCCGAA 57.026 30.769 19.38 0.00 0.00 4.30
2319 38573 3.600388 AGGGTTAAGCGACATTTCTGAG 58.400 45.455 0.00 0.00 0.00 3.35
2321 38575 3.181520 CGAAGGGTTAAGCGACATTTCTG 60.182 47.826 0.00 0.00 0.00 3.02
2322 38576 3.000727 CGAAGGGTTAAGCGACATTTCT 58.999 45.455 0.00 0.00 0.00 2.52
2327 38581 1.614903 TCTTCGAAGGGTTAAGCGACA 59.385 47.619 24.37 0.00 31.91 4.35
2328 38582 2.260481 CTCTTCGAAGGGTTAAGCGAC 58.740 52.381 24.37 0.00 31.91 5.19
2330 38584 2.365408 ACTCTTCGAAGGGTTAAGCG 57.635 50.000 25.07 6.09 35.90 4.68
2331 38585 3.556365 GCATACTCTTCGAAGGGTTAAGC 59.444 47.826 34.07 28.07 40.91 3.09
2332 38586 4.806247 CAGCATACTCTTCGAAGGGTTAAG 59.194 45.833 34.07 23.49 40.91 1.85
2333 38587 4.755411 CAGCATACTCTTCGAAGGGTTAA 58.245 43.478 34.07 18.99 40.91 2.01
2335 38589 2.678190 GCAGCATACTCTTCGAAGGGTT 60.678 50.000 34.07 19.24 40.91 4.11
2336 38590 1.134670 GCAGCATACTCTTCGAAGGGT 60.135 52.381 31.91 31.91 43.51 4.34
2337 38591 1.576356 GCAGCATACTCTTCGAAGGG 58.424 55.000 23.55 23.55 0.00 3.95
2338 38592 1.137872 AGGCAGCATACTCTTCGAAGG 59.862 52.381 24.37 16.92 0.00 3.46
2339 38593 2.159184 TCAGGCAGCATACTCTTCGAAG 60.159 50.000 19.35 19.35 0.00 3.79
2358 38612 8.227791 GTGCTTTAAGTTGTCGAAATTATCTCA 58.772 33.333 0.00 0.00 0.00 3.27
2371 38625 6.980397 CCTGAAATGAAAGTGCTTTAAGTTGT 59.020 34.615 0.09 0.00 32.11 3.32
2376 38630 5.738783 GCACCCTGAAATGAAAGTGCTTTAA 60.739 40.000 5.73 0.00 45.40 1.52
2462 38717 4.211920 CCACTTTGACCAAACTTCCCTTA 58.788 43.478 0.00 0.00 0.00 2.69
2480 38735 2.101249 CTCACAACAATTTGGCACCACT 59.899 45.455 0.78 0.00 37.00 4.00
2484 38739 3.316308 AGTCTCTCACAACAATTTGGCAC 59.684 43.478 0.78 0.00 37.00 5.01
2487 38742 3.567164 AGCAGTCTCTCACAACAATTTGG 59.433 43.478 0.78 0.00 37.00 3.28
2521 38776 8.086143 AGGAAAGCTATGTGGTTTAGTATACA 57.914 34.615 5.50 0.00 45.15 2.29
2525 38781 9.969001 AAAATAGGAAAGCTATGTGGTTTAGTA 57.031 29.630 0.00 0.00 45.15 1.82
2532 38788 7.630242 TTGAGAAAATAGGAAAGCTATGTGG 57.370 36.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.