Multiple sequence alignment - TraesCS1A01G316900

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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 TraesCS1A01G316900 chr1A 100.000 2782 0 0 1 2782 508526082 508528863 0.000000e+00 5138.0
1 TraesCS1A01G316900 chr1D 87.005 2147 160 61 1 2103 412021894 412023965 0.000000e+00 2309.0
2 TraesCS1A01G316900 chr1B 88.389 1266 75 27 1 1222 555292522 555293759 0.000000e+00 1458.0
3 TraesCS1A01G316900 chr1B 87.634 1027 81 28 1222 2216 555293787 555294799 0.000000e+00 1151.0
4 TraesCS1A01G316900 chr5D 92.481 532 27 2 2212 2731 537389270 537388740 0.000000e+00 749.0
5 TraesCS1A01G316900 chr5D 98.039 51 1 0 2732 2782 537388758 537388708 3.820000e-14 89.8
6 TraesCS1A01G316900 chr4D 92.264 530 28 2 2214 2731 311166859 311166331 0.000000e+00 739.0
7 TraesCS1A01G316900 chr4D 98.039 51 1 0 2732 2782 311166349 311166299 3.820000e-14 89.8
8 TraesCS1A01G316900 chr3B 93.028 502 22 2 2214 2703 717037725 717038225 0.000000e+00 721.0
9 TraesCS1A01G316900 chr3B 92.629 502 24 2 2214 2703 578631363 578631863 0.000000e+00 710.0
10 TraesCS1A01G316900 chr3B 91.929 508 28 2 2211 2706 578634525 578634019 0.000000e+00 699.0
11 TraesCS1A01G316900 chr3B 78.961 385 70 10 1270 1651 566835226 566834850 4.600000e-63 252.0
12 TraesCS1A01G316900 chr3B 97.778 45 1 0 2735 2779 578631858 578631902 8.260000e-11 78.7
13 TraesCS1A01G316900 chr3B 95.833 48 2 0 2735 2782 578634027 578633980 8.260000e-11 78.7
14 TraesCS1A01G316900 chr3B 97.778 45 1 0 2735 2779 717038220 717038264 8.260000e-11 78.7
15 TraesCS1A01G316900 chr6D 91.095 539 31 4 2205 2731 464073520 464074053 0.000000e+00 713.0
16 TraesCS1A01G316900 chr6D 80.000 135 27 0 2211 2345 308933115 308932981 1.760000e-17 100.0
17 TraesCS1A01G316900 chr6D 98.039 51 1 0 2732 2782 464074035 464074085 3.820000e-14 89.8
18 TraesCS1A01G316900 chr2D 83.796 216 35 0 1291 1506 192156799 192156584 3.630000e-49 206.0


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 TraesCS1A01G316900 chr1A 508526082 508528863 2781 False 5138.00 5138 100.0000 1 2782 1 chr1A.!!$F1 2781
1 TraesCS1A01G316900 chr1D 412021894 412023965 2071 False 2309.00 2309 87.0050 1 2103 1 chr1D.!!$F1 2102
2 TraesCS1A01G316900 chr1B 555292522 555294799 2277 False 1304.50 1458 88.0115 1 2216 2 chr1B.!!$F1 2215
3 TraesCS1A01G316900 chr5D 537388708 537389270 562 True 419.40 749 95.2600 2212 2782 2 chr5D.!!$R1 570
4 TraesCS1A01G316900 chr4D 311166299 311166859 560 True 414.40 739 95.1515 2214 2782 2 chr4D.!!$R1 568
5 TraesCS1A01G316900 chr3B 717037725 717038264 539 False 399.85 721 95.4030 2214 2779 2 chr3B.!!$F2 565
6 TraesCS1A01G316900 chr3B 578631363 578631902 539 False 394.35 710 95.2035 2214 2779 2 chr3B.!!$F1 565
7 TraesCS1A01G316900 chr3B 578633980 578634525 545 True 388.85 699 93.8810 2211 2782 2 chr3B.!!$R2 571
8 TraesCS1A01G316900 chr6D 464073520 464074085 565 False 401.40 713 94.5670 2205 2782 2 chr6D.!!$F1 577

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
802 851 0.250209 TACTAGGTCTCGGCTAGGCG 60.25 60.0 31.0 31.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2308 0.032952 TAAGCGGTGTGGTGTCAGAC 59.967 55.0 0.0 0.0 36.55 3.51 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
94 104 6.183360 CGGTTTGCCTAATTATACGTTTCCTT 60.183 38.462 0.00 0.00 0.00 3.36
157 167 0.535102 CCGCCTCTCTCTCTCTCTCC 60.535 65.000 0.00 0.00 0.00 3.71
158 168 0.469917 CGCCTCTCTCTCTCTCTCCT 59.530 60.000 0.00 0.00 0.00 3.69
216 250 1.623311 GGCCAGCAAAAAGGTAACCAT 59.377 47.619 0.00 0.00 37.17 3.55
358 394 3.577231 CGGATCTCGCAGCTGTAAT 57.423 52.632 16.64 3.82 0.00 1.89
359 395 2.706555 CGGATCTCGCAGCTGTAATA 57.293 50.000 16.64 0.00 0.00 0.98
360 396 2.590073 CGGATCTCGCAGCTGTAATAG 58.410 52.381 16.64 7.89 0.00 1.73
396 433 1.638529 TTTTGGTGCCCGGATTTGAT 58.361 45.000 0.73 0.00 0.00 2.57
417 454 1.127951 GCGATTGGTTGTCGATTTCGT 59.872 47.619 0.00 0.00 41.40 3.85
472 509 2.735134 GCGATCTGTGTCGGTTTAGTTT 59.265 45.455 0.00 0.00 41.72 2.66
568 607 1.852942 TGGTTATTCTCGCGATCTGC 58.147 50.000 10.36 0.00 41.47 4.26
637 676 2.297698 TGGGAGAACTTGGTCTCGTA 57.702 50.000 9.27 0.00 44.30 3.43
638 677 2.168496 TGGGAGAACTTGGTCTCGTAG 58.832 52.381 9.27 0.00 44.30 3.51
639 678 2.224942 TGGGAGAACTTGGTCTCGTAGA 60.225 50.000 9.27 0.00 44.30 2.59
659 699 3.780850 AGAGTCGGGGAAATGGTTAGATT 59.219 43.478 0.00 0.00 0.00 2.40
663 703 3.054948 TCGGGGAAATGGTTAGATTCGTT 60.055 43.478 0.00 0.00 0.00 3.85
715 756 3.179830 CTGTAATCCTCGGACAGTTTCG 58.820 50.000 0.00 0.00 36.62 3.46
732 773 5.235186 CAGTTTCGTCTCTGTTCATCTGTTT 59.765 40.000 0.00 0.00 0.00 2.83
735 776 3.574396 TCGTCTCTGTTCATCTGTTTCCT 59.426 43.478 0.00 0.00 0.00 3.36
755 804 3.370104 CTGGGAGGTCTGTAGATCTGTT 58.630 50.000 5.18 0.00 35.24 3.16
756 805 3.099905 TGGGAGGTCTGTAGATCTGTTG 58.900 50.000 5.18 0.00 35.24 3.33
757 806 3.245622 TGGGAGGTCTGTAGATCTGTTGA 60.246 47.826 5.18 0.00 35.24 3.18
758 807 3.769844 GGGAGGTCTGTAGATCTGTTGAA 59.230 47.826 5.18 0.00 35.24 2.69
759 808 4.382147 GGGAGGTCTGTAGATCTGTTGAAC 60.382 50.000 5.18 3.16 35.24 3.18
760 809 4.464597 GGAGGTCTGTAGATCTGTTGAACT 59.535 45.833 5.18 8.13 35.24 3.01
761 810 5.398603 AGGTCTGTAGATCTGTTGAACTG 57.601 43.478 5.18 0.00 33.50 3.16
762 811 3.929610 GGTCTGTAGATCTGTTGAACTGC 59.070 47.826 5.18 0.00 0.00 4.40
775 824 1.673920 TGAACTGCTTCGTTTTGGTCC 59.326 47.619 0.00 0.00 0.00 4.46
802 851 0.250209 TACTAGGTCTCGGCTAGGCG 60.250 60.000 31.00 31.00 0.00 5.52
803 852 2.905880 TAGGTCTCGGCTAGGCGC 60.906 66.667 31.86 18.68 38.13 6.53
846 895 3.552132 TTTGCTTCGGTCCTGCATATA 57.448 42.857 0.00 0.00 36.55 0.86
847 896 3.769739 TTGCTTCGGTCCTGCATATAT 57.230 42.857 0.00 0.00 36.55 0.86
958 1009 2.452600 AAGGCCAACAAGAGAAACCA 57.547 45.000 5.01 0.00 0.00 3.67
1048 1099 0.392461 TGCCTTCGGTATGCTTCCAC 60.392 55.000 0.00 0.00 0.00 4.02
1183 1239 8.419076 AAATTTGGAAATTTGTGTGTAGTCAC 57.581 30.769 8.88 0.00 44.46 3.67
1184 1240 5.508200 TTGGAAATTTGTGTGTAGTCACC 57.492 39.130 0.00 0.00 43.26 4.02
1185 1241 4.787551 TGGAAATTTGTGTGTAGTCACCT 58.212 39.130 0.00 0.00 43.26 4.00
1186 1242 4.578516 TGGAAATTTGTGTGTAGTCACCTG 59.421 41.667 0.00 0.00 43.26 4.00
1187 1243 4.819630 GGAAATTTGTGTGTAGTCACCTGA 59.180 41.667 0.00 0.00 43.26 3.86
1189 1245 6.348540 GGAAATTTGTGTGTAGTCACCTGATC 60.349 42.308 0.00 0.00 43.26 2.92
1190 1246 4.681074 TTTGTGTGTAGTCACCTGATCA 57.319 40.909 0.00 0.00 43.26 2.92
1191 1247 4.890158 TTGTGTGTAGTCACCTGATCAT 57.110 40.909 0.00 0.00 43.26 2.45
1192 1248 4.456280 TGTGTGTAGTCACCTGATCATC 57.544 45.455 0.00 0.00 43.26 2.92
1193 1249 3.195610 TGTGTGTAGTCACCTGATCATCC 59.804 47.826 0.00 0.00 43.26 3.51
1263 1349 2.906691 ACATGAGCTCTGCCTACATC 57.093 50.000 16.19 0.00 0.00 3.06
1266 1352 3.181467 ACATGAGCTCTGCCTACATCTTC 60.181 47.826 16.19 0.00 0.00 2.87
1278 1364 4.383552 GCCTACATCTTCTCTGACATGGTT 60.384 45.833 0.00 0.00 0.00 3.67
1491 1577 1.195115 GCACAGTAGTCCAGGATCCA 58.805 55.000 15.82 0.00 0.00 3.41
1507 1593 0.397254 TCCAGAGCTAGGCCAGGTAC 60.397 60.000 5.01 1.26 34.30 3.34
1511 1597 0.599060 GAGCTAGGCCAGGTACGATC 59.401 60.000 5.01 0.00 34.30 3.69
1512 1598 0.186386 AGCTAGGCCAGGTACGATCT 59.814 55.000 5.01 0.00 31.65 2.75
1513 1599 0.599060 GCTAGGCCAGGTACGATCTC 59.401 60.000 5.01 0.00 0.00 2.75
1514 1600 1.982660 CTAGGCCAGGTACGATCTCA 58.017 55.000 5.01 0.00 0.00 3.27
1515 1601 1.883275 CTAGGCCAGGTACGATCTCAG 59.117 57.143 5.01 0.00 0.00 3.35
1516 1602 0.259065 AGGCCAGGTACGATCTCAGA 59.741 55.000 5.01 0.00 0.00 3.27
1517 1603 1.133325 AGGCCAGGTACGATCTCAGAT 60.133 52.381 5.01 0.00 0.00 2.90
1518 1604 2.108425 AGGCCAGGTACGATCTCAGATA 59.892 50.000 5.01 0.00 0.00 1.98
1520 1606 3.150767 GCCAGGTACGATCTCAGATACT 58.849 50.000 0.00 0.00 0.00 2.12
1521 1607 3.570550 GCCAGGTACGATCTCAGATACTT 59.429 47.826 0.00 0.00 0.00 2.24
1523 1609 5.241064 GCCAGGTACGATCTCAGATACTTTA 59.759 44.000 0.00 0.00 0.00 1.85
1524 1610 6.238953 GCCAGGTACGATCTCAGATACTTTAA 60.239 42.308 0.00 0.00 0.00 1.52
1525 1611 7.140048 CCAGGTACGATCTCAGATACTTTAAC 58.860 42.308 0.00 0.00 0.00 2.01
1527 1613 8.407064 CAGGTACGATCTCAGATACTTTAACTT 58.593 37.037 0.00 0.00 0.00 2.66
1529 1615 9.662545 GGTACGATCTCAGATACTTTAACTTAC 57.337 37.037 0.00 0.00 0.00 2.34
1555 1642 5.600484 TCCATCTAGTTCTCAATTCTCTCCC 59.400 44.000 0.00 0.00 0.00 4.30
1557 1644 3.954904 TCTAGTTCTCAATTCTCTCCCGG 59.045 47.826 0.00 0.00 0.00 5.73
1577 1664 4.583489 CCGGTGTTGGTATACTGACTAGAT 59.417 45.833 2.25 0.00 0.00 1.98
1578 1665 5.766670 CCGGTGTTGGTATACTGACTAGATA 59.233 44.000 2.25 0.00 0.00 1.98
1579 1666 6.263842 CCGGTGTTGGTATACTGACTAGATAA 59.736 42.308 2.25 0.00 0.00 1.75
1581 1668 8.358148 CGGTGTTGGTATACTGACTAGATAATT 58.642 37.037 2.25 0.00 0.00 1.40
1651 1738 4.880164 TGCTACTTTCCTAGTCCAGGTAT 58.120 43.478 0.00 0.00 45.71 2.73
1659 1748 3.201487 TCCTAGTCCAGGTATCTTCGACA 59.799 47.826 3.42 0.00 45.71 4.35
1662 1751 2.959707 AGTCCAGGTATCTTCGACATCC 59.040 50.000 3.42 0.00 0.00 3.51
1681 1770 5.047802 ACATCCAACAAGATGAACACCATTC 60.048 40.000 8.44 0.00 45.43 2.67
1692 1781 6.845758 ATGAACACCATTCATCATTCTGTT 57.154 33.333 0.00 0.00 34.28 3.16
1705 1795 7.307694 TCATCATTCTGTTAATGTTTCTGTGC 58.692 34.615 0.00 0.00 0.00 4.57
1706 1796 6.631971 TCATTCTGTTAATGTTTCTGTGCA 57.368 33.333 0.00 0.00 0.00 4.57
1708 1798 8.334263 TCATTCTGTTAATGTTTCTGTGCATA 57.666 30.769 0.00 0.00 0.00 3.14
1713 1803 8.236586 TCTGTTAATGTTTCTGTGCATAATCAC 58.763 33.333 0.00 0.00 37.48 3.06
1714 1804 8.109705 TGTTAATGTTTCTGTGCATAATCACT 57.890 30.769 0.00 0.00 37.81 3.41
1716 1806 8.853345 GTTAATGTTTCTGTGCATAATCACTTG 58.147 33.333 0.00 0.00 37.81 3.16
1717 1807 6.579666 ATGTTTCTGTGCATAATCACTTGT 57.420 33.333 0.00 0.00 37.81 3.16
1718 1808 6.000891 TGTTTCTGTGCATAATCACTTGTC 57.999 37.500 0.00 0.00 37.81 3.18
1721 1811 2.684881 CTGTGCATAATCACTTGTCCCC 59.315 50.000 0.00 0.00 37.81 4.81
1724 1814 3.763897 GTGCATAATCACTTGTCCCCTTT 59.236 43.478 0.00 0.00 34.29 3.11
1725 1815 4.016444 TGCATAATCACTTGTCCCCTTTC 58.984 43.478 0.00 0.00 0.00 2.62
1726 1816 4.263905 TGCATAATCACTTGTCCCCTTTCT 60.264 41.667 0.00 0.00 0.00 2.52
1727 1817 4.336713 GCATAATCACTTGTCCCCTTTCTC 59.663 45.833 0.00 0.00 0.00 2.87
1728 1818 3.441500 AATCACTTGTCCCCTTTCTCC 57.558 47.619 0.00 0.00 0.00 3.71
1730 1820 1.978580 TCACTTGTCCCCTTTCTCCTC 59.021 52.381 0.00 0.00 0.00 3.71
1731 1821 1.981495 CACTTGTCCCCTTTCTCCTCT 59.019 52.381 0.00 0.00 0.00 3.69
1732 1822 1.981495 ACTTGTCCCCTTTCTCCTCTG 59.019 52.381 0.00 0.00 0.00 3.35
1733 1823 0.693049 TTGTCCCCTTTCTCCTCTGC 59.307 55.000 0.00 0.00 0.00 4.26
1734 1824 0.178891 TGTCCCCTTTCTCCTCTGCT 60.179 55.000 0.00 0.00 0.00 4.24
1742 1832 0.336392 TTCTCCTCTGCTAGGCTGGA 59.664 55.000 0.43 0.00 46.10 3.86
1806 1896 2.617274 GCCGCCTCCGATAAATGCC 61.617 63.158 0.00 0.00 36.29 4.40
1842 1932 6.016108 GCCGGTTCTACTCTATATTGAAGACT 60.016 42.308 1.90 0.00 0.00 3.24
1877 1969 4.383602 CGCCCGCTTGTTGAACCG 62.384 66.667 0.00 0.00 0.00 4.44
1880 1972 2.190841 CCCGCTTGTTGAACCGGTT 61.191 57.895 22.50 22.50 39.12 4.44
1912 2004 1.202290 GCAAGTTGTGTTGTCACCTGG 60.202 52.381 4.48 0.00 43.26 4.45
1957 2049 6.992123 CCAGCATATCAGTATGGTTTGTCTAA 59.008 38.462 0.00 0.00 44.37 2.10
2000 2092 4.330944 AATCCGTATCGTTTGGCTATGA 57.669 40.909 0.00 0.00 0.00 2.15
2005 2097 3.975670 CGTATCGTTTGGCTATGACTCTC 59.024 47.826 0.00 0.00 0.00 3.20
2006 2098 4.497507 CGTATCGTTTGGCTATGACTCTCA 60.498 45.833 0.00 0.00 0.00 3.27
2019 2111 3.486383 TGACTCTCATTTTGGTCCCAAC 58.514 45.455 0.00 0.00 35.46 3.77
2033 2125 2.292569 GTCCCAACTTTCGTTTCCTTCC 59.707 50.000 0.00 0.00 0.00 3.46
2045 2137 2.536761 TTCCTTCCGTTGTCGTGATT 57.463 45.000 0.00 0.00 35.01 2.57
2053 2145 1.464023 CGTTGTCGTGATTGTGGATGC 60.464 52.381 0.00 0.00 0.00 3.91
2091 2186 1.065272 TGATGAGCCTAATGTGCTGCA 60.065 47.619 0.00 0.00 39.69 4.41
2092 2187 1.332997 GATGAGCCTAATGTGCTGCAC 59.667 52.381 25.15 25.15 39.69 4.57
2099 2194 1.298157 TAATGTGCTGCACGCTGGTC 61.298 55.000 25.88 2.78 37.14 4.02
2107 2202 2.433145 CACGCTGGTCGCTGATGT 60.433 61.111 0.00 0.00 43.23 3.06
2108 2203 2.433145 ACGCTGGTCGCTGATGTG 60.433 61.111 0.00 0.00 43.23 3.21
2109 2204 2.433145 CGCTGGTCGCTGATGTGT 60.433 61.111 0.00 0.00 36.13 3.72
2110 2205 2.733671 CGCTGGTCGCTGATGTGTG 61.734 63.158 0.00 0.00 36.13 3.82
2111 2206 2.393768 GCTGGTCGCTGATGTGTGG 61.394 63.158 0.00 0.00 35.14 4.17
2112 2207 1.004560 CTGGTCGCTGATGTGTGGT 60.005 57.895 0.00 0.00 0.00 4.16
2116 2229 2.048222 CGCTGATGTGTGGTCCGT 60.048 61.111 0.00 0.00 0.00 4.69
2119 2232 1.291877 GCTGATGTGTGGTCCGTGTC 61.292 60.000 0.00 0.00 0.00 3.67
2122 2235 1.006571 ATGTGTGGTCCGTGTCGTC 60.007 57.895 0.00 0.00 0.00 4.20
2126 2239 1.663702 GTGGTCCGTGTCGTCTTGG 60.664 63.158 0.00 0.00 0.00 3.61
2131 2244 3.103911 CGTGTCGTCTTGGCGGAC 61.104 66.667 0.00 1.12 0.00 4.79
2173 2287 1.130561 GGCACGAACCAAATCTGTAGC 59.869 52.381 0.00 0.00 0.00 3.58
2177 2291 2.029290 ACGAACCAAATCTGTAGCTCGT 60.029 45.455 0.00 0.00 33.76 4.18
2185 2299 3.773860 ATCTGTAGCTCGTCAGACAAG 57.226 47.619 15.17 0.00 42.30 3.16
2194 2308 3.386379 GTCAGACAAGGACGAGTCG 57.614 57.895 11.85 11.85 39.67 4.18
2318 2432 5.365314 GGTGCCATAAAAATATTCCAGGGAA 59.635 40.000 2.75 2.75 38.59 3.97
2397 2511 9.642343 TTAAAGTATAACTGCCATCTCTAGAGA 57.358 33.333 24.36 24.36 42.37 3.10
2459 2573 5.587388 ATCCATACCAAACAGCATTCAAG 57.413 39.130 0.00 0.00 0.00 3.02
2487 2601 3.807553 CAAACCAGAGCACCCAAATTTT 58.192 40.909 0.00 0.00 0.00 1.82
2508 2622 0.534877 AGATGACCGTTGCACTGCAA 60.535 50.000 12.59 12.59 46.80 4.08
2521 2635 5.710513 TGCACTGCAATAGAAAAATCTGT 57.289 34.783 0.00 0.00 34.76 3.41
2608 2722 3.611025 AAACTCTCCCCCAAAACATGA 57.389 42.857 0.00 0.00 0.00 3.07
2644 2770 2.172293 AGCATGATGAACTCCTCCTTCC 59.828 50.000 0.00 0.00 0.00 3.46
2670 2796 1.005097 TCAGATGCACAGAGCCCAAAT 59.995 47.619 0.00 0.00 44.83 2.32
2695 2821 1.915141 ACAAAATCCACAGAGCCCAG 58.085 50.000 0.00 0.00 0.00 4.45
2720 2864 9.338622 AGTTAGTTTGCAGTACAATTCTAGTTT 57.661 29.630 0.00 0.00 38.31 2.66
2721 2865 9.595357 GTTAGTTTGCAGTACAATTCTAGTTTC 57.405 33.333 0.00 0.00 38.31 2.78
2722 2866 7.203255 AGTTTGCAGTACAATTCTAGTTTCC 57.797 36.000 0.00 0.00 38.31 3.13
2723 2867 6.770785 AGTTTGCAGTACAATTCTAGTTTCCA 59.229 34.615 0.00 0.00 38.31 3.53
2724 2868 7.448469 AGTTTGCAGTACAATTCTAGTTTCCAT 59.552 33.333 0.00 0.00 38.31 3.41
2725 2869 6.985188 TGCAGTACAATTCTAGTTTCCATC 57.015 37.500 0.00 0.00 0.00 3.51
2726 2870 5.880332 TGCAGTACAATTCTAGTTTCCATCC 59.120 40.000 0.00 0.00 0.00 3.51
2727 2871 5.297029 GCAGTACAATTCTAGTTTCCATCCC 59.703 44.000 0.00 0.00 0.00 3.85
2728 2872 5.823045 CAGTACAATTCTAGTTTCCATCCCC 59.177 44.000 0.00 0.00 0.00 4.81
2729 2873 4.946160 ACAATTCTAGTTTCCATCCCCA 57.054 40.909 0.00 0.00 0.00 4.96
2730 2874 5.472301 ACAATTCTAGTTTCCATCCCCAT 57.528 39.130 0.00 0.00 0.00 4.00
2731 2875 5.842339 ACAATTCTAGTTTCCATCCCCATT 58.158 37.500 0.00 0.00 0.00 3.16
2732 2876 6.263754 ACAATTCTAGTTTCCATCCCCATTT 58.736 36.000 0.00 0.00 0.00 2.32
2733 2877 6.381133 ACAATTCTAGTTTCCATCCCCATTTC 59.619 38.462 0.00 0.00 0.00 2.17
2734 2878 5.796502 TTCTAGTTTCCATCCCCATTTCT 57.203 39.130 0.00 0.00 0.00 2.52
2735 2879 6.901615 TTCTAGTTTCCATCCCCATTTCTA 57.098 37.500 0.00 0.00 0.00 2.10
2736 2880 6.500589 TCTAGTTTCCATCCCCATTTCTAG 57.499 41.667 0.00 0.00 0.00 2.43
2737 2881 5.970640 TCTAGTTTCCATCCCCATTTCTAGT 59.029 40.000 0.00 0.00 0.00 2.57
2738 2882 5.536497 AGTTTCCATCCCCATTTCTAGTT 57.464 39.130 0.00 0.00 0.00 2.24
2769 2913 7.185120 TCCCCATCATCCACATATGAATTATCT 59.815 37.037 10.38 0.00 39.25 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 104 0.812549 TGTCGCGCACTTATAGTGGA 59.187 50.000 8.75 0.00 46.01 4.02
128 138 1.227205 GAGAGGCGGATGTGAGCTG 60.227 63.158 0.00 0.00 0.00 4.24
203 237 3.257375 GGAAAGCGGATGGTTACCTTTTT 59.743 43.478 2.07 0.00 33.97 1.94
353 389 0.834612 CCCAAGTCCCCGCTATTACA 59.165 55.000 0.00 0.00 0.00 2.41
354 390 0.108019 CCCCAAGTCCCCGCTATTAC 59.892 60.000 0.00 0.00 0.00 1.89
355 391 1.057851 CCCCCAAGTCCCCGCTATTA 61.058 60.000 0.00 0.00 0.00 0.98
356 392 2.383601 CCCCCAAGTCCCCGCTATT 61.384 63.158 0.00 0.00 0.00 1.73
357 393 2.772622 CCCCCAAGTCCCCGCTAT 60.773 66.667 0.00 0.00 0.00 2.97
396 433 1.127766 CGAAATCGACAACCAATCGCA 59.872 47.619 0.00 0.00 43.02 5.10
403 440 1.523934 ACGAACACGAAATCGACAACC 59.476 47.619 10.16 0.00 41.43 3.77
407 444 0.179258 GCCACGAACACGAAATCGAC 60.179 55.000 10.16 0.00 41.43 4.20
417 454 2.031012 CCTCAGCAGCCACGAACA 59.969 61.111 0.00 0.00 0.00 3.18
472 509 1.600636 CAAAGCCTGACCAGCCGAA 60.601 57.895 0.00 0.00 0.00 4.30
568 607 5.878116 AGCTATATACGGAGTTCTAGCAGAG 59.122 44.000 0.00 0.00 37.78 3.35
637 676 2.829023 TCTAACCATTTCCCCGACTCT 58.171 47.619 0.00 0.00 0.00 3.24
638 677 3.840124 ATCTAACCATTTCCCCGACTC 57.160 47.619 0.00 0.00 0.00 3.36
639 678 3.431766 CGAATCTAACCATTTCCCCGACT 60.432 47.826 0.00 0.00 0.00 4.18
640 679 2.870411 CGAATCTAACCATTTCCCCGAC 59.130 50.000 0.00 0.00 0.00 4.79
641 680 2.502538 ACGAATCTAACCATTTCCCCGA 59.497 45.455 0.00 0.00 0.00 5.14
642 681 2.914059 ACGAATCTAACCATTTCCCCG 58.086 47.619 0.00 0.00 0.00 5.73
659 699 2.093625 GCATAGTGCGACAAATCAACGA 59.906 45.455 0.00 0.00 31.71 3.85
708 749 4.302455 ACAGATGAACAGAGACGAAACTG 58.698 43.478 0.00 0.00 39.65 3.16
715 756 3.999663 CCAGGAAACAGATGAACAGAGAC 59.000 47.826 0.00 0.00 0.00 3.36
732 773 2.091610 CAGATCTACAGACCTCCCAGGA 60.092 54.545 0.00 0.00 37.67 3.86
735 776 3.099905 CAACAGATCTACAGACCTCCCA 58.900 50.000 0.00 0.00 0.00 4.37
755 804 1.673920 GGACCAAAACGAAGCAGTTCA 59.326 47.619 0.00 0.00 32.43 3.18
756 805 1.673920 TGGACCAAAACGAAGCAGTTC 59.326 47.619 0.00 0.00 32.43 3.01
757 806 1.757682 TGGACCAAAACGAAGCAGTT 58.242 45.000 0.00 0.00 35.59 3.16
758 807 1.608590 CATGGACCAAAACGAAGCAGT 59.391 47.619 0.00 0.00 0.00 4.40
759 808 1.879380 TCATGGACCAAAACGAAGCAG 59.121 47.619 0.00 0.00 0.00 4.24
760 809 1.974265 TCATGGACCAAAACGAAGCA 58.026 45.000 0.00 0.00 0.00 3.91
761 810 2.293399 ACTTCATGGACCAAAACGAAGC 59.707 45.455 18.81 0.00 34.57 3.86
762 811 4.568152 AACTTCATGGACCAAAACGAAG 57.432 40.909 17.91 17.91 36.72 3.79
775 824 3.381908 AGCCGAGACCTAGTAACTTCATG 59.618 47.826 0.00 0.00 0.00 3.07
803 852 2.831742 TACCCTCACGCCTAGCCG 60.832 66.667 0.00 0.00 0.00 5.52
804 853 2.794028 GGTACCCTCACGCCTAGCC 61.794 68.421 0.00 0.00 0.00 3.93
805 854 1.757340 AGGTACCCTCACGCCTAGC 60.757 63.158 8.74 0.00 0.00 3.42
806 855 0.395311 TCAGGTACCCTCACGCCTAG 60.395 60.000 8.74 0.00 0.00 3.02
807 856 0.260816 ATCAGGTACCCTCACGCCTA 59.739 55.000 8.74 0.00 0.00 3.93
808 857 0.617820 AATCAGGTACCCTCACGCCT 60.618 55.000 8.74 0.00 0.00 5.52
809 858 0.252197 AAATCAGGTACCCTCACGCC 59.748 55.000 8.74 0.00 0.00 5.68
810 859 1.369625 CAAATCAGGTACCCTCACGC 58.630 55.000 8.74 0.00 0.00 5.34
811 860 1.066143 AGCAAATCAGGTACCCTCACG 60.066 52.381 8.74 0.00 0.00 4.35
812 861 2.789409 AGCAAATCAGGTACCCTCAC 57.211 50.000 8.74 0.00 0.00 3.51
846 895 7.425606 AGAAACAAATAACAAGTGAAAGCGAT 58.574 30.769 0.00 0.00 0.00 4.58
847 896 6.791303 AGAAACAAATAACAAGTGAAAGCGA 58.209 32.000 0.00 0.00 0.00 4.93
958 1009 2.308570 TGACTGGCACCCAACAGATTAT 59.691 45.455 0.00 0.00 38.09 1.28
1048 1099 4.511527 AGAAGCAACAGACATGGATGTAG 58.488 43.478 5.60 0.00 41.95 2.74
1263 1349 4.904241 AGGAAGAAACCATGTCAGAGAAG 58.096 43.478 0.00 0.00 0.00 2.85
1266 1352 4.823989 ACAAAGGAAGAAACCATGTCAGAG 59.176 41.667 0.00 0.00 30.37 3.35
1278 1364 6.207417 CAGCAAAAGGATCTACAAAGGAAGAA 59.793 38.462 0.00 0.00 0.00 2.52
1335 1421 1.135141 TGCACATAATCTTTTGCGCCC 60.135 47.619 4.18 0.00 37.82 6.13
1491 1577 0.186386 ATCGTACCTGGCCTAGCTCT 59.814 55.000 3.32 0.00 0.00 4.09
1507 1593 9.453325 GGAAGTAAGTTAAAGTATCTGAGATCG 57.547 37.037 0.00 0.00 0.00 3.69
1523 1609 9.660180 GAATTGAGAACTAGATGGAAGTAAGTT 57.340 33.333 0.00 0.00 33.26 2.66
1524 1610 9.041354 AGAATTGAGAACTAGATGGAAGTAAGT 57.959 33.333 0.00 0.00 0.00 2.24
1525 1611 9.528018 GAGAATTGAGAACTAGATGGAAGTAAG 57.472 37.037 0.00 0.00 0.00 2.34
1527 1613 8.830915 AGAGAATTGAGAACTAGATGGAAGTA 57.169 34.615 0.00 0.00 0.00 2.24
1529 1615 7.209475 GGAGAGAATTGAGAACTAGATGGAAG 58.791 42.308 0.00 0.00 0.00 3.46
1532 1618 5.508825 CGGGAGAGAATTGAGAACTAGATGG 60.509 48.000 0.00 0.00 0.00 3.51
1534 1620 4.586841 CCGGGAGAGAATTGAGAACTAGAT 59.413 45.833 0.00 0.00 0.00 1.98
1535 1621 3.954904 CCGGGAGAGAATTGAGAACTAGA 59.045 47.826 0.00 0.00 0.00 2.43
1536 1622 3.702045 ACCGGGAGAGAATTGAGAACTAG 59.298 47.826 6.32 0.00 0.00 2.57
1537 1623 3.447586 CACCGGGAGAGAATTGAGAACTA 59.552 47.826 6.32 0.00 0.00 2.24
1538 1624 2.234908 CACCGGGAGAGAATTGAGAACT 59.765 50.000 6.32 0.00 0.00 3.01
1539 1625 2.028020 ACACCGGGAGAGAATTGAGAAC 60.028 50.000 6.32 0.00 0.00 3.01
1555 1642 5.769484 ATCTAGTCAGTATACCAACACCG 57.231 43.478 0.00 0.00 0.00 4.94
1577 1664 6.417258 TGAATGACCTGCAGAAGATGAATTA 58.583 36.000 17.39 0.00 0.00 1.40
1578 1665 5.258841 TGAATGACCTGCAGAAGATGAATT 58.741 37.500 17.39 4.97 0.00 2.17
1579 1666 4.851843 TGAATGACCTGCAGAAGATGAAT 58.148 39.130 17.39 0.00 0.00 2.57
1581 1668 3.870274 CTGAATGACCTGCAGAAGATGA 58.130 45.455 17.39 0.00 0.00 2.92
1583 1670 2.239150 AGCTGAATGACCTGCAGAAGAT 59.761 45.455 17.39 0.00 34.07 2.40
1585 1672 2.110901 AGCTGAATGACCTGCAGAAG 57.889 50.000 17.39 1.02 34.07 2.85
1586 1673 2.224597 TGAAGCTGAATGACCTGCAGAA 60.225 45.455 17.39 0.00 34.07 3.02
1651 1738 4.535526 TCATCTTGTTGGATGTCGAAGA 57.464 40.909 0.00 0.00 42.45 2.87
1659 1748 5.078949 TGAATGGTGTTCATCTTGTTGGAT 58.921 37.500 0.00 0.00 34.44 3.41
1681 1770 7.085746 TGCACAGAAACATTAACAGAATGATG 58.914 34.615 4.36 1.28 39.69 3.07
1692 1781 8.109705 ACAAGTGATTATGCACAGAAACATTA 57.890 30.769 0.00 0.00 41.19 1.90
1705 1795 4.884164 GGAGAAAGGGGACAAGTGATTATG 59.116 45.833 0.00 0.00 0.00 1.90
1706 1796 4.790790 AGGAGAAAGGGGACAAGTGATTAT 59.209 41.667 0.00 0.00 0.00 1.28
1708 1798 2.989571 AGGAGAAAGGGGACAAGTGATT 59.010 45.455 0.00 0.00 0.00 2.57
1713 1803 1.339535 GCAGAGGAGAAAGGGGACAAG 60.340 57.143 0.00 0.00 0.00 3.16
1714 1804 0.693049 GCAGAGGAGAAAGGGGACAA 59.307 55.000 0.00 0.00 0.00 3.18
1716 1806 1.760029 CTAGCAGAGGAGAAAGGGGAC 59.240 57.143 0.00 0.00 0.00 4.46
1717 1807 2.166907 CTAGCAGAGGAGAAAGGGGA 57.833 55.000 0.00 0.00 0.00 4.81
1728 1818 1.307097 GCAATTCCAGCCTAGCAGAG 58.693 55.000 0.00 0.00 0.00 3.35
1730 1820 0.462581 TCGCAATTCCAGCCTAGCAG 60.463 55.000 0.00 0.00 0.00 4.24
1731 1821 0.035534 TTCGCAATTCCAGCCTAGCA 60.036 50.000 0.00 0.00 0.00 3.49
1732 1822 0.659957 CTTCGCAATTCCAGCCTAGC 59.340 55.000 0.00 0.00 0.00 3.42
1733 1823 2.315925 TCTTCGCAATTCCAGCCTAG 57.684 50.000 0.00 0.00 0.00 3.02
1734 1824 2.632377 CTTCTTCGCAATTCCAGCCTA 58.368 47.619 0.00 0.00 0.00 3.93
1742 1832 2.479566 TGAGCTCCTTCTTCGCAATT 57.520 45.000 12.15 0.00 0.00 2.32
1784 1874 0.468226 ATTTATCGGAGGCGGCTTCA 59.532 50.000 18.62 4.96 0.00 3.02
1826 1916 9.153479 AGATGCCTTAAGTCTTCAATATAGAGT 57.847 33.333 0.97 0.00 0.00 3.24
1912 2004 3.876914 TGGTACAGCAGCAGCATAATAAC 59.123 43.478 3.17 0.00 45.49 1.89
1957 2049 7.973944 GGATTTTTATTTAGTCGGCAACATCTT 59.026 33.333 0.00 0.00 0.00 2.40
2000 2092 3.884037 AGTTGGGACCAAAATGAGAGT 57.116 42.857 5.17 0.00 37.70 3.24
2005 2097 3.726291 ACGAAAGTTGGGACCAAAATG 57.274 42.857 5.17 0.00 46.40 2.32
2019 2111 2.348218 CGACAACGGAAGGAAACGAAAG 60.348 50.000 0.00 0.00 35.72 2.62
2033 2125 1.464023 GCATCCACAATCACGACAACG 60.464 52.381 0.00 0.00 45.75 4.10
2045 2137 2.106566 ACAACCAAACAAGCATCCACA 58.893 42.857 0.00 0.00 0.00 4.17
2053 2145 4.035091 TCATCAGACGAACAACCAAACAAG 59.965 41.667 0.00 0.00 0.00 3.16
2099 2194 2.048222 ACGGACCACACATCAGCG 60.048 61.111 0.00 0.00 0.00 5.18
2103 2198 1.006571 ACGACACGGACCACACATC 60.007 57.895 0.00 0.00 0.00 3.06
2104 2199 1.006571 GACGACACGGACCACACAT 60.007 57.895 0.00 0.00 0.00 3.21
2107 2202 1.066752 CAAGACGACACGGACCACA 59.933 57.895 0.00 0.00 0.00 4.17
2108 2203 1.663702 CCAAGACGACACGGACCAC 60.664 63.158 0.00 0.00 0.00 4.16
2109 2204 2.732016 CCAAGACGACACGGACCA 59.268 61.111 0.00 0.00 0.00 4.02
2110 2205 2.737376 GCCAAGACGACACGGACC 60.737 66.667 0.00 0.00 0.00 4.46
2111 2206 3.103911 CGCCAAGACGACACGGAC 61.104 66.667 0.00 0.00 34.06 4.79
2112 2207 4.351938 CCGCCAAGACGACACGGA 62.352 66.667 0.00 0.00 46.71 4.69
2116 2229 3.998672 GGGTCCGCCAAGACGACA 61.999 66.667 0.00 0.00 37.66 4.35
2119 2232 3.695022 CTACGGGTCCGCCAAGACG 62.695 68.421 9.55 0.00 44.19 4.18
2122 2235 2.183555 GACTACGGGTCCGCCAAG 59.816 66.667 9.55 7.30 44.19 3.61
2158 2272 3.585862 TGACGAGCTACAGATTTGGTTC 58.414 45.455 0.00 0.00 0.00 3.62
2161 2275 3.182967 GTCTGACGAGCTACAGATTTGG 58.817 50.000 16.80 0.00 43.46 3.28
2168 2282 1.540267 GTCCTTGTCTGACGAGCTACA 59.460 52.381 17.90 0.87 0.00 2.74
2169 2283 2.265647 GTCCTTGTCTGACGAGCTAC 57.734 55.000 17.90 13.99 0.00 3.58
2177 2291 3.016997 ACGACTCGTCCTTGTCTGA 57.983 52.632 0.00 0.00 33.69 3.27
2194 2308 0.032952 TAAGCGGTGTGGTGTCAGAC 59.967 55.000 0.00 0.00 36.55 3.51
2200 2314 2.746277 GGCCTAAGCGGTGTGGTG 60.746 66.667 0.00 0.00 41.24 4.17
2371 2485 9.642343 TCTCTAGAGATGGCAGTTATACTTTAA 57.358 33.333 18.76 0.00 31.41 1.52
2394 2508 3.017442 GGTTTGGGTAGGAATGCTTCTC 58.983 50.000 0.00 0.00 0.00 2.87
2397 2511 2.525368 GTGGTTTGGGTAGGAATGCTT 58.475 47.619 0.00 0.00 0.00 3.91
2411 2525 0.467290 ATGTTGCTCGGTGGTGGTTT 60.467 50.000 0.00 0.00 0.00 3.27
2459 2573 1.266989 GGTGCTCTGGTTTGCTGTAAC 59.733 52.381 0.00 0.00 0.00 2.50
2487 2601 0.950555 GCAGTGCAACGGTCATCTGA 60.951 55.000 11.09 0.00 45.86 3.27
2508 2622 6.472887 TCTCCAAACGGACAGATTTTTCTAT 58.527 36.000 0.00 0.00 0.00 1.98
2548 2662 4.082190 TGCTTCTACGAGCTTGTTCTGTAT 60.082 41.667 12.97 0.00 43.11 2.29
2608 2722 3.682696 TCATGCTTGAAGATGAGTGCTT 58.317 40.909 0.00 0.00 0.00 3.91
2644 2770 1.735386 CTCTGTGCATCTGAAGGTGG 58.265 55.000 0.00 0.00 0.00 4.61
2670 2796 4.566907 GGGCTCTGTGGATTTTGTAGGTTA 60.567 45.833 0.00 0.00 0.00 2.85
2695 2821 9.595357 GAAACTAGAATTGTACTGCAAACTAAC 57.405 33.333 0.00 0.00 40.91 2.34
2720 2864 3.855599 TGGAAACTAGAAATGGGGATGGA 59.144 43.478 0.00 0.00 0.00 3.41
2721 2865 4.249638 TGGAAACTAGAAATGGGGATGG 57.750 45.455 0.00 0.00 0.00 3.51
2722 2866 4.829492 GGATGGAAACTAGAAATGGGGATG 59.171 45.833 0.00 0.00 0.00 3.51
2723 2867 4.140924 GGGATGGAAACTAGAAATGGGGAT 60.141 45.833 0.00 0.00 0.00 3.85
2724 2868 3.204382 GGGATGGAAACTAGAAATGGGGA 59.796 47.826 0.00 0.00 0.00 4.81
2725 2869 3.566351 GGGATGGAAACTAGAAATGGGG 58.434 50.000 0.00 0.00 0.00 4.96
2726 2870 3.052944 TGGGGATGGAAACTAGAAATGGG 60.053 47.826 0.00 0.00 0.00 4.00
2727 2871 4.249638 TGGGGATGGAAACTAGAAATGG 57.750 45.455 0.00 0.00 0.00 3.16
2728 2872 5.448654 TGATGGGGATGGAAACTAGAAATG 58.551 41.667 0.00 0.00 0.00 2.32
2729 2873 5.732331 TGATGGGGATGGAAACTAGAAAT 57.268 39.130 0.00 0.00 0.00 2.17
2730 2874 5.399038 GGATGATGGGGATGGAAACTAGAAA 60.399 44.000 0.00 0.00 0.00 2.52
2731 2875 4.104738 GGATGATGGGGATGGAAACTAGAA 59.895 45.833 0.00 0.00 0.00 2.10
2732 2876 3.652869 GGATGATGGGGATGGAAACTAGA 59.347 47.826 0.00 0.00 0.00 2.43
2733 2877 3.395607 TGGATGATGGGGATGGAAACTAG 59.604 47.826 0.00 0.00 0.00 2.57
2734 2878 3.138283 GTGGATGATGGGGATGGAAACTA 59.862 47.826 0.00 0.00 0.00 2.24
2735 2879 2.091665 GTGGATGATGGGGATGGAAACT 60.092 50.000 0.00 0.00 0.00 2.66
2736 2880 2.310538 GTGGATGATGGGGATGGAAAC 58.689 52.381 0.00 0.00 0.00 2.78
2737 2881 1.928785 TGTGGATGATGGGGATGGAAA 59.071 47.619 0.00 0.00 0.00 3.13
2738 2882 1.606026 TGTGGATGATGGGGATGGAA 58.394 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.