Multiple sequence alignment - TraesCS7D01G459400

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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 TraesCS7D01G459400 chr7D 100.000 2743 0 0 1 2743 576687973 576685231 0.000000e+00 5066.0
1 TraesCS7D01G459400 chr7D 95.506 979 36 7 1769 2743 523253839 523254813 0.000000e+00 1557.0
2 TraesCS7D01G459400 chr7D 94.592 980 42 9 1769 2743 21983120 21982147 0.000000e+00 1506.0
3 TraesCS7D01G459400 chr7D 84.464 811 116 4 880 1686 576747571 576748375 0.000000e+00 791.0
4 TraesCS7D01G459400 chr1D 96.622 977 28 5 1769 2743 240741811 240740838 0.000000e+00 1616.0
5 TraesCS7D01G459400 chr5D 96.016 979 31 6 1769 2743 494801328 494800354 0.000000e+00 1585.0
6 TraesCS7D01G459400 chr5D 94.995 979 40 7 1769 2743 538544375 538545348 0.000000e+00 1528.0
7 TraesCS7D01G459400 chr5D 92.714 549 40 0 220 768 376700131 376699583 0.000000e+00 793.0
8 TraesCS7D01G459400 chr4D 95.914 979 31 6 1769 2743 249087913 249086940 0.000000e+00 1578.0
9 TraesCS7D01G459400 chr4D 96.070 967 32 4 1780 2743 471217163 471218126 0.000000e+00 1570.0
10 TraesCS7D01G459400 chr4D 95.714 980 33 7 1769 2743 369873537 369872562 0.000000e+00 1568.0
11 TraesCS7D01G459400 chr2D 94.990 978 40 7 1769 2743 643717441 643716470 0.000000e+00 1526.0
12 TraesCS7D01G459400 chr2D 94.909 550 28 0 220 769 33335911 33335362 0.000000e+00 861.0
13 TraesCS7D01G459400 chr2D 92.377 551 40 2 218 768 626591345 626590797 0.000000e+00 784.0
14 TraesCS7D01G459400 chr7A 84.293 955 116 15 769 1723 668311826 668310906 0.000000e+00 902.0
15 TraesCS7D01G459400 chr7A 83.046 755 106 7 889 1637 668528394 668529132 0.000000e+00 665.0
16 TraesCS7D01G459400 chr7A 93.750 128 4 4 1 126 668312303 668312178 3.610000e-44 189.0
17 TraesCS7D01G459400 chr7A 78.289 152 28 4 1343 1491 668990925 668991074 2.910000e-15 93.5
18 TraesCS7D01G459400 chr3D 93.989 549 33 0 220 768 21459579 21460127 0.000000e+00 832.0
19 TraesCS7D01G459400 chr3B 93.078 549 37 1 220 768 284567818 284567271 0.000000e+00 802.0
20 TraesCS7D01G459400 chr5A 92.909 550 39 0 219 768 510277943 510277394 0.000000e+00 800.0
21 TraesCS7D01G459400 chr4A 92.545 550 41 0 220 769 666946142 666946691 0.000000e+00 789.0
22 TraesCS7D01G459400 chr4A 92.350 549 41 1 220 768 537117079 537117626 0.000000e+00 780.0
23 TraesCS7D01G459400 chr6A 92.210 552 43 0 218 769 603562623 603562072 0.000000e+00 782.0
24 TraesCS7D01G459400 chr7B 83.046 755 104 8 889 1637 639379302 639378566 0.000000e+00 664.0


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 TraesCS7D01G459400 chr7D 576685231 576687973 2742 True 5066.0 5066 100.0000 1 2743 1 chr7D.!!$R2 2742
1 TraesCS7D01G459400 chr7D 523253839 523254813 974 False 1557.0 1557 95.5060 1769 2743 1 chr7D.!!$F1 974
2 TraesCS7D01G459400 chr7D 21982147 21983120 973 True 1506.0 1506 94.5920 1769 2743 1 chr7D.!!$R1 974
3 TraesCS7D01G459400 chr7D 576747571 576748375 804 False 791.0 791 84.4640 880 1686 1 chr7D.!!$F2 806
4 TraesCS7D01G459400 chr1D 240740838 240741811 973 True 1616.0 1616 96.6220 1769 2743 1 chr1D.!!$R1 974
5 TraesCS7D01G459400 chr5D 494800354 494801328 974 True 1585.0 1585 96.0160 1769 2743 1 chr5D.!!$R2 974
6 TraesCS7D01G459400 chr5D 538544375 538545348 973 False 1528.0 1528 94.9950 1769 2743 1 chr5D.!!$F1 974
7 TraesCS7D01G459400 chr5D 376699583 376700131 548 True 793.0 793 92.7140 220 768 1 chr5D.!!$R1 548
8 TraesCS7D01G459400 chr4D 249086940 249087913 973 True 1578.0 1578 95.9140 1769 2743 1 chr4D.!!$R1 974
9 TraesCS7D01G459400 chr4D 471217163 471218126 963 False 1570.0 1570 96.0700 1780 2743 1 chr4D.!!$F1 963
10 TraesCS7D01G459400 chr4D 369872562 369873537 975 True 1568.0 1568 95.7140 1769 2743 1 chr4D.!!$R2 974
11 TraesCS7D01G459400 chr2D 643716470 643717441 971 True 1526.0 1526 94.9900 1769 2743 1 chr2D.!!$R3 974
12 TraesCS7D01G459400 chr2D 33335362 33335911 549 True 861.0 861 94.9090 220 769 1 chr2D.!!$R1 549
13 TraesCS7D01G459400 chr2D 626590797 626591345 548 True 784.0 784 92.3770 218 768 1 chr2D.!!$R2 550
14 TraesCS7D01G459400 chr7A 668528394 668529132 738 False 665.0 665 83.0460 889 1637 1 chr7A.!!$F1 748
15 TraesCS7D01G459400 chr7A 668310906 668312303 1397 True 545.5 902 89.0215 1 1723 2 chr7A.!!$R1 1722
16 TraesCS7D01G459400 chr3D 21459579 21460127 548 False 832.0 832 93.9890 220 768 1 chr3D.!!$F1 548
17 TraesCS7D01G459400 chr3B 284567271 284567818 547 True 802.0 802 93.0780 220 768 1 chr3B.!!$R1 548
18 TraesCS7D01G459400 chr5A 510277394 510277943 549 True 800.0 800 92.9090 219 768 1 chr5A.!!$R1 549
19 TraesCS7D01G459400 chr4A 666946142 666946691 549 False 789.0 789 92.5450 220 769 1 chr4A.!!$F2 549
20 TraesCS7D01G459400 chr4A 537117079 537117626 547 False 780.0 780 92.3500 220 768 1 chr4A.!!$F1 548
21 TraesCS7D01G459400 chr6A 603562072 603562623 551 True 782.0 782 92.2100 218 769 1 chr6A.!!$R1 551
22 TraesCS7D01G459400 chr7B 639378566 639379302 736 True 664.0 664 83.0460 889 1637 1 chr7B.!!$R1 748

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
863 1131 0.250081 GGAAGCCCCAAGATAGCTCG 60.25 60.0 0.0 0.0 35.3 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 2887 0.892358 GGAAACGGGTGGAGGGAAAC 60.892 60.0 0.0 0.0 0.0 2.78 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
52 53 4.637574 GCGTTAGCATGATGTCAGATAC 57.362 45.455 0.00 0.00 44.35 2.24
53 54 3.120286 GCGTTAGCATGATGTCAGATACG 59.880 47.826 0.00 0.00 44.35 3.06
74 75 1.468520 GGCAGCGACTATTGCTTCAAA 59.531 47.619 0.00 0.00 41.72 2.69
122 123 4.605183 AGTGGGAGATCCTTCTATATCCG 58.395 47.826 0.00 0.00 38.00 4.18
129 397 4.701171 AGATCCTTCTATATCCGAACGTCC 59.299 45.833 0.00 0.00 0.00 4.79
137 405 1.321074 ATCCGAACGTCCTGGACTCC 61.321 60.000 23.49 11.57 33.91 3.85
161 429 1.815840 TTTGAGCACGTTCGTGGCA 60.816 52.632 23.27 0.00 36.70 4.92
164 432 2.943345 GAGCACGTTCGTGGCACTG 61.943 63.158 23.27 7.76 36.70 3.66
170 438 2.355837 TTCGTGGCACTGCGTCTC 60.356 61.111 16.72 0.00 0.00 3.36
188 456 4.249661 GTCTCATCTTTCTCAGTGAACCC 58.750 47.826 0.00 0.00 33.88 4.11
189 457 3.903714 TCTCATCTTTCTCAGTGAACCCA 59.096 43.478 0.00 0.00 33.88 4.51
190 458 4.020751 TCTCATCTTTCTCAGTGAACCCAG 60.021 45.833 0.00 0.00 33.88 4.45
194 462 0.318441 TTCTCAGTGAACCCAGAGCG 59.682 55.000 0.00 0.00 0.00 5.03
195 463 1.079543 CTCAGTGAACCCAGAGCGG 60.080 63.158 0.00 0.00 0.00 5.52
210 478 3.636231 CGGGGGCTGTGAGGACAA 61.636 66.667 0.00 0.00 0.00 3.18
211 479 2.034221 GGGGGCTGTGAGGACAAC 59.966 66.667 0.00 0.00 0.00 3.32
212 480 2.529744 GGGGGCTGTGAGGACAACT 61.530 63.158 0.00 0.00 0.00 3.16
213 481 1.003233 GGGGCTGTGAGGACAACTC 60.003 63.158 0.00 0.00 46.78 3.01
214 482 1.484444 GGGGCTGTGAGGACAACTCT 61.484 60.000 0.00 0.00 46.72 3.24
215 483 1.267121 GGGCTGTGAGGACAACTCTA 58.733 55.000 0.00 0.00 46.72 2.43
216 484 1.066787 GGGCTGTGAGGACAACTCTAC 60.067 57.143 0.00 0.00 46.72 2.59
324 592 1.816074 TGTCCTAATCCGTGGCAAAC 58.184 50.000 0.00 0.00 0.00 2.93
381 649 3.146847 GCTAAGCACCAAACTAACCAGT 58.853 45.455 0.00 0.00 36.19 4.00
596 864 1.525995 CACCGTGGCACCTGAAACT 60.526 57.895 12.86 0.00 0.00 2.66
691 959 5.949354 CCATGGATTAGGACAAAAGTGGTAA 59.051 40.000 5.56 0.00 0.00 2.85
698 966 9.974980 GATTAGGACAAAAGTGGTAATTTTTCA 57.025 29.630 0.00 0.00 0.00 2.69
777 1045 7.949903 TTTTGTTAAATACTCACTCTACGCA 57.050 32.000 0.00 0.00 0.00 5.24
778 1046 7.576750 TTTGTTAAATACTCACTCTACGCAG 57.423 36.000 0.00 0.00 0.00 5.18
795 1063 1.068055 GCAGTTGCTTGGTTGATCAGG 60.068 52.381 0.00 0.00 38.21 3.86
796 1064 2.507484 CAGTTGCTTGGTTGATCAGGA 58.493 47.619 0.00 0.00 0.00 3.86
805 1073 1.003580 GGTTGATCAGGAAGGAGTGCA 59.996 52.381 0.00 0.00 0.00 4.57
813 1081 1.065126 AGGAAGGAGTGCATAAGCCAC 60.065 52.381 0.00 0.00 41.13 5.01
814 1082 1.009829 GAAGGAGTGCATAAGCCACG 58.990 55.000 0.00 0.00 41.13 4.94
822 1090 0.455410 GCATAAGCCACGCCATGAAA 59.545 50.000 0.00 0.00 33.58 2.69
823 1091 1.135141 GCATAAGCCACGCCATGAAAA 60.135 47.619 0.00 0.00 33.58 2.29
826 1094 4.736168 GCATAAGCCACGCCATGAAAATTA 60.736 41.667 0.00 0.00 33.58 1.40
832 1100 4.601019 CCACGCCATGAAAATTATCAGAC 58.399 43.478 0.00 0.00 31.76 3.51
833 1101 4.336433 CCACGCCATGAAAATTATCAGACT 59.664 41.667 0.00 0.00 31.76 3.24
863 1131 0.250081 GGAAGCCCCAAGATAGCTCG 60.250 60.000 0.00 0.00 35.30 5.03
866 1134 0.691078 AGCCCCAAGATAGCTCGGAA 60.691 55.000 0.00 0.00 28.40 4.30
887 1155 8.047310 TCGGAAAGAATTAAGCTAGAAGGATTT 58.953 33.333 0.00 0.00 0.00 2.17
904 1172 7.946776 AGAAGGATTTGGTTATATCAAGGATGG 59.053 37.037 0.00 0.00 0.00 3.51
940 1208 2.189594 TGCACCCTTGATGTTCTCAG 57.810 50.000 0.00 0.00 34.68 3.35
961 1232 2.567615 GGGAACTAGCAGAGGAAACAGA 59.432 50.000 0.00 0.00 0.00 3.41
965 1236 0.895530 TAGCAGAGGAAACAGACCCG 59.104 55.000 0.00 0.00 0.00 5.28
972 1243 3.143728 GAGGAAACAGACCCGCTTAAAA 58.856 45.455 0.00 0.00 0.00 1.52
1025 1296 2.287248 GCAACTTGCTCAACTCCTTCAC 60.287 50.000 6.50 0.00 40.96 3.18
1028 1299 2.149578 CTTGCTCAACTCCTTCACAGG 58.850 52.381 0.00 0.00 42.50 4.00
1061 1332 1.905687 GACGTCAGATTTCTCGTGTCG 59.094 52.381 11.55 0.00 36.67 4.35
1086 1357 0.936297 GTCTTTTGCTGCGCACAAGG 60.936 55.000 20.96 16.87 43.76 3.61
1087 1358 2.279385 TTTTGCTGCGCACAAGGC 60.279 55.556 19.56 16.38 38.71 4.35
1130 1401 2.552315 TGTCTTCATGGCCGAGTTTTTC 59.448 45.455 0.00 0.00 0.00 2.29
1145 1416 4.911390 AGTTTTTCGGAGACATGAAGGAT 58.089 39.130 0.00 0.00 34.32 3.24
1149 1420 4.672587 TTCGGAGACATGAAGGATAAGG 57.327 45.455 0.00 0.00 34.32 2.69
1150 1421 3.910989 TCGGAGACATGAAGGATAAGGA 58.089 45.455 0.00 0.00 0.00 3.36
1151 1422 4.286707 TCGGAGACATGAAGGATAAGGAA 58.713 43.478 0.00 0.00 0.00 3.36
1152 1423 4.342378 TCGGAGACATGAAGGATAAGGAAG 59.658 45.833 0.00 0.00 0.00 3.46
1153 1424 4.502259 CGGAGACATGAAGGATAAGGAAGG 60.502 50.000 0.00 0.00 0.00 3.46
1154 1425 4.656112 GGAGACATGAAGGATAAGGAAGGA 59.344 45.833 0.00 0.00 0.00 3.36
1186 1457 1.063642 TGGAGATCGAGGACATGGAGT 60.064 52.381 0.00 0.00 0.00 3.85
1207 1478 2.919494 GCGGTGTTCAAGGCCCTTG 61.919 63.158 17.74 17.74 42.25 3.61
1260 1534 1.048601 TCAGACAACAGGAGTGGGAC 58.951 55.000 0.00 0.00 0.00 4.46
1262 1536 1.004918 GACAACAGGAGTGGGACGG 60.005 63.158 0.00 0.00 0.00 4.79
1286 1560 2.366916 AGGCCATATACACTGACTCTGC 59.633 50.000 5.01 0.00 0.00 4.26
1291 1565 0.608130 ATACACTGACTCTGCGCCAA 59.392 50.000 4.18 0.00 0.00 4.52
1296 1570 2.483877 CACTGACTCTGCGCCAAAATTA 59.516 45.455 4.18 0.00 0.00 1.40
1314 1588 0.041833 TAGAACAGCAGGAGGAGGCT 59.958 55.000 0.00 0.00 42.06 4.58
1328 1602 0.815615 GAGGCTGATACAAAGGCGGG 60.816 60.000 0.00 0.00 44.52 6.13
1332 1606 0.251916 CTGATACAAAGGCGGGGACA 59.748 55.000 0.00 0.00 0.00 4.02
1335 1609 0.252197 ATACAAAGGCGGGGACAGTC 59.748 55.000 0.00 0.00 0.00 3.51
1339 1613 1.488705 AAAGGCGGGGACAGTCATGA 61.489 55.000 2.17 0.00 0.00 3.07
1341 1615 2.125106 GCGGGGACAGTCATGACC 60.125 66.667 22.21 6.89 40.13 4.02
1356 1630 0.895100 TGACCCAACATCTGCTTGCC 60.895 55.000 0.00 0.00 0.00 4.52
1402 1676 0.883814 GCTCAAGCTCATATGCGCCT 60.884 55.000 13.93 0.00 38.21 5.52
1403 1677 1.590932 CTCAAGCTCATATGCGCCTT 58.409 50.000 13.93 5.49 38.13 4.35
1404 1678 2.759191 CTCAAGCTCATATGCGCCTTA 58.241 47.619 13.93 0.00 38.13 2.69
1413 1687 2.240493 TATGCGCCTTAAAGCTCTCC 57.760 50.000 4.18 0.00 0.00 3.71
1434 1708 0.884704 GTGGCATCAACGTGGACACT 60.885 55.000 0.00 0.00 0.00 3.55
1449 1723 0.531090 ACACTGCGGCGACAACTTTA 60.531 50.000 12.98 0.00 0.00 1.85
1450 1724 0.584396 CACTGCGGCGACAACTTTAA 59.416 50.000 12.98 0.00 0.00 1.52
1464 1738 4.577283 ACAACTTTAACTTTAGCCGAGCAA 59.423 37.500 0.00 0.00 0.00 3.91
1554 1828 1.079336 GTTGGCGACAGAGGGGTAC 60.079 63.158 0.00 0.00 44.54 3.34
1601 1875 3.407424 TGTGGTGATTGACCTTCTCAG 57.593 47.619 0.00 0.00 46.32 3.35
1628 1902 3.854045 GCGCGTGGGAGTAAAAATTGAAA 60.854 43.478 8.43 0.00 0.00 2.69
1641 1915 9.435688 AGTAAAAATTGAAATGTATCTTTGGCC 57.564 29.630 0.00 0.00 0.00 5.36
1642 1916 6.966435 AAAATTGAAATGTATCTTTGGCCG 57.034 33.333 0.00 0.00 0.00 6.13
1643 1917 5.659440 AATTGAAATGTATCTTTGGCCGT 57.341 34.783 0.00 0.00 0.00 5.68
1644 1918 6.767524 AATTGAAATGTATCTTTGGCCGTA 57.232 33.333 0.00 0.00 0.00 4.02
1665 1939 0.835971 GGGGCCAAGGTTTGATGGTT 60.836 55.000 4.39 0.00 39.00 3.67
1679 1953 7.619302 AGGTTTGATGGTTCATGGTATTGTATT 59.381 33.333 0.00 0.00 0.00 1.89
1687 1961 4.919206 TCATGGTATTGTATTTGCTTGCG 58.081 39.130 0.00 0.00 0.00 4.85
1692 1966 4.625311 GGTATTGTATTTGCTTGCGCTTTT 59.375 37.500 9.73 0.00 36.97 2.27
1700 1974 1.349259 GCTTGCGCTTTTCAGGCATG 61.349 55.000 9.73 0.00 36.66 4.06
1701 1975 1.349259 CTTGCGCTTTTCAGGCATGC 61.349 55.000 9.90 9.90 36.44 4.06
1704 1978 1.074872 GCGCTTTTCAGGCATGCTTC 61.075 55.000 18.92 1.03 0.00 3.86
1718 1992 5.047188 GGCATGCTTCTCTAGTTCTACTTC 58.953 45.833 18.92 0.00 0.00 3.01
1719 1993 5.163457 GGCATGCTTCTCTAGTTCTACTTCT 60.163 44.000 18.92 0.00 0.00 2.85
1720 1994 6.039941 GGCATGCTTCTCTAGTTCTACTTCTA 59.960 42.308 18.92 0.00 0.00 2.10
1721 1995 7.255801 GGCATGCTTCTCTAGTTCTACTTCTAT 60.256 40.741 18.92 0.00 0.00 1.98
1722 1996 7.594758 GCATGCTTCTCTAGTTCTACTTCTATG 59.405 40.741 11.37 0.00 0.00 2.23
1723 1997 8.845227 CATGCTTCTCTAGTTCTACTTCTATGA 58.155 37.037 0.00 0.00 0.00 2.15
1724 1998 8.215926 TGCTTCTCTAGTTCTACTTCTATGAC 57.784 38.462 0.00 0.00 0.00 3.06
1725 1999 7.283580 TGCTTCTCTAGTTCTACTTCTATGACC 59.716 40.741 0.00 0.00 0.00 4.02
1726 2000 7.519328 GCTTCTCTAGTTCTACTTCTATGACCG 60.519 44.444 0.00 0.00 0.00 4.79
1727 2001 6.887013 TCTCTAGTTCTACTTCTATGACCGT 58.113 40.000 0.00 0.00 0.00 4.83
1728 2002 6.985645 TCTCTAGTTCTACTTCTATGACCGTC 59.014 42.308 0.00 0.00 0.00 4.79
1729 2003 6.887013 TCTAGTTCTACTTCTATGACCGTCT 58.113 40.000 0.00 0.00 0.00 4.18
1730 2004 7.337167 TCTAGTTCTACTTCTATGACCGTCTT 58.663 38.462 0.00 0.00 0.00 3.01
1731 2005 6.837471 AGTTCTACTTCTATGACCGTCTTT 57.163 37.500 0.00 0.00 0.00 2.52
1732 2006 6.854778 AGTTCTACTTCTATGACCGTCTTTC 58.145 40.000 0.00 0.00 0.00 2.62
1733 2007 6.433404 AGTTCTACTTCTATGACCGTCTTTCA 59.567 38.462 0.00 0.00 0.00 2.69
1734 2008 6.829229 TCTACTTCTATGACCGTCTTTCAA 57.171 37.500 0.00 0.00 0.00 2.69
1735 2009 6.618811 TCTACTTCTATGACCGTCTTTCAAC 58.381 40.000 0.00 0.00 0.00 3.18
1736 2010 5.209818 ACTTCTATGACCGTCTTTCAACA 57.790 39.130 0.00 0.00 0.00 3.33
1737 2011 5.607477 ACTTCTATGACCGTCTTTCAACAA 58.393 37.500 0.00 0.00 0.00 2.83
1738 2012 6.053005 ACTTCTATGACCGTCTTTCAACAAA 58.947 36.000 0.00 0.00 0.00 2.83
1739 2013 6.710744 ACTTCTATGACCGTCTTTCAACAAAT 59.289 34.615 0.00 0.00 0.00 2.32
1740 2014 7.228706 ACTTCTATGACCGTCTTTCAACAAATT 59.771 33.333 0.00 0.00 0.00 1.82
1741 2015 8.610248 TTCTATGACCGTCTTTCAACAAATTA 57.390 30.769 0.00 0.00 0.00 1.40
1742 2016 8.610248 TCTATGACCGTCTTTCAACAAATTAA 57.390 30.769 0.00 0.00 0.00 1.40
1743 2017 8.717821 TCTATGACCGTCTTTCAACAAATTAAG 58.282 33.333 0.00 0.00 0.00 1.85
1744 2018 6.928979 TGACCGTCTTTCAACAAATTAAGA 57.071 33.333 0.00 0.00 0.00 2.10
1745 2019 7.323049 TGACCGTCTTTCAACAAATTAAGAA 57.677 32.000 0.00 0.00 0.00 2.52
1746 2020 7.190871 TGACCGTCTTTCAACAAATTAAGAAC 58.809 34.615 0.00 0.00 0.00 3.01
1747 2021 7.066525 TGACCGTCTTTCAACAAATTAAGAACT 59.933 33.333 0.00 0.00 0.00 3.01
1748 2022 7.768240 ACCGTCTTTCAACAAATTAAGAACTT 58.232 30.769 0.00 0.00 0.00 2.66
1749 2023 8.895737 ACCGTCTTTCAACAAATTAAGAACTTA 58.104 29.630 0.00 0.00 0.00 2.24
1750 2024 9.893305 CCGTCTTTCAACAAATTAAGAACTTAT 57.107 29.630 0.00 0.00 0.00 1.73
2072 2353 1.331756 CGACTGGTGCATGCCTATTTC 59.668 52.381 16.68 5.46 0.00 2.17
2307 2590 7.770366 ACCCACGTGATATGTGAGTATATTA 57.230 36.000 19.30 0.00 37.29 0.98
2442 2725 3.886505 AGTGGCACGAACCATTTCTTTTA 59.113 39.130 12.71 0.00 43.01 1.52
2446 2729 7.033185 GTGGCACGAACCATTTCTTTTAATAT 58.967 34.615 0.00 0.00 43.01 1.28
2549 2834 3.530535 ACATTTCCAAACTGCGCTTTTT 58.469 36.364 9.73 4.84 0.00 1.94
2588 2873 2.283532 CCATTTCCCGCCACCCAA 60.284 61.111 0.00 0.00 0.00 4.12
2602 2887 3.448340 CCAATTTCCCGCCACCCG 61.448 66.667 0.00 0.00 0.00 5.28
2616 2901 4.404098 CCCGTTTCCCTCCACCCG 62.404 72.222 0.00 0.00 0.00 5.28
2688 2988 1.844544 AACCTTTCCCGCCATACCGT 61.845 55.000 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.139734 GCCGTCGATCTTGAGCAGA 59.860 57.895 0.00 0.00 35.33 4.26
47 48 1.000163 CAATAGTCGCTGCCCGTATCT 60.000 52.381 0.00 0.00 38.35 1.98
49 50 0.600255 GCAATAGTCGCTGCCCGTAT 60.600 55.000 0.00 0.00 38.35 3.06
50 51 1.227147 GCAATAGTCGCTGCCCGTA 60.227 57.895 0.00 0.00 38.35 4.02
52 53 1.766143 GAAGCAATAGTCGCTGCCCG 61.766 60.000 0.00 0.00 40.35 6.13
53 54 0.744414 TGAAGCAATAGTCGCTGCCC 60.744 55.000 0.00 0.00 40.35 5.36
74 75 2.104792 CCCGTCCACAATCCATCTGTAT 59.895 50.000 0.00 0.00 0.00 2.29
137 405 1.841663 CGAACGTGCTCAAACCCCTG 61.842 60.000 0.00 0.00 0.00 4.45
161 429 7.237071 TTCACTGAGAAAGATGAGACGCAGT 62.237 44.000 0.00 0.00 42.13 4.40
164 432 3.223423 TCACTGAGAAAGATGAGACGC 57.777 47.619 0.00 0.00 0.00 5.19
170 438 4.252073 CTCTGGGTTCACTGAGAAAGATG 58.748 47.826 3.41 0.00 38.13 2.90
188 456 4.463879 CTCACAGCCCCCGCTCTG 62.464 72.222 0.00 0.00 43.95 3.35
194 462 2.034221 GTTGTCCTCACAGCCCCC 59.966 66.667 0.00 0.00 32.71 5.40
195 463 1.003233 GAGTTGTCCTCACAGCCCC 60.003 63.158 0.00 0.00 40.17 5.80
197 465 1.618837 TGTAGAGTTGTCCTCACAGCC 59.381 52.381 0.00 0.00 43.12 4.85
212 480 8.891671 AGTTTTTGGTTAAATACTCGTGTAGA 57.108 30.769 3.50 0.00 34.37 2.59
214 482 8.987890 GGTAGTTTTTGGTTAAATACTCGTGTA 58.012 33.333 0.00 0.00 38.47 2.90
215 483 7.498570 TGGTAGTTTTTGGTTAAATACTCGTGT 59.501 33.333 0.00 0.00 38.47 4.49
216 484 7.799914 GTGGTAGTTTTTGGTTAAATACTCGTG 59.200 37.037 0.00 0.00 38.47 4.35
300 568 1.132453 GCCACGGATTAGGACAAAAGC 59.868 52.381 0.00 0.00 0.00 3.51
324 592 2.729882 CGGTTTCGAGACTTGGTAGTTG 59.270 50.000 6.02 0.00 39.00 3.16
359 627 3.146066 CTGGTTAGTTTGGTGCTTAGCA 58.854 45.455 1.39 1.39 35.60 3.49
381 649 0.036164 CACCTGAAACATGGGACCGA 59.964 55.000 0.00 0.00 0.00 4.69
666 934 4.202673 ACCACTTTTGTCCTAATCCATGGT 60.203 41.667 12.58 0.00 31.91 3.55
691 959 7.762159 ACCACTTTACGATTTTGTGTGAAAAAT 59.238 29.630 0.00 0.00 34.34 1.82
698 966 6.930667 AACTACCACTTTACGATTTTGTGT 57.069 33.333 0.00 0.00 0.00 3.72
756 1024 6.263516 ACTGCGTAGAGTGAGTATTTAACA 57.736 37.500 7.78 0.00 0.00 2.41
777 1045 2.957402 TCCTGATCAACCAAGCAACT 57.043 45.000 0.00 0.00 0.00 3.16
778 1046 2.229784 CCTTCCTGATCAACCAAGCAAC 59.770 50.000 0.00 0.00 0.00 4.17
795 1063 1.009829 CGTGGCTTATGCACTCCTTC 58.990 55.000 2.72 0.00 41.91 3.46
796 1064 1.026718 GCGTGGCTTATGCACTCCTT 61.027 55.000 2.72 0.00 41.11 3.36
805 1073 5.301551 TGATAATTTTCATGGCGTGGCTTAT 59.698 36.000 6.90 5.50 0.00 1.73
813 1081 8.773645 TGTTATAGTCTGATAATTTTCATGGCG 58.226 33.333 0.00 0.00 0.00 5.69
823 1091 9.717942 GCTTCCTGAATGTTATAGTCTGATAAT 57.282 33.333 0.00 0.00 0.00 1.28
826 1094 6.465035 GGGCTTCCTGAATGTTATAGTCTGAT 60.465 42.308 0.00 0.00 0.00 2.90
832 1100 4.437682 TGGGGCTTCCTGAATGTTATAG 57.562 45.455 0.00 0.00 36.20 1.31
833 1101 4.476846 TCTTGGGGCTTCCTGAATGTTATA 59.523 41.667 0.00 0.00 36.20 0.98
844 1112 0.250081 CGAGCTATCTTGGGGCTTCC 60.250 60.000 0.00 0.00 36.37 3.46
863 1131 8.409371 CCAAATCCTTCTAGCTTAATTCTTTCC 58.591 37.037 0.00 0.00 0.00 3.13
866 1134 8.885693 AACCAAATCCTTCTAGCTTAATTCTT 57.114 30.769 0.00 0.00 0.00 2.52
887 1155 9.627123 CTAAAAGAACCATCCTTGATATAACCA 57.373 33.333 0.00 0.00 0.00 3.67
894 1162 5.183904 GCACACTAAAAGAACCATCCTTGAT 59.816 40.000 0.00 0.00 0.00 2.57
940 1208 2.567615 TCTGTTTCCTCTGCTAGTTCCC 59.432 50.000 0.00 0.00 0.00 3.97
972 1243 3.572682 TCGGACGATGGCAGATATAGTTT 59.427 43.478 0.00 0.00 0.00 2.66
977 1248 1.621992 AGTCGGACGATGGCAGATAT 58.378 50.000 1.89 0.00 0.00 1.63
978 1249 1.067060 CAAGTCGGACGATGGCAGATA 59.933 52.381 1.89 0.00 0.00 1.98
1008 1279 2.149578 CCTGTGAAGGAGTTGAGCAAG 58.850 52.381 0.00 0.00 0.00 4.01
1048 1319 1.153901 TCGCCCGACACGAGAAATC 60.154 57.895 0.00 0.00 33.96 2.17
1061 1332 2.563427 GCAGCAAAAGACTCGCCC 59.437 61.111 0.00 0.00 0.00 6.13
1087 1358 4.473520 ACCTTGCGGCGAGGATGG 62.474 66.667 36.97 16.34 37.20 3.51
1130 1401 4.502259 CCTTCCTTATCCTTCATGTCTCCG 60.502 50.000 0.00 0.00 0.00 4.63
1145 1416 2.367567 ACACTTTGCGAGTCCTTCCTTA 59.632 45.455 0.00 0.00 36.10 2.69
1149 1420 0.868406 CCACACTTTGCGAGTCCTTC 59.132 55.000 0.00 0.00 36.10 3.46
1150 1421 0.468226 TCCACACTTTGCGAGTCCTT 59.532 50.000 0.00 0.00 36.10 3.36
1151 1422 0.034059 CTCCACACTTTGCGAGTCCT 59.966 55.000 0.00 0.00 36.10 3.85
1152 1423 0.033504 TCTCCACACTTTGCGAGTCC 59.966 55.000 0.00 0.00 36.10 3.85
1153 1424 1.996191 GATCTCCACACTTTGCGAGTC 59.004 52.381 0.00 0.00 36.10 3.36
1154 1425 1.670087 CGATCTCCACACTTTGCGAGT 60.670 52.381 0.00 0.00 39.89 4.18
1186 1457 2.281484 GGCCTTGAACACCGCAGA 60.281 61.111 0.00 0.00 0.00 4.26
1207 1478 3.673809 GTGTCGGTGTAGATGAACTGAAC 59.326 47.826 0.00 0.00 33.59 3.18
1260 1534 0.321671 CAGTGTATATGGCCTCCCCG 59.678 60.000 3.32 0.00 35.87 5.73
1262 1536 2.300437 GAGTCAGTGTATATGGCCTCCC 59.700 54.545 3.32 0.00 0.00 4.30
1272 1546 0.608130 TTGGCGCAGAGTCAGTGTAT 59.392 50.000 10.83 0.00 34.99 2.29
1286 1560 2.487762 TCCTGCTGTTCTAATTTTGGCG 59.512 45.455 0.00 0.00 0.00 5.69
1291 1565 3.623453 GCCTCCTCCTGCTGTTCTAATTT 60.623 47.826 0.00 0.00 0.00 1.82
1296 1570 1.229464 AGCCTCCTCCTGCTGTTCT 60.229 57.895 0.00 0.00 36.23 3.01
1314 1588 0.251916 CTGTCCCCGCCTTTGTATCA 59.748 55.000 0.00 0.00 0.00 2.15
1318 1592 1.779061 ATGACTGTCCCCGCCTTTGT 61.779 55.000 5.17 0.00 0.00 2.83
1328 1602 2.026822 AGATGTTGGGTCATGACTGTCC 60.027 50.000 24.50 17.55 0.00 4.02
1332 1606 1.632409 AGCAGATGTTGGGTCATGACT 59.368 47.619 24.50 4.18 0.00 3.41
1335 1609 1.135199 GCAAGCAGATGTTGGGTCATG 60.135 52.381 0.00 0.00 0.00 3.07
1339 1613 1.973281 CGGCAAGCAGATGTTGGGT 60.973 57.895 0.00 0.00 0.00 4.51
1356 1630 0.807667 GTCCATACCTGTCAGCAGCG 60.808 60.000 0.00 0.00 41.26 5.18
1402 1676 0.618458 ATGCCACCGGAGAGCTTTAA 59.382 50.000 9.46 0.00 0.00 1.52
1403 1677 0.178068 GATGCCACCGGAGAGCTTTA 59.822 55.000 9.46 0.00 0.00 1.85
1404 1678 1.078143 GATGCCACCGGAGAGCTTT 60.078 57.895 9.46 0.00 0.00 3.51
1413 1687 2.358125 TCCACGTTGATGCCACCG 60.358 61.111 0.00 0.00 34.21 4.94
1434 1708 1.301423 AAGTTAAAGTTGTCGCCGCA 58.699 45.000 0.00 0.00 0.00 5.69
1449 1723 1.961793 TGTGTTGCTCGGCTAAAGTT 58.038 45.000 0.00 0.00 0.00 2.66
1450 1724 1.602377 GTTGTGTTGCTCGGCTAAAGT 59.398 47.619 0.00 0.00 0.00 2.66
1464 1738 1.072159 GAGCTCTGGGCAGTTGTGT 59.928 57.895 6.43 0.00 44.79 3.72
1554 1828 2.633509 GCTTGCCTCCAGGTGCTTG 61.634 63.158 5.50 0.67 37.57 4.01
1601 1875 2.775032 TTTACTCCCACGCGCAGACC 62.775 60.000 5.73 0.00 0.00 3.85
1617 1891 8.091449 ACGGCCAAAGATACATTTCAATTTTTA 58.909 29.630 2.24 0.00 0.00 1.52
1628 1902 2.224769 CCCCATACGGCCAAAGATACAT 60.225 50.000 2.24 0.00 0.00 2.29
1640 1914 1.000145 AAACCTTGGCCCCATACGG 60.000 57.895 0.00 0.00 0.00 4.02
1641 1915 0.322997 TCAAACCTTGGCCCCATACG 60.323 55.000 0.00 0.00 0.00 3.06
1642 1916 1.756538 CATCAAACCTTGGCCCCATAC 59.243 52.381 0.00 0.00 0.00 2.39
1643 1917 1.342874 CCATCAAACCTTGGCCCCATA 60.343 52.381 0.00 0.00 0.00 2.74
1644 1918 0.618393 CCATCAAACCTTGGCCCCAT 60.618 55.000 0.00 0.00 0.00 4.00
1655 1929 9.086336 CAAATACAATACCATGAACCATCAAAC 57.914 33.333 0.00 0.00 39.49 2.93
1665 1939 4.919206 CGCAAGCAAATACAATACCATGA 58.081 39.130 0.00 0.00 0.00 3.07
1687 1961 1.817447 AGAGAAGCATGCCTGAAAAGC 59.183 47.619 15.66 0.00 0.00 3.51
1692 1966 3.102972 AGAACTAGAGAAGCATGCCTGA 58.897 45.455 15.66 0.00 0.00 3.86
1700 1974 7.519328 CGGTCATAGAAGTAGAACTAGAGAAGC 60.519 44.444 0.00 0.00 0.00 3.86
1701 1975 7.496591 ACGGTCATAGAAGTAGAACTAGAGAAG 59.503 40.741 0.00 0.00 0.00 2.85
1704 1978 6.987992 AGACGGTCATAGAAGTAGAACTAGAG 59.012 42.308 11.27 0.00 0.00 2.43
1718 1992 8.717821 TCTTAATTTGTTGAAAGACGGTCATAG 58.282 33.333 11.27 0.00 0.00 2.23
1719 1993 8.610248 TCTTAATTTGTTGAAAGACGGTCATA 57.390 30.769 11.27 0.00 0.00 2.15
1720 1994 7.504924 TCTTAATTTGTTGAAAGACGGTCAT 57.495 32.000 11.27 0.00 0.00 3.06
1721 1995 6.928979 TCTTAATTTGTTGAAAGACGGTCA 57.071 33.333 11.27 0.00 0.00 4.02
1722 1996 7.415229 AGTTCTTAATTTGTTGAAAGACGGTC 58.585 34.615 0.00 0.00 0.00 4.79
1723 1997 7.329588 AGTTCTTAATTTGTTGAAAGACGGT 57.670 32.000 0.00 0.00 0.00 4.83
1724 1998 9.893305 ATAAGTTCTTAATTTGTTGAAAGACGG 57.107 29.630 0.00 0.00 0.00 4.79
2549 2834 2.191908 CGGGAAATGGATGGCGGA 59.808 61.111 0.00 0.00 0.00 5.54
2588 2873 1.974875 GAAACGGGTGGCGGGAAAT 60.975 57.895 0.00 0.00 0.00 2.17
2602 2887 0.892358 GGAAACGGGTGGAGGGAAAC 60.892 60.000 0.00 0.00 0.00 2.78
2616 2901 1.606994 GGAAATTGGTTGGCGGGAAAC 60.607 52.381 0.00 0.00 0.00 2.78
2688 2988 0.899720 ATGGCGGGAAAGAACGACTA 59.100 50.000 0.00 0.00 39.30 2.59


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

AutoCloner maintained by Alex Coulton.