Multiple sequence alignment - TraesCS2D01G116400

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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 TraesCS2D01G116400 chr2D 100.000 3870 0 0 1 3870 65534402 65538271 0.000000e+00 7147.0
1 TraesCS2D01G116400 chr2D 84.337 166 24 2 554 717 586150574 586150739 1.110000e-35 161.0
2 TraesCS2D01G116400 chr2D 78.067 269 45 11 511 769 606084534 606084798 1.440000e-34 158.0
3 TraesCS2D01G116400 chr2A 95.327 1819 64 10 1304 3109 69267625 69265815 0.000000e+00 2868.0
4 TraesCS2D01G116400 chr2A 88.326 1302 108 28 1 1287 69268880 69267608 0.000000e+00 1522.0
5 TraesCS2D01G116400 chr2A 98.291 351 5 1 3419 3769 69261804 69261455 7.110000e-172 614.0
6 TraesCS2D01G116400 chr2A 95.088 285 13 1 3099 3383 69264364 69264081 7.630000e-122 448.0
7 TraesCS2D01G116400 chr2A 76.154 260 45 9 506 753 28685782 28686036 1.890000e-23 121.0
8 TraesCS2D01G116400 chr2A 98.182 55 1 0 3379 3433 69261985 69261931 3.180000e-16 97.1
9 TraesCS2D01G116400 chr2B 94.187 1531 68 6 1351 2867 105765188 105763665 0.000000e+00 2314.0
10 TraesCS2D01G116400 chr2B 88.837 215 19 2 3556 3769 391174577 391174367 3.840000e-65 259.0
11 TraesCS2D01G116400 chr2B 81.116 233 36 4 510 735 41433388 41433157 3.070000e-41 180.0
12 TraesCS2D01G116400 chr5B 89.767 215 17 2 3556 3769 567295964 567296174 1.770000e-68 270.0
13 TraesCS2D01G116400 chr5B 88.837 215 19 2 3556 3769 567240301 567240091 3.840000e-65 259.0
14 TraesCS2D01G116400 chr5B 96.078 102 4 0 3768 3869 553923018 553923119 2.390000e-37 167.0
15 TraesCS2D01G116400 chr5B 92.929 99 5 2 3773 3870 513611398 513611301 4.030000e-30 143.0
16 TraesCS2D01G116400 chr3B 93.182 176 12 0 771 946 201514222 201514047 3.840000e-65 259.0
17 TraesCS2D01G116400 chr3B 92.655 177 12 1 771 946 201514759 201514583 1.780000e-63 254.0
18 TraesCS2D01G116400 chr3B 92.655 177 12 1 771 946 201515801 201515625 1.780000e-63 254.0
19 TraesCS2D01G116400 chr3B 97.959 98 2 0 3773 3870 722354849 722354752 1.850000e-38 171.0
20 TraesCS2D01G116400 chr3B 78.818 203 31 10 551 749 143267089 143267283 4.060000e-25 126.0
21 TraesCS2D01G116400 chr3B 100.000 29 0 0 13 41 642287598 642287570 2.000000e-03 54.7
22 TraesCS2D01G116400 chrUn 92.655 177 12 1 771 946 445811942 445812118 1.780000e-63 254.0
23 TraesCS2D01G116400 chrUn 91.573 178 12 3 771 946 30306230 30306406 3.860000e-60 243.0
24 TraesCS2D01G116400 chr7B 92.655 177 12 1 771 946 45215068 45215244 1.780000e-63 254.0
25 TraesCS2D01G116400 chr7B 97.561 41 1 0 18 58 20425466 20425506 1.930000e-08 71.3
26 TraesCS2D01G116400 chr6B 92.614 176 13 0 771 946 22427065 22426890 1.780000e-63 254.0
27 TraesCS2D01G116400 chr1D 91.573 178 12 3 771 946 318665601 318665425 3.860000e-60 243.0
28 TraesCS2D01G116400 chr1D 77.778 216 36 9 547 757 15517950 15517742 5.250000e-24 122.0
29 TraesCS2D01G116400 chr6D 96.875 96 3 0 3775 3870 143985692 143985597 1.110000e-35 161.0
30 TraesCS2D01G116400 chr6D 93.878 98 6 0 3773 3870 222772793 222772696 8.660000e-32 148.0
31 TraesCS2D01G116400 chr6D 91.176 102 9 0 3769 3870 302052386 302052487 5.210000e-29 139.0
32 TraesCS2D01G116400 chr6D 78.231 147 27 5 2307 2449 67384935 67384790 5.330000e-14 89.8
33 TraesCS2D01G116400 chr3D 79.911 224 36 8 551 769 445041124 445041343 5.180000e-34 156.0
34 TraesCS2D01G116400 chr3D 80.882 204 33 5 510 711 481533480 481533679 5.180000e-34 156.0
35 TraesCS2D01G116400 chr3D 80.000 100 15 4 13 108 481290352 481290254 6.940000e-08 69.4
36 TraesCS2D01G116400 chr5D 78.367 245 47 4 510 753 509672111 509672350 1.860000e-33 154.0
37 TraesCS2D01G116400 chr4B 93.137 102 5 2 3770 3870 299562186 299562286 8.660000e-32 148.0
38 TraesCS2D01G116400 chr7A 89.623 106 11 0 3765 3870 700170102 700169997 6.740000e-28 135.0
39 TraesCS2D01G116400 chr4D 90.196 102 10 0 3769 3870 150196492 150196593 2.430000e-27 134.0
40 TraesCS2D01G116400 chr5A 86.538 52 6 1 284 335 476026166 476026216 5.400000e-04 56.5
41 TraesCS2D01G116400 chr3A 94.444 36 2 0 302 337 595457020 595456985 5.400000e-04 56.5
42 TraesCS2D01G116400 chr3A 75.200 125 25 4 13 131 624045223 624045099 2.000000e-03 54.7


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 TraesCS2D01G116400 chr2D 65534402 65538271 3869 False 7147.000000 7147 100.000000 1 3870 1 chr2D.!!$F1 3869
1 TraesCS2D01G116400 chr2A 69261455 69268880 7425 True 1109.820000 2868 95.042800 1 3769 5 chr2A.!!$R1 3768
2 TraesCS2D01G116400 chr2B 105763665 105765188 1523 True 2314.000000 2314 94.187000 1351 2867 1 chr2B.!!$R2 1516
3 TraesCS2D01G116400 chr3B 201514047 201515801 1754 True 255.666667 259 92.830667 771 946 3 chr3B.!!$R3 175

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
767 773 0.108186 TGCGTTCATAGGGCTGACTG 60.108 55.0 0.00 0.0 0.00 3.51 F
1433 1723 0.030638 CGGCCAAGGTTTCACAACAG 59.969 55.0 2.24 0.0 34.15 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2519 0.108585 GTCTTGGAACTCAGTGCCCA 59.891 55.0 0.0 0.0 27.67 5.36 R
3153 4930 0.320508 GCTCGTTCGTCCTCCCTTTT 60.321 55.0 0.0 0.0 0.00 2.27 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
230 231 4.218417 ACCTTTCTTCATACATGGTTGCAC 59.782 41.667 0.00 0.00 0.00 4.57
290 292 4.445452 AGTGGCATGCTTTTATGTTGAG 57.555 40.909 18.92 0.00 0.00 3.02
377 379 7.011389 CGTTTGATAGCATATGAAGACAAAGGA 59.989 37.037 20.33 3.99 35.43 3.36
436 440 8.458843 TCTCCAAATTAAAGAACGAATGAATCC 58.541 33.333 0.00 0.00 0.00 3.01
437 441 8.348285 TCCAAATTAAAGAACGAATGAATCCT 57.652 30.769 0.00 0.00 0.00 3.24
537 542 4.723309 AGCTCAGATGGTGAAGTTCTTTT 58.277 39.130 4.17 0.00 33.60 2.27
567 572 2.552373 CCAACCTACCAGGGTTCAAGTC 60.552 54.545 0.00 0.00 46.58 3.01
673 679 2.279502 GACTACGGAGGCGCATGTGA 62.280 60.000 10.83 0.00 0.00 3.58
675 681 1.217585 CTACGGAGGCGCATGTGATG 61.218 60.000 10.83 0.00 0.00 3.07
701 707 7.605449 ACTTGGTCAATCTTAAAATGATGTGG 58.395 34.615 0.00 0.00 0.00 4.17
706 712 2.722094 TCTTAAAATGATGTGGCGGCT 58.278 42.857 11.43 0.00 0.00 5.52
707 713 2.682856 TCTTAAAATGATGTGGCGGCTC 59.317 45.455 11.43 7.43 0.00 4.70
729 735 5.510430 TCAGTCTCTCAGAGGTGCTTATAA 58.490 41.667 0.57 0.00 0.00 0.98
732 738 4.038642 GTCTCTCAGAGGTGCTTATAAGGG 59.961 50.000 14.28 0.00 0.00 3.95
741 747 3.006217 GGTGCTTATAAGGGTACGTAGGG 59.994 52.174 14.28 0.00 0.00 3.53
767 773 0.108186 TGCGTTCATAGGGCTGACTG 60.108 55.000 0.00 0.00 0.00 3.51
769 775 1.645034 CGTTCATAGGGCTGACTGTG 58.355 55.000 0.00 0.00 0.00 3.66
775 781 1.399714 TAGGGCTGACTGTGATACCG 58.600 55.000 0.00 0.00 0.00 4.02
926 1199 3.330701 TGCTGGAATCTTAGGTGGTTCTT 59.669 43.478 0.00 0.00 0.00 2.52
943 1216 6.016276 GTGGTTCTTGGAAGAAGATAGCAAAA 60.016 38.462 1.96 0.00 45.01 2.44
1012 1285 2.275253 CGTCTGCAACGTGTTGAAAAAC 59.725 45.455 16.48 6.41 46.42 2.43
1118 1392 8.735315 TCTTTAAAATCGTATGGAATGCTTTCA 58.265 29.630 13.72 0.00 33.23 2.69
1119 1393 9.352784 CTTTAAAATCGTATGGAATGCTTTCAA 57.647 29.630 13.72 3.28 33.23 2.69
1122 1396 7.992180 AAATCGTATGGAATGCTTTCAAATC 57.008 32.000 13.72 0.85 33.23 2.17
1198 1487 2.092429 CCTTTGGTAAGGCAGGCTATGA 60.092 50.000 0.00 0.00 44.27 2.15
1205 1494 0.326048 AGGCAGGCTATGAGACCACT 60.326 55.000 0.00 0.00 0.00 4.00
1212 1501 1.786937 CTATGAGACCACTGCTCCCT 58.213 55.000 0.00 0.00 0.00 4.20
1239 1528 6.966632 TGTCAAATCAACAAAGAAGAAGAACG 59.033 34.615 0.00 0.00 0.00 3.95
1246 1535 3.312697 ACAAAGAAGAAGAACGAAGGCAC 59.687 43.478 0.00 0.00 0.00 5.01
1251 1540 2.135933 AGAAGAACGAAGGCACGAAAG 58.864 47.619 10.66 0.00 37.03 2.62
1254 1543 1.865340 AGAACGAAGGCACGAAAGAAC 59.135 47.619 10.66 0.00 37.03 3.01
1287 1577 2.593725 CTCGCTCCATGGCCCATG 60.594 66.667 17.16 17.16 41.10 3.66
1295 1585 2.234586 CATGGCCCATGGAGTAGGT 58.765 57.895 16.33 0.00 38.11 3.08
1296 1586 0.179009 CATGGCCCATGGAGTAGGTG 60.179 60.000 16.33 0.27 38.11 4.00
1297 1587 1.355718 ATGGCCCATGGAGTAGGTGG 61.356 60.000 15.22 0.00 0.00 4.61
1298 1588 2.193248 GCCCATGGAGTAGGTGGC 59.807 66.667 15.22 0.69 0.00 5.01
1299 1589 2.505982 CCCATGGAGTAGGTGGCG 59.494 66.667 15.22 0.00 0.00 5.69
1300 1590 2.063979 CCCATGGAGTAGGTGGCGA 61.064 63.158 15.22 0.00 0.00 5.54
1301 1591 1.144057 CCATGGAGTAGGTGGCGAC 59.856 63.158 5.56 0.00 0.00 5.19
1302 1592 1.226974 CATGGAGTAGGTGGCGACG 60.227 63.158 0.00 0.00 0.00 5.12
1303 1593 1.379443 ATGGAGTAGGTGGCGACGA 60.379 57.895 0.00 0.00 0.00 4.20
1304 1594 1.664321 ATGGAGTAGGTGGCGACGAC 61.664 60.000 0.00 0.00 0.00 4.34
1305 1595 2.045131 GGAGTAGGTGGCGACGACT 61.045 63.158 0.65 4.98 0.00 4.18
1306 1596 1.428620 GAGTAGGTGGCGACGACTC 59.571 63.158 14.00 14.00 31.95 3.36
1307 1597 2.099831 GTAGGTGGCGACGACTCG 59.900 66.667 0.65 0.00 43.28 4.18
1315 1605 2.805353 CGACGACTCGCCACCAAG 60.805 66.667 0.00 0.00 31.91 3.61
1316 1606 2.432628 GACGACTCGCCACCAAGG 60.433 66.667 0.00 0.00 41.84 3.61
1317 1607 2.915659 ACGACTCGCCACCAAGGA 60.916 61.111 0.00 0.00 41.22 3.36
1318 1608 2.432628 CGACTCGCCACCAAGGAC 60.433 66.667 0.00 0.00 41.22 3.85
1319 1609 2.047179 GACTCGCCACCAAGGACC 60.047 66.667 0.00 0.00 41.22 4.46
1320 1610 3.607370 GACTCGCCACCAAGGACCC 62.607 68.421 0.00 0.00 41.22 4.46
1321 1611 3.636231 CTCGCCACCAAGGACCCA 61.636 66.667 0.00 0.00 41.22 4.51
1322 1612 3.901797 CTCGCCACCAAGGACCCAC 62.902 68.421 0.00 0.00 41.22 4.61
1334 1624 0.673985 GGACCCACAAACTTGAAGGC 59.326 55.000 0.00 0.00 0.00 4.35
1338 1628 1.370414 CACAAACTTGAAGGCGCCG 60.370 57.895 23.20 9.03 0.00 6.46
1433 1723 0.030638 CGGCCAAGGTTTCACAACAG 59.969 55.000 2.24 0.00 34.15 3.16
1621 1933 1.986575 GAGCATGAGCAGCCGGTTTC 61.987 60.000 1.90 0.00 45.49 2.78
1671 1983 4.740822 CCCGCCCCCTTCAACCTG 62.741 72.222 0.00 0.00 0.00 4.00
1686 1998 1.339097 ACCTGTACCGCATAGATCCC 58.661 55.000 0.00 0.00 0.00 3.85
1689 2001 1.080025 GTACCGCATAGATCCCGCC 60.080 63.158 0.00 0.00 0.00 6.13
1742 2054 4.093952 GGCGACGTCGTCCGAAGA 62.094 66.667 35.48 0.00 42.22 2.87
1747 2059 1.325647 GACGTCGTCCGAAGAAAGAC 58.674 55.000 14.60 0.00 40.70 3.01
1826 2138 1.603739 GGCCCTGCGAAAAGAACCT 60.604 57.895 0.00 0.00 0.00 3.50
1926 2238 1.410517 ACCATCCTGTATGACGCAGAG 59.589 52.381 0.00 0.00 37.86 3.35
2082 2394 2.811317 CTCCTCCGCGACAGCAAC 60.811 66.667 8.23 0.00 45.49 4.17
2633 2945 1.067283 CAGCGGGCTCACCTATGATAG 60.067 57.143 0.00 0.00 36.97 2.08
2658 2970 0.457166 CCACGACGAATCTTGCGGTA 60.457 55.000 0.00 0.00 0.00 4.02
2775 3087 1.188863 AAGCCCTGTGAATGAATGGC 58.811 50.000 0.00 0.00 39.17 4.40
2803 3115 0.808125 GCTCTCTCTCGTGCTTCTGA 59.192 55.000 0.00 0.00 0.00 3.27
3007 3322 8.668510 AGTGAATCTTGCAATAATAATCTCGT 57.331 30.769 0.00 0.00 0.00 4.18
3153 4930 2.041115 CGAGCTCGAGACTGACCCA 61.041 63.158 32.06 0.00 43.02 4.51
3164 4941 0.771755 ACTGACCCAAAAGGGAGGAC 59.228 55.000 7.71 0.00 41.63 3.85
3263 5040 0.814457 TGCCGCAAAGTTTCAACACT 59.186 45.000 0.00 0.00 0.00 3.55
3443 7575 3.290948 AGCTTCCTTGTTTGTGGTACA 57.709 42.857 0.00 0.00 0.00 2.90
3666 7798 1.516169 GCCTAAAAATGCCGCACCG 60.516 57.895 0.00 0.00 0.00 4.94
3715 7847 3.775316 AGCTGGTTAGTATTAGCTGGTGT 59.225 43.478 0.00 0.00 44.23 4.16
3769 7901 6.286758 GTGATCCACATGATTGTCTACATCT 58.713 40.000 0.00 0.00 32.34 2.90
3770 7902 6.423302 GTGATCCACATGATTGTCTACATCTC 59.577 42.308 0.00 0.00 32.34 2.75
3771 7903 4.936891 TCCACATGATTGTCTACATCTCG 58.063 43.478 0.00 0.00 32.34 4.04
3772 7904 4.644685 TCCACATGATTGTCTACATCTCGA 59.355 41.667 0.00 0.00 32.34 4.04
3773 7905 4.981054 CCACATGATTGTCTACATCTCGAG 59.019 45.833 5.93 5.93 32.34 4.04
3774 7906 5.221126 CCACATGATTGTCTACATCTCGAGA 60.221 44.000 19.19 19.19 32.34 4.04
3775 7907 6.445475 CACATGATTGTCTACATCTCGAGAT 58.555 40.000 22.32 22.32 32.34 2.75
3776 7908 6.362820 CACATGATTGTCTACATCTCGAGATG 59.637 42.308 40.66 40.66 44.73 2.90
3777 7909 8.469603 CACATGATTGTCTACATCTCGAGATGG 61.470 44.444 42.86 31.58 44.11 3.51
3784 7916 2.469274 CATCTCGAGATGGGAATGGG 57.531 55.000 37.19 16.88 46.09 4.00
3785 7917 0.689623 ATCTCGAGATGGGAATGGGC 59.310 55.000 26.78 0.00 32.68 5.36
3786 7918 1.072159 CTCGAGATGGGAATGGGCC 59.928 63.158 6.58 0.00 0.00 5.80
3787 7919 2.281070 CGAGATGGGAATGGGCCG 60.281 66.667 0.00 0.00 0.00 6.13
3788 7920 2.113986 GAGATGGGAATGGGCCGG 59.886 66.667 0.00 0.00 0.00 6.13
3789 7921 3.497884 GAGATGGGAATGGGCCGGG 62.498 68.421 2.18 0.00 0.00 5.73
3790 7922 3.820843 GATGGGAATGGGCCGGGT 61.821 66.667 2.18 0.00 0.00 5.28
3791 7923 3.792185 GATGGGAATGGGCCGGGTC 62.792 68.421 2.18 0.00 0.00 4.46
3818 7950 2.920912 GGTCACTGACCCGACCCA 60.921 66.667 16.54 0.00 46.19 4.51
3819 7951 2.657237 GTCACTGACCCGACCCAG 59.343 66.667 0.00 0.00 36.53 4.45
3820 7952 1.906824 GTCACTGACCCGACCCAGA 60.907 63.158 0.00 0.00 34.65 3.86
3821 7953 1.152419 TCACTGACCCGACCCAGAA 60.152 57.895 0.00 0.00 34.65 3.02
3822 7954 0.761323 TCACTGACCCGACCCAGAAA 60.761 55.000 0.00 0.00 34.65 2.52
3823 7955 0.320771 CACTGACCCGACCCAGAAAG 60.321 60.000 0.00 0.00 34.65 2.62
3824 7956 0.471211 ACTGACCCGACCCAGAAAGA 60.471 55.000 0.00 0.00 34.65 2.52
3825 7957 0.037232 CTGACCCGACCCAGAAAGAC 60.037 60.000 0.00 0.00 32.37 3.01
3826 7958 1.080025 GACCCGACCCAGAAAGACG 60.080 63.158 0.00 0.00 0.00 4.18
3827 7959 1.530013 GACCCGACCCAGAAAGACGA 61.530 60.000 0.00 0.00 0.00 4.20
3828 7960 1.215647 CCCGACCCAGAAAGACGAG 59.784 63.158 0.00 0.00 0.00 4.18
3829 7961 1.215647 CCGACCCAGAAAGACGAGG 59.784 63.158 0.00 0.00 0.00 4.63
3830 7962 1.446272 CGACCCAGAAAGACGAGGC 60.446 63.158 0.00 0.00 0.00 4.70
3831 7963 1.079057 GACCCAGAAAGACGAGGCC 60.079 63.158 0.00 0.00 0.00 5.19
3832 7964 1.827399 GACCCAGAAAGACGAGGCCA 61.827 60.000 5.01 0.00 0.00 5.36
3833 7965 1.374947 CCCAGAAAGACGAGGCCAA 59.625 57.895 5.01 0.00 0.00 4.52
3834 7966 0.035056 CCCAGAAAGACGAGGCCAAT 60.035 55.000 5.01 0.00 0.00 3.16
3835 7967 1.089920 CCAGAAAGACGAGGCCAATG 58.910 55.000 5.01 0.00 0.00 2.82
3836 7968 1.089920 CAGAAAGACGAGGCCAATGG 58.910 55.000 5.01 0.00 0.00 3.16
3837 7969 0.035056 AGAAAGACGAGGCCAATGGG 60.035 55.000 5.01 0.00 37.18 4.00
3847 7979 4.792066 CCAATGGGCCAAGTGGAT 57.208 55.556 27.56 1.26 37.39 3.41
3848 7980 2.995480 CCAATGGGCCAAGTGGATT 58.005 52.632 27.56 7.81 37.39 3.01
3849 7981 0.538118 CCAATGGGCCAAGTGGATTG 59.462 55.000 27.56 18.32 38.74 2.67
3859 7991 3.806625 CAAGTGGATTGGCCCTAAATG 57.193 47.619 0.00 0.00 35.08 2.32
3860 7992 3.364549 CAAGTGGATTGGCCCTAAATGA 58.635 45.455 0.00 0.00 35.08 2.57
3861 7993 3.962718 CAAGTGGATTGGCCCTAAATGAT 59.037 43.478 0.00 0.00 35.08 2.45
3862 7994 5.139727 CAAGTGGATTGGCCCTAAATGATA 58.860 41.667 0.00 0.00 35.08 2.15
3863 7995 5.605540 AGTGGATTGGCCCTAAATGATAT 57.394 39.130 0.00 0.00 34.97 1.63
3864 7996 6.718593 AGTGGATTGGCCCTAAATGATATA 57.281 37.500 0.00 0.00 34.97 0.86
3865 7997 7.289326 AGTGGATTGGCCCTAAATGATATAT 57.711 36.000 0.00 0.00 34.97 0.86
3866 7998 7.121382 AGTGGATTGGCCCTAAATGATATATG 58.879 38.462 0.00 0.00 34.97 1.78
3867 7999 6.322201 GTGGATTGGCCCTAAATGATATATGG 59.678 42.308 0.00 0.00 34.97 2.74
3868 8000 5.835280 GGATTGGCCCTAAATGATATATGGG 59.165 44.000 0.00 0.00 37.76 4.00
3869 8001 5.876691 TTGGCCCTAAATGATATATGGGT 57.123 39.130 0.00 0.00 37.09 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 8.100164 TCAGACAATCATGTTCCATACAACTAA 58.900 33.333 0.00 0.00 40.74 2.24
40 41 7.619965 TCAGACAATCATGTTCCATACAACTA 58.380 34.615 0.00 0.00 40.74 2.24
41 42 6.475504 TCAGACAATCATGTTCCATACAACT 58.524 36.000 0.00 0.00 40.74 3.16
197 198 5.705441 TGTATGAAGAAAGGTCCATCACAAC 59.295 40.000 0.00 0.00 0.00 3.32
203 204 5.456921 ACCATGTATGAAGAAAGGTCCAT 57.543 39.130 0.00 0.00 0.00 3.41
230 231 2.294074 TGAGAAAAACCCACCTCAACG 58.706 47.619 0.00 0.00 33.26 4.10
348 350 7.003939 TGTCTTCATATGCTATCAAACGTTG 57.996 36.000 0.00 0.00 0.00 4.10
351 353 7.011389 TCCTTTGTCTTCATATGCTATCAAACG 59.989 37.037 0.00 3.00 0.00 3.60
377 379 8.717717 TCATCCACTCAAACCTCTTGATATATT 58.282 33.333 0.00 0.00 0.00 1.28
537 542 2.423660 CCTGGTAGGTTGGTTCCACAAA 60.424 50.000 0.00 0.00 31.17 2.83
539 544 0.768622 CCTGGTAGGTTGGTTCCACA 59.231 55.000 0.00 0.00 0.00 4.17
554 559 2.541466 AGTCTAGGACTTGAACCCTGG 58.459 52.381 0.00 0.00 40.28 4.45
567 572 9.722184 AATATGATCATCAATGTCAAGTCTAGG 57.278 33.333 12.53 0.00 0.00 3.02
597 602 6.072948 TCGCCGAAAAGTCTGAAATAAATCAA 60.073 34.615 0.00 0.00 0.00 2.57
607 613 0.037326 AGCATCGCCGAAAAGTCTGA 60.037 50.000 0.00 0.00 0.00 3.27
616 622 2.351244 ACTGAAGGAGCATCGCCGA 61.351 57.895 0.00 0.00 34.37 5.54
667 673 5.892160 AAGATTGACCAAGTCATCACATG 57.108 39.130 0.00 0.00 42.40 3.21
673 679 9.028284 ACATCATTTTAAGATTGACCAAGTCAT 57.972 29.630 0.00 0.00 42.40 3.06
675 681 7.756722 CCACATCATTTTAAGATTGACCAAGTC 59.243 37.037 0.00 0.00 0.00 3.01
701 707 1.433064 CTCTGAGAGACTGAGCCGC 59.567 63.158 2.60 0.00 37.65 6.53
706 712 2.300956 AAGCACCTCTGAGAGACTGA 57.699 50.000 11.82 0.00 0.00 3.41
707 713 5.221224 CCTTATAAGCACCTCTGAGAGACTG 60.221 48.000 11.82 6.88 0.00 3.51
729 735 0.616679 ATGCACACCCTACGTACCCT 60.617 55.000 0.00 0.00 0.00 4.34
732 738 1.418342 CGCATGCACACCCTACGTAC 61.418 60.000 19.57 0.00 0.00 3.67
741 747 0.378257 CCCTATGAACGCATGCACAC 59.622 55.000 19.57 8.21 35.94 3.82
767 773 1.068816 GTTGCCCAAACACGGTATCAC 60.069 52.381 0.00 0.00 38.75 3.06
769 775 0.524414 GGTTGCCCAAACACGGTATC 59.476 55.000 0.00 0.00 40.86 2.24
840 1113 5.771165 AAGTCTCCGATATAGGAAGACTTCC 59.229 44.000 25.93 24.46 45.06 3.46
848 1121 9.857656 TTTAAGTAAGAAGTCTCCGATATAGGA 57.142 33.333 4.35 4.35 38.80 2.94
1092 1366 8.735315 TGAAAGCATTCCATACGATTTTAAAGA 58.265 29.630 0.00 0.00 34.49 2.52
1105 1379 6.363167 TCCTTTGATTTGAAAGCATTCCAT 57.637 33.333 0.00 0.00 34.49 3.41
1109 1383 4.564199 GGGCTCCTTTGATTTGAAAGCATT 60.564 41.667 0.00 0.00 32.45 3.56
1112 1386 2.354103 GGGGCTCCTTTGATTTGAAAGC 60.354 50.000 0.00 0.00 32.45 3.51
1113 1387 2.899256 TGGGGCTCCTTTGATTTGAAAG 59.101 45.455 3.07 0.00 33.42 2.62
1118 1392 2.158325 TCACTTGGGGCTCCTTTGATTT 60.158 45.455 3.07 0.00 0.00 2.17
1119 1393 1.428912 TCACTTGGGGCTCCTTTGATT 59.571 47.619 3.07 0.00 0.00 2.57
1122 1396 1.703411 TTTCACTTGGGGCTCCTTTG 58.297 50.000 3.07 0.00 0.00 2.77
1159 1440 3.644884 AGGTGTGTCACTTCGTAGAAG 57.355 47.619 4.27 8.11 45.90 2.85
1161 1442 3.491964 CCAAAGGTGTGTCACTTCGTAGA 60.492 47.826 4.27 0.00 34.40 2.59
1166 1451 3.564225 CCTTACCAAAGGTGTGTCACTTC 59.436 47.826 4.27 0.00 46.34 3.01
1198 1487 0.398318 GACAAAGGGAGCAGTGGTCT 59.602 55.000 20.97 0.64 0.00 3.85
1205 1494 3.295093 TGTTGATTTGACAAAGGGAGCA 58.705 40.909 6.77 0.00 0.00 4.26
1212 1501 9.139174 GTTCTTCTTCTTTGTTGATTTGACAAA 57.861 29.630 2.48 2.48 42.78 2.83
1246 1535 3.540738 GGTTCACAAAACACGTTCTTTCG 59.459 43.478 0.00 0.00 0.00 3.46
1287 1577 1.991099 GAGTCGTCGCCACCTACTCC 61.991 65.000 1.56 0.00 30.61 3.85
1288 1578 1.428620 GAGTCGTCGCCACCTACTC 59.571 63.158 0.00 0.00 0.00 2.59
1289 1579 2.396955 CGAGTCGTCGCCACCTACT 61.397 63.158 3.82 0.00 39.88 2.57
1290 1580 2.099831 CGAGTCGTCGCCACCTAC 59.900 66.667 3.82 0.00 39.88 3.18
1299 1589 2.432628 CCTTGGTGGCGAGTCGTC 60.433 66.667 10.93 10.93 0.00 4.20
1300 1590 2.915659 TCCTTGGTGGCGAGTCGT 60.916 61.111 15.08 0.00 35.26 4.34
1301 1591 2.432628 GTCCTTGGTGGCGAGTCG 60.433 66.667 8.54 8.54 35.26 4.18
1302 1592 2.047179 GGTCCTTGGTGGCGAGTC 60.047 66.667 0.00 0.00 35.26 3.36
1303 1593 3.637273 GGGTCCTTGGTGGCGAGT 61.637 66.667 0.00 0.00 35.26 4.18
1304 1594 3.636231 TGGGTCCTTGGTGGCGAG 61.636 66.667 0.00 0.00 35.26 5.03
1305 1595 3.948719 GTGGGTCCTTGGTGGCGA 61.949 66.667 0.00 0.00 35.26 5.54
1306 1596 3.783362 TTGTGGGTCCTTGGTGGCG 62.783 63.158 0.00 0.00 35.26 5.69
1307 1597 1.456705 TTTGTGGGTCCTTGGTGGC 60.457 57.895 0.00 0.00 35.26 5.01
1308 1598 0.106217 AGTTTGTGGGTCCTTGGTGG 60.106 55.000 0.00 0.00 37.10 4.61
1309 1599 1.408702 CAAGTTTGTGGGTCCTTGGTG 59.591 52.381 0.00 0.00 32.57 4.17
1310 1600 1.286553 TCAAGTTTGTGGGTCCTTGGT 59.713 47.619 0.00 0.00 35.98 3.67
1311 1601 2.065899 TCAAGTTTGTGGGTCCTTGG 57.934 50.000 0.00 0.00 35.98 3.61
1312 1602 2.362077 CCTTCAAGTTTGTGGGTCCTTG 59.638 50.000 0.00 0.00 36.49 3.61
1313 1603 2.666317 CCTTCAAGTTTGTGGGTCCTT 58.334 47.619 0.00 0.00 0.00 3.36
1314 1604 1.754201 GCCTTCAAGTTTGTGGGTCCT 60.754 52.381 0.00 0.00 0.00 3.85
1315 1605 0.673985 GCCTTCAAGTTTGTGGGTCC 59.326 55.000 8.06 0.00 0.00 4.46
1316 1606 0.310854 CGCCTTCAAGTTTGTGGGTC 59.689 55.000 8.06 2.23 0.00 4.46
1317 1607 1.734388 GCGCCTTCAAGTTTGTGGGT 61.734 55.000 0.00 0.00 0.00 4.51
1318 1608 1.007387 GCGCCTTCAAGTTTGTGGG 60.007 57.895 0.00 5.61 0.00 4.61
1319 1609 1.007387 GGCGCCTTCAAGTTTGTGG 60.007 57.895 22.15 0.00 0.00 4.17
1320 1610 1.370414 CGGCGCCTTCAAGTTTGTG 60.370 57.895 26.68 0.00 0.00 3.33
1321 1611 1.098712 TTCGGCGCCTTCAAGTTTGT 61.099 50.000 26.68 0.00 0.00 2.83
1322 1612 0.660300 GTTCGGCGCCTTCAAGTTTG 60.660 55.000 26.68 5.22 0.00 2.93
1334 1624 0.456221 ATCTGGTGAGTAGTTCGGCG 59.544 55.000 0.00 0.00 0.00 6.46
1338 1628 5.971763 AGATCAACATCTGGTGAGTAGTTC 58.028 41.667 4.04 0.00 46.01 3.01
1467 1764 7.712205 CCAAGAAATGAAAGAACCAAGACAATT 59.288 33.333 0.00 0.00 0.00 2.32
1468 1765 7.069826 TCCAAGAAATGAAAGAACCAAGACAAT 59.930 33.333 0.00 0.00 0.00 2.71
1469 1766 6.379703 TCCAAGAAATGAAAGAACCAAGACAA 59.620 34.615 0.00 0.00 0.00 3.18
1470 1767 5.890985 TCCAAGAAATGAAAGAACCAAGACA 59.109 36.000 0.00 0.00 0.00 3.41
1621 1933 0.250234 TTCCTCACCGCCAGATTCAG 59.750 55.000 0.00 0.00 0.00 3.02
1671 1983 1.080025 GGCGGGATCTATGCGGTAC 60.080 63.158 0.00 0.00 0.00 3.34
1686 1998 1.296056 CCGGGTAGAACAACTTGGCG 61.296 60.000 0.00 0.00 0.00 5.69
1689 2001 1.296056 CGGCCGGGTAGAACAACTTG 61.296 60.000 20.10 0.00 0.00 3.16
1742 2054 3.007940 TGTCGTTGGATCTGATGGTCTTT 59.992 43.478 0.00 0.00 0.00 2.52
1747 2059 3.534554 TCATTGTCGTTGGATCTGATGG 58.465 45.455 0.00 0.00 0.00 3.51
1887 2199 4.953868 CGGCCGACGTTGTCCACA 62.954 66.667 24.07 0.00 37.93 4.17
1926 2238 3.127533 GTGCGGATGGTGTGGAGC 61.128 66.667 0.00 0.00 0.00 4.70
2082 2394 1.166129 TCTTGAAGGACGAGGACGAG 58.834 55.000 0.00 0.00 42.66 4.18
2206 2518 0.843309 TCTTGGAACTCAGTGCCCAA 59.157 50.000 0.00 5.58 37.18 4.12
2207 2519 0.108585 GTCTTGGAACTCAGTGCCCA 59.891 55.000 0.00 0.00 27.67 5.36
2390 2702 1.335051 GCGAAAAGCCAAACCAGAGAC 60.335 52.381 0.00 0.00 40.81 3.36
2633 2945 0.949105 AAGATTCGTCGTGGTGTGGC 60.949 55.000 0.00 0.00 0.00 5.01
2691 3003 2.285368 ATCCTTCCCAGCCCGTGA 60.285 61.111 0.00 0.00 0.00 4.35
2775 3087 1.436195 CGAGAGAGAGCTCCTCCGTG 61.436 65.000 21.57 12.18 42.97 4.94
2803 3115 3.007940 ACCACACATATATAGCACGGCAT 59.992 43.478 0.00 0.00 0.00 4.40
2897 3211 4.128925 TGCAGTGCTATGAGTTCTAAGG 57.871 45.455 17.60 0.00 0.00 2.69
2982 3297 8.668510 ACGAGATTATTATTGCAAGATTCACT 57.331 30.769 4.94 0.00 0.00 3.41
3007 3322 4.697756 CCTTCGTTGCGGCCCTGA 62.698 66.667 0.00 0.00 0.00 3.86
3153 4930 0.320508 GCTCGTTCGTCCTCCCTTTT 60.321 55.000 0.00 0.00 0.00 2.27
3181 4958 5.009010 GGCTCAATTTTATCCGTCATGATGT 59.991 40.000 13.81 0.00 0.00 3.06
3182 4959 5.008911 TGGCTCAATTTTATCCGTCATGATG 59.991 40.000 8.03 8.03 0.00 3.07
3255 5032 2.429930 CTCCGGGCCAGTGTTGAA 59.570 61.111 4.39 0.00 0.00 2.69
3263 5040 2.449967 TAGTGTTCTCCTCCGGGCCA 62.450 60.000 4.39 0.00 0.00 5.36
3285 5062 5.944049 ACCGCGATATTATTTATGCGTAG 57.056 39.130 8.23 0.00 43.68 3.51
3288 5065 4.328983 AGGAACCGCGATATTATTTATGCG 59.671 41.667 8.23 0.00 44.68 4.73
3387 7378 6.625081 GCAAGGGTAAGTAAGCTAAAACATGG 60.625 42.308 0.00 0.00 0.00 3.66
3443 7575 5.826737 CCTTGATCAAGATAGCACATTCCTT 59.173 40.000 32.49 0.00 40.79 3.36
3482 7614 0.462789 CATTTTCTGCATCCCCAGCC 59.537 55.000 0.00 0.00 32.87 4.85
3695 7827 5.339008 TGACACCAGCTAATACTAACCAG 57.661 43.478 0.00 0.00 0.00 4.00
3715 7847 2.562298 GGTGAACCAATGCTCCATTTGA 59.438 45.455 0.00 0.00 31.05 2.69
3769 7901 2.807107 CGGCCCATTCCCATCTCGA 61.807 63.158 0.00 0.00 0.00 4.04
3770 7902 2.281070 CGGCCCATTCCCATCTCG 60.281 66.667 0.00 0.00 0.00 4.04
3771 7903 2.113986 CCGGCCCATTCCCATCTC 59.886 66.667 0.00 0.00 0.00 2.75
3772 7904 3.501911 CCCGGCCCATTCCCATCT 61.502 66.667 0.00 0.00 0.00 2.90
3773 7905 3.792185 GACCCGGCCCATTCCCATC 62.792 68.421 0.00 0.00 0.00 3.51
3774 7906 3.820843 GACCCGGCCCATTCCCAT 61.821 66.667 0.00 0.00 0.00 4.00
3802 7934 1.469335 TTCTGGGTCGGGTCAGTGAC 61.469 60.000 15.24 15.24 33.13 3.67
3803 7935 0.761323 TTTCTGGGTCGGGTCAGTGA 60.761 55.000 0.00 0.00 33.13 3.41
3804 7936 0.320771 CTTTCTGGGTCGGGTCAGTG 60.321 60.000 0.00 0.00 33.13 3.66
3805 7937 0.471211 TCTTTCTGGGTCGGGTCAGT 60.471 55.000 0.00 0.00 33.13 3.41
3806 7938 0.037232 GTCTTTCTGGGTCGGGTCAG 60.037 60.000 0.00 0.00 0.00 3.51
3807 7939 1.812686 CGTCTTTCTGGGTCGGGTCA 61.813 60.000 0.00 0.00 0.00 4.02
3808 7940 1.080025 CGTCTTTCTGGGTCGGGTC 60.080 63.158 0.00 0.00 0.00 4.46
3809 7941 1.532316 TCGTCTTTCTGGGTCGGGT 60.532 57.895 0.00 0.00 0.00 5.28
3810 7942 1.215647 CTCGTCTTTCTGGGTCGGG 59.784 63.158 0.00 0.00 0.00 5.14
3811 7943 1.215647 CCTCGTCTTTCTGGGTCGG 59.784 63.158 0.00 0.00 0.00 4.79
3812 7944 1.446272 GCCTCGTCTTTCTGGGTCG 60.446 63.158 0.00 0.00 0.00 4.79
3813 7945 1.079057 GGCCTCGTCTTTCTGGGTC 60.079 63.158 0.00 0.00 0.00 4.46
3814 7946 1.415672 TTGGCCTCGTCTTTCTGGGT 61.416 55.000 3.32 0.00 0.00 4.51
3815 7947 0.035056 ATTGGCCTCGTCTTTCTGGG 60.035 55.000 3.32 0.00 0.00 4.45
3816 7948 1.089920 CATTGGCCTCGTCTTTCTGG 58.910 55.000 3.32 0.00 0.00 3.86
3817 7949 1.089920 CCATTGGCCTCGTCTTTCTG 58.910 55.000 3.32 0.00 0.00 3.02
3818 7950 0.035056 CCCATTGGCCTCGTCTTTCT 60.035 55.000 3.32 0.00 0.00 2.52
3819 7951 2.482326 CCCATTGGCCTCGTCTTTC 58.518 57.895 3.32 0.00 0.00 2.62
3820 7952 4.743018 CCCATTGGCCTCGTCTTT 57.257 55.556 3.32 0.00 0.00 2.52
3830 7962 0.538118 CAATCCACTTGGCCCATTGG 59.462 55.000 6.87 6.87 34.44 3.16
3839 7971 3.364549 TCATTTAGGGCCAATCCACTTG 58.635 45.455 6.18 0.00 36.21 3.16
3840 7972 3.756082 TCATTTAGGGCCAATCCACTT 57.244 42.857 6.18 0.00 36.21 3.16
3841 7973 3.979501 ATCATTTAGGGCCAATCCACT 57.020 42.857 6.18 0.00 36.21 4.00
3842 7974 6.322201 CCATATATCATTTAGGGCCAATCCAC 59.678 42.308 6.18 0.00 36.21 4.02
3843 7975 6.434302 CCATATATCATTTAGGGCCAATCCA 58.566 40.000 6.18 0.00 36.21 3.41
3844 7976 5.835280 CCCATATATCATTTAGGGCCAATCC 59.165 44.000 6.18 0.00 0.00 3.01
3845 7977 6.435164 ACCCATATATCATTTAGGGCCAATC 58.565 40.000 6.18 0.00 39.97 2.67
3846 7978 6.421892 ACCCATATATCATTTAGGGCCAAT 57.578 37.500 6.18 0.00 39.97 3.16
3847 7979 5.876691 ACCCATATATCATTTAGGGCCAA 57.123 39.130 6.18 0.00 39.97 4.52


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

AutoCloner maintained by Alex Coulton.