Multiple sequence alignment - TraesCS7A01G145700

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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 TraesCS7A01G145700 chr7A 100.000 2361 0 0 1 2361 97252670 97250310 0.000000e+00 4361.0
1 TraesCS7A01G145700 chr7B 88.771 1318 78 24 685 1953 47620636 47619340 0.000000e+00 1550.0
2 TraesCS7A01G145700 chr7B 89.630 270 16 4 1951 2210 47619227 47618960 1.350000e-87 333.0
3 TraesCS7A01G145700 chr7B 89.308 159 16 1 433 590 47620912 47620754 5.150000e-47 198.0
4 TraesCS7A01G145700 chr7B 84.848 132 17 3 285 416 47621430 47621302 1.900000e-26 130.0
5 TraesCS7A01G145700 chr7B 87.736 106 9 3 2260 2361 47618962 47618857 1.150000e-23 121.0
6 TraesCS7A01G145700 chr7B 92.683 41 1 1 597 637 47620675 47620637 9.110000e-05 58.4
7 TraesCS7A01G145700 chr7D 89.920 1002 42 29 685 1636 93938630 93937638 0.000000e+00 1236.0
8 TraesCS7A01G145700 chr7D 86.332 717 55 10 1640 2349 93937445 93936765 0.000000e+00 741.0
9 TraesCS7A01G145700 chr7D 81.852 540 66 25 76 594 93980123 93979595 2.170000e-115 425.0
10 TraesCS7A01G145700 chr7D 97.297 37 1 0 433 469 377605982 377606018 1.960000e-06 63.9
11 TraesCS7A01G145700 chr6B 81.992 261 32 14 1109 1360 668245352 668245606 8.550000e-50 207.0
12 TraesCS7A01G145700 chr6A 81.579 266 30 18 1113 1366 591428115 591428373 3.980000e-48 202.0
13 TraesCS7A01G145700 chr6A 94.444 36 2 0 434 469 609118133 609118098 3.280000e-04 56.5
14 TraesCS7A01G145700 chr6D 81.369 263 33 14 1113 1366 443844686 443844941 1.430000e-47 200.0
15 TraesCS7A01G145700 chr4A 97.222 36 1 0 436 471 24215401 24215366 7.050000e-06 62.1
16 TraesCS7A01G145700 chr3A 97.222 36 1 0 436 471 203663520 203663485 7.050000e-06 62.1
17 TraesCS7A01G145700 chr3D 94.595 37 2 0 433 469 596846530 596846494 9.110000e-05 58.4
18 TraesCS7A01G145700 chr3D 92.308 39 3 0 434 472 11334583 11334545 3.280000e-04 56.5
19 TraesCS7A01G145700 chr5D 100.000 30 0 0 434 463 495349682 495349711 3.280000e-04 56.5
20 TraesCS7A01G145700 chr5A 92.308 39 3 0 434 472 59700847 59700885 3.280000e-04 56.5


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 TraesCS7A01G145700 chr7A 97250310 97252670 2360 True 4361.0 4361 100.000000 1 2361 1 chr7A.!!$R1 2360
1 TraesCS7A01G145700 chr7B 47618857 47621430 2573 True 398.4 1550 88.829333 285 2361 6 chr7B.!!$R1 2076
2 TraesCS7A01G145700 chr7D 93936765 93938630 1865 True 988.5 1236 88.126000 685 2349 2 chr7D.!!$R2 1664
3 TraesCS7A01G145700 chr7D 93979595 93980123 528 True 425.0 425 81.852000 76 594 1 chr7D.!!$R1 518

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
40 41 0.037605 ACTGTGTAGCAACTACCGGC 60.038 55.0 0.0 0.0 36.24 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2581 0.395586 AGCAACCACACAAGAGGCAA 60.396 50.0 0.0 0.0 0.0 4.52 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
17 18 3.127533 GCGCAAGGTGTGGCTAGG 61.128 66.667 0.30 0.00 38.28 3.02
18 19 2.436646 CGCAAGGTGTGGCTAGGG 60.437 66.667 0.00 0.00 0.00 3.53
19 20 2.954684 CGCAAGGTGTGGCTAGGGA 61.955 63.158 0.00 0.00 0.00 4.20
20 21 1.378762 GCAAGGTGTGGCTAGGGAA 59.621 57.895 0.00 0.00 0.00 3.97
21 22 0.251165 GCAAGGTGTGGCTAGGGAAA 60.251 55.000 0.00 0.00 0.00 3.13
22 23 1.534729 CAAGGTGTGGCTAGGGAAAC 58.465 55.000 0.00 0.00 0.00 2.78
23 24 1.073923 CAAGGTGTGGCTAGGGAAACT 59.926 52.381 0.00 0.00 0.00 2.66
24 25 0.693049 AGGTGTGGCTAGGGAAACTG 59.307 55.000 0.00 0.00 0.00 3.16
25 26 0.400594 GGTGTGGCTAGGGAAACTGT 59.599 55.000 0.00 0.00 0.00 3.55
26 27 1.523758 GTGTGGCTAGGGAAACTGTG 58.476 55.000 0.00 0.00 0.00 3.66
27 28 1.136828 TGTGGCTAGGGAAACTGTGT 58.863 50.000 0.00 0.00 0.00 3.72
28 29 2.038033 GTGTGGCTAGGGAAACTGTGTA 59.962 50.000 0.00 0.00 0.00 2.90
29 30 2.301870 TGTGGCTAGGGAAACTGTGTAG 59.698 50.000 0.00 0.00 0.00 2.74
30 31 1.278127 TGGCTAGGGAAACTGTGTAGC 59.722 52.381 0.00 0.00 36.23 3.58
31 32 1.278127 GGCTAGGGAAACTGTGTAGCA 59.722 52.381 0.00 0.00 38.28 3.49
32 33 2.290071 GGCTAGGGAAACTGTGTAGCAA 60.290 50.000 0.00 0.00 38.28 3.91
33 34 2.742589 GCTAGGGAAACTGTGTAGCAAC 59.257 50.000 0.00 0.00 36.83 4.17
34 35 3.557264 GCTAGGGAAACTGTGTAGCAACT 60.557 47.826 0.00 0.00 36.83 3.16
35 36 4.322499 GCTAGGGAAACTGTGTAGCAACTA 60.322 45.833 0.00 0.00 36.83 2.24
36 37 4.004196 AGGGAAACTGTGTAGCAACTAC 57.996 45.455 0.00 0.00 37.46 2.73
37 38 3.072211 GGGAAACTGTGTAGCAACTACC 58.928 50.000 2.49 0.00 36.24 3.18
38 39 2.735134 GGAAACTGTGTAGCAACTACCG 59.265 50.000 2.49 0.00 36.24 4.02
39 40 2.450609 AACTGTGTAGCAACTACCGG 57.549 50.000 0.00 0.00 36.24 5.28
40 41 0.037605 ACTGTGTAGCAACTACCGGC 60.038 55.000 0.00 0.00 36.24 6.13
41 42 0.037697 CTGTGTAGCAACTACCGGCA 60.038 55.000 0.00 0.00 36.24 5.69
42 43 0.393448 TGTGTAGCAACTACCGGCAA 59.607 50.000 0.00 0.00 36.24 4.52
43 44 1.076332 GTGTAGCAACTACCGGCAAG 58.924 55.000 0.00 1.09 36.24 4.01
53 54 2.672996 CCGGCAAGGTGGGACAAG 60.673 66.667 0.00 0.00 44.16 3.16
54 55 2.429930 CGGCAAGGTGGGACAAGA 59.570 61.111 0.00 0.00 44.16 3.02
55 56 1.672356 CGGCAAGGTGGGACAAGAG 60.672 63.158 0.00 0.00 44.16 2.85
56 57 1.303643 GGCAAGGTGGGACAAGAGG 60.304 63.158 0.00 0.00 44.16 3.69
57 58 1.456287 GCAAGGTGGGACAAGAGGT 59.544 57.895 0.00 0.00 44.16 3.85
58 59 0.890996 GCAAGGTGGGACAAGAGGTG 60.891 60.000 0.00 0.00 44.16 4.00
59 60 0.474184 CAAGGTGGGACAAGAGGTGT 59.526 55.000 0.00 0.00 44.16 4.16
60 61 0.474184 AAGGTGGGACAAGAGGTGTG 59.526 55.000 0.00 0.00 44.16 3.82
61 62 1.073199 GGTGGGACAAGAGGTGTGG 59.927 63.158 0.00 0.00 44.16 4.17
62 63 1.600916 GTGGGACAAGAGGTGTGGC 60.601 63.158 0.00 0.00 44.16 5.01
63 64 1.770110 TGGGACAAGAGGTGTGGCT 60.770 57.895 0.00 0.00 41.96 4.75
64 65 1.302832 GGGACAAGAGGTGTGGCTG 60.303 63.158 0.00 0.00 41.96 4.85
65 66 1.302832 GGACAAGAGGTGTGGCTGG 60.303 63.158 0.00 0.00 41.96 4.85
66 67 1.302832 GACAAGAGGTGTGGCTGGG 60.303 63.158 0.00 0.00 41.96 4.45
67 68 1.768684 GACAAGAGGTGTGGCTGGGA 61.769 60.000 0.00 0.00 41.96 4.37
68 69 1.002868 CAAGAGGTGTGGCTGGGAG 60.003 63.158 0.00 0.00 0.00 4.30
69 70 2.900106 AAGAGGTGTGGCTGGGAGC 61.900 63.158 0.00 0.00 41.46 4.70
70 71 4.767255 GAGGTGTGGCTGGGAGCG 62.767 72.222 0.00 0.00 43.62 5.03
108 109 1.992277 AGCTGAGAATGCGGGAGGT 60.992 57.895 0.00 0.00 35.28 3.85
109 110 1.817099 GCTGAGAATGCGGGAGGTG 60.817 63.158 0.00 0.00 0.00 4.00
115 116 3.335356 AATGCGGGAGGTGAGGCAG 62.335 63.158 0.00 0.00 39.00 4.85
118 119 3.775654 CGGGAGGTGAGGCAGGAC 61.776 72.222 0.00 0.00 0.00 3.85
119 120 3.403558 GGGAGGTGAGGCAGGACC 61.404 72.222 0.00 0.00 39.61 4.46
169 171 1.418637 GTGGGGATGGAGCGGTTATAA 59.581 52.381 0.00 0.00 0.00 0.98
174 176 3.009143 GGGATGGAGCGGTTATAAGGATT 59.991 47.826 0.00 0.00 0.00 3.01
175 177 4.003648 GGATGGAGCGGTTATAAGGATTG 58.996 47.826 0.00 0.00 0.00 2.67
177 179 2.152016 GGAGCGGTTATAAGGATTGCC 58.848 52.381 0.00 0.00 0.00 4.52
178 180 2.152016 GAGCGGTTATAAGGATTGCCC 58.848 52.381 0.00 0.00 33.31 5.36
179 181 1.202891 AGCGGTTATAAGGATTGCCCC 60.203 52.381 0.00 0.00 34.66 5.80
203 205 2.175715 CCCCCTCTCCTCTTTTTATGGG 59.824 54.545 0.00 0.00 0.00 4.00
209 211 4.086457 TCTCCTCTTTTTATGGGTTTGGC 58.914 43.478 0.00 0.00 0.00 4.52
225 227 0.776810 TGGCAAGTGGATTGGGAAGA 59.223 50.000 0.00 0.00 39.47 2.87
229 231 3.359950 GCAAGTGGATTGGGAAGAATCT 58.640 45.455 0.00 0.00 39.47 2.40
241 243 4.778579 GGGAAGAATCTACTTACCCCAAC 58.221 47.826 0.00 0.00 43.13 3.77
266 268 9.730705 ACAGGTAGGGTTTTTAGTAGAAAATAC 57.269 33.333 0.00 0.00 31.80 1.89
274 276 9.091784 GGTTTTTAGTAGAAAATACGTAGGGAG 57.908 37.037 0.08 0.00 31.80 4.30
282 284 2.679429 ATACGTAGGGAGAAGAGGGG 57.321 55.000 0.08 0.00 0.00 4.79
283 285 1.600058 TACGTAGGGAGAAGAGGGGA 58.400 55.000 0.00 0.00 0.00 4.81
342 345 6.609616 ACCCTTTACTTTCCAATTCTTGACAA 59.390 34.615 0.00 0.00 0.00 3.18
345 348 9.196552 CCTTTACTTTCCAATTCTTGACAATTC 57.803 33.333 0.00 0.00 0.00 2.17
346 349 9.748708 CTTTACTTTCCAATTCTTGACAATTCA 57.251 29.630 0.00 0.00 0.00 2.57
364 368 4.463050 TTCATTAGGTGAAGGGTTGGTT 57.537 40.909 0.00 0.00 41.79 3.67
416 716 3.262660 TGACATCCAAGAGACTCTGCATT 59.737 43.478 5.55 0.00 0.00 3.56
418 718 5.046376 TGACATCCAAGAGACTCTGCATTTA 60.046 40.000 5.55 0.00 0.00 1.40
419 719 5.426504 ACATCCAAGAGACTCTGCATTTAG 58.573 41.667 5.55 0.00 0.00 1.85
420 720 5.046014 ACATCCAAGAGACTCTGCATTTAGT 60.046 40.000 5.55 0.00 0.00 2.24
421 721 6.155221 ACATCCAAGAGACTCTGCATTTAGTA 59.845 38.462 5.55 0.00 0.00 1.82
422 722 6.798427 TCCAAGAGACTCTGCATTTAGTAT 57.202 37.500 5.55 0.00 0.00 2.12
423 723 7.898014 TCCAAGAGACTCTGCATTTAGTATA 57.102 36.000 5.55 0.00 0.00 1.47
468 846 9.976776 ATCTTATATTATGAGACGGAGGAAGTA 57.023 33.333 0.62 0.00 0.00 2.24
469 847 9.228949 TCTTATATTATGAGACGGAGGAAGTAC 57.771 37.037 0.00 0.00 0.00 2.73
470 848 8.929260 TTATATTATGAGACGGAGGAAGTACA 57.071 34.615 0.00 0.00 0.00 2.90
486 864 7.238710 AGGAAGTACATTGTAAAATCCAACCT 58.761 34.615 18.56 8.74 0.00 3.50
487 865 7.728532 AGGAAGTACATTGTAAAATCCAACCTT 59.271 33.333 18.56 7.84 0.00 3.50
590 969 4.609113 CGTGAAACTGCTCTGTAACACATG 60.609 45.833 0.00 0.00 31.75 3.21
592 971 4.273235 TGAAACTGCTCTGTAACACATGTG 59.727 41.667 24.25 24.25 0.00 3.21
625 1076 5.823570 TGTATTTGGAACTCGGAAACAGAAA 59.176 36.000 0.00 0.00 0.00 2.52
626 1077 5.845391 ATTTGGAACTCGGAAACAGAAAA 57.155 34.783 0.00 0.00 0.00 2.29
627 1078 4.893424 TTGGAACTCGGAAACAGAAAAG 57.107 40.909 0.00 0.00 0.00 2.27
628 1079 3.881220 TGGAACTCGGAAACAGAAAAGT 58.119 40.909 0.00 0.00 0.00 2.66
630 1081 4.334481 TGGAACTCGGAAACAGAAAAGTTC 59.666 41.667 4.83 4.83 41.02 3.01
631 1082 4.575236 GGAACTCGGAAACAGAAAAGTTCT 59.425 41.667 11.50 0.00 41.33 3.01
633 1084 5.485662 ACTCGGAAACAGAAAAGTTCTTG 57.514 39.130 0.00 0.00 38.11 3.02
634 1085 4.941873 ACTCGGAAACAGAAAAGTTCTTGT 59.058 37.500 0.00 0.00 38.11 3.16
635 1086 6.110707 ACTCGGAAACAGAAAAGTTCTTGTA 58.889 36.000 0.00 0.00 38.11 2.41
636 1087 6.258068 ACTCGGAAACAGAAAAGTTCTTGTAG 59.742 38.462 0.00 0.00 38.11 2.74
637 1088 6.110707 TCGGAAACAGAAAAGTTCTTGTAGT 58.889 36.000 0.00 0.00 38.11 2.73
638 1089 6.596497 TCGGAAACAGAAAAGTTCTTGTAGTT 59.404 34.615 0.00 0.00 38.11 2.24
639 1090 7.120138 TCGGAAACAGAAAAGTTCTTGTAGTTT 59.880 33.333 4.69 4.69 38.11 2.66
640 1091 7.753580 CGGAAACAGAAAAGTTCTTGTAGTTTT 59.246 33.333 0.00 0.00 38.11 2.43
641 1092 9.419297 GGAAACAGAAAAGTTCTTGTAGTTTTT 57.581 29.630 0.00 0.00 38.11 1.94
663 1114 6.500684 TTTTCTTGAATCAGGAGGAAATCG 57.499 37.500 0.00 0.00 0.00 3.34
664 1115 4.826274 TCTTGAATCAGGAGGAAATCGT 57.174 40.909 0.00 0.00 0.00 3.73
665 1116 5.165961 TCTTGAATCAGGAGGAAATCGTT 57.834 39.130 0.00 0.00 0.00 3.85
666 1117 6.294361 TCTTGAATCAGGAGGAAATCGTTA 57.706 37.500 0.00 0.00 0.00 3.18
667 1118 6.707290 TCTTGAATCAGGAGGAAATCGTTAA 58.293 36.000 0.00 0.00 0.00 2.01
668 1119 7.338710 TCTTGAATCAGGAGGAAATCGTTAAT 58.661 34.615 0.00 0.00 0.00 1.40
669 1120 7.829211 TCTTGAATCAGGAGGAAATCGTTAATT 59.171 33.333 0.00 0.00 0.00 1.40
670 1121 7.938140 TGAATCAGGAGGAAATCGTTAATTT 57.062 32.000 0.00 0.00 40.34 1.82
671 1122 8.348285 TGAATCAGGAGGAAATCGTTAATTTT 57.652 30.769 0.00 0.00 37.70 1.82
672 1123 8.802267 TGAATCAGGAGGAAATCGTTAATTTTT 58.198 29.630 0.00 0.00 37.70 1.94
732 1186 4.500035 GGAGGGAATCAGAGACGTAACATC 60.500 50.000 0.00 0.00 0.00 3.06
777 1232 4.447290 TCGATGTCTGTTTTCACAAAGGA 58.553 39.130 0.00 0.00 30.36 3.36
783 1238 5.037385 GTCTGTTTTCACAAAGGAAAGAGC 58.963 41.667 0.00 0.00 37.98 4.09
861 1316 0.969149 CACCAGCAGTAGTCAGTCCA 59.031 55.000 0.00 0.00 0.00 4.02
862 1317 1.344438 CACCAGCAGTAGTCAGTCCAA 59.656 52.381 0.00 0.00 0.00 3.53
863 1318 1.620819 ACCAGCAGTAGTCAGTCCAAG 59.379 52.381 0.00 0.00 0.00 3.61
938 1410 2.614013 ACGGCCTCCATTTCCCCT 60.614 61.111 0.00 0.00 0.00 4.79
1042 1514 1.075226 CCCCCGAATCTCTCTCCCA 60.075 63.158 0.00 0.00 0.00 4.37
1076 1548 2.284405 TCCCCGTGTTCCCTCCTC 60.284 66.667 0.00 0.00 0.00 3.71
1086 1558 0.401979 TTCCCTCCTCCATGGATCCC 60.402 60.000 16.63 0.00 45.16 3.85
1238 1710 2.124860 GTACCTTCCGCCGCCATT 60.125 61.111 0.00 0.00 0.00 3.16
1240 1712 0.250166 GTACCTTCCGCCGCCATTAT 60.250 55.000 0.00 0.00 0.00 1.28
1243 1722 0.951040 CCTTCCGCCGCCATTATCTC 60.951 60.000 0.00 0.00 0.00 2.75
1375 1882 0.469331 TCTAAGCCGGGGATGACGAT 60.469 55.000 2.18 0.00 0.00 3.73
1382 1889 0.664466 CGGGGATGACGATGATGACG 60.664 60.000 0.00 0.00 0.00 4.35
1478 1985 1.299976 GACTCCGGGATGCCTGTTT 59.700 57.895 0.00 0.00 0.00 2.83
1479 1986 0.322546 GACTCCGGGATGCCTGTTTT 60.323 55.000 0.00 0.00 0.00 2.43
1480 1987 0.988832 ACTCCGGGATGCCTGTTTTA 59.011 50.000 0.00 0.00 0.00 1.52
1481 1988 1.353022 ACTCCGGGATGCCTGTTTTAA 59.647 47.619 0.00 0.00 0.00 1.52
1482 1989 2.017049 CTCCGGGATGCCTGTTTTAAG 58.983 52.381 0.00 0.00 0.00 1.85
1483 1990 1.631388 TCCGGGATGCCTGTTTTAAGA 59.369 47.619 0.00 0.00 0.00 2.10
1505 2012 6.835914 AGATTAAGATTTCGCTTGTGTTGAG 58.164 36.000 0.00 0.00 0.00 3.02
1570 2079 8.361889 CCATCATATTTTGCTGATTATGGAACA 58.638 33.333 0.00 0.00 34.13 3.18
1571 2080 9.406828 CATCATATTTTGCTGATTATGGAACAG 57.593 33.333 0.00 0.00 33.39 3.16
1638 2336 2.744202 CTGACCAGTTGAAATCCTTCGG 59.256 50.000 0.00 0.00 33.94 4.30
1681 2379 7.490402 CCTACCTGCATTTTGAATGAATTTCTC 59.510 37.037 4.92 0.00 35.23 2.87
1703 2401 1.538075 TGTAGCGGTTTGGCTTTAAGC 59.462 47.619 8.66 8.66 41.39 3.09
1704 2402 1.810755 GTAGCGGTTTGGCTTTAAGCT 59.189 47.619 16.89 0.00 41.39 3.74
1705 2403 0.598065 AGCGGTTTGGCTTTAAGCTG 59.402 50.000 16.89 1.92 41.39 4.24
1714 2412 4.935352 TGGCTTTAAGCTGTTCATTTGT 57.065 36.364 16.89 0.00 41.99 2.83
1715 2413 5.275067 TGGCTTTAAGCTGTTCATTTGTT 57.725 34.783 16.89 0.00 41.99 2.83
1765 2463 6.100134 GGTAGGGGATAGTTGTATTGTGGTTA 59.900 42.308 0.00 0.00 0.00 2.85
1891 2589 9.023962 TCAATGTTCTACAATTATTTGCCTCTT 57.976 29.630 0.00 0.00 36.22 2.85
1892 2590 9.079833 CAATGTTCTACAATTATTTGCCTCTTG 57.920 33.333 0.00 0.00 36.22 3.02
1929 2627 7.582667 ACTTGTTCAGTATGGTTTTAAGCTT 57.417 32.000 3.48 3.48 36.16 3.74
1965 2778 1.064389 GCTTGGTAGGAGATTGCCCTT 60.064 52.381 0.00 0.00 35.30 3.95
1967 2780 2.806945 TGGTAGGAGATTGCCCTTTG 57.193 50.000 0.00 0.00 35.30 2.77
1968 2781 1.992557 TGGTAGGAGATTGCCCTTTGT 59.007 47.619 0.00 0.00 35.30 2.83
1969 2782 3.186283 TGGTAGGAGATTGCCCTTTGTA 58.814 45.455 0.00 0.00 35.30 2.41
1970 2783 3.199946 TGGTAGGAGATTGCCCTTTGTAG 59.800 47.826 0.00 0.00 35.30 2.74
1971 2784 3.200165 GGTAGGAGATTGCCCTTTGTAGT 59.800 47.826 0.00 0.00 35.30 2.73
1979 2793 4.440826 TTGCCCTTTGTAGTTCTACCAA 57.559 40.909 7.40 2.72 0.00 3.67
2005 2819 9.710900 AAACCTTGATTTATCAATGACCTTTTC 57.289 29.630 12.67 0.00 44.92 2.29
2016 2830 5.184864 TCAATGACCTTTTCGCCATTTGTAT 59.815 36.000 0.00 0.00 0.00 2.29
2031 2845 6.164876 CCATTTGTATTTCCTTTGTGCATGA 58.835 36.000 0.00 0.00 0.00 3.07
2113 2932 9.757227 TTTGGATGATTTAGTTGTTTTTAGTGG 57.243 29.630 0.00 0.00 0.00 4.00
2168 2989 8.804688 TGTTTGTGGTTTGCTACATATAAAAC 57.195 30.769 0.00 0.00 36.00 2.43
2231 3057 2.541588 CCAATTTTCTTATGCGCCCTCG 60.542 50.000 4.18 0.00 39.07 4.63
2239 3065 0.809636 TATGCGCCCTCGTTGTGATG 60.810 55.000 4.18 0.00 38.14 3.07
2240 3066 3.499737 GCGCCCTCGTTGTGATGG 61.500 66.667 0.00 0.00 38.14 3.51
2250 3076 1.202065 CGTTGTGATGGCGATTTGAGG 60.202 52.381 0.00 0.00 0.00 3.86
2253 3079 1.103398 GTGATGGCGATTTGAGGGGG 61.103 60.000 0.00 0.00 0.00 5.40
2255 3081 0.111253 GATGGCGATTTGAGGGGGAT 59.889 55.000 0.00 0.00 0.00 3.85
2256 3082 0.178981 ATGGCGATTTGAGGGGGATG 60.179 55.000 0.00 0.00 0.00 3.51
2257 3083 1.529244 GGCGATTTGAGGGGGATGG 60.529 63.158 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.127533 CCTAGCCACACCTTGCGC 61.128 66.667 0.00 0.00 0.00 6.09
1 2 2.436646 CCCTAGCCACACCTTGCG 60.437 66.667 0.00 0.00 0.00 4.85
2 3 0.251165 TTTCCCTAGCCACACCTTGC 60.251 55.000 0.00 0.00 0.00 4.01
3 4 1.073923 AGTTTCCCTAGCCACACCTTG 59.926 52.381 0.00 0.00 0.00 3.61
4 5 1.073923 CAGTTTCCCTAGCCACACCTT 59.926 52.381 0.00 0.00 0.00 3.50
5 6 0.693049 CAGTTTCCCTAGCCACACCT 59.307 55.000 0.00 0.00 0.00 4.00
6 7 0.400594 ACAGTTTCCCTAGCCACACC 59.599 55.000 0.00 0.00 0.00 4.16
7 8 1.202770 ACACAGTTTCCCTAGCCACAC 60.203 52.381 0.00 0.00 0.00 3.82
8 9 1.136828 ACACAGTTTCCCTAGCCACA 58.863 50.000 0.00 0.00 0.00 4.17
9 10 2.935676 GCTACACAGTTTCCCTAGCCAC 60.936 54.545 0.00 0.00 0.00 5.01
10 11 1.278127 GCTACACAGTTTCCCTAGCCA 59.722 52.381 0.00 0.00 0.00 4.75
11 12 1.278127 TGCTACACAGTTTCCCTAGCC 59.722 52.381 0.00 0.00 30.68 3.93
12 13 2.742589 GTTGCTACACAGTTTCCCTAGC 59.257 50.000 0.00 0.00 0.00 3.42
13 14 4.273148 AGTTGCTACACAGTTTCCCTAG 57.727 45.455 0.13 0.00 0.00 3.02
14 15 4.020839 GGTAGTTGCTACACAGTTTCCCTA 60.021 45.833 0.13 0.00 38.58 3.53
15 16 3.244457 GGTAGTTGCTACACAGTTTCCCT 60.244 47.826 0.13 0.00 38.58 4.20
16 17 3.072211 GGTAGTTGCTACACAGTTTCCC 58.928 50.000 0.13 0.00 38.58 3.97
17 18 2.735134 CGGTAGTTGCTACACAGTTTCC 59.265 50.000 0.13 0.00 38.58 3.13
18 19 2.735134 CCGGTAGTTGCTACACAGTTTC 59.265 50.000 0.13 0.00 38.58 2.78
19 20 2.762745 CCGGTAGTTGCTACACAGTTT 58.237 47.619 0.13 0.00 38.58 2.66
20 21 1.607251 GCCGGTAGTTGCTACACAGTT 60.607 52.381 1.90 0.00 38.58 3.16
21 22 0.037605 GCCGGTAGTTGCTACACAGT 60.038 55.000 1.90 0.00 38.58 3.55
22 23 0.037697 TGCCGGTAGTTGCTACACAG 60.038 55.000 1.90 0.00 38.58 3.66
23 24 0.393448 TTGCCGGTAGTTGCTACACA 59.607 50.000 1.90 1.53 38.58 3.72
24 25 1.076332 CTTGCCGGTAGTTGCTACAC 58.924 55.000 1.90 0.00 38.58 2.90
25 26 0.036765 CCTTGCCGGTAGTTGCTACA 60.037 55.000 1.90 0.00 38.58 2.74
26 27 0.036671 ACCTTGCCGGTAGTTGCTAC 60.037 55.000 1.90 0.00 46.73 3.58
27 28 0.036765 CACCTTGCCGGTAGTTGCTA 60.037 55.000 1.90 0.00 46.94 3.49
28 29 1.302511 CACCTTGCCGGTAGTTGCT 60.303 57.895 1.90 0.00 46.94 3.91
29 30 2.332654 CCACCTTGCCGGTAGTTGC 61.333 63.158 1.90 0.00 46.94 4.17
30 31 1.674322 CCCACCTTGCCGGTAGTTG 60.674 63.158 1.90 0.00 46.94 3.16
31 32 1.844289 TCCCACCTTGCCGGTAGTT 60.844 57.895 1.90 0.00 46.94 2.24
32 33 2.203877 TCCCACCTTGCCGGTAGT 60.204 61.111 1.90 0.00 46.94 2.73
33 34 2.119484 TTGTCCCACCTTGCCGGTAG 62.119 60.000 1.90 0.31 46.94 3.18
34 35 2.119484 CTTGTCCCACCTTGCCGGTA 62.119 60.000 1.90 0.00 46.94 4.02
36 37 2.672996 CTTGTCCCACCTTGCCGG 60.673 66.667 0.00 0.00 39.35 6.13
37 38 1.672356 CTCTTGTCCCACCTTGCCG 60.672 63.158 0.00 0.00 0.00 5.69
38 39 1.303643 CCTCTTGTCCCACCTTGCC 60.304 63.158 0.00 0.00 0.00 4.52
39 40 0.890996 CACCTCTTGTCCCACCTTGC 60.891 60.000 0.00 0.00 0.00 4.01
40 41 0.474184 ACACCTCTTGTCCCACCTTG 59.526 55.000 0.00 0.00 29.79 3.61
41 42 0.474184 CACACCTCTTGTCCCACCTT 59.526 55.000 0.00 0.00 35.67 3.50
42 43 1.418908 CCACACCTCTTGTCCCACCT 61.419 60.000 0.00 0.00 35.67 4.00
43 44 1.073199 CCACACCTCTTGTCCCACC 59.927 63.158 0.00 0.00 35.67 4.61
44 45 1.600916 GCCACACCTCTTGTCCCAC 60.601 63.158 0.00 0.00 35.67 4.61
45 46 1.770110 AGCCACACCTCTTGTCCCA 60.770 57.895 0.00 0.00 35.67 4.37
46 47 1.302832 CAGCCACACCTCTTGTCCC 60.303 63.158 0.00 0.00 35.67 4.46
47 48 1.302832 CCAGCCACACCTCTTGTCC 60.303 63.158 0.00 0.00 35.67 4.02
48 49 1.302832 CCCAGCCACACCTCTTGTC 60.303 63.158 0.00 0.00 35.67 3.18
49 50 1.770110 TCCCAGCCACACCTCTTGT 60.770 57.895 0.00 0.00 39.97 3.16
50 51 1.002868 CTCCCAGCCACACCTCTTG 60.003 63.158 0.00 0.00 0.00 3.02
51 52 2.900106 GCTCCCAGCCACACCTCTT 61.900 63.158 0.00 0.00 34.48 2.85
52 53 3.325753 GCTCCCAGCCACACCTCT 61.326 66.667 0.00 0.00 34.48 3.69
53 54 4.767255 CGCTCCCAGCCACACCTC 62.767 72.222 0.00 0.00 38.18 3.85
81 82 3.011635 ATTCTCAGCTGCTCGCCGT 62.012 57.895 9.47 0.00 40.39 5.68
85 86 2.523507 CCGCATTCTCAGCTGCTCG 61.524 63.158 9.47 5.57 36.23 5.03
161 163 1.905637 GGGGGCAATCCTTATAACCG 58.094 55.000 0.00 0.00 35.33 4.44
186 188 4.158579 GCCAAACCCATAAAAAGAGGAGAG 59.841 45.833 0.00 0.00 0.00 3.20
187 189 4.086457 GCCAAACCCATAAAAAGAGGAGA 58.914 43.478 0.00 0.00 0.00 3.71
188 190 3.831911 TGCCAAACCCATAAAAAGAGGAG 59.168 43.478 0.00 0.00 0.00 3.69
189 191 3.850752 TGCCAAACCCATAAAAAGAGGA 58.149 40.909 0.00 0.00 0.00 3.71
192 194 4.202305 CCACTTGCCAAACCCATAAAAAGA 60.202 41.667 0.00 0.00 0.00 2.52
203 205 1.337118 TCCCAATCCACTTGCCAAAC 58.663 50.000 0.00 0.00 33.20 2.93
209 211 5.749462 AGTAGATTCTTCCCAATCCACTTG 58.251 41.667 0.00 0.00 32.70 3.16
225 227 4.720273 CCTACCTGTTGGGGTAAGTAGATT 59.280 45.833 0.00 0.00 40.79 2.40
229 231 2.836667 CCCTACCTGTTGGGGTAAGTA 58.163 52.381 8.72 0.00 41.15 2.24
241 243 8.876790 CGTATTTTCTACTAAAAACCCTACCTG 58.123 37.037 0.00 0.00 31.35 4.00
266 268 0.259356 ACTCCCCTCTTCTCCCTACG 59.741 60.000 0.00 0.00 0.00 3.51
342 345 4.675063 ACCAACCCTTCACCTAATGAAT 57.325 40.909 0.00 0.00 46.37 2.57
345 348 3.089284 GGAACCAACCCTTCACCTAATG 58.911 50.000 0.00 0.00 0.00 1.90
346 349 3.451402 GGAACCAACCCTTCACCTAAT 57.549 47.619 0.00 0.00 0.00 1.73
364 368 3.453059 AACGAGGAGAGTCTAAAGGGA 57.547 47.619 0.00 0.00 0.00 4.20
454 832 3.870633 ACAATGTACTTCCTCCGTCTC 57.129 47.619 0.00 0.00 0.00 3.36
456 834 6.036844 GGATTTTACAATGTACTTCCTCCGTC 59.963 42.308 0.00 0.00 0.00 4.79
458 836 5.878116 TGGATTTTACAATGTACTTCCTCCG 59.122 40.000 13.32 0.00 0.00 4.63
490 868 8.537049 TGCAACACGTTTGTACTAATATACTT 57.463 30.769 10.65 0.00 33.55 2.24
491 869 8.712285 ATGCAACACGTTTGTACTAATATACT 57.288 30.769 0.00 0.00 33.55 2.12
567 946 2.863740 TGTGTTACAGAGCAGTTTCACG 59.136 45.455 0.00 0.00 31.45 4.35
590 969 4.216257 AGTTCCAAATACATGCACTCACAC 59.784 41.667 0.00 0.00 0.00 3.82
592 971 4.436050 CGAGTTCCAAATACATGCACTCAC 60.436 45.833 0.00 0.00 32.59 3.51
594 973 3.063997 CCGAGTTCCAAATACATGCACTC 59.936 47.826 0.00 0.00 0.00 3.51
595 974 3.009723 CCGAGTTCCAAATACATGCACT 58.990 45.455 0.00 0.00 0.00 4.40
639 1090 6.490040 ACGATTTCCTCCTGATTCAAGAAAAA 59.510 34.615 0.00 2.01 0.00 1.94
640 1091 6.003950 ACGATTTCCTCCTGATTCAAGAAAA 58.996 36.000 0.00 0.00 0.00 2.29
641 1092 5.560724 ACGATTTCCTCCTGATTCAAGAAA 58.439 37.500 0.00 0.00 0.00 2.52
642 1093 5.165961 ACGATTTCCTCCTGATTCAAGAA 57.834 39.130 0.00 0.00 0.00 2.52
643 1094 4.826274 ACGATTTCCTCCTGATTCAAGA 57.174 40.909 0.00 0.00 0.00 3.02
644 1095 6.985188 TTAACGATTTCCTCCTGATTCAAG 57.015 37.500 0.00 0.00 0.00 3.02
645 1096 7.938140 AATTAACGATTTCCTCCTGATTCAA 57.062 32.000 0.00 0.00 0.00 2.69
646 1097 7.938140 AAATTAACGATTTCCTCCTGATTCA 57.062 32.000 0.00 0.00 32.49 2.57
672 1123 5.890424 AACGACTTCCTTTGTCTCAAAAA 57.110 34.783 0.00 0.00 32.70 1.94
673 1124 7.066525 ACAATAACGACTTCCTTTGTCTCAAAA 59.933 33.333 0.00 0.00 32.70 2.44
674 1125 6.540914 ACAATAACGACTTCCTTTGTCTCAAA 59.459 34.615 0.00 0.00 32.70 2.69
675 1126 6.018262 CACAATAACGACTTCCTTTGTCTCAA 60.018 38.462 0.00 0.00 32.70 3.02
676 1127 5.465390 CACAATAACGACTTCCTTTGTCTCA 59.535 40.000 0.00 0.00 32.70 3.27
677 1128 5.694910 TCACAATAACGACTTCCTTTGTCTC 59.305 40.000 0.00 0.00 32.70 3.36
678 1129 5.607477 TCACAATAACGACTTCCTTTGTCT 58.393 37.500 0.00 0.00 32.70 3.41
679 1130 5.694910 TCTCACAATAACGACTTCCTTTGTC 59.305 40.000 0.00 0.00 0.00 3.18
680 1131 5.607477 TCTCACAATAACGACTTCCTTTGT 58.393 37.500 0.00 0.00 0.00 2.83
681 1132 6.363473 GTTCTCACAATAACGACTTCCTTTG 58.637 40.000 0.00 0.00 0.00 2.77
682 1133 6.541111 GTTCTCACAATAACGACTTCCTTT 57.459 37.500 0.00 0.00 0.00 3.11
732 1186 1.684983 CTGGGCTTTAATGGGCTCATG 59.315 52.381 0.00 0.00 38.33 3.07
777 1232 4.384846 CGTAACGTTATGTCTGTGCTCTTT 59.615 41.667 17.64 0.00 0.00 2.52
783 1238 2.597305 GGCTCGTAACGTTATGTCTGTG 59.403 50.000 23.27 12.51 0.00 3.66
836 1291 0.976073 GACTACTGCTGGTGGGCCTA 60.976 60.000 4.53 0.00 35.27 3.93
861 1316 1.198759 TGGGCTCGGCTAGTTTCCTT 61.199 55.000 0.00 0.00 0.00 3.36
862 1317 0.983378 ATGGGCTCGGCTAGTTTCCT 60.983 55.000 0.00 0.00 0.00 3.36
863 1318 0.107165 AATGGGCTCGGCTAGTTTCC 60.107 55.000 0.00 0.00 0.00 3.13
938 1410 1.280998 GAAACCCTTGGATCGGAGGAA 59.719 52.381 13.10 0.00 34.91 3.36
1042 1514 1.691434 GGGAGAGGAATCGAAGCAGAT 59.309 52.381 0.00 0.00 0.00 2.90
1076 1548 2.111878 GTCAGCGGGGATCCATGG 59.888 66.667 15.23 4.97 0.00 3.66
1238 1710 1.238615 ACTAACCGGGGGAGGAGATA 58.761 55.000 6.32 0.00 34.73 1.98
1240 1712 1.009997 TTACTAACCGGGGGAGGAGA 58.990 55.000 6.32 0.00 34.73 3.71
1243 1722 0.763035 CCATTACTAACCGGGGGAGG 59.237 60.000 6.32 0.00 37.30 4.30
1293 1800 1.134521 ACCTGAGACAGCAACGAAACA 60.135 47.619 0.00 0.00 0.00 2.83
1430 1937 1.512771 CTTGCAAAAACAACGAGACGC 59.487 47.619 0.00 0.00 0.00 5.19
1478 1985 8.779303 TCAACACAAGCGAAATCTTAATCTTAA 58.221 29.630 0.00 0.00 0.00 1.85
1479 1986 8.317891 TCAACACAAGCGAAATCTTAATCTTA 57.682 30.769 0.00 0.00 0.00 2.10
1480 1987 7.173218 TCTCAACACAAGCGAAATCTTAATCTT 59.827 33.333 0.00 0.00 0.00 2.40
1481 1988 6.650807 TCTCAACACAAGCGAAATCTTAATCT 59.349 34.615 0.00 0.00 0.00 2.40
1482 1989 6.831769 TCTCAACACAAGCGAAATCTTAATC 58.168 36.000 0.00 0.00 0.00 1.75
1483 1990 6.650807 TCTCTCAACACAAGCGAAATCTTAAT 59.349 34.615 0.00 0.00 0.00 1.40
1571 2080 4.637977 ACAGAGCTTAAGCAGGATAAAAGC 59.362 41.667 28.39 0.00 45.16 3.51
1681 2379 1.149987 TAAAGCCAAACCGCTACACG 58.850 50.000 0.00 0.00 38.44 4.49
1714 2412 7.341445 AGCAACCAGTTAACAATTCTACAAA 57.659 32.000 8.61 0.00 0.00 2.83
1715 2413 6.952773 AGCAACCAGTTAACAATTCTACAA 57.047 33.333 8.61 0.00 0.00 2.41
1731 2429 1.843851 CTATCCCCTACCAAGCAACCA 59.156 52.381 0.00 0.00 0.00 3.67
1765 2463 5.425539 ATGCCTACAACAGGTATTCTACACT 59.574 40.000 0.00 0.00 46.79 3.55
1844 2542 8.906867 CATTGAATCAACCTACATATCTGGTTT 58.093 33.333 0.00 0.00 41.57 3.27
1883 2581 0.395586 AGCAACCACACAAGAGGCAA 60.396 50.000 0.00 0.00 0.00 4.52
1891 2589 3.759086 TGAACAAGTAAAGCAACCACACA 59.241 39.130 0.00 0.00 0.00 3.72
1892 2590 4.142469 ACTGAACAAGTAAAGCAACCACAC 60.142 41.667 0.00 0.00 37.36 3.82
1929 2627 5.096443 ACCAAGCAAAAGGAAAACATCAA 57.904 34.783 0.00 0.00 0.00 2.57
1965 2778 8.528044 AAATCAAGGTTTTGGTAGAACTACAA 57.472 30.769 12.94 0.00 37.78 2.41
1969 2782 8.934023 TGATAAATCAAGGTTTTGGTAGAACT 57.066 30.769 0.00 0.00 34.97 3.01
1993 2807 3.652274 ACAAATGGCGAAAAGGTCATTG 58.348 40.909 0.00 0.00 41.11 2.82
2005 2819 3.367630 GCACAAAGGAAATACAAATGGCG 59.632 43.478 0.00 0.00 0.00 5.69
2016 2830 7.035004 GCATAAATAGTCATGCACAAAGGAAA 58.965 34.615 0.00 0.00 45.51 3.13
2095 2914 9.582648 AGGTATCACCACTAAAAACAACTAAAT 57.417 29.630 0.00 0.00 41.95 1.40
2131 2950 8.688151 AGCAAACCACAAACATTAAACTACTTA 58.312 29.630 0.00 0.00 0.00 2.24
2231 3057 1.133025 CCCTCAAATCGCCATCACAAC 59.867 52.381 0.00 0.00 0.00 3.32
2239 3065 1.529244 CCATCCCCCTCAAATCGCC 60.529 63.158 0.00 0.00 0.00 5.54
2240 3066 1.529244 CCCATCCCCCTCAAATCGC 60.529 63.158 0.00 0.00 0.00 4.58
2241 3067 1.151450 CCCCATCCCCCTCAAATCG 59.849 63.158 0.00 0.00 0.00 3.34
2250 3076 2.041216 GTCATACATAACCCCCATCCCC 59.959 54.545 0.00 0.00 0.00 4.81
2253 3079 3.650942 TGAGGTCATACATAACCCCCATC 59.349 47.826 0.00 0.00 36.11 3.51
2255 3081 3.045634 CTGAGGTCATACATAACCCCCA 58.954 50.000 0.00 0.00 36.11 4.96
2256 3082 2.372172 CCTGAGGTCATACATAACCCCC 59.628 54.545 0.00 0.00 36.11 5.40
2257 3083 2.372172 CCCTGAGGTCATACATAACCCC 59.628 54.545 0.00 0.00 36.11 4.95
2287 3113 0.752658 GCAAACCTTCCCAAACAGCT 59.247 50.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.