Multiple sequence alignment - TraesCS1A01G207600

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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 TraesCS1A01G207600 chr1A 100.000 2927 0 0 1 2927 369498763 369495837 0.000000e+00 5406.0
1 TraesCS1A01G207600 chr1B 89.613 1781 97 37 771 2503 398145476 398143736 0.000000e+00 2183.0
2 TraesCS1A01G207600 chr1B 91.736 484 39 1 1226 1709 683420957 683420475 0.000000e+00 671.0
3 TraesCS1A01G207600 chr1B 95.455 418 13 3 2514 2926 398143683 398143267 0.000000e+00 662.0
4 TraesCS1A01G207600 chr1D 94.839 1395 54 9 1119 2503 296979606 296978220 0.000000e+00 2161.0
5 TraesCS1A01G207600 chr1D 86.701 782 72 16 1 760 481494262 481493491 0.000000e+00 839.0
6 TraesCS1A01G207600 chr1D 90.385 416 30 6 2514 2927 296978158 296977751 3.320000e-149 538.0
7 TraesCS1A01G207600 chr1D 86.051 509 49 16 274 760 246950997 246951505 7.180000e-146 527.0
8 TraesCS1A01G207600 chr1D 91.367 139 9 1 1116 1254 46477134 46477269 1.380000e-43 187.0
9 TraesCS1A01G207600 chr1D 93.333 45 1 2 446 488 7374929 7374885 6.770000e-07 65.8
10 TraesCS1A01G207600 chr2D 88.123 783 69 13 1 760 533032572 533033353 0.000000e+00 909.0
11 TraesCS1A01G207600 chr2D 85.299 653 61 14 130 760 589887437 589888076 2.460000e-180 641.0
12 TraesCS1A01G207600 chr2D 89.912 456 42 3 1255 1709 36503273 36503725 4.200000e-163 584.0
13 TraesCS1A01G207600 chr2D 89.209 139 12 1 1116 1254 36499419 36499554 1.390000e-38 171.0
14 TraesCS1A01G207600 chr2D 94.286 35 2 0 1276 1310 448689700 448689666 1.000000e-03 54.7
15 TraesCS1A01G207600 chr7A 87.564 780 77 12 1 760 8806275 8807054 0.000000e+00 885.0
16 TraesCS1A01G207600 chr7A 87.561 410 47 1 354 759 162875673 162875264 3.410000e-129 472.0
17 TraesCS1A01G207600 chr7A 91.912 136 8 1 1119 1254 46898181 46898049 1.380000e-43 187.0
18 TraesCS1A01G207600 chr5D 87.598 766 69 11 1 760 431250249 431250994 0.000000e+00 865.0
19 TraesCS1A01G207600 chr5D 86.300 781 82 14 1 759 553045340 553046117 0.000000e+00 826.0
20 TraesCS1A01G207600 chr5D 85.531 781 71 23 3 760 397343532 397342771 0.000000e+00 778.0
21 TraesCS1A01G207600 chrUn 86.132 786 85 13 1 764 287444900 287444117 0.000000e+00 826.0
22 TraesCS1A01G207600 chrUn 84.918 736 87 13 49 762 40653220 40653953 0.000000e+00 723.0
23 TraesCS1A01G207600 chrUn 93.333 45 1 2 446 488 167012028 167012072 6.770000e-07 65.8
24 TraesCS1A01G207600 chr3B 86.132 786 85 13 1 764 736884578 736885361 0.000000e+00 826.0
25 TraesCS1A01G207600 chr3D 85.935 775 90 13 1 759 131491777 131491006 0.000000e+00 809.0
26 TraesCS1A01G207600 chr3D 91.176 136 9 1 1119 1254 12137617 12137485 6.440000e-42 182.0
27 TraesCS1A01G207600 chr3D 89.706 136 11 1 1119 1254 146280734 146280602 1.390000e-38 171.0
28 TraesCS1A01G207600 chr3D 93.333 45 1 2 446 488 19534555 19534599 6.770000e-07 65.8
29 TraesCS1A01G207600 chr4D 85.934 782 75 16 1 760 31018410 31017642 0.000000e+00 802.0
30 TraesCS1A01G207600 chr4D 93.534 232 15 0 223 454 446655348 446655117 2.160000e-91 346.0
31 TraesCS1A01G207600 chr4D 89.706 136 11 2 1119 1254 462822278 462822146 1.390000e-38 171.0
32 TraesCS1A01G207600 chr4D 93.333 45 1 2 446 488 58385554 58385598 6.770000e-07 65.8
33 TraesCS1A01G207600 chr6D 85.879 779 76 17 3 759 455626261 455627027 0.000000e+00 798.0
34 TraesCS1A01G207600 chr6D 85.077 784 80 16 3 762 54233599 54232829 0.000000e+00 765.0
35 TraesCS1A01G207600 chr6D 85.714 462 44 12 320 759 390026565 390026104 4.420000e-128 468.0
36 TraesCS1A01G207600 chr6D 93.333 45 1 2 446 488 381976174 381976130 6.770000e-07 65.8
37 TraesCS1A01G207600 chr2B 88.963 598 57 5 1118 1709 44986556 44987150 0.000000e+00 730.0
38 TraesCS1A01G207600 chr4B 88.007 592 68 3 1118 1709 365085752 365086340 0.000000e+00 697.0
39 TraesCS1A01G207600 chr4B 85.835 593 80 3 1118 1709 358486461 358485872 6.890000e-176 627.0
40 TraesCS1A01G207600 chr5B 90.855 503 45 1 1207 1709 679584413 679584914 0.000000e+00 673.0
41 TraesCS1A01G207600 chr6B 85.248 644 71 14 1 622 21871058 21870417 2.460000e-180 641.0
42 TraesCS1A01G207600 chr6B 84.957 585 66 12 1 563 664649497 664648913 9.100000e-160 573.0
43 TraesCS1A01G207600 chr7D 89.278 457 44 4 1255 1709 168797951 168798404 4.230000e-158 568.0
44 TraesCS1A01G207600 chr7D 89.706 136 11 1 1119 1254 32509750 32509618 1.390000e-38 171.0
45 TraesCS1A01G207600 chr7D 89.209 139 12 1 1116 1254 168795532 168795667 1.390000e-38 171.0
46 TraesCS1A01G207600 chr7D 93.333 45 1 2 446 488 205153846 205153802 6.770000e-07 65.8
47 TraesCS1A01G207600 chr3A 85.768 534 51 9 232 760 683475717 683475204 2.570000e-150 542.0
48 TraesCS1A01G207600 chr5A 91.912 136 8 1 1119 1254 299616761 299616629 1.380000e-43 187.0
49 TraesCS1A01G207600 chr5A 93.333 45 1 2 446 488 695934346 695934302 6.770000e-07 65.8
50 TraesCS1A01G207600 chr6A 93.333 45 1 2 446 488 98237071 98237115 6.770000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G207600 chr1A 369495837 369498763 2926 True 5406.0 5406 100.0000 1 2927 1 chr1A.!!$R1 2926
1 TraesCS1A01G207600 chr1B 398143267 398145476 2209 True 1422.5 2183 92.5340 771 2926 2 chr1B.!!$R2 2155
2 TraesCS1A01G207600 chr1D 296977751 296979606 1855 True 1349.5 2161 92.6120 1119 2927 2 chr1D.!!$R3 1808
3 TraesCS1A01G207600 chr1D 481493491 481494262 771 True 839.0 839 86.7010 1 760 1 chr1D.!!$R2 759
4 TraesCS1A01G207600 chr1D 246950997 246951505 508 False 527.0 527 86.0510 274 760 1 chr1D.!!$F2 486
5 TraesCS1A01G207600 chr2D 533032572 533033353 781 False 909.0 909 88.1230 1 760 1 chr2D.!!$F1 759
6 TraesCS1A01G207600 chr2D 589887437 589888076 639 False 641.0 641 85.2990 130 760 1 chr2D.!!$F2 630
7 TraesCS1A01G207600 chr2D 36499419 36503725 4306 False 377.5 584 89.5605 1116 1709 2 chr2D.!!$F3 593
8 TraesCS1A01G207600 chr7A 8806275 8807054 779 False 885.0 885 87.5640 1 760 1 chr7A.!!$F1 759
9 TraesCS1A01G207600 chr5D 431250249 431250994 745 False 865.0 865 87.5980 1 760 1 chr5D.!!$F1 759
10 TraesCS1A01G207600 chr5D 553045340 553046117 777 False 826.0 826 86.3000 1 759 1 chr5D.!!$F2 758
11 TraesCS1A01G207600 chr5D 397342771 397343532 761 True 778.0 778 85.5310 3 760 1 chr5D.!!$R1 757
12 TraesCS1A01G207600 chrUn 287444117 287444900 783 True 826.0 826 86.1320 1 764 1 chrUn.!!$R1 763
13 TraesCS1A01G207600 chrUn 40653220 40653953 733 False 723.0 723 84.9180 49 762 1 chrUn.!!$F1 713
14 TraesCS1A01G207600 chr3B 736884578 736885361 783 False 826.0 826 86.1320 1 764 1 chr3B.!!$F1 763
15 TraesCS1A01G207600 chr3D 131491006 131491777 771 True 809.0 809 85.9350 1 759 1 chr3D.!!$R2 758
16 TraesCS1A01G207600 chr4D 31017642 31018410 768 True 802.0 802 85.9340 1 760 1 chr4D.!!$R1 759
17 TraesCS1A01G207600 chr6D 455626261 455627027 766 False 798.0 798 85.8790 3 759 1 chr6D.!!$F1 756
18 TraesCS1A01G207600 chr6D 54232829 54233599 770 True 765.0 765 85.0770 3 762 1 chr6D.!!$R1 759
19 TraesCS1A01G207600 chr2B 44986556 44987150 594 False 730.0 730 88.9630 1118 1709 1 chr2B.!!$F1 591
20 TraesCS1A01G207600 chr4B 365085752 365086340 588 False 697.0 697 88.0070 1118 1709 1 chr4B.!!$F1 591
21 TraesCS1A01G207600 chr4B 358485872 358486461 589 True 627.0 627 85.8350 1118 1709 1 chr4B.!!$R1 591
22 TraesCS1A01G207600 chr5B 679584413 679584914 501 False 673.0 673 90.8550 1207 1709 1 chr5B.!!$F1 502
23 TraesCS1A01G207600 chr6B 21870417 21871058 641 True 641.0 641 85.2480 1 622 1 chr6B.!!$R1 621
24 TraesCS1A01G207600 chr6B 664648913 664649497 584 True 573.0 573 84.9570 1 563 1 chr6B.!!$R2 562
25 TraesCS1A01G207600 chr7D 168795532 168798404 2872 False 369.5 568 89.2435 1116 1709 2 chr7D.!!$F1 593
26 TraesCS1A01G207600 chr3A 683475204 683475717 513 True 542.0 542 85.7680 232 760 1 chr3A.!!$R1 528

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
105 106 0.034186 TTGATCTCCTTGCCCGCATT 60.034 50.0 0.0 0.0 0.0 3.56 F
896 978 0.038892 GAACACGTAGCTTGACCCGA 60.039 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 5745 0.027194 TATCTTCGTCTTCGTCGGCG 59.973 55.000 1.15 1.15 38.33 6.46 R
2323 6197 1.301479 AACAAGTTCGGACGGGCTC 60.301 57.895 0.00 0.00 0.00 4.70 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
21 22 1.645455 GCACTCATGCCGCTATGTG 59.355 57.895 0.00 0.00 46.97 3.21
35 36 2.665165 CTATGTGGAGCTCCTCTGTCT 58.335 52.381 32.28 16.76 36.82 3.41
37 38 1.722034 TGTGGAGCTCCTCTGTCTTT 58.278 50.000 32.28 0.00 36.82 2.52
66 67 0.764752 CCCTCCTATTCGCCCCTCTT 60.765 60.000 0.00 0.00 0.00 2.85
105 106 0.034186 TTGATCTCCTTGCCCGCATT 60.034 50.000 0.00 0.00 0.00 3.56
121 122 4.338682 CCCGCATTCTACTACACTAGAGTT 59.661 45.833 0.00 0.00 0.00 3.01
151 152 0.535335 TCGCTCATTTCGGCCTACTT 59.465 50.000 0.00 0.00 0.00 2.24
272 273 0.319383 CTCGATCATCTTGGCCTCCG 60.319 60.000 3.32 0.00 0.00 4.63
307 321 2.632996 CTCTTGTCCCACTACACTGGAA 59.367 50.000 0.00 0.00 32.30 3.53
330 344 2.271800 GTTTCTGGCGTCGATCATCTT 58.728 47.619 0.00 0.00 0.00 2.40
496 571 4.508128 CGGCGCCACGGACACTAT 62.508 66.667 28.98 0.00 0.00 2.12
497 572 2.585247 GGCGCCACGGACACTATC 60.585 66.667 24.80 0.00 0.00 2.08
498 573 2.585247 GCGCCACGGACACTATCC 60.585 66.667 0.00 0.00 45.20 2.59
508 583 2.279582 GACACTATCCACCACAGTCG 57.720 55.000 0.00 0.00 0.00 4.18
509 584 0.246635 ACACTATCCACCACAGTCGC 59.753 55.000 0.00 0.00 0.00 5.19
510 585 0.460284 CACTATCCACCACAGTCGCC 60.460 60.000 0.00 0.00 0.00 5.54
511 586 0.902984 ACTATCCACCACAGTCGCCA 60.903 55.000 0.00 0.00 0.00 5.69
512 587 0.465705 CTATCCACCACAGTCGCCAT 59.534 55.000 0.00 0.00 0.00 4.40
513 588 0.177836 TATCCACCACAGTCGCCATG 59.822 55.000 0.00 0.00 0.00 3.66
514 589 2.541547 ATCCACCACAGTCGCCATGG 62.542 60.000 7.63 7.63 39.57 3.66
516 591 1.600636 CACCACAGTCGCCATGGTT 60.601 57.895 14.67 0.00 44.51 3.67
517 592 1.302511 ACCACAGTCGCCATGGTTC 60.303 57.895 14.67 4.26 44.51 3.62
518 593 2.390599 CCACAGTCGCCATGGTTCG 61.391 63.158 14.67 9.64 0.00 3.95
519 594 2.047274 ACAGTCGCCATGGTTCGG 60.047 61.111 14.67 7.48 0.00 4.30
520 595 3.499737 CAGTCGCCATGGTTCGGC 61.500 66.667 14.67 11.08 46.62 5.54
539 614 2.030805 GGCGAACACTGCATTTCTTCTT 60.031 45.455 0.00 0.00 0.00 2.52
565 640 3.247006 TCCTTTGCTAGCTCTTAACCG 57.753 47.619 17.23 0.00 0.00 4.44
653 730 1.812235 ATGCGTTCAGACAATGCAGA 58.188 45.000 7.28 0.00 44.29 4.26
662 739 3.890756 TCAGACAATGCAGACAACCAAAT 59.109 39.130 0.00 0.00 0.00 2.32
677 754 6.821388 ACAACCAAATAATGTGCCAAAGTTA 58.179 32.000 0.00 0.00 0.00 2.24
722 801 6.294453 CCATATGCAGACAACCAAACAACTTA 60.294 38.462 0.00 0.00 0.00 2.24
739 818 8.846943 AACAACTTACAGATGTCACATATGAA 57.153 30.769 19.31 7.99 36.31 2.57
764 843 4.282496 TGTTTTTCCAGAGCCAGGTTAAA 58.718 39.130 0.00 0.00 0.00 1.52
765 844 4.098807 TGTTTTTCCAGAGCCAGGTTAAAC 59.901 41.667 0.00 0.00 34.36 2.01
766 845 3.586470 TTTCCAGAGCCAGGTTAAACA 57.414 42.857 0.00 0.00 0.00 2.83
767 846 3.586470 TTCCAGAGCCAGGTTAAACAA 57.414 42.857 0.00 0.00 0.00 2.83
768 847 2.858745 TCCAGAGCCAGGTTAAACAAC 58.141 47.619 0.00 0.00 0.00 3.32
769 848 2.441750 TCCAGAGCCAGGTTAAACAACT 59.558 45.455 0.00 0.00 0.00 3.16
788 867 2.154462 CTTGGAGTGCCTACTTGGTTG 58.846 52.381 0.00 0.00 37.25 3.77
811 891 4.830826 AAACCTCGAATCACCTTGTTTC 57.169 40.909 0.00 0.00 0.00 2.78
812 892 3.485463 ACCTCGAATCACCTTGTTTCA 57.515 42.857 0.00 0.00 0.00 2.69
817 897 5.008613 CCTCGAATCACCTTGTTTCAAGAAA 59.991 40.000 10.54 0.00 0.00 2.52
827 907 4.027572 TGTTTCAAGAAAGTTCCTTGCG 57.972 40.909 0.00 0.00 40.45 4.85
831 912 0.586802 AAGAAAGTTCCTTGCGCGAC 59.413 50.000 12.10 0.88 0.00 5.19
835 916 3.723348 GTTCCTTGCGCGACCACC 61.723 66.667 12.10 0.00 0.00 4.61
845 926 4.084888 CGACCACCCGCTTTTCGC 62.085 66.667 0.00 0.00 36.73 4.70
851 933 4.715523 CCCGCTTTTCGCCCTCCA 62.716 66.667 0.00 0.00 36.73 3.86
888 970 4.430765 CGCCGGGAACACGTAGCT 62.431 66.667 2.18 0.00 0.00 3.32
890 972 2.388232 GCCGGGAACACGTAGCTTG 61.388 63.158 2.18 0.00 0.00 4.01
894 976 0.672711 GGGAACACGTAGCTTGACCC 60.673 60.000 0.00 0.00 0.00 4.46
895 977 1.012486 GGAACACGTAGCTTGACCCG 61.012 60.000 0.00 0.00 0.00 5.28
896 978 0.038892 GAACACGTAGCTTGACCCGA 60.039 55.000 0.00 0.00 0.00 5.14
897 979 0.606604 AACACGTAGCTTGACCCGAT 59.393 50.000 0.00 0.00 0.00 4.18
916 998 2.047844 GAGCTGCGCTGTTCCTCA 60.048 61.111 18.24 0.00 39.88 3.86
949 1031 4.837860 AGGCCAGTAAGATAATCCAGAGAG 59.162 45.833 5.01 0.00 0.00 3.20
989 1071 4.373116 GCGACCCGAGCACCAGAA 62.373 66.667 0.00 0.00 34.19 3.02
991 1073 2.432628 GACCCGAGCACCAGAACG 60.433 66.667 0.00 0.00 0.00 3.95
1026 1108 1.359459 CCACCCGTCGCTTTAAGCTC 61.359 60.000 15.29 7.10 39.60 4.09
1060 1142 0.896019 CACCGGAGACACCTCACTCT 60.896 60.000 9.46 0.00 41.20 3.24
1064 1146 1.611936 CGGAGACACCTCACTCTCTCA 60.612 57.143 0.00 0.00 41.20 3.27
1068 1150 0.543174 ACACCTCACTCTCTCACCCC 60.543 60.000 0.00 0.00 0.00 4.95
1072 1156 0.252012 CTCACTCTCTCACCCCCACT 60.252 60.000 0.00 0.00 0.00 4.00
1102 1186 2.202851 CCTCGCATCGCAAGCTCT 60.203 61.111 0.00 0.00 37.18 4.09
1103 1187 2.236382 CCTCGCATCGCAAGCTCTC 61.236 63.158 0.00 0.00 37.18 3.20
1104 1188 1.517913 CTCGCATCGCAAGCTCTCA 60.518 57.895 0.00 0.00 37.18 3.27
1106 1190 1.059994 CGCATCGCAAGCTCTCAAC 59.940 57.895 0.00 0.00 37.18 3.18
1108 1192 1.712081 CATCGCAAGCTCTCAACCG 59.288 57.895 0.00 0.00 37.18 4.44
1109 1193 0.737367 CATCGCAAGCTCTCAACCGA 60.737 55.000 0.00 0.00 37.18 4.69
1110 1194 0.737715 ATCGCAAGCTCTCAACCGAC 60.738 55.000 0.00 0.00 37.18 4.79
1111 1195 2.383527 CGCAAGCTCTCAACCGACC 61.384 63.158 0.00 0.00 0.00 4.79
1112 1196 2.383527 GCAAGCTCTCAACCGACCG 61.384 63.158 0.00 0.00 0.00 4.79
1114 1198 1.009389 CAAGCTCTCAACCGACCGAC 61.009 60.000 0.00 0.00 0.00 4.79
1596 5448 2.288025 GGTGTTCACCGAGGGGCTA 61.288 63.158 6.22 0.00 36.48 3.93
1938 5790 3.522750 AGGATTCCTAGATGATCCCATGC 59.477 47.826 2.49 0.00 28.75 4.06
1941 5793 0.979665 CCTAGATGATCCCATGCCGT 59.020 55.000 0.00 0.00 32.09 5.68
1942 5794 1.066573 CCTAGATGATCCCATGCCGTC 60.067 57.143 0.00 0.00 32.09 4.79
1944 5796 2.281070 ATGATCCCATGCCGTCGC 60.281 61.111 0.00 0.00 0.00 5.19
2008 5868 4.391405 AGTTTGTTGCTTTTCTCCCTTG 57.609 40.909 0.00 0.00 0.00 3.61
2012 5872 1.178534 TTGCTTTTCTCCCTTGCCCG 61.179 55.000 0.00 0.00 0.00 6.13
2041 5901 4.454728 TGGCCATGTAAAATTTCTCAGC 57.545 40.909 0.00 0.00 0.00 4.26
2069 5934 1.804151 GTCAGCGAATGCAACTGGTAA 59.196 47.619 0.00 0.00 46.23 2.85
2070 5935 2.225491 GTCAGCGAATGCAACTGGTAAA 59.775 45.455 0.00 0.00 46.23 2.01
2096 5961 0.385473 GCACATTTACTTGCGTGCGT 60.385 50.000 0.00 0.00 44.54 5.24
2133 5999 4.136796 TGGGACTCTGAGTTTGAATGTTG 58.863 43.478 12.27 0.00 0.00 3.33
2158 6024 4.912187 GCTGAAAGTTTCCAAATTCGAGTC 59.088 41.667 13.01 0.00 35.30 3.36
2237 6103 3.243907 GGGGGAATCTCTGTCAATAGTCG 60.244 52.174 0.00 0.00 0.00 4.18
2307 6181 3.943958 TGTCGATATTACAACGTCGGAG 58.056 45.455 0.00 0.00 35.01 4.63
2323 6197 2.138320 CGGAGTCGGAATCCAATCATG 58.862 52.381 22.76 3.16 36.57 3.07
2347 6234 1.082756 GTCCGAACTTGTTGCGCTG 60.083 57.895 9.73 0.00 0.00 5.18
2348 6235 1.522806 TCCGAACTTGTTGCGCTGT 60.523 52.632 9.73 0.00 0.00 4.40
2349 6236 1.092921 TCCGAACTTGTTGCGCTGTT 61.093 50.000 9.73 6.00 0.00 3.16
2350 6237 0.929824 CCGAACTTGTTGCGCTGTTG 60.930 55.000 9.73 0.00 0.00 3.33
2351 6238 1.531522 CGAACTTGTTGCGCTGTTGC 61.532 55.000 9.73 0.00 0.00 4.17
2352 6239 0.248621 GAACTTGTTGCGCTGTTGCT 60.249 50.000 9.73 0.00 36.97 3.91
2353 6240 0.526096 AACTTGTTGCGCTGTTGCTG 60.526 50.000 9.73 0.00 36.97 4.41
2354 6241 2.278726 TTGTTGCGCTGTTGCTGC 60.279 55.556 9.73 0.00 38.50 5.25
2355 6242 2.672908 CTTGTTGCGCTGTTGCTGCT 62.673 55.000 9.73 0.00 38.69 4.24
2356 6243 2.728383 GTTGCGCTGTTGCTGCTG 60.728 61.111 9.73 0.00 38.69 4.41
2357 6244 4.634133 TTGCGCTGTTGCTGCTGC 62.634 61.111 9.73 8.89 38.69 5.25
2360 6247 4.400109 CGCTGTTGCTGCTGCCTG 62.400 66.667 13.47 3.99 38.71 4.85
2361 6248 4.719369 GCTGTTGCTGCTGCCTGC 62.719 66.667 13.47 10.04 43.25 4.85
2362 6249 2.984155 CTGTTGCTGCTGCCTGCT 60.984 61.111 13.47 0.00 43.37 4.24
2363 6250 3.268965 CTGTTGCTGCTGCCTGCTG 62.269 63.158 13.47 3.82 43.37 4.41
2364 6251 2.981909 GTTGCTGCTGCCTGCTGA 60.982 61.111 13.47 0.00 42.27 4.26
2365 6252 2.671963 TTGCTGCTGCCTGCTGAG 60.672 61.111 13.47 0.00 42.27 3.35
2366 6253 3.486905 TTGCTGCTGCCTGCTGAGT 62.487 57.895 13.47 0.00 42.27 3.41
2390 6277 1.577328 GCCGACTGATGTGGTGGTTG 61.577 60.000 0.00 0.00 0.00 3.77
2491 6378 1.108776 GCCGTCATCACAGGTACCTA 58.891 55.000 15.80 0.00 0.00 3.08
2496 6383 3.695060 CGTCATCACAGGTACCTACTTCT 59.305 47.826 15.80 0.00 0.00 2.85
2503 6390 6.550163 TCACAGGTACCTACTTCTACTTTCT 58.450 40.000 15.80 0.00 0.00 2.52
2505 6392 5.715753 ACAGGTACCTACTTCTACTTTCTGG 59.284 44.000 15.80 0.00 0.00 3.86
2507 6394 6.210984 CAGGTACCTACTTCTACTTTCTGGTT 59.789 42.308 15.80 0.00 0.00 3.67
2508 6395 6.786461 AGGTACCTACTTCTACTTTCTGGTTT 59.214 38.462 14.41 0.00 0.00 3.27
2512 6399 5.639931 CCTACTTCTACTTTCTGGTTTCAGC 59.360 44.000 0.00 0.00 40.69 4.26
2761 6699 1.515020 CAGAGTTCGCCTCCCTCAG 59.485 63.158 0.00 0.00 41.47 3.35
2780 6718 1.693640 CCTGCCCCTCAACATCCTT 59.306 57.895 0.00 0.00 0.00 3.36
2806 6746 5.924254 TGTAAGAACTAAGAACACATCCACG 59.076 40.000 0.00 0.00 0.00 4.94
2910 6854 5.351465 AGCTTAATTTCTCGCATTTTCTCGA 59.649 36.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.836636 AGACAGAGGAGCTCCACATA 57.163 50.000 33.90 0.00 38.89 2.29
21 22 1.003003 AGCAAAAGACAGAGGAGCTCC 59.997 52.381 26.22 26.22 0.00 4.70
35 36 1.656587 TAGGAGGGCTCTGAGCAAAA 58.343 50.000 28.95 7.06 44.75 2.44
37 38 1.765314 GAATAGGAGGGCTCTGAGCAA 59.235 52.381 28.95 8.86 44.75 3.91
66 67 2.112297 GGAAGGGCGTTGGTGTCA 59.888 61.111 0.00 0.00 0.00 3.58
105 106 5.413833 CCGGAAACAACTCTAGTGTAGTAGA 59.586 44.000 0.00 0.00 0.00 2.59
121 122 3.583276 ATGAGCGACGCCGGAAACA 62.583 57.895 17.79 7.93 36.06 2.83
151 152 1.174783 GCAGTAGGAGGACGACAGAA 58.825 55.000 0.00 0.00 0.00 3.02
253 254 0.319383 CGGAGGCCAAGATGATCGAG 60.319 60.000 5.01 0.00 0.00 4.04
272 273 1.756561 AAGAGAGAGGAGGCCGAGC 60.757 63.158 0.00 0.00 0.00 5.03
307 321 0.172578 TGATCGACGCCAGAAACGAT 59.827 50.000 0.00 0.00 45.77 3.73
330 344 1.279749 TAGGACGAGAGAGGAGGCCA 61.280 60.000 5.01 0.00 0.00 5.36
382 396 1.645710 GGTGGACAGAGGAGGAGAAA 58.354 55.000 0.00 0.00 0.00 2.52
489 564 1.736032 GCGACTGTGGTGGATAGTGTC 60.736 57.143 0.00 0.00 0.00 3.67
490 565 0.246635 GCGACTGTGGTGGATAGTGT 59.753 55.000 0.00 0.00 0.00 3.55
491 566 0.460284 GGCGACTGTGGTGGATAGTG 60.460 60.000 0.00 0.00 0.00 2.74
492 567 0.902984 TGGCGACTGTGGTGGATAGT 60.903 55.000 0.00 0.00 0.00 2.12
493 568 0.465705 ATGGCGACTGTGGTGGATAG 59.534 55.000 0.00 0.00 0.00 2.08
494 569 0.177836 CATGGCGACTGTGGTGGATA 59.822 55.000 0.00 0.00 0.00 2.59
495 570 1.078214 CATGGCGACTGTGGTGGAT 60.078 57.895 0.00 0.00 0.00 3.41
496 571 2.347114 CATGGCGACTGTGGTGGA 59.653 61.111 0.00 0.00 0.00 4.02
497 572 2.747460 CCATGGCGACTGTGGTGG 60.747 66.667 0.00 0.00 33.75 4.61
498 573 1.577328 GAACCATGGCGACTGTGGTG 61.577 60.000 17.82 0.00 45.25 4.17
500 575 2.390599 CGAACCATGGCGACTGTGG 61.391 63.158 13.04 11.16 40.98 4.17
501 576 2.390599 CCGAACCATGGCGACTGTG 61.391 63.158 13.04 0.00 0.00 3.66
502 577 2.047274 CCGAACCATGGCGACTGT 60.047 61.111 13.04 0.00 0.00 3.55
503 578 3.499737 GCCGAACCATGGCGACTG 61.500 66.667 13.04 1.09 43.70 3.51
509 584 1.671054 AGTGTTCGCCGAACCATGG 60.671 57.895 25.56 11.19 41.35 3.66
510 585 1.497278 CAGTGTTCGCCGAACCATG 59.503 57.895 25.56 19.46 41.35 3.66
511 586 2.325082 GCAGTGTTCGCCGAACCAT 61.325 57.895 25.56 12.32 41.35 3.55
512 587 2.970324 GCAGTGTTCGCCGAACCA 60.970 61.111 25.56 12.02 41.35 3.67
513 588 1.852067 AATGCAGTGTTCGCCGAACC 61.852 55.000 25.56 16.90 41.35 3.62
514 589 0.040425 AAATGCAGTGTTCGCCGAAC 60.040 50.000 22.39 22.39 42.26 3.95
515 590 0.237235 GAAATGCAGTGTTCGCCGAA 59.763 50.000 0.00 0.00 0.00 4.30
516 591 0.602638 AGAAATGCAGTGTTCGCCGA 60.603 50.000 0.00 0.00 0.00 5.54
517 592 0.238289 AAGAAATGCAGTGTTCGCCG 59.762 50.000 0.00 0.00 0.00 6.46
518 593 1.537202 AGAAGAAATGCAGTGTTCGCC 59.463 47.619 0.00 0.00 0.00 5.54
519 594 2.977405 AGAAGAAATGCAGTGTTCGC 57.023 45.000 0.00 0.00 0.00 4.70
520 595 3.365364 GGGAAGAAGAAATGCAGTGTTCG 60.365 47.826 0.00 0.00 0.00 3.95
521 596 3.057245 GGGGAAGAAGAAATGCAGTGTTC 60.057 47.826 0.00 0.00 0.00 3.18
522 597 2.893489 GGGGAAGAAGAAATGCAGTGTT 59.107 45.455 0.00 0.00 0.00 3.32
539 614 0.912486 GAGCTAGCAAAGGAAGGGGA 59.088 55.000 18.83 0.00 0.00 4.81
639 716 2.929641 TGGTTGTCTGCATTGTCTGAA 58.070 42.857 0.00 0.00 0.00 3.02
641 718 3.713858 TTTGGTTGTCTGCATTGTCTG 57.286 42.857 0.00 0.00 0.00 3.51
653 730 5.289083 ACTTTGGCACATTATTTGGTTGT 57.711 34.783 0.00 0.00 39.30 3.32
662 739 4.337145 ACGGGATTAACTTTGGCACATTA 58.663 39.130 0.00 0.00 39.30 1.90
677 754 4.035112 TGGACTTCCTACATTACGGGATT 58.965 43.478 0.00 0.00 36.82 3.01
722 801 7.750229 AAACAGTTTCATATGTGACATCTGT 57.250 32.000 0.00 5.43 39.34 3.41
739 818 2.310538 CCTGGCTCTGGAAAAACAGTT 58.689 47.619 0.00 0.00 39.48 3.16
764 843 2.487265 CCAAGTAGGCACTCCAAGTTGT 60.487 50.000 1.45 0.00 41.75 3.32
765 844 2.154462 CCAAGTAGGCACTCCAAGTTG 58.846 52.381 0.00 0.00 41.75 3.16
766 845 1.774856 ACCAAGTAGGCACTCCAAGTT 59.225 47.619 0.00 0.00 43.14 2.66
767 846 1.435256 ACCAAGTAGGCACTCCAAGT 58.565 50.000 0.00 0.00 43.14 3.16
768 847 2.154462 CAACCAAGTAGGCACTCCAAG 58.846 52.381 0.00 0.00 43.14 3.61
769 848 1.493022 ACAACCAAGTAGGCACTCCAA 59.507 47.619 0.00 0.00 43.14 3.53
788 867 5.237779 TGAAACAAGGTGATTCGAGGTTTAC 59.762 40.000 0.00 0.00 32.63 2.01
837 918 1.805428 TTGCTTGGAGGGCGAAAAGC 61.805 55.000 0.00 0.00 44.18 3.51
841 922 1.302511 GACTTGCTTGGAGGGCGAA 60.303 57.895 0.00 0.00 0.00 4.70
845 926 1.672356 CACGGACTTGCTTGGAGGG 60.672 63.158 0.00 0.00 0.00 4.30
851 933 0.179094 TGTCGTTCACGGACTTGCTT 60.179 50.000 0.00 0.00 40.29 3.91
888 970 2.184322 GCAGCTCGATCGGGTCAA 59.816 61.111 17.85 0.00 0.00 3.18
924 1006 3.574396 TCTGGATTATCTTACTGGCCTCG 59.426 47.826 3.32 0.00 0.00 4.63
1044 1126 1.091537 GAGAGAGTGAGGTGTCTCCG 58.908 60.000 0.00 0.00 40.20 4.63
1060 1142 2.607750 GGCAGAGTGGGGGTGAGA 60.608 66.667 0.00 0.00 0.00 3.27
1090 1174 0.737367 TCGGTTGAGAGCTTGCGATG 60.737 55.000 0.00 0.00 0.00 3.84
1092 1176 1.372997 GTCGGTTGAGAGCTTGCGA 60.373 57.895 0.00 0.00 0.00 5.10
1102 1186 2.027897 CGTTGGTCGGTCGGTTGA 59.972 61.111 0.00 0.00 35.71 3.18
1103 1187 3.708734 GCGTTGGTCGGTCGGTTG 61.709 66.667 0.00 0.00 40.26 3.77
1104 1188 4.974989 GGCGTTGGTCGGTCGGTT 62.975 66.667 0.00 0.00 40.26 4.44
1108 1192 3.186047 CATCGGCGTTGGTCGGTC 61.186 66.667 6.85 0.00 42.74 4.79
1109 1193 3.927163 GACATCGGCGTTGGTCGGT 62.927 63.158 20.71 0.52 42.74 4.69
1110 1194 3.186047 GACATCGGCGTTGGTCGG 61.186 66.667 20.71 0.00 42.74 4.79
1111 1195 3.186047 GGACATCGGCGTTGGTCG 61.186 66.667 20.71 0.00 44.20 4.79
1112 1196 3.186047 CGGACATCGGCGTTGGTC 61.186 66.667 20.71 18.08 34.75 4.02
1293 5135 4.003788 ACGGTGGTGGAGAAGGCG 62.004 66.667 0.00 0.00 0.00 5.52
1581 5433 1.078637 GGTTAGCCCCTCGGTGAAC 60.079 63.158 0.00 0.00 0.00 3.18
1647 5499 2.505498 GCGGACGCTGTACATCACG 61.505 63.158 9.76 10.46 38.26 4.35
1893 5745 0.027194 TATCTTCGTCTTCGTCGGCG 59.973 55.000 1.15 1.15 38.33 6.46
1895 5747 3.670311 TCTTATCTTCGTCTTCGTCGG 57.330 47.619 0.00 0.00 38.33 4.79
1897 5749 5.232610 TCCTTCTTATCTTCGTCTTCGTC 57.767 43.478 0.00 0.00 38.33 4.20
1901 5753 6.800072 AGGAATCCTTCTTATCTTCGTCTT 57.200 37.500 0.00 0.00 0.00 3.01
1902 5754 7.291566 TCTAGGAATCCTTCTTATCTTCGTCT 58.708 38.462 7.30 0.00 34.61 4.18
1934 5786 3.188100 ATCACACGCGACGGCATG 61.188 61.111 15.93 0.68 38.56 4.06
1935 5787 3.188100 CATCACACGCGACGGCAT 61.188 61.111 15.93 0.00 39.92 4.40
1944 5796 2.788176 CGTACGCAGCCATCACACG 61.788 63.158 0.52 0.00 0.00 4.49
1968 5825 5.941948 AACTACTGGAGTAAAACATGCAC 57.058 39.130 0.00 0.00 37.44 4.57
2008 5868 1.412343 ACATGGCCAAAATATTCGGGC 59.588 47.619 10.96 18.51 45.67 6.13
2041 5901 2.543641 TGCATTCGCTGACATCTACTG 58.456 47.619 0.00 0.00 39.64 2.74
2069 5934 4.722194 CGCAAGTAAATGTGCATACAGTT 58.278 39.130 0.00 0.00 45.85 3.16
2070 5935 4.340894 CGCAAGTAAATGTGCATACAGT 57.659 40.909 0.00 0.00 40.79 3.55
2096 5961 2.557924 AGTCCCATCACAAACGTACGTA 59.442 45.455 23.12 5.71 0.00 3.57
2133 5999 5.108385 TCGAATTTGGAAACTTTCAGCTC 57.892 39.130 3.93 0.00 0.00 4.09
2187 6053 1.450025 GGTGGATTCGGAACTGAACC 58.550 55.000 0.00 3.86 0.00 3.62
2251 6118 2.033755 GTGAGCTCAGCACTGCCAG 61.034 63.158 18.89 0.00 33.57 4.85
2307 6181 1.876156 GGCTCATGATTGGATTCCGAC 59.124 52.381 0.00 0.00 0.00 4.79
2323 6197 1.301479 AACAAGTTCGGACGGGCTC 60.301 57.895 0.00 0.00 0.00 4.70
2360 6247 4.385405 AGTCGGCCAGCACTCAGC 62.385 66.667 2.24 0.00 46.19 4.26
2361 6248 2.236223 ATCAGTCGGCCAGCACTCAG 62.236 60.000 2.24 0.00 0.00 3.35
2362 6249 2.285773 ATCAGTCGGCCAGCACTCA 61.286 57.895 2.24 0.00 0.00 3.41
2363 6250 1.812922 CATCAGTCGGCCAGCACTC 60.813 63.158 2.24 0.00 0.00 3.51
2364 6251 2.267006 CATCAGTCGGCCAGCACT 59.733 61.111 2.24 0.00 0.00 4.40
2365 6252 2.046892 ACATCAGTCGGCCAGCAC 60.047 61.111 2.24 0.00 0.00 4.40
2366 6253 2.046988 CACATCAGTCGGCCAGCA 60.047 61.111 2.24 0.00 0.00 4.41
2390 6277 4.484872 GAGGGCCCCTTGCGGTAC 62.485 72.222 21.43 0.00 42.61 3.34
2491 6378 4.390264 GGCTGAAACCAGAAAGTAGAAGT 58.610 43.478 0.00 0.00 33.56 3.01
2496 6383 2.103432 TCACGGCTGAAACCAGAAAGTA 59.897 45.455 0.00 0.00 33.56 2.24
2541 6479 3.978723 CTCTCGACGCACCTGCAGG 62.979 68.421 31.60 31.60 42.21 4.85
2688 6626 2.433838 CAGCTCCAGCACGTCCAG 60.434 66.667 0.48 0.00 45.16 3.86
2761 6699 2.440980 GGATGTTGAGGGGCAGGC 60.441 66.667 0.00 0.00 0.00 4.85
2780 6718 7.758076 CGTGGATGTGTTCTTAGTTCTTACATA 59.242 37.037 0.00 0.00 0.00 2.29
2806 6746 1.561542 AGAGGTGGATGGGATGTTGTC 59.438 52.381 0.00 0.00 0.00 3.18
2851 6795 1.734465 CCAATGGCGAGTTCTCTGTTC 59.266 52.381 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.