Multiple sequence alignment - TraesCS3A01G243000

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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 TraesCS3A01G243000 chr3A 100.000 3270 0 0 1 3270 456701897 456698628 0.000000e+00 6039.0
1 TraesCS3A01G243000 chr3A 89.923 1042 93 8 1241 2272 456452183 456453222 0.000000e+00 1332.0
2 TraesCS3A01G243000 chr3D 91.101 3225 155 52 119 3270 338350969 338347804 0.000000e+00 4244.0
3 TraesCS3A01G243000 chr3D 88.580 1042 107 6 1241 2272 338321155 338322194 0.000000e+00 1254.0
4 TraesCS3A01G243000 chr3B 92.189 1946 95 26 954 2887 436728339 436726439 0.000000e+00 2699.0
5 TraesCS3A01G243000 chr3B 89.913 1031 95 7 1249 2272 436574735 436575763 0.000000e+00 1319.0
6 TraesCS3A01G243000 chr3B 87.530 842 66 19 126 955 436729189 436728375 0.000000e+00 937.0
7 TraesCS3A01G243000 chr3B 92.308 364 18 4 2916 3270 436726442 436726080 2.910000e-140 508.0
8 TraesCS3A01G243000 chr3B 93.600 125 4 4 1 122 536413388 536413511 2.000000e-42 183.0
9 TraesCS3A01G243000 chr5A 98.347 121 1 1 1 120 645732699 645732819 9.190000e-51 211.0
10 TraesCS3A01G243000 chr5B 96.721 122 2 2 1 120 640427537 640427416 5.530000e-48 202.0
11 TraesCS3A01G243000 chr2D 93.284 134 8 1 1372 1504 536380670 536380803 2.570000e-46 196.0
12 TraesCS3A01G243000 chr4A 95.868 121 4 1 1 120 615001213 615001333 9.260000e-46 195.0
13 TraesCS3A01G243000 chr2A 95.868 121 4 1 1 120 103366540 103366420 9.260000e-46 195.0
14 TraesCS3A01G243000 chr2B 92.481 133 10 0 1372 1504 637775929 637776061 1.200000e-44 191.0
15 TraesCS3A01G243000 chr2B 94.167 120 3 4 4 120 664409421 664409303 2.590000e-41 180.0
16 TraesCS3A01G243000 chr7B 92.126 127 3 4 1 120 449508623 449508749 4.340000e-39 172.0
17 TraesCS3A01G243000 chr4B 93.277 119 5 3 4 120 644578172 644578055 4.340000e-39 172.0
18 TraesCS3A01G243000 chr1B 91.473 129 6 5 1 126 173596513 173596639 4.340000e-39 172.0
19 TraesCS3A01G243000 chr6B 92.308 65 5 0 1700 1764 347591962 347591898 3.470000e-15 93.5


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 TraesCS3A01G243000 chr3A 456698628 456701897 3269 True 6039.000000 6039 100.000000 1 3270 1 chr3A.!!$R1 3269
1 TraesCS3A01G243000 chr3A 456452183 456453222 1039 False 1332.000000 1332 89.923000 1241 2272 1 chr3A.!!$F1 1031
2 TraesCS3A01G243000 chr3D 338347804 338350969 3165 True 4244.000000 4244 91.101000 119 3270 1 chr3D.!!$R1 3151
3 TraesCS3A01G243000 chr3D 338321155 338322194 1039 False 1254.000000 1254 88.580000 1241 2272 1 chr3D.!!$F1 1031
4 TraesCS3A01G243000 chr3B 436726080 436729189 3109 True 1381.333333 2699 90.675667 126 3270 3 chr3B.!!$R1 3144
5 TraesCS3A01G243000 chr3B 436574735 436575763 1028 False 1319.000000 1319 89.913000 1249 2272 1 chr3B.!!$F1 1023

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
20 21 0.106708 ATAGCCATGGCACTACGGTG 59.893 55.0 37.18 0.0 44.88 4.94 F
682 692 0.251787 ACCCTCAACTGATTTGGGCC 60.252 55.0 0.00 0.0 41.44 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1341 0.776810 TTGGGGTTCTTCCTGCATCA 59.223 50.0 0.0 0.0 36.25 3.07 R
2352 2445 0.038166 GCAAGGACCCAACCATCTCA 59.962 55.0 0.0 0.0 0.00 3.27 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
19 20 1.712056 TATAGCCATGGCACTACGGT 58.288 50.000 37.18 18.07 44.88 4.83
20 21 0.106708 ATAGCCATGGCACTACGGTG 59.893 55.000 37.18 0.00 44.88 4.94
32 33 2.348666 CACTACGGTGCTCAATGTAAGC 59.651 50.000 0.00 0.00 40.26 3.09
33 34 2.233922 ACTACGGTGCTCAATGTAAGCT 59.766 45.455 0.00 0.00 40.50 3.74
34 35 2.185004 ACGGTGCTCAATGTAAGCTT 57.815 45.000 3.48 3.48 40.50 3.74
35 36 2.076863 ACGGTGCTCAATGTAAGCTTC 58.923 47.619 0.00 0.00 40.50 3.86
36 37 2.076100 CGGTGCTCAATGTAAGCTTCA 58.924 47.619 0.00 1.13 40.50 3.02
37 38 2.679837 CGGTGCTCAATGTAAGCTTCAT 59.320 45.455 0.00 3.80 40.50 2.57
38 39 3.486375 CGGTGCTCAATGTAAGCTTCATG 60.486 47.826 0.00 0.00 40.50 3.07
39 40 3.441572 GGTGCTCAATGTAAGCTTCATGT 59.558 43.478 0.00 0.00 40.50 3.21
40 41 4.635765 GGTGCTCAATGTAAGCTTCATGTA 59.364 41.667 0.00 0.00 40.50 2.29
41 42 5.123820 GGTGCTCAATGTAAGCTTCATGTAA 59.876 40.000 0.00 0.00 40.50 2.41
42 43 6.024049 GTGCTCAATGTAAGCTTCATGTAAC 58.976 40.000 0.00 0.00 40.50 2.50
43 44 5.939883 TGCTCAATGTAAGCTTCATGTAACT 59.060 36.000 0.00 0.00 40.50 2.24
44 45 6.128200 TGCTCAATGTAAGCTTCATGTAACTG 60.128 38.462 0.00 2.26 40.50 3.16
45 46 6.092670 GCTCAATGTAAGCTTCATGTAACTGA 59.907 38.462 0.00 6.22 36.80 3.41
46 47 7.364522 TCAATGTAAGCTTCATGTAACTGAC 57.635 36.000 0.00 0.00 0.00 3.51
47 48 6.371548 TCAATGTAAGCTTCATGTAACTGACC 59.628 38.462 0.00 0.00 0.00 4.02
48 49 4.575885 TGTAAGCTTCATGTAACTGACCC 58.424 43.478 0.00 0.00 0.00 4.46
49 50 4.286032 TGTAAGCTTCATGTAACTGACCCT 59.714 41.667 0.00 0.00 0.00 4.34
50 51 4.373156 AAGCTTCATGTAACTGACCCTT 57.627 40.909 0.00 0.00 0.00 3.95
51 52 4.373156 AGCTTCATGTAACTGACCCTTT 57.627 40.909 0.00 0.00 0.00 3.11
52 53 4.074970 AGCTTCATGTAACTGACCCTTTG 58.925 43.478 0.00 0.00 0.00 2.77
53 54 3.191371 GCTTCATGTAACTGACCCTTTGG 59.809 47.826 0.00 0.00 37.80 3.28
62 63 3.590574 ACCCTTTGGTCCCAGGCC 61.591 66.667 0.00 0.00 43.06 5.19
63 64 3.268032 CCCTTTGGTCCCAGGCCT 61.268 66.667 0.00 0.00 0.00 5.19
64 65 2.854076 CCTTTGGTCCCAGGCCTT 59.146 61.111 0.00 0.00 0.00 4.35
65 66 1.607467 CCTTTGGTCCCAGGCCTTG 60.607 63.158 0.00 0.00 0.00 3.61
67 68 3.826265 TTTGGTCCCAGGCCTTGGC 62.826 63.158 18.38 12.66 46.32 4.52
75 76 2.934369 AGGCCTTGGCCTGTTTGA 59.066 55.556 30.29 0.00 38.99 2.69
76 77 1.232792 AGGCCTTGGCCTGTTTGAA 59.767 52.632 30.29 0.00 38.99 2.69
77 78 0.398381 AGGCCTTGGCCTGTTTGAAA 60.398 50.000 30.29 0.00 38.99 2.69
78 79 0.686789 GGCCTTGGCCTGTTTGAAAT 59.313 50.000 22.47 0.00 0.00 2.17
79 80 1.899142 GGCCTTGGCCTGTTTGAAATA 59.101 47.619 22.47 0.00 0.00 1.40
80 81 2.501316 GGCCTTGGCCTGTTTGAAATAT 59.499 45.455 22.47 0.00 0.00 1.28
81 82 3.704061 GGCCTTGGCCTGTTTGAAATATA 59.296 43.478 22.47 0.00 0.00 0.86
82 83 4.344968 GGCCTTGGCCTGTTTGAAATATAT 59.655 41.667 22.47 0.00 0.00 0.86
83 84 5.538433 GGCCTTGGCCTGTTTGAAATATATA 59.462 40.000 22.47 0.00 0.00 0.86
84 85 6.041523 GGCCTTGGCCTGTTTGAAATATATAA 59.958 38.462 22.47 0.00 0.00 0.98
85 86 7.147976 GCCTTGGCCTGTTTGAAATATATAAG 58.852 38.462 3.32 0.00 0.00 1.73
86 87 7.661040 CCTTGGCCTGTTTGAAATATATAAGG 58.339 38.462 3.32 0.00 0.00 2.69
87 88 7.287696 CCTTGGCCTGTTTGAAATATATAAGGT 59.712 37.037 3.32 0.00 0.00 3.50
88 89 9.349713 CTTGGCCTGTTTGAAATATATAAGGTA 57.650 33.333 3.32 0.00 0.00 3.08
89 90 8.918202 TGGCCTGTTTGAAATATATAAGGTAG 57.082 34.615 3.32 0.00 0.00 3.18
90 91 8.719596 TGGCCTGTTTGAAATATATAAGGTAGA 58.280 33.333 3.32 0.00 0.00 2.59
91 92 9.569122 GGCCTGTTTGAAATATATAAGGTAGAA 57.431 33.333 0.00 0.00 0.00 2.10
142 143 7.639062 AAGGATATGTAGATCCCTTGATTGT 57.361 36.000 2.06 0.00 45.85 2.71
379 380 0.320771 TCCTCAAGAAGCGCCTTGAC 60.321 55.000 20.72 2.50 45.25 3.18
400 401 3.132646 ACAAGTTGATGGCTGAAAAGCAA 59.867 39.130 10.54 0.00 36.33 3.91
409 410 2.029649 GGCTGAAAAGCAAGCATCTTCA 60.030 45.455 0.00 0.00 36.33 3.02
412 413 2.248487 GAAAAGCAAGCATCTTCAGCG 58.752 47.619 0.00 0.00 37.01 5.18
428 429 0.396435 AGCGAGTGATGACCAACCAA 59.604 50.000 0.00 0.00 0.00 3.67
429 430 1.202758 AGCGAGTGATGACCAACCAAA 60.203 47.619 0.00 0.00 0.00 3.28
436 437 5.815581 AGTGATGACCAACCAAATAGCTAA 58.184 37.500 0.00 0.00 0.00 3.09
442 443 5.105106 TGACCAACCAAATAGCTAATCGAGA 60.105 40.000 0.00 0.00 0.00 4.04
458 461 9.031360 GCTAATCGAGATTTTGTATGTCTTACA 57.969 33.333 3.49 0.00 34.40 2.41
471 474 1.071699 GTCTTACACTTGTGCCCAGGA 59.928 52.381 0.10 0.00 0.00 3.86
472 475 1.771854 TCTTACACTTGTGCCCAGGAA 59.228 47.619 0.10 0.00 0.00 3.36
486 489 1.537202 CCAGGAAGCAGTTGTTGTAGC 59.463 52.381 0.00 0.00 0.00 3.58
494 497 2.095567 GCAGTTGTTGTAGCTCATGTGG 60.096 50.000 0.00 0.00 0.00 4.17
496 499 4.314961 CAGTTGTTGTAGCTCATGTGGTA 58.685 43.478 2.68 2.68 0.00 3.25
498 501 5.412594 CAGTTGTTGTAGCTCATGTGGTAAT 59.587 40.000 8.17 0.00 0.00 1.89
513 516 3.505680 GTGGTAATGGTTCATGCAACTGA 59.494 43.478 0.00 0.00 35.06 3.41
523 526 5.984926 GGTTCATGCAACTGAAAATGAGAAA 59.015 36.000 4.34 0.00 36.92 2.52
525 528 7.339953 GTTCATGCAACTGAAAATGAGAAAAC 58.660 34.615 4.34 0.00 36.92 2.43
529 532 5.291614 TGCAACTGAAAATGAGAAAACTTGC 59.708 36.000 0.00 0.00 0.00 4.01
531 534 4.948847 ACTGAAAATGAGAAAACTTGCCC 58.051 39.130 0.00 0.00 0.00 5.36
534 537 3.391506 AAATGAGAAAACTTGCCCTGC 57.608 42.857 0.00 0.00 0.00 4.85
535 538 1.999648 ATGAGAAAACTTGCCCTGCA 58.000 45.000 0.00 0.00 36.47 4.41
542 545 1.180029 AACTTGCCCTGCATGTGATC 58.820 50.000 8.16 0.00 44.18 2.92
543 546 0.330604 ACTTGCCCTGCATGTGATCT 59.669 50.000 6.78 0.00 43.50 2.75
545 548 0.622136 TTGCCCTGCATGTGATCTCT 59.378 50.000 0.00 0.00 38.76 3.10
547 550 1.022735 GCCCTGCATGTGATCTCTTG 58.977 55.000 6.35 6.35 0.00 3.02
548 551 1.407851 GCCCTGCATGTGATCTCTTGA 60.408 52.381 13.19 0.79 0.00 3.02
549 552 2.748798 GCCCTGCATGTGATCTCTTGAT 60.749 50.000 13.19 0.00 35.26 2.57
550 553 3.139850 CCCTGCATGTGATCTCTTGATC 58.860 50.000 13.19 0.00 46.89 2.92
551 554 3.181453 CCCTGCATGTGATCTCTTGATCT 60.181 47.826 13.19 0.00 46.84 2.75
552 555 4.040095 CCCTGCATGTGATCTCTTGATCTA 59.960 45.833 13.19 0.00 46.84 1.98
593 597 2.078849 TGTCTTGGCATGTACAGTCG 57.921 50.000 0.33 0.00 0.00 4.18
594 598 1.337728 TGTCTTGGCATGTACAGTCGG 60.338 52.381 0.33 0.00 0.00 4.79
595 599 0.973632 TCTTGGCATGTACAGTCGGT 59.026 50.000 0.33 0.00 0.00 4.69
596 600 1.346395 TCTTGGCATGTACAGTCGGTT 59.654 47.619 0.33 0.00 0.00 4.44
597 601 1.732259 CTTGGCATGTACAGTCGGTTC 59.268 52.381 0.33 0.00 0.00 3.62
598 602 0.682292 TGGCATGTACAGTCGGTTCA 59.318 50.000 0.33 0.00 0.00 3.18
599 603 1.277842 TGGCATGTACAGTCGGTTCAT 59.722 47.619 0.33 0.00 37.93 2.57
600 604 1.933853 GGCATGTACAGTCGGTTCATC 59.066 52.381 0.33 0.00 35.58 2.92
601 605 2.616960 GCATGTACAGTCGGTTCATCA 58.383 47.619 0.33 0.00 35.58 3.07
602 606 3.198068 GCATGTACAGTCGGTTCATCAT 58.802 45.455 0.33 0.00 35.58 2.45
603 607 3.246226 GCATGTACAGTCGGTTCATCATC 59.754 47.826 0.33 0.00 35.58 2.92
604 608 4.432712 CATGTACAGTCGGTTCATCATCA 58.567 43.478 0.33 0.00 35.58 3.07
605 609 4.736126 TGTACAGTCGGTTCATCATCAT 57.264 40.909 0.00 0.00 0.00 2.45
606 610 5.845391 TGTACAGTCGGTTCATCATCATA 57.155 39.130 0.00 0.00 0.00 2.15
607 611 6.405278 TGTACAGTCGGTTCATCATCATAT 57.595 37.500 0.00 0.00 0.00 1.78
608 612 6.816136 TGTACAGTCGGTTCATCATCATATT 58.184 36.000 0.00 0.00 0.00 1.28
609 613 6.701400 TGTACAGTCGGTTCATCATCATATTG 59.299 38.462 0.00 0.00 0.00 1.90
610 614 5.674525 ACAGTCGGTTCATCATCATATTGT 58.325 37.500 0.00 0.00 0.00 2.71
611 615 6.115446 ACAGTCGGTTCATCATCATATTGTT 58.885 36.000 0.00 0.00 0.00 2.83
612 616 7.272244 ACAGTCGGTTCATCATCATATTGTTA 58.728 34.615 0.00 0.00 0.00 2.41
613 617 7.933577 ACAGTCGGTTCATCATCATATTGTTAT 59.066 33.333 0.00 0.00 0.00 1.89
614 618 9.423061 CAGTCGGTTCATCATCATATTGTTATA 57.577 33.333 0.00 0.00 0.00 0.98
615 619 9.424319 AGTCGGTTCATCATCATATTGTTATAC 57.576 33.333 0.00 0.00 0.00 1.47
616 620 9.203421 GTCGGTTCATCATCATATTGTTATACA 57.797 33.333 0.00 0.00 0.00 2.29
617 621 9.771534 TCGGTTCATCATCATATTGTTATACAA 57.228 29.630 0.00 0.00 42.95 2.41
656 663 4.954092 AATTTGAATCTTCTGACGAGGC 57.046 40.909 0.00 0.00 0.00 4.70
657 664 3.401033 TTTGAATCTTCTGACGAGGCA 57.599 42.857 0.00 0.00 0.00 4.75
664 671 3.067106 TCTTCTGACGAGGCATTTTGAC 58.933 45.455 0.00 0.00 0.00 3.18
669 676 0.400213 ACGAGGCATTTTGACCCTCA 59.600 50.000 6.71 0.00 44.24 3.86
682 692 0.251787 ACCCTCAACTGATTTGGGCC 60.252 55.000 0.00 0.00 41.44 5.80
711 725 4.761739 CAGATTCCTGCAACCTTGTTTCTA 59.238 41.667 0.00 0.00 33.07 2.10
735 749 2.039818 TAGATGCTTCTCGTCGAGGT 57.960 50.000 21.63 3.90 35.85 3.85
738 752 1.994507 ATGCTTCTCGTCGAGGTCGG 61.995 60.000 21.63 10.46 40.29 4.79
745 759 1.081376 CGTCGAGGTCGGGCATATC 60.081 63.158 0.00 0.00 40.29 1.63
747 761 0.603569 GTCGAGGTCGGGCATATCAT 59.396 55.000 0.00 0.00 40.29 2.45
750 764 1.270305 CGAGGTCGGGCATATCATTGT 60.270 52.381 0.00 0.00 35.37 2.71
752 766 2.037772 GAGGTCGGGCATATCATTGTCT 59.962 50.000 0.00 0.00 0.00 3.41
761 775 5.311265 GGCATATCATTGTCTTCTCCATCA 58.689 41.667 0.00 0.00 0.00 3.07
762 776 5.411977 GGCATATCATTGTCTTCTCCATCAG 59.588 44.000 0.00 0.00 0.00 2.90
792 806 2.731691 ATCGTGTGCGCCCAACTCTT 62.732 55.000 4.18 0.00 38.14 2.85
793 807 1.666553 CGTGTGCGCCCAACTCTTA 60.667 57.895 4.18 0.00 0.00 2.10
805 819 4.323562 GCCCAACTCTTACTGTAATCCACT 60.324 45.833 0.00 0.00 0.00 4.00
822 840 3.884091 TCCACTAGTTCTAATCTCTCGGC 59.116 47.826 0.00 0.00 0.00 5.54
860 878 0.911769 CAGGTTCCATGCTACCCTGA 59.088 55.000 11.42 0.00 44.39 3.86
861 879 1.281867 CAGGTTCCATGCTACCCTGAA 59.718 52.381 11.42 0.00 44.39 3.02
909 927 1.782028 AAAGTTTCGCCGCGCTTTCT 61.782 50.000 8.21 0.98 0.00 2.52
911 929 4.383602 TTTCGCCGCGCTTTCTGC 62.384 61.111 8.21 0.00 38.57 4.26
932 950 3.358993 GCGATTCTTTTCAGCTTGAAACG 59.641 43.478 9.83 8.88 45.03 3.60
988 1043 3.733960 CTCGCGACTCCACGGTGA 61.734 66.667 3.71 0.00 0.00 4.02
999 1054 0.739813 CCACGGTGAAGGAACGATCC 60.740 60.000 10.28 2.97 46.98 3.36
1265 1341 1.339929 GGGAGTTTGTTGCGATGGTTT 59.660 47.619 0.00 0.00 0.00 3.27
2291 2379 2.201732 CACGTGTGCCATGGTACTATC 58.798 52.381 29.82 19.41 0.00 2.08
2304 2392 8.198109 GCCATGGTACTATCGACTTATTATCAT 58.802 37.037 14.67 0.00 0.00 2.45
2305 2393 9.737427 CCATGGTACTATCGACTTATTATCATC 57.263 37.037 2.57 0.00 0.00 2.92
2306 2394 9.439537 CATGGTACTATCGACTTATTATCATCG 57.560 37.037 0.00 0.00 35.91 3.84
2307 2395 8.557592 TGGTACTATCGACTTATTATCATCGT 57.442 34.615 0.00 0.00 36.03 3.73
2308 2396 9.006839 TGGTACTATCGACTTATTATCATCGTT 57.993 33.333 0.00 0.00 36.03 3.85
2350 2443 2.442212 TGCCATTGTTGCTGTTCATG 57.558 45.000 0.00 0.00 0.00 3.07
2351 2444 1.687660 TGCCATTGTTGCTGTTCATGT 59.312 42.857 0.00 0.00 0.00 3.21
2352 2445 2.102757 TGCCATTGTTGCTGTTCATGTT 59.897 40.909 0.00 0.00 0.00 2.71
2353 2446 2.477375 GCCATTGTTGCTGTTCATGTTG 59.523 45.455 0.00 0.00 0.00 3.33
2354 2447 3.799574 GCCATTGTTGCTGTTCATGTTGA 60.800 43.478 0.00 0.00 0.00 3.18
2355 2448 3.985279 CCATTGTTGCTGTTCATGTTGAG 59.015 43.478 0.00 0.00 0.00 3.02
2356 2449 4.261698 CCATTGTTGCTGTTCATGTTGAGA 60.262 41.667 0.00 0.00 0.00 3.27
2357 2450 5.466819 CATTGTTGCTGTTCATGTTGAGAT 58.533 37.500 0.00 0.00 0.00 2.75
2358 2451 4.492791 TGTTGCTGTTCATGTTGAGATG 57.507 40.909 0.00 0.00 0.00 2.90
2398 2493 3.181466 GGGGTTAATGATGTGCCCAATTC 60.181 47.826 0.00 0.00 41.02 2.17
2399 2494 3.706086 GGGTTAATGATGTGCCCAATTCT 59.294 43.478 0.00 0.00 39.13 2.40
2490 2586 7.698836 CAAGCTATGTTAACTTGCAAAAAGT 57.301 32.000 7.22 0.00 34.90 2.66
2491 2587 7.777425 CAAGCTATGTTAACTTGCAAAAAGTC 58.223 34.615 7.22 0.00 34.90 3.01
2492 2588 7.277174 AGCTATGTTAACTTGCAAAAAGTCT 57.723 32.000 7.22 0.00 0.00 3.24
2493 2589 7.716612 AGCTATGTTAACTTGCAAAAAGTCTT 58.283 30.769 7.22 0.00 0.00 3.01
2494 2590 8.846211 AGCTATGTTAACTTGCAAAAAGTCTTA 58.154 29.630 7.22 0.00 0.00 2.10
2495 2591 9.626045 GCTATGTTAACTTGCAAAAAGTCTTAT 57.374 29.630 7.22 0.00 0.00 1.73
2563 2659 1.661112 GTCGTCTCTAACTTGCATGGC 59.339 52.381 4.44 0.00 0.00 4.40
2569 2665 1.550524 TCTAACTTGCATGGCGTCTCT 59.449 47.619 4.44 0.00 0.00 3.10
2585 2683 5.921408 GGCGTCTCTACCATTGACTATAAAG 59.079 44.000 0.00 0.00 0.00 1.85
2595 2693 8.078060 ACCATTGACTATAAAGAAAATTGGGG 57.922 34.615 0.00 0.00 0.00 4.96
2695 2793 9.489084 CCTTTGATCACGGATGAATAGTTATTA 57.511 33.333 0.00 0.00 38.69 0.98
2700 2798 9.562583 GATCACGGATGAATAGTTATTAGAGAC 57.437 37.037 0.00 0.00 38.69 3.36
2873 2973 4.655963 AGTGTGGAGTGCTAACATCAAAT 58.344 39.130 0.00 0.00 0.00 2.32
2881 2981 3.063997 GTGCTAACATCAAATGGACCTCG 59.936 47.826 0.00 0.00 33.60 4.63
2887 2987 2.194201 TCAAATGGACCTCGGGAAAC 57.806 50.000 0.00 0.00 0.00 2.78
2904 3022 5.003160 GGGAAACAAATTGGAAGATTTGGG 58.997 41.667 13.10 0.00 46.36 4.12
2932 3050 8.273780 TGCTTGAAGAAATCTAATCTTTCTCC 57.726 34.615 0.00 0.00 41.01 3.71
2959 3077 5.248020 TGACCAATATGGCAGGAAATGTTTT 59.752 36.000 0.00 0.00 42.67 2.43
2961 3079 6.639563 ACCAATATGGCAGGAAATGTTTTAC 58.360 36.000 0.00 0.00 42.67 2.01
2989 3107 9.652114 AAAAGGGCTTTCTTTCATATCTATGAT 57.348 29.630 0.93 0.00 36.02 2.45
3020 3138 6.879458 AGATTTTAGTTTCGCATAACAGGTCT 59.121 34.615 1.37 0.00 0.00 3.85
3069 3187 5.762218 TGCCAACACTAAATTTTTCCATTGG 59.238 36.000 0.00 6.32 37.67 3.16
3215 3333 2.224159 TTTGGCGAGAAGGAGGCCT 61.224 57.895 3.86 3.86 46.97 5.19
3216 3334 2.469465 TTTGGCGAGAAGGAGGCCTG 62.469 60.000 12.00 0.00 46.97 4.85
3231 3358 2.092538 AGGCCTGAAGAATGATGTGGAG 60.093 50.000 3.11 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.343142 CACCGTAGTGCCATGGCTATA 59.657 52.381 35.53 24.51 42.51 1.31
1 2 0.106708 CACCGTAGTGCCATGGCTAT 59.893 55.000 35.53 25.53 42.51 2.97
2 3 1.520192 CACCGTAGTGCCATGGCTA 59.480 57.895 35.53 19.30 42.51 3.93
3 4 2.268920 CACCGTAGTGCCATGGCT 59.731 61.111 35.53 20.42 42.51 4.75
12 13 2.233922 AGCTTACATTGAGCACCGTAGT 59.766 45.455 0.00 0.00 42.56 2.73
13 14 2.893637 AGCTTACATTGAGCACCGTAG 58.106 47.619 0.00 0.00 42.56 3.51
14 15 3.259064 GAAGCTTACATTGAGCACCGTA 58.741 45.455 0.00 0.00 42.56 4.02
15 16 2.076863 GAAGCTTACATTGAGCACCGT 58.923 47.619 0.00 0.00 42.56 4.83
16 17 2.076100 TGAAGCTTACATTGAGCACCG 58.924 47.619 0.00 0.00 42.56 4.94
17 18 3.441572 ACATGAAGCTTACATTGAGCACC 59.558 43.478 0.00 0.00 42.56 5.01
18 19 4.691860 ACATGAAGCTTACATTGAGCAC 57.308 40.909 0.00 0.00 42.56 4.40
19 20 5.939883 AGTTACATGAAGCTTACATTGAGCA 59.060 36.000 0.00 0.00 42.56 4.26
20 21 6.092670 TCAGTTACATGAAGCTTACATTGAGC 59.907 38.462 0.00 0.00 40.43 4.26
21 22 7.413438 GGTCAGTTACATGAAGCTTACATTGAG 60.413 40.741 0.00 0.00 0.00 3.02
22 23 6.371548 GGTCAGTTACATGAAGCTTACATTGA 59.628 38.462 0.00 3.05 0.00 2.57
23 24 6.403636 GGGTCAGTTACATGAAGCTTACATTG 60.404 42.308 0.00 0.00 0.00 2.82
24 25 5.648092 GGGTCAGTTACATGAAGCTTACATT 59.352 40.000 0.00 0.16 0.00 2.71
25 26 5.045578 AGGGTCAGTTACATGAAGCTTACAT 60.046 40.000 0.00 2.09 0.00 2.29
26 27 4.286032 AGGGTCAGTTACATGAAGCTTACA 59.714 41.667 0.00 0.00 0.00 2.41
27 28 4.833390 AGGGTCAGTTACATGAAGCTTAC 58.167 43.478 0.00 0.00 0.00 2.34
28 29 5.499004 AAGGGTCAGTTACATGAAGCTTA 57.501 39.130 0.00 0.00 0.00 3.09
29 30 4.373156 AAGGGTCAGTTACATGAAGCTT 57.627 40.909 0.00 0.00 0.00 3.74
30 31 4.074970 CAAAGGGTCAGTTACATGAAGCT 58.925 43.478 0.00 0.00 0.00 3.74
31 32 3.191371 CCAAAGGGTCAGTTACATGAAGC 59.809 47.826 0.00 0.00 0.00 3.86
46 47 2.856937 AAGGCCTGGGACCAAAGGG 61.857 63.158 5.69 3.40 41.29 3.95
47 48 1.607467 CAAGGCCTGGGACCAAAGG 60.607 63.158 5.69 7.91 36.58 3.11
48 49 1.607467 CCAAGGCCTGGGACCAAAG 60.607 63.158 23.53 0.00 42.17 2.77
49 50 2.525592 CCAAGGCCTGGGACCAAA 59.474 61.111 23.53 0.00 42.17 3.28
50 51 4.299796 GCCAAGGCCTGGGACCAA 62.300 66.667 32.15 0.00 46.54 3.67
60 61 3.893326 ATATTTCAAACAGGCCAAGGC 57.107 42.857 5.01 1.52 41.06 4.35
61 62 7.287696 ACCTTATATATTTCAAACAGGCCAAGG 59.712 37.037 5.01 5.62 34.00 3.61
62 63 8.237811 ACCTTATATATTTCAAACAGGCCAAG 57.762 34.615 5.01 0.00 0.00 3.61
63 64 9.349713 CTACCTTATATATTTCAAACAGGCCAA 57.650 33.333 5.01 0.00 0.00 4.52
64 65 8.719596 TCTACCTTATATATTTCAAACAGGCCA 58.280 33.333 5.01 0.00 0.00 5.36
65 66 9.569122 TTCTACCTTATATATTTCAAACAGGCC 57.431 33.333 0.00 0.00 0.00 5.19
115 116 9.359653 CAATCAAGGGATCTACATATCCTTTTT 57.640 33.333 3.09 0.00 41.22 1.94
116 117 8.506083 ACAATCAAGGGATCTACATATCCTTTT 58.494 33.333 3.09 0.00 41.22 2.27
117 118 8.050316 ACAATCAAGGGATCTACATATCCTTT 57.950 34.615 3.09 0.00 43.90 3.11
142 143 9.715119 ATGGTAGCATCTGGTAATGATAGTATA 57.285 33.333 0.40 0.00 28.77 1.47
152 153 6.405731 GCAAATTCAATGGTAGCATCTGGTAA 60.406 38.462 8.07 0.00 0.00 2.85
379 380 3.374220 TGCTTTTCAGCCATCAACTTG 57.626 42.857 0.00 0.00 46.74 3.16
400 401 1.479730 TCATCACTCGCTGAAGATGCT 59.520 47.619 0.00 0.00 38.15 3.79
409 410 0.396435 TTGGTTGGTCATCACTCGCT 59.604 50.000 0.00 0.00 0.00 4.93
412 413 4.265073 AGCTATTTGGTTGGTCATCACTC 58.735 43.478 0.00 0.00 0.00 3.51
428 429 9.988815 AGACATACAAAATCTCGATTAGCTATT 57.011 29.630 0.00 0.00 0.00 1.73
429 430 9.988815 AAGACATACAAAATCTCGATTAGCTAT 57.011 29.630 0.00 0.00 0.00 2.97
436 437 8.873830 CAAGTGTAAGACATACAAAATCTCGAT 58.126 33.333 0.00 0.00 45.81 3.59
442 443 6.294508 GGGCACAAGTGTAAGACATACAAAAT 60.295 38.462 1.79 0.00 45.81 1.82
458 461 1.228367 CTGCTTCCTGGGCACAAGT 60.228 57.895 0.00 0.00 35.71 3.16
459 462 0.825010 AACTGCTTCCTGGGCACAAG 60.825 55.000 0.00 0.00 35.71 3.16
471 474 3.251729 CACATGAGCTACAACAACTGCTT 59.748 43.478 0.00 0.00 35.76 3.91
472 475 2.810274 CACATGAGCTACAACAACTGCT 59.190 45.455 0.00 0.00 38.59 4.24
486 489 3.695556 TGCATGAACCATTACCACATGAG 59.304 43.478 0.00 0.00 40.13 2.90
494 497 6.867816 TCATTTTCAGTTGCATGAACCATTAC 59.132 34.615 2.20 0.00 38.87 1.89
496 499 5.856156 TCATTTTCAGTTGCATGAACCATT 58.144 33.333 2.20 0.00 38.87 3.16
498 501 4.583907 TCTCATTTTCAGTTGCATGAACCA 59.416 37.500 2.20 0.00 38.87 3.67
513 516 3.134442 TGCAGGGCAAGTTTTCTCATTTT 59.866 39.130 0.00 0.00 34.76 1.82
523 526 1.180029 GATCACATGCAGGGCAAGTT 58.820 50.000 2.31 0.00 43.62 2.66
525 528 1.022735 GAGATCACATGCAGGGCAAG 58.977 55.000 2.31 0.00 43.62 4.01
529 532 2.704464 TCAAGAGATCACATGCAGGG 57.296 50.000 2.31 0.00 0.00 4.45
542 545 7.913423 TGAATTTGATTTCGCTAGATCAAGAG 58.087 34.615 4.67 0.00 41.67 2.85
543 546 7.765819 TCTGAATTTGATTTCGCTAGATCAAGA 59.234 33.333 4.67 0.00 41.67 3.02
545 548 7.848223 TCTGAATTTGATTTCGCTAGATCAA 57.152 32.000 0.59 0.59 39.71 2.57
547 550 9.727627 ATTTTCTGAATTTGATTTCGCTAGATC 57.272 29.630 0.00 0.00 0.00 2.75
549 552 9.345517 CAATTTTCTGAATTTGATTTCGCTAGA 57.654 29.630 0.00 0.00 31.12 2.43
550 553 9.132521 ACAATTTTCTGAATTTGATTTCGCTAG 57.867 29.630 16.04 0.00 32.91 3.42
551 554 9.128107 GACAATTTTCTGAATTTGATTTCGCTA 57.872 29.630 16.04 0.00 32.91 4.26
552 555 7.869429 AGACAATTTTCTGAATTTGATTTCGCT 59.131 29.630 16.04 5.24 32.91 4.93
574 578 1.337728 CCGACTGTACATGCCAAGACA 60.338 52.381 0.00 0.00 0.00 3.41
608 612 9.320352 ACATCTACGTTGCATAATTGTATAACA 57.680 29.630 0.00 0.00 0.00 2.41
614 618 9.502145 CAAATTACATCTACGTTGCATAATTGT 57.498 29.630 0.00 0.00 0.00 2.71
615 619 9.715123 TCAAATTACATCTACGTTGCATAATTG 57.285 29.630 0.00 0.00 0.00 2.32
618 622 9.929722 GATTCAAATTACATCTACGTTGCATAA 57.070 29.630 0.00 0.00 0.00 1.90
619 623 9.325198 AGATTCAAATTACATCTACGTTGCATA 57.675 29.630 0.00 0.00 0.00 3.14
620 624 8.213518 AGATTCAAATTACATCTACGTTGCAT 57.786 30.769 0.00 0.00 0.00 3.96
621 625 7.609760 AGATTCAAATTACATCTACGTTGCA 57.390 32.000 0.00 0.00 0.00 4.08
626 630 8.262588 CGTCAGAAGATTCAAATTACATCTACG 58.737 37.037 0.00 0.00 0.00 3.51
632 636 5.351465 GCCTCGTCAGAAGATTCAAATTACA 59.649 40.000 0.00 0.00 0.00 2.41
656 663 5.232463 CCAAATCAGTTGAGGGTCAAAATG 58.768 41.667 0.00 0.00 38.22 2.32
657 664 4.284234 CCCAAATCAGTTGAGGGTCAAAAT 59.716 41.667 0.00 0.00 38.22 1.82
664 671 0.040204 AGGCCCAAATCAGTTGAGGG 59.960 55.000 0.00 0.00 39.87 4.30
669 676 1.194121 GCCCAAGGCCCAAATCAGTT 61.194 55.000 0.00 0.00 44.06 3.16
705 715 7.461677 CGACGAGAAGCATCTAAAAGTAGAAAC 60.462 40.741 0.00 0.00 39.81 2.78
711 725 4.416620 CTCGACGAGAAGCATCTAAAAGT 58.583 43.478 20.25 0.00 35.54 2.66
735 749 3.244215 GGAGAAGACAATGATATGCCCGA 60.244 47.826 0.00 0.00 0.00 5.14
738 752 5.311265 TGATGGAGAAGACAATGATATGCC 58.689 41.667 0.00 0.00 0.00 4.40
752 766 1.623311 TCGCCAACTTCTGATGGAGAA 59.377 47.619 0.00 0.00 40.66 2.87
761 775 1.148310 CACACGATTCGCCAACTTCT 58.852 50.000 5.86 0.00 0.00 2.85
762 776 0.452784 GCACACGATTCGCCAACTTC 60.453 55.000 5.86 0.00 0.00 3.01
793 807 9.127277 GAGAGATTAGAACTAGTGGATTACAGT 57.873 37.037 0.00 0.00 36.50 3.55
805 819 4.524053 TCTGTGCCGAGAGATTAGAACTA 58.476 43.478 0.00 0.00 0.00 2.24
817 831 0.891373 TTTCTCCTCTCTGTGCCGAG 59.109 55.000 0.00 0.00 0.00 4.63
818 832 0.891373 CTTTCTCCTCTCTGTGCCGA 59.109 55.000 0.00 0.00 0.00 5.54
822 840 3.587923 CTGCTTCTTTCTCCTCTCTGTG 58.412 50.000 0.00 0.00 0.00 3.66
860 878 5.940617 TCGGTCTTTATTCCATCATCCATT 58.059 37.500 0.00 0.00 0.00 3.16
861 879 5.513788 CCTCGGTCTTTATTCCATCATCCAT 60.514 44.000 0.00 0.00 0.00 3.41
909 927 4.290155 GTTTCAAGCTGAAAAGAATCGCA 58.710 39.130 11.33 0.00 46.53 5.10
911 929 4.772434 TCGTTTCAAGCTGAAAAGAATCG 58.228 39.130 17.72 13.71 46.36 3.34
932 950 2.211353 AGCTTCCGCGAGAATAGTTC 57.789 50.000 8.23 0.00 42.32 3.01
980 1035 0.739813 GGATCGTTCCTTCACCGTGG 60.740 60.000 5.21 0.00 39.14 4.94
981 1036 0.037697 TGGATCGTTCCTTCACCGTG 60.038 55.000 13.55 0.00 43.07 4.94
988 1043 0.331278 TTGGCCATGGATCGTTCCTT 59.669 50.000 18.40 4.66 43.07 3.36
1221 1278 1.566018 AAGCTACGCGAAGGTGCAAC 61.566 55.000 15.93 0.00 34.15 4.17
1228 1285 1.143969 CCCGGTAAAGCTACGCGAAG 61.144 60.000 15.93 0.00 0.00 3.79
1265 1341 0.776810 TTGGGGTTCTTCCTGCATCA 59.223 50.000 0.00 0.00 36.25 3.07
2350 2443 2.162681 CAAGGACCCAACCATCTCAAC 58.837 52.381 0.00 0.00 0.00 3.18
2351 2444 1.547675 GCAAGGACCCAACCATCTCAA 60.548 52.381 0.00 0.00 0.00 3.02
2352 2445 0.038166 GCAAGGACCCAACCATCTCA 59.962 55.000 0.00 0.00 0.00 3.27
2353 2446 1.026718 CGCAAGGACCCAACCATCTC 61.027 60.000 0.00 0.00 0.00 2.75
2354 2447 1.002134 CGCAAGGACCCAACCATCT 60.002 57.895 0.00 0.00 0.00 2.90
2355 2448 3.590824 CGCAAGGACCCAACCATC 58.409 61.111 0.00 0.00 0.00 3.51
2441 2536 9.612066 TGCAGAAACATCTTATATTATGACACA 57.388 29.630 2.69 0.00 0.00 3.72
2444 2539 9.604626 GCTTGCAGAAACATCTTATATTATGAC 57.395 33.333 0.00 0.00 0.00 3.06
2445 2540 9.565090 AGCTTGCAGAAACATCTTATATTATGA 57.435 29.630 0.00 0.00 0.00 2.15
2487 2583 9.793259 TTTTCTCTGTTCCACAATATAAGACTT 57.207 29.630 0.00 0.00 0.00 3.01
2488 2584 9.965902 ATTTTCTCTGTTCCACAATATAAGACT 57.034 29.630 0.00 0.00 0.00 3.24
2526 2622 8.226819 AGAGACGACAACTTTGATATGATCTA 57.773 34.615 0.00 0.00 0.00 1.98
2532 2628 7.063544 GCAAGTTAGAGACGACAACTTTGATAT 59.936 37.037 0.00 0.00 39.78 1.63
2534 2630 5.177696 GCAAGTTAGAGACGACAACTTTGAT 59.822 40.000 0.00 0.00 39.78 2.57
2537 2633 4.439057 TGCAAGTTAGAGACGACAACTTT 58.561 39.130 0.00 0.00 39.78 2.66
2540 2636 3.123621 CCATGCAAGTTAGAGACGACAAC 59.876 47.826 0.00 0.00 0.00 3.32
2541 2637 3.325870 CCATGCAAGTTAGAGACGACAA 58.674 45.455 0.00 0.00 0.00 3.18
2542 2638 2.930887 GCCATGCAAGTTAGAGACGACA 60.931 50.000 0.00 0.00 0.00 4.35
2563 2659 9.582431 TTTTCTTTATAGTCAATGGTAGAGACG 57.418 33.333 0.00 0.00 37.36 4.18
2569 2665 9.196139 CCCCAATTTTCTTTATAGTCAATGGTA 57.804 33.333 0.00 0.00 0.00 3.25
2585 2683 4.285775 TGGATTTGGTCTTCCCCAATTTTC 59.714 41.667 0.00 0.00 43.77 2.29
2595 2693 1.808411 TGCGAGTGGATTTGGTCTTC 58.192 50.000 0.00 0.00 0.00 2.87
2695 2793 5.946377 CCATAAGCCTTGGTTTTTAGTCTCT 59.054 40.000 0.00 0.00 0.00 3.10
2708 2806 7.396540 AACTAGATTCAAACCATAAGCCTTG 57.603 36.000 0.00 0.00 0.00 3.61
2873 2973 2.235016 CAATTTGTTTCCCGAGGTCCA 58.765 47.619 0.00 0.00 0.00 4.02
2881 2981 5.003160 CCCAAATCTTCCAATTTGTTTCCC 58.997 41.667 8.15 0.00 42.50 3.97
2887 2987 3.752747 GCAACCCCAAATCTTCCAATTTG 59.247 43.478 3.02 3.02 43.28 2.32
2904 3022 8.518702 AGAAAGATTAGATTTCTTCAAGCAACC 58.481 33.333 0.00 0.00 42.86 3.77
2932 3050 0.180171 TCCTGCCATATTGGTCACCG 59.820 55.000 0.00 0.00 40.46 4.94
2959 3077 7.182060 AGATATGAAAGAAAGCCCTTTTGGTA 58.818 34.615 0.00 0.00 36.58 3.25
2961 3079 6.535963 AGATATGAAAGAAAGCCCTTTTGG 57.464 37.500 0.00 0.00 36.58 3.28
2989 3107 7.389330 TGTTATGCGAAACTAAAATCTTCCTCA 59.611 33.333 0.00 0.00 0.00 3.86
3020 3138 2.361757 CTGCAACAATCACCTTTCACCA 59.638 45.455 0.00 0.00 0.00 4.17
3069 3187 2.505407 CCCCCTTTTCCCATTTTCCATC 59.495 50.000 0.00 0.00 0.00 3.51
3093 3211 8.048514 TGTTTAAAAGTGTACATAGTATCCCCC 58.951 37.037 0.00 0.00 0.00 5.40
3191 3309 2.494059 CTCCTTCTCGCCAAACAAAGA 58.506 47.619 0.00 0.00 0.00 2.52
3215 3333 3.986996 TCAGCTCCACATCATTCTTCA 57.013 42.857 0.00 0.00 0.00 3.02
3216 3334 4.511527 TCTTCAGCTCCACATCATTCTTC 58.488 43.478 0.00 0.00 0.00 2.87
3231 3358 7.066766 ACCATCTTCTGATAAACATTCTTCAGC 59.933 37.037 0.00 0.00 36.41 4.26


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

AutoCloner maintained by Alex Coulton.