Multiple sequence alignment - TraesCS4A01G406000

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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 TraesCS4A01G406000 chr4A 100.000 3416 0 0 1 3416 679076539 679073124 0.000000e+00 6309
1 TraesCS4A01G406000 chr4D 91.702 3049 159 31 114 3131 472166651 472163666 0.000000e+00 4143
2 TraesCS4A01G406000 chr4D 89.552 268 24 3 3136 3402 472163473 472163209 1.520000e-88 337
3 TraesCS4A01G406000 chr4B 88.771 3028 224 57 112 3087 594359705 594356742 0.000000e+00 3602
4 TraesCS4A01G406000 chr7D 94.331 829 32 2 1338 2166 538599681 538598868 0.000000e+00 1256
5 TraesCS4A01G406000 chr7D 94.951 713 33 1 1454 2166 159703171 159703880 0.000000e+00 1114
6 TraesCS4A01G406000 chr7D 93.798 129 8 0 1395 1523 137915408 137915536 9.670000e-46 195
7 TraesCS4A01G406000 chr2D 95.481 686 31 0 1444 2129 442056969 442056284 0.000000e+00 1096
8 TraesCS4A01G406000 chr3D 93.607 610 35 2 1557 2166 320413817 320413212 0.000000e+00 907
9 TraesCS4A01G406000 chr2A 91.610 584 46 1 1583 2166 85584677 85585257 0.000000e+00 804
10 TraesCS4A01G406000 chr2A 92.667 150 11 0 1438 1587 85537649 85537798 2.060000e-52 217
11 TraesCS4A01G406000 chr1B 91.473 129 11 0 1395 1523 167949602 167949474 9.740000e-41 178
12 TraesCS4A01G406000 chr6D 90.769 130 12 0 1395 1524 157661293 157661164 1.260000e-39 174


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 TraesCS4A01G406000 chr4A 679073124 679076539 3415 True 6309 6309 100.000 1 3416 1 chr4A.!!$R1 3415
1 TraesCS4A01G406000 chr4D 472163209 472166651 3442 True 2240 4143 90.627 114 3402 2 chr4D.!!$R1 3288
2 TraesCS4A01G406000 chr4B 594356742 594359705 2963 True 3602 3602 88.771 112 3087 1 chr4B.!!$R1 2975
3 TraesCS4A01G406000 chr7D 538598868 538599681 813 True 1256 1256 94.331 1338 2166 1 chr7D.!!$R1 828
4 TraesCS4A01G406000 chr7D 159703171 159703880 709 False 1114 1114 94.951 1454 2166 1 chr7D.!!$F2 712
5 TraesCS4A01G406000 chr2D 442056284 442056969 685 True 1096 1096 95.481 1444 2129 1 chr2D.!!$R1 685
6 TraesCS4A01G406000 chr3D 320413212 320413817 605 True 907 907 93.607 1557 2166 1 chr3D.!!$R1 609
7 TraesCS4A01G406000 chr2A 85584677 85585257 580 False 804 804 91.610 1583 2166 1 chr2A.!!$F2 583

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
743 770 0.034574 TCAGTGCCACCAGTTGTGTT 60.035 50.0 0.0 0.0 43.85 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2721 2779 0.036105 TGCTGTCTAGTGTGGGCATG 60.036 55.0 0.0 0.0 0.0 4.06 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
35 36 3.869272 CTGGCGGCGCTCATGAAC 61.869 66.667 32.30 13.58 0.00 3.18
38 39 3.264897 GCGGCGCTCATGAACGAT 61.265 61.111 26.86 0.00 0.00 3.73
39 40 2.622629 CGGCGCTCATGAACGATG 59.377 61.111 22.00 9.10 0.00 3.84
40 41 2.325857 GGCGCTCATGAACGATGC 59.674 61.111 22.00 8.21 31.32 3.91
41 42 2.325857 GCGCTCATGAACGATGCC 59.674 61.111 22.00 0.49 31.32 4.40
42 43 2.176273 GCGCTCATGAACGATGCCT 61.176 57.895 22.00 0.00 31.32 4.75
43 44 1.709147 GCGCTCATGAACGATGCCTT 61.709 55.000 22.00 0.00 31.32 4.35
44 45 0.302890 CGCTCATGAACGATGCCTTC 59.697 55.000 13.15 0.00 31.32 3.46
45 46 0.659957 GCTCATGAACGATGCCTTCC 59.340 55.000 0.00 0.00 31.32 3.46
46 47 2.013563 GCTCATGAACGATGCCTTCCA 61.014 52.381 0.00 0.00 31.32 3.53
47 48 1.938577 CTCATGAACGATGCCTTCCAG 59.061 52.381 0.00 0.00 31.32 3.86
48 49 1.554617 TCATGAACGATGCCTTCCAGA 59.445 47.619 0.00 0.00 31.32 3.86
49 50 1.938577 CATGAACGATGCCTTCCAGAG 59.061 52.381 0.00 0.00 0.00 3.35
50 51 0.391661 TGAACGATGCCTTCCAGAGC 60.392 55.000 0.00 0.00 0.00 4.09
51 52 0.107945 GAACGATGCCTTCCAGAGCT 60.108 55.000 0.00 0.00 0.00 4.09
52 53 0.107945 AACGATGCCTTCCAGAGCTC 60.108 55.000 5.27 5.27 0.00 4.09
53 54 1.227497 CGATGCCTTCCAGAGCTCC 60.227 63.158 10.93 0.00 0.00 4.70
54 55 1.148048 GATGCCTTCCAGAGCTCCC 59.852 63.158 10.93 0.00 0.00 4.30
55 56 2.657102 GATGCCTTCCAGAGCTCCCG 62.657 65.000 10.93 1.35 0.00 5.14
56 57 4.168291 GCCTTCCAGAGCTCCCGG 62.168 72.222 10.93 11.94 0.00 5.73
57 58 4.168291 CCTTCCAGAGCTCCCGGC 62.168 72.222 10.93 0.00 42.19 6.13
58 59 4.168291 CTTCCAGAGCTCCCGGCC 62.168 72.222 10.93 0.00 43.05 6.13
63 64 4.541648 AGAGCTCCCGGCCGGTAT 62.542 66.667 40.52 23.95 43.05 2.73
64 65 4.301027 GAGCTCCCGGCCGGTATG 62.301 72.222 40.52 29.13 43.05 2.39
67 68 4.910585 CTCCCGGCCGGTATGCAC 62.911 72.222 40.52 0.00 0.00 4.57
70 71 4.769063 CCGGCCGGTATGCACACA 62.769 66.667 36.64 0.00 0.00 3.72
71 72 3.496131 CGGCCGGTATGCACACAC 61.496 66.667 20.10 0.00 0.00 3.82
72 73 2.359354 GGCCGGTATGCACACACA 60.359 61.111 1.90 0.00 0.00 3.72
73 74 2.686816 GGCCGGTATGCACACACAC 61.687 63.158 1.90 0.00 0.00 3.82
74 75 1.963855 GCCGGTATGCACACACACA 60.964 57.895 1.90 0.00 0.00 3.72
75 76 1.866237 CCGGTATGCACACACACAC 59.134 57.895 0.00 0.00 0.00 3.82
76 77 0.882484 CCGGTATGCACACACACACA 60.882 55.000 0.00 0.00 0.00 3.72
77 78 0.234625 CGGTATGCACACACACACAC 59.765 55.000 0.00 0.00 0.00 3.82
78 79 1.304254 GGTATGCACACACACACACA 58.696 50.000 0.00 0.00 0.00 3.72
79 80 1.002900 GGTATGCACACACACACACAC 60.003 52.381 0.00 0.00 0.00 3.82
80 81 1.668237 GTATGCACACACACACACACA 59.332 47.619 0.00 0.00 0.00 3.72
81 82 0.451383 ATGCACACACACACACACAC 59.549 50.000 0.00 0.00 0.00 3.82
82 83 0.886490 TGCACACACACACACACACA 60.886 50.000 0.00 0.00 0.00 3.72
83 84 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
84 85 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
85 86 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
86 87 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
87 88 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
88 89 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
89 90 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
90 91 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
91 92 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
92 93 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
93 94 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
94 95 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
95 96 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
96 97 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
97 98 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
98 99 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
99 100 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
100 101 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
101 102 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
102 103 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
103 104 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
104 105 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
105 106 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
106 107 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
107 108 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
108 109 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
109 110 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
110 111 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
128 129 0.586319 CACACACACACATTCGTCCC 59.414 55.000 0.00 0.00 0.00 4.46
146 147 2.022195 CCCTCTGTCATGCAAAGATGG 58.978 52.381 0.00 0.00 0.00 3.51
147 148 2.356432 CCCTCTGTCATGCAAAGATGGA 60.356 50.000 0.00 0.00 29.84 3.41
168 169 2.479566 TTCACTTCCTGACATGGCTC 57.520 50.000 0.00 0.00 0.00 4.70
311 312 0.322816 TGAAGCCCAAGCAGGACATC 60.323 55.000 0.00 0.00 43.56 3.06
389 408 5.667539 TCGAGAGGTTTTGATTCAGAGAT 57.332 39.130 0.00 0.00 0.00 2.75
394 413 8.721478 CGAGAGGTTTTGATTCAGAGATTTTTA 58.279 33.333 0.00 0.00 0.00 1.52
396 415 9.354673 AGAGGTTTTGATTCAGAGATTTTTACA 57.645 29.630 0.00 0.00 0.00 2.41
398 417 9.918630 AGGTTTTGATTCAGAGATTTTTACATG 57.081 29.630 0.00 0.00 0.00 3.21
399 418 9.696917 GGTTTTGATTCAGAGATTTTTACATGT 57.303 29.630 2.69 2.69 0.00 3.21
403 422 9.681692 TTGATTCAGAGATTTTTACATGTGTTG 57.318 29.630 9.11 0.00 0.00 3.33
405 424 9.121517 GATTCAGAGATTTTTACATGTGTTGTG 57.878 33.333 9.11 0.00 39.48 3.33
408 427 6.857964 CAGAGATTTTTACATGTGTTGTGGTC 59.142 38.462 9.11 0.00 39.48 4.02
410 429 7.936847 AGAGATTTTTACATGTGTTGTGGTCTA 59.063 33.333 9.11 0.00 39.48 2.59
411 430 8.635765 AGATTTTTACATGTGTTGTGGTCTAT 57.364 30.769 9.11 0.00 39.48 1.98
419 438 4.724399 TGTGTTGTGGTCTATTTGGACAT 58.276 39.130 0.00 0.00 37.91 3.06
420 439 4.518590 TGTGTTGTGGTCTATTTGGACATG 59.481 41.667 0.00 0.00 37.91 3.21
484 503 2.100631 CGAGGACATCAACACGGCC 61.101 63.158 0.00 0.00 0.00 6.13
548 567 2.161855 GGATGGACAAGTGACAATGCA 58.838 47.619 0.00 0.00 0.00 3.96
549 568 2.557924 GGATGGACAAGTGACAATGCAA 59.442 45.455 0.00 0.00 0.00 4.08
551 570 1.680735 TGGACAAGTGACAATGCAACC 59.319 47.619 0.00 0.00 0.00 3.77
556 575 3.181487 ACAAGTGACAATGCAACCTGAAC 60.181 43.478 0.00 0.00 0.00 3.18
561 580 2.622942 GACAATGCAACCTGAACCTGAA 59.377 45.455 0.00 0.00 0.00 3.02
562 581 3.030291 ACAATGCAACCTGAACCTGAAA 58.970 40.909 0.00 0.00 0.00 2.69
563 582 3.450457 ACAATGCAACCTGAACCTGAAAA 59.550 39.130 0.00 0.00 0.00 2.29
564 583 3.733443 ATGCAACCTGAACCTGAAAAC 57.267 42.857 0.00 0.00 0.00 2.43
565 584 1.754226 TGCAACCTGAACCTGAAAACC 59.246 47.619 0.00 0.00 0.00 3.27
566 585 1.754226 GCAACCTGAACCTGAAAACCA 59.246 47.619 0.00 0.00 0.00 3.67
568 587 3.799917 GCAACCTGAACCTGAAAACCATG 60.800 47.826 0.00 0.00 0.00 3.66
569 588 1.963515 ACCTGAACCTGAAAACCATGC 59.036 47.619 0.00 0.00 0.00 4.06
570 589 1.962807 CCTGAACCTGAAAACCATGCA 59.037 47.619 0.00 0.00 0.00 3.96
571 590 2.288395 CCTGAACCTGAAAACCATGCAC 60.288 50.000 0.00 0.00 0.00 4.57
572 591 2.361757 CTGAACCTGAAAACCATGCACA 59.638 45.455 0.00 0.00 0.00 4.57
573 592 2.100584 TGAACCTGAAAACCATGCACAC 59.899 45.455 0.00 0.00 0.00 3.82
576 595 1.000060 CCTGAAAACCATGCACACAGG 60.000 52.381 0.00 0.00 37.63 4.00
577 596 0.388659 TGAAAACCATGCACACAGGC 59.611 50.000 0.00 0.00 0.00 4.85
578 597 0.675633 GAAAACCATGCACACAGGCT 59.324 50.000 0.00 0.00 34.04 4.58
579 598 0.390124 AAAACCATGCACACAGGCTG 59.610 50.000 14.16 14.16 34.04 4.85
580 599 0.756442 AAACCATGCACACAGGCTGT 60.756 50.000 15.88 15.88 34.04 4.40
581 600 0.756442 AACCATGCACACAGGCTGTT 60.756 50.000 19.43 6.96 34.04 3.16
582 601 1.174712 ACCATGCACACAGGCTGTTC 61.175 55.000 19.43 10.69 34.04 3.18
583 602 1.208358 CATGCACACAGGCTGTTCG 59.792 57.895 19.43 13.00 34.04 3.95
584 603 2.620112 ATGCACACAGGCTGTTCGC 61.620 57.895 24.29 24.29 38.13 4.70
585 604 2.974698 GCACACAGGCTGTTCGCT 60.975 61.111 23.95 4.78 39.13 4.93
586 605 2.959357 GCACACAGGCTGTTCGCTC 61.959 63.158 23.95 8.15 39.13 5.03
587 606 2.356313 ACACAGGCTGTTCGCTCG 60.356 61.111 19.43 8.20 39.13 5.03
588 607 2.049156 CACAGGCTGTTCGCTCGA 60.049 61.111 19.43 0.00 39.13 4.04
589 608 2.091112 CACAGGCTGTTCGCTCGAG 61.091 63.158 19.43 8.45 39.13 4.04
590 609 2.259818 CAGGCTGTTCGCTCGAGT 59.740 61.111 15.13 0.00 39.13 4.18
591 610 1.373497 CAGGCTGTTCGCTCGAGTT 60.373 57.895 15.13 0.00 39.13 3.01
592 611 0.946221 CAGGCTGTTCGCTCGAGTTT 60.946 55.000 15.13 0.00 39.13 2.66
593 612 0.946221 AGGCTGTTCGCTCGAGTTTG 60.946 55.000 15.13 4.71 39.13 2.93
594 613 1.154580 GCTGTTCGCTCGAGTTTGC 60.155 57.895 15.13 6.74 35.14 3.68
621 640 6.208402 TGCTGCTCATTCCAGTACAAAATAAA 59.792 34.615 0.00 0.00 32.93 1.40
623 642 7.761249 GCTGCTCATTCCAGTACAAAATAAATT 59.239 33.333 0.00 0.00 32.93 1.82
624 643 9.643693 CTGCTCATTCCAGTACAAAATAAATTT 57.356 29.630 0.00 0.00 0.00 1.82
685 707 3.305267 GCATGTGTTGACTTAATGTGCCA 60.305 43.478 0.00 0.00 0.00 4.92
687 709 4.991153 TGTGTTGACTTAATGTGCCAAA 57.009 36.364 0.00 0.00 0.00 3.28
689 711 4.202101 TGTGTTGACTTAATGTGCCAAAGG 60.202 41.667 0.00 0.00 0.00 3.11
707 729 0.744771 GGAACTTCATCCCTCCGTGC 60.745 60.000 0.00 0.00 33.05 5.34
710 732 1.794714 ACTTCATCCCTCCGTGCTAT 58.205 50.000 0.00 0.00 0.00 2.97
729 751 7.404985 GTGCTATACTTCATTGTTCATCAGTG 58.595 38.462 0.00 0.00 35.51 3.66
743 770 0.034574 TCAGTGCCACCAGTTGTGTT 60.035 50.000 0.00 0.00 43.85 3.32
749 776 2.021457 GCCACCAGTTGTGTTAACTGT 58.979 47.619 16.00 4.70 44.52 3.55
782 809 3.244078 TGTCTGTCTCCGTTAGTGCAATT 60.244 43.478 0.00 0.00 0.00 2.32
783 810 3.368236 GTCTGTCTCCGTTAGTGCAATTC 59.632 47.826 0.00 0.00 0.00 2.17
833 862 0.721718 GTCTCGGCCGTGATCTTTTG 59.278 55.000 30.35 8.87 0.00 2.44
879 909 6.206634 TCACATGTTCCTAAACCAAAGCTAAG 59.793 38.462 0.00 0.00 34.28 2.18
921 951 3.298320 GCCCAAATTTAGGCTCCCA 57.702 52.632 19.01 0.00 46.14 4.37
922 952 1.567357 GCCCAAATTTAGGCTCCCAA 58.433 50.000 19.01 0.00 46.14 4.12
945 975 4.323569 TCCCAGCCACATATTTACCAAA 57.676 40.909 0.00 0.00 0.00 3.28
947 977 3.132111 CCCAGCCACATATTTACCAAACC 59.868 47.826 0.00 0.00 0.00 3.27
950 980 5.197451 CAGCCACATATTTACCAAACCCTA 58.803 41.667 0.00 0.00 0.00 3.53
951 981 5.299279 CAGCCACATATTTACCAAACCCTAG 59.701 44.000 0.00 0.00 0.00 3.02
988 1018 2.158740 GCACCTCCCTCTTTTATCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
1010 1040 2.102578 CTTCCCCCACATGCCTAAAAG 58.897 52.381 0.00 0.00 0.00 2.27
1052 1082 0.811616 CACCGTTATGGCCTGAGAGC 60.812 60.000 3.32 0.00 43.94 4.09
1056 1086 1.269517 CGTTATGGCCTGAGAGCTCTC 60.270 57.143 32.73 32.73 43.15 3.20
1302 1342 3.318555 CGCATGCTCGAGTCGCTC 61.319 66.667 17.13 2.16 0.00 5.03
1365 1405 4.570663 GAGGCCCGGATCGACGTG 62.571 72.222 0.73 0.00 0.00 4.49
2171 2211 4.194720 GACGCCGACGGATCAGCT 62.195 66.667 20.50 0.00 46.04 4.24
2271 2311 1.380650 GGAGAGCTTCGAGGGGTCT 60.381 63.158 17.72 17.72 43.06 3.85
2483 2525 4.657013 TGTACAATGTCCTTGGTATTGCA 58.343 39.130 14.39 0.00 39.30 4.08
2484 2526 4.457603 TGTACAATGTCCTTGGTATTGCAC 59.542 41.667 14.39 13.05 39.30 4.57
2485 2527 3.766545 ACAATGTCCTTGGTATTGCACT 58.233 40.909 14.39 0.00 39.30 4.40
2486 2528 4.917385 ACAATGTCCTTGGTATTGCACTA 58.083 39.130 14.39 0.00 39.30 2.74
2487 2529 5.509498 ACAATGTCCTTGGTATTGCACTAT 58.491 37.500 14.39 0.00 39.30 2.12
2488 2530 5.951747 ACAATGTCCTTGGTATTGCACTATT 59.048 36.000 14.39 0.00 39.30 1.73
2489 2531 6.127647 ACAATGTCCTTGGTATTGCACTATTG 60.128 38.462 14.39 0.00 39.30 1.90
2490 2532 9.447596 ACAATGTCCTTGGTATTGCACTATTGC 62.448 40.741 14.39 0.00 43.31 3.56
2547 2590 1.164041 GGTGGGCGGGATATTTCGTG 61.164 60.000 0.00 0.00 0.00 4.35
2548 2591 0.179067 GTGGGCGGGATATTTCGTGA 60.179 55.000 0.00 0.00 0.00 4.35
2581 2624 8.296713 TGATAAAAATTGCTCTTGTAAGTGACC 58.703 33.333 0.00 0.00 0.00 4.02
2642 2688 0.393267 TATTTTACAGCGCCGGCCTT 60.393 50.000 23.46 6.11 41.24 4.35
2643 2689 1.654023 ATTTTACAGCGCCGGCCTTC 61.654 55.000 23.46 10.59 41.24 3.46
2644 2690 2.741486 TTTTACAGCGCCGGCCTTCT 62.741 55.000 23.46 13.00 41.24 2.85
2645 2691 3.659089 TTACAGCGCCGGCCTTCTC 62.659 63.158 23.46 4.96 41.24 2.87
2674 2732 0.541063 TGTCAAGCCCGAGGTGAGTA 60.541 55.000 0.00 0.00 0.00 2.59
2698 2756 3.423996 TTGTTTGTAACGGAGGCAAAC 57.576 42.857 15.29 15.29 46.95 2.93
2720 2778 2.993899 GTTGTACCCTGTCTCATTCACG 59.006 50.000 0.00 0.00 0.00 4.35
2721 2779 1.067142 TGTACCCTGTCTCATTCACGC 60.067 52.381 0.00 0.00 0.00 5.34
2730 2788 1.303155 TCATTCACGCATGCCCACA 60.303 52.632 13.15 0.00 0.00 4.17
2765 2823 4.488879 GAACATGAAATTCTCCAAGGCAC 58.511 43.478 0.00 0.00 0.00 5.01
2778 2836 0.468226 AAGGCACACTCTCGACCAAA 59.532 50.000 0.00 0.00 0.00 3.28
2798 2856 9.821662 GACCAAACTATCTTACAACAAATACAC 57.178 33.333 0.00 0.00 0.00 2.90
2839 2918 8.621286 CAAGATAAATAAACGGCAGAGGTTATT 58.379 33.333 0.00 0.00 0.00 1.40
2843 2922 1.722011 AACGGCAGAGGTTATTGTCG 58.278 50.000 0.00 0.00 46.92 4.35
2853 2932 2.496470 AGGTTATTGTCGTCACTCCTCC 59.504 50.000 0.00 0.00 0.00 4.30
2889 2968 1.190984 CGATTTCATCATCGGCGACAG 59.809 52.381 13.76 8.50 42.03 3.51
2902 2981 1.675310 CGACAGCCAATGAAGCCCA 60.675 57.895 0.00 0.00 0.00 5.36
2908 2987 1.891722 GCCAATGAAGCCCACCCAAG 61.892 60.000 0.00 0.00 0.00 3.61
2909 2988 0.542702 CCAATGAAGCCCACCCAAGT 60.543 55.000 0.00 0.00 0.00 3.16
2910 2989 0.890683 CAATGAAGCCCACCCAAGTC 59.109 55.000 0.00 0.00 0.00 3.01
2912 2991 1.142688 ATGAAGCCCACCCAAGTCCT 61.143 55.000 0.00 0.00 0.00 3.85
2919 2999 1.519408 CCACCCAAGTCCTAACAACG 58.481 55.000 0.00 0.00 0.00 4.10
2941 3021 3.814577 GCGTGAAGCCACTCTAAGA 57.185 52.632 0.00 0.00 41.06 2.10
2968 3048 4.263727 ACCAAATAGTTGTCCACATAGGCA 60.264 41.667 1.80 0.00 32.40 4.75
2999 3082 0.949105 GGGTGTGTGCTTGAGTACGG 60.949 60.000 0.00 0.00 33.15 4.02
3084 3167 8.327271 CAAGGATCATTCTCATATACCAAGGAT 58.673 37.037 0.00 0.00 0.00 3.24
3087 3170 8.492782 GGATCATTCTCATATACCAAGGATCAT 58.507 37.037 12.63 0.00 37.65 2.45
3088 3171 9.545105 GATCATTCTCATATACCAAGGATCATC 57.455 37.037 0.00 0.00 36.51 2.92
3089 3172 7.855375 TCATTCTCATATACCAAGGATCATCC 58.145 38.462 0.00 0.00 36.58 3.51
3090 3173 6.627087 TTCTCATATACCAAGGATCATCCC 57.373 41.667 0.00 0.00 37.19 3.85
3091 3174 4.711846 TCTCATATACCAAGGATCATCCCG 59.288 45.833 0.00 0.00 37.19 5.14
3092 3175 4.683643 TCATATACCAAGGATCATCCCGA 58.316 43.478 0.00 0.00 37.19 5.14
3093 3176 5.090845 TCATATACCAAGGATCATCCCGAA 58.909 41.667 0.00 0.00 37.19 4.30
3094 3177 5.546110 TCATATACCAAGGATCATCCCGAAA 59.454 40.000 0.00 0.00 37.19 3.46
3101 3184 5.594317 CCAAGGATCATCCCGAAAACTATTT 59.406 40.000 0.00 0.00 37.19 1.40
3102 3185 6.096846 CCAAGGATCATCCCGAAAACTATTTT 59.903 38.462 0.00 0.00 37.19 1.82
3105 3188 6.543831 AGGATCATCCCGAAAACTATTTTGAG 59.456 38.462 0.00 0.00 37.19 3.02
3127 3210 2.165437 GGCATGGGCGAAAAGTTTATCA 59.835 45.455 0.00 0.00 42.47 2.15
3131 3214 2.040545 TGGGCGAAAAGTTTATCAGGGA 59.959 45.455 0.00 0.00 0.00 4.20
3133 3216 3.315470 GGGCGAAAAGTTTATCAGGGATC 59.685 47.826 0.00 0.00 0.00 3.36
3134 3217 3.945285 GGCGAAAAGTTTATCAGGGATCA 59.055 43.478 0.00 0.00 0.00 2.92
3148 3419 2.641815 AGGGATCATTCCAGGCTATGTC 59.358 50.000 0.00 0.00 44.60 3.06
3150 3421 2.613977 GGATCATTCCAGGCTATGTCGG 60.614 54.545 0.00 0.00 42.12 4.79
3152 3423 1.069765 ATTCCAGGCTATGTCGGCG 59.930 57.895 0.00 0.00 34.19 6.46
3154 3425 2.572095 TTCCAGGCTATGTCGGCGTG 62.572 60.000 6.85 0.00 42.76 5.34
3183 3454 7.023575 GTGTTCTTTCATACATTGGTGTGATC 58.976 38.462 0.00 0.00 43.45 2.92
3184 3455 6.150976 TGTTCTTTCATACATTGGTGTGATCC 59.849 38.462 0.00 0.00 43.45 3.36
3214 3485 3.494398 GCCTCGATTCATGCTAGGGTTAA 60.494 47.826 0.00 0.00 0.00 2.01
3215 3486 4.703897 CCTCGATTCATGCTAGGGTTAAA 58.296 43.478 0.00 0.00 0.00 1.52
3299 3570 1.904287 TGGCCACAACTGTTATGGAC 58.096 50.000 21.42 19.17 42.43 4.02
3302 3573 2.890945 GGCCACAACTGTTATGGACTTT 59.109 45.455 21.42 0.00 38.62 2.66
3312 3583 7.480760 ACTGTTATGGACTTTGCCAATATTT 57.519 32.000 0.00 0.00 42.16 1.40
3313 3584 7.547227 ACTGTTATGGACTTTGCCAATATTTC 58.453 34.615 0.00 0.00 42.16 2.17
3314 3585 7.397192 ACTGTTATGGACTTTGCCAATATTTCT 59.603 33.333 0.00 0.00 42.16 2.52
3380 3652 9.698309 TCAAAGAACAACATAACTTCAAACAAA 57.302 25.926 0.00 0.00 0.00 2.83
3402 3674 1.879575 TGGGTCTAGCTTGTAGGCAT 58.120 50.000 0.00 0.00 34.17 4.40
3403 3675 1.486310 TGGGTCTAGCTTGTAGGCATG 59.514 52.381 0.00 0.00 34.17 4.06
3404 3676 1.202698 GGGTCTAGCTTGTAGGCATGG 60.203 57.143 0.00 0.00 34.17 3.66
3405 3677 1.762957 GGTCTAGCTTGTAGGCATGGA 59.237 52.381 0.00 0.00 34.17 3.41
3406 3678 2.170607 GGTCTAGCTTGTAGGCATGGAA 59.829 50.000 0.00 0.00 34.17 3.53
3407 3679 3.370527 GGTCTAGCTTGTAGGCATGGAAA 60.371 47.826 0.00 0.00 34.17 3.13
3408 3680 3.873952 GTCTAGCTTGTAGGCATGGAAAG 59.126 47.826 0.00 0.00 34.17 2.62
3409 3681 2.134789 AGCTTGTAGGCATGGAAAGG 57.865 50.000 0.00 0.00 34.17 3.11
3410 3682 1.635487 AGCTTGTAGGCATGGAAAGGA 59.365 47.619 0.00 0.00 34.17 3.36
3411 3683 2.243221 AGCTTGTAGGCATGGAAAGGAT 59.757 45.455 0.00 0.00 34.17 3.24
3412 3684 2.360165 GCTTGTAGGCATGGAAAGGATG 59.640 50.000 0.00 0.00 0.00 3.51
3413 3685 2.057137 TGTAGGCATGGAAAGGATGC 57.943 50.000 0.00 0.00 44.65 3.91
3414 3686 1.565759 TGTAGGCATGGAAAGGATGCT 59.434 47.619 0.00 0.00 44.75 3.79
3415 3687 2.225467 GTAGGCATGGAAAGGATGCTC 58.775 52.381 0.00 0.00 44.75 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.869272 GTTCATGAGCGCCGCCAG 61.869 66.667 4.98 0.00 0.00 4.85
21 22 3.264897 ATCGTTCATGAGCGCCGC 61.265 61.111 25.04 0.00 34.98 6.53
22 23 2.622629 CATCGTTCATGAGCGCCG 59.377 61.111 25.04 14.99 33.80 6.46
23 24 2.325857 GCATCGTTCATGAGCGCC 59.674 61.111 25.04 12.86 33.80 6.53
24 25 1.709147 AAGGCATCGTTCATGAGCGC 61.709 55.000 25.04 12.45 33.80 5.92
25 26 0.302890 GAAGGCATCGTTCATGAGCG 59.697 55.000 24.06 24.06 33.80 5.03
26 27 0.659957 GGAAGGCATCGTTCATGAGC 59.340 55.000 0.00 0.00 33.80 4.26
27 28 1.938577 CTGGAAGGCATCGTTCATGAG 59.061 52.381 0.00 0.00 33.80 2.90
28 29 1.554617 TCTGGAAGGCATCGTTCATGA 59.445 47.619 0.00 0.00 33.80 3.07
29 30 1.938577 CTCTGGAAGGCATCGTTCATG 59.061 52.381 0.00 0.00 35.29 3.07
30 31 1.745141 GCTCTGGAAGGCATCGTTCAT 60.745 52.381 0.00 0.00 31.60 2.57
31 32 0.391661 GCTCTGGAAGGCATCGTTCA 60.392 55.000 0.00 0.00 31.60 3.18
32 33 0.107945 AGCTCTGGAAGGCATCGTTC 60.108 55.000 0.00 0.00 33.36 3.95
33 34 0.107945 GAGCTCTGGAAGGCATCGTT 60.108 55.000 6.43 0.00 33.36 3.85
34 35 1.519719 GAGCTCTGGAAGGCATCGT 59.480 57.895 6.43 0.00 33.36 3.73
35 36 1.227497 GGAGCTCTGGAAGGCATCG 60.227 63.158 14.64 0.00 33.36 3.84
36 37 1.148048 GGGAGCTCTGGAAGGCATC 59.852 63.158 14.64 0.00 33.36 3.91
37 38 2.739996 CGGGAGCTCTGGAAGGCAT 61.740 63.158 14.64 0.00 33.36 4.40
38 39 3.393970 CGGGAGCTCTGGAAGGCA 61.394 66.667 14.64 0.00 33.36 4.75
39 40 4.168291 CCGGGAGCTCTGGAAGGC 62.168 72.222 14.64 0.00 44.90 4.35
40 41 4.168291 GCCGGGAGCTCTGGAAGG 62.168 72.222 24.09 16.02 44.90 3.46
41 42 4.168291 GGCCGGGAGCTCTGGAAG 62.168 72.222 24.09 7.39 44.90 3.46
46 47 4.541648 ATACCGGCCGGGAGCTCT 62.542 66.667 44.99 27.21 43.05 4.09
47 48 4.301027 CATACCGGCCGGGAGCTC 62.301 72.222 44.99 4.71 43.05 4.09
50 51 4.910585 GTGCATACCGGCCGGGAG 62.911 72.222 44.99 33.36 39.97 4.30
53 54 4.769063 TGTGTGCATACCGGCCGG 62.769 66.667 42.17 42.17 42.03 6.13
54 55 3.496131 GTGTGTGCATACCGGCCG 61.496 66.667 21.04 21.04 0.00 6.13
55 56 2.359354 TGTGTGTGCATACCGGCC 60.359 61.111 11.39 0.00 0.00 6.13
56 57 1.963855 TGTGTGTGTGCATACCGGC 60.964 57.895 11.39 2.38 36.12 6.13
57 58 0.882484 TGTGTGTGTGTGCATACCGG 60.882 55.000 11.39 0.00 36.12 5.28
58 59 0.234625 GTGTGTGTGTGTGCATACCG 59.765 55.000 11.39 0.00 36.12 4.02
59 60 1.002900 GTGTGTGTGTGTGTGCATACC 60.003 52.381 11.39 3.32 36.12 2.73
60 61 1.668237 TGTGTGTGTGTGTGTGCATAC 59.332 47.619 6.65 6.65 37.26 2.39
61 62 1.668237 GTGTGTGTGTGTGTGTGCATA 59.332 47.619 0.00 0.00 0.00 3.14
62 63 0.451383 GTGTGTGTGTGTGTGTGCAT 59.549 50.000 0.00 0.00 0.00 3.96
63 64 0.886490 TGTGTGTGTGTGTGTGTGCA 60.886 50.000 0.00 0.00 0.00 4.57
64 65 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
65 66 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
66 67 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
67 68 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
68 69 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
69 70 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
70 71 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
71 72 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
72 73 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
73 74 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
74 75 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
75 76 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
76 77 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
77 78 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
78 79 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
79 80 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
80 81 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
81 82 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
82 83 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
83 84 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
84 85 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
85 86 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
86 87 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
87 88 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
88 89 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
89 90 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
90 91 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
91 92 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
92 93 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
93 94 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
94 95 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
95 96 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
96 97 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
97 98 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
98 99 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
99 100 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
100 101 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
101 102 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
102 103 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
103 104 2.784505 GAATGTGTGTGTGTGTGTGTG 58.215 47.619 0.00 0.00 0.00 3.82
104 105 1.396648 CGAATGTGTGTGTGTGTGTGT 59.603 47.619 0.00 0.00 0.00 3.72
105 106 1.396648 ACGAATGTGTGTGTGTGTGTG 59.603 47.619 0.00 0.00 0.00 3.82
106 107 1.663643 GACGAATGTGTGTGTGTGTGT 59.336 47.619 0.00 0.00 0.00 3.72
107 108 1.003972 GGACGAATGTGTGTGTGTGTG 60.004 52.381 0.00 0.00 0.00 3.82
108 109 1.295792 GGACGAATGTGTGTGTGTGT 58.704 50.000 0.00 0.00 0.00 3.72
109 110 0.586319 GGGACGAATGTGTGTGTGTG 59.414 55.000 0.00 0.00 0.00 3.82
110 111 0.468226 AGGGACGAATGTGTGTGTGT 59.532 50.000 0.00 0.00 0.00 3.72
128 129 5.124936 TGAAATCCATCTTTGCATGACAGAG 59.875 40.000 0.00 0.00 0.00 3.35
146 147 3.350833 AGCCATGTCAGGAAGTGAAATC 58.649 45.455 0.00 0.00 36.74 2.17
147 148 3.009916 AGAGCCATGTCAGGAAGTGAAAT 59.990 43.478 0.00 0.00 36.74 2.17
377 396 9.681692 CAACACATGTAAAAATCTCTGAATCAA 57.318 29.630 0.00 0.00 0.00 2.57
389 408 7.923344 CCAAATAGACCACAACACATGTAAAAA 59.077 33.333 0.00 0.00 41.46 1.94
394 413 4.518970 GTCCAAATAGACCACAACACATGT 59.481 41.667 0.00 0.00 45.34 3.21
396 415 4.724399 TGTCCAAATAGACCACAACACAT 58.276 39.130 0.00 0.00 35.83 3.21
397 416 4.157849 TGTCCAAATAGACCACAACACA 57.842 40.909 0.00 0.00 35.83 3.72
398 417 4.759693 TCATGTCCAAATAGACCACAACAC 59.240 41.667 0.00 0.00 35.83 3.32
399 418 4.759693 GTCATGTCCAAATAGACCACAACA 59.240 41.667 0.00 0.00 35.83 3.33
400 419 4.759693 TGTCATGTCCAAATAGACCACAAC 59.240 41.667 0.00 0.00 35.83 3.32
401 420 4.979335 TGTCATGTCCAAATAGACCACAA 58.021 39.130 0.00 0.00 35.83 3.33
403 422 3.941483 CCTGTCATGTCCAAATAGACCAC 59.059 47.826 0.00 0.00 35.83 4.16
405 424 4.446371 CTCCTGTCATGTCCAAATAGACC 58.554 47.826 0.00 0.00 35.83 3.85
408 427 3.875727 CAGCTCCTGTCATGTCCAAATAG 59.124 47.826 0.00 0.00 0.00 1.73
410 429 2.619849 CCAGCTCCTGTCATGTCCAAAT 60.620 50.000 0.00 0.00 0.00 2.32
411 430 1.271543 CCAGCTCCTGTCATGTCCAAA 60.272 52.381 0.00 0.00 0.00 3.28
460 479 1.519455 GTTGATGTCCTCGAGGCCG 60.519 63.158 27.39 3.42 34.44 6.13
467 486 0.321653 AAGGCCGTGTTGATGTCCTC 60.322 55.000 0.00 0.00 0.00 3.71
548 567 2.365293 GCATGGTTTTCAGGTTCAGGTT 59.635 45.455 0.00 0.00 0.00 3.50
549 568 1.963515 GCATGGTTTTCAGGTTCAGGT 59.036 47.619 0.00 0.00 0.00 4.00
551 570 2.361757 TGTGCATGGTTTTCAGGTTCAG 59.638 45.455 0.00 0.00 0.00 3.02
556 575 1.000060 CCTGTGTGCATGGTTTTCAGG 60.000 52.381 0.00 0.00 35.72 3.86
561 580 0.756442 ACAGCCTGTGTGCATGGTTT 60.756 50.000 0.00 0.00 38.28 3.27
562 581 0.756442 AACAGCCTGTGTGCATGGTT 60.756 50.000 0.00 0.00 40.26 3.67
563 582 1.152694 AACAGCCTGTGTGCATGGT 60.153 52.632 0.00 0.00 40.26 3.55
564 583 1.582968 GAACAGCCTGTGTGCATGG 59.417 57.895 0.00 0.00 40.26 3.66
565 584 1.208358 CGAACAGCCTGTGTGCATG 59.792 57.895 0.00 0.00 40.26 4.06
566 585 2.620112 GCGAACAGCCTGTGTGCAT 61.620 57.895 14.59 0.00 40.26 3.96
577 596 0.861837 AAGCAAACTCGAGCGAACAG 59.138 50.000 13.61 0.00 35.48 3.16
578 597 0.581529 CAAGCAAACTCGAGCGAACA 59.418 50.000 13.61 0.00 35.48 3.18
579 598 0.722799 GCAAGCAAACTCGAGCGAAC 60.723 55.000 13.61 0.00 35.48 3.95
580 599 0.880278 AGCAAGCAAACTCGAGCGAA 60.880 50.000 13.61 0.00 35.48 4.70
581 600 1.300931 AGCAAGCAAACTCGAGCGA 60.301 52.632 13.61 0.00 35.48 4.93
582 601 1.154525 CAGCAAGCAAACTCGAGCG 60.155 57.895 13.61 2.18 35.48 5.03
583 602 1.441682 GCAGCAAGCAAACTCGAGC 60.442 57.895 13.61 0.00 44.79 5.03
584 603 4.834828 GCAGCAAGCAAACTCGAG 57.165 55.556 11.84 11.84 44.79 4.04
593 612 1.399791 GTACTGGAATGAGCAGCAAGC 59.600 52.381 0.00 0.00 46.19 4.01
594 613 2.703416 TGTACTGGAATGAGCAGCAAG 58.297 47.619 0.00 0.00 0.00 4.01
621 640 1.940752 GCGGCAGCAATGAAACCAAAT 60.941 47.619 3.18 0.00 44.35 2.32
623 642 1.006337 GCGGCAGCAATGAAACCAA 60.006 52.632 3.18 0.00 44.35 3.67
624 643 2.650196 GCGGCAGCAATGAAACCA 59.350 55.556 3.18 0.00 44.35 3.67
685 707 1.985895 ACGGAGGGATGAAGTTCCTTT 59.014 47.619 0.00 0.00 35.97 3.11
687 709 0.905357 CACGGAGGGATGAAGTTCCT 59.095 55.000 0.00 0.00 35.97 3.36
689 711 0.250513 AGCACGGAGGGATGAAGTTC 59.749 55.000 0.00 0.00 0.00 3.01
700 722 5.109210 TGAACAATGAAGTATAGCACGGAG 58.891 41.667 0.00 0.00 0.00 4.63
707 729 6.539826 TGGCACTGATGAACAATGAAGTATAG 59.460 38.462 0.00 0.00 0.00 1.31
710 732 4.455533 GTGGCACTGATGAACAATGAAGTA 59.544 41.667 11.13 0.00 0.00 2.24
782 809 7.282901 TGAATCACTGAAGAAACAAGTCAATGA 59.717 33.333 0.00 0.00 32.68 2.57
783 810 7.420002 TGAATCACTGAAGAAACAAGTCAATG 58.580 34.615 0.00 0.00 0.00 2.82
833 862 6.811170 TGTGAAAGTTCTGGTTTTTCATCAAC 59.189 34.615 2.68 0.00 41.31 3.18
879 909 1.295792 TGACAAGTTGAGACGGTTGC 58.704 50.000 10.54 0.00 0.00 4.17
917 947 1.303898 TATGTGGCTGGGAATTGGGA 58.696 50.000 0.00 0.00 0.00 4.37
921 951 4.877773 TGGTAAATATGTGGCTGGGAATT 58.122 39.130 0.00 0.00 0.00 2.17
922 952 4.534647 TGGTAAATATGTGGCTGGGAAT 57.465 40.909 0.00 0.00 0.00 3.01
945 975 4.430765 CGCGTGCGTTCCTAGGGT 62.431 66.667 9.46 0.00 34.35 4.34
963 993 3.481453 GATAAAAGAGGGAGGTGCATCC 58.519 50.000 0.00 0.00 38.76 3.51
964 994 3.137360 AGGATAAAAGAGGGAGGTGCATC 59.863 47.826 0.00 0.00 0.00 3.91
988 1018 0.918983 TTAGGCATGTGGGGGAAGAG 59.081 55.000 0.00 0.00 0.00 2.85
1010 1040 1.070471 CGGTTGGCAATGCGCTAAAC 61.070 55.000 9.73 4.05 44.89 2.01
1287 1327 4.300457 GAGAGCGACTCGAGCATG 57.700 61.111 13.61 3.35 35.84 4.06
1302 1342 2.357881 TGCTTGGTCTGCAGCGAG 60.358 61.111 9.47 6.53 39.04 5.03
1494 1534 0.737715 CCCGCTTGTTCTTCTCCTCG 60.738 60.000 0.00 0.00 0.00 4.63
2314 2354 0.390735 ATCCTCGTAAACACGCCCAC 60.391 55.000 0.00 0.00 0.00 4.61
2325 2365 1.652563 CATCGTCGGCATCCTCGTA 59.347 57.895 0.00 0.00 0.00 3.43
2328 2368 2.663188 GGCATCGTCGGCATCCTC 60.663 66.667 0.00 0.00 0.00 3.71
2547 2590 6.934048 AGAGCAATTTTTATCACTAGGCTC 57.066 37.500 0.00 0.00 44.04 4.70
2548 2591 6.660949 ACAAGAGCAATTTTTATCACTAGGCT 59.339 34.615 0.00 0.00 0.00 4.58
2581 2624 6.340522 TCAGGTGATCACATATACACACTTG 58.659 40.000 26.47 4.64 36.93 3.16
2642 2688 2.550855 GGCTTGACATGTCACCTTGAGA 60.551 50.000 27.88 10.79 39.66 3.27
2643 2689 1.808945 GGCTTGACATGTCACCTTGAG 59.191 52.381 27.88 21.54 39.66 3.02
2644 2690 1.545428 GGGCTTGACATGTCACCTTGA 60.545 52.381 27.88 12.26 39.66 3.02
2645 2691 0.883833 GGGCTTGACATGTCACCTTG 59.116 55.000 27.88 17.84 39.66 3.61
2674 2732 4.657436 TGCCTCCGTTACAAACAAAAAT 57.343 36.364 0.00 0.00 0.00 1.82
2698 2756 2.993899 GTGAATGAGACAGGGTACAACG 59.006 50.000 0.00 0.00 0.00 4.10
2720 2778 1.372087 GCTGTCTAGTGTGGGCATGC 61.372 60.000 9.90 9.90 0.00 4.06
2721 2779 0.036105 TGCTGTCTAGTGTGGGCATG 60.036 55.000 0.00 0.00 0.00 4.06
2730 2788 4.558226 TTCATGTTCCATGCTGTCTAGT 57.442 40.909 0.00 0.00 0.00 2.57
2758 2816 0.249868 TTGGTCGAGAGTGTGCCTTG 60.250 55.000 0.00 0.00 0.00 3.61
2765 2823 5.950883 TGTAAGATAGTTTGGTCGAGAGTG 58.049 41.667 0.00 0.00 0.00 3.51
2778 2836 7.934665 TGTGTGGTGTATTTGTTGTAAGATAGT 59.065 33.333 0.00 0.00 0.00 2.12
2798 2856 0.395036 TCTTGTGGGGTTGTGTGTGG 60.395 55.000 0.00 0.00 0.00 4.17
2839 2918 0.673985 CTTGTGGAGGAGTGACGACA 59.326 55.000 0.00 0.00 0.00 4.35
2843 2922 1.230324 GTTGCTTGTGGAGGAGTGAC 58.770 55.000 0.00 0.00 0.00 3.67
2853 2932 0.670546 ATCGGAGTCGGTTGCTTGTG 60.671 55.000 0.00 0.00 36.95 3.33
2883 2962 2.486966 GGCTTCATTGGCTGTCGC 59.513 61.111 0.00 0.00 0.00 5.19
2889 2968 1.891722 CTTGGGTGGGCTTCATTGGC 61.892 60.000 0.00 0.00 0.00 4.52
2892 2971 0.251787 GGACTTGGGTGGGCTTCATT 60.252 55.000 0.00 0.00 0.00 2.57
2902 2981 3.867216 GCATACGTTGTTAGGACTTGGGT 60.867 47.826 0.00 0.00 0.00 4.51
2919 2999 2.579207 TAGAGTGGCTTCACGCATAC 57.421 50.000 3.42 0.00 45.55 2.39
2935 3015 7.606456 GTGGACAACTATTTGGTTGATCTTAGA 59.394 37.037 12.93 0.00 46.55 2.10
2941 3021 6.603201 CCTATGTGGACAACTATTTGGTTGAT 59.397 38.462 12.93 0.00 46.38 2.57
2968 3048 4.666512 AGCACACACCCATCTTATTTTCT 58.333 39.130 0.00 0.00 0.00 2.52
2999 3082 3.423571 CGACACTCGGTAACATGAGTAC 58.576 50.000 0.00 0.99 43.33 2.73
3022 3105 1.475280 GGTTAATTTTGGGGAGTCGGC 59.525 52.381 0.00 0.00 0.00 5.54
3025 3108 6.184789 TCATGTAGGTTAATTTTGGGGAGTC 58.815 40.000 0.00 0.00 0.00 3.36
3084 3167 4.947388 CCCTCAAAATAGTTTTCGGGATGA 59.053 41.667 11.70 0.00 40.37 2.92
3087 3170 3.086282 GCCCTCAAAATAGTTTTCGGGA 58.914 45.455 18.40 0.00 40.37 5.14
3088 3171 2.823154 TGCCCTCAAAATAGTTTTCGGG 59.177 45.455 12.46 12.46 40.66 5.14
3089 3172 4.423732 CATGCCCTCAAAATAGTTTTCGG 58.576 43.478 0.00 0.00 0.00 4.30
3090 3173 4.423732 CCATGCCCTCAAAATAGTTTTCG 58.576 43.478 0.00 0.00 0.00 3.46
3091 3174 4.758688 CCCATGCCCTCAAAATAGTTTTC 58.241 43.478 0.00 0.00 0.00 2.29
3092 3175 3.055167 GCCCATGCCCTCAAAATAGTTTT 60.055 43.478 0.00 0.00 0.00 2.43
3093 3176 2.501316 GCCCATGCCCTCAAAATAGTTT 59.499 45.455 0.00 0.00 0.00 2.66
3094 3177 2.110578 GCCCATGCCCTCAAAATAGTT 58.889 47.619 0.00 0.00 0.00 2.24
3101 3184 1.228706 TTTTCGCCCATGCCCTCAA 60.229 52.632 0.00 0.00 0.00 3.02
3102 3185 1.678635 CTTTTCGCCCATGCCCTCA 60.679 57.895 0.00 0.00 0.00 3.86
3105 3188 0.892063 TAAACTTTTCGCCCATGCCC 59.108 50.000 0.00 0.00 0.00 5.36
3127 3210 2.641815 GACATAGCCTGGAATGATCCCT 59.358 50.000 14.24 0.00 45.95 4.20
3131 3214 1.271054 GCCGACATAGCCTGGAATGAT 60.271 52.381 14.24 1.92 0.00 2.45
3133 3216 1.224069 CGCCGACATAGCCTGGAATG 61.224 60.000 0.00 2.70 0.00 2.67
3134 3217 1.069765 CGCCGACATAGCCTGGAAT 59.930 57.895 0.00 0.00 0.00 3.01
3148 3419 2.018717 GAAAGAACACTTTCACGCCG 57.981 50.000 14.98 0.00 44.90 6.46
3154 3425 7.379529 CACACCAATGTATGAAAGAACACTTTC 59.620 37.037 13.55 13.55 41.94 2.62
3184 3455 2.513897 GAATCGAGGCCCCAACGG 60.514 66.667 0.00 0.00 0.00 4.44
3197 3468 7.389053 CCTACTGATTTAACCCTAGCATGAATC 59.611 40.741 0.00 0.00 0.00 2.52
3214 3485 3.055094 GTGTCATCACCCACCTACTGATT 60.055 47.826 0.00 0.00 38.51 2.57
3215 3486 2.501723 GTGTCATCACCCACCTACTGAT 59.498 50.000 0.00 0.00 38.51 2.90
3250 3521 9.362151 TCCCATTGGGACAAAATATATCTAAAC 57.638 33.333 21.00 0.00 46.17 2.01
3273 3544 0.827507 ACAGTTGTGGCCAATGTCCC 60.828 55.000 7.24 0.00 32.11 4.46
3352 3623 9.352784 TGTTTGAAGTTATGTTGTTCTTTGAAG 57.647 29.630 0.00 0.00 0.00 3.02
3359 3630 9.701355 CCATTTTTGTTTGAAGTTATGTTGTTC 57.299 29.630 0.00 0.00 0.00 3.18
3360 3631 8.672815 CCCATTTTTGTTTGAAGTTATGTTGTT 58.327 29.630 0.00 0.00 0.00 2.83
3362 3633 8.207521 ACCCATTTTTGTTTGAAGTTATGTTG 57.792 30.769 0.00 0.00 0.00 3.33
3367 3639 7.286775 AGCTAGACCCATTTTTGTTTGAAGTTA 59.713 33.333 0.00 0.00 0.00 2.24
3374 3646 5.869649 ACAAGCTAGACCCATTTTTGTTT 57.130 34.783 0.00 0.00 0.00 2.83
3376 3648 5.010282 CCTACAAGCTAGACCCATTTTTGT 58.990 41.667 0.00 0.00 0.00 2.83
3380 3652 2.576191 TGCCTACAAGCTAGACCCATTT 59.424 45.455 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.