Multiple sequence alignment - TraesCS7B01G345500

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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 TraesCS7B01G345500 chr7B 100.000 3344 0 0 1 3344 601227584 601230927 0.000000e+00 6176
1 TraesCS7B01G345500 chr7A 90.646 1176 75 24 747 1913 641010619 641011768 0.000000e+00 1530
2 TraesCS7B01G345500 chr7A 83.784 1443 122 48 1942 3328 641011835 641013221 0.000000e+00 1266
3 TraesCS7B01G345500 chr7A 88.235 408 43 3 1510 1912 177284966 177285373 1.800000e-132 483
4 TraesCS7B01G345500 chr7D 89.810 1158 67 22 792 1913 554908577 554907435 0.000000e+00 1437
5 TraesCS7B01G345500 chr7D 85.068 1480 136 50 1913 3322 554907407 554905943 0.000000e+00 1430
6 TraesCS7B01G345500 chr7D 85.837 466 42 12 2499 2947 21699119 21698661 1.090000e-129 473
7 TraesCS7B01G345500 chr3A 100.000 527 0 0 129 655 46601946 46602472 0.000000e+00 974
8 TraesCS7B01G345500 chr3A 99.811 530 1 0 129 658 533086317 533085788 0.000000e+00 974
9 TraesCS7B01G345500 chr3A 99.811 529 1 0 130 658 60235813 60235285 0.000000e+00 972
10 TraesCS7B01G345500 chr3A 83.893 596 62 19 1510 2072 182399130 182399724 3.800000e-149 538
11 TraesCS7B01G345500 chr3A 83.752 597 62 19 1510 2072 282056167 282056762 1.770000e-147 532
12 TraesCS7B01G345500 chr3A 87.160 405 47 3 1510 1909 688958958 688959362 3.930000e-124 455
13 TraesCS7B01G345500 chr3A 90.683 161 13 2 1913 2072 34783024 34782865 2.610000e-51 213
14 TraesCS7B01G345500 chr3A 90.683 161 13 2 1913 2072 688959396 688959555 2.610000e-51 213
15 TraesCS7B01G345500 chr2B 99.810 526 1 0 130 655 40532582 40533107 0.000000e+00 966
16 TraesCS7B01G345500 chr3B 99.621 528 2 0 131 658 585599271 585598744 0.000000e+00 965
17 TraesCS7B01G345500 chr4B 86.926 849 69 25 954 1772 592719147 592718311 0.000000e+00 915
18 TraesCS7B01G345500 chr4B 94.363 408 23 0 248 655 170977551 170977958 7.880000e-176 627
19 TraesCS7B01G345500 chr3D 96.552 522 17 1 133 654 393017201 393016681 0.000000e+00 863
20 TraesCS7B01G345500 chr1B 85.787 788 69 21 954 1709 615996708 615997484 0.000000e+00 795
21 TraesCS7B01G345500 chr6B 88.167 600 42 16 954 1528 648691110 648690515 0.000000e+00 688
22 TraesCS7B01G345500 chr2A 83.838 594 60 21 1513 2072 37152148 37151557 1.770000e-147 532
23 TraesCS7B01G345500 chr6A 83.585 597 63 19 1510 2072 50953408 50954003 8.220000e-146 527
24 TraesCS7B01G345500 chr1A 89.737 419 25 11 240 658 291560497 291560097 1.380000e-143 520
25 TraesCS7B01G345500 chr1D 91.123 383 32 2 134 516 224569351 224568971 4.950000e-143 518
26 TraesCS7B01G345500 chr1D 94.656 131 5 1 126 254 472420172 472420042 5.660000e-48 202
27 TraesCS7B01G345500 chr1D 93.860 114 7 0 545 658 224568393 224568280 4.440000e-39 172
28 TraesCS7B01G345500 chr5A 88.089 403 42 4 1515 1912 61255022 61254621 1.090000e-129 473
29 TraesCS7B01G345500 chrUn 85.714 469 40 15 2499 2947 92824294 92824755 1.400000e-128 470
30 TraesCS7B01G345500 chr4A 86.765 408 49 4 1510 1912 83558242 83558649 1.830000e-122 449


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 TraesCS7B01G345500 chr7B 601227584 601230927 3343 False 6176.0 6176 100.0000 1 3344 1 chr7B.!!$F1 3343
1 TraesCS7B01G345500 chr7A 641010619 641013221 2602 False 1398.0 1530 87.2150 747 3328 2 chr7A.!!$F2 2581
2 TraesCS7B01G345500 chr7D 554905943 554908577 2634 True 1433.5 1437 87.4390 792 3322 2 chr7D.!!$R2 2530
3 TraesCS7B01G345500 chr3A 46601946 46602472 526 False 974.0 974 100.0000 129 655 1 chr3A.!!$F1 526
4 TraesCS7B01G345500 chr3A 533085788 533086317 529 True 974.0 974 99.8110 129 658 1 chr3A.!!$R3 529
5 TraesCS7B01G345500 chr3A 60235285 60235813 528 True 972.0 972 99.8110 130 658 1 chr3A.!!$R2 528
6 TraesCS7B01G345500 chr3A 182399130 182399724 594 False 538.0 538 83.8930 1510 2072 1 chr3A.!!$F2 562
7 TraesCS7B01G345500 chr3A 282056167 282056762 595 False 532.0 532 83.7520 1510 2072 1 chr3A.!!$F3 562
8 TraesCS7B01G345500 chr3A 688958958 688959555 597 False 334.0 455 88.9215 1510 2072 2 chr3A.!!$F4 562
9 TraesCS7B01G345500 chr2B 40532582 40533107 525 False 966.0 966 99.8100 130 655 1 chr2B.!!$F1 525
10 TraesCS7B01G345500 chr3B 585598744 585599271 527 True 965.0 965 99.6210 131 658 1 chr3B.!!$R1 527
11 TraesCS7B01G345500 chr4B 592718311 592719147 836 True 915.0 915 86.9260 954 1772 1 chr4B.!!$R1 818
12 TraesCS7B01G345500 chr3D 393016681 393017201 520 True 863.0 863 96.5520 133 654 1 chr3D.!!$R1 521
13 TraesCS7B01G345500 chr1B 615996708 615997484 776 False 795.0 795 85.7870 954 1709 1 chr1B.!!$F1 755
14 TraesCS7B01G345500 chr6B 648690515 648691110 595 True 688.0 688 88.1670 954 1528 1 chr6B.!!$R1 574
15 TraesCS7B01G345500 chr2A 37151557 37152148 591 True 532.0 532 83.8380 1513 2072 1 chr2A.!!$R1 559
16 TraesCS7B01G345500 chr6A 50953408 50954003 595 False 527.0 527 83.5850 1510 2072 1 chr6A.!!$F1 562
17 TraesCS7B01G345500 chr1D 224568280 224569351 1071 True 345.0 518 92.4915 134 658 2 chr1D.!!$R2 524

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
56 57 0.037697 GACATGTGGTGACGGCTGTA 60.038 55.0 1.15 0.0 0.0 2.74 F
658 659 0.037697 TCGCGAACATTGCAGGTAGT 60.038 50.0 6.20 0.0 0.0 2.73 F
685 686 0.040425 GCGACCTGTGCGTGAATTTT 60.040 50.0 0.00 0.0 0.0 1.82 F
1179 1184 0.106619 AGGTCGCCGAGAAGGACTAT 60.107 55.0 0.00 0.0 45.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1425 0.307453 GCTTGCATTCACACACGACA 59.693 50.000 0.0 0.0 0.00 4.35 R
1539 1570 0.815213 AACTGCTCACTCGCTTGCAA 60.815 50.000 0.0 0.0 34.90 4.08 R
2118 2575 1.471119 ATGCCAGGTCATTCTGCAAG 58.529 50.000 0.0 0.0 33.64 4.01 R
2815 3438 1.268743 GCGCTCCCAAGTTAATGCATC 60.269 52.381 0.0 0.0 0.00 3.91 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
33 34 4.972751 AAAAATTAAAAGGAGCCCAGCA 57.027 36.364 0.00 0.00 0.00 4.41
34 35 3.961480 AAATTAAAAGGAGCCCAGCAC 57.039 42.857 0.00 0.00 0.00 4.40
35 36 2.603075 ATTAAAAGGAGCCCAGCACA 57.397 45.000 0.00 0.00 0.00 4.57
36 37 2.603075 TTAAAAGGAGCCCAGCACAT 57.397 45.000 0.00 0.00 0.00 3.21
37 38 1.838112 TAAAAGGAGCCCAGCACATG 58.162 50.000 0.00 0.00 0.00 3.21
38 39 0.112995 AAAAGGAGCCCAGCACATGA 59.887 50.000 0.00 0.00 0.00 3.07
39 40 0.610232 AAAGGAGCCCAGCACATGAC 60.610 55.000 0.00 0.00 0.00 3.06
40 41 1.782201 AAGGAGCCCAGCACATGACA 61.782 55.000 0.00 0.00 0.00 3.58
41 42 1.077212 GGAGCCCAGCACATGACAT 60.077 57.895 0.00 0.00 0.00 3.06
42 43 1.381928 GGAGCCCAGCACATGACATG 61.382 60.000 14.02 14.02 0.00 3.21
43 44 0.679002 GAGCCCAGCACATGACATGT 60.679 55.000 15.48 15.48 46.22 3.21
51 52 3.231734 ACATGACATGTGGTGACGG 57.768 52.632 20.21 0.00 43.01 4.79
52 53 0.955428 ACATGACATGTGGTGACGGC 60.955 55.000 20.21 0.00 43.01 5.68
53 54 0.674581 CATGACATGTGGTGACGGCT 60.675 55.000 1.15 0.00 0.00 5.52
54 55 0.674581 ATGACATGTGGTGACGGCTG 60.675 55.000 1.15 0.00 0.00 4.85
55 56 1.301716 GACATGTGGTGACGGCTGT 60.302 57.895 1.15 0.00 0.00 4.40
56 57 0.037697 GACATGTGGTGACGGCTGTA 60.038 55.000 1.15 0.00 0.00 2.74
57 58 0.320421 ACATGTGGTGACGGCTGTAC 60.320 55.000 0.00 0.00 0.00 2.90
58 59 0.320334 CATGTGGTGACGGCTGTACA 60.320 55.000 0.00 0.00 0.00 2.90
59 60 0.320421 ATGTGGTGACGGCTGTACAC 60.320 55.000 16.53 16.53 0.00 2.90
60 61 1.068417 GTGGTGACGGCTGTACACA 59.932 57.895 21.78 10.00 36.42 3.72
61 62 1.068417 TGGTGACGGCTGTACACAC 59.932 57.895 21.78 15.63 36.42 3.82
62 63 1.666872 GGTGACGGCTGTACACACC 60.667 63.158 16.73 16.73 42.83 4.16
63 64 1.068417 GTGACGGCTGTACACACCA 59.932 57.895 17.88 1.68 35.06 4.17
64 65 1.068417 TGACGGCTGTACACACCAC 59.932 57.895 0.00 4.83 0.00 4.16
65 66 1.366366 GACGGCTGTACACACCACT 59.634 57.895 0.00 0.00 0.00 4.00
66 67 0.249741 GACGGCTGTACACACCACTT 60.250 55.000 0.00 0.00 0.00 3.16
67 68 0.531974 ACGGCTGTACACACCACTTG 60.532 55.000 0.00 0.00 0.00 3.16
68 69 1.227999 CGGCTGTACACACCACTTGG 61.228 60.000 10.12 0.00 42.17 3.61
69 70 1.515521 GGCTGTACACACCACTTGGC 61.516 60.000 5.46 0.00 39.32 4.52
70 71 1.841663 GCTGTACACACCACTTGGCG 61.842 60.000 0.00 0.00 39.32 5.69
71 72 0.531974 CTGTACACACCACTTGGCGT 60.532 55.000 0.00 0.00 39.32 5.68
74 75 2.901840 CACACCACTTGGCGTGCT 60.902 61.111 3.53 0.00 40.79 4.40
75 76 2.591715 ACACCACTTGGCGTGCTC 60.592 61.111 0.00 0.00 42.42 4.26
76 77 2.281070 CACCACTTGGCGTGCTCT 60.281 61.111 0.00 0.00 42.42 4.09
77 78 1.005037 CACCACTTGGCGTGCTCTA 60.005 57.895 0.00 0.00 42.42 2.43
78 79 1.004918 ACCACTTGGCGTGCTCTAC 60.005 57.895 0.00 0.00 42.42 2.59
79 80 1.293498 CCACTTGGCGTGCTCTACT 59.707 57.895 0.00 0.00 42.42 2.57
80 81 0.737715 CCACTTGGCGTGCTCTACTC 60.738 60.000 0.00 0.00 42.42 2.59
81 82 0.244994 CACTTGGCGTGCTCTACTCT 59.755 55.000 0.00 0.00 36.72 3.24
82 83 1.472878 CACTTGGCGTGCTCTACTCTA 59.527 52.381 0.00 0.00 36.72 2.43
83 84 2.094700 CACTTGGCGTGCTCTACTCTAA 60.095 50.000 0.00 0.00 36.72 2.10
84 85 2.561419 ACTTGGCGTGCTCTACTCTAAA 59.439 45.455 0.00 0.00 0.00 1.85
85 86 2.941453 TGGCGTGCTCTACTCTAAAG 57.059 50.000 0.00 0.00 0.00 1.85
86 87 1.135083 TGGCGTGCTCTACTCTAAAGC 60.135 52.381 0.00 0.00 36.56 3.51
87 88 1.562017 GCGTGCTCTACTCTAAAGCC 58.438 55.000 0.00 0.00 35.12 4.35
88 89 1.135083 GCGTGCTCTACTCTAAAGCCA 60.135 52.381 0.00 0.00 35.12 4.75
89 90 2.531206 CGTGCTCTACTCTAAAGCCAC 58.469 52.381 0.00 0.00 35.12 5.01
90 91 2.735762 CGTGCTCTACTCTAAAGCCACC 60.736 54.545 0.00 0.00 35.12 4.61
91 92 1.476891 TGCTCTACTCTAAAGCCACCG 59.523 52.381 0.00 0.00 35.12 4.94
92 93 1.749634 GCTCTACTCTAAAGCCACCGA 59.250 52.381 0.00 0.00 0.00 4.69
93 94 2.165845 GCTCTACTCTAAAGCCACCGAA 59.834 50.000 0.00 0.00 0.00 4.30
94 95 3.368116 GCTCTACTCTAAAGCCACCGAAA 60.368 47.826 0.00 0.00 0.00 3.46
95 96 4.425520 CTCTACTCTAAAGCCACCGAAAG 58.574 47.826 0.00 0.00 0.00 2.62
96 97 3.830755 TCTACTCTAAAGCCACCGAAAGT 59.169 43.478 0.00 0.00 0.00 2.66
97 98 2.767505 ACTCTAAAGCCACCGAAAGTG 58.232 47.619 0.00 0.00 46.83 3.16
105 106 2.665185 ACCGAAAGTGACCGCTGC 60.665 61.111 0.00 0.00 0.00 5.25
106 107 2.664851 CCGAAAGTGACCGCTGCA 60.665 61.111 0.00 0.00 0.00 4.41
107 108 2.671177 CCGAAAGTGACCGCTGCAG 61.671 63.158 10.11 10.11 0.00 4.41
108 109 2.671177 CGAAAGTGACCGCTGCAGG 61.671 63.158 17.12 2.55 37.30 4.85
115 116 2.603473 ACCGCTGCAGGTCAGGTA 60.603 61.111 17.12 0.00 41.46 3.08
116 117 2.214216 ACCGCTGCAGGTCAGGTAA 61.214 57.895 17.12 0.00 41.46 2.85
117 118 1.221840 CCGCTGCAGGTCAGGTAAT 59.778 57.895 17.12 0.00 43.06 1.89
118 119 0.811616 CCGCTGCAGGTCAGGTAATC 60.812 60.000 17.12 0.00 43.06 1.75
119 120 1.148157 CGCTGCAGGTCAGGTAATCG 61.148 60.000 17.12 2.03 43.06 3.34
120 121 0.108138 GCTGCAGGTCAGGTAATCGT 60.108 55.000 17.12 0.00 43.06 3.73
121 122 1.927895 CTGCAGGTCAGGTAATCGTC 58.072 55.000 5.57 0.00 39.15 4.20
122 123 1.204704 CTGCAGGTCAGGTAATCGTCA 59.795 52.381 5.57 0.00 39.15 4.35
123 124 1.204704 TGCAGGTCAGGTAATCGTCAG 59.795 52.381 0.00 0.00 0.00 3.51
124 125 1.471676 GCAGGTCAGGTAATCGTCAGG 60.472 57.143 0.00 0.00 0.00 3.86
125 126 1.825474 CAGGTCAGGTAATCGTCAGGT 59.175 52.381 0.00 0.00 0.00 4.00
126 127 3.021695 CAGGTCAGGTAATCGTCAGGTA 58.978 50.000 0.00 0.00 0.00 3.08
127 128 3.066900 CAGGTCAGGTAATCGTCAGGTAG 59.933 52.174 0.00 0.00 0.00 3.18
655 656 1.574428 GTTCGCGAACATTGCAGGT 59.426 52.632 39.21 0.00 40.84 4.00
658 659 0.037697 TCGCGAACATTGCAGGTAGT 60.038 50.000 6.20 0.00 0.00 2.73
659 660 0.796312 CGCGAACATTGCAGGTAGTT 59.204 50.000 0.00 0.00 0.00 2.24
660 661 1.464023 CGCGAACATTGCAGGTAGTTG 60.464 52.381 0.00 0.00 0.00 3.16
661 662 1.729149 GCGAACATTGCAGGTAGTTGC 60.729 52.381 0.00 0.00 44.33 4.17
662 663 1.806542 CGAACATTGCAGGTAGTTGCT 59.193 47.619 0.00 0.00 44.38 3.91
663 664 2.159653 CGAACATTGCAGGTAGTTGCTC 60.160 50.000 0.00 0.00 44.38 4.26
664 665 2.867109 ACATTGCAGGTAGTTGCTCT 57.133 45.000 0.00 0.00 44.38 4.09
665 666 2.704572 ACATTGCAGGTAGTTGCTCTC 58.295 47.619 0.00 0.00 44.38 3.20
666 667 1.662629 CATTGCAGGTAGTTGCTCTCG 59.337 52.381 0.00 0.00 44.38 4.04
667 668 0.670546 TTGCAGGTAGTTGCTCTCGC 60.671 55.000 0.00 0.00 44.38 5.03
668 669 2.161486 GCAGGTAGTTGCTCTCGCG 61.161 63.158 0.00 0.00 40.89 5.87
669 670 1.506718 CAGGTAGTTGCTCTCGCGA 59.493 57.895 9.26 9.26 39.65 5.87
674 675 2.049063 GTTGCTCTCGCGACCTGT 60.049 61.111 3.71 0.00 43.44 4.00
675 676 2.049156 TTGCTCTCGCGACCTGTG 60.049 61.111 3.71 0.00 39.65 3.66
676 677 4.724602 TGCTCTCGCGACCTGTGC 62.725 66.667 3.71 9.41 39.65 4.57
683 684 3.253955 GCGACCTGTGCGTGAATT 58.746 55.556 0.00 0.00 0.00 2.17
684 685 1.574428 GCGACCTGTGCGTGAATTT 59.426 52.632 0.00 0.00 0.00 1.82
685 686 0.040425 GCGACCTGTGCGTGAATTTT 60.040 50.000 0.00 0.00 0.00 1.82
686 687 1.599419 GCGACCTGTGCGTGAATTTTT 60.599 47.619 0.00 0.00 0.00 1.94
709 710 6.827586 TTTTTAGGGAAGTGCGTGAAATAT 57.172 33.333 0.00 0.00 0.00 1.28
710 711 7.925043 TTTTTAGGGAAGTGCGTGAAATATA 57.075 32.000 0.00 0.00 0.00 0.86
711 712 7.548196 TTTTAGGGAAGTGCGTGAAATATAG 57.452 36.000 0.00 0.00 0.00 1.31
712 713 4.073293 AGGGAAGTGCGTGAAATATAGG 57.927 45.455 0.00 0.00 0.00 2.57
713 714 3.709653 AGGGAAGTGCGTGAAATATAGGA 59.290 43.478 0.00 0.00 0.00 2.94
714 715 4.058817 GGGAAGTGCGTGAAATATAGGAG 58.941 47.826 0.00 0.00 0.00 3.69
715 716 3.495001 GGAAGTGCGTGAAATATAGGAGC 59.505 47.826 0.00 0.00 0.00 4.70
716 717 4.372656 GAAGTGCGTGAAATATAGGAGCT 58.627 43.478 0.00 0.00 0.00 4.09
717 718 3.983741 AGTGCGTGAAATATAGGAGCTC 58.016 45.455 4.71 4.71 0.00 4.09
718 719 3.060602 GTGCGTGAAATATAGGAGCTCC 58.939 50.000 26.22 26.22 0.00 4.70
719 720 2.037251 TGCGTGAAATATAGGAGCTCCC 59.963 50.000 29.54 12.44 36.42 4.30
720 721 2.613223 GCGTGAAATATAGGAGCTCCCC 60.613 54.545 29.54 6.19 36.42 4.81
721 722 2.632996 CGTGAAATATAGGAGCTCCCCA 59.367 50.000 29.54 17.98 36.42 4.96
722 723 3.071023 CGTGAAATATAGGAGCTCCCCAA 59.929 47.826 29.54 15.61 36.42 4.12
723 724 4.444306 CGTGAAATATAGGAGCTCCCCAAA 60.444 45.833 29.54 12.94 36.42 3.28
724 725 5.066593 GTGAAATATAGGAGCTCCCCAAAG 58.933 45.833 29.54 0.00 36.42 2.77
725 726 4.726825 TGAAATATAGGAGCTCCCCAAAGT 59.273 41.667 29.54 12.24 36.42 2.66
726 727 4.713792 AATATAGGAGCTCCCCAAAGTG 57.286 45.455 29.54 0.00 36.42 3.16
727 728 2.270434 ATAGGAGCTCCCCAAAGTGA 57.730 50.000 29.54 5.00 36.42 3.41
728 729 1.573108 TAGGAGCTCCCCAAAGTGAG 58.427 55.000 29.54 0.00 36.42 3.51
729 730 0.178891 AGGAGCTCCCCAAAGTGAGA 60.179 55.000 29.54 0.00 36.42 3.27
730 731 0.251634 GGAGCTCCCCAAAGTGAGAG 59.748 60.000 23.19 0.00 0.00 3.20
731 732 4.310288 GCTCCCCAAAGTGAGAGC 57.690 61.111 0.00 0.00 44.36 4.09
732 733 1.377856 GCTCCCCAAAGTGAGAGCC 60.378 63.158 0.00 0.00 44.76 4.70
733 734 1.846712 GCTCCCCAAAGTGAGAGCCT 61.847 60.000 0.00 0.00 44.76 4.58
734 735 1.573108 CTCCCCAAAGTGAGAGCCTA 58.427 55.000 0.00 0.00 0.00 3.93
735 736 2.122768 CTCCCCAAAGTGAGAGCCTAT 58.877 52.381 0.00 0.00 0.00 2.57
736 737 2.507471 CTCCCCAAAGTGAGAGCCTATT 59.493 50.000 0.00 0.00 0.00 1.73
737 738 3.711704 CTCCCCAAAGTGAGAGCCTATTA 59.288 47.826 0.00 0.00 0.00 0.98
738 739 4.108570 TCCCCAAAGTGAGAGCCTATTAA 58.891 43.478 0.00 0.00 0.00 1.40
739 740 4.538490 TCCCCAAAGTGAGAGCCTATTAAA 59.462 41.667 0.00 0.00 0.00 1.52
740 741 4.884164 CCCCAAAGTGAGAGCCTATTAAAG 59.116 45.833 0.00 0.00 0.00 1.85
741 742 5.339200 CCCCAAAGTGAGAGCCTATTAAAGA 60.339 44.000 0.00 0.00 0.00 2.52
742 743 6.180472 CCCAAAGTGAGAGCCTATTAAAGAA 58.820 40.000 0.00 0.00 0.00 2.52
743 744 6.094186 CCCAAAGTGAGAGCCTATTAAAGAAC 59.906 42.308 0.00 0.00 0.00 3.01
744 745 6.655003 CCAAAGTGAGAGCCTATTAAAGAACA 59.345 38.462 0.00 0.00 0.00 3.18
745 746 7.361286 CCAAAGTGAGAGCCTATTAAAGAACAC 60.361 40.741 0.00 0.00 0.00 3.32
757 758 1.341080 AAGAACACCATGGGCCAAAG 58.659 50.000 18.09 7.59 0.00 2.77
923 925 2.907179 CGCCTTTCCCCACCTTCCT 61.907 63.158 0.00 0.00 0.00 3.36
1102 1107 2.580601 CCTCCGGGGTTCTGACGTT 61.581 63.158 0.00 0.00 0.00 3.99
1179 1184 0.106619 AGGTCGCCGAGAAGGACTAT 60.107 55.000 0.00 0.00 45.00 2.12
1202 1207 1.135373 CGAGGTATGCTGTCGTTCTGT 60.135 52.381 0.00 0.00 0.00 3.41
1346 1351 7.294584 TGATTCGTTAGGGGGATATGAATTTT 58.705 34.615 0.00 0.00 0.00 1.82
1406 1411 6.211384 ACTGGAATCTTGTCAAAATTAAGGGG 59.789 38.462 0.00 0.00 0.00 4.79
1410 1415 5.799827 TCTTGTCAAAATTAAGGGGTTGG 57.200 39.130 0.00 0.00 0.00 3.77
1420 1425 6.508030 AATTAAGGGGTTGGTGAATGTTTT 57.492 33.333 0.00 0.00 0.00 2.43
1424 1429 2.544903 GGGGTTGGTGAATGTTTTGTCG 60.545 50.000 0.00 0.00 0.00 4.35
1427 1432 3.428316 GGTTGGTGAATGTTTTGTCGTGT 60.428 43.478 0.00 0.00 0.00 4.49
1435 1466 2.791567 TGTTTTGTCGTGTGTGAATGC 58.208 42.857 0.00 0.00 0.00 3.56
1439 1470 0.307453 TGTCGTGTGTGAATGCAAGC 59.693 50.000 0.00 0.00 0.00 4.01
1441 1472 0.878086 TCGTGTGTGAATGCAAGCGA 60.878 50.000 0.00 0.00 0.00 4.93
1446 1477 4.225984 GTGTGTGAATGCAAGCGAAATTA 58.774 39.130 0.00 0.00 0.00 1.40
1539 1570 1.890489 GAATTTTGGGGCGGTAGTGTT 59.110 47.619 0.00 0.00 0.00 3.32
1690 1725 8.413309 AATTGGTCATGGATTATCTAATGTGG 57.587 34.615 0.00 0.00 0.00 4.17
1762 1797 6.672593 TCCTTTCTTTATGCCATTCCTGTAT 58.327 36.000 0.00 0.00 0.00 2.29
1875 2268 8.301002 GGTGTATTTATTTAGTTGTTTGAGCCA 58.699 33.333 0.00 0.00 0.00 4.75
1876 2269 9.124807 GTGTATTTATTTAGTTGTTTGAGCCAC 57.875 33.333 0.00 0.00 0.00 5.01
1925 2349 3.634448 ACTCTCAATCACTACCATCCTCG 59.366 47.826 0.00 0.00 0.00 4.63
1975 2410 6.772360 ATTATGCCATGTGTTGTGATGTTA 57.228 33.333 0.00 0.00 0.00 2.41
1998 2433 3.245766 TGAGGAAGAGGAAGGTGATCTGA 60.246 47.826 0.00 0.00 0.00 3.27
2002 2437 5.104569 AGGAAGAGGAAGGTGATCTGAATTC 60.105 44.000 0.00 0.00 0.00 2.17
2057 2496 3.703556 TGCTTGAAAAACCAGTCCATGAA 59.296 39.130 0.00 0.00 0.00 2.57
2118 2575 5.514274 TCATTGTTTTGGTTTCCTCTGTC 57.486 39.130 0.00 0.00 0.00 3.51
2195 2652 5.394738 ACCACTAGCAGCTATCCAGTATTA 58.605 41.667 1.54 0.00 0.00 0.98
2196 2653 5.839063 ACCACTAGCAGCTATCCAGTATTAA 59.161 40.000 1.54 0.00 0.00 1.40
2227 2687 2.027192 TGCTTGTCCTATGACCCTTGTC 60.027 50.000 0.00 0.00 41.01 3.18
2358 2975 1.668826 AATGAGTCTGCCCACCCTTA 58.331 50.000 0.00 0.00 0.00 2.69
2361 2978 0.690762 GAGTCTGCCCACCCTTACAA 59.309 55.000 0.00 0.00 0.00 2.41
2429 3046 4.688879 CGCTTCACTATCTGTGGTTGTAAA 59.311 41.667 0.00 0.00 46.20 2.01
2457 3074 4.460263 ACCTTCAGTTGTGTTGAGCATTA 58.540 39.130 0.00 0.00 0.00 1.90
2458 3075 4.887071 ACCTTCAGTTGTGTTGAGCATTAA 59.113 37.500 0.00 0.00 0.00 1.40
2472 3089 1.332377 GCATTAAGCATCGTCGCAGTC 60.332 52.381 1.90 0.00 44.79 3.51
2473 3090 1.071894 CATTAAGCATCGTCGCAGTCG 60.072 52.381 1.90 0.00 41.01 4.18
2476 3093 2.765250 AAGCATCGTCGCAGTCGGTT 62.765 55.000 1.90 0.00 39.90 4.44
2494 3111 3.874392 GTTGCTGAAACCTATGGCATT 57.126 42.857 4.78 0.00 32.13 3.56
2496 3113 3.872511 TGCTGAAACCTATGGCATTTG 57.127 42.857 4.78 0.00 0.00 2.32
2523 3140 3.808726 GCCTCTTCTGCTTATCTGTGATG 59.191 47.826 0.00 0.00 0.00 3.07
2603 3220 4.828939 TGTGCATCAAGTCTTCCAATTTCT 59.171 37.500 0.00 0.00 0.00 2.52
2620 3238 4.998671 TTTCTTTGTGTTGATTGCCTGA 57.001 36.364 0.00 0.00 0.00 3.86
2641 3259 4.154737 TGATCTGGTTCTGCTTCATTTTCG 59.845 41.667 0.00 0.00 0.00 3.46
2648 3266 5.452777 GTTCTGCTTCATTTTCGTTAGCTT 58.547 37.500 0.00 0.00 33.15 3.74
2672 3290 3.626930 TCCACTTTGTTAGTTGGTTGCT 58.373 40.909 0.00 0.00 33.85 3.91
2783 3406 6.886459 TGCATTCCTTGGCTTCTATATTATCC 59.114 38.462 0.00 0.00 0.00 2.59
2787 3410 5.045578 TCCTTGGCTTCTATATTATCCAGGC 60.046 44.000 0.00 0.00 0.00 4.85
2798 3421 4.696479 ATTATCCAGGCGTCTCTCAAAT 57.304 40.909 0.00 0.00 0.00 2.32
2802 3425 1.757118 CCAGGCGTCTCTCAAATAGGA 59.243 52.381 0.00 0.00 0.00 2.94
2804 3427 1.757699 AGGCGTCTCTCAAATAGGACC 59.242 52.381 0.00 0.00 0.00 4.46
2811 3434 5.699915 CGTCTCTCAAATAGGACCGTATCTA 59.300 44.000 0.00 0.00 0.00 1.98
2820 3450 4.955811 AGGACCGTATCTATTTGATGCA 57.044 40.909 0.00 0.00 37.59 3.96
2821 3451 5.489792 AGGACCGTATCTATTTGATGCAT 57.510 39.130 0.00 0.00 37.59 3.96
2843 3473 2.479566 ACTTGGGAGCGCATATATGG 57.520 50.000 11.47 5.93 0.00 2.74
2854 3484 4.633126 AGCGCATATATGGTTGATGATGTC 59.367 41.667 11.47 0.00 0.00 3.06
2855 3485 4.633126 GCGCATATATGGTTGATGATGTCT 59.367 41.667 14.51 0.00 0.00 3.41
2857 3487 6.674037 GCGCATATATGGTTGATGATGTCTTC 60.674 42.308 14.51 0.00 0.00 2.87
2858 3488 6.592994 CGCATATATGGTTGATGATGTCTTCT 59.407 38.462 14.51 0.00 0.00 2.85
2859 3489 7.201504 CGCATATATGGTTGATGATGTCTTCTC 60.202 40.741 14.51 0.00 0.00 2.87
2871 3501 9.521503 TGATGATGTCTTCTCTAAGTTTATTCG 57.478 33.333 0.00 0.00 34.13 3.34
2921 3556 9.350357 TGTGTAGAATCGATACAACTTTAACTC 57.650 33.333 0.00 0.00 35.04 3.01
2930 3565 6.453396 CGATACAACTTTAACTCGTTACAGCC 60.453 42.308 3.56 0.00 0.00 4.85
2948 3583 1.836802 GCCTCCTTGTGATCTTCCTCT 59.163 52.381 0.00 0.00 0.00 3.69
2980 3625 4.235372 CCATAGAACCCTTCCTGGAGTAT 58.765 47.826 0.00 0.00 35.89 2.12
2988 3633 2.424956 CCTTCCTGGAGTATTTGCTTGC 59.575 50.000 0.00 0.00 38.35 4.01
2989 3634 2.877097 TCCTGGAGTATTTGCTTGCA 57.123 45.000 0.00 0.00 0.00 4.08
2990 3635 3.370840 TCCTGGAGTATTTGCTTGCAT 57.629 42.857 0.00 0.00 0.00 3.96
2991 3636 3.700538 TCCTGGAGTATTTGCTTGCATT 58.299 40.909 0.00 0.00 0.00 3.56
2993 3638 4.082081 TCCTGGAGTATTTGCTTGCATTTG 60.082 41.667 0.00 0.00 0.00 2.32
2994 3639 4.178540 CTGGAGTATTTGCTTGCATTTGG 58.821 43.478 0.00 0.00 0.00 3.28
2997 3642 2.905736 AGTATTTGCTTGCATTTGGGGT 59.094 40.909 0.00 0.00 0.00 4.95
2998 3643 2.955342 ATTTGCTTGCATTTGGGGTT 57.045 40.000 0.00 0.00 0.00 4.11
2999 3644 2.725221 TTTGCTTGCATTTGGGGTTT 57.275 40.000 0.00 0.00 0.00 3.27
3000 3645 2.725221 TTGCTTGCATTTGGGGTTTT 57.275 40.000 0.00 0.00 0.00 2.43
3001 3646 1.964552 TGCTTGCATTTGGGGTTTTG 58.035 45.000 0.00 0.00 0.00 2.44
3002 3647 0.592637 GCTTGCATTTGGGGTTTTGC 59.407 50.000 0.00 0.00 35.67 3.68
3003 3648 1.237533 CTTGCATTTGGGGTTTTGCC 58.762 50.000 0.00 0.00 34.20 4.52
3011 3656 3.941704 TTGGGGTTTTGCCTTTCATTT 57.058 38.095 0.00 0.00 37.43 2.32
3024 3669 6.355747 TGCCTTTCATTTGTCAAGGAAAATT 58.644 32.000 12.67 0.00 41.03 1.82
3060 3705 8.974060 TTTTCCTGAAACCTATATATGGTGTC 57.026 34.615 13.54 13.54 41.13 3.67
3073 3718 7.759489 ATATATGGTGTCTCAGTCTCTTCTC 57.241 40.000 0.00 0.00 0.00 2.87
3076 3729 3.161866 GGTGTCTCAGTCTCTTCTCCTT 58.838 50.000 0.00 0.00 0.00 3.36
3090 3743 9.515226 GTCTCTTCTCCTTATCTATGATACAGT 57.485 37.037 0.00 0.00 0.00 3.55
3104 3784 4.172807 TGATACAGTTGGTTCCCCTAAGT 58.827 43.478 0.00 0.00 0.00 2.24
3105 3785 2.951229 ACAGTTGGTTCCCCTAAGTG 57.049 50.000 0.00 0.00 32.73 3.16
3116 3796 1.004745 CCCCTAAGTGTTCATGCACCT 59.995 52.381 0.00 0.00 40.04 4.00
3118 3798 2.002586 CCTAAGTGTTCATGCACCTCG 58.997 52.381 0.00 0.00 40.04 4.63
3124 3804 3.118629 AGTGTTCATGCACCTCGTATCAT 60.119 43.478 0.00 0.00 40.04 2.45
3130 3810 1.762370 TGCACCTCGTATCATCATGGT 59.238 47.619 0.00 0.00 0.00 3.55
3131 3811 2.170397 TGCACCTCGTATCATCATGGTT 59.830 45.455 0.00 0.00 0.00 3.67
3138 3818 3.871006 TCGTATCATCATGGTTGTTGCTC 59.129 43.478 0.00 0.00 0.00 4.26
3160 3840 9.773328 TGCTCGAGTAGATTTATTTTCATTTTG 57.227 29.630 15.13 0.00 0.00 2.44
3183 3863 1.869754 CGAACCATATCACAGCTCCCG 60.870 57.143 0.00 0.00 0.00 5.14
3187 3867 0.969149 CATATCACAGCTCCCGCCTA 59.031 55.000 0.00 0.00 36.60 3.93
3225 3905 7.419750 CCCTGATAAACTTATTGGCTAGTGGTA 60.420 40.741 0.00 0.00 0.00 3.25
3238 3918 3.008704 GCTAGTGGTACCTTTCCCTTTGA 59.991 47.826 14.36 0.00 0.00 2.69
3243 3923 2.522185 GTACCTTTCCCTTTGAACCCC 58.478 52.381 0.00 0.00 31.05 4.95
3250 3930 1.920351 TCCCTTTGAACCCCTGGTATC 59.080 52.381 0.00 0.00 33.12 2.24
3328 4011 1.075601 TGCATTCCTGGAAGTCCCTT 58.924 50.000 15.34 0.00 35.38 3.95
3329 4012 1.428912 TGCATTCCTGGAAGTCCCTTT 59.571 47.619 15.34 0.00 35.38 3.11
3330 4013 2.158325 TGCATTCCTGGAAGTCCCTTTT 60.158 45.455 15.34 0.00 35.38 2.27
3331 4014 2.232208 GCATTCCTGGAAGTCCCTTTTG 59.768 50.000 15.34 6.65 35.38 2.44
3332 4015 3.500343 CATTCCTGGAAGTCCCTTTTGT 58.500 45.455 15.34 0.00 35.38 2.83
3333 4016 3.680777 TTCCTGGAAGTCCCTTTTGTT 57.319 42.857 4.68 0.00 35.38 2.83
3334 4017 2.944129 TCCTGGAAGTCCCTTTTGTTG 58.056 47.619 0.00 0.00 35.38 3.33
3335 4018 2.512056 TCCTGGAAGTCCCTTTTGTTGA 59.488 45.455 0.00 0.00 35.38 3.18
3336 4019 3.140144 TCCTGGAAGTCCCTTTTGTTGAT 59.860 43.478 0.00 0.00 35.38 2.57
3337 4020 3.897505 CCTGGAAGTCCCTTTTGTTGATT 59.102 43.478 0.00 0.00 35.38 2.57
3338 4021 4.262164 CCTGGAAGTCCCTTTTGTTGATTG 60.262 45.833 0.00 0.00 35.38 2.67
3339 4022 4.541705 TGGAAGTCCCTTTTGTTGATTGA 58.458 39.130 0.00 0.00 35.38 2.57
3340 4023 5.147032 TGGAAGTCCCTTTTGTTGATTGAT 58.853 37.500 0.00 0.00 35.38 2.57
3341 4024 5.010922 TGGAAGTCCCTTTTGTTGATTGATG 59.989 40.000 0.00 0.00 35.38 3.07
3342 4025 5.243730 GGAAGTCCCTTTTGTTGATTGATGA 59.756 40.000 0.00 0.00 0.00 2.92
3343 4026 6.071165 GGAAGTCCCTTTTGTTGATTGATGAT 60.071 38.462 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.102367 TGTGCTGGGCTCCTTTTAATTTTT 59.898 37.500 0.00 0.00 0.00 1.94
13 14 3.645687 TGTGCTGGGCTCCTTTTAATTTT 59.354 39.130 0.00 0.00 0.00 1.82
14 15 3.238597 TGTGCTGGGCTCCTTTTAATTT 58.761 40.909 0.00 0.00 0.00 1.82
15 16 2.888212 TGTGCTGGGCTCCTTTTAATT 58.112 42.857 0.00 0.00 0.00 1.40
16 17 2.603075 TGTGCTGGGCTCCTTTTAAT 57.397 45.000 0.00 0.00 0.00 1.40
17 18 2.170166 CATGTGCTGGGCTCCTTTTAA 58.830 47.619 0.00 0.00 0.00 1.52
18 19 1.354031 TCATGTGCTGGGCTCCTTTTA 59.646 47.619 0.00 0.00 0.00 1.52
19 20 0.112995 TCATGTGCTGGGCTCCTTTT 59.887 50.000 0.00 0.00 0.00 2.27
20 21 0.610232 GTCATGTGCTGGGCTCCTTT 60.610 55.000 0.00 0.00 0.00 3.11
21 22 1.001641 GTCATGTGCTGGGCTCCTT 60.002 57.895 0.00 0.00 0.00 3.36
22 23 1.569030 ATGTCATGTGCTGGGCTCCT 61.569 55.000 0.00 0.00 0.00 3.69
23 24 1.077212 ATGTCATGTGCTGGGCTCC 60.077 57.895 0.00 0.00 0.00 4.70
24 25 0.679002 ACATGTCATGTGCTGGGCTC 60.679 55.000 17.74 0.00 43.01 4.70
25 26 1.381463 ACATGTCATGTGCTGGGCT 59.619 52.632 17.74 0.00 43.01 5.19
26 27 4.007457 ACATGTCATGTGCTGGGC 57.993 55.556 17.74 0.00 43.01 5.36
33 34 0.955428 GCCGTCACCACATGTCATGT 60.955 55.000 12.87 12.87 46.22 3.21
34 35 0.674581 AGCCGTCACCACATGTCATG 60.675 55.000 11.41 11.41 0.00 3.07
35 36 0.674581 CAGCCGTCACCACATGTCAT 60.675 55.000 0.00 0.00 0.00 3.06
36 37 1.301637 CAGCCGTCACCACATGTCA 60.302 57.895 0.00 0.00 0.00 3.58
37 38 0.037697 TACAGCCGTCACCACATGTC 60.038 55.000 0.00 0.00 0.00 3.06
38 39 0.320421 GTACAGCCGTCACCACATGT 60.320 55.000 0.00 0.00 0.00 3.21
39 40 0.320334 TGTACAGCCGTCACCACATG 60.320 55.000 0.00 0.00 0.00 3.21
40 41 0.320421 GTGTACAGCCGTCACCACAT 60.320 55.000 0.00 0.00 0.00 3.21
41 42 1.068417 GTGTACAGCCGTCACCACA 59.932 57.895 0.00 0.00 0.00 4.17
42 43 1.068417 TGTGTACAGCCGTCACCAC 59.932 57.895 0.00 0.00 0.00 4.16
43 44 1.068417 GTGTGTACAGCCGTCACCA 59.932 57.895 0.00 0.00 0.00 4.17
44 45 1.666872 GGTGTGTACAGCCGTCACC 60.667 63.158 14.67 14.67 40.99 4.02
45 46 1.068417 TGGTGTGTACAGCCGTCAC 59.932 57.895 11.23 0.00 43.22 3.67
46 47 1.068417 GTGGTGTGTACAGCCGTCA 59.932 57.895 11.23 0.00 43.22 4.35
47 48 0.249741 AAGTGGTGTGTACAGCCGTC 60.250 55.000 11.23 0.07 43.22 4.79
48 49 0.531974 CAAGTGGTGTGTACAGCCGT 60.532 55.000 11.23 0.00 43.22 5.68
49 50 1.227999 CCAAGTGGTGTGTACAGCCG 61.228 60.000 11.23 0.00 43.22 5.52
50 51 1.515521 GCCAAGTGGTGTGTACAGCC 61.516 60.000 11.23 2.27 43.22 4.85
51 52 1.841663 CGCCAAGTGGTGTGTACAGC 61.842 60.000 7.23 7.23 44.06 4.40
52 53 2.234613 CGCCAAGTGGTGTGTACAG 58.765 57.895 0.00 0.00 40.69 2.74
53 54 4.447544 CGCCAAGTGGTGTGTACA 57.552 55.556 2.56 0.00 40.69 2.90
63 64 1.835494 TAGAGTAGAGCACGCCAAGT 58.165 50.000 0.00 0.00 0.00 3.16
64 65 2.941453 TTAGAGTAGAGCACGCCAAG 57.059 50.000 0.00 0.00 0.00 3.61
65 66 2.674177 GCTTTAGAGTAGAGCACGCCAA 60.674 50.000 0.00 0.00 36.45 4.52
66 67 1.135083 GCTTTAGAGTAGAGCACGCCA 60.135 52.381 0.00 0.00 36.45 5.69
67 68 1.562017 GCTTTAGAGTAGAGCACGCC 58.438 55.000 0.00 0.00 36.45 5.68
68 69 1.135083 TGGCTTTAGAGTAGAGCACGC 60.135 52.381 0.00 0.00 38.14 5.34
69 70 2.531206 GTGGCTTTAGAGTAGAGCACG 58.469 52.381 0.00 0.00 38.14 5.34
70 71 2.735762 CGGTGGCTTTAGAGTAGAGCAC 60.736 54.545 0.00 0.00 38.14 4.40
71 72 1.476891 CGGTGGCTTTAGAGTAGAGCA 59.523 52.381 0.00 0.00 38.14 4.26
72 73 1.749634 TCGGTGGCTTTAGAGTAGAGC 59.250 52.381 0.00 0.00 35.71 4.09
73 74 4.082136 ACTTTCGGTGGCTTTAGAGTAGAG 60.082 45.833 0.00 0.00 0.00 2.43
74 75 3.830755 ACTTTCGGTGGCTTTAGAGTAGA 59.169 43.478 0.00 0.00 0.00 2.59
75 76 3.927142 CACTTTCGGTGGCTTTAGAGTAG 59.073 47.826 0.00 0.00 41.90 2.57
76 77 3.575256 TCACTTTCGGTGGCTTTAGAGTA 59.425 43.478 0.00 0.00 45.38 2.59
77 78 2.367567 TCACTTTCGGTGGCTTTAGAGT 59.632 45.455 0.00 0.00 45.38 3.24
78 79 2.737252 GTCACTTTCGGTGGCTTTAGAG 59.263 50.000 0.00 0.00 46.12 2.43
79 80 2.762745 GTCACTTTCGGTGGCTTTAGA 58.237 47.619 0.00 0.00 46.12 2.10
86 87 2.030562 AGCGGTCACTTTCGGTGG 59.969 61.111 0.00 0.00 45.38 4.61
87 88 3.244105 CAGCGGTCACTTTCGGTG 58.756 61.111 0.00 0.00 45.78 4.94
88 89 2.665185 GCAGCGGTCACTTTCGGT 60.665 61.111 0.00 0.00 37.61 4.69
89 90 2.664851 TGCAGCGGTCACTTTCGG 60.665 61.111 0.00 0.00 0.00 4.30
90 91 2.671177 CCTGCAGCGGTCACTTTCG 61.671 63.158 8.66 0.00 0.00 3.46
91 92 1.598130 ACCTGCAGCGGTCACTTTC 60.598 57.895 8.66 0.00 29.14 2.62
92 93 2.510906 ACCTGCAGCGGTCACTTT 59.489 55.556 8.66 0.00 29.14 2.66
98 99 1.553690 ATTACCTGACCTGCAGCGGT 61.554 55.000 8.66 13.51 43.50 5.68
99 100 0.811616 GATTACCTGACCTGCAGCGG 60.812 60.000 8.66 8.06 43.50 5.52
100 101 1.148157 CGATTACCTGACCTGCAGCG 61.148 60.000 8.66 4.27 43.50 5.18
101 102 0.108138 ACGATTACCTGACCTGCAGC 60.108 55.000 8.66 0.00 43.50 5.25
102 103 1.204704 TGACGATTACCTGACCTGCAG 59.795 52.381 6.78 6.78 44.49 4.41
103 104 1.204704 CTGACGATTACCTGACCTGCA 59.795 52.381 0.00 0.00 0.00 4.41
104 105 1.471676 CCTGACGATTACCTGACCTGC 60.472 57.143 0.00 0.00 0.00 4.85
105 106 1.825474 ACCTGACGATTACCTGACCTG 59.175 52.381 0.00 0.00 0.00 4.00
106 107 2.233305 ACCTGACGATTACCTGACCT 57.767 50.000 0.00 0.00 0.00 3.85
107 108 3.022406 ACTACCTGACGATTACCTGACC 58.978 50.000 0.00 0.00 0.00 4.02
108 109 4.715527 AACTACCTGACGATTACCTGAC 57.284 45.455 0.00 0.00 0.00 3.51
109 110 5.733620 AAAACTACCTGACGATTACCTGA 57.266 39.130 0.00 0.00 0.00 3.86
666 667 0.040425 AAAATTCACGCACAGGTCGC 60.040 50.000 0.00 0.00 0.00 5.19
667 668 2.399396 AAAAATTCACGCACAGGTCG 57.601 45.000 0.00 0.00 0.00 4.79
686 687 6.827586 ATATTTCACGCACTTCCCTAAAAA 57.172 33.333 0.00 0.00 0.00 1.94
687 688 6.540914 CCTATATTTCACGCACTTCCCTAAAA 59.459 38.462 0.00 0.00 0.00 1.52
688 689 6.053005 CCTATATTTCACGCACTTCCCTAAA 58.947 40.000 0.00 0.00 0.00 1.85
689 690 5.364446 TCCTATATTTCACGCACTTCCCTAA 59.636 40.000 0.00 0.00 0.00 2.69
690 691 4.897076 TCCTATATTTCACGCACTTCCCTA 59.103 41.667 0.00 0.00 0.00 3.53
691 692 3.709653 TCCTATATTTCACGCACTTCCCT 59.290 43.478 0.00 0.00 0.00 4.20
692 693 4.058817 CTCCTATATTTCACGCACTTCCC 58.941 47.826 0.00 0.00 0.00 3.97
693 694 3.495001 GCTCCTATATTTCACGCACTTCC 59.505 47.826 0.00 0.00 0.00 3.46
694 695 4.372656 AGCTCCTATATTTCACGCACTTC 58.627 43.478 0.00 0.00 0.00 3.01
695 696 4.372656 GAGCTCCTATATTTCACGCACTT 58.627 43.478 0.87 0.00 0.00 3.16
696 697 3.243907 GGAGCTCCTATATTTCACGCACT 60.244 47.826 26.25 0.00 0.00 4.40
697 698 3.060602 GGAGCTCCTATATTTCACGCAC 58.939 50.000 26.25 0.00 0.00 5.34
698 699 2.037251 GGGAGCTCCTATATTTCACGCA 59.963 50.000 31.36 0.00 35.95 5.24
699 700 2.613223 GGGGAGCTCCTATATTTCACGC 60.613 54.545 31.36 10.49 35.95 5.34
700 701 2.632996 TGGGGAGCTCCTATATTTCACG 59.367 50.000 31.36 0.00 35.95 4.35
701 702 4.706842 TTGGGGAGCTCCTATATTTCAC 57.293 45.455 31.36 11.76 35.95 3.18
702 703 4.726825 ACTTTGGGGAGCTCCTATATTTCA 59.273 41.667 31.36 15.00 35.95 2.69
703 704 5.066593 CACTTTGGGGAGCTCCTATATTTC 58.933 45.833 31.36 13.25 35.95 2.17
704 705 4.726825 TCACTTTGGGGAGCTCCTATATTT 59.273 41.667 31.36 10.37 35.95 1.40
705 706 4.307259 TCACTTTGGGGAGCTCCTATATT 58.693 43.478 31.36 9.85 35.95 1.28
706 707 3.906846 CTCACTTTGGGGAGCTCCTATAT 59.093 47.826 31.36 10.49 35.95 0.86
707 708 3.052109 TCTCACTTTGGGGAGCTCCTATA 60.052 47.826 31.36 15.48 35.95 1.31
708 709 2.122768 CTCACTTTGGGGAGCTCCTAT 58.877 52.381 31.36 8.72 35.95 2.57
709 710 1.078823 TCTCACTTTGGGGAGCTCCTA 59.921 52.381 31.36 18.38 35.95 2.94
710 711 0.178891 TCTCACTTTGGGGAGCTCCT 60.179 55.000 31.36 8.54 35.95 3.69
711 712 0.251634 CTCTCACTTTGGGGAGCTCC 59.748 60.000 25.59 25.59 0.00 4.70
712 713 0.392327 GCTCTCACTTTGGGGAGCTC 60.392 60.000 4.71 4.71 45.15 4.09
713 714 1.682257 GCTCTCACTTTGGGGAGCT 59.318 57.895 7.75 0.00 45.15 4.09
714 715 4.310288 GCTCTCACTTTGGGGAGC 57.690 61.111 0.00 0.00 43.07 4.70
715 716 1.573108 TAGGCTCTCACTTTGGGGAG 58.427 55.000 0.00 0.00 0.00 4.30
716 717 2.270434 ATAGGCTCTCACTTTGGGGA 57.730 50.000 0.00 0.00 0.00 4.81
717 718 4.503714 TTAATAGGCTCTCACTTTGGGG 57.496 45.455 0.00 0.00 0.00 4.96
718 719 5.745227 TCTTTAATAGGCTCTCACTTTGGG 58.255 41.667 0.00 0.00 0.00 4.12
719 720 6.655003 TGTTCTTTAATAGGCTCTCACTTTGG 59.345 38.462 0.00 0.00 0.00 3.28
720 721 7.361286 GGTGTTCTTTAATAGGCTCTCACTTTG 60.361 40.741 0.00 0.00 0.00 2.77
721 722 6.655425 GGTGTTCTTTAATAGGCTCTCACTTT 59.345 38.462 0.00 0.00 0.00 2.66
722 723 6.174049 GGTGTTCTTTAATAGGCTCTCACTT 58.826 40.000 0.00 0.00 0.00 3.16
723 724 5.248477 TGGTGTTCTTTAATAGGCTCTCACT 59.752 40.000 0.00 0.00 0.00 3.41
724 725 5.488341 TGGTGTTCTTTAATAGGCTCTCAC 58.512 41.667 0.00 0.00 0.00 3.51
725 726 5.755409 TGGTGTTCTTTAATAGGCTCTCA 57.245 39.130 0.00 0.00 0.00 3.27
726 727 5.529060 CCATGGTGTTCTTTAATAGGCTCTC 59.471 44.000 2.57 0.00 0.00 3.20
727 728 5.440610 CCATGGTGTTCTTTAATAGGCTCT 58.559 41.667 2.57 0.00 0.00 4.09
728 729 4.580580 CCCATGGTGTTCTTTAATAGGCTC 59.419 45.833 11.73 0.00 0.00 4.70
729 730 4.536765 CCCATGGTGTTCTTTAATAGGCT 58.463 43.478 11.73 0.00 0.00 4.58
730 731 3.068165 GCCCATGGTGTTCTTTAATAGGC 59.932 47.826 11.73 0.00 0.00 3.93
731 732 3.636764 GGCCCATGGTGTTCTTTAATAGG 59.363 47.826 11.73 0.00 0.00 2.57
732 733 4.277476 TGGCCCATGGTGTTCTTTAATAG 58.723 43.478 11.73 0.00 0.00 1.73
733 734 4.323569 TGGCCCATGGTGTTCTTTAATA 57.676 40.909 11.73 0.00 0.00 0.98
734 735 3.182887 TGGCCCATGGTGTTCTTTAAT 57.817 42.857 11.73 0.00 0.00 1.40
735 736 2.685106 TGGCCCATGGTGTTCTTTAA 57.315 45.000 11.73 0.00 0.00 1.52
736 737 2.685106 TTGGCCCATGGTGTTCTTTA 57.315 45.000 11.73 0.00 0.00 1.85
737 738 1.693606 CTTTGGCCCATGGTGTTCTTT 59.306 47.619 11.73 0.00 0.00 2.52
738 739 1.341080 CTTTGGCCCATGGTGTTCTT 58.659 50.000 11.73 0.00 0.00 2.52
739 740 0.542702 CCTTTGGCCCATGGTGTTCT 60.543 55.000 11.73 0.00 0.00 3.01
740 741 1.974543 CCTTTGGCCCATGGTGTTC 59.025 57.895 11.73 0.00 0.00 3.18
741 742 2.216331 GCCTTTGGCCCATGGTGTT 61.216 57.895 11.73 0.00 44.06 3.32
742 743 2.604382 GCCTTTGGCCCATGGTGT 60.604 61.111 11.73 0.00 44.06 4.16
766 768 2.189594 TGATGGGCACTGTTCTCTTG 57.810 50.000 0.00 0.00 0.00 3.02
777 779 0.964860 CACGGGTTTGATGATGGGCA 60.965 55.000 0.00 0.00 0.00 5.36
1179 1184 0.885879 AACGACAGCATACCTCGTCA 59.114 50.000 0.00 0.00 39.68 4.35
1346 1351 1.308047 CATAAGCATAGCAACCCGCA 58.692 50.000 0.00 0.00 46.13 5.69
1377 1382 4.998671 TTTTGACAAGATTCCAGTGCAA 57.001 36.364 0.00 0.00 0.00 4.08
1406 1411 3.545873 CACACGACAAAACATTCACCAAC 59.454 43.478 0.00 0.00 0.00 3.77
1410 1415 4.009798 TCACACACGACAAAACATTCAC 57.990 40.909 0.00 0.00 0.00 3.18
1420 1425 0.307453 GCTTGCATTCACACACGACA 59.693 50.000 0.00 0.00 0.00 4.35
1424 1429 2.118228 TTTCGCTTGCATTCACACAC 57.882 45.000 0.00 0.00 0.00 3.82
1427 1432 4.668941 CGACTAATTTCGCTTGCATTCACA 60.669 41.667 0.00 0.00 31.03 3.58
1435 1466 4.651994 AGCAATTCGACTAATTTCGCTTG 58.348 39.130 0.00 8.87 38.95 4.01
1439 1470 8.993852 AATTCATAGCAATTCGACTAATTTCG 57.006 30.769 0.00 0.00 35.54 3.46
1446 1477 6.707608 TCAGCATAATTCATAGCAATTCGACT 59.292 34.615 0.00 0.00 0.00 4.18
1517 1548 1.889829 CACTACCGCCCCAAAATTCAA 59.110 47.619 0.00 0.00 0.00 2.69
1539 1570 0.815213 AACTGCTCACTCGCTTGCAA 60.815 50.000 0.00 0.00 34.90 4.08
1573 1605 2.441750 TCCCAAGTCTAACCAAGCAACT 59.558 45.455 0.00 0.00 0.00 3.16
1686 1721 6.155221 AGCAAGTTCTACTTCAGATATCCACA 59.845 38.462 0.00 0.00 36.03 4.17
1690 1725 6.045318 TGCAGCAAGTTCTACTTCAGATATC 58.955 40.000 0.00 0.00 36.03 1.63
1762 1797 4.079980 TGTTAGTGCCTAGCAAACAGAA 57.920 40.909 3.37 0.00 41.47 3.02
1789 1824 7.661847 AGTTGACTTTTAAGATGGACTAACTGG 59.338 37.037 0.00 0.00 0.00 4.00
1925 2349 5.919141 CCACAGTCAAGCCTACGTATTATAC 59.081 44.000 0.00 0.00 0.00 1.47
1975 2410 3.710677 CAGATCACCTTCCTCTTCCTCAT 59.289 47.826 0.00 0.00 0.00 2.90
2057 2496 3.054139 TCACTGGCCATTGCTTCTATCTT 60.054 43.478 17.94 0.00 37.74 2.40
2118 2575 1.471119 ATGCCAGGTCATTCTGCAAG 58.529 50.000 0.00 0.00 33.64 4.01
2195 2652 5.246203 TCATAGGACAAGCAGTGTAGAAGTT 59.754 40.000 0.00 0.00 41.96 2.66
2196 2653 4.772624 TCATAGGACAAGCAGTGTAGAAGT 59.227 41.667 0.00 0.00 41.96 3.01
2358 2975 7.854337 AGATTATCATTTTCTGGGCATTTTGT 58.146 30.769 0.00 0.00 0.00 2.83
2361 2978 9.597681 AGATAGATTATCATTTTCTGGGCATTT 57.402 29.630 0.00 0.00 37.65 2.32
2429 3046 5.353394 TCAACACAACTGAAGGTAGTCTT 57.647 39.130 0.00 0.00 38.65 3.01
2457 3074 2.507102 CCGACTGCGACGATGCTT 60.507 61.111 0.00 0.00 40.82 3.91
2458 3075 3.282745 AACCGACTGCGACGATGCT 62.283 57.895 0.00 0.00 40.82 3.79
2476 3093 3.429492 TCAAATGCCATAGGTTTCAGCA 58.571 40.909 0.00 0.00 37.94 4.41
2523 3140 4.891992 TTATTAGCTAGGGACCATCTGC 57.108 45.455 0.00 0.00 0.00 4.26
2603 3220 3.256383 CCAGATCAGGCAATCAACACAAA 59.744 43.478 0.00 0.00 0.00 2.83
2620 3238 4.074970 ACGAAAATGAAGCAGAACCAGAT 58.925 39.130 0.00 0.00 0.00 2.90
2641 3259 6.862711 ACTAACAAAGTGGAAGAAGCTAAC 57.137 37.500 0.00 0.00 36.93 2.34
2648 3266 4.097286 GCAACCAACTAACAAAGTGGAAGA 59.903 41.667 0.00 0.00 38.88 2.87
2734 3357 4.243007 AGCAATCAACTAACAAAGTGGC 57.757 40.909 0.00 0.00 38.88 5.01
2769 3392 5.126384 AGAGACGCCTGGATAATATAGAAGC 59.874 44.000 0.00 0.00 0.00 3.86
2783 3406 2.482142 GGTCCTATTTGAGAGACGCCTG 60.482 54.545 0.00 0.00 0.00 4.85
2787 3410 4.515944 AGATACGGTCCTATTTGAGAGACG 59.484 45.833 0.00 0.00 0.00 4.18
2798 3421 6.605471 ATGCATCAAATAGATACGGTCCTA 57.395 37.500 0.00 0.00 34.43 2.94
2802 3425 8.559536 CAAGTTAATGCATCAAATAGATACGGT 58.440 33.333 0.00 0.00 34.43 4.83
2804 3427 8.017373 CCCAAGTTAATGCATCAAATAGATACG 58.983 37.037 0.00 0.00 34.43 3.06
2811 3434 4.440525 CGCTCCCAAGTTAATGCATCAAAT 60.441 41.667 0.00 0.00 0.00 2.32
2815 3438 1.268743 GCGCTCCCAAGTTAATGCATC 60.269 52.381 0.00 0.00 0.00 3.91
2820 3450 4.943705 CCATATATGCGCTCCCAAGTTAAT 59.056 41.667 9.73 0.00 0.00 1.40
2821 3451 4.202419 ACCATATATGCGCTCCCAAGTTAA 60.202 41.667 9.73 0.00 0.00 2.01
2854 3484 9.413048 AGACTTTGACGAATAAACTTAGAGAAG 57.587 33.333 0.00 0.00 38.76 2.85
2855 3485 9.408069 GAGACTTTGACGAATAAACTTAGAGAA 57.592 33.333 0.00 0.00 0.00 2.87
2857 3487 8.973835 AGAGACTTTGACGAATAAACTTAGAG 57.026 34.615 0.00 0.00 0.00 2.43
2858 3488 9.760077 AAAGAGACTTTGACGAATAAACTTAGA 57.240 29.630 0.00 0.00 0.00 2.10
2871 3501 7.063544 ACAGCGAACATATAAAGAGACTTTGAC 59.936 37.037 6.95 0.00 0.00 3.18
2921 3556 2.093973 AGATCACAAGGAGGCTGTAACG 60.094 50.000 0.00 0.00 0.00 3.18
2925 3560 1.280421 GGAAGATCACAAGGAGGCTGT 59.720 52.381 0.00 0.00 0.00 4.40
2930 3565 2.836981 ACCAGAGGAAGATCACAAGGAG 59.163 50.000 0.00 0.00 0.00 3.69
2980 3625 2.686915 CAAAACCCCAAATGCAAGCAAA 59.313 40.909 0.00 0.00 0.00 3.68
2988 3633 3.205784 TGAAAGGCAAAACCCCAAATG 57.794 42.857 0.00 0.00 40.58 2.32
2989 3634 4.451891 AATGAAAGGCAAAACCCCAAAT 57.548 36.364 0.00 0.00 40.58 2.32
2990 3635 3.941704 AATGAAAGGCAAAACCCCAAA 57.058 38.095 0.00 0.00 40.58 3.28
2991 3636 3.054065 ACAAATGAAAGGCAAAACCCCAA 60.054 39.130 0.00 0.00 40.58 4.12
2993 3638 3.138304 GACAAATGAAAGGCAAAACCCC 58.862 45.455 0.00 0.00 40.58 4.95
2994 3639 3.802866 TGACAAATGAAAGGCAAAACCC 58.197 40.909 0.00 0.00 40.58 4.11
2997 3642 5.350504 TCCTTGACAAATGAAAGGCAAAA 57.649 34.783 12.05 0.00 40.31 2.44
2998 3643 5.350504 TTCCTTGACAAATGAAAGGCAAA 57.649 34.783 12.05 3.73 40.31 3.68
2999 3644 5.350504 TTTCCTTGACAAATGAAAGGCAA 57.649 34.783 12.05 7.34 40.31 4.52
3000 3645 5.350504 TTTTCCTTGACAAATGAAAGGCA 57.649 34.783 12.05 2.81 40.31 4.75
3001 3646 6.260714 ACAATTTTCCTTGACAAATGAAAGGC 59.739 34.615 12.05 0.00 40.31 4.35
3002 3647 7.280652 ACACAATTTTCCTTGACAAATGAAAGG 59.719 33.333 10.65 11.14 41.60 3.11
3003 3648 8.200364 ACACAATTTTCCTTGACAAATGAAAG 57.800 30.769 10.65 5.15 33.32 2.62
3011 3656 5.105392 AGCTGAAACACAATTTTCCTTGACA 60.105 36.000 0.00 0.00 35.01 3.58
3051 3696 4.892934 GGAGAAGAGACTGAGACACCATAT 59.107 45.833 0.00 0.00 0.00 1.78
3052 3697 4.017958 AGGAGAAGAGACTGAGACACCATA 60.018 45.833 0.00 0.00 0.00 2.74
3053 3698 3.096092 GGAGAAGAGACTGAGACACCAT 58.904 50.000 0.00 0.00 0.00 3.55
3054 3699 2.109128 AGGAGAAGAGACTGAGACACCA 59.891 50.000 0.00 0.00 0.00 4.17
3060 3705 8.868522 ATCATAGATAAGGAGAAGAGACTGAG 57.131 38.462 0.00 0.00 0.00 3.35
3104 3784 3.118811 TGATGATACGAGGTGCATGAACA 60.119 43.478 6.08 0.00 0.00 3.18
3105 3785 3.457234 TGATGATACGAGGTGCATGAAC 58.543 45.455 0.00 0.00 0.00 3.18
3116 3796 3.871006 GAGCAACAACCATGATGATACGA 59.129 43.478 0.00 0.00 31.40 3.43
3118 3798 3.871006 TCGAGCAACAACCATGATGATAC 59.129 43.478 0.00 0.00 31.40 2.24
3124 3804 2.560981 TCTACTCGAGCAACAACCATGA 59.439 45.455 13.61 0.00 0.00 3.07
3130 3810 8.317891 TGAAAATAAATCTACTCGAGCAACAA 57.682 30.769 13.61 0.00 0.00 2.83
3131 3811 7.899178 TGAAAATAAATCTACTCGAGCAACA 57.101 32.000 13.61 0.00 0.00 3.33
3138 3818 9.210426 CGGACAAAATGAAAATAAATCTACTCG 57.790 33.333 0.00 0.00 0.00 4.18
3159 3839 1.831106 AGCTGTGATATGGTTCGGACA 59.169 47.619 0.00 0.00 0.00 4.02
3160 3840 2.474816 GAGCTGTGATATGGTTCGGAC 58.525 52.381 0.00 0.00 0.00 4.79
3163 3843 1.869754 CGGGAGCTGTGATATGGTTCG 60.870 57.143 0.00 0.00 0.00 3.95
3183 3863 4.689612 TCAGGGATCAACTAACATAGGC 57.310 45.455 0.00 0.00 0.00 3.93
3212 3892 2.241430 GGGAAAGGTACCACTAGCCAAT 59.759 50.000 15.94 0.00 0.00 3.16
3225 3905 1.133167 CAGGGGTTCAAAGGGAAAGGT 60.133 52.381 0.00 0.00 37.23 3.50
3238 3918 5.077564 GTTCAGAAAAAGATACCAGGGGTT 58.922 41.667 0.00 0.00 37.09 4.11
3243 3923 4.690748 TGCTCGTTCAGAAAAAGATACCAG 59.309 41.667 0.00 0.00 0.00 4.00
3250 3930 1.597663 ACCGTGCTCGTTCAGAAAAAG 59.402 47.619 7.47 0.00 35.01 2.27


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

AutoCloner maintained by Alex Coulton.