Multiple sequence alignment - TraesCS2D01G584600

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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 TraesCS2D01G584600 chr2D 100.000 3483 0 0 1 3483 643877344 643880826 0.000000e+00 6433.0
1 TraesCS2D01G584600 chr2D 82.368 777 121 10 1729 2491 643901665 643902439 0.000000e+00 662.0
2 TraesCS2D01G584600 chr2D 79.843 635 120 5 1759 2386 644016788 644017421 1.140000e-124 457.0
3 TraesCS2D01G584600 chr2D 97.101 138 4 0 4 141 609844023 609844160 2.090000e-57 233.0
4 TraesCS2D01G584600 chr2D 81.448 221 33 7 1064 1277 643901092 643901311 1.290000e-39 174.0
5 TraesCS2D01G584600 chr2A 90.217 1380 79 18 1341 2708 769003627 769004962 0.000000e+00 1749.0
6 TraesCS2D01G584600 chr2A 85.160 721 68 20 642 1343 769002693 769003393 0.000000e+00 702.0
7 TraesCS2D01G584600 chr2A 95.500 400 11 3 206 600 769002297 769002694 1.760000e-177 632.0
8 TraesCS2D01G584600 chr2A 80.724 773 128 11 1736 2489 769020848 769021618 1.800000e-162 582.0
9 TraesCS2D01G584600 chr2A 79.461 594 122 0 1759 2352 769145322 769145915 4.160000e-114 422.0
10 TraesCS2D01G584600 chr2A 75.000 768 106 36 2753 3483 769004961 769005679 3.420000e-70 276.0
11 TraesCS2D01G584600 chr2A 98.485 132 2 0 1 132 485395144 485395013 2.090000e-57 233.0
12 TraesCS2D01G584600 chr2A 84.404 218 28 5 1063 1277 769144924 769145138 3.520000e-50 209.0
13 TraesCS2D01G584600 chr2A 81.532 222 31 8 1064 1277 769020358 769020577 1.290000e-39 174.0
14 TraesCS2D01G584600 chr2A 78.390 236 36 9 1064 1284 769473973 769473738 4.690000e-29 139.0
15 TraesCS2D01G584600 chr2A 97.917 48 1 0 128 175 769002243 769002290 2.230000e-12 84.2
16 TraesCS2D01G584600 chr2A 82.474 97 13 2 3390 3483 769016458 769016553 8.010000e-12 82.4
17 TraesCS2D01G584600 chr2A 91.525 59 4 1 3389 3447 769016540 769016597 2.880000e-11 80.5
18 TraesCS2D01G584600 chr2B 94.479 1123 49 6 1404 2514 793169505 793168384 0.000000e+00 1718.0
19 TraesCS2D01G584600 chr2B 86.159 932 71 32 387 1282 793170512 793169603 0.000000e+00 953.0
20 TraesCS2D01G584600 chr2B 80.971 783 128 11 1729 2491 793141613 793140832 4.970000e-168 601.0
21 TraesCS2D01G584600 chr2B 83.358 673 68 24 2807 3467 793168333 793167693 1.800000e-162 582.0
22 TraesCS2D01G584600 chr2B 78.707 634 127 4 1759 2385 793034678 793034046 1.930000e-112 416.0
23 TraesCS2D01G584600 chr2B 77.837 564 117 6 1760 2319 792877160 792877719 3.330000e-90 342.0
24 TraesCS2D01G584600 chr2B 91.403 221 13 2 128 342 793170747 793170527 7.310000e-77 298.0
25 TraesCS2D01G584600 chr2B 95.172 145 5 2 1 144 675976866 675976723 9.730000e-56 228.0
26 TraesCS2D01G584600 chr2B 84.862 218 27 5 1063 1277 793035076 793034862 7.570000e-52 215.0
27 TraesCS2D01G584600 chr2B 81.900 221 32 5 1064 1277 793142141 793141922 2.760000e-41 180.0
28 TraesCS2D01G584600 chr2B 89.844 128 13 0 1476 1603 793034808 793034681 7.730000e-37 165.0
29 TraesCS2D01G584600 chr2B 77.350 234 35 13 1064 1279 792876619 792876852 4.720000e-24 122.0
30 TraesCS2D01G584600 chr3B 95.238 147 4 3 1 146 56982292 56982436 2.700000e-56 230.0
31 TraesCS2D01G584600 chr3B 97.727 132 3 0 1 132 469397551 469397682 9.730000e-56 228.0
32 TraesCS2D01G584600 chr3B 94.286 35 1 1 1417 1450 448314246 448314212 6.000000e-03 52.8
33 TraesCS2D01G584600 chr6B 96.403 139 4 1 1 139 58416825 58416688 9.730000e-56 228.0
34 TraesCS2D01G584600 chr6B 95.105 143 5 2 1 143 298992549 298992409 1.260000e-54 224.0
35 TraesCS2D01G584600 chr6B 90.196 51 5 0 2713 2763 287601714 287601664 2.240000e-07 67.6
36 TraesCS2D01G584600 chr1B 95.205 146 3 3 1 144 656809124 656809267 9.730000e-56 228.0
37 TraesCS2D01G584600 chr7D 95.714 140 5 1 1 140 545253932 545253794 1.260000e-54 224.0
38 TraesCS2D01G584600 chr7B 97.619 42 1 0 2714 2755 230218369 230218410 4.820000e-09 73.1
39 TraesCS2D01G584600 chr7B 95.556 45 2 0 2713 2757 710460648 710460604 4.820000e-09 73.1
40 TraesCS2D01G584600 chr3D 95.556 45 2 0 2714 2758 43735637 43735681 4.820000e-09 73.1
41 TraesCS2D01G584600 chr3D 94.595 37 1 1 1415 1450 348912666 348912630 4.860000e-04 56.5
42 TraesCS2D01G584600 chr4A 91.837 49 4 0 2713 2761 337145542 337145494 6.240000e-08 69.4
43 TraesCS2D01G584600 chr1D 89.286 56 5 1 2714 2768 367413221 367413166 6.240000e-08 69.4
44 TraesCS2D01G584600 chr5B 86.885 61 6 2 2704 2762 678663216 678663276 2.240000e-07 67.6
45 TraesCS2D01G584600 chr5B 85.938 64 5 2 2699 2758 485809909 485809972 8.070000e-07 65.8
46 TraesCS2D01G584600 chr1A 85.714 63 8 1 2714 2776 457958554 457958493 8.070000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G584600 chr2D 643877344 643880826 3482 False 6433.000000 6433 100.00000 1 3483 1 chr2D.!!$F2 3482
1 TraesCS2D01G584600 chr2D 644016788 644017421 633 False 457.000000 457 79.84300 1759 2386 1 chr2D.!!$F3 627
2 TraesCS2D01G584600 chr2D 643901092 643902439 1347 False 418.000000 662 81.90800 1064 2491 2 chr2D.!!$F4 1427
3 TraesCS2D01G584600 chr2A 769002243 769005679 3436 False 688.640000 1749 88.75880 128 3483 5 chr2A.!!$F1 3355
4 TraesCS2D01G584600 chr2A 769144924 769145915 991 False 315.500000 422 81.93250 1063 2352 2 chr2A.!!$F3 1289
5 TraesCS2D01G584600 chr2A 769016458 769021618 5160 False 229.725000 582 84.06375 1064 3483 4 chr2A.!!$F2 2419
6 TraesCS2D01G584600 chr2B 793167693 793170747 3054 True 887.750000 1718 88.84975 128 3467 4 chr2B.!!$R4 3339
7 TraesCS2D01G584600 chr2B 793140832 793142141 1309 True 390.500000 601 81.43550 1064 2491 2 chr2B.!!$R3 1427
8 TraesCS2D01G584600 chr2B 793034046 793035076 1030 True 265.333333 416 84.47100 1063 2385 3 chr2B.!!$R2 1322
9 TraesCS2D01G584600 chr2B 792876619 792877719 1100 False 232.000000 342 77.59350 1064 2319 2 chr2B.!!$F1 1255

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
627 650 0.174845 AATCGATCCGCTTCACCGAA 59.825 50.0 0.0 0.0 32.84 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 5789 0.174389 CAGGATGACTGTGACCGAGG 59.826 60.0 0.0 0.0 42.42 4.63 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
34 35 9.077885 TGAGAAAAACAAGAGCATTAATTAGGT 57.922 29.630 0.00 0.00 0.00 3.08
35 36 9.346725 GAGAAAAACAAGAGCATTAATTAGGTG 57.653 33.333 0.00 0.00 0.00 4.00
36 37 8.306761 AGAAAAACAAGAGCATTAATTAGGTGG 58.693 33.333 0.00 0.00 0.00 4.61
37 38 7.539034 AAAACAAGAGCATTAATTAGGTGGT 57.461 32.000 4.83 4.83 0.00 4.16
38 39 7.539034 AAACAAGAGCATTAATTAGGTGGTT 57.461 32.000 6.22 0.00 0.00 3.67
39 40 7.539034 AACAAGAGCATTAATTAGGTGGTTT 57.461 32.000 6.22 0.00 0.00 3.27
41 42 7.378181 ACAAGAGCATTAATTAGGTGGTTTTG 58.622 34.615 20.96 20.96 39.70 2.44
42 43 5.965922 AGAGCATTAATTAGGTGGTTTTGC 58.034 37.500 6.22 0.00 0.00 3.68
43 44 5.480073 AGAGCATTAATTAGGTGGTTTTGCA 59.520 36.000 6.22 0.00 0.00 4.08
44 45 6.014669 AGAGCATTAATTAGGTGGTTTTGCAA 60.015 34.615 0.00 0.00 0.00 4.08
45 46 6.529220 AGCATTAATTAGGTGGTTTTGCAAA 58.471 32.000 8.05 8.05 0.00 3.68
46 47 6.426633 AGCATTAATTAGGTGGTTTTGCAAAC 59.573 34.615 12.39 7.26 0.00 2.93
49 50 8.921670 CATTAATTAGGTGGTTTTGCAAACTAC 58.078 33.333 12.39 14.14 0.00 2.73
50 51 6.472686 AATTAGGTGGTTTTGCAAACTACA 57.527 33.333 12.39 8.40 33.92 2.74
51 52 5.916661 TTAGGTGGTTTTGCAAACTACAA 57.083 34.783 12.39 0.00 33.92 2.41
52 53 4.810191 AGGTGGTTTTGCAAACTACAAA 57.190 36.364 12.39 0.00 33.92 2.83
53 54 5.153950 AGGTGGTTTTGCAAACTACAAAA 57.846 34.783 12.39 0.00 42.93 2.44
54 55 5.552178 AGGTGGTTTTGCAAACTACAAAAA 58.448 33.333 12.39 0.00 45.64 1.94
55 56 5.641636 AGGTGGTTTTGCAAACTACAAAAAG 59.358 36.000 12.39 0.00 45.64 2.27
57 58 6.590677 GGTGGTTTTGCAAACTACAAAAAGTA 59.409 34.615 12.39 0.00 45.64 2.24
58 59 7.279090 GGTGGTTTTGCAAACTACAAAAAGTAT 59.721 33.333 12.39 0.00 45.64 2.12
61 62 8.332464 GGTTTTGCAAACTACAAAAAGTATTCC 58.668 33.333 12.39 0.00 45.64 3.01
62 63 8.874816 GTTTTGCAAACTACAAAAAGTATTCCA 58.125 29.630 12.39 0.00 45.64 3.53
63 64 7.995463 TTGCAAACTACAAAAAGTATTCCAC 57.005 32.000 0.00 0.00 30.93 4.02
64 65 6.508777 TGCAAACTACAAAAAGTATTCCACC 58.491 36.000 0.00 0.00 30.93 4.61
65 66 6.096987 TGCAAACTACAAAAAGTATTCCACCA 59.903 34.615 0.00 0.00 30.93 4.17
66 67 6.419710 GCAAACTACAAAAAGTATTCCACCAC 59.580 38.462 0.00 0.00 30.93 4.16
67 68 7.683463 GCAAACTACAAAAAGTATTCCACCACT 60.683 37.037 0.00 0.00 30.93 4.00
68 69 7.506328 AACTACAAAAAGTATTCCACCACTC 57.494 36.000 0.00 0.00 30.93 3.51
71 72 4.583073 ACAAAAAGTATTCCACCACTCACC 59.417 41.667 0.00 0.00 0.00 4.02
72 73 4.447138 AAAAGTATTCCACCACTCACCA 57.553 40.909 0.00 0.00 0.00 4.17
73 74 4.657814 AAAGTATTCCACCACTCACCAT 57.342 40.909 0.00 0.00 0.00 3.55
74 75 3.914426 AGTATTCCACCACTCACCATC 57.086 47.619 0.00 0.00 0.00 3.51
75 76 3.454858 AGTATTCCACCACTCACCATCT 58.545 45.455 0.00 0.00 0.00 2.90
77 78 3.914426 ATTCCACCACTCACCATCTAC 57.086 47.619 0.00 0.00 0.00 2.59
78 79 1.568504 TCCACCACTCACCATCTACC 58.431 55.000 0.00 0.00 0.00 3.18
79 80 1.078823 TCCACCACTCACCATCTACCT 59.921 52.381 0.00 0.00 0.00 3.08
80 81 1.909302 CCACCACTCACCATCTACCTT 59.091 52.381 0.00 0.00 0.00 3.50
81 82 2.355108 CCACCACTCACCATCTACCTTG 60.355 54.545 0.00 0.00 0.00 3.61
84 85 2.305927 CCACTCACCATCTACCTTGGTT 59.694 50.000 0.00 0.00 45.19 3.67
85 86 3.338249 CACTCACCATCTACCTTGGTTG 58.662 50.000 0.00 0.00 45.19 3.77
86 87 2.305927 ACTCACCATCTACCTTGGTTGG 59.694 50.000 7.30 7.30 45.19 3.77
87 88 2.305927 CTCACCATCTACCTTGGTTGGT 59.694 50.000 8.42 8.42 45.19 3.67
88 89 2.436417 CACCATCTACCTTGGTTGGTG 58.564 52.381 20.88 20.88 45.19 4.17
90 91 2.305927 ACCATCTACCTTGGTTGGTGAG 59.694 50.000 14.37 8.18 45.19 3.51
91 92 2.571653 CCATCTACCTTGGTTGGTGAGA 59.428 50.000 14.37 4.26 41.05 3.27
94 95 4.993705 TCTACCTTGGTTGGTGAGATTT 57.006 40.909 0.00 0.00 41.05 2.17
95 96 5.319043 TCTACCTTGGTTGGTGAGATTTT 57.681 39.130 0.00 0.00 41.05 1.82
96 97 5.701224 TCTACCTTGGTTGGTGAGATTTTT 58.299 37.500 0.00 0.00 41.05 1.94
97 98 4.670896 ACCTTGGTTGGTGAGATTTTTG 57.329 40.909 0.00 0.00 39.17 2.44
100 101 5.366477 ACCTTGGTTGGTGAGATTTTTGAAT 59.634 36.000 0.00 0.00 39.17 2.57
101 102 6.126796 ACCTTGGTTGGTGAGATTTTTGAATT 60.127 34.615 0.00 0.00 39.17 2.17
102 103 6.203338 CCTTGGTTGGTGAGATTTTTGAATTG 59.797 38.462 0.00 0.00 0.00 2.32
103 104 6.477053 TGGTTGGTGAGATTTTTGAATTGA 57.523 33.333 0.00 0.00 0.00 2.57
104 105 6.514947 TGGTTGGTGAGATTTTTGAATTGAG 58.485 36.000 0.00 0.00 0.00 3.02
106 107 5.138125 TGGTGAGATTTTTGAATTGAGCC 57.862 39.130 0.00 0.00 0.00 4.70
107 108 4.021192 TGGTGAGATTTTTGAATTGAGCCC 60.021 41.667 0.00 0.00 0.00 5.19
108 109 4.221482 GGTGAGATTTTTGAATTGAGCCCT 59.779 41.667 0.00 0.00 0.00 5.19
109 110 5.418840 GGTGAGATTTTTGAATTGAGCCCTA 59.581 40.000 0.00 0.00 0.00 3.53
110 111 6.097412 GGTGAGATTTTTGAATTGAGCCCTAT 59.903 38.462 0.00 0.00 0.00 2.57
111 112 7.285401 GGTGAGATTTTTGAATTGAGCCCTATA 59.715 37.037 0.00 0.00 0.00 1.31
112 113 8.686334 GTGAGATTTTTGAATTGAGCCCTATAA 58.314 33.333 0.00 0.00 0.00 0.98
113 114 9.253832 TGAGATTTTTGAATTGAGCCCTATAAA 57.746 29.630 0.00 0.00 0.00 1.40
114 115 9.521503 GAGATTTTTGAATTGAGCCCTATAAAC 57.478 33.333 0.00 0.00 0.00 2.01
115 116 8.478066 AGATTTTTGAATTGAGCCCTATAAACC 58.522 33.333 0.00 0.00 0.00 3.27
116 117 5.828299 TTTGAATTGAGCCCTATAAACCG 57.172 39.130 0.00 0.00 0.00 4.44
117 118 3.815809 TGAATTGAGCCCTATAAACCGG 58.184 45.455 0.00 0.00 0.00 5.28
118 119 3.456644 TGAATTGAGCCCTATAAACCGGA 59.543 43.478 9.46 0.00 0.00 5.14
120 121 4.513406 ATTGAGCCCTATAAACCGGAAA 57.487 40.909 9.46 0.00 0.00 3.13
121 122 3.553828 TGAGCCCTATAAACCGGAAAG 57.446 47.619 9.46 0.00 0.00 2.62
123 124 2.436911 GAGCCCTATAAACCGGAAAGGA 59.563 50.000 9.46 0.00 45.00 3.36
124 125 2.438392 AGCCCTATAAACCGGAAAGGAG 59.562 50.000 9.46 0.00 45.00 3.69
125 126 2.486727 GCCCTATAAACCGGAAAGGAGG 60.487 54.545 9.46 9.03 45.00 4.30
126 127 2.105993 CCCTATAAACCGGAAAGGAGGG 59.894 54.545 9.46 14.71 45.00 4.30
175 176 2.740981 GAGAAGGGCAATCAGATATGCG 59.259 50.000 9.90 0.00 43.47 4.73
188 189 3.256879 CAGATATGCGAAGAGGAGCCTTA 59.743 47.826 0.00 0.00 0.00 2.69
200 201 2.496470 AGGAGCCTTAACTTCCGTGTAG 59.504 50.000 0.00 0.00 0.00 2.74
329 336 3.525268 TCTAGCATGTCGATCTTGCAA 57.475 42.857 19.88 0.00 45.70 4.08
374 382 2.102252 GGGAGATGAGACACACTCCATC 59.898 54.545 19.59 0.00 44.34 3.51
394 406 2.632996 TCCATCGATCCCATCTAACCAC 59.367 50.000 0.00 0.00 0.00 4.16
409 421 7.257053 CCATCTAACCACCCCTAGCTAATTAAT 60.257 40.741 0.00 0.00 0.00 1.40
605 625 2.910199 TCCAAGGAATCAATCGAGCAG 58.090 47.619 0.00 0.00 0.00 4.24
612 635 1.224075 ATCAATCGAGCAGCCAATCG 58.776 50.000 0.00 0.00 40.26 3.34
616 639 1.068083 TCGAGCAGCCAATCGATCC 59.932 57.895 0.00 0.00 42.61 3.36
627 650 0.174845 AATCGATCCGCTTCACCGAA 59.825 50.000 0.00 0.00 32.84 4.30
692 715 6.148645 CGCCCTTAATTGCATACACATGTATA 59.851 38.462 0.00 0.00 39.06 1.47
757 780 0.537371 CACGAAAGCCCCAGGAAAGT 60.537 55.000 0.00 0.00 0.00 2.66
766 789 0.682852 CCCAGGAAAGTGACACCGTA 59.317 55.000 0.84 0.00 0.00 4.02
768 791 2.413837 CCAGGAAAGTGACACCGTAAG 58.586 52.381 0.84 0.00 0.00 2.34
769 792 2.036733 CCAGGAAAGTGACACCGTAAGA 59.963 50.000 0.84 0.00 43.02 2.10
771 794 4.315803 CAGGAAAGTGACACCGTAAGATT 58.684 43.478 0.84 0.00 43.02 2.40
774 797 4.329256 GGAAAGTGACACCGTAAGATTAGC 59.671 45.833 0.84 0.00 43.02 3.09
775 798 4.803098 AAGTGACACCGTAAGATTAGCT 57.197 40.909 0.84 0.00 43.02 3.32
776 799 4.373348 AGTGACACCGTAAGATTAGCTC 57.627 45.455 0.84 0.00 43.02 4.09
779 802 4.799428 GTGACACCGTAAGATTAGCTCTTC 59.201 45.833 0.00 0.00 43.32 2.87
781 804 5.000012 ACACCGTAAGATTAGCTCTTCTG 58.000 43.478 0.00 0.00 43.32 3.02
783 806 5.038033 CACCGTAAGATTAGCTCTTCTGAC 58.962 45.833 0.00 0.00 43.32 3.51
785 808 5.419471 ACCGTAAGATTAGCTCTTCTGACTT 59.581 40.000 10.24 0.00 43.32 3.01
787 810 6.326375 CGTAAGATTAGCTCTTCTGACTTGT 58.674 40.000 10.24 0.00 43.32 3.16
788 811 7.415318 CCGTAAGATTAGCTCTTCTGACTTGTA 60.415 40.741 10.24 0.00 43.32 2.41
790 813 6.215495 AGATTAGCTCTTCTGACTTGTACC 57.785 41.667 0.00 0.00 0.00 3.34
791 814 4.803098 TTAGCTCTTCTGACTTGTACCC 57.197 45.455 0.00 0.00 0.00 3.69
792 815 1.903183 AGCTCTTCTGACTTGTACCCC 59.097 52.381 0.00 0.00 0.00 4.95
796 819 3.578716 CTCTTCTGACTTGTACCCCTCAA 59.421 47.826 0.00 0.00 0.00 3.02
797 820 3.323979 TCTTCTGACTTGTACCCCTCAAC 59.676 47.826 0.00 0.00 0.00 3.18
799 822 3.042682 TCTGACTTGTACCCCTCAACAA 58.957 45.455 0.00 0.00 34.57 2.83
800 823 3.650942 TCTGACTTGTACCCCTCAACAAT 59.349 43.478 0.00 0.00 35.21 2.71
801 824 4.841813 TCTGACTTGTACCCCTCAACAATA 59.158 41.667 0.00 0.00 35.21 1.90
802 825 5.308497 TCTGACTTGTACCCCTCAACAATAA 59.692 40.000 0.00 0.00 35.21 1.40
804 827 6.366340 TGACTTGTACCCCTCAACAATAAAA 58.634 36.000 0.00 0.00 35.21 1.52
805 828 6.834451 TGACTTGTACCCCTCAACAATAAAAA 59.166 34.615 0.00 0.00 35.21 1.94
841 868 0.804364 TTGTAGCTTCAAGCCATGCG 59.196 50.000 5.53 0.00 43.77 4.73
883 910 2.796593 GTTTGTAAGCAACGTACGTCCT 59.203 45.455 23.05 17.60 33.82 3.85
976 1021 6.042437 AGGACCGACCGATTATAAATACCTTT 59.958 38.462 0.00 0.00 44.74 3.11
978 1023 5.467735 ACCGACCGATTATAAATACCTTTGC 59.532 40.000 0.00 0.00 0.00 3.68
1016 1065 0.250166 GCCACACGACACCCTTTAGT 60.250 55.000 0.00 0.00 0.00 2.24
1019 1068 2.611224 CCACACGACACCCTTTAGTACC 60.611 54.545 0.00 0.00 0.00 3.34
1020 1069 2.298163 CACACGACACCCTTTAGTACCT 59.702 50.000 0.00 0.00 0.00 3.08
1021 1070 2.298163 ACACGACACCCTTTAGTACCTG 59.702 50.000 0.00 0.00 0.00 4.00
1024 1073 2.564062 CGACACCCTTTAGTACCTGGAA 59.436 50.000 0.00 0.00 0.00 3.53
1027 1076 5.175388 ACACCCTTTAGTACCTGGAAATC 57.825 43.478 0.00 0.00 0.00 2.17
1028 1077 4.018688 ACACCCTTTAGTACCTGGAAATCC 60.019 45.833 0.00 0.00 0.00 3.01
1029 1078 4.227527 CACCCTTTAGTACCTGGAAATCCT 59.772 45.833 0.00 0.00 36.82 3.24
1030 1079 5.427481 CACCCTTTAGTACCTGGAAATCCTA 59.573 44.000 0.00 0.00 36.82 2.94
1032 1081 7.291651 CACCCTTTAGTACCTGGAAATCCTATA 59.708 40.741 0.00 0.00 36.82 1.31
1164 4023 2.737376 GACTTCCACGCGGTGTCC 60.737 66.667 12.47 0.00 33.68 4.02
1200 4059 2.223876 ACACATCGTCAAGTACCACGTT 60.224 45.455 8.86 0.00 37.30 3.99
1311 4170 6.910433 GGCACAAGTATACAATTTTCGTATGG 59.090 38.462 5.50 0.00 32.01 2.74
1312 4171 7.414762 GGCACAAGTATACAATTTTCGTATGGT 60.415 37.037 5.50 0.00 32.01 3.55
1364 4463 8.623310 TGTATGTATGTATGACACTTGTTACG 57.377 34.615 0.00 0.00 0.00 3.18
1370 4469 5.647589 TGTATGACACTTGTTACGATCCTC 58.352 41.667 0.00 0.00 0.00 3.71
1371 4470 3.587797 TGACACTTGTTACGATCCTCC 57.412 47.619 0.00 0.00 0.00 4.30
1377 4476 5.238650 ACACTTGTTACGATCCTCCAAAAAG 59.761 40.000 0.00 0.00 0.00 2.27
1379 4478 6.017440 CACTTGTTACGATCCTCCAAAAAGAA 60.017 38.462 0.00 0.00 0.00 2.52
1399 4502 8.597662 AAAGAAAGTATGACGCTTGTTACTTA 57.402 30.769 0.00 0.00 34.64 2.24
1400 4503 7.578169 AGAAAGTATGACGCTTGTTACTTAC 57.422 36.000 0.00 0.00 34.64 2.34
1401 4504 7.376615 AGAAAGTATGACGCTTGTTACTTACT 58.623 34.615 0.00 0.00 34.64 2.24
1402 4505 6.946229 AAGTATGACGCTTGTTACTTACTG 57.054 37.500 0.00 0.00 34.12 2.74
1403 4506 6.022163 AGTATGACGCTTGTTACTTACTGT 57.978 37.500 0.00 0.00 0.00 3.55
1453 4556 1.912971 GGTGCTCCTAACCGGGAAT 59.087 57.895 6.32 0.00 34.66 3.01
1671 4781 1.402787 ACGGCCATCAATCCAAATCC 58.597 50.000 2.24 0.00 0.00 3.01
1963 5122 2.759795 GCCCACTGCTCCTCCTTT 59.240 61.111 0.00 0.00 36.87 3.11
2341 5500 1.255667 ACAGCCGTGTCGAGGGTATT 61.256 55.000 0.00 0.00 37.77 1.89
2411 5576 3.349006 CGCCGTGCTTGCTGAAGT 61.349 61.111 0.00 0.00 0.00 3.01
2433 5621 0.874175 GTGAGCGTGTGTGTGCTACA 60.874 55.000 0.00 0.00 42.60 2.74
2439 5627 1.124297 CGTGTGTGTGCTACAATCGTC 59.876 52.381 0.00 0.00 41.89 4.20
2514 5710 4.040829 TCAGACATCATGCCCCAAGTATAG 59.959 45.833 0.00 0.00 0.00 1.31
2525 5721 3.116862 CCCCAAGTATAGGAGTCCTACCA 60.117 52.174 21.46 9.51 39.10 3.25
2564 5760 9.650371 CACCATACATCGTAAAATATGTCTTTG 57.350 33.333 0.00 0.00 37.50 2.77
2586 5789 3.565902 GGCTATGGTTCCAGAAATGCTAC 59.434 47.826 0.00 0.00 0.00 3.58
2590 5793 2.280628 GGTTCCAGAAATGCTACCTCG 58.719 52.381 0.00 0.00 0.00 4.63
2596 5799 1.899814 AGAAATGCTACCTCGGTCACA 59.100 47.619 0.00 0.00 0.00 3.58
2615 5818 3.407424 CAGTCATCCTGTTTCCTGTCA 57.593 47.619 0.00 0.00 36.37 3.58
2616 5819 3.070018 CAGTCATCCTGTTTCCTGTCAC 58.930 50.000 0.00 0.00 36.37 3.67
2617 5820 2.975489 AGTCATCCTGTTTCCTGTCACT 59.025 45.455 0.00 0.00 0.00 3.41
2618 5821 4.021104 CAGTCATCCTGTTTCCTGTCACTA 60.021 45.833 0.00 0.00 36.37 2.74
2619 5822 4.021016 AGTCATCCTGTTTCCTGTCACTAC 60.021 45.833 0.00 0.00 0.00 2.73
2646 5849 1.105457 TCAATGCAGCATAAGGCCAC 58.895 50.000 8.75 0.00 46.50 5.01
2647 5850 0.818938 CAATGCAGCATAAGGCCACA 59.181 50.000 8.75 0.00 46.50 4.17
2651 5854 0.456653 GCAGCATAAGGCCACAAACG 60.457 55.000 5.01 0.00 46.50 3.60
2684 5887 7.977293 ACCAAAACTTACCATTTCAAGTGTAAC 59.023 33.333 0.00 0.00 35.23 2.50
2686 5889 7.648039 AAACTTACCATTTCAAGTGTAACCA 57.352 32.000 0.00 0.00 37.80 3.67
2709 5912 9.696572 ACCAACGGTGTATAGATATGATATACT 57.303 33.333 0.00 0.00 37.13 2.12
2732 5935 8.653036 ACTTCCTAGTATAAAGTTGAGTCACT 57.347 34.615 0.00 0.00 31.21 3.41
2733 5936 9.091220 ACTTCCTAGTATAAAGTTGAGTCACTT 57.909 33.333 0.00 0.00 33.78 3.16
2742 5945 8.934023 ATAAAGTTGAGTCACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
2743 5946 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2744 5947 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
2745 5948 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
2746 5949 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
2747 5950 4.202377 TGAGTCACTTATTTTGGGACGGAA 60.202 41.667 0.00 0.00 33.84 4.30
2748 5951 4.721132 AGTCACTTATTTTGGGACGGAAA 58.279 39.130 0.00 0.00 33.84 3.13
2749 5952 4.760204 AGTCACTTATTTTGGGACGGAAAG 59.240 41.667 0.00 0.00 33.84 2.62
2750 5953 4.758165 GTCACTTATTTTGGGACGGAAAGA 59.242 41.667 0.00 0.00 0.00 2.52
2751 5954 5.001232 TCACTTATTTTGGGACGGAAAGAG 58.999 41.667 0.00 0.00 0.00 2.85
2752 5955 4.760204 CACTTATTTTGGGACGGAAAGAGT 59.240 41.667 0.00 0.00 0.00 3.24
2753 5956 5.935789 CACTTATTTTGGGACGGAAAGAGTA 59.064 40.000 0.00 0.00 0.00 2.59
2762 5965 4.395231 GGGACGGAAAGAGTAGAAAATTGG 59.605 45.833 0.00 0.00 0.00 3.16
2795 5998 4.722700 TGAAAGGGCTGCTCCGGC 62.723 66.667 0.00 0.00 39.26 6.13
2819 6022 0.388520 CAGACGGACGTTGCAGATCA 60.389 55.000 0.00 0.00 0.00 2.92
2844 6047 0.537188 AGCAGAAATCGGACGGACAT 59.463 50.000 0.00 0.00 0.00 3.06
2848 6051 3.243301 GCAGAAATCGGACGGACATACTA 60.243 47.826 0.00 0.00 0.00 1.82
2870 6080 3.536917 CCGATGGCCTGGCGAGTA 61.537 66.667 13.40 0.00 0.00 2.59
2885 6095 4.078516 GTAAGGCGCGGTGGAGGT 62.079 66.667 8.83 0.00 0.00 3.85
2910 6120 5.517054 CGAGAAGACATGCTACCTAGAAAAC 59.483 44.000 0.00 0.00 0.00 2.43
2919 6129 0.669625 ACCTAGAAAACCTGTCGCGC 60.670 55.000 0.00 0.00 0.00 6.86
2941 6151 7.145323 GCGCCCACAATACTTAAATCATTTAT 58.855 34.615 0.00 0.00 0.00 1.40
2942 6152 7.651704 GCGCCCACAATACTTAAATCATTTATT 59.348 33.333 0.00 0.00 0.00 1.40
2943 6153 9.528018 CGCCCACAATACTTAAATCATTTATTT 57.472 29.630 0.00 0.00 40.87 1.40
2991 6201 2.082366 GTGCGTTGCAGCGGAAATG 61.082 57.895 24.49 0.00 40.08 2.32
2999 6213 2.431454 TGCAGCGGAAATGTCATACAA 58.569 42.857 0.00 0.00 0.00 2.41
3000 6214 2.161410 TGCAGCGGAAATGTCATACAAC 59.839 45.455 0.00 0.00 0.00 3.32
3011 6225 4.991153 TGTCATACAACTCCTCTAGCTG 57.009 45.455 0.00 0.00 0.00 4.24
3045 6259 0.539438 AAACCATTGCGAGCCTTGGA 60.539 50.000 16.82 0.00 33.36 3.53
3048 6262 0.819582 CCATTGCGAGCCTTGGATTT 59.180 50.000 7.39 0.00 0.00 2.17
3049 6263 2.023673 CCATTGCGAGCCTTGGATTTA 58.976 47.619 7.39 0.00 0.00 1.40
3063 6277 5.465724 CCTTGGATTTATAGTGTAGGAACGC 59.534 44.000 0.00 0.00 36.31 4.84
3064 6278 5.601583 TGGATTTATAGTGTAGGAACGCA 57.398 39.130 0.00 0.00 38.65 5.24
3121 6335 3.031660 GCTTAGCTAGCGTCAACGT 57.968 52.632 9.55 0.00 40.71 3.99
3258 6475 9.626045 CAAACTTTGTTAGGAATGGAGTAAATC 57.374 33.333 0.00 0.00 0.00 2.17
3273 6493 7.280356 TGGAGTAAATCTATTTAGGCCTTCAC 58.720 38.462 12.58 0.00 33.31 3.18
3305 6525 3.117663 TCAGTAGGAACCTGTTTTTGCCT 60.118 43.478 3.36 0.00 0.00 4.75
3341 6561 1.255667 CCCTTGAAGCTGCTGCCAAT 61.256 55.000 12.44 0.00 40.80 3.16
3367 6609 7.589958 TTTTGCATTGTTTTTCCTAGTAGGA 57.410 32.000 15.33 15.33 44.10 2.94
3373 6615 6.999705 TTGTTTTTCCTAGTAGGACCACTA 57.000 37.500 18.97 9.47 45.78 2.74
3380 6622 4.434545 CTAGTAGGACCACTAGGCAGTA 57.565 50.000 17.06 0.00 42.85 2.74
3381 6623 3.015675 AGTAGGACCACTAGGCAGTAC 57.984 52.381 0.00 0.00 39.06 2.73
3383 6625 0.039326 AGGACCACTAGGCAGTACGT 59.961 55.000 0.00 0.00 39.06 3.57
3384 6626 1.283029 AGGACCACTAGGCAGTACGTA 59.717 52.381 0.00 0.00 39.06 3.57
3385 6627 2.094675 GGACCACTAGGCAGTACGTAA 58.905 52.381 0.00 0.00 39.06 3.18
3386 6628 2.098770 GGACCACTAGGCAGTACGTAAG 59.901 54.545 0.00 0.00 41.20 2.34
3387 6629 3.012518 GACCACTAGGCAGTACGTAAGA 58.987 50.000 0.00 0.00 38.98 2.10
3388 6630 3.015327 ACCACTAGGCAGTACGTAAGAG 58.985 50.000 0.00 0.00 38.98 2.85
3455 6703 0.539986 TGTTCTTCCTCGTATGGCCC 59.460 55.000 0.00 0.00 0.00 5.80
3461 6709 0.399949 TCCTCGTATGGCCCCTTGAT 60.400 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.912634 CCTAATTAATGCTCTTGTTTTTCTCAA 57.087 29.630 0.00 0.00 0.00 3.02
9 10 9.346725 CACCTAATTAATGCTCTTGTTTTTCTC 57.653 33.333 0.00 0.00 0.00 2.87
10 11 8.306761 CCACCTAATTAATGCTCTTGTTTTTCT 58.693 33.333 0.00 0.00 0.00 2.52
12 13 7.962441 ACCACCTAATTAATGCTCTTGTTTTT 58.038 30.769 0.00 0.00 0.00 1.94
17 18 6.311200 GCAAAACCACCTAATTAATGCTCTTG 59.689 38.462 0.00 0.00 0.00 3.02
20 21 5.719173 TGCAAAACCACCTAATTAATGCTC 58.281 37.500 0.00 0.00 32.74 4.26
22 23 6.426633 AGTTTGCAAAACCACCTAATTAATGC 59.573 34.615 14.67 0.00 0.00 3.56
25 26 8.008513 TGTAGTTTGCAAAACCACCTAATTAA 57.991 30.769 14.67 0.00 0.00 1.40
26 27 7.584122 TGTAGTTTGCAAAACCACCTAATTA 57.416 32.000 14.67 0.00 0.00 1.40
27 28 6.472686 TGTAGTTTGCAAAACCACCTAATT 57.527 33.333 14.67 0.00 0.00 1.40
28 29 6.472686 TTGTAGTTTGCAAAACCACCTAAT 57.527 33.333 14.67 0.00 0.00 1.73
29 30 5.916661 TTGTAGTTTGCAAAACCACCTAA 57.083 34.783 14.67 0.82 0.00 2.69
30 31 5.916661 TTTGTAGTTTGCAAAACCACCTA 57.083 34.783 14.67 7.87 33.51 3.08
31 32 4.810191 TTTGTAGTTTGCAAAACCACCT 57.190 36.364 14.67 8.91 33.51 4.00
34 35 8.779354 AATACTTTTTGTAGTTTGCAAAACCA 57.221 26.923 14.67 7.96 42.99 3.67
35 36 8.332464 GGAATACTTTTTGTAGTTTGCAAAACC 58.668 33.333 14.67 2.18 42.99 3.27
36 37 8.874816 TGGAATACTTTTTGTAGTTTGCAAAAC 58.125 29.630 14.67 10.26 42.99 2.43
37 38 8.874816 GTGGAATACTTTTTGTAGTTTGCAAAA 58.125 29.630 14.67 0.00 42.03 2.44
38 39 7.492994 GGTGGAATACTTTTTGTAGTTTGCAAA 59.507 33.333 8.05 8.05 34.24 3.68
39 40 6.981559 GGTGGAATACTTTTTGTAGTTTGCAA 59.018 34.615 0.00 0.00 34.24 4.08
41 42 6.419710 GTGGTGGAATACTTTTTGTAGTTTGC 59.580 38.462 0.00 0.00 34.24 3.68
42 43 7.712797 AGTGGTGGAATACTTTTTGTAGTTTG 58.287 34.615 0.00 0.00 34.24 2.93
43 44 7.558444 TGAGTGGTGGAATACTTTTTGTAGTTT 59.442 33.333 0.00 0.00 34.24 2.66
44 45 7.012989 GTGAGTGGTGGAATACTTTTTGTAGTT 59.987 37.037 0.00 0.00 34.24 2.24
45 46 6.485648 GTGAGTGGTGGAATACTTTTTGTAGT 59.514 38.462 0.00 0.00 34.24 2.73
46 47 6.072673 GGTGAGTGGTGGAATACTTTTTGTAG 60.073 42.308 0.00 0.00 34.24 2.74
49 50 4.582656 TGGTGAGTGGTGGAATACTTTTTG 59.417 41.667 0.00 0.00 0.00 2.44
50 51 4.798882 TGGTGAGTGGTGGAATACTTTTT 58.201 39.130 0.00 0.00 0.00 1.94
51 52 4.447138 TGGTGAGTGGTGGAATACTTTT 57.553 40.909 0.00 0.00 0.00 2.27
52 53 4.289672 AGATGGTGAGTGGTGGAATACTTT 59.710 41.667 0.00 0.00 0.00 2.66
53 54 3.846588 AGATGGTGAGTGGTGGAATACTT 59.153 43.478 0.00 0.00 0.00 2.24
54 55 3.454858 AGATGGTGAGTGGTGGAATACT 58.545 45.455 0.00 0.00 0.00 2.12
55 56 3.914426 AGATGGTGAGTGGTGGAATAC 57.086 47.619 0.00 0.00 0.00 1.89
57 58 2.505819 GGTAGATGGTGAGTGGTGGAAT 59.494 50.000 0.00 0.00 0.00 3.01
58 59 1.906574 GGTAGATGGTGAGTGGTGGAA 59.093 52.381 0.00 0.00 0.00 3.53
61 62 2.355108 CCAAGGTAGATGGTGAGTGGTG 60.355 54.545 0.00 0.00 33.08 4.17
62 63 1.909302 CCAAGGTAGATGGTGAGTGGT 59.091 52.381 0.00 0.00 33.08 4.16
63 64 2.698855 CCAAGGTAGATGGTGAGTGG 57.301 55.000 0.00 0.00 33.08 4.00
71 72 3.981071 TCTCACCAACCAAGGTAGATG 57.019 47.619 0.00 0.00 40.77 2.90
72 73 5.520748 AAATCTCACCAACCAAGGTAGAT 57.479 39.130 0.00 0.00 40.77 1.98
73 74 4.993705 AAATCTCACCAACCAAGGTAGA 57.006 40.909 0.00 0.00 40.77 2.59
74 75 5.534654 TCAAAAATCTCACCAACCAAGGTAG 59.465 40.000 0.00 0.00 40.77 3.18
75 76 5.450453 TCAAAAATCTCACCAACCAAGGTA 58.550 37.500 0.00 0.00 40.77 3.08
77 78 4.935352 TCAAAAATCTCACCAACCAAGG 57.065 40.909 0.00 0.00 0.00 3.61
78 79 6.985645 TCAATTCAAAAATCTCACCAACCAAG 59.014 34.615 0.00 0.00 0.00 3.61
79 80 6.882656 TCAATTCAAAAATCTCACCAACCAA 58.117 32.000 0.00 0.00 0.00 3.67
80 81 6.477053 TCAATTCAAAAATCTCACCAACCA 57.523 33.333 0.00 0.00 0.00 3.67
81 82 5.406477 GCTCAATTCAAAAATCTCACCAACC 59.594 40.000 0.00 0.00 0.00 3.77
84 85 4.021192 GGGCTCAATTCAAAAATCTCACCA 60.021 41.667 0.00 0.00 0.00 4.17
85 86 4.221482 AGGGCTCAATTCAAAAATCTCACC 59.779 41.667 0.00 0.00 0.00 4.02
86 87 5.397142 AGGGCTCAATTCAAAAATCTCAC 57.603 39.130 0.00 0.00 0.00 3.51
87 88 8.821686 TTATAGGGCTCAATTCAAAAATCTCA 57.178 30.769 0.00 0.00 0.00 3.27
88 89 9.521503 GTTTATAGGGCTCAATTCAAAAATCTC 57.478 33.333 0.00 0.00 0.00 2.75
90 91 7.435192 CGGTTTATAGGGCTCAATTCAAAAATC 59.565 37.037 0.00 0.00 0.00 2.17
91 92 7.264947 CGGTTTATAGGGCTCAATTCAAAAAT 58.735 34.615 0.00 0.00 0.00 1.82
94 95 4.642885 CCGGTTTATAGGGCTCAATTCAAA 59.357 41.667 0.00 0.00 0.00 2.69
95 96 4.080243 TCCGGTTTATAGGGCTCAATTCAA 60.080 41.667 0.00 0.00 0.00 2.69
96 97 3.456644 TCCGGTTTATAGGGCTCAATTCA 59.543 43.478 0.00 0.00 0.00 2.57
97 98 4.081322 TCCGGTTTATAGGGCTCAATTC 57.919 45.455 0.00 0.00 0.00 2.17
100 101 3.371166 CCTTTCCGGTTTATAGGGCTCAA 60.371 47.826 0.00 0.00 0.00 3.02
101 102 2.171870 CCTTTCCGGTTTATAGGGCTCA 59.828 50.000 0.00 0.00 0.00 4.26
102 103 2.436911 TCCTTTCCGGTTTATAGGGCTC 59.563 50.000 0.00 0.00 0.00 4.70
103 104 2.438392 CTCCTTTCCGGTTTATAGGGCT 59.562 50.000 0.00 0.00 0.00 5.19
104 105 2.486727 CCTCCTTTCCGGTTTATAGGGC 60.487 54.545 0.00 0.00 0.00 5.19
106 107 3.043418 TCCCTCCTTTCCGGTTTATAGG 58.957 50.000 0.00 4.62 0.00 2.57
107 108 3.710165 ACTCCCTCCTTTCCGGTTTATAG 59.290 47.826 0.00 0.00 0.00 1.31
108 109 3.727948 ACTCCCTCCTTTCCGGTTTATA 58.272 45.455 0.00 0.00 0.00 0.98
109 110 2.558974 ACTCCCTCCTTTCCGGTTTAT 58.441 47.619 0.00 0.00 0.00 1.40
110 111 2.034436 ACTCCCTCCTTTCCGGTTTA 57.966 50.000 0.00 0.00 0.00 2.01
111 112 1.907255 CTACTCCCTCCTTTCCGGTTT 59.093 52.381 0.00 0.00 0.00 3.27
112 113 1.569653 CTACTCCCTCCTTTCCGGTT 58.430 55.000 0.00 0.00 0.00 4.44
113 114 0.976590 GCTACTCCCTCCTTTCCGGT 60.977 60.000 0.00 0.00 0.00 5.28
114 115 0.688087 AGCTACTCCCTCCTTTCCGG 60.688 60.000 0.00 0.00 0.00 5.14
115 116 1.957877 CTAGCTACTCCCTCCTTTCCG 59.042 57.143 0.00 0.00 0.00 4.30
116 117 1.689813 GCTAGCTACTCCCTCCTTTCC 59.310 57.143 7.70 0.00 0.00 3.13
117 118 2.673258 AGCTAGCTACTCCCTCCTTTC 58.327 52.381 17.69 0.00 0.00 2.62
118 119 2.858787 AGCTAGCTACTCCCTCCTTT 57.141 50.000 17.69 0.00 0.00 3.11
120 121 2.708759 TCTAGCTAGCTACTCCCTCCT 58.291 52.381 20.67 0.00 0.00 3.69
121 122 3.512219 TTCTAGCTAGCTACTCCCTCC 57.488 52.381 20.67 0.00 0.00 4.30
122 123 3.192633 GCATTCTAGCTAGCTACTCCCTC 59.807 52.174 20.67 5.10 0.00 4.30
123 124 3.161866 GCATTCTAGCTAGCTACTCCCT 58.838 50.000 20.67 0.00 0.00 4.20
124 125 2.232696 GGCATTCTAGCTAGCTACTCCC 59.767 54.545 20.67 12.18 34.17 4.30
125 126 3.161866 AGGCATTCTAGCTAGCTACTCC 58.838 50.000 20.67 15.26 34.17 3.85
126 127 4.279671 TGAAGGCATTCTAGCTAGCTACTC 59.720 45.833 20.67 7.68 36.33 2.59
175 176 2.234168 ACGGAAGTTAAGGCTCCTCTTC 59.766 50.000 13.40 13.40 46.40 2.87
200 201 1.114627 GCCAATCATCCCCTTGTTCC 58.885 55.000 0.00 0.00 0.00 3.62
329 336 5.163519 CGGAGGAATAATTTTGAATGGCACT 60.164 40.000 0.00 0.00 0.00 4.40
374 382 2.289694 GGTGGTTAGATGGGATCGATGG 60.290 54.545 0.54 0.00 0.00 3.51
394 406 4.163458 TGGCGGATATTAATTAGCTAGGGG 59.837 45.833 0.00 0.00 0.00 4.79
409 421 1.227943 GGCAGCTTGATGGCGGATA 60.228 57.895 0.00 0.00 35.90 2.59
605 625 1.643832 GTGAAGCGGATCGATTGGC 59.356 57.895 12.22 12.22 35.04 4.52
637 660 0.734253 CAAAGAGCTGACCGGACTCG 60.734 60.000 9.46 0.00 35.56 4.18
641 664 2.048222 CGCAAAGAGCTGACCGGA 60.048 61.111 9.46 0.00 42.61 5.14
692 715 3.332034 GGCGACATGTTACCAAACTAGT 58.668 45.455 12.02 0.00 36.51 2.57
768 791 5.353111 GGGTACAAGTCAGAAGAGCTAATC 58.647 45.833 0.00 0.00 0.00 1.75
769 792 4.162509 GGGGTACAAGTCAGAAGAGCTAAT 59.837 45.833 0.00 0.00 0.00 1.73
771 794 3.097614 GGGGTACAAGTCAGAAGAGCTA 58.902 50.000 0.00 0.00 0.00 3.32
774 797 3.165875 TGAGGGGTACAAGTCAGAAGAG 58.834 50.000 0.00 0.00 0.00 2.85
775 798 3.254093 TGAGGGGTACAAGTCAGAAGA 57.746 47.619 0.00 0.00 0.00 2.87
776 799 3.071023 TGTTGAGGGGTACAAGTCAGAAG 59.929 47.826 0.00 0.00 0.00 2.85
779 802 3.485463 TTGTTGAGGGGTACAAGTCAG 57.515 47.619 0.00 0.00 0.00 3.51
781 804 6.887626 TTTTATTGTTGAGGGGTACAAGTC 57.112 37.500 0.00 0.00 0.00 3.01
806 829 6.456795 AGCTACAAGTCAGAAAAGCTTTTT 57.543 33.333 24.58 12.30 36.98 1.94
807 830 6.456795 AAGCTACAAGTCAGAAAAGCTTTT 57.543 33.333 24.08 24.08 45.37 2.27
824 851 0.375106 GTCGCATGGCTTGAAGCTAC 59.625 55.000 17.59 1.56 41.99 3.58
828 855 0.455633 GCAAGTCGCATGGCTTGAAG 60.456 55.000 13.33 0.00 43.29 3.02
841 868 2.413239 CGTGGATCAACATGTGCAAGTC 60.413 50.000 0.00 0.00 0.00 3.01
854 881 2.222213 CGTTGCTTACAAACGTGGATCA 59.778 45.455 0.00 0.00 37.58 2.92
883 910 1.374631 CCACAAGTCGCAGCTAGCA 60.375 57.895 18.83 0.00 46.13 3.49
1016 1065 5.087923 TGGAGCTATAGGATTTCCAGGTA 57.912 43.478 1.04 0.00 38.89 3.08
1019 1068 4.533707 TGGATGGAGCTATAGGATTTCCAG 59.466 45.833 1.04 0.00 40.93 3.86
1020 1069 4.502415 TGGATGGAGCTATAGGATTTCCA 58.498 43.478 1.04 0.00 41.75 3.53
1021 1070 5.428131 AGATGGATGGAGCTATAGGATTTCC 59.572 44.000 1.04 0.00 0.00 3.13
1024 1073 4.163839 GCAGATGGATGGAGCTATAGGATT 59.836 45.833 1.04 0.00 0.00 3.01
1027 1076 3.106054 AGCAGATGGATGGAGCTATAGG 58.894 50.000 1.04 0.00 33.06 2.57
1028 1077 3.679361 GCAGCAGATGGATGGAGCTATAG 60.679 52.174 0.00 0.00 33.59 1.31
1029 1078 2.235650 GCAGCAGATGGATGGAGCTATA 59.764 50.000 0.00 0.00 33.59 1.31
1030 1079 1.003349 GCAGCAGATGGATGGAGCTAT 59.997 52.381 0.00 0.00 33.59 2.97
1032 1081 1.148723 GCAGCAGATGGATGGAGCT 59.851 57.895 0.00 0.00 35.63 4.09
1164 4023 3.636231 TGTTCCAGGTCCGGGCAG 61.636 66.667 9.07 0.00 0.00 4.85
1311 4170 2.152489 CACTTAGTCACGTACGCACAAC 59.848 50.000 16.72 8.41 0.00 3.32
1312 4171 2.033174 TCACTTAGTCACGTACGCACAA 59.967 45.455 16.72 8.48 0.00 3.33
1364 4463 6.675728 GCGTCATACTTTCTTTTTGGAGGATC 60.676 42.308 0.00 0.00 0.00 3.36
1370 4469 5.519722 ACAAGCGTCATACTTTCTTTTTGG 58.480 37.500 0.00 0.00 0.00 3.28
1371 4470 7.855904 AGTAACAAGCGTCATACTTTCTTTTTG 59.144 33.333 0.00 0.00 0.00 2.44
1377 4476 7.115947 ACAGTAAGTAACAAGCGTCATACTTTC 59.884 37.037 10.45 7.06 38.92 2.62
1379 4478 6.453092 ACAGTAAGTAACAAGCGTCATACTT 58.547 36.000 10.17 10.17 40.59 2.24
1399 4502 4.518970 CCCTGCAACAACAGTAAATACAGT 59.481 41.667 0.00 0.00 35.83 3.55
1400 4503 4.615912 GCCCTGCAACAACAGTAAATACAG 60.616 45.833 0.00 0.00 35.83 2.74
1401 4504 3.254657 GCCCTGCAACAACAGTAAATACA 59.745 43.478 0.00 0.00 35.83 2.29
1402 4505 3.506067 AGCCCTGCAACAACAGTAAATAC 59.494 43.478 0.00 0.00 35.83 1.89
1403 4506 3.505680 CAGCCCTGCAACAACAGTAAATA 59.494 43.478 0.00 0.00 35.83 1.40
1453 4556 1.522092 CATCCCCTGCTCGCTGTTA 59.478 57.895 0.00 0.00 0.00 2.41
1652 4755 1.402787 GGATTTGGATTGATGGCCGT 58.597 50.000 0.00 0.00 0.00 5.68
1653 4756 0.311790 CGGATTTGGATTGATGGCCG 59.688 55.000 0.00 0.00 0.00 6.13
1671 4781 3.533606 ACCATCCAATCTGAAGACTCG 57.466 47.619 0.00 0.00 0.00 4.18
2077 5236 2.202570 GGCGTACGCACATCGAGT 60.203 61.111 37.99 0.00 44.11 4.18
2191 5350 2.103538 GAGAACCGCGTCGCCATA 59.896 61.111 12.44 0.00 0.00 2.74
2382 5547 1.995991 CACGGCGACTAACCAATCG 59.004 57.895 16.62 0.00 41.32 3.34
2411 5576 2.460275 GCACACACACGCTCACACA 61.460 57.895 0.00 0.00 0.00 3.72
2433 5621 2.159043 CCACTAGCACCATGAGACGATT 60.159 50.000 0.00 0.00 0.00 3.34
2439 5627 3.058016 CACAAAACCACTAGCACCATGAG 60.058 47.826 0.00 0.00 0.00 2.90
2514 5710 4.215908 TCACACTGATATGGTAGGACTCC 58.784 47.826 0.00 0.00 0.00 3.85
2525 5721 6.015095 ACGATGTATGGTGATCACACTGATAT 60.015 38.462 26.47 13.04 45.32 1.63
2564 5760 2.659428 AGCATTTCTGGAACCATAGCC 58.341 47.619 0.00 0.00 0.00 3.93
2586 5789 0.174389 CAGGATGACTGTGACCGAGG 59.826 60.000 0.00 0.00 42.42 4.63
2596 5799 2.975489 AGTGACAGGAAACAGGATGACT 59.025 45.455 0.00 0.00 39.69 3.41
2610 5813 4.034858 GCATTGACCATCATGTAGTGACAG 59.965 45.833 0.00 0.00 40.28 3.51
2611 5814 3.940852 GCATTGACCATCATGTAGTGACA 59.059 43.478 0.00 0.00 40.28 3.58
2613 5816 4.193865 CTGCATTGACCATCATGTAGTGA 58.806 43.478 0.00 0.00 42.06 3.41
2614 5817 3.242969 GCTGCATTGACCATCATGTAGTG 60.243 47.826 0.00 0.00 0.00 2.74
2615 5818 2.947652 GCTGCATTGACCATCATGTAGT 59.052 45.455 0.00 0.00 0.00 2.73
2616 5819 2.946990 TGCTGCATTGACCATCATGTAG 59.053 45.455 0.00 0.00 0.00 2.74
2617 5820 3.002038 TGCTGCATTGACCATCATGTA 57.998 42.857 0.00 0.00 0.00 2.29
2618 5821 1.842052 TGCTGCATTGACCATCATGT 58.158 45.000 0.00 0.00 0.00 3.21
2619 5822 4.546570 CTTATGCTGCATTGACCATCATG 58.453 43.478 21.56 0.00 0.00 3.07
2646 5849 5.627780 GGTAAGTTTTGGTAGCATTCGTTTG 59.372 40.000 0.00 0.00 0.00 2.93
2647 5850 5.299782 TGGTAAGTTTTGGTAGCATTCGTTT 59.700 36.000 0.00 0.00 0.00 3.60
2651 5854 7.375053 TGAAATGGTAAGTTTTGGTAGCATTC 58.625 34.615 8.15 0.00 43.85 2.67
2717 5920 8.793592 GTCCCAAAATAAGTGACTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
2718 5921 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
2719 5922 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2720 5923 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2721 5924 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2722 5925 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2723 5926 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2724 5927 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2725 5928 3.934068 TCCGTCCCAAAATAAGTGACTC 58.066 45.455 0.00 0.00 0.00 3.36
2726 5929 4.360951 TTCCGTCCCAAAATAAGTGACT 57.639 40.909 0.00 0.00 0.00 3.41
2727 5930 4.758165 TCTTTCCGTCCCAAAATAAGTGAC 59.242 41.667 0.00 0.00 0.00 3.67
2728 5931 4.975631 TCTTTCCGTCCCAAAATAAGTGA 58.024 39.130 0.00 0.00 0.00 3.41
2729 5932 4.760204 ACTCTTTCCGTCCCAAAATAAGTG 59.240 41.667 0.00 0.00 0.00 3.16
2730 5933 4.981812 ACTCTTTCCGTCCCAAAATAAGT 58.018 39.130 0.00 0.00 0.00 2.24
2731 5934 6.403878 TCTACTCTTTCCGTCCCAAAATAAG 58.596 40.000 0.00 0.00 0.00 1.73
2732 5935 6.363167 TCTACTCTTTCCGTCCCAAAATAA 57.637 37.500 0.00 0.00 0.00 1.40
2733 5936 6.363167 TTCTACTCTTTCCGTCCCAAAATA 57.637 37.500 0.00 0.00 0.00 1.40
2734 5937 4.903045 TCTACTCTTTCCGTCCCAAAAT 57.097 40.909 0.00 0.00 0.00 1.82
2735 5938 4.693042 TTCTACTCTTTCCGTCCCAAAA 57.307 40.909 0.00 0.00 0.00 2.44
2736 5939 4.693042 TTTCTACTCTTTCCGTCCCAAA 57.307 40.909 0.00 0.00 0.00 3.28
2737 5940 4.693042 TTTTCTACTCTTTCCGTCCCAA 57.307 40.909 0.00 0.00 0.00 4.12
2738 5941 4.903045 ATTTTCTACTCTTTCCGTCCCA 57.097 40.909 0.00 0.00 0.00 4.37
2739 5942 4.395231 CCAATTTTCTACTCTTTCCGTCCC 59.605 45.833 0.00 0.00 0.00 4.46
2740 5943 5.001874 ACCAATTTTCTACTCTTTCCGTCC 58.998 41.667 0.00 0.00 0.00 4.79
2741 5944 5.469084 ACACCAATTTTCTACTCTTTCCGTC 59.531 40.000 0.00 0.00 0.00 4.79
2742 5945 5.374071 ACACCAATTTTCTACTCTTTCCGT 58.626 37.500 0.00 0.00 0.00 4.69
2743 5946 5.941948 ACACCAATTTTCTACTCTTTCCG 57.058 39.130 0.00 0.00 0.00 4.30
2744 5947 6.713450 TGGTACACCAATTTTCTACTCTTTCC 59.287 38.462 0.00 0.00 44.35 3.13
2745 5948 7.739498 TGGTACACCAATTTTCTACTCTTTC 57.261 36.000 0.00 0.00 44.35 2.62
2773 5976 1.376466 GAGCAGCCCTTTCACTCCA 59.624 57.895 0.00 0.00 0.00 3.86
2795 5998 2.084681 GCAACGTCCGTCTGTACCG 61.085 63.158 0.00 0.00 0.00 4.02
2819 6022 3.132289 TCCGTCCGATTTCTGCTAAGATT 59.868 43.478 0.00 0.00 30.72 2.40
2865 6075 4.124351 TCCACCGCGCCTTACTCG 62.124 66.667 0.00 0.00 0.00 4.18
2879 6089 0.532573 GCATGTCTTCTCGACCTCCA 59.467 55.000 0.00 0.00 42.13 3.86
2880 6090 0.820871 AGCATGTCTTCTCGACCTCC 59.179 55.000 0.00 0.00 42.13 4.30
2885 6095 4.152284 TCTAGGTAGCATGTCTTCTCGA 57.848 45.455 0.00 0.00 0.00 4.04
2910 6120 2.125310 TATTGTGGGCGCGACAGG 60.125 61.111 17.00 0.00 0.00 4.00
2941 6151 7.261325 TCATTGTTGTTTGCTTAGCTACAAAA 58.739 30.769 20.47 15.44 37.50 2.44
2942 6152 6.800543 TCATTGTTGTTTGCTTAGCTACAAA 58.199 32.000 20.47 11.18 36.32 2.83
2943 6153 6.384258 TCATTGTTGTTTGCTTAGCTACAA 57.616 33.333 16.88 16.88 33.87 2.41
2944 6154 6.384258 TTCATTGTTGTTTGCTTAGCTACA 57.616 33.333 5.60 7.18 0.00 2.74
2945 6155 7.619982 GCAATTCATTGTTGTTTGCTTAGCTAC 60.620 37.037 5.60 4.49 38.67 3.58
2946 6156 6.365789 GCAATTCATTGTTGTTTGCTTAGCTA 59.634 34.615 5.60 0.00 38.67 3.32
2948 6158 5.178067 AGCAATTCATTGTTGTTTGCTTAGC 59.822 36.000 0.00 0.00 43.88 3.09
2949 6159 6.586751 CAGCAATTCATTGTTGTTTGCTTAG 58.413 36.000 5.77 0.00 43.88 2.18
2950 6160 6.528014 CAGCAATTCATTGTTGTTTGCTTA 57.472 33.333 5.77 0.00 43.88 3.09
2951 6161 5.412526 CAGCAATTCATTGTTGTTTGCTT 57.587 34.783 5.77 0.00 43.88 3.91
2972 6182 2.551006 ATTTCCGCTGCAACGCACA 61.551 52.632 3.43 0.00 33.79 4.57
2985 6195 5.755861 GCTAGAGGAGTTGTATGACATTTCC 59.244 44.000 0.00 3.07 33.62 3.13
2991 6201 3.491792 GCCAGCTAGAGGAGTTGTATGAC 60.492 52.174 5.89 0.00 34.69 3.06
2999 6213 2.534042 TTGTAGCCAGCTAGAGGAGT 57.466 50.000 0.00 0.00 0.00 3.85
3000 6214 3.895232 TTTTGTAGCCAGCTAGAGGAG 57.105 47.619 0.00 0.00 0.00 3.69
3011 6225 5.277297 GCAATGGTTTGAAGTTTTTGTAGCC 60.277 40.000 0.00 0.00 34.60 3.93
3045 6259 4.802039 CGTGTGCGTTCCTACACTATAAAT 59.198 41.667 0.00 0.00 43.73 1.40
3048 6262 3.409851 CGTGTGCGTTCCTACACTATA 57.590 47.619 0.00 0.00 43.73 1.31
3049 6263 2.273370 CGTGTGCGTTCCTACACTAT 57.727 50.000 0.00 0.00 43.73 2.12
3069 6283 2.353889 GCGTCAGTCTTAGTCACGGATA 59.646 50.000 0.00 0.00 0.00 2.59
3074 6288 1.071567 GCCGCGTCAGTCTTAGTCAC 61.072 60.000 4.92 0.00 0.00 3.67
3166 6383 2.455557 TCCCGTATTTCTCGGTAACCA 58.544 47.619 3.78 0.00 45.63 3.67
3230 6447 8.934023 TTACTCCATTCCTAACAAAGTTTGAT 57.066 30.769 22.23 12.93 0.00 2.57
3252 6469 6.486993 CCCAGTGAAGGCCTAAATAGATTTAC 59.513 42.308 5.16 0.00 0.00 2.01
3258 6475 2.576615 GCCCAGTGAAGGCCTAAATAG 58.423 52.381 5.16 0.00 45.16 1.73
3273 6493 1.541310 TTCCTACTGACACGGCCCAG 61.541 60.000 0.00 0.21 36.53 4.45
3281 6501 3.630312 GCAAAAACAGGTTCCTACTGACA 59.370 43.478 0.00 0.00 39.24 3.58
3367 6609 3.015327 CTCTTACGTACTGCCTAGTGGT 58.985 50.000 0.00 0.00 37.78 4.16
3455 6703 2.496470 GTCTATACGCCCCCTATCAAGG 59.504 54.545 0.00 0.00 43.25 3.61
3461 6709 2.322658 CAAAGGTCTATACGCCCCCTA 58.677 52.381 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.