Multiple sequence alignment - TraesCS6D01G286100

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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 TraesCS6D01G286100 chr6D 100.000 5369 0 0 1856 7224 394624850 394619482 0.000000e+00 9878.0
1 TraesCS6D01G286100 chr6D 100.000 1462 0 0 1 1462 394626705 394625244 0.000000e+00 2700.0
2 TraesCS6D01G286100 chr6D 84.795 901 81 28 11 878 394630913 394630036 0.000000e+00 854.0
3 TraesCS6D01G286100 chr6D 98.513 269 4 0 2324 2592 394624065 394623797 6.560000e-130 475.0
4 TraesCS6D01G286100 chr6D 98.513 269 4 0 2641 2909 394624382 394624114 6.560000e-130 475.0
5 TraesCS6D01G286100 chr6D 100.000 165 0 0 2603 2767 394623977 394623813 9.100000e-79 305.0
6 TraesCS6D01G286100 chr6D 100.000 165 0 0 2729 2893 394624103 394623939 9.100000e-79 305.0
7 TraesCS6D01G286100 chr6D 100.000 165 0 0 2412 2576 394624103 394623939 9.100000e-79 305.0
8 TraesCS6D01G286100 chr6D 100.000 165 0 0 2603 2767 394624294 394624130 9.100000e-79 305.0
9 TraesCS6D01G286100 chr6D 83.039 283 44 3 8 289 394633994 394633715 3.340000e-63 254.0
10 TraesCS6D01G286100 chr6D 96.850 127 4 0 2324 2450 394623939 394623813 5.680000e-51 213.0
11 TraesCS6D01G286100 chr6D 96.850 127 4 0 2324 2450 394624256 394624130 5.680000e-51 213.0
12 TraesCS6D01G286100 chr6D 96.850 127 4 0 2767 2893 394624382 394624256 5.680000e-51 213.0
13 TraesCS6D01G286100 chr6D 96.850 127 4 0 2450 2576 394624382 394624256 5.680000e-51 213.0
14 TraesCS6D01G286100 chr6D 91.111 90 8 0 1307 1396 394625333 394625244 9.840000e-24 122.0
15 TraesCS6D01G286100 chr6D 91.111 90 8 0 1373 1462 394625399 394625310 9.840000e-24 122.0
16 TraesCS6D01G286100 chr6D 86.301 73 8 1 845 915 394625827 394625755 2.160000e-10 78.7
17 TraesCS6D01G286100 chr6D 86.301 73 8 1 879 951 394625861 394625791 2.160000e-10 78.7
18 TraesCS6D01G286100 chr6D 100.000 39 0 0 2603 2641 394623851 394623813 1.010000e-08 73.1
19 TraesCS6D01G286100 chr6D 100.000 39 0 0 2855 2893 394624103 394624065 1.010000e-08 73.1
20 TraesCS6D01G286100 chr6D 100.000 39 0 0 2538 2576 394624103 394624065 1.010000e-08 73.1
21 TraesCS6D01G286100 chr6D 100.000 39 0 0 2603 2641 394624168 394624130 1.010000e-08 73.1
22 TraesCS6D01G286100 chr6A 94.373 3519 121 21 2641 6104 540622989 540619493 0.000000e+00 5330.0
23 TraesCS6D01G286100 chr6A 92.308 1079 45 15 414 1462 540624770 540623700 0.000000e+00 1498.0
24 TraesCS6D01G286100 chr6A 97.372 723 18 1 1870 2592 540623443 540622722 0.000000e+00 1229.0
25 TraesCS6D01G286100 chr6A 90.095 525 22 15 6716 7224 540618709 540618199 0.000000e+00 654.0
26 TraesCS6D01G286100 chr6A 83.881 639 76 13 11 641 540628238 540627619 1.040000e-162 584.0
27 TraesCS6D01G286100 chr6A 81.696 743 96 21 18 744 540663411 540662693 3.760000e-162 582.0
28 TraesCS6D01G286100 chr6A 93.059 389 13 4 6341 6724 540619258 540618879 2.280000e-154 556.0
29 TraesCS6D01G286100 chr6A 97.500 280 5 2 6135 6413 540619495 540619217 1.820000e-130 477.0
30 TraesCS6D01G286100 chr6A 97.576 165 4 0 2603 2767 540622902 540622738 4.270000e-72 283.0
31 TraesCS6D01G286100 chr6A 97.638 127 3 0 2324 2450 540622864 540622738 1.220000e-52 219.0
32 TraesCS6D01G286100 chr6A 95.276 127 5 1 2767 2893 540622989 540622864 4.420000e-47 200.0
33 TraesCS6D01G286100 chr6A 95.276 127 5 1 2450 2576 540622989 540622864 4.420000e-47 200.0
34 TraesCS6D01G286100 chr6A 90.000 90 9 0 1373 1462 540623855 540623766 4.580000e-22 117.0
35 TraesCS6D01G286100 chr6A 92.000 75 6 0 1856 1930 540623801 540623727 9.910000e-19 106.0
36 TraesCS6D01G286100 chr6A 89.041 73 6 1 845 915 540624278 540624206 9.980000e-14 89.8
37 TraesCS6D01G286100 chr6A 94.545 55 3 0 1408 1462 540623443 540623389 1.290000e-12 86.1
38 TraesCS6D01G286100 chr6A 90.164 61 6 0 1342 1402 540623443 540623383 6.010000e-11 80.5
39 TraesCS6D01G286100 chr6A 86.301 73 8 1 878 950 540624313 540624243 2.160000e-10 78.7
40 TraesCS6D01G286100 chr6A 100.000 39 0 0 2603 2641 540622776 540622738 1.010000e-08 73.1
41 TraesCS6D01G286100 chr6B 92.120 1967 95 29 3833 5771 590672374 590670440 0.000000e+00 2719.0
42 TraesCS6D01G286100 chr6B 88.914 1326 87 24 145 1435 590675121 590673821 0.000000e+00 1580.0
43 TraesCS6D01G286100 chr6B 92.955 1022 58 11 2873 3888 590673382 590672369 0.000000e+00 1476.0
44 TraesCS6D01G286100 chr6B 93.844 601 27 4 5922 6519 590670137 590669544 0.000000e+00 896.0
45 TraesCS6D01G286100 chr6B 92.193 538 42 0 1861 2398 590673923 590673386 0.000000e+00 761.0
46 TraesCS6D01G286100 chr6B 81.782 752 99 21 8 745 590682698 590681971 4.820000e-166 595.0
47 TraesCS6D01G286100 chr6B 86.704 534 34 22 6709 7224 590669231 590668717 6.330000e-155 558.0
48 TraesCS6D01G286100 chr6B 81.073 634 72 22 11 602 590677282 590676655 5.110000e-126 462.0
49 TraesCS6D01G286100 chr6B 90.244 123 12 0 1340 1462 590673949 590673827 2.090000e-35 161.0
50 TraesCS6D01G286100 chr6B 94.792 96 5 0 1307 1402 590673916 590673821 4.510000e-32 150.0
51 TraesCS6D01G286100 chr6B 88.889 90 10 0 1373 1462 590673949 590673860 2.130000e-20 111.0
52 TraesCS6D01G286100 chr6B 97.619 42 1 0 1856 1897 590673862 590673821 1.010000e-08 73.1
53 TraesCS6D01G286100 chr3B 83.704 135 8 9 3968 4092 370933053 370933183 1.650000e-21 115.0
54 TraesCS6D01G286100 chr3A 82.963 135 9 7 3968 4092 359662875 359663005 7.660000e-20 110.0
55 TraesCS6D01G286100 chr2B 77.143 210 30 11 3917 4113 214585453 214585249 9.910000e-19 106.0
56 TraesCS6D01G286100 chr2B 83.333 102 15 2 3989 4090 546932116 546932215 7.720000e-15 93.5
57 TraesCS6D01G286100 chr1B 76.068 234 32 15 3911 4125 344046426 344046198 4.610000e-17 100.0
58 TraesCS6D01G286100 chr3D 81.481 135 11 7 3968 4092 279199859 279199729 1.660000e-16 99.0
59 TraesCS6D01G286100 chr1D 77.596 183 23 11 3956 4125 389215312 389215135 2.150000e-15 95.3


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 TraesCS6D01G286100 chr6D 394619482 394626705 7223 True 814.690000 9878 96.962500 1 7224 20 chr6D.!!$R1 7223
1 TraesCS6D01G286100 chr6D 394630036 394633994 3958 True 554.000000 854 83.917000 8 878 2 chr6D.!!$R2 870
2 TraesCS6D01G286100 chr6A 540618199 540628238 10039 True 658.955556 5330 93.133611 11 7224 18 chr6A.!!$R2 7213
3 TraesCS6D01G286100 chr6A 540662693 540663411 718 True 582.000000 582 81.696000 18 744 1 chr6A.!!$R1 726
4 TraesCS6D01G286100 chr6B 590668717 590677282 8565 True 813.372727 2719 90.849727 11 7224 11 chr6B.!!$R2 7213
5 TraesCS6D01G286100 chr6B 590681971 590682698 727 True 595.000000 595 81.782000 8 745 1 chr6B.!!$R1 737

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
648 5779 0.329138 CCTATAAACCCCCACCCCCT 60.329 60.0 0.0 0.0 0.00 4.79 F
1408 9850 0.172578 TGATGGCACTAAGTCCGTCG 59.827 55.0 0.0 0.0 40.42 5.12 F
2374 11028 0.038709 TTGTTTGCGTGCTTATGGCC 60.039 50.0 0.0 0.0 40.92 5.36 F
2691 11345 0.038709 TTGTTTGCGTGCTTATGGCC 60.039 50.0 0.0 0.0 40.92 5.36 F
2817 11471 0.038709 TTGTTTGCGTGCTTATGGCC 60.039 50.0 0.0 0.0 40.92 5.36 F
2822 11476 0.106967 TGCGTGCTTATGGCCCATTA 60.107 50.0 0.0 0.0 40.92 1.90 F
4730 13457 1.029681 AAACCGTGTTGAAAGGCTCC 58.970 50.0 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 10316 0.773644 ACTGCCATCACCCTTGTTCT 59.226 50.000 0.00 0.0 0.00 3.01 R
2672 11326 0.038709 GGCCATAAGCACGCAAACAA 60.039 50.000 0.00 0.0 46.50 2.83 R
4257 12975 0.958822 GGCTAAAACACCCCACACTG 59.041 55.000 0.00 0.0 0.00 3.66 R
4730 13457 4.394300 CCTTTCTTCAACATAGTGAGGCAG 59.606 45.833 0.00 0.0 0.00 4.85 R
4828 13555 4.984146 ATCATAGGCTAACCTCCTTTCC 57.016 45.455 0.00 0.0 46.34 3.13 R
4900 13627 3.005155 GTGGCTGAGCTTCTTCAACAAAT 59.995 43.478 3.72 0.0 0.00 2.32 R
6782 16009 0.041135 CTGCGTAGTAGTAGAGCGGC 60.041 60.000 0.00 0.0 34.87 6.53 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
62 3093 5.914033 TCCAATCTAAACTGTTATCCTCGG 58.086 41.667 0.00 0.00 0.00 4.63
116 5145 2.095768 CACTGCCGACACACATTTAAGG 60.096 50.000 0.00 0.00 0.00 2.69
165 5223 7.388776 GCATAAAGACAACATGCTCCATAGATA 59.611 37.037 0.00 0.00 41.44 1.98
194 5252 6.801862 CGTTTTCATTAAACTGTTCATCCTCC 59.198 38.462 0.00 0.00 43.21 4.30
218 5276 4.799564 AAAACTCACAAAAGTGAAGCCA 57.200 36.364 0.00 0.00 32.43 4.75
223 5281 3.734463 TCACAAAAGTGAAGCCATACGA 58.266 40.909 0.00 0.00 0.00 3.43
252 5310 4.569162 CCACTAACAAACGTCAAGAACAGA 59.431 41.667 0.00 0.00 0.00 3.41
270 5328 3.067106 CAGAGTGTCGCCATGTTTAAGT 58.933 45.455 0.00 0.00 0.00 2.24
288 5353 2.551270 AGTTGTGGGAGCTAGGATTCA 58.449 47.619 0.00 0.00 0.00 2.57
333 5403 6.417635 CCATTTGATTGTTGAATATACCGCAC 59.582 38.462 0.00 0.00 0.00 5.34
347 5417 3.870633 ACCGCACAAAGGTTGTTAAAA 57.129 38.095 0.00 0.00 43.23 1.52
395 5469 1.802069 GTCTCCTTGCCACAAGAGAC 58.198 55.000 8.87 13.79 45.94 3.36
486 5598 7.175119 GGCATAGAATAGACCAGGAAAAATACC 59.825 40.741 0.00 0.00 0.00 2.73
524 5636 0.802607 GCGTTCGATCCAGACAGTCC 60.803 60.000 0.00 0.00 0.00 3.85
533 5645 0.965866 CCAGACAGTCCAGCCGTCTA 60.966 60.000 0.00 0.00 37.92 2.59
575 5697 0.898326 AAAGGATTTGGGGTCCGCAC 60.898 55.000 8.40 0.00 40.76 5.34
602 5731 2.961721 CGCACCGGATGTCCATCG 60.962 66.667 9.46 0.00 38.69 3.84
603 5732 2.499205 GCACCGGATGTCCATCGA 59.501 61.111 9.46 0.00 38.69 3.59
604 5733 1.592669 GCACCGGATGTCCATCGAG 60.593 63.158 9.46 0.00 38.69 4.04
628 5757 3.077556 CCTCCCTGTCTCCCCACG 61.078 72.222 0.00 0.00 0.00 4.94
647 5778 2.015243 GCCTATAAACCCCCACCCCC 62.015 65.000 0.00 0.00 0.00 5.40
648 5779 0.329138 CCTATAAACCCCCACCCCCT 60.329 60.000 0.00 0.00 0.00 4.79
649 5780 0.850784 CTATAAACCCCCACCCCCTG 59.149 60.000 0.00 0.00 0.00 4.45
650 5781 0.426437 TATAAACCCCCACCCCCTGA 59.574 55.000 0.00 0.00 0.00 3.86
651 5782 1.219131 ATAAACCCCCACCCCCTGAC 61.219 60.000 0.00 0.00 0.00 3.51
670 9079 4.463879 CAGAGCGGAGGCCACAGG 62.464 72.222 5.01 0.00 41.24 4.00
703 9113 2.592308 GCCCTGACAGTCATCCCC 59.408 66.667 2.97 0.00 0.00 4.81
909 9344 4.692129 CGCGAGTAGATTCAGCGT 57.308 55.556 0.00 0.00 44.96 5.07
914 9349 3.436496 GCGAGTAGATTCAGCGTAGTTT 58.564 45.455 0.00 0.00 0.00 2.66
1397 9839 1.168714 GAGAACAAGGGTGATGGCAC 58.831 55.000 0.00 0.00 44.39 5.01
1408 9850 0.172578 TGATGGCACTAAGTCCGTCG 59.827 55.000 0.00 0.00 40.42 5.12
1410 9852 2.508663 GGCACTAAGTCCGTCGCC 60.509 66.667 0.00 0.00 0.00 5.54
1411 9853 2.260434 GCACTAAGTCCGTCGCCA 59.740 61.111 0.00 0.00 0.00 5.69
1414 9856 0.736325 CACTAAGTCCGTCGCCAAGG 60.736 60.000 0.00 0.00 0.00 3.61
1438 9880 0.462047 GGGTGATGGCAGTAAGTCCG 60.462 60.000 0.00 0.00 0.00 4.79
1874 10316 1.211969 GCAGTAAGTCTGTCGCCGA 59.788 57.895 0.00 0.00 45.23 5.54
1893 10335 0.773644 AGAACAAGGGTGATGGCAGT 59.226 50.000 0.00 0.00 0.00 4.40
1899 10553 1.958288 AGGGTGATGGCAGTAAGTCT 58.042 50.000 0.00 0.00 0.00 3.24
1910 10564 1.088306 AGTAAGTCTGTCGCCGAGAG 58.912 55.000 4.66 4.66 0.00 3.20
2089 10743 2.820787 GAGAAGGAGAAGAAGGACGACA 59.179 50.000 0.00 0.00 0.00 4.35
2136 10790 4.142093 GCTGGGTTTATCTTCATGTGCAAT 60.142 41.667 0.00 0.00 0.00 3.56
2374 11028 0.038709 TTGTTTGCGTGCTTATGGCC 60.039 50.000 0.00 0.00 40.92 5.36
2376 11030 1.604879 TTTGCGTGCTTATGGCCCA 60.605 52.632 0.00 0.00 40.92 5.36
2379 11033 1.066257 GCGTGCTTATGGCCCATTG 59.934 57.895 0.00 0.00 40.92 2.82
2400 11054 8.095169 CCATTGTTATGGTAGTAGAAGTATCCC 58.905 40.741 0.00 0.00 45.34 3.85
2485 11139 6.183360 TGCTCAGGTAATTTTTGGTCATTGTT 60.183 34.615 0.00 0.00 0.00 2.83
2511 11165 4.458989 CGTGCTTATGGCCCATTATTATGT 59.541 41.667 0.00 0.00 40.92 2.29
2576 11230 7.200434 ACAACCTGTCCTGAAGATATTATGT 57.800 36.000 0.00 0.00 0.00 2.29
2577 11231 7.050377 ACAACCTGTCCTGAAGATATTATGTG 58.950 38.462 0.00 0.00 0.00 3.21
2578 11232 5.615289 ACCTGTCCTGAAGATATTATGTGC 58.385 41.667 0.00 0.00 0.00 4.57
2579 11233 5.367937 ACCTGTCCTGAAGATATTATGTGCT 59.632 40.000 0.00 0.00 0.00 4.40
2580 11234 6.554982 ACCTGTCCTGAAGATATTATGTGCTA 59.445 38.462 0.00 0.00 0.00 3.49
2581 11235 7.236432 ACCTGTCCTGAAGATATTATGTGCTAT 59.764 37.037 0.00 0.00 0.00 2.97
2582 11236 8.753133 CCTGTCCTGAAGATATTATGTGCTATA 58.247 37.037 0.00 0.00 0.00 1.31
2585 11239 9.457110 GTCCTGAAGATATTATGTGCTATATCG 57.543 37.037 0.00 0.00 38.30 2.92
2586 11240 9.190317 TCCTGAAGATATTATGTGCTATATCGT 57.810 33.333 0.00 0.00 38.30 3.73
2641 11295 6.595682 ACAACCTGTCCTGAAGATATTATGG 58.404 40.000 0.00 0.00 0.00 2.74
2642 11296 5.832539 ACCTGTCCTGAAGATATTATGGG 57.167 43.478 0.00 0.00 0.00 4.00
2643 11297 5.476983 ACCTGTCCTGAAGATATTATGGGA 58.523 41.667 0.00 0.00 0.00 4.37
2644 11298 5.911178 ACCTGTCCTGAAGATATTATGGGAA 59.089 40.000 0.00 0.00 0.00 3.97
2645 11299 6.389869 ACCTGTCCTGAAGATATTATGGGAAA 59.610 38.462 0.00 0.00 0.00 3.13
2646 11300 7.074237 ACCTGTCCTGAAGATATTATGGGAAAT 59.926 37.037 0.00 0.00 0.00 2.17
2647 11301 7.946776 CCTGTCCTGAAGATATTATGGGAAATT 59.053 37.037 0.00 0.00 0.00 1.82
2648 11302 8.924511 TGTCCTGAAGATATTATGGGAAATTC 57.075 34.615 0.00 0.00 0.00 2.17
2649 11303 7.944554 TGTCCTGAAGATATTATGGGAAATTCC 59.055 37.037 2.79 2.79 35.23 3.01
2663 11317 4.281657 GGAAATTCCCTGCTCAGGTAATT 58.718 43.478 12.05 12.05 45.41 1.40
2667 11321 6.041423 AATTCCCTGCTCAGGTAATTTTTG 57.959 37.500 12.05 0.00 42.27 2.44
2668 11322 5.046376 AATTCCCTGCTCAGGTAATTTTTGG 60.046 40.000 12.05 0.00 42.27 3.28
2669 11323 7.433929 AATTCCCTGCTCAGGTAATTTTTGGT 61.434 38.462 12.05 0.00 42.27 3.67
2670 11324 4.440839 CCTGCTCAGGTAATTTTTGGTC 57.559 45.455 7.75 0.00 43.61 4.02
2671 11325 3.826157 CCTGCTCAGGTAATTTTTGGTCA 59.174 43.478 7.75 0.00 43.61 4.02
2672 11326 4.463891 CCTGCTCAGGTAATTTTTGGTCAT 59.536 41.667 7.75 0.00 43.61 3.06
2673 11327 5.047092 CCTGCTCAGGTAATTTTTGGTCATT 60.047 40.000 7.75 0.00 43.61 2.57
2674 11328 5.782047 TGCTCAGGTAATTTTTGGTCATTG 58.218 37.500 0.00 0.00 0.00 2.82
2675 11329 5.304101 TGCTCAGGTAATTTTTGGTCATTGT 59.696 36.000 0.00 0.00 0.00 2.71
2676 11330 6.183360 TGCTCAGGTAATTTTTGGTCATTGTT 60.183 34.615 0.00 0.00 0.00 2.83
2677 11331 6.705825 GCTCAGGTAATTTTTGGTCATTGTTT 59.294 34.615 0.00 0.00 0.00 2.83
2678 11332 7.307337 GCTCAGGTAATTTTTGGTCATTGTTTG 60.307 37.037 0.00 0.00 0.00 2.93
2679 11333 6.481644 TCAGGTAATTTTTGGTCATTGTTTGC 59.518 34.615 0.00 0.00 0.00 3.68
2680 11334 5.465056 AGGTAATTTTTGGTCATTGTTTGCG 59.535 36.000 0.00 0.00 0.00 4.85
2681 11335 5.235401 GGTAATTTTTGGTCATTGTTTGCGT 59.765 36.000 0.00 0.00 0.00 5.24
2682 11336 4.792528 ATTTTTGGTCATTGTTTGCGTG 57.207 36.364 0.00 0.00 0.00 5.34
2683 11337 1.565305 TTTGGTCATTGTTTGCGTGC 58.435 45.000 0.00 0.00 0.00 5.34
2684 11338 0.743688 TTGGTCATTGTTTGCGTGCT 59.256 45.000 0.00 0.00 0.00 4.40
2685 11339 0.743688 TGGTCATTGTTTGCGTGCTT 59.256 45.000 0.00 0.00 0.00 3.91
2686 11340 1.950216 TGGTCATTGTTTGCGTGCTTA 59.050 42.857 0.00 0.00 0.00 3.09
2687 11341 2.556189 TGGTCATTGTTTGCGTGCTTAT 59.444 40.909 0.00 0.00 0.00 1.73
2688 11342 2.916716 GGTCATTGTTTGCGTGCTTATG 59.083 45.455 0.00 0.00 0.00 1.90
2689 11343 2.916716 GTCATTGTTTGCGTGCTTATGG 59.083 45.455 0.00 0.00 0.00 2.74
2690 11344 1.655099 CATTGTTTGCGTGCTTATGGC 59.345 47.619 0.00 0.00 42.22 4.40
2691 11345 0.038709 TTGTTTGCGTGCTTATGGCC 60.039 50.000 0.00 0.00 40.92 5.36
2692 11346 1.153842 GTTTGCGTGCTTATGGCCC 60.154 57.895 0.00 0.00 40.92 5.80
2693 11347 1.604879 TTTGCGTGCTTATGGCCCA 60.605 52.632 0.00 0.00 40.92 5.36
2694 11348 0.969917 TTTGCGTGCTTATGGCCCAT 60.970 50.000 0.00 0.00 40.92 4.00
2695 11349 0.969917 TTGCGTGCTTATGGCCCATT 60.970 50.000 0.00 0.00 40.92 3.16
2696 11350 0.106967 TGCGTGCTTATGGCCCATTA 60.107 50.000 0.00 0.00 40.92 1.90
2697 11351 1.247567 GCGTGCTTATGGCCCATTAT 58.752 50.000 0.00 0.00 40.92 1.28
2698 11352 1.613437 GCGTGCTTATGGCCCATTATT 59.387 47.619 0.00 0.00 40.92 1.40
2699 11353 2.817258 GCGTGCTTATGGCCCATTATTA 59.183 45.455 0.00 0.00 40.92 0.98
2700 11354 3.443681 GCGTGCTTATGGCCCATTATTAT 59.556 43.478 0.00 0.00 40.92 1.28
2701 11355 4.675146 GCGTGCTTATGGCCCATTATTATG 60.675 45.833 0.00 0.00 40.92 1.90
2702 11356 4.458989 CGTGCTTATGGCCCATTATTATGT 59.541 41.667 0.00 0.00 40.92 2.29
2703 11357 5.048083 CGTGCTTATGGCCCATTATTATGTT 60.048 40.000 0.00 0.00 40.92 2.71
2704 11358 6.150307 CGTGCTTATGGCCCATTATTATGTTA 59.850 38.462 0.00 0.00 40.92 2.41
2705 11359 7.538575 GTGCTTATGGCCCATTATTATGTTAG 58.461 38.462 0.00 0.00 40.92 2.34
2706 11360 7.176690 GTGCTTATGGCCCATTATTATGTTAGT 59.823 37.037 0.00 0.00 40.92 2.24
2707 11361 8.387039 TGCTTATGGCCCATTATTATGTTAGTA 58.613 33.333 0.00 0.00 40.92 1.82
2708 11362 8.893727 GCTTATGGCCCATTATTATGTTAGTAG 58.106 37.037 0.00 0.00 34.27 2.57
2712 11366 8.041143 TGGCCCATTATTATGTTAGTAGAAGT 57.959 34.615 0.00 0.00 0.00 3.01
2713 11367 9.161572 TGGCCCATTATTATGTTAGTAGAAGTA 57.838 33.333 0.00 0.00 0.00 2.24
2767 11421 6.595682 ACAACCTGTCCTGAAGATATTATGG 58.404 40.000 0.00 0.00 0.00 2.74
2768 11422 5.832539 ACCTGTCCTGAAGATATTATGGG 57.167 43.478 0.00 0.00 0.00 4.00
2769 11423 5.476983 ACCTGTCCTGAAGATATTATGGGA 58.523 41.667 0.00 0.00 0.00 4.37
2770 11424 5.911178 ACCTGTCCTGAAGATATTATGGGAA 59.089 40.000 0.00 0.00 0.00 3.97
2771 11425 6.389869 ACCTGTCCTGAAGATATTATGGGAAA 59.610 38.462 0.00 0.00 0.00 3.13
2772 11426 7.074237 ACCTGTCCTGAAGATATTATGGGAAAT 59.926 37.037 0.00 0.00 0.00 2.17
2773 11427 7.946776 CCTGTCCTGAAGATATTATGGGAAATT 59.053 37.037 0.00 0.00 0.00 1.82
2774 11428 8.924511 TGTCCTGAAGATATTATGGGAAATTC 57.075 34.615 0.00 0.00 0.00 2.17
2775 11429 7.944554 TGTCCTGAAGATATTATGGGAAATTCC 59.055 37.037 2.79 2.79 35.23 3.01
2789 11443 4.281657 GGAAATTCCCTGCTCAGGTAATT 58.718 43.478 12.05 12.05 45.41 1.40
2793 11447 6.041423 AATTCCCTGCTCAGGTAATTTTTG 57.959 37.500 12.05 0.00 42.27 2.44
2794 11448 5.046376 AATTCCCTGCTCAGGTAATTTTTGG 60.046 40.000 12.05 0.00 42.27 3.28
2795 11449 7.433929 AATTCCCTGCTCAGGTAATTTTTGGT 61.434 38.462 12.05 0.00 42.27 3.67
2796 11450 4.440839 CCTGCTCAGGTAATTTTTGGTC 57.559 45.455 7.75 0.00 43.61 4.02
2797 11451 3.826157 CCTGCTCAGGTAATTTTTGGTCA 59.174 43.478 7.75 0.00 43.61 4.02
2798 11452 4.463891 CCTGCTCAGGTAATTTTTGGTCAT 59.536 41.667 7.75 0.00 43.61 3.06
2799 11453 5.047092 CCTGCTCAGGTAATTTTTGGTCATT 60.047 40.000 7.75 0.00 43.61 2.57
2800 11454 5.782047 TGCTCAGGTAATTTTTGGTCATTG 58.218 37.500 0.00 0.00 0.00 2.82
2801 11455 5.304101 TGCTCAGGTAATTTTTGGTCATTGT 59.696 36.000 0.00 0.00 0.00 2.71
2802 11456 6.183360 TGCTCAGGTAATTTTTGGTCATTGTT 60.183 34.615 0.00 0.00 0.00 2.83
2803 11457 6.705825 GCTCAGGTAATTTTTGGTCATTGTTT 59.294 34.615 0.00 0.00 0.00 2.83
2804 11458 7.307337 GCTCAGGTAATTTTTGGTCATTGTTTG 60.307 37.037 0.00 0.00 0.00 2.93
2805 11459 6.481644 TCAGGTAATTTTTGGTCATTGTTTGC 59.518 34.615 0.00 0.00 0.00 3.68
2806 11460 5.465056 AGGTAATTTTTGGTCATTGTTTGCG 59.535 36.000 0.00 0.00 0.00 4.85
2807 11461 5.235401 GGTAATTTTTGGTCATTGTTTGCGT 59.765 36.000 0.00 0.00 0.00 5.24
2808 11462 4.792528 ATTTTTGGTCATTGTTTGCGTG 57.207 36.364 0.00 0.00 0.00 5.34
2809 11463 1.565305 TTTGGTCATTGTTTGCGTGC 58.435 45.000 0.00 0.00 0.00 5.34
2810 11464 0.743688 TTGGTCATTGTTTGCGTGCT 59.256 45.000 0.00 0.00 0.00 4.40
2811 11465 0.743688 TGGTCATTGTTTGCGTGCTT 59.256 45.000 0.00 0.00 0.00 3.91
2812 11466 1.950216 TGGTCATTGTTTGCGTGCTTA 59.050 42.857 0.00 0.00 0.00 3.09
2813 11467 2.556189 TGGTCATTGTTTGCGTGCTTAT 59.444 40.909 0.00 0.00 0.00 1.73
2814 11468 2.916716 GGTCATTGTTTGCGTGCTTATG 59.083 45.455 0.00 0.00 0.00 1.90
2815 11469 2.916716 GTCATTGTTTGCGTGCTTATGG 59.083 45.455 0.00 0.00 0.00 2.74
2816 11470 1.655099 CATTGTTTGCGTGCTTATGGC 59.345 47.619 0.00 0.00 42.22 4.40
2817 11471 0.038709 TTGTTTGCGTGCTTATGGCC 60.039 50.000 0.00 0.00 40.92 5.36
2818 11472 1.153842 GTTTGCGTGCTTATGGCCC 60.154 57.895 0.00 0.00 40.92 5.80
2819 11473 1.604879 TTTGCGTGCTTATGGCCCA 60.605 52.632 0.00 0.00 40.92 5.36
2820 11474 0.969917 TTTGCGTGCTTATGGCCCAT 60.970 50.000 0.00 0.00 40.92 4.00
2821 11475 0.969917 TTGCGTGCTTATGGCCCATT 60.970 50.000 0.00 0.00 40.92 3.16
2822 11476 0.106967 TGCGTGCTTATGGCCCATTA 60.107 50.000 0.00 0.00 40.92 1.90
2823 11477 1.247567 GCGTGCTTATGGCCCATTAT 58.752 50.000 0.00 0.00 40.92 1.28
2824 11478 1.613437 GCGTGCTTATGGCCCATTATT 59.387 47.619 0.00 0.00 40.92 1.40
2825 11479 2.817258 GCGTGCTTATGGCCCATTATTA 59.183 45.455 0.00 0.00 40.92 0.98
2826 11480 3.443681 GCGTGCTTATGGCCCATTATTAT 59.556 43.478 0.00 0.00 40.92 1.28
2827 11481 4.675146 GCGTGCTTATGGCCCATTATTATG 60.675 45.833 0.00 0.00 40.92 1.90
2828 11482 4.458989 CGTGCTTATGGCCCATTATTATGT 59.541 41.667 0.00 0.00 40.92 2.29
2829 11483 5.048083 CGTGCTTATGGCCCATTATTATGTT 60.048 40.000 0.00 0.00 40.92 2.71
2830 11484 6.150307 CGTGCTTATGGCCCATTATTATGTTA 59.850 38.462 0.00 0.00 40.92 2.41
2831 11485 7.538575 GTGCTTATGGCCCATTATTATGTTAG 58.461 38.462 0.00 0.00 40.92 2.34
2832 11486 7.176690 GTGCTTATGGCCCATTATTATGTTAGT 59.823 37.037 0.00 0.00 40.92 2.24
2833 11487 8.387039 TGCTTATGGCCCATTATTATGTTAGTA 58.613 33.333 0.00 0.00 40.92 1.82
2834 11488 8.893727 GCTTATGGCCCATTATTATGTTAGTAG 58.106 37.037 0.00 0.00 34.27 2.57
2838 11492 8.041143 TGGCCCATTATTATGTTAGTAGAAGT 57.959 34.615 0.00 0.00 0.00 3.01
2839 11493 9.161572 TGGCCCATTATTATGTTAGTAGAAGTA 57.838 33.333 0.00 0.00 0.00 2.24
2961 11615 1.473965 CGCAGACAATGGCCTGATAGT 60.474 52.381 3.32 0.00 32.37 2.12
2962 11616 2.648059 GCAGACAATGGCCTGATAGTT 58.352 47.619 3.32 0.00 32.37 2.24
3011 11666 6.749118 GCTCATTAGTGATGTGTTGAAATTCC 59.251 38.462 0.00 0.00 37.06 3.01
3074 11729 5.063438 TGCGTGTATGCTTATTGAAGAGAAC 59.937 40.000 0.00 0.00 34.25 3.01
3348 12007 3.942748 GCAAAGGTCGTGGTATATTGGAA 59.057 43.478 0.00 0.00 0.00 3.53
3466 12125 9.897744 GAAACACACATGATCTTTTTATGAGAA 57.102 29.630 0.00 0.00 0.00 2.87
3593 12253 3.127895 TGCACAGTAACCGAATTAATGGC 59.872 43.478 10.30 10.35 42.05 4.40
3606 12266 4.833478 ATTAATGGCGATCTCAGGCTAT 57.167 40.909 0.00 0.00 35.01 2.97
3626 12286 8.049721 AGGCTATGTAGAAAGAAATAGCTGTTT 58.950 33.333 8.32 8.32 44.45 2.83
3713 12373 1.094785 AAAATCGGCGGATGACCTTG 58.905 50.000 7.21 0.00 31.83 3.61
3716 12376 2.329539 ATCGGCGGATGACCTTGCAT 62.330 55.000 7.21 0.00 0.00 3.96
3861 12521 7.648112 GCAAACACTACTGATCATCTATAACGA 59.352 37.037 0.00 0.00 0.00 3.85
3953 12655 5.990996 CCAACATCACCAAAATTTTGCTAGT 59.009 36.000 22.90 13.89 36.86 2.57
4169 12880 5.984725 TGCCGTGGAATTCTAATTTCTCTA 58.015 37.500 5.23 0.00 0.00 2.43
4172 12883 7.656137 TGCCGTGGAATTCTAATTTCTCTATAC 59.344 37.037 5.23 0.00 0.00 1.47
4266 12984 4.662278 TCTTTTATCCTTTCAGTGTGGGG 58.338 43.478 0.00 0.00 0.00 4.96
4296 13014 3.690460 CCTTGGAAAGCTAACATGGAGT 58.310 45.455 10.01 0.00 44.44 3.85
4365 13083 4.414337 AAGGAGATGATGCTAAGGACAC 57.586 45.455 0.00 0.00 0.00 3.67
4475 13202 5.316158 AGCATGCCATTAAGGAGAACTAT 57.684 39.130 15.66 0.00 41.22 2.12
4476 13203 5.068636 AGCATGCCATTAAGGAGAACTATG 58.931 41.667 15.66 0.00 41.22 2.23
4728 13455 1.404035 GACAAACCGTGTTGAAAGGCT 59.596 47.619 2.61 0.00 41.96 4.58
4730 13457 1.029681 AAACCGTGTTGAAAGGCTCC 58.970 50.000 0.00 0.00 0.00 4.70
4828 13555 2.746269 CAACACCCACAATTTGCTGAG 58.254 47.619 0.00 0.00 0.00 3.35
4837 13564 3.057033 CACAATTTGCTGAGGAAAGGAGG 60.057 47.826 5.21 0.00 0.00 4.30
4900 13627 1.533731 GAAGAAATTCGACGCCCACAA 59.466 47.619 0.00 0.00 0.00 3.33
4932 13659 3.314307 AGCTCAGCCACCTACATACTA 57.686 47.619 0.00 0.00 0.00 1.82
4933 13660 3.850752 AGCTCAGCCACCTACATACTAT 58.149 45.455 0.00 0.00 0.00 2.12
4934 13661 3.829601 AGCTCAGCCACCTACATACTATC 59.170 47.826 0.00 0.00 0.00 2.08
5142 13874 4.354893 TGGCTGCTTCCAAATTGAATTT 57.645 36.364 0.00 0.00 32.18 1.82
5144 13876 5.131784 TGGCTGCTTCCAAATTGAATTTTT 58.868 33.333 0.00 0.00 32.18 1.94
5146 13878 6.769822 TGGCTGCTTCCAAATTGAATTTTTAA 59.230 30.769 0.00 0.00 32.18 1.52
5147 13879 7.447853 TGGCTGCTTCCAAATTGAATTTTTAAT 59.552 29.630 0.00 0.00 32.18 1.40
5148 13880 8.298854 GGCTGCTTCCAAATTGAATTTTTAATT 58.701 29.630 0.00 0.00 0.00 1.40
5187 13919 9.796120 TTTCACCATATTTTCGTCCATTTTATC 57.204 29.630 0.00 0.00 0.00 1.75
5338 14080 3.221771 TGGGTTGTTTCTGTGGATTCTG 58.778 45.455 0.00 0.00 0.00 3.02
5351 14093 3.057526 GTGGATTCTGTTAGTTTGGTGCC 60.058 47.826 0.00 0.00 0.00 5.01
5391 14134 9.899226 CTAACCAATTCACCTCTTTCTAAAAAG 57.101 33.333 0.00 0.00 42.77 2.27
5542 14285 6.816140 TGTTCATTCTTTCCAAAAGTTTGTCC 59.184 34.615 3.26 0.00 36.45 4.02
5559 14302 4.336889 TGTCCGACTCATCAAAGAAAGT 57.663 40.909 0.00 0.00 0.00 2.66
5667 14412 7.631717 AGAAATAAGAAGTTTACCCTCATGC 57.368 36.000 0.00 0.00 0.00 4.06
5680 14425 1.005215 CCTCATGCCAGAACCTTTCCT 59.995 52.381 0.00 0.00 0.00 3.36
5720 14470 6.639671 TGCGTATTTGTTTGGCAATTAATC 57.360 33.333 0.00 0.00 36.89 1.75
5785 14618 9.964303 TGGCATGTATTAATATTTGAACATGTC 57.036 29.630 21.99 21.99 45.50 3.06
5839 14693 7.443575 AGGTTTATATCATGCTGTCTTGATGAC 59.556 37.037 0.00 0.00 45.54 3.06
5849 14704 2.224281 TGTCTTGATGACTGCGGTCTTT 60.224 45.455 25.54 13.65 45.54 2.52
5855 14710 4.130857 TGATGACTGCGGTCTTTTACAAA 58.869 39.130 25.54 3.88 42.54 2.83
5864 14719 5.067413 TGCGGTCTTTTACAAATGTAAACCA 59.933 36.000 16.16 5.45 46.48 3.67
5869 14724 7.095816 GGTCTTTTACAAATGTAAACCATGCAC 60.096 37.037 16.16 8.19 46.48 4.57
5877 14732 6.588719 AATGTAAACCATGCACTACAACAT 57.411 33.333 0.00 0.00 32.82 2.71
6040 14951 4.814294 GACTACAGGGTGCCGCCG 62.814 72.222 0.00 0.00 38.44 6.46
6097 15011 1.219935 CTACCGTGGTGCTTACCCC 59.780 63.158 0.72 0.00 0.00 4.95
6511 15507 1.955080 GGTAGCTGGTAGTGCGTAGAT 59.045 52.381 0.00 0.00 35.28 1.98
6536 15532 4.513442 TCGGTTGATCCATCTTCGAAATT 58.487 39.130 0.00 0.00 35.57 1.82
6537 15533 4.570772 TCGGTTGATCCATCTTCGAAATTC 59.429 41.667 0.00 0.00 35.57 2.17
6552 15548 8.965172 TCTTCGAAATTCGCAGTTTAGATATAC 58.035 33.333 13.97 0.00 40.21 1.47
6553 15549 8.867112 TTCGAAATTCGCAGTTTAGATATACT 57.133 30.769 10.93 0.00 40.21 2.12
6554 15550 9.955208 TTCGAAATTCGCAGTTTAGATATACTA 57.045 29.630 10.93 0.00 40.21 1.82
6555 15551 9.390795 TCGAAATTCGCAGTTTAGATATACTAC 57.609 33.333 10.93 0.00 40.21 2.73
6577 15573 9.978044 ACTACTTTAGTGATCTAAAACGTCTTT 57.022 29.630 0.00 0.00 42.97 2.52
6598 15594 1.729284 ATTAGTTTACGGCGGTGGTG 58.271 50.000 13.24 0.00 0.00 4.17
6667 15713 3.053619 AGAAAGTGGTTCCTGGTCAAGTT 60.054 43.478 0.00 0.00 36.86 2.66
6678 15724 1.578206 GGTCAAGTTCGGCAGGAAGC 61.578 60.000 0.00 0.00 44.65 3.86
6712 15758 0.391130 TTCCGTCGCAATCTTCTGGG 60.391 55.000 0.00 0.00 0.00 4.45
6782 16009 1.690219 AATGGACTCGGGCTAGGCTG 61.690 60.000 18.88 18.88 0.00 4.85
6793 16020 1.173444 GCTAGGCTGCCGCTCTACTA 61.173 60.000 13.96 0.00 36.09 1.82
6795 16022 0.183014 TAGGCTGCCGCTCTACTACT 59.817 55.000 13.96 0.00 36.09 2.57
6796 16023 0.183014 AGGCTGCCGCTCTACTACTA 59.817 55.000 13.96 0.00 36.09 1.82
6797 16024 0.311477 GGCTGCCGCTCTACTACTAC 59.689 60.000 1.35 0.00 36.09 2.73
6810 16037 5.198965 TCTACTACTACGCAGGAAGGAAAT 58.801 41.667 0.00 0.00 0.00 2.17
6811 16038 4.388378 ACTACTACGCAGGAAGGAAATC 57.612 45.455 0.00 0.00 0.00 2.17
6812 16039 4.024670 ACTACTACGCAGGAAGGAAATCT 58.975 43.478 0.00 0.00 0.00 2.40
6813 16040 3.528597 ACTACGCAGGAAGGAAATCTC 57.471 47.619 0.00 0.00 0.00 2.75
7100 16358 0.610687 GCGCCTATATTCCAGCCTCT 59.389 55.000 0.00 0.00 0.00 3.69
7101 16359 1.674221 GCGCCTATATTCCAGCCTCTG 60.674 57.143 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.506708 ACAGTTTAGATTGGATGGTTACCC 58.493 41.667 0.00 0.00 0.00 3.69
38 39 6.525629 CCGAGGATAACAGTTTAGATTGGAT 58.474 40.000 0.00 0.00 0.00 3.41
99 3130 0.170339 GGCCTTAAATGTGTGTCGGC 59.830 55.000 0.00 0.00 35.41 5.54
116 5145 2.154462 AGTGTTGTTACTGCTCATGGC 58.846 47.619 0.00 0.00 42.22 4.40
183 5241 5.935945 TGTGAGTTTTAAGGAGGATGAACA 58.064 37.500 0.00 0.00 0.00 3.18
218 5276 0.528924 TGTTAGTGGTGCGCTCGTAT 59.471 50.000 9.73 0.00 0.00 3.06
223 5281 0.812412 ACGTTTGTTAGTGGTGCGCT 60.812 50.000 9.73 0.00 0.00 5.92
270 5328 4.298626 ACTATGAATCCTAGCTCCCACAA 58.701 43.478 0.00 0.00 0.00 3.33
329 5399 3.553511 TGCATTTTAACAACCTTTGTGCG 59.446 39.130 0.00 0.00 44.59 5.34
347 5417 6.126478 ACCTGTGGGTCTTTATACTATTGCAT 60.126 38.462 0.00 0.00 43.38 3.96
364 5434 0.900647 AAGGAGACGAGACCTGTGGG 60.901 60.000 0.00 0.00 36.56 4.61
377 5447 0.687354 GGTCTCTTGTGGCAAGGAGA 59.313 55.000 8.74 10.04 33.19 3.71
395 5469 1.267433 CGTTCTAGTAGCACGTCTCGG 60.267 57.143 13.33 0.00 30.48 4.63
466 5573 4.275196 GGCGGTATTTTTCCTGGTCTATTC 59.725 45.833 0.00 0.00 0.00 1.75
486 5598 1.939838 GCCGTGGAGGAAATATAGGCG 60.940 57.143 0.00 0.00 45.00 5.52
524 5636 1.315690 TTCGACCCTATAGACGGCTG 58.684 55.000 0.00 0.00 0.00 4.85
533 5645 1.738030 CGGTTCGCTTTTCGACCCTAT 60.738 52.381 0.00 0.00 46.20 2.57
604 5733 1.382009 GAGACAGGGAGGGGAGTCC 60.382 68.421 0.00 0.00 35.64 3.85
628 5757 1.540166 GGGGTGGGGGTTTATAGGC 59.460 63.158 0.00 0.00 0.00 3.93
653 5784 4.463879 CCTGTGGCCTCCGCTCTG 62.464 72.222 3.32 0.00 34.70 3.35
683 9092 1.690219 GGGATGACTGTCAGGGCGAT 61.690 60.000 16.46 0.00 0.00 4.58
684 9093 2.359169 GGGATGACTGTCAGGGCGA 61.359 63.158 16.46 0.00 0.00 5.54
686 9095 1.566298 AAGGGGATGACTGTCAGGGC 61.566 60.000 16.46 7.91 0.00 5.19
691 9101 1.740718 GCGAGAAAGGGGATGACTGTC 60.741 57.143 0.00 0.00 0.00 3.51
703 9113 2.790468 CGTACCTTCGGTAGCGAGAAAG 60.790 54.545 17.37 11.90 39.02 2.62
726 9136 1.439644 GATGACGGAGGTGAGGAGC 59.560 63.158 0.00 0.00 0.00 4.70
1397 9839 0.458025 GTCCTTGGCGACGGACTTAG 60.458 60.000 15.89 0.00 44.90 2.18
1408 9850 0.967380 CCATCACCCTTGTCCTTGGC 60.967 60.000 0.00 0.00 0.00 4.52
1410 9852 0.251297 TGCCATCACCCTTGTCCTTG 60.251 55.000 0.00 0.00 0.00 3.61
1411 9853 0.038744 CTGCCATCACCCTTGTCCTT 59.961 55.000 0.00 0.00 0.00 3.36
1414 9856 2.290323 ACTTACTGCCATCACCCTTGTC 60.290 50.000 0.00 0.00 0.00 3.18
1438 9880 2.027625 CACCCTTGTTCTCGGCGAC 61.028 63.158 4.99 0.00 0.00 5.19
1860 10302 1.241165 TGTTCTCGGCGACAGACTTA 58.759 50.000 4.99 0.00 0.00 2.24
1866 10308 2.342279 CCCTTGTTCTCGGCGACA 59.658 61.111 4.99 0.00 0.00 4.35
1874 10316 0.773644 ACTGCCATCACCCTTGTTCT 59.226 50.000 0.00 0.00 0.00 3.01
1893 10335 0.958876 TGCTCTCGGCGACAGACTTA 60.959 55.000 16.53 0.00 45.43 2.24
1899 10553 4.069232 CCCTTGCTCTCGGCGACA 62.069 66.667 4.99 0.00 45.43 4.35
1910 10564 2.378038 TCTTAATGCCATCACCCTTGC 58.622 47.619 0.00 0.00 0.00 4.01
2063 10717 2.115427 CCTTCTTCTCCTTCTCCTCCC 58.885 57.143 0.00 0.00 0.00 4.30
2089 10743 4.787280 CCTCTCCTCCCCCGCTGT 62.787 72.222 0.00 0.00 0.00 4.40
2136 10790 1.292223 CTCCGGCTTCGTCTTTCCA 59.708 57.895 0.00 0.00 0.00 3.53
2189 10843 4.339530 TCTTCTCCACCACATCTATCTTCG 59.660 45.833 0.00 0.00 0.00 3.79
2374 11028 8.095169 GGGATACTTCTACTACCATAACAATGG 58.905 40.741 2.84 2.84 46.92 3.16
2376 11030 7.508296 ACGGGATACTTCTACTACCATAACAAT 59.492 37.037 0.00 0.00 0.00 2.71
2379 11033 6.890979 ACGGGATACTTCTACTACCATAAC 57.109 41.667 0.00 0.00 0.00 1.89
2429 11083 5.476983 TCCCATAATATCTTCAGGACAGGT 58.523 41.667 0.00 0.00 0.00 4.00
2473 11127 1.135915 AGCACGCAAACAATGACCAAA 59.864 42.857 0.00 0.00 0.00 3.28
2615 11269 8.378565 CCATAATATCTTCAGGACAGGTTGTAT 58.621 37.037 0.00 0.00 0.00 2.29
2616 11270 7.202093 CCCATAATATCTTCAGGACAGGTTGTA 60.202 40.741 0.00 0.00 0.00 2.41
2617 11271 6.409695 CCCATAATATCTTCAGGACAGGTTGT 60.410 42.308 0.00 0.00 0.00 3.32
2618 11272 6.000219 CCCATAATATCTTCAGGACAGGTTG 59.000 44.000 0.00 0.00 0.00 3.77
2619 11273 5.911178 TCCCATAATATCTTCAGGACAGGTT 59.089 40.000 0.00 0.00 0.00 3.50
2620 11274 5.476983 TCCCATAATATCTTCAGGACAGGT 58.523 41.667 0.00 0.00 0.00 4.00
2621 11275 6.439636 TTCCCATAATATCTTCAGGACAGG 57.560 41.667 0.00 0.00 0.00 4.00
2622 11276 8.930846 AATTTCCCATAATATCTTCAGGACAG 57.069 34.615 0.00 0.00 0.00 3.51
2623 11277 7.944554 GGAATTTCCCATAATATCTTCAGGACA 59.055 37.037 3.89 0.00 0.00 4.02
2624 11278 8.341892 GGAATTTCCCATAATATCTTCAGGAC 57.658 38.462 3.89 0.00 0.00 3.85
2650 11304 5.649782 ATGACCAAAAATTACCTGAGCAG 57.350 39.130 0.00 0.00 0.00 4.24
2651 11305 5.304101 ACAATGACCAAAAATTACCTGAGCA 59.696 36.000 0.00 0.00 0.00 4.26
2652 11306 5.783111 ACAATGACCAAAAATTACCTGAGC 58.217 37.500 0.00 0.00 0.00 4.26
2653 11307 7.307337 GCAAACAATGACCAAAAATTACCTGAG 60.307 37.037 0.00 0.00 0.00 3.35
2654 11308 6.481644 GCAAACAATGACCAAAAATTACCTGA 59.518 34.615 0.00 0.00 0.00 3.86
2655 11309 6.563753 CGCAAACAATGACCAAAAATTACCTG 60.564 38.462 0.00 0.00 0.00 4.00
2656 11310 5.465056 CGCAAACAATGACCAAAAATTACCT 59.535 36.000 0.00 0.00 0.00 3.08
2657 11311 5.235401 ACGCAAACAATGACCAAAAATTACC 59.765 36.000 0.00 0.00 0.00 2.85
2658 11312 6.126079 CACGCAAACAATGACCAAAAATTAC 58.874 36.000 0.00 0.00 0.00 1.89
2659 11313 5.277058 GCACGCAAACAATGACCAAAAATTA 60.277 36.000 0.00 0.00 0.00 1.40
2660 11314 4.495514 GCACGCAAACAATGACCAAAAATT 60.496 37.500 0.00 0.00 0.00 1.82
2661 11315 3.002144 GCACGCAAACAATGACCAAAAAT 59.998 39.130 0.00 0.00 0.00 1.82
2662 11316 2.349886 GCACGCAAACAATGACCAAAAA 59.650 40.909 0.00 0.00 0.00 1.94
2663 11317 1.929836 GCACGCAAACAATGACCAAAA 59.070 42.857 0.00 0.00 0.00 2.44
2664 11318 1.135915 AGCACGCAAACAATGACCAAA 59.864 42.857 0.00 0.00 0.00 3.28
2665 11319 0.743688 AGCACGCAAACAATGACCAA 59.256 45.000 0.00 0.00 0.00 3.67
2666 11320 0.743688 AAGCACGCAAACAATGACCA 59.256 45.000 0.00 0.00 0.00 4.02
2667 11321 2.697431 TAAGCACGCAAACAATGACC 57.303 45.000 0.00 0.00 0.00 4.02
2668 11322 2.916716 CCATAAGCACGCAAACAATGAC 59.083 45.455 0.00 0.00 0.00 3.06
2669 11323 2.670789 GCCATAAGCACGCAAACAATGA 60.671 45.455 0.00 0.00 42.97 2.57
2670 11324 1.655099 GCCATAAGCACGCAAACAATG 59.345 47.619 0.00 0.00 42.97 2.82
2671 11325 1.404047 GGCCATAAGCACGCAAACAAT 60.404 47.619 0.00 0.00 46.50 2.71
2672 11326 0.038709 GGCCATAAGCACGCAAACAA 60.039 50.000 0.00 0.00 46.50 2.83
2673 11327 1.583986 GGCCATAAGCACGCAAACA 59.416 52.632 0.00 0.00 46.50 2.83
2674 11328 1.153842 GGGCCATAAGCACGCAAAC 60.154 57.895 4.39 0.00 46.50 2.93
2675 11329 3.283303 GGGCCATAAGCACGCAAA 58.717 55.556 4.39 0.00 46.50 3.68
2681 11335 7.237982 ACTAACATAATAATGGGCCATAAGCA 58.762 34.615 21.54 6.35 38.87 3.91
2682 11336 7.703058 ACTAACATAATAATGGGCCATAAGC 57.297 36.000 21.54 0.00 37.43 3.09
2686 11340 8.669571 ACTTCTACTAACATAATAATGGGCCAT 58.330 33.333 14.78 14.78 37.43 4.40
2687 11341 8.041143 ACTTCTACTAACATAATAATGGGCCA 57.959 34.615 9.61 9.61 37.43 5.36
2741 11395 8.378565 CCATAATATCTTCAGGACAGGTTGTAT 58.621 37.037 0.00 0.00 0.00 2.29
2742 11396 7.202093 CCCATAATATCTTCAGGACAGGTTGTA 60.202 40.741 0.00 0.00 0.00 2.41
2743 11397 6.409695 CCCATAATATCTTCAGGACAGGTTGT 60.410 42.308 0.00 0.00 0.00 3.32
2744 11398 6.000219 CCCATAATATCTTCAGGACAGGTTG 59.000 44.000 0.00 0.00 0.00 3.77
2745 11399 5.911178 TCCCATAATATCTTCAGGACAGGTT 59.089 40.000 0.00 0.00 0.00 3.50
2746 11400 5.476983 TCCCATAATATCTTCAGGACAGGT 58.523 41.667 0.00 0.00 0.00 4.00
2747 11401 6.439636 TTCCCATAATATCTTCAGGACAGG 57.560 41.667 0.00 0.00 0.00 4.00
2748 11402 8.930846 AATTTCCCATAATATCTTCAGGACAG 57.069 34.615 0.00 0.00 0.00 3.51
2749 11403 7.944554 GGAATTTCCCATAATATCTTCAGGACA 59.055 37.037 3.89 0.00 0.00 4.02
2750 11404 8.341892 GGAATTTCCCATAATATCTTCAGGAC 57.658 38.462 3.89 0.00 0.00 3.85
2776 11430 5.649782 ATGACCAAAAATTACCTGAGCAG 57.350 39.130 0.00 0.00 0.00 4.24
2777 11431 5.304101 ACAATGACCAAAAATTACCTGAGCA 59.696 36.000 0.00 0.00 0.00 4.26
2778 11432 5.783111 ACAATGACCAAAAATTACCTGAGC 58.217 37.500 0.00 0.00 0.00 4.26
2779 11433 7.307337 GCAAACAATGACCAAAAATTACCTGAG 60.307 37.037 0.00 0.00 0.00 3.35
2780 11434 6.481644 GCAAACAATGACCAAAAATTACCTGA 59.518 34.615 0.00 0.00 0.00 3.86
2781 11435 6.563753 CGCAAACAATGACCAAAAATTACCTG 60.564 38.462 0.00 0.00 0.00 4.00
2782 11436 5.465056 CGCAAACAATGACCAAAAATTACCT 59.535 36.000 0.00 0.00 0.00 3.08
2783 11437 5.235401 ACGCAAACAATGACCAAAAATTACC 59.765 36.000 0.00 0.00 0.00 2.85
2784 11438 6.126079 CACGCAAACAATGACCAAAAATTAC 58.874 36.000 0.00 0.00 0.00 1.89
2785 11439 5.277058 GCACGCAAACAATGACCAAAAATTA 60.277 36.000 0.00 0.00 0.00 1.40
2786 11440 4.495514 GCACGCAAACAATGACCAAAAATT 60.496 37.500 0.00 0.00 0.00 1.82
2787 11441 3.002144 GCACGCAAACAATGACCAAAAAT 59.998 39.130 0.00 0.00 0.00 1.82
2788 11442 2.349886 GCACGCAAACAATGACCAAAAA 59.650 40.909 0.00 0.00 0.00 1.94
2789 11443 1.929836 GCACGCAAACAATGACCAAAA 59.070 42.857 0.00 0.00 0.00 2.44
2790 11444 1.135915 AGCACGCAAACAATGACCAAA 59.864 42.857 0.00 0.00 0.00 3.28
2791 11445 0.743688 AGCACGCAAACAATGACCAA 59.256 45.000 0.00 0.00 0.00 3.67
2792 11446 0.743688 AAGCACGCAAACAATGACCA 59.256 45.000 0.00 0.00 0.00 4.02
2793 11447 2.697431 TAAGCACGCAAACAATGACC 57.303 45.000 0.00 0.00 0.00 4.02
2794 11448 2.916716 CCATAAGCACGCAAACAATGAC 59.083 45.455 0.00 0.00 0.00 3.06
2795 11449 2.670789 GCCATAAGCACGCAAACAATGA 60.671 45.455 0.00 0.00 42.97 2.57
2796 11450 1.655099 GCCATAAGCACGCAAACAATG 59.345 47.619 0.00 0.00 42.97 2.82
2797 11451 1.404047 GGCCATAAGCACGCAAACAAT 60.404 47.619 0.00 0.00 46.50 2.71
2798 11452 0.038709 GGCCATAAGCACGCAAACAA 60.039 50.000 0.00 0.00 46.50 2.83
2799 11453 1.583986 GGCCATAAGCACGCAAACA 59.416 52.632 0.00 0.00 46.50 2.83
2800 11454 1.153842 GGGCCATAAGCACGCAAAC 60.154 57.895 4.39 0.00 46.50 2.93
2801 11455 3.283303 GGGCCATAAGCACGCAAA 58.717 55.556 4.39 0.00 46.50 3.68
2807 11461 7.237982 ACTAACATAATAATGGGCCATAAGCA 58.762 34.615 21.54 6.35 38.87 3.91
2808 11462 7.703058 ACTAACATAATAATGGGCCATAAGC 57.297 36.000 21.54 0.00 37.43 3.09
2812 11466 8.669571 ACTTCTACTAACATAATAATGGGCCAT 58.330 33.333 14.78 14.78 37.43 4.40
2813 11467 8.041143 ACTTCTACTAACATAATAATGGGCCA 57.959 34.615 9.61 9.61 37.43 5.36
2867 11521 8.938883 ACATAATATCTTCAGGACAGGTTGTAT 58.061 33.333 0.00 0.00 0.00 2.29
2868 11522 8.204160 CACATAATATCTTCAGGACAGGTTGTA 58.796 37.037 0.00 0.00 0.00 2.41
2869 11523 7.050377 CACATAATATCTTCAGGACAGGTTGT 58.950 38.462 0.00 0.00 0.00 3.32
2870 11524 6.017605 GCACATAATATCTTCAGGACAGGTTG 60.018 42.308 0.00 0.00 0.00 3.77
2871 11525 6.058183 GCACATAATATCTTCAGGACAGGTT 58.942 40.000 0.00 0.00 0.00 3.50
2872 11526 5.367937 AGCACATAATATCTTCAGGACAGGT 59.632 40.000 0.00 0.00 0.00 4.00
2873 11527 5.862845 AGCACATAATATCTTCAGGACAGG 58.137 41.667 0.00 0.00 0.00 4.00
2876 11530 9.457110 CGATATAGCACATAATATCTTCAGGAC 57.543 37.037 0.00 0.00 34.35 3.85
2877 11531 9.190317 ACGATATAGCACATAATATCTTCAGGA 57.810 33.333 0.00 0.00 34.35 3.86
2911 11565 0.928229 GTGCGGCTTTCTACATACCG 59.072 55.000 0.00 0.00 46.50 4.02
3011 11666 1.268896 GCATGCCATCGGAATCAACAG 60.269 52.381 6.36 0.00 0.00 3.16
3074 11729 3.446184 GACAAGAAGAACATGTCGCTG 57.554 47.619 0.00 0.00 37.45 5.18
3086 11741 3.209410 AGTTGCCAAGTGAGACAAGAAG 58.791 45.455 0.00 0.00 0.00 2.85
3348 12007 5.557576 ACATCATGTATGCTAGGATGTGT 57.442 39.130 7.05 0.16 44.84 3.72
3466 12125 6.715280 AGATAGTTCAGGACATGTGACATTT 58.285 36.000 1.15 0.00 0.00 2.32
3593 12253 5.697473 TCTTTCTACATAGCCTGAGATCG 57.303 43.478 0.00 0.00 0.00 3.69
3606 12266 8.677148 AAGACAAACAGCTATTTCTTTCTACA 57.323 30.769 0.00 0.00 0.00 2.74
3626 12286 4.431416 TTAGGCCAGAAACTCAAAGACA 57.569 40.909 5.01 0.00 0.00 3.41
3764 12424 3.430929 CCTTGCCATCTACCAGTACTCAC 60.431 52.174 0.00 0.00 0.00 3.51
3953 12655 7.309770 ACCAAAACCTTAGCCAATATTTTGA 57.690 32.000 12.29 0.00 38.64 2.69
4169 12880 6.805016 TGCAAATTAATCAACATGGGGTAT 57.195 33.333 0.00 0.00 0.00 2.73
4172 12883 8.680039 AATAATGCAAATTAATCAACATGGGG 57.320 30.769 0.00 0.00 0.00 4.96
4254 12972 2.691011 GCTAAAACACCCCACACTGAAA 59.309 45.455 0.00 0.00 0.00 2.69
4257 12975 0.958822 GGCTAAAACACCCCACACTG 59.041 55.000 0.00 0.00 0.00 3.66
4266 12984 5.447624 TTAGCTTTCCAAGGCTAAAACAC 57.552 39.130 12.15 0.00 44.63 3.32
4475 13202 4.904251 TGGGTGAATTTTCCCTTTGAATCA 59.096 37.500 16.36 0.00 43.74 2.57
4476 13203 5.482163 TGGGTGAATTTTCCCTTTGAATC 57.518 39.130 16.36 0.00 43.74 2.52
4728 13455 3.173151 TCTTCAACATAGTGAGGCAGGA 58.827 45.455 0.00 0.00 0.00 3.86
4730 13457 4.394300 CCTTTCTTCAACATAGTGAGGCAG 59.606 45.833 0.00 0.00 0.00 4.85
4828 13555 4.984146 ATCATAGGCTAACCTCCTTTCC 57.016 45.455 0.00 0.00 46.34 3.13
4900 13627 3.005155 GTGGCTGAGCTTCTTCAACAAAT 59.995 43.478 3.72 0.00 0.00 2.32
4932 13659 0.917533 AGGAGCAGGAGCAACATGAT 59.082 50.000 0.00 0.00 45.49 2.45
4933 13660 0.251354 GAGGAGCAGGAGCAACATGA 59.749 55.000 0.00 0.00 45.49 3.07
4934 13661 0.035725 TGAGGAGCAGGAGCAACATG 60.036 55.000 0.00 0.00 45.49 3.21
5142 13874 7.090173 GGTGAAAAGCTATGCTCACAATTAAA 58.910 34.615 15.27 0.00 38.25 1.52
5144 13876 5.709631 TGGTGAAAAGCTATGCTCACAATTA 59.290 36.000 15.27 1.80 38.25 1.40
5146 13878 4.081406 TGGTGAAAAGCTATGCTCACAAT 58.919 39.130 15.27 0.00 38.25 2.71
5147 13879 3.485394 TGGTGAAAAGCTATGCTCACAA 58.515 40.909 15.27 5.46 38.25 3.33
5148 13880 3.138884 TGGTGAAAAGCTATGCTCACA 57.861 42.857 15.27 2.49 38.25 3.58
5153 13885 6.265577 ACGAAAATATGGTGAAAAGCTATGC 58.734 36.000 0.00 0.00 0.00 3.14
5187 13919 7.234384 GGACACAACTTATCAAACATACTTCG 58.766 38.462 0.00 0.00 0.00 3.79
5338 14080 2.165319 AGACTCGGCACCAAACTAAC 57.835 50.000 0.00 0.00 0.00 2.34
5351 14093 7.380065 GTGAATTGGTTAGCTATCTTAGACTCG 59.620 40.741 0.00 0.00 0.00 4.18
5433 14176 4.081586 GCCTATACTAGGGTAATCAGCACC 60.082 50.000 2.54 0.00 46.32 5.01
5452 14195 5.428457 TCCCAGATTCTCATAAAACAGCCTA 59.572 40.000 0.00 0.00 0.00 3.93
5542 14285 8.390354 TGCATTAATACTTTCTTTGATGAGTCG 58.610 33.333 0.00 0.00 0.00 4.18
5559 14302 1.144913 GGGGCCTCCAGTGCATTAATA 59.855 52.381 0.84 0.00 35.00 0.98
5654 14399 2.092323 GGTTCTGGCATGAGGGTAAAC 58.908 52.381 0.00 0.00 0.00 2.01
5667 14412 5.259632 AGAATCATGAAGGAAAGGTTCTGG 58.740 41.667 0.00 0.00 0.00 3.86
5680 14425 9.720667 CAAATACGCAAATTCTAGAATCATGAA 57.279 29.630 24.64 14.45 0.00 2.57
5720 14470 9.612620 GTTCCTAAATGTTTTAGTCTGTTCATG 57.387 33.333 6.34 0.00 0.00 3.07
5785 14618 3.315191 AGATGTCAAAAACACCCTCAACG 59.685 43.478 0.00 0.00 41.75 4.10
5849 14704 7.511959 TGTAGTGCATGGTTTACATTTGTAA 57.488 32.000 0.00 0.00 37.84 2.41
5855 14710 7.695480 TTATGTTGTAGTGCATGGTTTACAT 57.305 32.000 0.00 0.00 41.57 2.29
5864 14719 9.539825 TCAAAACATTTTTATGTTGTAGTGCAT 57.460 25.926 4.45 0.00 43.29 3.96
5909 14769 6.925718 GCATCGGAGCATATGTGTATGTATAT 59.074 38.462 4.29 0.00 39.90 0.86
5910 14770 6.096846 AGCATCGGAGCATATGTGTATGTATA 59.903 38.462 4.29 0.00 39.90 1.47
5929 14840 3.875727 AGGTCAGAATTCATCAAGCATCG 59.124 43.478 8.44 0.00 0.00 3.84
6097 15011 4.803426 GACAGGTCCTGAGCGGCG 62.803 72.222 26.18 0.51 35.18 6.46
6133 15047 2.359478 AGGTTTGCCGGGTAAGCG 60.359 61.111 2.18 0.00 40.50 4.68
6390 15335 1.662044 ACGACACGTTCCAGTACCC 59.338 57.895 0.00 0.00 36.35 3.69
6511 15507 4.929819 TCGAAGATGGATCAACCGAATA 57.070 40.909 0.00 0.00 42.61 1.75
6577 15573 3.260740 CACCACCGCCGTAAACTAATTA 58.739 45.455 0.00 0.00 0.00 1.40
6578 15574 2.078392 CACCACCGCCGTAAACTAATT 58.922 47.619 0.00 0.00 0.00 1.40
6667 15713 2.665000 CTCCTTGCTTCCTGCCGA 59.335 61.111 0.00 0.00 42.00 5.54
6678 15724 1.089920 CGGAACTTGATGGCTCCTTG 58.910 55.000 0.00 0.00 0.00 3.61
6732 15955 1.164041 CGTTGCTCGTTTGACCCCTT 61.164 55.000 0.00 0.00 34.52 3.95
6782 16009 0.041135 CTGCGTAGTAGTAGAGCGGC 60.041 60.000 0.00 0.00 34.87 6.53
6793 16020 2.832129 TGAGATTTCCTTCCTGCGTAGT 59.168 45.455 0.00 0.00 0.00 2.73
6795 16022 3.706594 AGATGAGATTTCCTTCCTGCGTA 59.293 43.478 0.00 0.00 0.00 4.42
6796 16023 2.503356 AGATGAGATTTCCTTCCTGCGT 59.497 45.455 0.00 0.00 0.00 5.24
6797 16024 3.191078 AGATGAGATTTCCTTCCTGCG 57.809 47.619 0.00 0.00 0.00 5.18
6810 16037 3.351794 AGACCACGACAGTAGATGAGA 57.648 47.619 0.00 0.00 0.00 3.27
6811 16038 3.440522 TGAAGACCACGACAGTAGATGAG 59.559 47.826 0.00 0.00 0.00 2.90
6812 16039 3.190744 GTGAAGACCACGACAGTAGATGA 59.809 47.826 0.00 0.00 35.86 2.92
6813 16040 3.502920 GTGAAGACCACGACAGTAGATG 58.497 50.000 0.00 0.00 35.86 2.90
6880 16121 2.668212 CGGTGGCGATGTTGTGGT 60.668 61.111 0.00 0.00 0.00 4.16
7146 16404 0.250727 TTGGAGGACTTTTCAGCGGG 60.251 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.