Multiple sequence alignment - TraesCS2B01G511200

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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 TraesCS2B01G511200 chr2B 100.000 5316 0 0 1 5316 706926372 706921057 0.000000e+00 9817.0
1 TraesCS2B01G511200 chr2B 97.133 2686 72 5 2434 5116 706732005 706729322 0.000000e+00 4529.0
2 TraesCS2B01G511200 chr2B 95.947 2023 56 11 298 2294 706734074 706732052 0.000000e+00 3258.0
3 TraesCS2B01G511200 chr2B 81.873 2146 297 57 2434 4528 759440414 759442518 0.000000e+00 1724.0
4 TraesCS2B01G511200 chr2B 82.552 1983 260 58 2435 4360 759346163 759348116 0.000000e+00 1666.0
5 TraesCS2B01G511200 chr2B 83.486 1423 209 12 906 2305 759438997 759440416 0.000000e+00 1303.0
6 TraesCS2B01G511200 chr2B 83.007 153 25 1 2616 2768 759346185 759346336 2.580000e-28 137.0
7 TraesCS2B01G511200 chr2B 93.258 89 6 0 41 129 56779809 56779897 1.200000e-26 132.0
8 TraesCS2B01G511200 chr2B 88.636 44 5 0 5230 5273 758899537 758899580 3.000000e-03 54.7
9 TraesCS2B01G511200 chr2D 93.733 2617 121 16 2636 5234 585687839 585685248 0.000000e+00 3884.0
10 TraesCS2B01G511200 chr2D 92.641 1848 122 8 298 2139 585691008 585689169 0.000000e+00 2647.0
11 TraesCS2B01G511200 chr2D 81.540 2546 345 75 2434 4914 619702240 619704725 0.000000e+00 1982.0
12 TraesCS2B01G511200 chr2D 83.052 1422 218 11 906 2305 619700822 619702242 0.000000e+00 1269.0
13 TraesCS2B01G511200 chr2D 91.244 217 16 3 2428 2641 585688964 585688748 5.210000e-75 292.0
14 TraesCS2B01G511200 chr2D 89.759 166 12 4 134 299 585691261 585691101 1.940000e-49 207.0
15 TraesCS2B01G511200 chr2D 86.014 143 19 1 2616 2758 619702263 619702404 9.220000e-33 152.0
16 TraesCS2B01G511200 chr2D 93.617 94 6 0 41 134 2564869 2564962 2.000000e-29 141.0
17 TraesCS2B01G511200 chr2D 85.156 128 17 2 2302 2428 76534962 76535088 4.320000e-26 130.0
18 TraesCS2B01G511200 chr2D 80.672 119 22 1 2616 2734 619664299 619664416 2.040000e-14 91.6
19 TraesCS2B01G511200 chr2A 94.762 2100 97 9 2434 4528 719730708 719728617 0.000000e+00 3256.0
20 TraesCS2B01G511200 chr2A 94.702 1491 68 7 649 2135 719732435 719730952 0.000000e+00 2305.0
21 TraesCS2B01G511200 chr2A 82.191 2145 299 50 2434 4528 751268515 751270626 0.000000e+00 1768.0
22 TraesCS2B01G511200 chr2A 82.060 2146 301 50 2434 4528 751238128 751240240 0.000000e+00 1753.0
23 TraesCS2B01G511200 chr2A 82.771 1985 250 58 2434 4360 751208748 751210698 0.000000e+00 1687.0
24 TraesCS2B01G511200 chr2A 82.059 2079 268 62 2638 4668 751233149 751235170 0.000000e+00 1676.0
25 TraesCS2B01G511200 chr2A 82.095 1642 238 31 702 2299 751236496 751238125 0.000000e+00 1352.0
26 TraesCS2B01G511200 chr2A 84.479 1295 197 3 1008 2299 751267219 751268512 0.000000e+00 1275.0
27 TraesCS2B01G511200 chr2A 84.479 1295 198 2 1008 2299 751288144 751289438 0.000000e+00 1275.0
28 TraesCS2B01G511200 chr2A 87.135 684 61 15 4572 5234 719728612 719727935 0.000000e+00 750.0
29 TraesCS2B01G511200 chr2A 87.571 354 25 10 300 634 719734851 719734498 4.990000e-105 392.0
30 TraesCS2B01G511200 chr2A 88.194 144 12 4 156 299 719735083 719734945 3.290000e-37 167.0
31 TraesCS2B01G511200 chr2A 87.413 143 17 1 2616 2758 751268538 751268679 4.260000e-36 163.0
32 TraesCS2B01G511200 chr2A 87.413 143 17 1 2616 2758 751289464 751289605 4.260000e-36 163.0
33 TraesCS2B01G511200 chr2A 82.105 95 3 6 41 135 770926072 770925992 9.550000e-08 69.4
34 TraesCS2B01G511200 chrUn 84.508 1291 196 3 1013 2299 337511521 337512811 0.000000e+00 1273.0
35 TraesCS2B01G511200 chrUn 87.413 143 17 1 2616 2758 337512837 337512978 4.260000e-36 163.0
36 TraesCS2B01G511200 chr3A 88.806 134 15 0 2303 2436 712629935 712629802 1.180000e-36 165.0
37 TraesCS2B01G511200 chr3A 88.393 112 10 3 2318 2428 97191989 97192098 1.200000e-26 132.0
38 TraesCS2B01G511200 chr7A 91.150 113 9 1 2323 2434 67729558 67729670 9.220000e-33 152.0
39 TraesCS2B01G511200 chr7A 78.626 131 21 6 494 620 700797952 700797825 4.410000e-11 80.5
40 TraesCS2B01G511200 chr5D 95.745 94 4 0 41 134 305988913 305988820 9.220000e-33 152.0
41 TraesCS2B01G511200 chr5D 86.325 117 15 1 2318 2434 300141307 300141422 5.590000e-25 126.0
42 TraesCS2B01G511200 chr5B 91.150 113 9 1 2323 2434 369480724 369480836 9.220000e-33 152.0
43 TraesCS2B01G511200 chr3D 94.845 97 5 0 41 137 448983434 448983338 9.220000e-33 152.0
44 TraesCS2B01G511200 chr3D 89.565 115 11 1 2323 2436 577341617 577341503 1.540000e-30 145.0
45 TraesCS2B01G511200 chr6D 93.617 94 6 0 41 134 11573722 11573815 2.000000e-29 141.0
46 TraesCS2B01G511200 chr5A 92.553 94 7 0 41 134 18944897 18944990 9.290000e-28 135.0
47 TraesCS2B01G511200 chr5A 88.393 112 10 3 2318 2428 579851094 579851203 1.200000e-26 132.0
48 TraesCS2B01G511200 chr4A 92.553 94 7 0 41 134 708534621 708534714 9.290000e-28 135.0
49 TraesCS2B01G511200 chr6B 87.288 118 12 3 2318 2434 650917304 650917189 1.200000e-26 132.0
50 TraesCS2B01G511200 chr3B 87.379 103 11 2 41 142 70911257 70911156 3.360000e-22 117.0
51 TraesCS2B01G511200 chr3B 79.699 133 21 6 491 620 815205466 815205337 2.040000e-14 91.6
52 TraesCS2B01G511200 chr7D 94.118 51 3 0 45 95 606657163 606657213 1.590000e-10 78.7
53 TraesCS2B01G511200 chr7B 100.000 34 0 0 491 524 613866944 613866977 4.440000e-06 63.9
54 TraesCS2B01G511200 chr4B 77.869 122 14 11 491 605 425178670 425178785 4.440000e-06 63.9


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 TraesCS2B01G511200 chr2B 706921057 706926372 5315 True 9817.000000 9817 100.000000 1 5316 1 chr2B.!!$R1 5315
1 TraesCS2B01G511200 chr2B 706729322 706734074 4752 True 3893.500000 4529 96.540000 298 5116 2 chr2B.!!$R2 4818
2 TraesCS2B01G511200 chr2B 759438997 759442518 3521 False 1513.500000 1724 82.679500 906 4528 2 chr2B.!!$F4 3622
3 TraesCS2B01G511200 chr2B 759346163 759348116 1953 False 901.500000 1666 82.779500 2435 4360 2 chr2B.!!$F3 1925
4 TraesCS2B01G511200 chr2D 585685248 585691261 6013 True 1757.500000 3884 91.844250 134 5234 4 chr2D.!!$R1 5100
5 TraesCS2B01G511200 chr2D 619700822 619704725 3903 False 1134.333333 1982 83.535333 906 4914 3 chr2D.!!$F4 4008
6 TraesCS2B01G511200 chr2A 751208748 751210698 1950 False 1687.000000 1687 82.771000 2434 4360 1 chr2A.!!$F1 1926
7 TraesCS2B01G511200 chr2A 751233149 751240240 7091 False 1593.666667 1753 82.071333 702 4668 3 chr2A.!!$F2 3966
8 TraesCS2B01G511200 chr2A 719727935 719735083 7148 True 1374.000000 3256 90.472800 156 5234 5 chr2A.!!$R2 5078
9 TraesCS2B01G511200 chr2A 751267219 751270626 3407 False 1068.666667 1768 84.694333 1008 4528 3 chr2A.!!$F3 3520
10 TraesCS2B01G511200 chr2A 751288144 751289605 1461 False 719.000000 1275 85.946000 1008 2758 2 chr2A.!!$F4 1750
11 TraesCS2B01G511200 chrUn 337511521 337512978 1457 False 718.000000 1273 85.960500 1013 2758 2 chrUn.!!$F1 1745

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
22 23 0.246635 TCTCACTCGTTTAGCTGGGC 59.753 55.000 0.00 0.0 0.00 5.36 F
115 116 0.465460 TGGCTAATGGGCGCTAAAGG 60.465 55.000 7.64 0.0 44.11 3.11 F
240 241 1.229400 TGCCTTCCCTCCGTTACCT 60.229 57.895 0.00 0.0 0.00 3.08 F
1897 4605 1.002366 CTACTGTGATGCCGCTGAAC 58.998 55.000 0.00 0.0 0.00 3.18 F
2388 5175 0.046242 ATCCACCTCAATCCCCTCCA 59.954 55.000 0.00 0.0 0.00 3.86 F
2399 5186 0.104144 TCCCCTCCAAACCTCTCCAA 60.104 55.000 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 4264 0.817013 GAGGTCTGAGCTGGAGTCAG 59.183 60.000 14.96 0.0 42.51 3.51 R
1617 4325 1.050988 ATGACCCATCCCACGGAGAG 61.051 60.000 0.00 0.0 34.05 3.20 R
2122 4830 1.067354 CCTGCTGCCATTTTTCAGGTC 60.067 52.381 0.00 0.0 39.45 3.85 R
3685 7610 0.034337 ACTACGTCCCAACAATGCGT 59.966 50.000 0.00 0.0 39.23 5.24 R
4055 7984 2.069273 GTTCTCCACAATGGACGAGTG 58.931 52.381 0.00 0.0 42.67 3.51 R
4408 8347 8.938883 ACCAGGATTACAATGTACTCAATAGAT 58.061 33.333 11.89 0.0 0.00 1.98 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
21 22 2.743636 TTCTCACTCGTTTAGCTGGG 57.256 50.000 0.00 0.00 0.00 4.45
22 23 0.246635 TCTCACTCGTTTAGCTGGGC 59.753 55.000 0.00 0.00 0.00 5.36
23 24 0.741221 CTCACTCGTTTAGCTGGGCC 60.741 60.000 0.00 0.00 0.00 5.80
24 25 1.003839 CACTCGTTTAGCTGGGCCA 60.004 57.895 5.85 5.85 0.00 5.36
25 26 1.021390 CACTCGTTTAGCTGGGCCAG 61.021 60.000 29.44 29.44 34.12 4.85
79 80 2.123428 CCAGGCCCATGCAAGCTAC 61.123 63.158 0.00 0.00 40.13 3.58
80 81 2.124570 AGGCCCATGCAAGCTACG 60.125 61.111 0.00 0.00 40.13 3.51
81 82 3.892581 GGCCCATGCAAGCTACGC 61.893 66.667 0.00 1.11 40.13 4.42
82 83 3.133464 GCCCATGCAAGCTACGCA 61.133 61.111 12.67 12.67 44.94 5.24
83 84 3.104766 CCCATGCAAGCTACGCAG 58.895 61.111 15.18 8.17 43.88 5.18
103 104 2.830370 GGCGCTGGCTTGGCTAAT 60.830 61.111 7.64 0.00 39.81 1.73
104 105 2.410469 GCGCTGGCTTGGCTAATG 59.590 61.111 0.00 0.00 35.83 1.90
106 107 2.484062 CGCTGGCTTGGCTAATGGG 61.484 63.158 0.00 0.00 0.00 4.00
107 108 2.789715 GCTGGCTTGGCTAATGGGC 61.790 63.158 0.00 0.00 41.27 5.36
108 109 2.440065 TGGCTTGGCTAATGGGCG 60.440 61.111 0.00 0.00 44.11 6.13
109 110 3.904479 GGCTTGGCTAATGGGCGC 61.904 66.667 0.00 0.00 44.11 6.53
112 113 1.101049 GCTTGGCTAATGGGCGCTAA 61.101 55.000 7.64 0.00 44.11 3.09
113 114 1.388547 CTTGGCTAATGGGCGCTAAA 58.611 50.000 7.64 0.00 44.11 1.85
114 115 1.334869 CTTGGCTAATGGGCGCTAAAG 59.665 52.381 7.64 0.00 44.11 1.85
115 116 0.465460 TGGCTAATGGGCGCTAAAGG 60.465 55.000 7.64 0.00 44.11 3.11
125 126 2.586357 GCTAAAGGCGCCGAGGAG 60.586 66.667 23.20 17.72 0.00 3.69
126 127 2.107141 CTAAAGGCGCCGAGGAGG 59.893 66.667 23.20 6.79 44.97 4.30
240 241 1.229400 TGCCTTCCCTCCGTTACCT 60.229 57.895 0.00 0.00 0.00 3.08
286 287 3.533691 CTTCGTCGCGCCTTCGTC 61.534 66.667 0.00 0.00 38.14 4.20
310 405 3.007940 TCATACCCCGCCAATAATCTCTG 59.992 47.826 0.00 0.00 0.00 3.35
400 495 2.289819 TGACTGACGGTAACCCATTTCC 60.290 50.000 0.00 0.00 0.00 3.13
407 502 3.206150 CGGTAACCCATTTCCTCTCATG 58.794 50.000 0.00 0.00 0.00 3.07
439 534 5.249393 TCTTCTTCTTTGTAATGCTCCCTCT 59.751 40.000 0.00 0.00 0.00 3.69
451 546 8.271458 TGTAATGCTCCCTCTGTTTCATATTAA 58.729 33.333 0.00 0.00 0.00 1.40
630 768 9.942850 TCTGTAATCTTGATCACTAATTGTTGA 57.057 29.630 0.00 0.00 0.00 3.18
1556 4264 1.521681 GCGACTACTCCATGGGTGC 60.522 63.158 13.02 4.94 0.00 5.01
1897 4605 1.002366 CTACTGTGATGCCGCTGAAC 58.998 55.000 0.00 0.00 0.00 3.18
2010 4718 7.876068 TGTGGTAAAGACAATAATTTCTCGACT 59.124 33.333 0.00 0.00 0.00 4.18
2122 4830 0.786581 CTCCGCGTATGCTTATGCTG 59.213 55.000 18.49 13.53 38.06 4.41
2136 4844 4.427312 CTTATGCTGACCTGAAAAATGGC 58.573 43.478 0.00 0.00 0.00 4.40
2139 4847 1.670967 GCTGACCTGAAAAATGGCAGC 60.671 52.381 0.23 0.23 41.88 5.25
2140 4848 1.614903 CTGACCTGAAAAATGGCAGCA 59.385 47.619 0.00 0.00 0.00 4.41
2187 4922 2.452600 TTTGGTTGGGAGAGCTTGTT 57.547 45.000 0.00 0.00 0.00 2.83
2223 4961 1.339055 CGTGATGGTGGTGGTGAGAAT 60.339 52.381 0.00 0.00 0.00 2.40
2295 5081 7.201556 CGCTTATTGATTGTACAGTGTGATCTT 60.202 37.037 5.88 2.72 0.00 2.40
2302 5089 3.650942 TGTACAGTGTGATCTTTCCCCTT 59.349 43.478 5.88 0.00 0.00 3.95
2303 5090 3.884037 ACAGTGTGATCTTTCCCCTTT 57.116 42.857 0.00 0.00 0.00 3.11
2304 5091 4.993705 ACAGTGTGATCTTTCCCCTTTA 57.006 40.909 0.00 0.00 0.00 1.85
2305 5092 4.911390 ACAGTGTGATCTTTCCCCTTTAG 58.089 43.478 0.00 0.00 0.00 1.85
2306 5093 4.263506 ACAGTGTGATCTTTCCCCTTTAGG 60.264 45.833 0.00 0.00 0.00 2.69
2319 5106 3.385193 CCTTTAGGGCTTGTTTGGTTG 57.615 47.619 0.00 0.00 0.00 3.77
2320 5107 2.547855 CCTTTAGGGCTTGTTTGGTTGC 60.548 50.000 0.00 0.00 0.00 4.17
2321 5108 1.781786 TTAGGGCTTGTTTGGTTGCA 58.218 45.000 0.00 0.00 0.00 4.08
2322 5109 1.781786 TAGGGCTTGTTTGGTTGCAA 58.218 45.000 0.00 0.00 0.00 4.08
2323 5110 0.908198 AGGGCTTGTTTGGTTGCAAA 59.092 45.000 0.00 0.00 0.00 3.68
2324 5111 1.134431 AGGGCTTGTTTGGTTGCAAAG 60.134 47.619 0.00 0.00 0.00 2.77
2325 5112 1.298602 GGCTTGTTTGGTTGCAAAGG 58.701 50.000 0.00 0.00 0.00 3.11
2326 5113 1.298602 GCTTGTTTGGTTGCAAAGGG 58.701 50.000 0.00 0.00 0.00 3.95
2327 5114 1.406751 GCTTGTTTGGTTGCAAAGGGT 60.407 47.619 0.00 0.00 0.00 4.34
2328 5115 2.939198 GCTTGTTTGGTTGCAAAGGGTT 60.939 45.455 0.00 0.00 0.00 4.11
2329 5116 3.342719 CTTGTTTGGTTGCAAAGGGTTT 58.657 40.909 0.00 0.00 0.00 3.27
2330 5117 2.704572 TGTTTGGTTGCAAAGGGTTTG 58.295 42.857 0.00 0.00 43.44 2.93
2331 5118 2.303022 TGTTTGGTTGCAAAGGGTTTGA 59.697 40.909 0.00 0.00 43.26 2.69
2332 5119 3.244561 TGTTTGGTTGCAAAGGGTTTGAA 60.245 39.130 0.00 0.00 43.26 2.69
2333 5120 2.977772 TGGTTGCAAAGGGTTTGAAG 57.022 45.000 0.00 0.00 43.26 3.02
2334 5121 2.183679 TGGTTGCAAAGGGTTTGAAGT 58.816 42.857 0.00 0.00 43.26 3.01
2335 5122 2.093764 TGGTTGCAAAGGGTTTGAAGTG 60.094 45.455 0.00 0.00 43.26 3.16
2336 5123 2.549926 GTTGCAAAGGGTTTGAAGTGG 58.450 47.619 0.00 0.00 43.26 4.00
2337 5124 2.151502 TGCAAAGGGTTTGAAGTGGA 57.848 45.000 3.56 0.00 43.26 4.02
2338 5125 2.676748 TGCAAAGGGTTTGAAGTGGAT 58.323 42.857 3.56 0.00 43.26 3.41
2339 5126 3.037549 TGCAAAGGGTTTGAAGTGGATT 58.962 40.909 3.56 0.00 43.26 3.01
2340 5127 3.181467 TGCAAAGGGTTTGAAGTGGATTG 60.181 43.478 3.56 0.00 43.26 2.67
2341 5128 3.803368 GCAAAGGGTTTGAAGTGGATTGG 60.803 47.826 3.56 0.00 43.26 3.16
2342 5129 2.309136 AGGGTTTGAAGTGGATTGGG 57.691 50.000 0.00 0.00 0.00 4.12
2343 5130 1.203174 AGGGTTTGAAGTGGATTGGGG 60.203 52.381 0.00 0.00 0.00 4.96
2344 5131 1.203125 GGGTTTGAAGTGGATTGGGGA 60.203 52.381 0.00 0.00 0.00 4.81
2345 5132 2.171003 GGTTTGAAGTGGATTGGGGAG 58.829 52.381 0.00 0.00 0.00 4.30
2346 5133 2.171003 GTTTGAAGTGGATTGGGGAGG 58.829 52.381 0.00 0.00 0.00 4.30
2347 5134 1.753903 TTGAAGTGGATTGGGGAGGA 58.246 50.000 0.00 0.00 0.00 3.71
2348 5135 1.985622 TGAAGTGGATTGGGGAGGAT 58.014 50.000 0.00 0.00 0.00 3.24
2349 5136 2.287584 TGAAGTGGATTGGGGAGGATT 58.712 47.619 0.00 0.00 0.00 3.01
2350 5137 3.469859 TGAAGTGGATTGGGGAGGATTA 58.530 45.455 0.00 0.00 0.00 1.75
2351 5138 3.855599 TGAAGTGGATTGGGGAGGATTAA 59.144 43.478 0.00 0.00 0.00 1.40
2352 5139 4.293634 TGAAGTGGATTGGGGAGGATTAAA 59.706 41.667 0.00 0.00 0.00 1.52
2353 5140 5.043432 TGAAGTGGATTGGGGAGGATTAAAT 60.043 40.000 0.00 0.00 0.00 1.40
2354 5141 5.066913 AGTGGATTGGGGAGGATTAAATC 57.933 43.478 0.00 0.00 0.00 2.17
2375 5162 8.753497 AAATCCTCTATAAGTGAAAATCCACC 57.247 34.615 0.00 0.00 37.76 4.61
2376 5163 7.698163 ATCCTCTATAAGTGAAAATCCACCT 57.302 36.000 0.00 0.00 37.76 4.00
2377 5164 7.125792 TCCTCTATAAGTGAAAATCCACCTC 57.874 40.000 0.00 0.00 37.76 3.85
2378 5165 6.672218 TCCTCTATAAGTGAAAATCCACCTCA 59.328 38.462 0.00 0.00 37.76 3.86
2379 5166 7.182026 TCCTCTATAAGTGAAAATCCACCTCAA 59.818 37.037 0.00 0.00 37.76 3.02
2380 5167 7.995488 CCTCTATAAGTGAAAATCCACCTCAAT 59.005 37.037 0.00 0.00 37.76 2.57
2381 5168 8.964476 TCTATAAGTGAAAATCCACCTCAATC 57.036 34.615 0.00 0.00 37.76 2.67
2382 5169 7.993183 TCTATAAGTGAAAATCCACCTCAATCC 59.007 37.037 0.00 0.00 37.76 3.01
2383 5170 3.701664 AGTGAAAATCCACCTCAATCCC 58.298 45.455 0.00 0.00 37.76 3.85
2384 5171 2.760650 GTGAAAATCCACCTCAATCCCC 59.239 50.000 0.00 0.00 0.00 4.81
2385 5172 2.654385 TGAAAATCCACCTCAATCCCCT 59.346 45.455 0.00 0.00 0.00 4.79
2386 5173 3.291584 GAAAATCCACCTCAATCCCCTC 58.708 50.000 0.00 0.00 0.00 4.30
2387 5174 1.226311 AATCCACCTCAATCCCCTCC 58.774 55.000 0.00 0.00 0.00 4.30
2388 5175 0.046242 ATCCACCTCAATCCCCTCCA 59.954 55.000 0.00 0.00 0.00 3.86
2389 5176 0.178846 TCCACCTCAATCCCCTCCAA 60.179 55.000 0.00 0.00 0.00 3.53
2390 5177 0.704076 CCACCTCAATCCCCTCCAAA 59.296 55.000 0.00 0.00 0.00 3.28
2391 5178 1.616994 CCACCTCAATCCCCTCCAAAC 60.617 57.143 0.00 0.00 0.00 2.93
2392 5179 0.704664 ACCTCAATCCCCTCCAAACC 59.295 55.000 0.00 0.00 0.00 3.27
2393 5180 1.002857 CCTCAATCCCCTCCAAACCT 58.997 55.000 0.00 0.00 0.00 3.50
2394 5181 1.064389 CCTCAATCCCCTCCAAACCTC 60.064 57.143 0.00 0.00 0.00 3.85
2395 5182 1.918957 CTCAATCCCCTCCAAACCTCT 59.081 52.381 0.00 0.00 0.00 3.69
2396 5183 1.916181 TCAATCCCCTCCAAACCTCTC 59.084 52.381 0.00 0.00 0.00 3.20
2397 5184 1.064389 CAATCCCCTCCAAACCTCTCC 60.064 57.143 0.00 0.00 0.00 3.71
2398 5185 0.121197 ATCCCCTCCAAACCTCTCCA 59.879 55.000 0.00 0.00 0.00 3.86
2399 5186 0.104144 TCCCCTCCAAACCTCTCCAA 60.104 55.000 0.00 0.00 0.00 3.53
2400 5187 1.002857 CCCCTCCAAACCTCTCCAAT 58.997 55.000 0.00 0.00 0.00 3.16
2401 5188 1.064389 CCCCTCCAAACCTCTCCAATC 60.064 57.143 0.00 0.00 0.00 2.67
2402 5189 1.064389 CCCTCCAAACCTCTCCAATCC 60.064 57.143 0.00 0.00 0.00 3.01
2403 5190 1.918957 CCTCCAAACCTCTCCAATCCT 59.081 52.381 0.00 0.00 0.00 3.24
2404 5191 2.092699 CCTCCAAACCTCTCCAATCCTC 60.093 54.545 0.00 0.00 0.00 3.71
2405 5192 2.843113 CTCCAAACCTCTCCAATCCTCT 59.157 50.000 0.00 0.00 0.00 3.69
2406 5193 2.840651 TCCAAACCTCTCCAATCCTCTC 59.159 50.000 0.00 0.00 0.00 3.20
2407 5194 2.092699 CCAAACCTCTCCAATCCTCTCC 60.093 54.545 0.00 0.00 0.00 3.71
2408 5195 2.573462 CAAACCTCTCCAATCCTCTCCA 59.427 50.000 0.00 0.00 0.00 3.86
2409 5196 2.649742 ACCTCTCCAATCCTCTCCAA 57.350 50.000 0.00 0.00 0.00 3.53
2410 5197 2.476199 ACCTCTCCAATCCTCTCCAAG 58.524 52.381 0.00 0.00 0.00 3.61
2411 5198 2.045047 ACCTCTCCAATCCTCTCCAAGA 59.955 50.000 0.00 0.00 0.00 3.02
2412 5199 2.699846 CCTCTCCAATCCTCTCCAAGAG 59.300 54.545 0.00 0.00 41.96 2.85
2413 5200 3.629539 CCTCTCCAATCCTCTCCAAGAGA 60.630 52.174 5.54 0.00 45.07 3.10
2423 5210 1.618837 TCTCCAAGAGAGGTTGAACCG 59.381 52.381 8.98 0.00 44.90 4.44
2424 5211 1.618837 CTCCAAGAGAGGTTGAACCGA 59.381 52.381 8.98 0.00 44.90 4.69
2425 5212 2.037251 CTCCAAGAGAGGTTGAACCGAA 59.963 50.000 8.98 0.00 44.90 4.30
2426 5213 2.143925 CCAAGAGAGGTTGAACCGAAC 58.856 52.381 8.98 5.02 44.90 3.95
2427 5214 2.484770 CCAAGAGAGGTTGAACCGAACA 60.485 50.000 8.98 0.00 44.90 3.18
2428 5215 3.403038 CAAGAGAGGTTGAACCGAACAT 58.597 45.455 8.98 0.00 44.90 2.71
2429 5216 4.562757 CCAAGAGAGGTTGAACCGAACATA 60.563 45.833 8.98 0.00 44.90 2.29
2430 5217 4.457834 AGAGAGGTTGAACCGAACATAG 57.542 45.455 8.98 0.00 44.90 2.23
2431 5218 2.930682 GAGAGGTTGAACCGAACATAGC 59.069 50.000 8.98 0.00 44.90 2.97
2432 5219 2.007608 GAGGTTGAACCGAACATAGCC 58.992 52.381 8.98 0.00 44.90 3.93
2451 5238 9.717942 ACATAGCCTTATGTTGAATTCTAGATC 57.282 33.333 7.05 0.00 45.92 2.75
2460 5248 6.349300 TGTTGAATTCTAGATCTGGTTAGGC 58.651 40.000 5.18 0.00 0.00 3.93
2523 5312 4.922692 TGCTGTTAAATTTTGGAAGCATCG 59.077 37.500 11.31 0.00 34.46 3.84
2553 5343 5.798132 TGCTGGACTATATATCTGGCTTTG 58.202 41.667 0.00 0.00 0.00 2.77
2623 5414 5.836024 TGTGGTTAGGAAACTTAGGATGT 57.164 39.130 0.00 0.00 43.67 3.06
2654 6359 2.590073 TCAACAAACACAACACTTGCG 58.410 42.857 0.00 0.00 0.00 4.85
2659 6364 3.437395 ACAAACACAACACTTGCGAGTAA 59.563 39.130 6.21 0.00 33.90 2.24
2727 6612 2.309613 TGGCTTTCTGCAGTTGACAAT 58.690 42.857 14.67 0.00 45.15 2.71
2747 6632 9.371136 TGACAATGAGAGTAATGTATTGAAGAC 57.629 33.333 0.00 0.00 33.98 3.01
2768 6656 6.806217 AGACTATACTCCCAATAGTGGCTAT 58.194 40.000 2.94 1.08 44.46 2.97
2799 6687 2.840038 ACTCACATCCATCTGCCTTGTA 59.160 45.455 0.00 0.00 0.00 2.41
2824 6712 6.997655 TGGATATGCAAGTCAAGAGGTATAG 58.002 40.000 0.00 0.00 0.00 1.31
2917 6808 3.469008 CCTGTCAGTGTCAGGTAAACA 57.531 47.619 23.61 2.97 45.09 2.83
3744 7671 5.183228 TGGTAAGGCTTAACATGCTAGTTC 58.817 41.667 20.69 0.00 33.07 3.01
3769 7696 9.640963 TCTCTACAGCTTAACTAATTCAAGTTC 57.359 33.333 0.00 0.00 40.20 3.01
3931 7858 6.618287 TCATGACAGACTTTACAAACCTTG 57.382 37.500 0.00 0.00 0.00 3.61
4055 7984 3.256558 GGAAATGCAAGAGAATTGGTGC 58.743 45.455 0.00 0.00 37.51 5.01
4757 8708 3.864003 GCCCGAAGTCTGACAATAGTAAC 59.136 47.826 10.88 0.00 0.00 2.50
4971 8934 8.832521 CGAATCATATATACCTCCTCTGTAGTC 58.167 40.741 0.00 0.00 0.00 2.59
5121 9089 4.972568 TGATGGCCTGGTAACTTTAGGATA 59.027 41.667 3.32 0.00 33.33 2.59
5165 9134 5.455326 GGTCTTCAGTATATCCATGGTGCTT 60.455 44.000 12.58 0.00 0.00 3.91
5240 9212 5.255710 TGTTGTTGAACATTGTAAGTGGG 57.744 39.130 0.00 0.00 37.15 4.61
5241 9213 4.707448 TGTTGTTGAACATTGTAAGTGGGT 59.293 37.500 0.00 0.00 37.15 4.51
5242 9214 5.186021 TGTTGTTGAACATTGTAAGTGGGTT 59.814 36.000 0.00 0.00 37.15 4.11
5243 9215 5.255710 TGTTGAACATTGTAAGTGGGTTG 57.744 39.130 0.00 0.00 0.00 3.77
5244 9216 4.950475 TGTTGAACATTGTAAGTGGGTTGA 59.050 37.500 0.00 0.00 0.00 3.18
5245 9217 5.419155 TGTTGAACATTGTAAGTGGGTTGAA 59.581 36.000 0.00 0.00 0.00 2.69
5246 9218 5.766150 TGAACATTGTAAGTGGGTTGAAG 57.234 39.130 0.00 0.00 0.00 3.02
5247 9219 5.441500 TGAACATTGTAAGTGGGTTGAAGA 58.558 37.500 0.00 0.00 0.00 2.87
5248 9220 6.068010 TGAACATTGTAAGTGGGTTGAAGAT 58.932 36.000 0.00 0.00 0.00 2.40
5249 9221 6.206634 TGAACATTGTAAGTGGGTTGAAGATC 59.793 38.462 0.00 0.00 0.00 2.75
5250 9222 5.630121 ACATTGTAAGTGGGTTGAAGATCA 58.370 37.500 0.00 0.00 0.00 2.92
5251 9223 5.707298 ACATTGTAAGTGGGTTGAAGATCAG 59.293 40.000 0.00 0.00 0.00 2.90
5252 9224 3.674997 TGTAAGTGGGTTGAAGATCAGC 58.325 45.455 0.00 0.00 0.00 4.26
5253 9225 3.327757 TGTAAGTGGGTTGAAGATCAGCT 59.672 43.478 0.00 0.00 0.00 4.24
5254 9226 2.777832 AGTGGGTTGAAGATCAGCTC 57.222 50.000 0.00 0.00 0.00 4.09
5255 9227 1.980765 AGTGGGTTGAAGATCAGCTCA 59.019 47.619 0.00 0.00 35.67 4.26
5256 9228 2.479566 TGGGTTGAAGATCAGCTCAC 57.520 50.000 0.00 0.00 33.02 3.51
5257 9229 1.003580 TGGGTTGAAGATCAGCTCACC 59.996 52.381 0.00 0.00 33.02 4.02
5258 9230 1.280421 GGGTTGAAGATCAGCTCACCT 59.720 52.381 0.00 0.00 27.72 4.00
5259 9231 2.626840 GGTTGAAGATCAGCTCACCTC 58.373 52.381 0.00 0.00 0.00 3.85
5260 9232 2.027745 GGTTGAAGATCAGCTCACCTCA 60.028 50.000 0.00 0.00 0.00 3.86
5261 9233 2.999355 GTTGAAGATCAGCTCACCTCAC 59.001 50.000 0.00 0.00 0.00 3.51
5262 9234 1.552337 TGAAGATCAGCTCACCTCACC 59.448 52.381 0.00 0.00 0.00 4.02
5263 9235 1.552337 GAAGATCAGCTCACCTCACCA 59.448 52.381 0.00 0.00 0.00 4.17
5264 9236 1.876849 AGATCAGCTCACCTCACCAT 58.123 50.000 0.00 0.00 0.00 3.55
5265 9237 3.037851 AGATCAGCTCACCTCACCATA 57.962 47.619 0.00 0.00 0.00 2.74
5266 9238 2.697751 AGATCAGCTCACCTCACCATAC 59.302 50.000 0.00 0.00 0.00 2.39
5267 9239 2.238084 TCAGCTCACCTCACCATACT 57.762 50.000 0.00 0.00 0.00 2.12
5268 9240 3.382083 TCAGCTCACCTCACCATACTA 57.618 47.619 0.00 0.00 0.00 1.82
5269 9241 3.916035 TCAGCTCACCTCACCATACTAT 58.084 45.455 0.00 0.00 0.00 2.12
5270 9242 3.638627 TCAGCTCACCTCACCATACTATG 59.361 47.826 0.00 0.00 0.00 2.23
5271 9243 3.638627 CAGCTCACCTCACCATACTATGA 59.361 47.826 0.00 0.00 0.00 2.15
5272 9244 3.894427 AGCTCACCTCACCATACTATGAG 59.106 47.826 0.00 0.00 41.75 2.90
5280 9252 5.555017 CTCACCATACTATGAGGGATTTGG 58.445 45.833 0.00 0.00 38.97 3.28
5281 9253 4.074970 CACCATACTATGAGGGATTTGGC 58.925 47.826 0.00 0.00 0.00 4.52
5282 9254 3.721575 ACCATACTATGAGGGATTTGGCA 59.278 43.478 0.00 0.00 0.00 4.92
5283 9255 4.167892 ACCATACTATGAGGGATTTGGCAA 59.832 41.667 0.00 0.00 0.00 4.52
5284 9256 5.139727 CCATACTATGAGGGATTTGGCAAA 58.860 41.667 16.01 16.01 0.00 3.68
5285 9257 5.010012 CCATACTATGAGGGATTTGGCAAAC 59.990 44.000 16.00 9.19 0.00 2.93
5286 9258 4.322057 ACTATGAGGGATTTGGCAAACT 57.678 40.909 16.00 8.09 0.00 2.66
5287 9259 4.273318 ACTATGAGGGATTTGGCAAACTC 58.727 43.478 16.00 16.93 0.00 3.01
5288 9260 2.673775 TGAGGGATTTGGCAAACTCA 57.326 45.000 21.15 21.15 33.05 3.41
5289 9261 2.956132 TGAGGGATTTGGCAAACTCAA 58.044 42.857 22.18 10.98 32.60 3.02
5290 9262 2.892852 TGAGGGATTTGGCAAACTCAAG 59.107 45.455 22.18 0.00 32.60 3.02
5291 9263 2.893489 GAGGGATTTGGCAAACTCAAGT 59.107 45.455 16.00 0.00 0.00 3.16
5292 9264 4.079253 GAGGGATTTGGCAAACTCAAGTA 58.921 43.478 16.00 0.00 0.00 2.24
5293 9265 3.826729 AGGGATTTGGCAAACTCAAGTAC 59.173 43.478 16.00 0.00 0.00 2.73
5294 9266 3.572255 GGGATTTGGCAAACTCAAGTACA 59.428 43.478 16.00 0.00 0.00 2.90
5295 9267 4.038642 GGGATTTGGCAAACTCAAGTACAA 59.961 41.667 16.00 0.00 0.00 2.41
5296 9268 4.982295 GGATTTGGCAAACTCAAGTACAAC 59.018 41.667 16.00 0.00 0.00 3.32
5297 9269 5.451242 GGATTTGGCAAACTCAAGTACAACA 60.451 40.000 16.00 0.00 0.00 3.33
5298 9270 4.364415 TTGGCAAACTCAAGTACAACAC 57.636 40.909 0.00 0.00 0.00 3.32
5299 9271 3.348119 TGGCAAACTCAAGTACAACACA 58.652 40.909 0.00 0.00 0.00 3.72
5300 9272 3.376859 TGGCAAACTCAAGTACAACACAG 59.623 43.478 0.00 0.00 0.00 3.66
5301 9273 3.363178 GCAAACTCAAGTACAACACAGC 58.637 45.455 0.00 0.00 0.00 4.40
5302 9274 3.607439 CAAACTCAAGTACAACACAGCG 58.393 45.455 0.00 0.00 0.00 5.18
5303 9275 1.865865 ACTCAAGTACAACACAGCGG 58.134 50.000 0.00 0.00 0.00 5.52
5304 9276 1.411246 ACTCAAGTACAACACAGCGGA 59.589 47.619 0.00 0.00 0.00 5.54
5305 9277 2.037251 ACTCAAGTACAACACAGCGGAT 59.963 45.455 0.00 0.00 0.00 4.18
5306 9278 3.257375 ACTCAAGTACAACACAGCGGATA 59.743 43.478 0.00 0.00 0.00 2.59
5307 9279 4.242475 CTCAAGTACAACACAGCGGATAA 58.758 43.478 0.00 0.00 0.00 1.75
5308 9280 4.633175 TCAAGTACAACACAGCGGATAAA 58.367 39.130 0.00 0.00 0.00 1.40
5309 9281 5.057819 TCAAGTACAACACAGCGGATAAAA 58.942 37.500 0.00 0.00 0.00 1.52
5310 9282 5.527951 TCAAGTACAACACAGCGGATAAAAA 59.472 36.000 0.00 0.00 0.00 1.94
5311 9283 6.205853 TCAAGTACAACACAGCGGATAAAAAT 59.794 34.615 0.00 0.00 0.00 1.82
5312 9284 7.388224 TCAAGTACAACACAGCGGATAAAAATA 59.612 33.333 0.00 0.00 0.00 1.40
5313 9285 7.068692 AGTACAACACAGCGGATAAAAATAC 57.931 36.000 0.00 0.00 0.00 1.89
5314 9286 6.877322 AGTACAACACAGCGGATAAAAATACT 59.123 34.615 0.00 0.00 0.00 2.12
5315 9287 8.036575 AGTACAACACAGCGGATAAAAATACTA 58.963 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.870435 GCCCAGCTAAACGAGTGAGAAA 60.870 50.000 0.00 0.00 0.00 2.52
3 4 0.246635 GCCCAGCTAAACGAGTGAGA 59.753 55.000 0.00 0.00 0.00 3.27
4 5 0.741221 GGCCCAGCTAAACGAGTGAG 60.741 60.000 0.00 0.00 0.00 3.51
5 6 1.295423 GGCCCAGCTAAACGAGTGA 59.705 57.895 0.00 0.00 0.00 3.41
6 7 1.003839 TGGCCCAGCTAAACGAGTG 60.004 57.895 0.00 0.00 0.00 3.51
7 8 1.296715 CTGGCCCAGCTAAACGAGT 59.703 57.895 0.00 0.00 0.00 4.18
8 9 4.208632 CTGGCCCAGCTAAACGAG 57.791 61.111 0.00 0.00 0.00 4.18
61 62 2.123428 GTAGCTTGCATGGGCCTGG 61.123 63.158 4.53 0.00 40.13 4.45
62 63 2.475466 CGTAGCTTGCATGGGCCTG 61.475 63.158 4.53 1.41 40.13 4.85
63 64 2.124570 CGTAGCTTGCATGGGCCT 60.125 61.111 4.53 0.00 40.13 5.19
86 87 2.830370 ATTAGCCAAGCCAGCGCC 60.830 61.111 2.29 0.00 34.57 6.53
87 88 2.410469 CATTAGCCAAGCCAGCGC 59.590 61.111 0.00 0.00 34.64 5.92
88 89 2.484062 CCCATTAGCCAAGCCAGCG 61.484 63.158 0.00 0.00 34.64 5.18
89 90 2.789715 GCCCATTAGCCAAGCCAGC 61.790 63.158 0.00 0.00 0.00 4.85
90 91 2.484062 CGCCCATTAGCCAAGCCAG 61.484 63.158 0.00 0.00 0.00 4.85
91 92 2.440065 CGCCCATTAGCCAAGCCA 60.440 61.111 0.00 0.00 0.00 4.75
93 94 1.101049 TTAGCGCCCATTAGCCAAGC 61.101 55.000 2.29 0.00 0.00 4.01
94 95 1.334869 CTTTAGCGCCCATTAGCCAAG 59.665 52.381 2.29 0.00 0.00 3.61
95 96 1.388547 CTTTAGCGCCCATTAGCCAA 58.611 50.000 2.29 0.00 0.00 4.52
98 99 1.654774 GCCTTTAGCGCCCATTAGC 59.345 57.895 2.29 0.00 0.00 3.09
108 109 2.586357 CTCCTCGGCGCCTTTAGC 60.586 66.667 26.68 0.00 38.52 3.09
109 110 2.107141 CCTCCTCGGCGCCTTTAG 59.893 66.667 26.68 18.25 0.00 1.85
117 118 3.213402 CGAGACCTCCTCCTCGGC 61.213 72.222 0.00 0.00 45.93 5.54
120 121 0.034863 AGTGACGAGACCTCCTCCTC 60.035 60.000 0.00 0.00 38.71 3.71
122 123 1.939769 GCAGTGACGAGACCTCCTCC 61.940 65.000 0.00 0.00 38.71 4.30
123 124 1.509004 GCAGTGACGAGACCTCCTC 59.491 63.158 0.00 0.00 38.55 3.71
124 125 1.979693 GGCAGTGACGAGACCTCCT 60.980 63.158 0.00 0.00 0.00 3.69
125 126 2.276116 TGGCAGTGACGAGACCTCC 61.276 63.158 0.00 0.00 0.00 4.30
126 127 1.080434 GTGGCAGTGACGAGACCTC 60.080 63.158 0.00 0.00 0.00 3.85
129 130 2.016704 CGTGTGGCAGTGACGAGAC 61.017 63.158 7.65 0.00 35.05 3.36
130 131 2.011741 AACGTGTGGCAGTGACGAGA 62.012 55.000 17.55 0.00 36.90 4.04
221 222 1.221021 GGTAACGGAGGGAAGGCAG 59.779 63.158 0.00 0.00 0.00 4.85
234 235 2.027100 CACCCTGGAGAGGAAAGGTAAC 60.027 54.545 0.00 0.00 42.93 2.50
240 241 3.107601 CTGATACACCCTGGAGAGGAAA 58.892 50.000 0.00 0.00 42.93 3.13
286 287 4.003648 GAGATTATTGGCGGGGTATGAAG 58.996 47.826 0.00 0.00 0.00 3.02
400 495 4.224818 AGAAGAAGAAAGGGGACATGAGAG 59.775 45.833 0.00 0.00 0.00 3.20
407 502 6.570571 GCATTACAAAGAAGAAGAAAGGGGAC 60.571 42.308 0.00 0.00 0.00 4.46
621 759 9.891828 CAAGCACAAATAGTACTTCAACAATTA 57.108 29.630 0.00 0.00 31.36 1.40
622 760 8.413229 ACAAGCACAAATAGTACTTCAACAATT 58.587 29.630 0.00 0.00 31.36 2.32
623 761 7.940850 ACAAGCACAAATAGTACTTCAACAAT 58.059 30.769 0.00 0.00 31.36 2.71
624 762 7.328277 ACAAGCACAAATAGTACTTCAACAA 57.672 32.000 0.00 0.00 31.36 2.83
626 764 8.770828 TCTTACAAGCACAAATAGTACTTCAAC 58.229 33.333 0.00 0.00 31.36 3.18
630 768 7.172703 GTGGTCTTACAAGCACAAATAGTACTT 59.827 37.037 0.00 0.00 44.90 2.24
1556 4264 0.817013 GAGGTCTGAGCTGGAGTCAG 59.183 60.000 14.96 0.00 42.51 3.51
1617 4325 1.050988 ATGACCCATCCCACGGAGAG 61.051 60.000 0.00 0.00 34.05 3.20
1621 4329 1.453745 CCAATGACCCATCCCACGG 60.454 63.158 0.00 0.00 0.00 4.94
2010 4718 4.019858 CAGGTGTCTTCATACCTCTCAGA 58.980 47.826 0.00 0.00 45.26 3.27
2122 4830 1.067354 CCTGCTGCCATTTTTCAGGTC 60.067 52.381 0.00 0.00 39.45 3.85
2139 4847 4.767255 GACTGGTCCGCAGCCCTG 62.767 72.222 0.00 0.00 0.00 4.45
2157 4892 3.161866 TCCCAACCAAATTAAGCACCTC 58.838 45.455 0.00 0.00 0.00 3.85
2187 4922 3.201353 TCACGAAATTTCCCTGTGTCA 57.799 42.857 18.32 4.27 32.55 3.58
2223 4961 2.656069 GGCAAGGCGGAGGTACAGA 61.656 63.158 0.00 0.00 0.00 3.41
2302 5089 1.781786 TGCAACCAAACAAGCCCTAA 58.218 45.000 0.00 0.00 0.00 2.69
2303 5090 1.781786 TTGCAACCAAACAAGCCCTA 58.218 45.000 0.00 0.00 0.00 3.53
2304 5091 0.908198 TTTGCAACCAAACAAGCCCT 59.092 45.000 0.00 0.00 36.09 5.19
2305 5092 1.298602 CTTTGCAACCAAACAAGCCC 58.701 50.000 0.00 0.00 36.09 5.19
2306 5093 1.298602 CCTTTGCAACCAAACAAGCC 58.701 50.000 0.00 0.00 36.09 4.35
2307 5094 1.298602 CCCTTTGCAACCAAACAAGC 58.701 50.000 0.00 0.00 36.09 4.01
2308 5095 2.689553 ACCCTTTGCAACCAAACAAG 57.310 45.000 0.00 0.00 36.09 3.16
2309 5096 3.077359 CAAACCCTTTGCAACCAAACAA 58.923 40.909 0.00 0.00 36.09 2.83
2310 5097 2.303022 TCAAACCCTTTGCAACCAAACA 59.697 40.909 0.00 0.00 40.43 2.83
2311 5098 2.979240 TCAAACCCTTTGCAACCAAAC 58.021 42.857 0.00 0.00 40.43 2.93
2312 5099 3.008485 ACTTCAAACCCTTTGCAACCAAA 59.992 39.130 0.00 0.00 40.43 3.28
2313 5100 2.569404 ACTTCAAACCCTTTGCAACCAA 59.431 40.909 0.00 0.00 40.43 3.67
2314 5101 2.093764 CACTTCAAACCCTTTGCAACCA 60.094 45.455 0.00 0.00 40.43 3.67
2315 5102 2.549926 CACTTCAAACCCTTTGCAACC 58.450 47.619 0.00 0.00 40.43 3.77
2316 5103 2.167487 TCCACTTCAAACCCTTTGCAAC 59.833 45.455 0.00 0.00 40.43 4.17
2317 5104 2.461695 TCCACTTCAAACCCTTTGCAA 58.538 42.857 0.00 0.00 40.43 4.08
2318 5105 2.151502 TCCACTTCAAACCCTTTGCA 57.848 45.000 0.00 0.00 40.43 4.08
2319 5106 3.392882 CAATCCACTTCAAACCCTTTGC 58.607 45.455 0.00 0.00 40.43 3.68
2320 5107 3.244181 CCCAATCCACTTCAAACCCTTTG 60.244 47.826 0.00 0.00 41.96 2.77
2321 5108 2.972021 CCCAATCCACTTCAAACCCTTT 59.028 45.455 0.00 0.00 0.00 3.11
2322 5109 2.608623 CCCAATCCACTTCAAACCCTT 58.391 47.619 0.00 0.00 0.00 3.95
2323 5110 1.203174 CCCCAATCCACTTCAAACCCT 60.203 52.381 0.00 0.00 0.00 4.34
2324 5111 1.203125 TCCCCAATCCACTTCAAACCC 60.203 52.381 0.00 0.00 0.00 4.11
2325 5112 2.171003 CTCCCCAATCCACTTCAAACC 58.829 52.381 0.00 0.00 0.00 3.27
2326 5113 2.171003 CCTCCCCAATCCACTTCAAAC 58.829 52.381 0.00 0.00 0.00 2.93
2327 5114 2.069775 TCCTCCCCAATCCACTTCAAA 58.930 47.619 0.00 0.00 0.00 2.69
2328 5115 1.753903 TCCTCCCCAATCCACTTCAA 58.246 50.000 0.00 0.00 0.00 2.69
2329 5116 1.985622 ATCCTCCCCAATCCACTTCA 58.014 50.000 0.00 0.00 0.00 3.02
2330 5117 4.519906 TTAATCCTCCCCAATCCACTTC 57.480 45.455 0.00 0.00 0.00 3.01
2331 5118 4.965283 TTTAATCCTCCCCAATCCACTT 57.035 40.909 0.00 0.00 0.00 3.16
2332 5119 4.140924 GGATTTAATCCTCCCCAATCCACT 60.141 45.833 16.16 0.00 46.19 4.00
2333 5120 4.152647 GGATTTAATCCTCCCCAATCCAC 58.847 47.826 16.16 0.00 46.19 4.02
2334 5121 4.469469 GGATTTAATCCTCCCCAATCCA 57.531 45.455 16.16 0.00 46.19 3.41
2349 5136 9.847224 GGTGGATTTTCACTTATAGAGGATTTA 57.153 33.333 0.00 0.00 37.75 1.40
2350 5137 8.560903 AGGTGGATTTTCACTTATAGAGGATTT 58.439 33.333 0.00 0.00 37.75 2.17
2351 5138 8.107196 AGGTGGATTTTCACTTATAGAGGATT 57.893 34.615 0.00 0.00 37.75 3.01
2352 5139 7.348274 TGAGGTGGATTTTCACTTATAGAGGAT 59.652 37.037 0.00 0.00 37.75 3.24
2353 5140 6.672218 TGAGGTGGATTTTCACTTATAGAGGA 59.328 38.462 0.00 0.00 37.75 3.71
2354 5141 6.889198 TGAGGTGGATTTTCACTTATAGAGG 58.111 40.000 0.00 0.00 37.75 3.69
2355 5142 8.970859 ATTGAGGTGGATTTTCACTTATAGAG 57.029 34.615 0.00 0.00 37.75 2.43
2356 5143 7.993183 GGATTGAGGTGGATTTTCACTTATAGA 59.007 37.037 0.00 0.00 37.75 1.98
2357 5144 7.229506 GGGATTGAGGTGGATTTTCACTTATAG 59.770 40.741 0.00 0.00 37.75 1.31
2358 5145 7.060421 GGGATTGAGGTGGATTTTCACTTATA 58.940 38.462 0.00 0.00 37.75 0.98
2359 5146 5.893824 GGGATTGAGGTGGATTTTCACTTAT 59.106 40.000 0.00 0.00 37.75 1.73
2360 5147 5.261216 GGGATTGAGGTGGATTTTCACTTA 58.739 41.667 0.00 0.00 37.75 2.24
2361 5148 4.089361 GGGATTGAGGTGGATTTTCACTT 58.911 43.478 0.00 0.00 37.75 3.16
2362 5149 3.564352 GGGGATTGAGGTGGATTTTCACT 60.564 47.826 0.00 0.00 37.75 3.41
2363 5150 2.760650 GGGGATTGAGGTGGATTTTCAC 59.239 50.000 0.00 0.00 36.95 3.18
2364 5151 2.654385 AGGGGATTGAGGTGGATTTTCA 59.346 45.455 0.00 0.00 0.00 2.69
2365 5152 3.291584 GAGGGGATTGAGGTGGATTTTC 58.708 50.000 0.00 0.00 0.00 2.29
2366 5153 2.023984 GGAGGGGATTGAGGTGGATTTT 60.024 50.000 0.00 0.00 0.00 1.82
2367 5154 1.570979 GGAGGGGATTGAGGTGGATTT 59.429 52.381 0.00 0.00 0.00 2.17
2368 5155 1.226311 GGAGGGGATTGAGGTGGATT 58.774 55.000 0.00 0.00 0.00 3.01
2369 5156 0.046242 TGGAGGGGATTGAGGTGGAT 59.954 55.000 0.00 0.00 0.00 3.41
2370 5157 0.178846 TTGGAGGGGATTGAGGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
2371 5158 0.704076 TTTGGAGGGGATTGAGGTGG 59.296 55.000 0.00 0.00 0.00 4.61
2372 5159 1.616994 GGTTTGGAGGGGATTGAGGTG 60.617 57.143 0.00 0.00 0.00 4.00
2373 5160 0.704664 GGTTTGGAGGGGATTGAGGT 59.295 55.000 0.00 0.00 0.00 3.85
2374 5161 1.002857 AGGTTTGGAGGGGATTGAGG 58.997 55.000 0.00 0.00 0.00 3.86
2375 5162 1.918957 AGAGGTTTGGAGGGGATTGAG 59.081 52.381 0.00 0.00 0.00 3.02
2376 5163 1.916181 GAGAGGTTTGGAGGGGATTGA 59.084 52.381 0.00 0.00 0.00 2.57
2377 5164 1.064389 GGAGAGGTTTGGAGGGGATTG 60.064 57.143 0.00 0.00 0.00 2.67
2378 5165 1.299939 GGAGAGGTTTGGAGGGGATT 58.700 55.000 0.00 0.00 0.00 3.01
2379 5166 0.121197 TGGAGAGGTTTGGAGGGGAT 59.879 55.000 0.00 0.00 0.00 3.85
2380 5167 0.104144 TTGGAGAGGTTTGGAGGGGA 60.104 55.000 0.00 0.00 0.00 4.81
2381 5168 1.002857 ATTGGAGAGGTTTGGAGGGG 58.997 55.000 0.00 0.00 0.00 4.79
2382 5169 1.064389 GGATTGGAGAGGTTTGGAGGG 60.064 57.143 0.00 0.00 0.00 4.30
2383 5170 1.918957 AGGATTGGAGAGGTTTGGAGG 59.081 52.381 0.00 0.00 0.00 4.30
2384 5171 2.843113 AGAGGATTGGAGAGGTTTGGAG 59.157 50.000 0.00 0.00 0.00 3.86
2385 5172 2.840651 GAGAGGATTGGAGAGGTTTGGA 59.159 50.000 0.00 0.00 0.00 3.53
2386 5173 2.092699 GGAGAGGATTGGAGAGGTTTGG 60.093 54.545 0.00 0.00 0.00 3.28
2387 5174 2.573462 TGGAGAGGATTGGAGAGGTTTG 59.427 50.000 0.00 0.00 0.00 2.93
2388 5175 2.921221 TGGAGAGGATTGGAGAGGTTT 58.079 47.619 0.00 0.00 0.00 3.27
2389 5176 2.649742 TGGAGAGGATTGGAGAGGTT 57.350 50.000 0.00 0.00 0.00 3.50
2390 5177 2.045047 TCTTGGAGAGGATTGGAGAGGT 59.955 50.000 0.00 0.00 0.00 3.85
2391 5178 2.699846 CTCTTGGAGAGGATTGGAGAGG 59.300 54.545 0.00 0.00 38.67 3.69
2392 5179 3.641046 TCTCTTGGAGAGGATTGGAGAG 58.359 50.000 5.22 0.00 42.54 3.20
2393 5180 3.765432 TCTCTTGGAGAGGATTGGAGA 57.235 47.619 5.22 0.00 42.54 3.71
2403 5190 1.618837 CGGTTCAACCTCTCTTGGAGA 59.381 52.381 4.68 0.00 44.45 3.71
2404 5191 1.618837 TCGGTTCAACCTCTCTTGGAG 59.381 52.381 4.68 0.00 41.51 3.86
2405 5192 1.712056 TCGGTTCAACCTCTCTTGGA 58.288 50.000 4.68 0.00 35.66 3.53
2406 5193 2.143925 GTTCGGTTCAACCTCTCTTGG 58.856 52.381 4.68 0.00 35.66 3.61
2407 5194 2.833794 TGTTCGGTTCAACCTCTCTTG 58.166 47.619 4.68 0.00 35.66 3.02
2408 5195 3.771577 ATGTTCGGTTCAACCTCTCTT 57.228 42.857 4.68 0.00 35.66 2.85
2409 5196 3.368531 GCTATGTTCGGTTCAACCTCTCT 60.369 47.826 4.68 0.00 35.66 3.10
2410 5197 2.930682 GCTATGTTCGGTTCAACCTCTC 59.069 50.000 4.68 0.00 35.66 3.20
2411 5198 2.354805 GGCTATGTTCGGTTCAACCTCT 60.355 50.000 4.68 0.00 35.66 3.69
2412 5199 2.007608 GGCTATGTTCGGTTCAACCTC 58.992 52.381 4.68 0.00 35.66 3.85
2413 5200 1.628846 AGGCTATGTTCGGTTCAACCT 59.371 47.619 4.68 0.00 35.66 3.50
2414 5201 2.109425 AGGCTATGTTCGGTTCAACC 57.891 50.000 0.00 0.00 34.05 3.77
2415 5202 4.634443 ACATAAGGCTATGTTCGGTTCAAC 59.366 41.667 0.00 0.00 44.77 3.18
2416 5203 4.839121 ACATAAGGCTATGTTCGGTTCAA 58.161 39.130 0.00 0.00 44.77 2.69
2417 5204 4.481368 ACATAAGGCTATGTTCGGTTCA 57.519 40.909 0.00 0.00 44.77 3.18
2426 5213 9.941325 AGATCTAGAATTCAACATAAGGCTATG 57.059 33.333 8.44 0.00 40.78 2.23
2427 5214 9.941325 CAGATCTAGAATTCAACATAAGGCTAT 57.059 33.333 8.44 0.00 0.00 2.97
2428 5215 8.370940 CCAGATCTAGAATTCAACATAAGGCTA 58.629 37.037 8.44 0.00 0.00 3.93
2429 5216 7.147408 ACCAGATCTAGAATTCAACATAAGGCT 60.147 37.037 8.44 0.00 0.00 4.58
2430 5217 6.995091 ACCAGATCTAGAATTCAACATAAGGC 59.005 38.462 8.44 0.00 0.00 4.35
2431 5218 8.970859 AACCAGATCTAGAATTCAACATAAGG 57.029 34.615 8.44 4.72 0.00 2.69
2451 5238 6.161855 TGATTAGTATGTCAGCCTAACCAG 57.838 41.667 0.00 0.00 0.00 4.00
2460 5248 5.521735 GCAGTTGTCCTGATTAGTATGTCAG 59.478 44.000 6.23 6.23 44.49 3.51
2543 5332 5.234466 ACTCTCTTTGTACAAAGCCAGAT 57.766 39.130 33.93 21.04 45.48 2.90
2547 5336 6.862711 AACTTACTCTCTTTGTACAAAGCC 57.137 37.500 33.93 0.00 45.48 4.35
2571 5361 6.543831 GCCATTACAGGAGTACAATCTTCAAT 59.456 38.462 0.00 0.00 0.00 2.57
2573 5363 5.189736 AGCCATTACAGGAGTACAATCTTCA 59.810 40.000 0.00 0.00 0.00 3.02
2623 5414 9.891828 GTGTTGTGTTTGTTGAGATTATTATGA 57.108 29.630 0.00 0.00 0.00 2.15
2634 6339 2.226674 TCGCAAGTGTTGTGTTTGTTGA 59.773 40.909 0.48 0.00 41.72 3.18
2747 6632 7.551585 CAGAATAGCCACTATTGGGAGTATAG 58.448 42.308 4.64 0.00 44.15 1.31
2799 6687 4.785346 ACCTCTTGACTTGCATATCCAT 57.215 40.909 0.00 0.00 0.00 3.41
2824 6712 9.346725 CATCCTAAAAAGTGAAGTAAATCTTGC 57.653 33.333 0.00 0.00 36.40 4.01
2917 6808 7.979444 TTGTTCTTAATCTCCTTGATTCGTT 57.021 32.000 0.00 0.00 43.69 3.85
3685 7610 0.034337 ACTACGTCCCAACAATGCGT 59.966 50.000 0.00 0.00 39.23 5.24
3744 7671 8.874816 GGAACTTGAATTAGTTAAGCTGTAGAG 58.125 37.037 0.00 0.00 38.43 2.43
3769 7696 4.217550 ACCACTGTTTTAATCATTCCACGG 59.782 41.667 0.00 0.00 0.00 4.94
3931 7858 9.680946 GCATTTTAGTTTACTTACGTAAGCTAC 57.319 33.333 30.47 24.14 44.09 3.58
4055 7984 2.069273 GTTCTCCACAATGGACGAGTG 58.931 52.381 0.00 0.00 42.67 3.51
4407 8346 9.784531 CCAGGATTACAATGTACTCAATAGATT 57.215 33.333 11.89 0.00 0.00 2.40
4408 8347 8.938883 ACCAGGATTACAATGTACTCAATAGAT 58.061 33.333 11.89 0.00 0.00 1.98
4669 8609 2.869801 TGGATTTTACGCTAAGATGCCG 59.130 45.455 0.00 0.00 0.00 5.69
4757 8708 8.352942 GCCCACTCTACCTGAATAAATAAAATG 58.647 37.037 0.00 0.00 0.00 2.32
4917 8871 5.124036 AGTTAGGCTGGCAATTTATACCA 57.876 39.130 3.38 0.00 0.00 3.25
5165 9134 2.771943 AGCACCTTTATGATTCTCCGGA 59.228 45.455 2.93 2.93 0.00 5.14
5234 9206 2.373169 TGAGCTGATCTTCAACCCACTT 59.627 45.455 0.00 0.00 0.00 3.16
5235 9207 1.980765 TGAGCTGATCTTCAACCCACT 59.019 47.619 0.00 0.00 0.00 4.00
5236 9208 2.079925 GTGAGCTGATCTTCAACCCAC 58.920 52.381 0.00 0.00 0.00 4.61
5237 9209 1.003580 GGTGAGCTGATCTTCAACCCA 59.996 52.381 0.00 0.00 0.00 4.51
5238 9210 1.280421 AGGTGAGCTGATCTTCAACCC 59.720 52.381 0.00 2.21 0.00 4.11
5239 9211 2.027745 TGAGGTGAGCTGATCTTCAACC 60.028 50.000 0.00 0.00 0.00 3.77
5240 9212 2.999355 GTGAGGTGAGCTGATCTTCAAC 59.001 50.000 0.00 0.00 0.00 3.18
5241 9213 2.027745 GGTGAGGTGAGCTGATCTTCAA 60.028 50.000 0.00 0.00 0.00 2.69
5242 9214 1.552337 GGTGAGGTGAGCTGATCTTCA 59.448 52.381 0.00 0.00 0.00 3.02
5243 9215 1.552337 TGGTGAGGTGAGCTGATCTTC 59.448 52.381 0.00 0.00 0.00 2.87
5244 9216 1.649321 TGGTGAGGTGAGCTGATCTT 58.351 50.000 0.00 0.00 0.00 2.40
5245 9217 1.876849 ATGGTGAGGTGAGCTGATCT 58.123 50.000 0.00 0.00 0.00 2.75
5246 9218 2.697751 AGTATGGTGAGGTGAGCTGATC 59.302 50.000 0.00 0.00 0.00 2.92
5247 9219 2.756907 AGTATGGTGAGGTGAGCTGAT 58.243 47.619 0.00 0.00 0.00 2.90
5248 9220 2.238084 AGTATGGTGAGGTGAGCTGA 57.762 50.000 0.00 0.00 0.00 4.26
5249 9221 3.638627 TCATAGTATGGTGAGGTGAGCTG 59.361 47.826 10.26 0.00 0.00 4.24
5250 9222 3.894427 CTCATAGTATGGTGAGGTGAGCT 59.106 47.826 10.26 0.00 38.50 4.09
5251 9223 4.250116 CTCATAGTATGGTGAGGTGAGC 57.750 50.000 10.26 0.00 38.50 4.26
5257 9229 5.555017 CCAAATCCCTCATAGTATGGTGAG 58.445 45.833 10.26 1.57 41.13 3.51
5258 9230 4.202461 GCCAAATCCCTCATAGTATGGTGA 60.202 45.833 10.26 5.22 0.00 4.02
5259 9231 4.074970 GCCAAATCCCTCATAGTATGGTG 58.925 47.826 10.26 4.10 0.00 4.17
5260 9232 3.721575 TGCCAAATCCCTCATAGTATGGT 59.278 43.478 10.26 0.00 0.00 3.55
5261 9233 4.371624 TGCCAAATCCCTCATAGTATGG 57.628 45.455 10.26 1.54 0.00 2.74
5262 9234 5.829924 AGTTTGCCAAATCCCTCATAGTATG 59.170 40.000 3.55 3.55 0.00 2.39
5263 9235 6.018433 AGTTTGCCAAATCCCTCATAGTAT 57.982 37.500 0.00 0.00 0.00 2.12
5264 9236 5.045213 TGAGTTTGCCAAATCCCTCATAGTA 60.045 40.000 5.21 0.00 0.00 1.82
5265 9237 4.263905 TGAGTTTGCCAAATCCCTCATAGT 60.264 41.667 5.21 0.00 0.00 2.12
5266 9238 4.272489 TGAGTTTGCCAAATCCCTCATAG 58.728 43.478 5.21 0.00 0.00 2.23
5267 9239 4.314522 TGAGTTTGCCAAATCCCTCATA 57.685 40.909 5.21 0.00 0.00 2.15
5268 9240 3.173953 TGAGTTTGCCAAATCCCTCAT 57.826 42.857 5.21 0.00 0.00 2.90
5269 9241 2.673775 TGAGTTTGCCAAATCCCTCA 57.326 45.000 5.21 5.21 0.00 3.86
5270 9242 2.893489 ACTTGAGTTTGCCAAATCCCTC 59.107 45.455 0.00 0.00 0.00 4.30
5271 9243 2.962859 ACTTGAGTTTGCCAAATCCCT 58.037 42.857 0.00 0.00 0.00 4.20
5272 9244 3.572255 TGTACTTGAGTTTGCCAAATCCC 59.428 43.478 0.00 0.00 0.00 3.85
5273 9245 4.846779 TGTACTTGAGTTTGCCAAATCC 57.153 40.909 0.00 0.00 0.00 3.01
5274 9246 5.458779 GTGTTGTACTTGAGTTTGCCAAATC 59.541 40.000 0.00 0.00 0.00 2.17
5275 9247 5.105554 TGTGTTGTACTTGAGTTTGCCAAAT 60.106 36.000 0.00 0.00 0.00 2.32
5276 9248 4.218635 TGTGTTGTACTTGAGTTTGCCAAA 59.781 37.500 0.00 0.00 0.00 3.28
5277 9249 3.759086 TGTGTTGTACTTGAGTTTGCCAA 59.241 39.130 0.00 0.00 0.00 4.52
5278 9250 3.348119 TGTGTTGTACTTGAGTTTGCCA 58.652 40.909 0.00 0.00 0.00 4.92
5279 9251 3.792124 GCTGTGTTGTACTTGAGTTTGCC 60.792 47.826 0.00 0.00 0.00 4.52
5280 9252 3.363178 GCTGTGTTGTACTTGAGTTTGC 58.637 45.455 0.00 0.00 0.00 3.68
5281 9253 3.546020 CCGCTGTGTTGTACTTGAGTTTG 60.546 47.826 0.00 0.00 0.00 2.93
5282 9254 2.612212 CCGCTGTGTTGTACTTGAGTTT 59.388 45.455 0.00 0.00 0.00 2.66
5283 9255 2.159014 TCCGCTGTGTTGTACTTGAGTT 60.159 45.455 0.00 0.00 0.00 3.01
5284 9256 1.411246 TCCGCTGTGTTGTACTTGAGT 59.589 47.619 0.00 0.00 0.00 3.41
5285 9257 2.148916 TCCGCTGTGTTGTACTTGAG 57.851 50.000 0.00 0.00 0.00 3.02
5286 9258 2.831685 ATCCGCTGTGTTGTACTTGA 57.168 45.000 0.00 0.00 0.00 3.02
5287 9259 5.351233 TTTTATCCGCTGTGTTGTACTTG 57.649 39.130 0.00 0.00 0.00 3.16
5288 9260 6.569179 ATTTTTATCCGCTGTGTTGTACTT 57.431 33.333 0.00 0.00 0.00 2.24
5289 9261 6.877322 AGTATTTTTATCCGCTGTGTTGTACT 59.123 34.615 0.00 0.00 0.00 2.73
5290 9262 7.068692 AGTATTTTTATCCGCTGTGTTGTAC 57.931 36.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.