Multiple sequence alignment - TraesCS5A01G494100

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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 TraesCS5A01G494100 chr5A 100.000 5817 0 0 1 5817 662732219 662726403 0.000000e+00 10743
1 TraesCS5A01G494100 chr5A 92.661 109 3 5 558 666 395758399 395758502 1.010000e-32 152
2 TraesCS5A01G494100 chr5A 91.765 85 6 1 5154 5237 662726983 662726899 3.680000e-22 117
3 TraesCS5A01G494100 chr5A 91.765 85 6 1 5237 5321 662727066 662726983 3.680000e-22 117
4 TraesCS5A01G494100 chr4B 94.483 3172 121 20 2669 5817 608671213 608674353 0.000000e+00 4839
5 TraesCS5A01G494100 chr4B 95.156 1156 51 5 1521 2675 608670029 608671180 0.000000e+00 1820
6 TraesCS5A01G494100 chr4B 85.911 1015 76 40 335 1342 608668723 608669677 0.000000e+00 1020
7 TraesCS5A01G494100 chr4B 82.469 559 46 29 61 591 608668193 608668727 5.350000e-120 442
8 TraesCS5A01G494100 chr4B 92.105 190 13 1 1336 1525 608669810 608669997 3.460000e-67 267
9 TraesCS5A01G494100 chr4B 92.453 106 5 2 557 659 416440468 416440573 1.310000e-31 148
10 TraesCS5A01G494100 chr4B 91.765 85 7 0 5237 5321 608673678 608673762 1.020000e-22 119
11 TraesCS5A01G494100 chr4B 90.476 84 7 1 5154 5237 608673762 608673844 6.160000e-20 110
12 TraesCS5A01G494100 chr4D 94.543 3170 109 18 2669 5811 480826344 480829476 0.000000e+00 4837
13 TraesCS5A01G494100 chr4D 96.031 1159 40 4 1521 2675 480825155 480826311 0.000000e+00 1881
14 TraesCS5A01G494100 chr4D 86.280 1086 87 39 449 1519 480824079 480825117 0.000000e+00 1123
15 TraesCS5A01G494100 chr4D 83.610 421 33 19 66 465 480823656 480824061 4.280000e-96 363
16 TraesCS5A01G494100 chr4D 90.741 162 15 0 3748 3909 85011280 85011119 3.530000e-52 217
17 TraesCS5A01G494100 chr4D 92.941 85 5 1 5154 5237 480828889 480828973 7.920000e-24 122
18 TraesCS5A01G494100 chr4D 89.412 85 8 1 5237 5321 480828806 480828889 7.970000e-19 106
19 TraesCS5A01G494100 chr6D 90.303 165 16 0 3747 3911 472535990 472535826 3.530000e-52 217
20 TraesCS5A01G494100 chr6D 93.137 102 4 3 558 658 82588639 82588540 4.700000e-31 147
21 TraesCS5A01G494100 chr2D 88.415 164 17 2 3746 3908 35507244 35507082 4.600000e-46 196
22 TraesCS5A01G494100 chr2D 84.663 163 21 4 3743 3903 97873240 97873080 6.030000e-35 159
23 TraesCS5A01G494100 chr2D 77.885 208 31 9 5558 5751 107932483 107932689 1.320000e-21 115
24 TraesCS5A01G494100 chr7A 85.714 168 20 3 3750 3915 86235170 86235005 2.150000e-39 174
25 TraesCS5A01G494100 chr2A 86.061 165 20 3 3746 3908 38596864 38596701 2.150000e-39 174
26 TraesCS5A01G494100 chr5D 86.076 158 17 3 3747 3902 176102085 176102239 1.300000e-36 165
27 TraesCS5A01G494100 chr1D 96.970 99 2 1 561 659 267593128 267593031 1.300000e-36 165
28 TraesCS5A01G494100 chr3A 78.671 286 32 20 5558 5817 521633071 521633353 4.660000e-36 163
29 TraesCS5A01G494100 chr3A 76.491 285 41 16 5558 5817 714773585 714773302 1.320000e-26 132
30 TraesCS5A01G494100 chr3D 78.246 285 35 19 5558 5817 401175453 401175735 2.170000e-34 158
31 TraesCS5A01G494100 chr3B 78.169 284 36 16 5558 5817 526964451 526964732 2.170000e-34 158
32 TraesCS5A01G494100 chr6A 94.118 102 6 0 557 658 80820458 80820357 7.800000e-34 156
33 TraesCS5A01G494100 chr1A 81.250 208 26 7 5557 5751 532736809 532737016 7.800000e-34 156
34 TraesCS5A01G494100 chr1B 94.118 102 4 2 558 659 345411252 345411351 2.810000e-33 154
35 TraesCS5A01G494100 chr4A 91.589 107 6 3 556 659 135355038 135354932 1.690000e-30 145
36 TraesCS5A01G494100 chr6B 79.703 202 27 8 5557 5747 204445865 204445667 3.660000e-27 134


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 TraesCS5A01G494100 chr5A 662726403 662732219 5816 True 10743.000000 10743 100.000000 1 5817 1 chr5A.!!$R1 5816
1 TraesCS5A01G494100 chr4B 608668193 608674353 6160 False 1231.000000 4839 90.337857 61 5817 7 chr4B.!!$F2 5756
2 TraesCS5A01G494100 chr4D 480823656 480829476 5820 False 1405.333333 4837 90.469500 66 5811 6 chr4D.!!$F1 5745

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
256 271 0.037160 GTACCACGGTGATTTGGGGT 59.963 55.000 10.28 0.00 37.18 4.95 F
445 476 0.247814 CCGAGAATGTGCGTGATTGC 60.248 55.000 0.00 0.00 0.00 3.56 F
1176 1461 0.319813 GAATGTTTGGTGTGCCTGGC 60.320 55.000 12.87 12.87 35.27 4.85 F
2032 2492 0.247460 TGCGCTGACAGCAATCTACT 59.753 50.000 26.32 0.00 42.58 2.57 F
2943 3446 1.267261 AGTCTGTGTGCTACGACTGTC 59.733 52.381 13.52 0.00 39.73 3.51 F
3571 4080 1.068127 GGTGTGCTATACCACCCTACG 59.932 57.143 0.00 0.00 38.12 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1571 0.530744 TAGCTACACGAACAGGCTGG 59.469 55.000 20.34 3.36 34.88 4.85 R
1539 1999 1.282248 AATCGAACACGCAGTCACCG 61.282 55.000 0.00 0.00 41.61 4.94 R
2936 3439 1.135915 AGCAGCAGAATAGGACAGTCG 59.864 52.381 0.00 0.00 0.00 4.18 R
3486 3995 1.910819 GACAAATTGCGTAACCATGCG 59.089 47.619 0.00 0.00 39.74 4.73 R
4622 5136 0.407528 TCAATAGGGCCTGCCAAACA 59.592 50.000 18.53 0.00 37.98 2.83 R
5333 5852 0.178981 ACTGCCTGCAGATTGTTGGT 60.179 50.000 24.88 1.10 46.30 3.67 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
18 19 4.682334 TCCGTGTGAGCCCGGGTA 62.682 66.667 24.63 6.20 44.32 3.69
19 20 4.446413 CCGTGTGAGCCCGGGTAC 62.446 72.222 24.63 18.96 40.54 3.34
20 21 4.789075 CGTGTGAGCCCGGGTACG 62.789 72.222 24.63 19.95 40.55 3.67
21 22 3.688159 GTGTGAGCCCGGGTACGT 61.688 66.667 24.63 4.14 38.78 3.57
22 23 2.035469 TGTGAGCCCGGGTACGTA 59.965 61.111 24.63 3.28 38.78 3.57
23 24 2.342650 TGTGAGCCCGGGTACGTAC 61.343 63.158 24.63 17.56 38.78 3.67
24 25 3.133464 TGAGCCCGGGTACGTACG 61.133 66.667 24.63 15.01 38.78 3.67
25 26 3.134127 GAGCCCGGGTACGTACGT 61.134 66.667 25.98 25.98 38.78 3.57
26 27 3.401243 GAGCCCGGGTACGTACGTG 62.401 68.421 30.25 13.56 38.78 4.49
27 28 4.496927 GCCCGGGTACGTACGTGG 62.497 72.222 30.25 22.18 38.78 4.94
28 29 3.825611 CCCGGGTACGTACGTGGG 61.826 72.222 28.81 28.81 38.78 4.61
29 30 3.825611 CCGGGTACGTACGTGGGG 61.826 72.222 30.25 19.99 38.78 4.96
30 31 3.825611 CGGGTACGTACGTGGGGG 61.826 72.222 30.25 13.26 34.81 5.40
31 32 2.679996 GGGTACGTACGTGGGGGT 60.680 66.667 30.25 5.02 0.00 4.95
32 33 2.710902 GGGTACGTACGTGGGGGTC 61.711 68.421 30.25 12.34 0.00 4.46
33 34 1.976474 GGTACGTACGTGGGGGTCA 60.976 63.158 30.25 5.88 0.00 4.02
34 35 1.212751 GTACGTACGTGGGGGTCAC 59.787 63.158 30.25 14.82 42.74 3.67
35 36 1.074775 TACGTACGTGGGGGTCACT 59.925 57.895 30.25 1.85 43.94 3.41
36 37 1.243342 TACGTACGTGGGGGTCACTG 61.243 60.000 30.25 0.00 43.94 3.66
37 38 2.567497 CGTACGTGGGGGTCACTGT 61.567 63.158 7.22 0.00 43.94 3.55
38 39 1.750297 GTACGTGGGGGTCACTGTT 59.250 57.895 0.00 0.00 43.94 3.16
39 40 0.601841 GTACGTGGGGGTCACTGTTG 60.602 60.000 0.00 0.00 43.94 3.33
40 41 1.760479 TACGTGGGGGTCACTGTTGG 61.760 60.000 0.00 0.00 43.94 3.77
41 42 2.813726 CGTGGGGGTCACTGTTGGA 61.814 63.158 0.00 0.00 43.94 3.53
42 43 1.073199 GTGGGGGTCACTGTTGGAG 59.927 63.158 0.00 0.00 42.86 3.86
43 44 1.074090 TGGGGGTCACTGTTGGAGA 60.074 57.895 0.00 0.00 0.00 3.71
44 45 1.127567 TGGGGGTCACTGTTGGAGAG 61.128 60.000 0.00 0.00 0.00 3.20
45 46 1.679898 GGGGTCACTGTTGGAGAGG 59.320 63.158 0.00 0.00 0.00 3.69
46 47 0.836400 GGGGTCACTGTTGGAGAGGA 60.836 60.000 0.00 0.00 0.00 3.71
47 48 0.610687 GGGTCACTGTTGGAGAGGAG 59.389 60.000 0.00 0.00 0.00 3.69
48 49 1.633774 GGTCACTGTTGGAGAGGAGA 58.366 55.000 0.00 0.00 0.00 3.71
49 50 1.548269 GGTCACTGTTGGAGAGGAGAG 59.452 57.143 0.00 0.00 0.00 3.20
50 51 1.548269 GTCACTGTTGGAGAGGAGAGG 59.452 57.143 0.00 0.00 0.00 3.69
51 52 1.429299 TCACTGTTGGAGAGGAGAGGA 59.571 52.381 0.00 0.00 0.00 3.71
52 53 1.824230 CACTGTTGGAGAGGAGAGGAG 59.176 57.143 0.00 0.00 0.00 3.69
53 54 1.713647 ACTGTTGGAGAGGAGAGGAGA 59.286 52.381 0.00 0.00 0.00 3.71
54 55 2.291540 ACTGTTGGAGAGGAGAGGAGAG 60.292 54.545 0.00 0.00 0.00 3.20
55 56 1.006519 TGTTGGAGAGGAGAGGAGAGG 59.993 57.143 0.00 0.00 0.00 3.69
56 57 1.286553 GTTGGAGAGGAGAGGAGAGGA 59.713 57.143 0.00 0.00 0.00 3.71
57 58 1.221635 TGGAGAGGAGAGGAGAGGAG 58.778 60.000 0.00 0.00 0.00 3.69
58 59 1.274708 TGGAGAGGAGAGGAGAGGAGA 60.275 57.143 0.00 0.00 0.00 3.71
59 60 1.421646 GGAGAGGAGAGGAGAGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
74 75 1.663695 GAGAGGAGGAGAGTGAGTCG 58.336 60.000 0.00 0.00 0.00 4.18
88 89 0.319641 GAGTCGCCACGTTTCTCCTT 60.320 55.000 0.00 0.00 0.00 3.36
89 90 0.319641 AGTCGCCACGTTTCTCCTTC 60.320 55.000 0.00 0.00 0.00 3.46
90 91 1.005394 TCGCCACGTTTCTCCTTCC 60.005 57.895 0.00 0.00 0.00 3.46
91 92 2.380410 CGCCACGTTTCTCCTTCCG 61.380 63.158 0.00 0.00 0.00 4.30
100 101 0.966920 TTCTCCTTCCGGTCTGTCAC 59.033 55.000 0.00 0.00 0.00 3.67
121 122 2.997485 CAGCACTTTTCTGCCTAACC 57.003 50.000 0.00 0.00 37.96 2.85
122 123 2.508526 CAGCACTTTTCTGCCTAACCT 58.491 47.619 0.00 0.00 37.96 3.50
123 124 3.674997 CAGCACTTTTCTGCCTAACCTA 58.325 45.455 0.00 0.00 37.96 3.08
124 125 4.072131 CAGCACTTTTCTGCCTAACCTAA 58.928 43.478 0.00 0.00 37.96 2.69
125 126 4.072839 AGCACTTTTCTGCCTAACCTAAC 58.927 43.478 0.00 0.00 37.96 2.34
128 129 2.103537 TTTCTGCCTAACCTAACGCC 57.896 50.000 0.00 0.00 0.00 5.68
135 142 3.668980 TAACCTAACGCCGGCTGCC 62.669 63.158 26.68 9.11 36.24 4.85
151 158 3.822735 GGCTGCCAGCAAATAATATCTCA 59.177 43.478 19.95 0.00 44.75 3.27
175 182 4.487412 GCAAGCTGCGGTCATGGC 62.487 66.667 0.00 0.00 31.71 4.40
204 211 0.596083 CGTGGATGGATCAGAGTCGC 60.596 60.000 0.00 0.00 0.00 5.19
224 231 1.674908 GAAAGAGACCGCGCAAAAAG 58.325 50.000 8.75 0.00 0.00 2.27
229 236 2.044135 GAGACCGCGCAAAAAGAAAAG 58.956 47.619 8.75 0.00 0.00 2.27
234 249 2.542824 CCGCGCAAAAAGAAAAGGAAGA 60.543 45.455 8.75 0.00 0.00 2.87
236 251 3.735746 CGCGCAAAAAGAAAAGGAAGAAT 59.264 39.130 8.75 0.00 0.00 2.40
239 254 5.689961 GCGCAAAAAGAAAAGGAAGAATGTA 59.310 36.000 0.30 0.00 0.00 2.29
241 256 6.143919 CGCAAAAAGAAAAGGAAGAATGTACC 59.856 38.462 0.00 0.00 0.00 3.34
243 258 7.042725 GCAAAAAGAAAAGGAAGAATGTACCAC 60.043 37.037 0.00 0.00 0.00 4.16
246 261 3.782656 AAAGGAAGAATGTACCACGGT 57.217 42.857 0.00 0.00 0.00 4.83
252 267 4.142687 GGAAGAATGTACCACGGTGATTTG 60.143 45.833 10.28 0.00 0.00 2.32
256 271 0.037160 GTACCACGGTGATTTGGGGT 59.963 55.000 10.28 0.00 37.18 4.95
305 331 0.750850 ATTGCATGCAGATTCCAGCC 59.249 50.000 21.50 0.00 0.00 4.85
339 366 2.162408 GGTCAAAGAATGTGTAGCTGGC 59.838 50.000 0.00 0.00 0.00 4.85
370 397 3.621558 TGATCACTGGAGTACGTCTGAT 58.378 45.455 0.00 0.00 0.00 2.90
382 409 6.869388 GGAGTACGTCTGATTTCTTCTTCTTT 59.131 38.462 0.00 0.00 0.00 2.52
383 410 7.062488 GGAGTACGTCTGATTTCTTCTTCTTTC 59.938 40.741 0.00 0.00 0.00 2.62
389 420 7.800847 CGTCTGATTTCTTCTTCTTTCCTTTTC 59.199 37.037 0.00 0.00 0.00 2.29
410 441 6.767524 TTCTTTTTGCAAGTTGGAGTAAGA 57.232 33.333 14.83 14.83 0.00 2.10
411 442 6.767524 TCTTTTTGCAAGTTGGAGTAAGAA 57.232 33.333 15.84 0.00 0.00 2.52
412 443 6.795399 TCTTTTTGCAAGTTGGAGTAAGAAG 58.205 36.000 15.84 6.27 0.00 2.85
413 444 6.377146 TCTTTTTGCAAGTTGGAGTAAGAAGT 59.623 34.615 15.84 0.00 0.00 3.01
414 445 5.751243 TTTGCAAGTTGGAGTAAGAAGTC 57.249 39.130 4.75 0.00 0.00 3.01
415 446 4.689612 TGCAAGTTGGAGTAAGAAGTCT 57.310 40.909 4.75 0.00 0.00 3.24
419 450 5.178438 GCAAGTTGGAGTAAGAAGTCTTGAG 59.822 44.000 4.75 0.00 37.40 3.02
443 474 1.337728 TGACCGAGAATGTGCGTGATT 60.338 47.619 0.00 0.00 0.00 2.57
445 476 0.247814 CCGAGAATGTGCGTGATTGC 60.248 55.000 0.00 0.00 0.00 3.56
446 477 0.723414 CGAGAATGTGCGTGATTGCT 59.277 50.000 0.00 0.00 35.36 3.91
470 535 4.338400 CCATCTGATAGACAGGTTGACGTA 59.662 45.833 0.00 0.00 45.76 3.57
476 541 5.417894 TGATAGACAGGTTGACGTACAAGAT 59.582 40.000 0.00 0.00 39.30 2.40
494 559 4.706842 AGATAACCCATCCATGTACACC 57.293 45.455 0.00 0.00 33.75 4.16
495 560 4.044308 AGATAACCCATCCATGTACACCA 58.956 43.478 0.00 0.00 33.75 4.17
513 578 4.021016 ACACCACTGTTATCTGAAGGAGAC 60.021 45.833 0.00 0.00 31.75 3.36
524 589 1.829849 TGAAGGAGACAGGCAGATGAG 59.170 52.381 0.00 0.00 0.00 2.90
528 593 1.552337 GGAGACAGGCAGATGAGTCAA 59.448 52.381 0.00 0.00 33.56 3.18
539 605 4.379186 GCAGATGAGTCAACCTTGAACATG 60.379 45.833 0.00 0.00 39.21 3.21
540 606 4.999311 CAGATGAGTCAACCTTGAACATGA 59.001 41.667 0.00 0.00 39.21 3.07
541 607 4.999950 AGATGAGTCAACCTTGAACATGAC 59.000 41.667 0.00 0.00 41.88 3.06
554 620 4.041049 TGAACATGACGCACAAATTTCAC 58.959 39.130 0.00 0.00 0.00 3.18
555 621 3.706802 ACATGACGCACAAATTTCACA 57.293 38.095 0.00 0.00 0.00 3.58
660 943 3.059352 ACTACAGCCACTTTGATGTCC 57.941 47.619 0.00 0.00 0.00 4.02
661 944 2.639839 ACTACAGCCACTTTGATGTCCT 59.360 45.455 0.00 0.00 0.00 3.85
662 945 1.901591 ACAGCCACTTTGATGTCCTG 58.098 50.000 0.00 0.00 0.00 3.86
663 946 1.171308 CAGCCACTTTGATGTCCTGG 58.829 55.000 0.00 0.00 0.00 4.45
664 947 0.610232 AGCCACTTTGATGTCCTGGC 60.610 55.000 0.00 0.00 46.65 4.85
665 948 0.610232 GCCACTTTGATGTCCTGGCT 60.610 55.000 0.00 0.00 43.52 4.75
666 949 1.340017 GCCACTTTGATGTCCTGGCTA 60.340 52.381 0.00 0.00 43.52 3.93
700 983 9.918630 ATCCTATTTGTATACAATACGTACACC 57.081 33.333 18.69 0.00 35.55 4.16
705 988 5.659463 TGTATACAATACGTACACCCCAAC 58.341 41.667 2.20 0.00 31.27 3.77
743 1026 3.258622 AGAAACTTCTCCTTCTGTACGGG 59.741 47.826 0.85 0.00 29.94 5.28
747 1030 0.324091 TCTCCTTCTGTACGGGTCCC 60.324 60.000 0.85 0.00 0.00 4.46
764 1047 1.483595 CCCAGCCCAAGACAGTCTGA 61.484 60.000 6.91 0.00 0.00 3.27
778 1061 1.207329 AGTCTGAATGGGTTACGGAGC 59.793 52.381 0.00 0.00 0.00 4.70
779 1062 1.066430 GTCTGAATGGGTTACGGAGCA 60.066 52.381 0.00 0.00 0.00 4.26
788 1071 2.966732 TTACGGAGCAAGGCCCAGG 61.967 63.158 0.00 0.00 0.00 4.45
878 1161 2.746277 CGGCTCAAAACCCCCTCG 60.746 66.667 0.00 0.00 0.00 4.63
909 1192 3.983821 TCTTAGGGTTTCCTCTCTCTCC 58.016 50.000 0.00 0.00 43.66 3.71
910 1193 3.598782 TCTTAGGGTTTCCTCTCTCTCCT 59.401 47.826 0.00 0.00 43.66 3.69
911 1194 2.543037 AGGGTTTCCTCTCTCTCCTC 57.457 55.000 0.00 0.00 39.80 3.71
912 1195 1.107945 GGGTTTCCTCTCTCTCCTCG 58.892 60.000 0.00 0.00 0.00 4.63
913 1196 1.107945 GGTTTCCTCTCTCTCCTCGG 58.892 60.000 0.00 0.00 0.00 4.63
919 1202 3.591835 CTCTCTCCTCGGCTCCGC 61.592 72.222 2.96 0.00 39.59 5.54
1088 1373 1.997606 GAAGCAAATGGTACGTACGCT 59.002 47.619 16.72 17.48 0.00 5.07
1089 1374 2.945447 AGCAAATGGTACGTACGCTA 57.055 45.000 19.30 10.02 0.00 4.26
1090 1375 2.533266 AGCAAATGGTACGTACGCTAC 58.467 47.619 19.30 15.81 0.00 3.58
1103 1388 4.849329 GCTACGCGGTCCCTGACG 62.849 72.222 12.47 0.00 32.65 4.35
1119 1404 4.933064 CGCGATCACCTCCTCGGC 62.933 72.222 0.00 0.00 35.48 5.54
1143 1428 8.124199 GGCGGAAATTTACGATTAGAAAATGTA 58.876 33.333 26.70 0.00 36.35 2.29
1144 1429 9.155053 GCGGAAATTTACGATTAGAAAATGTAG 57.845 33.333 26.70 0.00 36.35 2.74
1176 1461 0.319813 GAATGTTTGGTGTGCCTGGC 60.320 55.000 12.87 12.87 35.27 4.85
1199 1484 3.362706 TCGACTTGGCAAGGTAGACTAT 58.637 45.455 29.26 7.30 0.00 2.12
1207 1492 5.017490 TGGCAAGGTAGACTATATAGAGCC 58.983 45.833 16.79 14.05 37.75 4.70
1238 1523 6.587226 GCATTCAGTAATTCATTTGAGTTGCA 59.413 34.615 6.65 0.00 33.95 4.08
1286 1571 2.128771 TTCCAGGAGTTGCTATTGGC 57.871 50.000 0.00 0.00 42.22 4.52
1321 1606 6.400727 CGTGTAGCTAGCAACTTTCGTTAATT 60.401 38.462 18.83 0.00 0.00 1.40
1430 1854 8.439286 GGAGAAGCTAAAATTTATGCTATCTCG 58.561 37.037 25.25 0.00 38.71 4.04
1469 1893 9.665719 TGCACACAGAGTATGATTTATCTAAAA 57.334 29.630 0.00 0.00 0.00 1.52
1493 1917 4.461992 TCGAGGTTTTTCTTAGCAAACG 57.538 40.909 0.00 0.00 34.27 3.60
1519 1943 5.948481 ATGAGGGGTATGGATAAATTGGT 57.052 39.130 0.00 0.00 0.00 3.67
1539 1999 4.393680 TGGTGTTTGTCAAGTTGTACTGAC 59.606 41.667 2.11 6.13 31.49 3.51
1550 2010 1.285023 GTACTGACGGTGACTGCGT 59.715 57.895 0.00 0.00 0.00 5.24
1569 2029 4.142988 TGCGTGTTCGATTTAGAAATGGTC 60.143 41.667 0.00 0.00 39.71 4.02
1574 2034 7.846107 CGTGTTCGATTTAGAAATGGTCTATTG 59.154 37.037 0.00 0.00 37.71 1.90
1592 2052 7.178274 GGTCTATTGTACTGATCTCTCCATGAT 59.822 40.741 0.00 0.00 0.00 2.45
1597 2057 7.517614 TGTACTGATCTCTCCATGATTAGTC 57.482 40.000 0.00 0.38 40.00 2.59
1600 2060 7.673641 ACTGATCTCTCCATGATTAGTCTTT 57.326 36.000 0.00 0.00 36.47 2.52
1601 2061 7.725251 ACTGATCTCTCCATGATTAGTCTTTC 58.275 38.462 0.00 0.00 36.47 2.62
1732 2192 6.238239 GCTTAGCTCTTTGTAGAAATACTGCC 60.238 42.308 0.00 0.00 0.00 4.85
1775 2235 9.102757 TGAGTAAAGAAGCATATTTGTCTGATC 57.897 33.333 0.00 0.00 0.00 2.92
1801 2261 1.299976 GGTGGGGTCGCTGAAATCT 59.700 57.895 0.00 0.00 0.00 2.40
1940 2400 5.869753 TTCTTTTCTCTGCTGCTTGTATC 57.130 39.130 0.00 0.00 0.00 2.24
1948 2408 6.585416 TCTCTGCTGCTTGTATCAATGAATA 58.415 36.000 0.00 0.00 0.00 1.75
1950 2410 7.718314 TCTCTGCTGCTTGTATCAATGAATAAT 59.282 33.333 0.00 0.00 0.00 1.28
1980 2440 7.335171 TCAAGTGTCTGATCATGTCCTTTTATG 59.665 37.037 0.00 0.00 0.00 1.90
2032 2492 0.247460 TGCGCTGACAGCAATCTACT 59.753 50.000 26.32 0.00 42.58 2.57
2075 2535 7.414429 GCATGAAAAGTCTGCATGTATGTTCTA 60.414 37.037 0.00 0.00 41.01 2.10
2245 2705 1.281419 TGGTCTCGCCCCTAATTTCA 58.719 50.000 0.00 0.00 36.04 2.69
2246 2706 1.631388 TGGTCTCGCCCCTAATTTCAA 59.369 47.619 0.00 0.00 36.04 2.69
2413 2873 4.526650 TGTCAGGCAATCTACTTAGTGTCA 59.473 41.667 0.00 0.00 0.00 3.58
2471 2931 7.930217 CCATGTGGTTAACCTGTAATATCTTG 58.070 38.462 24.78 11.85 36.82 3.02
2597 3057 2.987547 CAGGGTGCAGGTTGGCAG 60.988 66.667 0.00 0.00 45.96 4.85
2727 3229 6.418101 AGATTCCAGAATGCTTGCTAGTTTA 58.582 36.000 0.00 0.00 31.97 2.01
2759 3261 9.301153 GGTTATCGATAATTTTGCATGTTTTCT 57.699 29.630 20.21 0.00 0.00 2.52
2928 3431 6.055588 TGAACTTGGTTAGAAAGGAAGTCTG 58.944 40.000 0.00 0.00 0.00 3.51
2934 3437 4.381411 GTTAGAAAGGAAGTCTGTGTGCT 58.619 43.478 0.00 0.00 0.00 4.40
2936 3439 3.996480 AGAAAGGAAGTCTGTGTGCTAC 58.004 45.455 0.00 0.00 0.00 3.58
2937 3440 2.440539 AAGGAAGTCTGTGTGCTACG 57.559 50.000 0.00 0.00 0.00 3.51
2938 3441 1.617322 AGGAAGTCTGTGTGCTACGA 58.383 50.000 0.00 0.00 0.00 3.43
2939 3442 1.269998 AGGAAGTCTGTGTGCTACGAC 59.730 52.381 0.00 0.00 34.92 4.34
2940 3443 1.269998 GGAAGTCTGTGTGCTACGACT 59.730 52.381 0.00 10.65 41.51 4.18
2941 3444 2.320367 GAAGTCTGTGTGCTACGACTG 58.680 52.381 14.36 0.00 40.47 3.51
2942 3445 1.319541 AGTCTGTGTGCTACGACTGT 58.680 50.000 13.52 0.00 39.73 3.55
2943 3446 1.267261 AGTCTGTGTGCTACGACTGTC 59.733 52.381 13.52 0.00 39.73 3.51
3267 3776 4.323417 CCTTGTTCAGGTTAGTATGCACA 58.677 43.478 0.00 0.00 37.99 4.57
3307 3816 5.476945 TGATGTCTTACTGTCAGCTCTGTTA 59.523 40.000 0.00 0.00 0.00 2.41
3388 3897 4.259356 TGATGATTCTGGAAGCTTGTCAG 58.741 43.478 2.10 11.78 0.00 3.51
3441 3950 5.545658 TTTCATTTGGCTGAGATTACGTC 57.454 39.130 0.00 0.00 0.00 4.34
3476 3985 6.039605 TCACTTGAAGCATTGAATTTCTGTGA 59.960 34.615 11.24 11.24 35.23 3.58
3571 4080 1.068127 GGTGTGCTATACCACCCTACG 59.932 57.143 0.00 0.00 38.12 3.51
3577 4086 4.038402 GTGCTATACCACCCTACGTGTAAT 59.962 45.833 0.00 0.00 41.26 1.89
3590 4099 1.809547 CGTGTAATGGTGGTTCATGCA 59.190 47.619 0.00 0.00 0.00 3.96
3704 4213 3.133141 GGTCAATGAGGCCTAGATTCC 57.867 52.381 4.42 2.10 39.61 3.01
3764 4274 5.603170 ACATTAGGGATGCAAATTTGGAG 57.397 39.130 19.47 5.20 39.47 3.86
4013 4526 7.283127 ACACATAATAACCGATTCTCAAAGCAT 59.717 33.333 0.00 0.00 0.00 3.79
4441 4955 3.861840 GTGTGAGGCACTGAAGCTTATA 58.138 45.455 0.00 0.00 41.55 0.98
4540 5054 3.627577 TCAAGGAAGCTGTTGAAGAACAC 59.372 43.478 4.38 0.00 37.15 3.32
4622 5136 7.012044 GGAAGGTATATAACGCTTCACATTGTT 59.988 37.037 0.00 0.00 37.24 2.83
4663 5177 9.836864 ATTGATACATGTAGATTAAGCTTGTCA 57.163 29.630 9.86 2.79 0.00 3.58
4719 5233 4.397420 TCTCATCTAAGCTTTTGTTGCCA 58.603 39.130 3.20 0.00 0.00 4.92
4748 5262 8.078596 GCTTACATCTGATTCACTTTTCTTGTT 58.921 33.333 0.00 0.00 0.00 2.83
4801 5315 0.786435 ATCTGGAGGGCAAAAGGGTT 59.214 50.000 0.00 0.00 0.00 4.11
4839 5353 2.470821 CAAATACGAAGCCTACGGGAG 58.529 52.381 0.00 0.00 34.93 4.30
4895 5409 7.318909 GTCATATATTTGTCGATTGTTGCTTCG 59.681 37.037 0.00 0.00 36.72 3.79
5226 5742 6.091076 TGATCATCAACTATTTTTCCCCCT 57.909 37.500 0.00 0.00 0.00 4.79
5231 5748 3.075283 TCAACTATTTTTCCCCCTGCTCA 59.925 43.478 0.00 0.00 0.00 4.26
5327 5846 0.108186 CCAGCTCAGCATCGGTGTTA 60.108 55.000 0.00 0.00 32.43 2.41
5333 5852 4.941263 AGCTCAGCATCGGTGTTAATTTAA 59.059 37.500 0.00 0.00 32.43 1.52
5345 5864 6.088883 CGGTGTTAATTTAACCAACAATCTGC 59.911 38.462 14.99 0.00 37.88 4.26
5353 5872 0.524862 CCAACAATCTGCAGGCAGTC 59.475 55.000 19.75 0.00 43.96 3.51
5376 5895 7.893302 AGTCATGGGGATATTTGTTCAGTTAAA 59.107 33.333 0.00 0.00 0.00 1.52
5377 5896 8.695456 GTCATGGGGATATTTGTTCAGTTAAAT 58.305 33.333 0.00 0.00 0.00 1.40
5427 5948 5.630121 TGTTGAACCTTGATACACCTCATT 58.370 37.500 0.00 0.00 0.00 2.57
5464 5985 5.437289 TGAATCTTCTTGCGTGTTTTCAT 57.563 34.783 0.00 0.00 0.00 2.57
5477 5998 4.285292 GTGTTTTCATTGTGCTGTCTGAG 58.715 43.478 0.00 0.00 0.00 3.35
5497 6018 4.202398 TGAGTCTTCAGGCTTGAGTGAATT 60.202 41.667 0.00 0.00 34.15 2.17
5645 6166 6.785337 TTCCTAGGATAGTCGTTTGATTCA 57.215 37.500 13.57 0.00 36.82 2.57
5646 6167 6.145338 TCCTAGGATAGTCGTTTGATTCAC 57.855 41.667 7.62 0.00 36.82 3.18
5676 6197 8.885494 TTGAAATCCTTACAAGTTTTTCCATG 57.115 30.769 9.53 0.00 30.31 3.66
5687 6208 8.831715 ACAAGTTTTTCCATGGTATTCATTTC 57.168 30.769 12.58 0.00 32.92 2.17
5699 6220 7.747155 TGGTATTCATTTCGTTGGAAACTTA 57.253 32.000 0.00 0.00 46.99 2.24
5732 6254 8.299990 TCAAACCTCTTTGTTGAATTCCTTTA 57.700 30.769 2.27 0.00 38.38 1.85
5781 6315 3.432252 GGTACAAAAGGACATGACACTCG 59.568 47.826 0.00 0.00 0.00 4.18
5782 6316 3.469008 ACAAAAGGACATGACACTCGA 57.531 42.857 0.00 0.00 0.00 4.04
5786 6320 4.543590 AAAGGACATGACACTCGATTCT 57.456 40.909 0.00 0.00 0.00 2.40
5787 6321 3.791973 AGGACATGACACTCGATTCTC 57.208 47.619 0.00 0.00 0.00 2.87
5812 6346 8.538856 TCGTGTTTTTCTTATTCTTGCATTTTG 58.461 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.789075 CGTACCCGGGCTCACACG 62.789 72.222 24.08 18.31 0.00 4.49
4 5 2.342650 TACGTACCCGGGCTCACAC 61.343 63.158 24.08 10.06 38.78 3.82
5 6 2.035469 TACGTACCCGGGCTCACA 59.965 61.111 24.08 0.00 38.78 3.58
6 7 2.491621 GTACGTACCCGGGCTCAC 59.508 66.667 24.08 15.58 38.78 3.51
7 8 3.133464 CGTACGTACCCGGGCTCA 61.133 66.667 24.08 2.33 38.78 4.26
8 9 3.134127 ACGTACGTACCCGGGCTC 61.134 66.667 24.08 13.33 38.78 4.70
9 10 3.443045 CACGTACGTACCCGGGCT 61.443 66.667 24.08 10.93 38.78 5.19
10 11 4.496927 CCACGTACGTACCCGGGC 62.497 72.222 24.08 3.66 38.78 6.13
11 12 3.825611 CCCACGTACGTACCCGGG 61.826 72.222 25.01 25.01 38.78 5.73
12 13 3.825611 CCCCACGTACGTACCCGG 61.826 72.222 22.34 17.50 38.78 5.73
13 14 3.825611 CCCCCACGTACGTACCCG 61.826 72.222 22.34 11.78 40.83 5.28
14 15 2.679996 ACCCCCACGTACGTACCC 60.680 66.667 22.34 0.00 0.00 3.69
15 16 1.976474 TGACCCCCACGTACGTACC 60.976 63.158 22.34 7.19 0.00 3.34
16 17 1.212751 GTGACCCCCACGTACGTAC 59.787 63.158 22.34 15.90 35.86 3.67
17 18 3.680156 GTGACCCCCACGTACGTA 58.320 61.111 22.34 0.00 35.86 3.57
24 25 1.073199 CTCCAACAGTGACCCCCAC 59.927 63.158 0.00 0.00 46.03 4.61
25 26 1.074090 TCTCCAACAGTGACCCCCA 60.074 57.895 0.00 0.00 0.00 4.96
26 27 1.679898 CTCTCCAACAGTGACCCCC 59.320 63.158 0.00 0.00 0.00 5.40
27 28 0.836400 TCCTCTCCAACAGTGACCCC 60.836 60.000 0.00 0.00 0.00 4.95
28 29 0.610687 CTCCTCTCCAACAGTGACCC 59.389 60.000 0.00 0.00 0.00 4.46
29 30 1.548269 CTCTCCTCTCCAACAGTGACC 59.452 57.143 0.00 0.00 0.00 4.02
30 31 1.548269 CCTCTCCTCTCCAACAGTGAC 59.452 57.143 0.00 0.00 0.00 3.67
31 32 1.429299 TCCTCTCCTCTCCAACAGTGA 59.571 52.381 0.00 0.00 0.00 3.41
32 33 1.824230 CTCCTCTCCTCTCCAACAGTG 59.176 57.143 0.00 0.00 0.00 3.66
33 34 1.713647 TCTCCTCTCCTCTCCAACAGT 59.286 52.381 0.00 0.00 0.00 3.55
34 35 2.378038 CTCTCCTCTCCTCTCCAACAG 58.622 57.143 0.00 0.00 0.00 3.16
35 36 1.006519 CCTCTCCTCTCCTCTCCAACA 59.993 57.143 0.00 0.00 0.00 3.33
36 37 1.286553 TCCTCTCCTCTCCTCTCCAAC 59.713 57.143 0.00 0.00 0.00 3.77
37 38 1.568597 CTCCTCTCCTCTCCTCTCCAA 59.431 57.143 0.00 0.00 0.00 3.53
38 39 1.221635 CTCCTCTCCTCTCCTCTCCA 58.778 60.000 0.00 0.00 0.00 3.86
39 40 1.421646 CTCTCCTCTCCTCTCCTCTCC 59.578 61.905 0.00 0.00 0.00 3.71
40 41 1.421646 CCTCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
41 42 1.010793 TCCTCTCCTCTCCTCTCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
42 43 1.421646 CTCCTCTCCTCTCCTCTCCTC 59.578 61.905 0.00 0.00 0.00 3.71
43 44 1.522900 CTCCTCTCCTCTCCTCTCCT 58.477 60.000 0.00 0.00 0.00 3.69
44 45 0.478507 CCTCCTCTCCTCTCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
45 46 1.421646 CTCCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
46 47 1.010793 TCTCCTCCTCTCCTCTCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
47 48 1.421646 CTCTCCTCCTCTCCTCTCCTC 59.578 61.905 0.00 0.00 0.00 3.71
48 49 1.275002 ACTCTCCTCCTCTCCTCTCCT 60.275 57.143 0.00 0.00 0.00 3.69
49 50 1.133792 CACTCTCCTCCTCTCCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
50 51 1.843851 TCACTCTCCTCCTCTCCTCTC 59.156 57.143 0.00 0.00 0.00 3.20
51 52 1.846439 CTCACTCTCCTCCTCTCCTCT 59.154 57.143 0.00 0.00 0.00 3.69
52 53 1.564348 ACTCACTCTCCTCCTCTCCTC 59.436 57.143 0.00 0.00 0.00 3.71
53 54 1.564348 GACTCACTCTCCTCCTCTCCT 59.436 57.143 0.00 0.00 0.00 3.69
54 55 1.745827 CGACTCACTCTCCTCCTCTCC 60.746 61.905 0.00 0.00 0.00 3.71
55 56 1.663695 CGACTCACTCTCCTCCTCTC 58.336 60.000 0.00 0.00 0.00 3.20
56 57 0.393808 GCGACTCACTCTCCTCCTCT 60.394 60.000 0.00 0.00 0.00 3.69
57 58 1.381165 GGCGACTCACTCTCCTCCTC 61.381 65.000 0.00 0.00 0.00 3.71
58 59 1.379309 GGCGACTCACTCTCCTCCT 60.379 63.158 0.00 0.00 0.00 3.69
59 60 1.679305 TGGCGACTCACTCTCCTCC 60.679 63.158 0.00 0.00 0.00 4.30
74 75 3.562635 CGGAAGGAGAAACGTGGC 58.437 61.111 0.00 0.00 0.00 5.01
128 129 2.816087 AGATATTATTTGCTGGCAGCCG 59.184 45.455 34.58 1.85 41.51 5.52
135 142 4.083643 CCGGTGCTGAGATATTATTTGCTG 60.084 45.833 0.00 0.00 0.00 4.41
175 182 5.183904 TCTGATCCATCCACGTATACATCAG 59.816 44.000 14.76 14.76 38.13 2.90
204 211 0.041663 TTTTTGCGCGGTCTCTTTCG 60.042 50.000 8.83 0.00 0.00 3.46
224 231 4.070009 ACCGTGGTACATTCTTCCTTTTC 58.930 43.478 0.00 0.00 44.52 2.29
229 236 2.754946 TCACCGTGGTACATTCTTCC 57.245 50.000 0.00 0.00 44.52 3.46
234 249 2.442413 CCCAAATCACCGTGGTACATT 58.558 47.619 0.00 0.00 44.52 2.71
236 251 0.037017 CCCCAAATCACCGTGGTACA 59.963 55.000 0.00 0.00 32.60 2.90
239 254 0.326927 CTACCCCAAATCACCGTGGT 59.673 55.000 0.00 0.00 32.60 4.16
241 256 0.616371 TCCTACCCCAAATCACCGTG 59.384 55.000 0.00 0.00 0.00 4.94
243 258 0.909623 ACTCCTACCCCAAATCACCG 59.090 55.000 0.00 0.00 0.00 4.94
246 261 2.352561 TGGACTCCTACCCCAAATCA 57.647 50.000 0.00 0.00 0.00 2.57
252 267 0.106669 GGCAAATGGACTCCTACCCC 60.107 60.000 0.00 0.00 0.00 4.95
256 271 0.174845 CGTCGGCAAATGGACTCCTA 59.825 55.000 0.00 0.00 0.00 2.94
283 309 2.727777 CTGGAATCTGCATGCAATTCG 58.272 47.619 28.90 18.44 31.56 3.34
287 313 1.659622 CGGCTGGAATCTGCATGCAA 61.660 55.000 22.88 13.05 39.25 4.08
305 331 4.758251 TGACCGTGCATCCAGGCG 62.758 66.667 0.00 0.00 36.28 5.52
363 390 6.793492 AAGGAAAGAAGAAGAAATCAGACG 57.207 37.500 0.00 0.00 0.00 4.18
370 397 8.935844 GCAAAAAGAAAAGGAAAGAAGAAGAAA 58.064 29.630 0.00 0.00 0.00 2.52
382 409 5.046663 ACTCCAACTTGCAAAAAGAAAAGGA 60.047 36.000 0.00 0.00 0.00 3.36
383 410 5.178061 ACTCCAACTTGCAAAAAGAAAAGG 58.822 37.500 0.00 0.00 0.00 3.11
389 420 6.564328 ACTTCTTACTCCAACTTGCAAAAAG 58.436 36.000 0.00 0.00 0.00 2.27
393 424 5.036117 AGACTTCTTACTCCAACTTGCAA 57.964 39.130 0.00 0.00 0.00 4.08
410 441 3.223435 TCTCGGTCAGAACTCAAGACTT 58.777 45.455 0.00 0.00 32.98 3.01
411 442 2.865079 TCTCGGTCAGAACTCAAGACT 58.135 47.619 0.00 0.00 32.98 3.24
412 443 3.644884 TTCTCGGTCAGAACTCAAGAC 57.355 47.619 0.00 0.00 36.08 3.01
413 444 3.574396 ACATTCTCGGTCAGAACTCAAGA 59.426 43.478 0.00 0.00 44.28 3.02
414 445 3.677121 CACATTCTCGGTCAGAACTCAAG 59.323 47.826 0.00 0.00 44.28 3.02
415 446 3.653344 CACATTCTCGGTCAGAACTCAA 58.347 45.455 0.00 0.00 44.28 3.02
419 450 0.716108 CGCACATTCTCGGTCAGAAC 59.284 55.000 0.00 0.00 44.28 3.01
443 474 3.037851 ACCTGTCTATCAGATGGAGCA 57.962 47.619 0.00 0.00 46.27 4.26
445 476 4.498850 CGTCAACCTGTCTATCAGATGGAG 60.499 50.000 0.00 0.00 46.27 3.86
446 477 3.381590 CGTCAACCTGTCTATCAGATGGA 59.618 47.826 0.00 0.00 46.27 3.41
470 535 5.437060 GTGTACATGGATGGGTTATCTTGT 58.563 41.667 0.00 0.00 36.63 3.16
476 541 3.054728 CAGTGGTGTACATGGATGGGTTA 60.055 47.826 0.00 0.00 0.00 2.85
494 559 4.753233 CCTGTCTCCTTCAGATAACAGTG 58.247 47.826 0.00 0.00 36.85 3.66
495 560 3.196685 GCCTGTCTCCTTCAGATAACAGT 59.803 47.826 0.00 0.00 36.85 3.55
513 578 2.082231 CAAGGTTGACTCATCTGCCTG 58.918 52.381 0.00 0.00 32.46 4.85
524 589 1.601903 TGCGTCATGTTCAAGGTTGAC 59.398 47.619 0.00 0.00 36.83 3.18
528 593 1.674359 TTGTGCGTCATGTTCAAGGT 58.326 45.000 0.00 0.00 0.00 3.50
567 633 2.104792 AGCAGCCACACTTCACTTCTTA 59.895 45.455 0.00 0.00 0.00 2.10
570 636 0.590195 CAGCAGCCACACTTCACTTC 59.410 55.000 0.00 0.00 0.00 3.01
573 639 2.263741 CCCAGCAGCCACACTTCAC 61.264 63.158 0.00 0.00 0.00 3.18
574 640 1.782201 ATCCCAGCAGCCACACTTCA 61.782 55.000 0.00 0.00 0.00 3.02
677 960 8.143193 TGGGGTGTACGTATTGTATACAAATAG 58.857 37.037 21.57 16.44 44.43 1.73
686 969 3.613671 CGTGTTGGGGTGTACGTATTGTA 60.614 47.826 0.00 0.00 0.00 2.41
687 970 2.769893 GTGTTGGGGTGTACGTATTGT 58.230 47.619 0.00 0.00 0.00 2.71
688 971 1.727880 CGTGTTGGGGTGTACGTATTG 59.272 52.381 0.00 0.00 0.00 1.90
689 972 1.940752 GCGTGTTGGGGTGTACGTATT 60.941 52.381 0.00 0.00 38.67 1.89
692 975 2.280321 GCGTGTTGGGGTGTACGT 60.280 61.111 0.00 0.00 38.67 3.57
693 976 3.408020 CGCGTGTTGGGGTGTACG 61.408 66.667 0.00 0.00 39.37 3.67
696 979 2.438795 AAACGCGTGTTGGGGTGT 60.439 55.556 14.98 0.00 38.62 4.16
698 981 1.313812 TTTGAAACGCGTGTTGGGGT 61.314 50.000 14.98 0.00 38.62 4.95
699 982 0.179134 TTTTGAAACGCGTGTTGGGG 60.179 50.000 14.98 0.00 38.62 4.96
700 983 1.846541 ATTTTGAAACGCGTGTTGGG 58.153 45.000 14.98 0.00 38.62 4.12
730 1013 0.613853 CTGGGACCCGTACAGAAGGA 60.614 60.000 5.91 0.00 34.21 3.36
731 1014 1.898154 CTGGGACCCGTACAGAAGG 59.102 63.158 5.91 0.00 34.21 3.46
743 1026 1.003233 GACTGTCTTGGGCTGGGAC 60.003 63.158 0.00 0.00 0.00 4.46
747 1030 2.082231 CATTCAGACTGTCTTGGGCTG 58.918 52.381 7.77 0.00 0.00 4.85
764 1047 0.679960 GCCTTGCTCCGTAACCCATT 60.680 55.000 0.00 0.00 0.00 3.16
833 1116 2.656651 CCTGGAGATTCGCGCTCG 60.657 66.667 5.56 0.00 33.19 5.03
878 1161 0.743345 AACCCTAAGAATGCGCGGTC 60.743 55.000 8.83 1.79 0.00 4.79
919 1202 4.366684 GGGGTGGAGTTGCCTGGG 62.367 72.222 0.00 0.00 37.63 4.45
922 1205 2.155197 GATTGGGGGTGGAGTTGCCT 62.155 60.000 0.00 0.00 37.63 4.75
1092 1377 3.822192 TGATCGCGTCAGGGACCG 61.822 66.667 5.77 0.00 42.26 4.79
1148 1433 6.997476 AGGCACACCAAACATTCATAATTTTT 59.003 30.769 0.00 0.00 39.06 1.94
1149 1434 6.427547 CAGGCACACCAAACATTCATAATTTT 59.572 34.615 0.00 0.00 39.06 1.82
1166 1451 3.537206 AAGTCGAGGCCAGGCACAC 62.537 63.158 15.19 3.40 0.00 3.82
1168 1453 2.743928 CAAGTCGAGGCCAGGCAC 60.744 66.667 15.19 2.09 0.00 5.01
1169 1454 4.020617 CCAAGTCGAGGCCAGGCA 62.021 66.667 15.19 0.00 0.00 4.75
1176 1461 0.895530 TCTACCTTGCCAAGTCGAGG 59.104 55.000 3.37 0.00 42.27 4.63
1182 1467 6.350612 GGCTCTATATAGTCTACCTTGCCAAG 60.351 46.154 9.58 0.00 35.94 3.61
1187 1472 4.944930 AGCGGCTCTATATAGTCTACCTTG 59.055 45.833 9.58 0.00 0.00 3.61
1199 1484 3.574396 ACTGAATGCTAAGCGGCTCTATA 59.426 43.478 1.45 0.00 0.00 1.31
1207 1492 7.188834 TCAAATGAATTACTGAATGCTAAGCG 58.811 34.615 0.00 0.00 0.00 4.68
1238 1523 8.746052 TTAACTGTAAACAAGCCTGCATATAT 57.254 30.769 0.00 0.00 0.00 0.86
1286 1571 0.530744 TAGCTACACGAACAGGCTGG 59.469 55.000 20.34 3.36 34.88 4.85
1469 1893 5.912955 CGTTTGCTAAGAAAAACCTCGAAAT 59.087 36.000 0.00 0.00 33.61 2.17
1472 1896 3.872771 ACGTTTGCTAAGAAAAACCTCGA 59.127 39.130 0.00 0.00 33.61 4.04
1473 1897 3.966218 CACGTTTGCTAAGAAAAACCTCG 59.034 43.478 0.00 0.00 33.61 4.63
1477 1901 6.577427 CCTCATACACGTTTGCTAAGAAAAAC 59.423 38.462 0.00 0.00 33.80 2.43
1493 1917 6.659242 CCAATTTATCCATACCCCTCATACAC 59.341 42.308 0.00 0.00 0.00 2.90
1519 1943 3.619483 CCGTCAGTACAACTTGACAAACA 59.381 43.478 12.01 0.00 30.79 2.83
1539 1999 1.282248 AATCGAACACGCAGTCACCG 61.282 55.000 0.00 0.00 41.61 4.94
1550 2010 8.786826 ACAATAGACCATTTCTAAATCGAACA 57.213 30.769 0.00 0.00 40.38 3.18
1574 2034 7.759489 AGACTAATCATGGAGAGATCAGTAC 57.241 40.000 0.00 0.00 0.00 2.73
1592 2052 6.235231 ACCACACAAGAAGAGAAAGACTAA 57.765 37.500 0.00 0.00 0.00 2.24
1597 2057 4.040461 TCCCTACCACACAAGAAGAGAAAG 59.960 45.833 0.00 0.00 0.00 2.62
1600 2060 3.254093 TCCCTACCACACAAGAAGAGA 57.746 47.619 0.00 0.00 0.00 3.10
1601 2061 3.369892 CCATCCCTACCACACAAGAAGAG 60.370 52.174 0.00 0.00 0.00 2.85
1732 2192 8.020819 TCTTTACTCAACAAATGCTTAAATCGG 58.979 33.333 0.00 0.00 0.00 4.18
1801 2261 1.905637 TGCGTAGGAGAACAGACTCA 58.094 50.000 0.00 0.00 38.51 3.41
1948 2408 6.318144 GGACATGATCAGACACTTGAATCATT 59.682 38.462 0.00 0.00 30.24 2.57
1950 2410 5.046087 AGGACATGATCAGACACTTGAATCA 60.046 40.000 0.00 0.00 0.00 2.57
1980 2440 7.351981 GCCATTACCAAATGACAAAGAAAAAC 58.648 34.615 0.00 0.00 44.50 2.43
2269 2729 7.864108 TCTGTAAGAAATAATGGTGTGATGG 57.136 36.000 0.00 0.00 42.31 3.51
2413 2873 6.550854 TCTGAAGGAGGAAACAAATGTTCATT 59.449 34.615 0.00 0.00 37.25 2.57
2471 2931 7.704472 TGTTCCAACACAATGTTTCAATCTTAC 59.296 33.333 0.00 0.00 38.77 2.34
2597 3057 5.762218 AGTTAAAGGACATATGCAGATGAGC 59.238 40.000 27.19 17.19 0.00 4.26
2727 3229 6.119536 TGCAAAATTATCGATAACCAGACCT 58.880 36.000 19.73 0.00 0.00 3.85
2928 3431 3.128938 AGAATAGGACAGTCGTAGCACAC 59.871 47.826 8.84 0.00 0.00 3.82
2934 3437 2.099263 GCAGCAGAATAGGACAGTCGTA 59.901 50.000 5.45 5.45 0.00 3.43
2936 3439 1.135915 AGCAGCAGAATAGGACAGTCG 59.864 52.381 0.00 0.00 0.00 4.18
2937 3440 2.977772 AGCAGCAGAATAGGACAGTC 57.022 50.000 0.00 0.00 0.00 3.51
2938 3441 4.508662 GTTAAGCAGCAGAATAGGACAGT 58.491 43.478 0.00 0.00 0.00 3.55
2939 3442 3.873952 GGTTAAGCAGCAGAATAGGACAG 59.126 47.826 0.00 0.00 0.00 3.51
2940 3443 3.263170 TGGTTAAGCAGCAGAATAGGACA 59.737 43.478 2.54 0.00 0.00 4.02
2941 3444 3.873910 TGGTTAAGCAGCAGAATAGGAC 58.126 45.455 2.54 0.00 0.00 3.85
2942 3445 4.568072 TTGGTTAAGCAGCAGAATAGGA 57.432 40.909 7.51 0.00 33.34 2.94
2943 3446 5.643379 TTTTGGTTAAGCAGCAGAATAGG 57.357 39.130 7.51 0.00 33.34 2.57
3341 3850 4.715534 TTGACAAGATACCAACAAGGGA 57.284 40.909 0.00 0.00 43.89 4.20
3441 3950 6.094464 TCAATGCTTCAAGTGAGAATGTATGG 59.906 38.462 0.00 0.00 0.00 2.74
3476 3985 3.857093 GCGTAACCATGCGAAATTTCATT 59.143 39.130 17.99 4.93 36.72 2.57
3486 3995 1.910819 GACAAATTGCGTAACCATGCG 59.089 47.619 0.00 0.00 39.74 4.73
3571 4080 4.454728 AATGCATGAACCACCATTACAC 57.545 40.909 0.00 0.00 0.00 2.90
3577 4086 5.015515 TGAATCTTAATGCATGAACCACCA 58.984 37.500 0.00 0.00 0.00 4.17
3636 4145 5.899631 AGGGTTGACTTTCTTAAGGTGTA 57.100 39.130 1.85 0.00 35.61 2.90
3704 4213 6.623486 TGAAATTAATGATTGAGTGGCAGTG 58.377 36.000 0.00 0.00 0.00 3.66
3997 4510 2.026822 AGGTCATGCTTTGAGAATCGGT 60.027 45.455 0.00 0.00 38.61 4.69
4013 4526 4.442332 CCGCTTGTTATATACCACAGGTCA 60.442 45.833 0.00 0.00 37.09 4.02
4106 4620 2.538437 CTTTGTCCTGCAGAGAGATCG 58.462 52.381 17.39 0.00 31.54 3.69
4441 4955 4.139786 ACATCATGTGTTCAACAGCTTCT 58.860 39.130 0.00 0.00 43.64 2.85
4540 5054 5.348997 GGAGAAGTCGGACAAAATAGTTGAG 59.651 44.000 11.27 0.00 0.00 3.02
4622 5136 0.407528 TCAATAGGGCCTGCCAAACA 59.592 50.000 18.53 0.00 37.98 2.83
4663 5177 3.452990 TCCAAATGGATTTGCATGAGCAT 59.547 39.130 0.00 0.00 44.86 3.79
4719 5233 8.345724 AGAAAAGTGAATCAGATGTAAGCAAT 57.654 30.769 0.00 0.00 0.00 3.56
4748 5262 1.710244 TCCCTGGAGCTGGAAAATTCA 59.290 47.619 0.00 0.00 0.00 2.57
4801 5315 7.710475 TCGTATTTGCTTCATGATACAAGATGA 59.290 33.333 0.00 4.99 0.00 2.92
4839 5353 3.547468 GCCACACGCAAAATCATATTGTC 59.453 43.478 0.00 0.00 37.47 3.18
4895 5409 3.568853 ACAGCCTGTATGTATACTCGTCC 59.431 47.826 0.00 0.00 34.41 4.79
5221 5737 1.706995 ATGAGATGCTGAGCAGGGGG 61.707 60.000 14.36 0.00 43.65 5.40
5226 5742 3.450096 AGACTTGTATGAGATGCTGAGCA 59.550 43.478 10.59 10.59 44.86 4.26
5231 5748 5.181748 GTTTGGAGACTTGTATGAGATGCT 58.818 41.667 0.00 0.00 0.00 3.79
5305 5824 3.473647 CCGATGCTGAGCTGGGGA 61.474 66.667 5.83 0.00 0.00 4.81
5306 5825 3.790437 ACCGATGCTGAGCTGGGG 61.790 66.667 5.83 6.34 0.00 4.96
5315 5834 5.241949 TGTTGGTTAAATTAACACCGATGCT 59.758 36.000 16.55 0.00 40.39 3.79
5327 5846 4.040217 TGCCTGCAGATTGTTGGTTAAATT 59.960 37.500 17.39 0.00 0.00 1.82
5333 5852 0.178981 ACTGCCTGCAGATTGTTGGT 60.179 50.000 24.88 1.10 46.30 3.67
5345 5864 2.889045 CAAATATCCCCATGACTGCCTG 59.111 50.000 0.00 0.00 0.00 4.85
5353 5872 8.917088 AGATTTAACTGAACAAATATCCCCATG 58.083 33.333 0.00 0.00 0.00 3.66
5376 5895 7.550906 GGTTTAGAACTCTATGCTTTGTCAGAT 59.449 37.037 0.00 0.00 0.00 2.90
5377 5896 6.874134 GGTTTAGAACTCTATGCTTTGTCAGA 59.126 38.462 0.00 0.00 0.00 3.27
5427 5948 9.467258 CAAGAAGATTCAACTATTTGCAGAAAA 57.533 29.630 0.00 0.00 32.17 2.29
5477 5998 3.365767 GCAATTCACTCAAGCCTGAAGAC 60.366 47.826 0.00 0.00 30.04 3.01
5486 6007 6.088173 TGATTCGAAATGCAATTCACTCAAG 58.912 36.000 14.62 0.00 33.67 3.02
5497 6018 6.089685 CACAAACATGATTGATTCGAAATGCA 59.910 34.615 21.13 0.00 34.38 3.96
5584 6105 7.148590 GGATCCAAATCCTTCAAAAATCAAACG 60.149 37.037 6.95 0.00 46.97 3.60
5620 6141 7.548075 GTGAATCAAACGACTATCCTAGGAAAA 59.452 37.037 17.30 6.28 0.00 2.29
5663 6184 7.598493 ACGAAATGAATACCATGGAAAAACTTG 59.402 33.333 21.47 2.00 35.24 3.16
5664 6185 7.666623 ACGAAATGAATACCATGGAAAAACTT 58.333 30.769 21.47 3.02 35.24 2.66
5676 6197 7.586747 TGTAAGTTTCCAACGAAATGAATACC 58.413 34.615 0.00 0.00 40.08 2.73
5687 6208 4.062293 TGAGTGGATGTAAGTTTCCAACG 58.938 43.478 0.00 0.00 43.42 4.10
5699 6220 4.170468 ACAAAGAGGTTTGAGTGGATGT 57.830 40.909 4.91 0.00 45.22 3.06
5781 6315 7.803189 TGCAAGAATAAGAAAAACACGAGAATC 59.197 33.333 0.00 0.00 0.00 2.52
5782 6316 7.648142 TGCAAGAATAAGAAAAACACGAGAAT 58.352 30.769 0.00 0.00 0.00 2.40
5786 6320 8.538856 CAAAATGCAAGAATAAGAAAAACACGA 58.461 29.630 0.00 0.00 0.00 4.35
5787 6321 8.538856 TCAAAATGCAAGAATAAGAAAAACACG 58.461 29.630 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.