Multiple sequence alignment - TraesCS5A01G455100

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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 TraesCS5A01G455100 chr5A 100.000 4803 0 0 1 4803 635781280 635776478 0.000000e+00 8870
1 TraesCS5A01G455100 chr5A 90.811 185 12 5 4065 4248 33127681 33127501 4.800000e-60 243
2 TraesCS5A01G455100 chr5A 89.617 183 14 3 4065 4246 428152202 428152024 1.340000e-55 228
3 TraesCS5A01G455100 chr5A 80.117 171 20 6 3891 4048 521246703 521246534 1.090000e-21 115
4 TraesCS5A01G455100 chr5A 79.532 171 21 7 3891 4048 521228028 521227859 5.080000e-20 110
5 TraesCS5A01G455100 chr5D 91.754 3335 177 47 589 3876 508120406 508117123 0.000000e+00 4545
6 TraesCS5A01G455100 chr5D 93.243 148 4 1 4662 4803 508115740 508115593 3.770000e-51 213
7 TraesCS5A01G455100 chr5B 90.965 2291 146 33 600 2868 638831758 638834009 0.000000e+00 3027
8 TraesCS5A01G455100 chr5B 90.259 1468 95 27 2931 4368 638834126 638835575 0.000000e+00 1875
9 TraesCS5A01G455100 chr4D 84.962 532 42 21 1185 1679 150650711 150650181 5.550000e-139 505
10 TraesCS5A01G455100 chr4D 83.179 541 44 25 1185 1679 166137206 166137745 7.330000e-123 451
11 TraesCS5A01G455100 chr4D 91.573 178 11 2 4065 4241 469158614 469158440 4.800000e-60 243
12 TraesCS5A01G455100 chr2A 81.520 579 82 14 41 597 66767772 66767197 2.040000e-123 453
13 TraesCS5A01G455100 chr6B 91.319 288 16 6 1055 1335 170169281 170168996 7.540000e-103 385
14 TraesCS5A01G455100 chr6B 87.390 341 30 3 1381 1720 170168998 170168670 3.510000e-101 379
15 TraesCS5A01G455100 chr6B 79.249 559 96 14 52 597 713474448 713473897 5.870000e-99 372
16 TraesCS5A01G455100 chr6D 79.887 532 98 9 52 577 816554 816026 9.750000e-102 381
17 TraesCS5A01G455100 chr6D 81.221 426 69 8 180 599 333365920 333366340 2.770000e-87 333
18 TraesCS5A01G455100 chr7D 79.385 553 103 9 29 575 590860199 590859652 3.510000e-101 379
19 TraesCS5A01G455100 chrUn 86.628 344 31 4 1381 1721 77549682 77550013 2.730000e-97 366
20 TraesCS5A01G455100 chrUn 92.517 147 5 6 1193 1335 77549540 77549684 6.300000e-49 206
21 TraesCS5A01G455100 chr7B 80.364 494 85 9 90 576 384764885 384764397 9.820000e-97 364
22 TraesCS5A01G455100 chr2D 79.568 509 94 7 76 578 611164857 611164353 5.910000e-94 355
23 TraesCS5A01G455100 chr2D 77.509 578 101 23 37 597 603661384 603660819 2.160000e-83 320
24 TraesCS5A01G455100 chr2D 91.061 179 12 2 4065 4242 640367485 640367310 6.210000e-59 239
25 TraesCS5A01G455100 chr4A 79.026 534 99 10 52 577 674361708 674361180 2.130000e-93 353
26 TraesCS5A01G455100 chr6A 92.090 177 10 3 4063 4238 89598812 89598639 3.710000e-61 246
27 TraesCS5A01G455100 chr7A 90.811 185 12 3 4065 4248 127763007 127763187 4.800000e-60 243
28 TraesCS5A01G455100 chr3B 90.857 175 12 2 4065 4238 4683090 4683261 1.040000e-56 231
29 TraesCS5A01G455100 chr3B 90.449 178 13 2 4065 4241 614906096 614905922 1.040000e-56 231
30 TraesCS5A01G455100 chr1A 75.284 352 60 14 38 368 345105613 345105268 5.010000e-30 143


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 TraesCS5A01G455100 chr5A 635776478 635781280 4802 True 8870 8870 100.0000 1 4803 1 chr5A.!!$R5 4802
1 TraesCS5A01G455100 chr5D 508115593 508120406 4813 True 2379 4545 92.4985 589 4803 2 chr5D.!!$R1 4214
2 TraesCS5A01G455100 chr5B 638831758 638835575 3817 False 2451 3027 90.6120 600 4368 2 chr5B.!!$F1 3768
3 TraesCS5A01G455100 chr4D 150650181 150650711 530 True 505 505 84.9620 1185 1679 1 chr4D.!!$R1 494
4 TraesCS5A01G455100 chr4D 166137206 166137745 539 False 451 451 83.1790 1185 1679 1 chr4D.!!$F1 494
5 TraesCS5A01G455100 chr2A 66767197 66767772 575 True 453 453 81.5200 41 597 1 chr2A.!!$R1 556
6 TraesCS5A01G455100 chr6B 170168670 170169281 611 True 382 385 89.3545 1055 1720 2 chr6B.!!$R2 665
7 TraesCS5A01G455100 chr6B 713473897 713474448 551 True 372 372 79.2490 52 597 1 chr6B.!!$R1 545
8 TraesCS5A01G455100 chr6D 816026 816554 528 True 381 381 79.8870 52 577 1 chr6D.!!$R1 525
9 TraesCS5A01G455100 chr7D 590859652 590860199 547 True 379 379 79.3850 29 575 1 chr7D.!!$R1 546
10 TraesCS5A01G455100 chr2D 611164353 611164857 504 True 355 355 79.5680 76 578 1 chr2D.!!$R2 502
11 TraesCS5A01G455100 chr2D 603660819 603661384 565 True 320 320 77.5090 37 597 1 chr2D.!!$R1 560
12 TraesCS5A01G455100 chr4A 674361180 674361708 528 True 353 353 79.0260 52 577 1 chr4A.!!$R1 525

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
505 534 0.036105 TGTAGTCGTCGCTAGGTGGA 60.036 55.0 0.00 0.0 0.00 4.02 F
702 734 0.039527 AGAAAATTCAACCGCGTGCC 60.040 50.0 4.92 0.0 0.00 5.01 F
1933 2042 0.107703 TGGCCTTCTGCGATTACCTG 60.108 55.0 3.32 0.0 42.61 4.00 F
3185 3388 0.695803 CCTATGCTGGGAGGGTCCTT 60.696 60.0 0.00 0.0 36.57 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1421 0.112412 GTGGCCTTTCCTCCTTTGGA 59.888 55.0 3.32 0.0 35.26 3.53 R
2663 2789 0.529378 GGCTTGCCCAGAAGAATGTG 59.471 55.0 0.00 0.0 0.00 3.21 R
3368 3571 0.397816 AGAAGAGCCGCTGGAGGTAT 60.398 55.0 0.00 0.0 0.00 2.73 R
4567 4816 0.040958 CACTTGGCAAGCACGACTTC 60.041 55.0 26.45 0.0 36.04 3.01 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
20 21 2.807676 CCTGCAATGTTTAGGGTTCCT 58.192 47.619 0.00 0.00 37.71 3.36
21 22 2.755103 CCTGCAATGTTTAGGGTTCCTC 59.245 50.000 0.00 0.00 34.61 3.71
22 23 2.420022 CTGCAATGTTTAGGGTTCCTCG 59.580 50.000 0.00 0.00 34.61 4.63
23 24 1.743394 GCAATGTTTAGGGTTCCTCGG 59.257 52.381 0.00 0.00 34.61 4.63
24 25 2.878526 GCAATGTTTAGGGTTCCTCGGT 60.879 50.000 0.00 0.00 34.61 4.69
25 26 3.007635 CAATGTTTAGGGTTCCTCGGTC 58.992 50.000 0.00 0.00 34.61 4.79
26 27 2.019807 TGTTTAGGGTTCCTCGGTCT 57.980 50.000 0.00 0.00 34.61 3.85
27 28 1.897802 TGTTTAGGGTTCCTCGGTCTC 59.102 52.381 0.00 0.00 34.61 3.36
50 51 3.537874 GCCCCGCCTCGTATCTGT 61.538 66.667 0.00 0.00 0.00 3.41
60 61 2.693591 CCTCGTATCTGTTGGCCTTAGA 59.306 50.000 3.32 5.40 0.00 2.10
62 63 3.362706 TCGTATCTGTTGGCCTTAGAGT 58.637 45.455 3.32 0.00 0.00 3.24
67 68 3.173151 TCTGTTGGCCTTAGAGTCATGA 58.827 45.455 3.32 0.00 0.00 3.07
72 73 0.175760 GCCTTAGAGTCATGACGGCA 59.824 55.000 27.08 12.75 34.40 5.69
86 87 4.101448 GGCACGGTGGATCCTGCT 62.101 66.667 19.74 0.00 39.00 4.24
117 118 4.825634 GGTGGGAGGGCTATGTTTTTATAC 59.174 45.833 0.00 0.00 0.00 1.47
120 121 5.163131 TGGGAGGGCTATGTTTTTATACCTC 60.163 44.000 0.00 0.00 41.86 3.85
129 131 7.169476 GCTATGTTTTTATACCTCCTTCGAGTC 59.831 40.741 0.00 0.00 33.93 3.36
135 141 6.600882 TTATACCTCCTTCGAGTCTTGTTT 57.399 37.500 0.00 0.00 33.93 2.83
146 152 3.119637 CGAGTCTTGTTTGGGTTTGTGTT 60.120 43.478 0.00 0.00 0.00 3.32
165 171 4.023021 GTGTTCTACTCAGAAAGACGAGGT 60.023 45.833 0.00 0.00 42.41 3.85
173 180 2.710724 GAAAGACGAGGTGGTGCGGT 62.711 60.000 0.00 0.00 0.00 5.68
195 203 3.048600 TCCCTGAAGATGGATAAGGGTG 58.951 50.000 5.97 0.00 46.59 4.61
219 228 2.281091 CCTAGCCCCGTCCTGGTA 59.719 66.667 0.00 0.00 35.15 3.25
243 252 1.831106 TGTCTAGCATCGTTGGTGGAT 59.169 47.619 13.70 0.00 41.89 3.41
251 260 0.690192 TCGTTGGTGGATGTGTGGAT 59.310 50.000 0.00 0.00 0.00 3.41
252 261 1.086696 CGTTGGTGGATGTGTGGATC 58.913 55.000 0.00 0.00 0.00 3.36
260 286 3.197766 GTGGATGTGTGGATCTGTCCTTA 59.802 47.826 0.00 0.00 45.32 2.69
264 290 3.506398 TGTGTGGATCTGTCCTTAGTGA 58.494 45.455 0.00 0.00 45.32 3.41
265 291 3.511540 TGTGTGGATCTGTCCTTAGTGAG 59.488 47.826 0.00 0.00 45.32 3.51
282 308 1.347707 TGAGTTTGCTCGGATCTGGTT 59.652 47.619 0.62 0.00 44.48 3.67
286 312 4.694339 AGTTTGCTCGGATCTGGTTATAC 58.306 43.478 0.62 0.00 0.00 1.47
319 345 5.804979 CGTTTGTGTTTCTTCAGGTTGAATT 59.195 36.000 0.00 0.00 35.59 2.17
345 373 4.611310 CGATCTACGGTACTCTTCACAA 57.389 45.455 0.00 0.00 38.46 3.33
352 380 1.000506 GGTACTCTTCACAAGTGGCGA 59.999 52.381 0.00 0.00 0.00 5.54
384 413 1.288508 TGCATTGGTCCTATGGGGCT 61.289 55.000 14.17 0.00 37.39 5.19
401 430 1.415374 GCTTTAGCACGACGACTTCA 58.585 50.000 0.00 0.00 41.59 3.02
407 436 0.110509 GCACGACGACTTCACGACTA 60.111 55.000 0.00 0.00 37.03 2.59
434 463 4.939439 ACTACAACAAGTTTTGTCCGACTT 59.061 37.500 0.00 0.00 44.59 3.01
448 477 4.698625 ACTTCGGCGAGGGAGGGT 62.699 66.667 23.15 7.74 0.00 4.34
450 479 4.689549 TTCGGCGAGGGAGGGTCA 62.690 66.667 10.46 0.00 0.00 4.02
505 534 0.036105 TGTAGTCGTCGCTAGGTGGA 60.036 55.000 0.00 0.00 0.00 4.02
553 582 7.829378 ATTATTTCTGGTCTTCGTTGTACTC 57.171 36.000 0.00 0.00 0.00 2.59
555 584 4.931661 TTCTGGTCTTCGTTGTACTCTT 57.068 40.909 0.00 0.00 0.00 2.85
556 585 4.931661 TCTGGTCTTCGTTGTACTCTTT 57.068 40.909 0.00 0.00 0.00 2.52
615 647 2.427232 ATATATTACGGCGCGTGTGT 57.573 45.000 6.90 6.61 41.39 3.72
616 648 2.206815 TATATTACGGCGCGTGTGTT 57.793 45.000 6.90 1.99 41.39 3.32
632 664 2.739913 TGTGTTTAGGATTTCCGCGAAG 59.260 45.455 8.23 0.00 42.08 3.79
654 686 7.519168 CGAAGGAAAGGAAAGAAGAAGAAGAAC 60.519 40.741 0.00 0.00 0.00 3.01
702 734 0.039527 AGAAAATTCAACCGCGTGCC 60.040 50.000 4.92 0.00 0.00 5.01
714 746 1.153958 GCGTGCCAAATCAAGAGCC 60.154 57.895 0.00 0.00 0.00 4.70
725 757 6.335777 CCAAATCAAGAGCCAGGATTTAAAG 58.664 40.000 0.00 0.00 38.74 1.85
760 792 3.325135 AGAACCTTCCGAAGTCACAATCT 59.675 43.478 7.37 0.00 0.00 2.40
894 938 1.856265 GCAGACCGCCAAGAAACCAG 61.856 60.000 0.00 0.00 32.94 4.00
972 1016 0.895530 CACCGCTCCTCCTACAAGAA 59.104 55.000 0.00 0.00 0.00 2.52
1037 1088 1.142870 ACCTCTCCTCTCCATCTCTCG 59.857 57.143 0.00 0.00 0.00 4.04
1038 1089 1.142870 CCTCTCCTCTCCATCTCTCGT 59.857 57.143 0.00 0.00 0.00 4.18
1039 1090 2.221169 CTCTCCTCTCCATCTCTCGTG 58.779 57.143 0.00 0.00 0.00 4.35
1040 1091 1.133945 TCTCCTCTCCATCTCTCGTGG 60.134 57.143 0.00 0.00 38.11 4.94
1338 1404 1.334689 GCTTTTTCCACCTCGTTTCCG 60.335 52.381 0.00 0.00 0.00 4.30
1355 1421 1.004918 CGCCAACGGAAGGTTCTCT 60.005 57.895 0.00 0.00 36.49 3.10
1375 1441 1.244019 CCAAAGGAGGAAAGGCCACG 61.244 60.000 5.01 0.00 40.02 4.94
1402 1476 1.259840 CCAGTTCCTGCATTTGGGGG 61.260 60.000 0.00 0.00 0.00 5.40
1408 1482 1.494721 TCCTGCATTTGGGGGTATCTC 59.505 52.381 0.00 0.00 0.00 2.75
1413 1487 1.676006 CATTTGGGGGTATCTCGTTGC 59.324 52.381 0.00 0.00 0.00 4.17
1546 1645 2.616842 GGCTTGAAACAAACGAGGAGAA 59.383 45.455 0.00 0.00 0.00 2.87
1547 1646 3.253432 GGCTTGAAACAAACGAGGAGAAT 59.747 43.478 0.00 0.00 0.00 2.40
1548 1647 4.261614 GGCTTGAAACAAACGAGGAGAATT 60.262 41.667 0.00 0.00 0.00 2.17
1589 1692 6.477669 AAACATCGATGACATCTATGATGC 57.522 37.500 31.33 0.00 37.35 3.91
1732 1840 0.390866 CTTCTCCGTGCTGTCATGCT 60.391 55.000 0.00 0.00 0.00 3.79
1834 1942 4.275936 GTGGCACATTAATCGCCTCTTATT 59.724 41.667 20.79 0.00 46.39 1.40
1849 1957 6.292596 CGCCTCTTATTCTGCTTCTGTAATTC 60.293 42.308 0.00 0.00 0.00 2.17
1860 1968 5.532406 TGCTTCTGTAATTCTGAGCTGTTTT 59.468 36.000 0.00 0.00 0.00 2.43
1864 1972 5.177511 TCTGTAATTCTGAGCTGTTTTCGTG 59.822 40.000 0.00 0.00 0.00 4.35
1868 1976 2.416747 TCTGAGCTGTTTTCGTGGATG 58.583 47.619 0.00 0.00 0.00 3.51
1933 2042 0.107703 TGGCCTTCTGCGATTACCTG 60.108 55.000 3.32 0.00 42.61 4.00
1952 2061 1.008538 GGCAACGCTGTCAAGGTTG 60.009 57.895 10.02 10.02 42.89 3.77
2026 2135 1.479709 TTGGTTGTTGACACCTTGGG 58.520 50.000 0.00 0.00 0.00 4.12
2036 2145 2.316108 GACACCTTGGGAATTTGTGGT 58.684 47.619 0.00 0.00 0.00 4.16
2177 2286 3.257127 CACCGTTTGTTTGATGGGGTATT 59.743 43.478 0.00 0.00 0.00 1.89
2188 2297 5.004361 TGATGGGGTATTTTCCTGTTTCA 57.996 39.130 0.00 0.00 0.00 2.69
2189 2298 5.398236 TGATGGGGTATTTTCCTGTTTCAA 58.602 37.500 0.00 0.00 0.00 2.69
2228 2346 2.252535 ATTGGGTTTGCCTGGCTAAT 57.747 45.000 21.03 7.90 34.45 1.73
2229 2347 2.022718 TTGGGTTTGCCTGGCTAATT 57.977 45.000 21.03 0.00 34.45 1.40
2234 2352 2.164422 GGTTTGCCTGGCTAATTCTGAC 59.836 50.000 21.03 6.05 0.00 3.51
2235 2353 2.819608 GTTTGCCTGGCTAATTCTGACA 59.180 45.455 21.03 0.00 0.00 3.58
2258 2376 8.065473 ACATGGAAAAATGCAGATACATGTTA 57.935 30.769 2.30 0.00 43.41 2.41
2345 2463 4.496360 TCATGCTCGTTACGTTAATTGGA 58.504 39.130 4.24 0.00 0.00 3.53
2357 2475 6.009115 ACGTTAATTGGAATTGGTGAGTTC 57.991 37.500 0.00 0.00 0.00 3.01
2370 2494 6.554334 TTGGTGAGTTCTTTTATTTCTCCG 57.446 37.500 0.00 0.00 0.00 4.63
2467 2592 1.499056 CATGCACAGCTTGACCGAC 59.501 57.895 0.00 0.00 36.06 4.79
2551 2676 1.464997 GTTGATGCCTTTGTCGTCTCC 59.535 52.381 0.00 0.00 0.00 3.71
2595 2720 4.973168 TGCCTCAACATTACTTTGACTCT 58.027 39.130 0.00 0.00 0.00 3.24
2596 2721 6.109156 TGCCTCAACATTACTTTGACTCTA 57.891 37.500 0.00 0.00 0.00 2.43
2597 2722 6.166279 TGCCTCAACATTACTTTGACTCTAG 58.834 40.000 0.00 0.00 0.00 2.43
2598 2723 6.166982 GCCTCAACATTACTTTGACTCTAGT 58.833 40.000 0.00 0.00 0.00 2.57
2635 2761 7.872113 ATTGTGATATCCAAAGGAGAAGAAC 57.128 36.000 9.69 0.00 34.05 3.01
2663 2789 6.425114 TCTCATAGTTGTTTTCTTCTGCAGTC 59.575 38.462 14.67 0.00 0.00 3.51
2713 2839 3.090790 TGCTCTGCTTTGCATATCCAAA 58.909 40.909 0.00 0.00 38.13 3.28
2806 2932 4.667573 ACTCTGACCTCTCTGTGTATGAA 58.332 43.478 0.00 0.00 0.00 2.57
2850 2976 7.849804 AGATTGTATTGCTCGTAATCTTGTT 57.150 32.000 0.00 0.00 35.25 2.83
2924 3121 9.480053 AAATTCAGTTACCATTCACATTTGAAG 57.520 29.630 0.23 0.00 45.07 3.02
2928 3125 7.717436 TCAGTTACCATTCACATTTGAAGTGTA 59.283 33.333 0.23 2.01 45.07 2.90
2933 3130 7.596494 ACCATTCACATTTGAAGTGTAATCAG 58.404 34.615 0.23 0.00 45.07 2.90
2969 3166 8.607459 GTCTTCACCATTGACTGAATATAGTTG 58.393 37.037 0.00 0.00 0.00 3.16
2990 3188 5.529581 TGACCCAAAAGAATTCTTGGAAC 57.470 39.130 22.66 16.58 44.16 3.62
3013 3211 7.591421 ACTAAATCTAGCTCTAGTTTCTCCC 57.409 40.000 0.00 0.00 34.84 4.30
3016 3214 6.418057 AATCTAGCTCTAGTTTCTCCCATG 57.582 41.667 0.00 0.00 34.84 3.66
3075 3278 5.580998 TCTGACACTGTTCTCTACCCTTAT 58.419 41.667 0.00 0.00 0.00 1.73
3095 3298 0.866061 CGATTCAGGTCTACGGCGTG 60.866 60.000 24.86 12.87 0.00 5.34
3167 3370 1.049289 ATCAACTACCCCTCCTCGCC 61.049 60.000 0.00 0.00 0.00 5.54
3173 3376 2.020100 TACCCCTCCTCGCCTATGCT 62.020 60.000 0.00 0.00 34.43 3.79
3185 3388 0.695803 CCTATGCTGGGAGGGTCCTT 60.696 60.000 0.00 0.00 36.57 3.36
3218 3421 1.450312 CATCCTGGCCGTGAAGTCC 60.450 63.158 0.00 0.00 0.00 3.85
3221 3424 2.743718 CTGGCCGTGAAGTCCTGT 59.256 61.111 0.00 0.00 0.00 4.00
3296 3499 0.869068 CGATCGTCTCGTCCTGCTAT 59.131 55.000 7.03 0.00 42.56 2.97
3378 3581 4.301027 CCGGCGGATACCTCCAGC 62.301 72.222 24.41 0.00 42.19 4.85
3381 3584 4.971125 GCGGATACCTCCAGCGGC 62.971 72.222 0.00 0.00 42.19 6.53
3383 3586 2.737830 GGATACCTCCAGCGGCTC 59.262 66.667 0.00 0.00 41.64 4.70
3413 3616 2.088104 TCCCTCAGAAGGCGTATGAT 57.912 50.000 0.00 0.00 41.85 2.45
3416 3619 2.628178 CCCTCAGAAGGCGTATGATGTA 59.372 50.000 0.00 0.00 41.85 2.29
3422 3625 3.068307 AGAAGGCGTATGATGTAGACACC 59.932 47.826 0.00 0.00 0.00 4.16
3429 3632 1.190643 TGATGTAGACACCGGCATCA 58.809 50.000 14.01 14.01 43.44 3.07
3722 3931 4.042398 CGAGGAAAGTATACACGTGATGG 58.958 47.826 25.01 0.00 0.00 3.51
3733 3942 2.126467 CACGTGATGGCCTTGTTTTTG 58.874 47.619 10.90 0.00 0.00 2.44
3734 3943 1.754226 ACGTGATGGCCTTGTTTTTGT 59.246 42.857 3.32 0.00 0.00 2.83
3735 3944 2.126467 CGTGATGGCCTTGTTTTTGTG 58.874 47.619 3.32 0.00 0.00 3.33
3736 3945 2.481104 CGTGATGGCCTTGTTTTTGTGT 60.481 45.455 3.32 0.00 0.00 3.72
3737 3946 2.865551 GTGATGGCCTTGTTTTTGTGTG 59.134 45.455 3.32 0.00 0.00 3.82
3738 3947 2.762887 TGATGGCCTTGTTTTTGTGTGA 59.237 40.909 3.32 0.00 0.00 3.58
3852 4063 3.206150 TGCTTCCTTATCGCCTTTCATC 58.794 45.455 0.00 0.00 0.00 2.92
3853 4064 3.206150 GCTTCCTTATCGCCTTTCATCA 58.794 45.455 0.00 0.00 0.00 3.07
3854 4065 3.817647 GCTTCCTTATCGCCTTTCATCAT 59.182 43.478 0.00 0.00 0.00 2.45
3855 4066 4.083590 GCTTCCTTATCGCCTTTCATCATC 60.084 45.833 0.00 0.00 0.00 2.92
3859 4070 2.267174 ATCGCCTTTCATCATCCCTG 57.733 50.000 0.00 0.00 0.00 4.45
3887 4098 0.774908 TGGGTTTGTTAGTCCCTGGG 59.225 55.000 6.33 6.33 41.58 4.45
3888 4099 0.039180 GGGTTTGTTAGTCCCTGGGG 59.961 60.000 14.00 2.42 38.29 4.96
3890 4101 1.546998 GGTTTGTTAGTCCCTGGGGTG 60.547 57.143 14.00 0.00 36.47 4.61
3997 4216 5.300034 ACACATGTATGCAAGGATGTAATGG 59.700 40.000 0.00 0.39 0.00 3.16
3998 4217 5.532032 CACATGTATGCAAGGATGTAATGGA 59.468 40.000 0.00 0.00 0.00 3.41
4001 4220 7.391554 ACATGTATGCAAGGATGTAATGGATAC 59.608 37.037 0.00 8.97 44.06 2.24
4009 4228 4.404394 AGGATGTAATGGATACGTGTGACA 59.596 41.667 0.00 0.00 37.32 3.58
4023 4247 5.305585 ACGTGTGACAAAGGATGAAATACT 58.694 37.500 0.00 0.00 41.45 2.12
4148 4379 9.133627 CATTATGTATCTAGGTATATGCGCATC 57.866 37.037 29.11 12.98 0.00 3.91
4213 4444 2.148446 TCAAATGAAGGCCTCCATGG 57.852 50.000 4.72 4.97 39.35 3.66
4238 4469 0.313987 GGTCTCCGTTTGGCCTTTTG 59.686 55.000 3.32 0.00 34.14 2.44
4262 4493 5.120674 GGCTGTATTTTGGATCAAACTTTGC 59.879 40.000 0.00 0.00 32.79 3.68
4276 4507 7.581213 TCAAACTTTGCCCATAGGTTATATG 57.419 36.000 0.00 0.00 34.57 1.78
4281 4512 2.713708 TGCCCATAGGTTATATGCCACA 59.286 45.455 1.77 0.00 34.57 4.17
4291 4522 5.483583 AGGTTATATGCCACAAAAACCATGT 59.516 36.000 4.99 0.00 39.05 3.21
4298 4529 3.866651 CCACAAAAACCATGTTGTTGGA 58.133 40.909 12.97 0.00 39.25 3.53
4408 4653 8.988064 TGATCAAAGATACAAGTGAGACTTAC 57.012 34.615 0.00 0.00 36.03 2.34
4415 4660 4.772886 ACAAGTGAGACTTACAAACCCT 57.227 40.909 0.00 0.00 36.03 4.34
4417 4662 6.243216 ACAAGTGAGACTTACAAACCCTAA 57.757 37.500 0.00 0.00 36.03 2.69
4418 4663 6.053650 ACAAGTGAGACTTACAAACCCTAAC 58.946 40.000 0.00 0.00 36.03 2.34
4420 4665 3.992427 GTGAGACTTACAAACCCTAACGG 59.008 47.826 0.00 0.00 37.81 4.44
4421 4666 3.896888 TGAGACTTACAAACCCTAACGGA 59.103 43.478 0.00 0.00 34.64 4.69
4422 4667 4.021719 TGAGACTTACAAACCCTAACGGAG 60.022 45.833 0.00 0.00 34.64 4.63
4423 4668 3.260128 AGACTTACAAACCCTAACGGAGG 59.740 47.826 0.00 0.00 46.25 4.30
4435 4680 4.367386 CTAACGGAGGAAGTATGTCGTT 57.633 45.455 0.00 0.00 42.28 3.85
4436 4681 5.490139 CTAACGGAGGAAGTATGTCGTTA 57.510 43.478 0.00 0.00 40.51 3.18
4437 4682 3.772060 ACGGAGGAAGTATGTCGTTAC 57.228 47.619 0.00 0.00 0.00 2.50
4438 4683 3.350833 ACGGAGGAAGTATGTCGTTACT 58.649 45.455 0.00 0.00 33.85 2.24
4439 4684 3.128242 ACGGAGGAAGTATGTCGTTACTG 59.872 47.826 0.00 0.00 32.78 2.74
4440 4685 3.128242 CGGAGGAAGTATGTCGTTACTGT 59.872 47.826 0.00 0.00 32.78 3.55
4441 4686 4.380233 CGGAGGAAGTATGTCGTTACTGTT 60.380 45.833 0.00 0.00 32.78 3.16
4442 4687 5.163723 CGGAGGAAGTATGTCGTTACTGTTA 60.164 44.000 0.00 0.00 32.78 2.41
4443 4688 6.459298 CGGAGGAAGTATGTCGTTACTGTTAT 60.459 42.308 0.00 0.00 32.78 1.89
4444 4689 7.263496 GGAGGAAGTATGTCGTTACTGTTATT 58.737 38.462 0.00 0.00 32.78 1.40
4445 4690 8.408601 GGAGGAAGTATGTCGTTACTGTTATTA 58.591 37.037 0.00 0.00 32.78 0.98
4446 4691 9.962783 GAGGAAGTATGTCGTTACTGTTATTAT 57.037 33.333 0.00 0.00 32.78 1.28
4447 4692 9.962783 AGGAAGTATGTCGTTACTGTTATTATC 57.037 33.333 0.00 0.00 32.78 1.75
4448 4693 9.962783 GGAAGTATGTCGTTACTGTTATTATCT 57.037 33.333 0.00 0.00 32.78 1.98
4483 4728 2.631427 GCGGATAGCGGAGTCTAGT 58.369 57.895 0.00 0.00 35.41 2.57
4484 4729 0.953003 GCGGATAGCGGAGTCTAGTT 59.047 55.000 0.00 0.00 35.41 2.24
4521 4766 7.255346 GCTGATGATGAAATATGAATGTGTGGA 60.255 37.037 0.00 0.00 0.00 4.02
4529 4774 8.245491 TGAAATATGAATGTGTGGATTGACTTG 58.755 33.333 0.00 0.00 0.00 3.16
4554 4799 3.554934 ACATTGACTGTGAACCATGTGT 58.445 40.909 0.00 0.00 36.48 3.72
4567 4816 0.514255 CATGTGTGACTGCCGTTGAG 59.486 55.000 0.00 0.00 0.00 3.02
4591 4840 1.363807 GTGCTTGCCAAGTGGAACC 59.636 57.895 6.28 0.00 37.80 3.62
4594 4843 1.662044 CTTGCCAAGTGGAACCTGC 59.338 57.895 0.18 0.00 37.80 4.85
4630 4901 4.778143 GCGGCCGTGGGTGAGATT 62.778 66.667 28.70 0.00 0.00 2.40
4694 5953 1.291877 CGTTGGGAGTGGAAAGCGAG 61.292 60.000 0.00 0.00 0.00 5.03
4733 5992 1.286880 GACATGCCTGCACAACCAC 59.713 57.895 0.00 0.00 0.00 4.16
4737 5996 4.332637 GCCTGCACAACCACAGCG 62.333 66.667 0.00 0.00 32.37 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.755103 GAGGAACCCTAAACATTGCAGG 59.245 50.000 0.00 0.00 31.76 4.85
1 2 2.420022 CGAGGAACCCTAAACATTGCAG 59.580 50.000 0.00 0.00 31.76 4.41
2 3 2.432444 CGAGGAACCCTAAACATTGCA 58.568 47.619 0.00 0.00 31.76 4.08
3 4 1.743394 CCGAGGAACCCTAAACATTGC 59.257 52.381 0.00 0.00 31.76 3.56
4 5 3.007635 GACCGAGGAACCCTAAACATTG 58.992 50.000 0.00 0.00 31.76 2.82
5 6 2.910977 AGACCGAGGAACCCTAAACATT 59.089 45.455 0.00 0.00 31.76 2.71
6 7 2.500504 GAGACCGAGGAACCCTAAACAT 59.499 50.000 0.00 0.00 31.76 2.71
7 8 1.897802 GAGACCGAGGAACCCTAAACA 59.102 52.381 0.00 0.00 31.76 2.83
8 9 1.206610 GGAGACCGAGGAACCCTAAAC 59.793 57.143 0.00 0.00 31.76 2.01
9 10 1.565067 GGAGACCGAGGAACCCTAAA 58.435 55.000 0.00 0.00 31.76 1.85
10 11 0.325016 GGGAGACCGAGGAACCCTAA 60.325 60.000 12.67 0.00 43.64 2.69
11 12 1.309006 GGGAGACCGAGGAACCCTA 59.691 63.158 12.67 0.00 43.64 3.53
12 13 2.039137 GGGAGACCGAGGAACCCT 59.961 66.667 12.67 0.00 43.64 4.34
34 35 1.227263 CAACAGATACGAGGCGGGG 60.227 63.158 0.00 0.00 0.00 5.73
35 36 1.227263 CCAACAGATACGAGGCGGG 60.227 63.158 0.00 0.00 0.00 6.13
45 46 3.776969 TCATGACTCTAAGGCCAACAGAT 59.223 43.478 5.01 0.00 0.00 2.90
48 49 2.353704 CGTCATGACTCTAAGGCCAACA 60.354 50.000 22.95 0.00 0.00 3.33
50 51 1.207089 CCGTCATGACTCTAAGGCCAA 59.793 52.381 22.95 0.00 0.00 4.52
60 61 2.048222 CACCGTGCCGTCATGACT 60.048 61.111 22.95 0.00 0.00 3.41
62 63 2.572095 GATCCACCGTGCCGTCATGA 62.572 60.000 0.00 0.00 0.00 3.07
67 68 4.082523 CAGGATCCACCGTGCCGT 62.083 66.667 15.82 0.00 44.74 5.68
72 73 0.036010 CAAAGAGCAGGATCCACCGT 60.036 55.000 15.82 0.00 44.74 4.83
85 86 2.045926 CCTCCCACCGGCAAAGAG 60.046 66.667 0.00 2.52 0.00 2.85
86 87 3.646715 CCCTCCCACCGGCAAAGA 61.647 66.667 0.00 0.00 0.00 2.52
106 107 7.184067 AGACTCGAAGGAGGTATAAAAACAT 57.816 36.000 0.00 0.00 44.93 2.71
107 108 6.600882 AGACTCGAAGGAGGTATAAAAACA 57.399 37.500 0.00 0.00 44.93 2.83
117 118 2.417719 CCAAACAAGACTCGAAGGAGG 58.582 52.381 0.00 0.00 44.93 4.30
120 121 2.256117 ACCCAAACAAGACTCGAAGG 57.744 50.000 0.00 0.00 0.00 3.46
129 131 5.124776 TGAGTAGAACACAAACCCAAACAAG 59.875 40.000 0.00 0.00 0.00 3.16
135 141 4.764050 TTCTGAGTAGAACACAAACCCA 57.236 40.909 0.00 0.00 37.99 4.51
146 152 3.082548 CCACCTCGTCTTTCTGAGTAGA 58.917 50.000 0.00 0.00 0.00 2.59
173 180 3.459598 CACCCTTATCCATCTTCAGGGAA 59.540 47.826 9.61 0.00 46.61 3.97
215 224 2.443416 ACGATGCTAGACACACTACCA 58.557 47.619 0.00 0.00 0.00 3.25
219 228 1.618837 ACCAACGATGCTAGACACACT 59.381 47.619 0.00 0.00 0.00 3.55
251 260 3.305403 CGAGCAAACTCACTAAGGACAGA 60.305 47.826 0.00 0.00 43.66 3.41
252 261 2.989840 CGAGCAAACTCACTAAGGACAG 59.010 50.000 0.00 0.00 43.66 3.51
260 286 1.066573 CCAGATCCGAGCAAACTCACT 60.067 52.381 0.00 0.00 43.66 3.41
264 290 3.914426 ATAACCAGATCCGAGCAAACT 57.086 42.857 0.00 0.00 0.00 2.66
265 291 4.694339 AGTATAACCAGATCCGAGCAAAC 58.306 43.478 0.00 0.00 0.00 2.93
286 312 5.005012 TGAAGAAACACAAACGTAGACGAAG 59.995 40.000 9.41 0.72 43.02 3.79
335 363 2.146342 CAATCGCCACTTGTGAAGAGT 58.854 47.619 1.89 0.00 36.97 3.24
338 366 3.389741 GCAATCGCCACTTGTGAAG 57.610 52.632 1.89 0.00 36.97 3.02
357 385 0.957395 AGGACCAATGCAGCAGAACG 60.957 55.000 0.00 0.00 0.00 3.95
384 413 1.002576 TCGTGAAGTCGTCGTGCTAAA 60.003 47.619 0.00 0.00 0.00 1.85
401 430 8.139989 ACAAAACTTGTTGTAGTAGATAGTCGT 58.860 33.333 0.00 0.00 42.22 4.34
407 436 6.423001 GTCGGACAAAACTTGTTGTAGTAGAT 59.577 38.462 2.62 0.00 45.52 1.98
434 463 3.976490 ATTGACCCTCCCTCGCCGA 62.976 63.158 0.00 0.00 0.00 5.54
475 504 2.604855 CGACGACTACAAGCACTGAAGT 60.605 50.000 0.00 0.00 0.00 3.01
505 534 9.847224 AATAAAAATTACATCCAGATCCGTAGT 57.153 29.630 0.00 0.00 0.00 2.73
541 570 8.835467 TTTCAATCAAAAAGAGTACAACGAAG 57.165 30.769 0.00 0.00 0.00 3.79
632 664 5.828328 TGGTTCTTCTTCTTCTTTCCTTTCC 59.172 40.000 0.00 0.00 0.00 3.13
637 669 7.333174 CAGAGTATGGTTCTTCTTCTTCTTTCC 59.667 40.741 0.00 0.00 0.00 3.13
654 686 0.313672 GAGAGCGAGGCAGAGTATGG 59.686 60.000 0.00 0.00 0.00 2.74
702 734 6.928520 ACTTTAAATCCTGGCTCTTGATTTG 58.071 36.000 6.90 0.00 38.70 2.32
714 746 2.238898 ACTCCCGGGACTTTAAATCCTG 59.761 50.000 22.63 7.86 41.66 3.86
725 757 1.273759 AGGTTCTAAACTCCCGGGAC 58.726 55.000 22.63 7.75 0.00 4.46
760 792 2.370849 GGCTATTTAATCCCGGGAGTCA 59.629 50.000 29.80 15.05 0.00 3.41
945 989 4.787280 AGGAGCGGTGGAGGGGAG 62.787 72.222 0.00 0.00 0.00 4.30
946 990 4.779733 GAGGAGCGGTGGAGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
1037 1088 2.494918 CGAGATCCCCACGACCAC 59.505 66.667 0.00 0.00 0.00 4.16
1038 1089 3.458163 GCGAGATCCCCACGACCA 61.458 66.667 0.00 0.00 0.00 4.02
1039 1090 4.570663 CGCGAGATCCCCACGACC 62.571 72.222 0.00 0.00 0.00 4.79
1338 1404 0.673956 GGAGAGAACCTTCCGTTGGC 60.674 60.000 0.00 0.00 33.74 4.52
1355 1421 0.112412 GTGGCCTTTCCTCCTTTGGA 59.888 55.000 3.32 0.00 35.26 3.53
1402 1476 1.258982 CCAGATTGCGCAACGAGATAC 59.741 52.381 27.64 10.63 0.00 2.24
1408 1482 0.304705 GGTATCCAGATTGCGCAACG 59.695 55.000 27.64 16.61 0.00 4.10
1413 1487 3.074412 GGGTAATGGTATCCAGATTGCG 58.926 50.000 0.00 0.00 36.75 4.85
1546 1645 9.988350 GATGTTTTTGTACAAGACGATGATAAT 57.012 29.630 8.56 0.71 0.00 1.28
1547 1646 8.166066 CGATGTTTTTGTACAAGACGATGATAA 58.834 33.333 8.56 0.00 0.00 1.75
1548 1647 7.542824 TCGATGTTTTTGTACAAGACGATGATA 59.457 33.333 8.56 0.00 32.18 2.15
1589 1692 6.598850 AGGCCAGGTTTAAAATAAAATGCATG 59.401 34.615 5.01 0.00 0.00 4.06
1732 1840 4.500887 CGTGTAGAAAGGGACAGAGACAAA 60.501 45.833 0.00 0.00 0.00 2.83
1816 1924 5.615289 AGCAGAATAAGAGGCGATTAATGT 58.385 37.500 0.00 0.00 0.00 2.71
1821 1929 4.125703 CAGAAGCAGAATAAGAGGCGATT 58.874 43.478 0.00 0.00 0.00 3.34
1834 1942 4.020751 ACAGCTCAGAATTACAGAAGCAGA 60.021 41.667 0.00 0.00 0.00 4.26
1849 1957 2.096069 CACATCCACGAAAACAGCTCAG 60.096 50.000 0.00 0.00 0.00 3.35
1860 1968 1.816835 GTCCACTCTACACATCCACGA 59.183 52.381 0.00 0.00 0.00 4.35
1864 1972 2.743183 GCCATGTCCACTCTACACATCC 60.743 54.545 0.00 0.00 0.00 3.51
1868 1976 2.350522 CTTGCCATGTCCACTCTACAC 58.649 52.381 0.00 0.00 0.00 2.90
1933 2042 2.193536 AACCTTGACAGCGTTGCCC 61.194 57.895 0.00 0.00 0.00 5.36
1952 2061 4.380867 CCCATTTTTGTGTGAGTAGATGGC 60.381 45.833 0.00 0.00 33.22 4.40
2026 2135 7.882179 ACACTAAATCCTACAACCACAAATTC 58.118 34.615 0.00 0.00 0.00 2.17
2036 2145 4.777896 AGGAGCTGACACTAAATCCTACAA 59.222 41.667 0.00 0.00 35.43 2.41
2086 2195 2.425312 CTCATCTTCGGTAGCTGTGACT 59.575 50.000 0.00 0.00 0.00 3.41
2177 2286 6.042143 GCAACTCTTTGATTGAAACAGGAAA 58.958 36.000 0.00 0.00 34.24 3.13
2188 2297 8.253113 CCCAATAAATACAGCAACTCTTTGATT 58.747 33.333 0.00 0.00 34.24 2.57
2189 2298 7.397192 ACCCAATAAATACAGCAACTCTTTGAT 59.603 33.333 0.00 0.00 34.24 2.57
2228 2346 5.988310 ATCTGCATTTTTCCATGTCAGAA 57.012 34.783 10.02 0.00 39.06 3.02
2229 2347 5.945191 TGTATCTGCATTTTTCCATGTCAGA 59.055 36.000 0.00 8.98 39.49 3.27
2234 2352 7.975058 TGTAACATGTATCTGCATTTTTCCATG 59.025 33.333 0.00 0.00 35.69 3.66
2235 2353 8.065473 TGTAACATGTATCTGCATTTTTCCAT 57.935 30.769 0.00 0.00 0.00 3.41
2296 2414 0.673644 AGAAAGACCCGTGGCAATCG 60.674 55.000 0.00 0.00 0.00 3.34
2345 2463 7.593825 CGGAGAAATAAAAGAACTCACCAATT 58.406 34.615 0.00 0.00 0.00 2.32
2357 2475 5.049405 AGACAGTTGTGCGGAGAAATAAAAG 60.049 40.000 0.00 0.00 0.00 2.27
2428 2553 3.094572 GCCCAAGTATACCCTCGCTATA 58.905 50.000 0.00 0.00 0.00 1.31
2467 2592 2.802787 AAGAGATCCCAGCGATAACG 57.197 50.000 0.00 0.00 42.93 3.18
2551 2676 1.468985 TGGACATACCATTTTGGCCG 58.531 50.000 0.00 0.00 44.59 6.13
2578 2703 7.027760 TCGCTACTAGAGTCAAAGTAATGTTG 58.972 38.462 0.00 0.00 0.00 3.33
2621 2746 7.108847 ACTATGAGAATGTTCTTCTCCTTTGG 58.891 38.462 11.36 3.30 43.14 3.28
2628 2753 9.566432 AGAAAACAACTATGAGAATGTTCTTCT 57.434 29.630 0.00 0.00 37.73 2.85
2635 2761 7.587629 TGCAGAAGAAAACAACTATGAGAATG 58.412 34.615 0.00 0.00 0.00 2.67
2663 2789 0.529378 GGCTTGCCCAGAAGAATGTG 59.471 55.000 0.00 0.00 0.00 3.21
2713 2839 1.376649 AGGAGTTGGGAATTCTGGCT 58.623 50.000 5.23 0.00 0.00 4.75
2806 2932 9.479549 ACAATCTTTGGATCAAGTAACCATATT 57.520 29.630 0.00 0.00 33.56 1.28
2850 2976 4.265904 TCCGTGTGAGCAGAATTCTAAA 57.734 40.909 7.86 0.00 0.00 1.85
2924 3121 7.221838 GTGAAGACTATTCTCTGCTGATTACAC 59.778 40.741 0.00 0.00 0.00 2.90
2928 3125 5.188555 TGGTGAAGACTATTCTCTGCTGATT 59.811 40.000 0.00 0.00 0.00 2.57
2933 3130 5.293079 GTCAATGGTGAAGACTATTCTCTGC 59.707 44.000 0.00 0.00 34.87 4.26
2969 3166 5.791336 AGTTCCAAGAATTCTTTTGGGTC 57.209 39.130 21.06 15.32 43.22 4.46
2990 3188 7.589958 TGGGAGAAACTAGAGCTAGATTTAG 57.410 40.000 11.28 4.13 36.97 1.85
3013 3211 5.885230 TTATCAACAACTGGAAGAGCATG 57.115 39.130 0.00 0.00 37.43 4.06
3016 3214 6.500684 TGATTTATCAACAACTGGAAGAGC 57.499 37.500 0.00 0.00 33.34 4.09
3075 3278 1.028330 ACGCCGTAGACCTGAATCGA 61.028 55.000 0.00 0.00 0.00 3.59
3095 3298 2.809601 CGGGTGTACGTCTGCTGC 60.810 66.667 0.00 0.00 0.00 5.25
3167 3370 0.471617 CAAGGACCCTCCCAGCATAG 59.528 60.000 0.00 0.00 37.19 2.23
3173 3376 2.531685 CCCACAAGGACCCTCCCA 60.532 66.667 0.00 0.00 37.19 4.37
3185 3388 2.042095 ATGGTCGGGATCCCCACA 59.958 61.111 27.45 21.70 45.83 4.17
3335 3538 2.032681 GCCTCGTCCTTGTTGCCT 59.967 61.111 0.00 0.00 0.00 4.75
3368 3571 0.397816 AGAAGAGCCGCTGGAGGTAT 60.398 55.000 0.00 0.00 0.00 2.73
3378 3581 1.681486 GGGAAGAGGGAGAAGAGCCG 61.681 65.000 0.00 0.00 0.00 5.52
3381 3584 2.024464 TCTGAGGGAAGAGGGAGAAGAG 60.024 54.545 0.00 0.00 0.00 2.85
3383 3586 2.541233 TCTGAGGGAAGAGGGAGAAG 57.459 55.000 0.00 0.00 0.00 2.85
3410 3613 1.136891 CTGATGCCGGTGTCTACATCA 59.863 52.381 16.24 16.24 44.86 3.07
3413 3616 0.902984 ACCTGATGCCGGTGTCTACA 60.903 55.000 1.90 0.00 32.41 2.74
3416 3619 1.296715 GAACCTGATGCCGGTGTCT 59.703 57.895 1.90 0.00 34.33 3.41
3422 3625 2.741985 TGCACGAACCTGATGCCG 60.742 61.111 0.00 0.00 38.63 5.69
3722 3931 4.211794 CCATCAATCACACAAAAACAAGGC 59.788 41.667 0.00 0.00 0.00 4.35
3733 3942 2.440409 AGCTGTTCCCATCAATCACAC 58.560 47.619 0.00 0.00 0.00 3.82
3734 3943 2.885135 AGCTGTTCCCATCAATCACA 57.115 45.000 0.00 0.00 0.00 3.58
3735 3944 3.624861 CAGTAGCTGTTCCCATCAATCAC 59.375 47.826 0.00 0.00 0.00 3.06
3736 3945 3.519107 TCAGTAGCTGTTCCCATCAATCA 59.481 43.478 0.00 0.00 32.61 2.57
3737 3946 3.873952 GTCAGTAGCTGTTCCCATCAATC 59.126 47.826 0.00 0.00 32.61 2.67
3738 3947 3.521126 AGTCAGTAGCTGTTCCCATCAAT 59.479 43.478 0.00 0.00 32.61 2.57
3852 4063 1.988107 ACCCAGCCATATACAGGGATG 59.012 52.381 11.19 0.97 41.64 3.51
3853 4064 2.440494 ACCCAGCCATATACAGGGAT 57.560 50.000 11.19 0.00 42.25 3.85
3854 4065 2.174639 CAAACCCAGCCATATACAGGGA 59.825 50.000 11.19 0.00 42.25 4.20
3855 4066 2.091885 ACAAACCCAGCCATATACAGGG 60.092 50.000 0.00 0.00 45.20 4.45
3859 4070 4.820173 GGACTAACAAACCCAGCCATATAC 59.180 45.833 0.00 0.00 0.00 1.47
3887 4098 1.545841 GGTCTCCAAAATGACCCACC 58.454 55.000 0.00 0.00 45.03 4.61
3997 4216 5.856126 TTTCATCCTTTGTCACACGTATC 57.144 39.130 0.00 0.00 0.00 2.24
3998 4217 7.103641 AGTATTTCATCCTTTGTCACACGTAT 58.896 34.615 0.00 0.00 0.00 3.06
4001 4220 5.862924 AGTATTTCATCCTTTGTCACACG 57.137 39.130 0.00 0.00 0.00 4.49
4009 4228 7.601856 TCGCAATTCAAAGTATTTCATCCTTT 58.398 30.769 0.00 0.00 35.03 3.11
4050 4274 4.091549 ACACAAAAAGATGAGGCCATGAT 58.908 39.130 5.01 0.00 32.09 2.45
4063 4287 7.855904 ACGTTAAAATGAGAGCTACACAAAAAG 59.144 33.333 0.00 0.00 0.00 2.27
4195 4426 2.029623 CTCCATGGAGGCCTTCATTTG 58.970 52.381 31.14 17.86 38.51 2.32
4200 4431 1.148048 GAGCTCCATGGAGGCCTTC 59.852 63.158 36.92 22.63 42.19 3.46
4233 4464 6.930722 AGTTTGATCCAAAATACAGCCAAAAG 59.069 34.615 0.00 0.00 35.03 2.27
4238 4469 5.120674 GCAAAGTTTGATCCAAAATACAGCC 59.879 40.000 19.82 0.00 35.03 4.85
4262 4493 6.462347 GGTTTTTGTGGCATATAACCTATGGG 60.462 42.308 16.40 0.00 33.84 4.00
4276 4507 2.354199 CCAACAACATGGTTTTTGTGGC 59.646 45.455 0.00 0.00 36.08 5.01
4311 4542 9.550406 CACGGGGAACTTGTTTAGAATAATATA 57.450 33.333 0.00 0.00 0.00 0.86
4312 4543 7.501225 CCACGGGGAACTTGTTTAGAATAATAT 59.499 37.037 0.00 0.00 35.59 1.28
4325 4556 2.535588 CGTTACCACGGGGAACTTG 58.464 57.895 12.96 0.00 43.16 3.16
4382 4616 9.593134 GTAAGTCTCACTTGTATCTTTGATCAT 57.407 33.333 0.00 0.00 39.11 2.45
4391 4625 6.465084 AGGGTTTGTAAGTCTCACTTGTATC 58.535 40.000 0.00 0.00 39.11 2.24
4393 4638 5.881923 AGGGTTTGTAAGTCTCACTTGTA 57.118 39.130 0.00 0.00 39.11 2.41
4395 4640 5.176958 CGTTAGGGTTTGTAAGTCTCACTTG 59.823 44.000 0.00 0.00 39.11 3.16
4398 4643 3.992427 CCGTTAGGGTTTGTAAGTCTCAC 59.008 47.826 0.00 0.00 0.00 3.51
4399 4644 3.896888 TCCGTTAGGGTTTGTAAGTCTCA 59.103 43.478 0.00 0.00 38.33 3.27
4403 4648 3.242011 TCCTCCGTTAGGGTTTGTAAGT 58.758 45.455 1.53 0.00 46.55 2.24
4408 4653 2.853235 ACTTCCTCCGTTAGGGTTTG 57.147 50.000 1.53 0.00 46.55 2.93
4415 4660 4.943705 AGTAACGACATACTTCCTCCGTTA 59.056 41.667 0.00 0.00 40.16 3.18
4417 4662 3.128242 CAGTAACGACATACTTCCTCCGT 59.872 47.826 0.00 0.00 33.90 4.69
4418 4663 3.128242 ACAGTAACGACATACTTCCTCCG 59.872 47.826 0.00 0.00 33.90 4.63
4420 4665 9.962783 ATAATAACAGTAACGACATACTTCCTC 57.037 33.333 0.00 0.00 33.90 3.71
4421 4666 9.962783 GATAATAACAGTAACGACATACTTCCT 57.037 33.333 0.00 0.00 33.90 3.36
4422 4667 9.962783 AGATAATAACAGTAACGACATACTTCC 57.037 33.333 0.00 0.00 33.90 3.46
4456 4701 3.069729 ACTCCGCTATCCGCTATCTTTTT 59.930 43.478 0.00 0.00 36.13 1.94
4457 4702 2.628657 ACTCCGCTATCCGCTATCTTTT 59.371 45.455 0.00 0.00 36.13 2.27
4458 4703 2.229302 GACTCCGCTATCCGCTATCTTT 59.771 50.000 0.00 0.00 36.13 2.52
4459 4704 1.813786 GACTCCGCTATCCGCTATCTT 59.186 52.381 0.00 0.00 36.13 2.40
4460 4705 1.003812 AGACTCCGCTATCCGCTATCT 59.996 52.381 0.00 0.00 36.13 1.98
4461 4706 1.455248 AGACTCCGCTATCCGCTATC 58.545 55.000 0.00 0.00 36.13 2.08
4462 4707 2.027007 ACTAGACTCCGCTATCCGCTAT 60.027 50.000 0.00 0.00 36.13 2.97
4463 4708 1.347050 ACTAGACTCCGCTATCCGCTA 59.653 52.381 0.00 0.00 36.13 4.26
4464 4709 0.108963 ACTAGACTCCGCTATCCGCT 59.891 55.000 0.00 0.00 36.13 5.52
4465 4710 0.953003 AACTAGACTCCGCTATCCGC 59.047 55.000 0.00 0.00 35.03 5.54
4466 4711 3.712091 AAAACTAGACTCCGCTATCCG 57.288 47.619 0.00 0.00 0.00 4.18
4495 4740 6.861572 CCACACATTCATATTTCATCATCAGC 59.138 38.462 0.00 0.00 0.00 4.26
4496 4741 8.161699 TCCACACATTCATATTTCATCATCAG 57.838 34.615 0.00 0.00 0.00 2.90
4509 4754 4.157289 GCTCAAGTCAATCCACACATTCAT 59.843 41.667 0.00 0.00 0.00 2.57
4521 4766 4.139786 ACAGTCAATGTGCTCAAGTCAAT 58.860 39.130 0.00 0.00 41.91 2.57
4547 4792 0.884259 TCAACGGCAGTCACACATGG 60.884 55.000 0.00 0.00 0.00 3.66
4551 4796 0.861837 CTTCTCAACGGCAGTCACAC 59.138 55.000 0.00 0.00 0.00 3.82
4552 4797 0.464036 ACTTCTCAACGGCAGTCACA 59.536 50.000 0.00 0.00 0.00 3.58
4553 4798 1.140816 GACTTCTCAACGGCAGTCAC 58.859 55.000 0.00 0.00 36.46 3.67
4554 4799 0.318699 CGACTTCTCAACGGCAGTCA 60.319 55.000 0.00 0.00 36.25 3.41
4567 4816 0.040958 CACTTGGCAAGCACGACTTC 60.041 55.000 26.45 0.00 36.04 3.01
4591 4840 2.021584 TGCGTACGAGCACAAGCAG 61.022 57.895 21.65 0.00 45.49 4.24
4618 4889 2.483714 CCCTGACATAATCTCACCCACG 60.484 54.545 0.00 0.00 0.00 4.94
4626 4897 4.286813 TTCTCCCTCCCTGACATAATCT 57.713 45.455 0.00 0.00 0.00 2.40
4630 4901 3.199442 TGTTTCTCCCTCCCTGACATA 57.801 47.619 0.00 0.00 0.00 2.29
4675 4947 1.291877 CTCGCTTTCCACTCCCAACG 61.292 60.000 0.00 0.00 0.00 4.10
4694 5953 1.153469 CAGCTTCTTCCTCCCTCGC 60.153 63.158 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.