Multiple sequence alignment - TraesCS5A01G425300

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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 TraesCS5A01G425300 chr5A 100.000 8144 0 0 1 8144 610482101 610490244 0.000000e+00 15040.0
1 TraesCS5A01G425300 chr5A 83.582 67 11 0 866 932 196838802 196838736 6.820000e-06 63.9
2 TraesCS5A01G425300 chr5B 93.465 2479 115 13 2923 5371 603638646 603641107 0.000000e+00 3637.0
3 TraesCS5A01G425300 chr5B 93.116 2266 106 25 699 2921 603636135 603638393 0.000000e+00 3275.0
4 TraesCS5A01G425300 chr5B 93.856 2067 73 20 5370 7402 603641212 603643258 0.000000e+00 3064.0
5 TraesCS5A01G425300 chr5B 87.403 643 37 14 17 645 603635526 603636138 0.000000e+00 699.0
6 TraesCS5A01G425300 chr5B 82.944 428 38 14 7680 8082 603643549 603643966 3.620000e-93 353.0
7 TraesCS5A01G425300 chr5B 88.372 86 9 1 105 190 603635711 603635795 1.450000e-17 102.0
8 TraesCS5A01G425300 chr5D 97.034 1787 47 3 4232 6017 489354791 489356572 0.000000e+00 3001.0
9 TraesCS5A01G425300 chr5D 91.223 1823 79 42 6059 7861 489356851 489358612 0.000000e+00 2405.0
10 TraesCS5A01G425300 chr5D 93.014 1231 51 15 1662 2870 489351331 489352548 0.000000e+00 1764.0
11 TraesCS5A01G425300 chr5D 97.400 846 15 2 2867 3710 489353309 489354149 0.000000e+00 1434.0
12 TraesCS5A01G425300 chr5D 95.531 895 31 7 695 1586 489350235 489351123 0.000000e+00 1423.0
13 TraesCS5A01G425300 chr5D 95.133 637 23 4 3481 4116 489354164 489354793 0.000000e+00 998.0
14 TraesCS5A01G425300 chr5D 88.113 530 28 17 197 702 489349619 489350137 1.510000e-166 597.0
15 TraesCS5A01G425300 chr5D 92.529 174 13 0 17 190 489349538 489349711 4.880000e-62 250.0
16 TraesCS5A01G425300 chr2B 88.302 265 28 3 17 281 482186478 482186739 1.710000e-81 315.0
17 TraesCS5A01G425300 chr6A 90.588 85 8 0 4144 4228 37441652 37441568 6.680000e-21 113.0
18 TraesCS5A01G425300 chr3A 81.061 132 12 3 4121 4240 353624472 353624602 8.700000e-15 93.5
19 TraesCS5A01G425300 chr3A 80.315 127 13 2 4121 4235 204885521 204885395 1.460000e-12 86.1
20 TraesCS5A01G425300 chr3A 95.556 45 2 0 4190 4234 534991153 534991197 1.130000e-08 73.1
21 TraesCS5A01G425300 chr1B 81.481 108 18 2 866 972 596548627 596548521 4.050000e-13 87.9
22 TraesCS5A01G425300 chr1B 93.878 49 2 1 865 912 412898673 412898721 1.130000e-08 73.1
23 TraesCS5A01G425300 chr1B 90.196 51 3 2 880 929 366567148 366567099 1.900000e-06 65.8
24 TraesCS5A01G425300 chr7D 87.013 77 8 2 4121 4196 126882378 126882303 1.460000e-12 86.1
25 TraesCS5A01G425300 chr7D 93.617 47 3 0 4189 4235 320291043 320291089 4.080000e-08 71.3
26 TraesCS5A01G425300 chr1A 87.879 66 8 0 867 932 268242697 268242632 2.440000e-10 78.7
27 TraesCS5A01G425300 chr7A 95.455 44 2 0 4190 4233 170908116 170908073 4.080000e-08 71.3
28 TraesCS5A01G425300 chr4B 81.132 106 4 4 4144 4235 66626315 66626212 4.080000e-08 71.3
29 TraesCS5A01G425300 chr4B 86.364 66 7 2 867 931 661676207 661676143 4.080000e-08 71.3
30 TraesCS5A01G425300 chr2A 80.556 108 5 4 4141 4234 459084817 459084922 1.470000e-07 69.4
31 TraesCS5A01G425300 chr2A 90.000 50 5 0 880 929 750084641 750084592 1.900000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G425300 chr5A 610482101 610490244 8143 False 15040 15040 100.000000 1 8144 1 chr5A.!!$F1 8143
1 TraesCS5A01G425300 chr5B 603635526 603643966 8440 False 1855 3637 89.859333 17 8082 6 chr5B.!!$F1 8065
2 TraesCS5A01G425300 chr5D 489349538 489358612 9074 False 1484 3001 93.747125 17 7861 8 chr5D.!!$F1 7844

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
847 985 0.038310 GGGGCTTCTAGCACTGGTTT 59.962 55.000 0.45 0.00 45.92 3.27 F
1613 1751 0.836606 TGGTGATCAGGTGTGTGTGT 59.163 50.000 0.00 0.00 0.00 3.72 F
1727 1997 0.528924 TGTTGCCAGCGTACGTATCT 59.471 50.000 17.90 2.27 0.00 1.98 F
2637 2935 1.352352 AGGTAGCTTGCAACTGATGGT 59.648 47.619 0.00 0.00 0.00 3.55 F
3503 4827 1.559682 ACAGCTGGGTACTTGTATGGG 59.440 52.381 19.93 0.00 0.00 4.00 F
3982 5547 0.768221 TGGAGCTCCATGGGGTATCC 60.768 60.000 32.00 24.12 42.01 2.59 F
5477 7162 1.001378 CAGGCAAGGACAAAACTTCCG 60.001 52.381 0.00 0.00 38.29 4.30 F
6036 7723 1.062962 CAGGTTGGATTATTGCCCCCT 60.063 52.381 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1977 0.643820 GATACGTACGCTGGCAACAC 59.356 55.000 16.72 0.0 46.17 3.32 R
2970 4285 0.606944 GACCCCACACATAAACGCCA 60.607 55.000 0.00 0.0 0.00 5.69 R
3471 4793 7.999450 AGTACCCAGCTGTATAGTAATAGAC 57.001 40.000 13.81 0.0 0.00 2.59 R
3982 5547 2.287644 TGTGACACTGCATTCAAGAACG 59.712 45.455 7.20 0.0 0.00 3.95 R
5471 7156 2.270352 TTTCAATGCCAGTCGGAAGT 57.730 45.000 0.00 0.0 0.00 3.01 R
5743 7430 1.815003 GCCAGTAGCTGCAATTCAACT 59.185 47.619 4.12 0.0 38.99 3.16 R
6283 8207 1.477700 TGATTAACCAAGCTGCATGCC 59.522 47.619 16.68 0.0 44.23 4.40 R
7694 9775 0.178068 GGGATGGCTAGTCGCTTTGA 59.822 55.000 0.00 0.0 39.13 2.69 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
99 100 6.850752 TTCTTACTGGATGTGAGTGTATGA 57.149 37.500 0.00 0.00 34.35 2.15
111 112 3.435327 TGAGTGTATGACAACGATTTGCC 59.565 43.478 0.00 0.00 36.00 4.52
150 151 8.239314 TCTCTTATGTTGTTCTTGATGCATTTC 58.761 33.333 0.00 0.00 0.00 2.17
190 191 2.806434 TGATGCCTGCTTGGTTGTATT 58.194 42.857 0.00 0.00 38.35 1.89
206 207 5.473039 GTTGTATTTGAGCTGGCAGATTTT 58.527 37.500 20.86 0.00 0.00 1.82
250 251 4.202040 TGTTGTTCTTGATGCACTTGAAGG 60.202 41.667 0.00 0.00 0.00 3.46
257 258 2.079925 GATGCACTTGAAGGGTGAGTC 58.920 52.381 0.00 0.00 36.89 3.36
271 272 1.002430 GTGAGTCTGGCTGGTTGATGA 59.998 52.381 0.00 0.00 0.00 2.92
277 278 0.983467 TGGCTGGTTGATGACTGCTA 59.017 50.000 0.00 0.00 0.00 3.49
278 279 1.561076 TGGCTGGTTGATGACTGCTAT 59.439 47.619 0.00 0.00 0.00 2.97
292 305 0.179037 TGCTATGATGTCAGCTGGCC 60.179 55.000 17.28 6.61 38.63 5.36
309 322 4.020662 GCTGGCCTTCTAGCTAGATTGTAT 60.021 45.833 23.81 0.00 43.55 2.29
317 330 6.639563 TTCTAGCTAGATTGTATGTGCAACA 58.360 36.000 23.81 1.14 41.41 3.33
319 332 7.793648 TTCTAGCTAGATTGTATGTGCAACACA 60.794 37.037 23.81 2.45 40.44 3.72
330 343 2.719531 TGCAACACACACTCCCTTTA 57.280 45.000 0.00 0.00 0.00 1.85
331 344 2.571212 TGCAACACACACTCCCTTTAG 58.429 47.619 0.00 0.00 0.00 1.85
332 345 1.266989 GCAACACACACTCCCTTTAGC 59.733 52.381 0.00 0.00 0.00 3.09
334 347 3.149196 CAACACACACTCCCTTTAGCAT 58.851 45.455 0.00 0.00 0.00 3.79
335 348 3.508845 ACACACACTCCCTTTAGCATT 57.491 42.857 0.00 0.00 0.00 3.56
341 354 5.823045 ACACACTCCCTTTAGCATTATTAGC 59.177 40.000 0.00 0.00 0.00 3.09
376 399 1.334243 GCGTTCATCGGTAGCTAGTCT 59.666 52.381 0.00 0.00 40.26 3.24
377 400 2.223525 GCGTTCATCGGTAGCTAGTCTT 60.224 50.000 0.00 0.00 40.26 3.01
379 402 3.707793 GTTCATCGGTAGCTAGTCTTGG 58.292 50.000 0.00 0.00 0.00 3.61
380 403 1.681793 TCATCGGTAGCTAGTCTTGGC 59.318 52.381 0.00 0.00 0.00 4.52
381 404 1.409064 CATCGGTAGCTAGTCTTGGCA 59.591 52.381 0.00 0.00 32.40 4.92
382 405 1.776662 TCGGTAGCTAGTCTTGGCAT 58.223 50.000 0.00 0.00 32.40 4.40
383 406 1.681793 TCGGTAGCTAGTCTTGGCATC 59.318 52.381 0.00 0.00 32.40 3.91
384 407 1.683917 CGGTAGCTAGTCTTGGCATCT 59.316 52.381 0.00 0.00 32.40 2.90
385 408 2.287909 CGGTAGCTAGTCTTGGCATCTC 60.288 54.545 0.00 0.00 32.40 2.75
386 409 2.036604 GGTAGCTAGTCTTGGCATCTCC 59.963 54.545 0.00 0.00 32.40 3.71
387 410 1.871418 AGCTAGTCTTGGCATCTCCA 58.129 50.000 0.00 0.00 44.85 3.86
417 440 7.763172 ATATTCTCAAGAAACATCGTGTCTC 57.237 36.000 0.00 0.00 37.61 3.36
418 441 4.855715 TCTCAAGAAACATCGTGTCTCT 57.144 40.909 0.00 0.00 27.27 3.10
421 444 5.692204 TCTCAAGAAACATCGTGTCTCTTTC 59.308 40.000 4.60 0.41 27.27 2.62
422 445 5.601662 TCAAGAAACATCGTGTCTCTTTCT 58.398 37.500 4.60 2.22 27.27 2.52
423 446 5.463392 TCAAGAAACATCGTGTCTCTTTCTG 59.537 40.000 4.60 0.00 27.27 3.02
424 447 4.950050 AGAAACATCGTGTCTCTTTCTGT 58.050 39.130 0.00 0.00 26.63 3.41
426 449 5.817816 AGAAACATCGTGTCTCTTTCTGTTT 59.182 36.000 0.00 0.00 37.87 2.83
427 450 6.984474 AGAAACATCGTGTCTCTTTCTGTTTA 59.016 34.615 0.00 0.00 35.98 2.01
428 451 7.657761 AGAAACATCGTGTCTCTTTCTGTTTAT 59.342 33.333 0.00 0.00 35.98 1.40
430 453 7.121974 ACATCGTGTCTCTTTCTGTTTATTG 57.878 36.000 0.00 0.00 0.00 1.90
471 496 5.253330 CCTATGCAACCTTCAACCTTCTTA 58.747 41.667 0.00 0.00 0.00 2.10
472 497 5.888161 CCTATGCAACCTTCAACCTTCTTAT 59.112 40.000 0.00 0.00 0.00 1.73
660 685 7.358352 CCGATGCAATACTTTTCTGTTTTGTTC 60.358 37.037 0.00 0.00 33.52 3.18
696 832 7.791029 CCCCCAAATATAAGCTGTATTTGTTT 58.209 34.615 26.71 11.79 43.23 2.83
799 937 9.381027 CATTGCATGCATCATGAAATAATTTTC 57.619 29.630 23.37 0.00 45.32 2.29
830 968 0.762418 TATCTGGTATTGGTGCGGGG 59.238 55.000 0.00 0.00 0.00 5.73
847 985 0.038310 GGGGCTTCTAGCACTGGTTT 59.962 55.000 0.45 0.00 45.92 3.27
861 999 6.649155 AGCACTGGTTTTGTCCTTTAATTTT 58.351 32.000 0.00 0.00 0.00 1.82
863 1001 7.279981 AGCACTGGTTTTGTCCTTTAATTTTTC 59.720 33.333 0.00 0.00 0.00 2.29
1017 1155 8.815565 TTTCATGTATAGGTCAGCCAAAATTA 57.184 30.769 0.00 0.00 37.19 1.40
1169 1307 3.689649 GTCTGATGCTCCCACGTTAATTT 59.310 43.478 0.00 0.00 0.00 1.82
1180 1318 4.218852 CCCACGTTAATTTTTAAGCCTGGA 59.781 41.667 0.00 0.00 0.00 3.86
1316 1454 3.764237 TTAGTGGGTCAAAGTCCAGAC 57.236 47.619 0.00 0.00 33.13 3.51
1364 1502 5.007921 GCAAAGAACATGGCAAGATTTTTGT 59.992 36.000 14.25 0.74 0.00 2.83
1438 1576 7.647907 ATGTCAAGAATGTTGCAAATCTTTC 57.352 32.000 16.49 11.92 30.01 2.62
1586 1724 6.057533 TGTTGCAAGCTCTTGTGCTATATAT 58.942 36.000 0.00 0.00 43.24 0.86
1588 1726 7.386025 TGTTGCAAGCTCTTGTGCTATATATAG 59.614 37.037 14.45 14.45 43.24 1.31
1590 1728 7.670364 TGCAAGCTCTTGTGCTATATATAGAA 58.330 34.615 21.65 10.06 43.24 2.10
1591 1729 8.150296 TGCAAGCTCTTGTGCTATATATAGAAA 58.850 33.333 21.65 11.68 43.24 2.52
1607 1745 5.965033 ATAGAAATCTGGTGATCAGGTGT 57.035 39.130 0.00 0.00 43.53 4.16
1609 1747 3.328931 AGAAATCTGGTGATCAGGTGTGT 59.671 43.478 0.00 0.00 43.53 3.72
1611 1749 1.423584 TCTGGTGATCAGGTGTGTGT 58.576 50.000 0.00 0.00 43.53 3.72
1613 1751 0.836606 TGGTGATCAGGTGTGTGTGT 59.163 50.000 0.00 0.00 0.00 3.72
1635 1773 4.152402 GTGTGTACATGTGTGGAGATGAAC 59.848 45.833 9.11 0.00 0.00 3.18
1638 1776 5.577164 GTGTACATGTGTGGAGATGAACTAC 59.423 44.000 9.11 0.00 0.00 2.73
1639 1777 5.480422 TGTACATGTGTGGAGATGAACTACT 59.520 40.000 9.11 0.00 0.00 2.57
1640 1778 6.661805 TGTACATGTGTGGAGATGAACTACTA 59.338 38.462 9.11 0.00 0.00 1.82
1641 1779 5.967088 ACATGTGTGGAGATGAACTACTAC 58.033 41.667 0.00 0.00 0.00 2.73
1642 1780 5.717178 ACATGTGTGGAGATGAACTACTACT 59.283 40.000 0.00 0.00 0.00 2.57
1643 1781 5.644977 TGTGTGGAGATGAACTACTACTG 57.355 43.478 0.00 0.00 0.00 2.74
1644 1782 5.321927 TGTGTGGAGATGAACTACTACTGA 58.678 41.667 0.00 0.00 0.00 3.41
1645 1783 5.183331 TGTGTGGAGATGAACTACTACTGAC 59.817 44.000 0.00 0.00 0.00 3.51
1646 1784 4.705507 TGTGGAGATGAACTACTACTGACC 59.294 45.833 0.00 0.00 0.00 4.02
1653 1802 4.338879 TGAACTACTACTGACCTACACCC 58.661 47.826 0.00 0.00 0.00 4.61
1707 1977 4.922692 TGTTGCTTTCAAATAAATCCGCAG 59.077 37.500 0.00 0.00 33.37 5.18
1722 1992 2.853210 CAGTGTTGCCAGCGTACG 59.147 61.111 11.84 11.84 0.00 3.67
1727 1997 0.528924 TGTTGCCAGCGTACGTATCT 59.471 50.000 17.90 2.27 0.00 1.98
1870 2141 6.916360 TGAATCCTAAGCAACAATCCTTTT 57.084 33.333 0.00 0.00 0.00 2.27
1902 2173 9.455144 TCATTAAATCCTACTATCACCCCTTTA 57.545 33.333 0.00 0.00 0.00 1.85
1948 2219 2.564771 TGTGGATCAGGCGAATGATTC 58.435 47.619 4.53 0.00 40.02 2.52
2021 2292 9.850628 GCTTAATGATGCATATGTGTTCAATAT 57.149 29.630 0.00 0.67 0.00 1.28
2048 2329 6.546034 GGATTAACAAATGTGTGGCCTATACT 59.454 38.462 3.32 0.00 38.27 2.12
2101 2382 7.582667 ATGTCAATGGGTAAAGGCTAAATAC 57.417 36.000 0.00 0.00 0.00 1.89
2126 2407 8.136165 ACGGTTACTGAATGTATTATGTCTCTC 58.864 37.037 0.00 0.00 0.00 3.20
2137 2418 2.483583 ATGTCTCTCTCATCGCGTTC 57.516 50.000 5.77 0.00 0.00 3.95
2164 2445 8.828644 TCATGTTTTGATTCACTTGGATTTTTG 58.171 29.630 0.00 0.00 0.00 2.44
2243 2524 6.271159 AGGAATGTACTTGTCTTCTCTTTCCT 59.729 38.462 0.00 0.00 35.85 3.36
2314 2610 8.358582 AGAGGATCACTGCAATTAAAATTTCT 57.641 30.769 0.00 0.00 37.82 2.52
2552 2848 9.935241 TCTGATATTCCAGATTATCTAAAGCAC 57.065 33.333 0.00 0.00 38.18 4.40
2578 2874 6.322491 CGGAGGTAATGATTGGTTTCTTTTC 58.678 40.000 0.00 0.00 0.00 2.29
2637 2935 1.352352 AGGTAGCTTGCAACTGATGGT 59.648 47.619 0.00 0.00 0.00 3.55
2739 3037 5.269505 AGCCACTTATAGCAACTACAGAG 57.730 43.478 0.00 0.00 0.00 3.35
2872 3170 9.331282 GAACAGTATTCTTGTTGGCTATAAGAT 57.669 33.333 8.71 3.35 31.21 2.40
2874 3172 7.653713 ACAGTATTCTTGTTGGCTATAAGATCG 59.346 37.037 8.71 0.69 31.21 3.69
2970 4285 8.463930 TCCACTTATGAATCTTTGTGTTTCTT 57.536 30.769 0.00 0.00 0.00 2.52
3471 4793 3.616379 GGTCAGCATTTTCTTCTCTCTCG 59.384 47.826 0.00 0.00 0.00 4.04
3503 4827 1.559682 ACAGCTGGGTACTTGTATGGG 59.440 52.381 19.93 0.00 0.00 4.00
3726 5290 4.036734 CCAGATATTGGTTGTTATGCGCTT 59.963 41.667 9.73 4.59 42.41 4.68
3982 5547 0.768221 TGGAGCTCCATGGGGTATCC 60.768 60.000 32.00 24.12 42.01 2.59
4046 5611 4.578105 CCTGTCATATCTTCTCTTTTGGGC 59.422 45.833 0.00 0.00 0.00 5.36
4110 5675 7.549488 GGTCATACTTTTAGTCTTGTACAGCAT 59.451 37.037 0.00 0.00 0.00 3.79
4135 5702 6.267471 TGCTTTATGTTTCAAGTCCTGGAAAT 59.733 34.615 0.00 0.00 35.66 2.17
4139 5706 3.751175 TGTTTCAAGTCCTGGAAATAGCG 59.249 43.478 0.00 0.00 35.66 4.26
4162 5729 1.259609 TGCAGAAATGCAGGGAAAGG 58.740 50.000 0.00 0.00 40.23 3.11
4193 5760 1.752833 GACCCAAAGTGGTCGGACT 59.247 57.895 8.23 0.00 44.98 3.85
4342 5921 9.187455 CACATTGTTAACTGGGTAAAATTGTAC 57.813 33.333 7.22 0.00 0.00 2.90
4345 5924 7.188468 TGTTAACTGGGTAAAATTGTACGTC 57.812 36.000 7.22 0.00 0.00 4.34
4352 5931 5.167845 GGGTAAAATTGTACGTCGGTCTTA 58.832 41.667 0.00 0.00 0.00 2.10
4353 5932 5.637387 GGGTAAAATTGTACGTCGGTCTTAA 59.363 40.000 0.00 0.00 0.00 1.85
4469 6048 1.871080 ATCGACCGGCTGAATTGATC 58.129 50.000 0.00 0.00 0.00 2.92
4589 6168 9.088512 CGATTTATACAAGTAAGTCTTTGAGCT 57.911 33.333 0.00 0.00 33.63 4.09
4861 6440 2.378038 GTGATGCTAGGCCAAATTCCA 58.622 47.619 5.01 0.00 0.00 3.53
4904 6483 7.123547 ACATTACAGAGCTAGTAAGAGAAGCTT 59.876 37.037 14.36 0.00 46.29 3.74
5003 6583 9.628500 AACCTAAATGTACATCCCTTTATTCTC 57.372 33.333 9.23 0.00 0.00 2.87
5090 6670 4.343814 ACAAGAAGGATCTAGCTAAGAGGC 59.656 45.833 0.00 0.00 37.74 4.70
5113 6693 1.451028 GCTGGGAAAGAGCGCATCT 60.451 57.895 11.47 6.88 41.27 2.90
5272 6852 6.513720 GCGGAAGTCAATTTACCAACAAACTA 60.514 38.462 0.00 0.00 0.00 2.24
5293 6873 2.912956 AGAGGGAATGTTCAAGGTAGCA 59.087 45.455 0.00 0.00 0.00 3.49
5310 6890 5.701290 AGGTAGCATAGTTTTTGTCACTGAC 59.299 40.000 1.86 1.86 0.00 3.51
5322 6902 5.657470 TTGTCACTGACGATTCTCTTTTG 57.343 39.130 4.71 0.00 34.95 2.44
5471 7156 3.507162 TCATCTCAGGCAAGGACAAAA 57.493 42.857 0.00 0.00 0.00 2.44
5477 7162 1.001378 CAGGCAAGGACAAAACTTCCG 60.001 52.381 0.00 0.00 38.29 4.30
5547 7232 2.212812 TGCCCTCACATTTACATGCA 57.787 45.000 0.00 0.00 33.05 3.96
5550 7235 3.119065 TGCCCTCACATTTACATGCATTG 60.119 43.478 0.00 0.00 33.05 2.82
5614 7301 7.868415 GTCTGAGTCTGAAACTGTTACTTGTAT 59.132 37.037 0.70 0.00 38.74 2.29
5868 7555 5.961263 GCAGCAAATTTGAAGTCTGTTTTTG 59.039 36.000 22.31 0.00 0.00 2.44
5988 7675 2.881111 AAGTAGAGTTCCCCAAAGGC 57.119 50.000 0.00 0.00 34.51 4.35
6032 7719 6.321181 TCACTATTTCAGGTTGGATTATTGCC 59.679 38.462 0.00 0.00 0.00 4.52
6035 7722 1.063266 TCAGGTTGGATTATTGCCCCC 60.063 52.381 0.00 0.00 0.00 5.40
6036 7723 1.062962 CAGGTTGGATTATTGCCCCCT 60.063 52.381 0.00 0.00 0.00 4.79
6055 7742 1.413077 CTCCCCCTCTCGTGGTTTATC 59.587 57.143 0.00 0.00 0.00 1.75
6209 8133 8.785329 AGGATAAAGAATTGAGAAGAACACTC 57.215 34.615 0.00 0.00 35.26 3.51
6252 8176 3.462205 AGTTAGGGTTCTCCAAAAGGTGT 59.538 43.478 0.00 0.00 38.24 4.16
6289 8213 3.740321 TCTTTGACAAATTTTCGGCATGC 59.260 39.130 9.90 9.90 0.00 4.06
6465 8389 3.935203 AGATGGCATCGAGTTTAAGTGTG 59.065 43.478 21.01 0.00 0.00 3.82
6484 8408 4.211374 GTGTGTAACTAAGGTGCTGTTCTG 59.789 45.833 0.00 0.00 38.04 3.02
6636 8560 8.023021 ACTGTCAGAATAGGCAGATAAATACA 57.977 34.615 6.91 0.00 33.57 2.29
6668 8592 5.855740 ATCCCTGTAAGACTAGTAGTTGC 57.144 43.478 3.85 0.00 34.07 4.17
6669 8593 4.669700 TCCCTGTAAGACTAGTAGTTGCA 58.330 43.478 3.85 1.73 34.07 4.08
6670 8594 5.269991 TCCCTGTAAGACTAGTAGTTGCAT 58.730 41.667 3.85 0.00 34.07 3.96
6671 8595 5.127194 TCCCTGTAAGACTAGTAGTTGCATG 59.873 44.000 3.85 0.12 34.07 4.06
6672 8596 5.352284 CCTGTAAGACTAGTAGTTGCATGG 58.648 45.833 3.85 3.22 34.07 3.66
6673 8597 5.105310 CCTGTAAGACTAGTAGTTGCATGGT 60.105 44.000 3.85 0.00 34.07 3.55
6674 8598 5.962433 TGTAAGACTAGTAGTTGCATGGTC 58.038 41.667 3.85 0.00 0.00 4.02
6675 8599 3.784701 AGACTAGTAGTTGCATGGTCG 57.215 47.619 3.85 0.00 0.00 4.79
6676 8600 3.353557 AGACTAGTAGTTGCATGGTCGA 58.646 45.455 3.85 0.00 0.00 4.20
6677 8601 3.954904 AGACTAGTAGTTGCATGGTCGAT 59.045 43.478 3.85 0.00 0.00 3.59
6678 8602 4.045104 GACTAGTAGTTGCATGGTCGATG 58.955 47.826 3.85 0.00 34.84 3.84
6679 8603 3.447586 ACTAGTAGTTGCATGGTCGATGT 59.552 43.478 0.00 0.00 34.14 3.06
6680 8604 4.643334 ACTAGTAGTTGCATGGTCGATGTA 59.357 41.667 0.00 0.00 34.14 2.29
6681 8605 4.046938 AGTAGTTGCATGGTCGATGTAG 57.953 45.455 0.00 0.00 34.14 2.74
6720 8648 7.446319 ACATTTGCTTGCTCTGCTGATATTATA 59.554 33.333 0.00 0.00 0.00 0.98
6742 8670 7.986085 ATAGTGCTTTATTGCTTATGGTAGG 57.014 36.000 0.00 0.00 0.00 3.18
6747 8675 6.321181 TGCTTTATTGCTTATGGTAGGAAAGG 59.679 38.462 0.00 0.00 0.00 3.11
6765 8711 8.080363 AGGAAAGGTAGTCCTCTGTATAAAAG 57.920 38.462 0.00 0.00 42.02 2.27
6803 8749 2.821378 TGATTGCCAGTCATGTCTTTGG 59.179 45.455 0.00 0.00 0.00 3.28
6819 8765 6.533730 TGTCTTTGGTGTCTTACAATCTCAT 58.466 36.000 0.00 0.00 0.00 2.90
6965 8911 4.872691 ACTCGGAGTGATTGACATGATTTC 59.127 41.667 10.41 0.00 0.00 2.17
7243 9199 3.558931 TTGCTGTTCCTTGTTCTCTCA 57.441 42.857 0.00 0.00 0.00 3.27
7284 9241 6.955963 CAGTTGCATCTTTTCTGTATACGAAC 59.044 38.462 8.88 0.00 0.00 3.95
7363 9321 8.528643 TGATATTCCCTATAATTCACCACTACG 58.471 37.037 0.00 0.00 0.00 3.51
7443 9405 2.303311 AGTTCTTCACCAAGTAGAGGGC 59.697 50.000 0.00 0.00 0.00 5.19
7463 9425 5.104360 AGGGCAATTTACTTCAGATAGCAGA 60.104 40.000 0.00 0.00 0.00 4.26
7468 9430 8.400947 GCAATTTACTTCAGATAGCAGATTTCA 58.599 33.333 0.00 0.00 0.00 2.69
7471 9433 8.484641 TTTACTTCAGATAGCAGATTTCACTG 57.515 34.615 0.00 0.00 40.43 3.66
7521 9483 4.202050 GCAAGATGAATGGATAAACCGCTT 60.202 41.667 0.00 0.00 42.61 4.68
7561 9564 9.537192 TCAGTAGATAAACGAAAAGAAAGACAA 57.463 29.630 0.00 0.00 0.00 3.18
7569 9572 7.796958 AACGAAAAGAAAGACAACAGAAAAG 57.203 32.000 0.00 0.00 0.00 2.27
7570 9573 6.322491 ACGAAAAGAAAGACAACAGAAAAGG 58.678 36.000 0.00 0.00 0.00 3.11
7572 9575 7.148069 ACGAAAAGAAAGACAACAGAAAAGGAT 60.148 33.333 0.00 0.00 0.00 3.24
7573 9576 7.702348 CGAAAAGAAAGACAACAGAAAAGGATT 59.298 33.333 0.00 0.00 0.00 3.01
7574 9577 9.371136 GAAAAGAAAGACAACAGAAAAGGATTT 57.629 29.630 0.00 0.00 42.41 2.17
7575 9578 8.707938 AAAGAAAGACAACAGAAAAGGATTTG 57.292 30.769 0.00 0.00 39.02 2.32
7576 9579 6.276091 AGAAAGACAACAGAAAAGGATTTGC 58.724 36.000 0.00 0.00 39.02 3.68
7577 9580 4.590850 AGACAACAGAAAAGGATTTGCC 57.409 40.909 0.00 0.00 39.02 4.52
7582 9594 5.942826 ACAACAGAAAAGGATTTGCCAAAAA 59.057 32.000 0.00 0.00 39.02 1.94
7607 9688 6.850752 AAAGACAACAGAAAAAGAGGGAAA 57.149 33.333 0.00 0.00 0.00 3.13
7611 9692 4.645136 ACAACAGAAAAAGAGGGAAAGACC 59.355 41.667 0.00 0.00 38.08 3.85
7613 9694 5.066913 ACAGAAAAAGAGGGAAAGACCAT 57.933 39.130 0.00 0.00 41.20 3.55
7615 9696 6.794534 ACAGAAAAAGAGGGAAAGACCATAT 58.205 36.000 0.00 0.00 41.20 1.78
7642 9723 8.504812 AAAAAGAAGATAAAGAGAGAGATGGC 57.495 34.615 0.00 0.00 0.00 4.40
7643 9724 5.452078 AGAAGATAAAGAGAGAGATGGCG 57.548 43.478 0.00 0.00 0.00 5.69
7644 9725 5.136828 AGAAGATAAAGAGAGAGATGGCGA 58.863 41.667 0.00 0.00 0.00 5.54
7645 9726 5.241506 AGAAGATAAAGAGAGAGATGGCGAG 59.758 44.000 0.00 0.00 0.00 5.03
7646 9727 3.826157 AGATAAAGAGAGAGATGGCGAGG 59.174 47.826 0.00 0.00 0.00 4.63
7647 9728 0.463620 AAAGAGAGAGATGGCGAGGC 59.536 55.000 0.00 0.00 0.00 4.70
7677 9758 0.402121 AACCCTTGCCCTCTTGAGTC 59.598 55.000 0.00 0.00 0.00 3.36
7678 9759 0.768221 ACCCTTGCCCTCTTGAGTCA 60.768 55.000 0.00 0.00 0.00 3.41
7694 9775 6.663093 TCTTGAGTCAAAGAGAGAGATAAGCT 59.337 38.462 7.06 0.00 32.42 3.74
7731 9812 3.624305 CGACACACGGAGATGTAGG 57.376 57.895 0.00 0.00 38.46 3.18
7732 9813 1.092348 CGACACACGGAGATGTAGGA 58.908 55.000 0.00 0.00 38.46 2.94
7733 9814 1.676529 CGACACACGGAGATGTAGGAT 59.323 52.381 0.00 0.00 38.46 3.24
7734 9815 2.876550 CGACACACGGAGATGTAGGATA 59.123 50.000 0.00 0.00 38.46 2.59
7738 9819 6.235231 ACACACGGAGATGTAGGATATTTT 57.765 37.500 0.00 0.00 0.00 1.82
7739 9820 6.049149 ACACACGGAGATGTAGGATATTTTG 58.951 40.000 0.00 0.00 0.00 2.44
7740 9821 6.049149 CACACGGAGATGTAGGATATTTTGT 58.951 40.000 0.00 0.00 0.00 2.83
7741 9822 7.147794 ACACACGGAGATGTAGGATATTTTGTA 60.148 37.037 0.00 0.00 0.00 2.41
7742 9823 7.169308 CACACGGAGATGTAGGATATTTTGTAC 59.831 40.741 0.00 0.00 0.00 2.90
7743 9824 7.147794 ACACGGAGATGTAGGATATTTTGTACA 60.148 37.037 0.00 0.00 0.00 2.90
7744 9825 7.872993 CACGGAGATGTAGGATATTTTGTACAT 59.127 37.037 0.00 0.00 38.52 2.29
7745 9826 7.872993 ACGGAGATGTAGGATATTTTGTACATG 59.127 37.037 0.00 0.00 36.47 3.21
7746 9827 8.088365 CGGAGATGTAGGATATTTTGTACATGA 58.912 37.037 0.00 0.00 36.47 3.07
7747 9828 9.209175 GGAGATGTAGGATATTTTGTACATGAC 57.791 37.037 0.00 0.00 36.47 3.06
7765 9846 7.889873 ACATGACAGGCCTATAGATACTATC 57.110 40.000 3.98 0.00 0.00 2.08
7767 9848 8.782927 ACATGACAGGCCTATAGATACTATCTA 58.217 37.037 3.98 8.03 45.23 1.98
7848 9935 3.726557 TCCACAAATTGAGATGGAGCT 57.273 42.857 0.00 0.00 36.30 4.09
7874 9961 4.749310 CTCGGCAGCTCGGCACTT 62.749 66.667 9.65 0.00 41.26 3.16
7905 9992 2.005451 CCAAGCAGAAATCGGTGAGAG 58.995 52.381 0.00 0.00 0.00 3.20
7906 9993 2.354103 CCAAGCAGAAATCGGTGAGAGA 60.354 50.000 0.00 0.00 0.00 3.10
7907 9994 3.529533 CAAGCAGAAATCGGTGAGAGAT 58.470 45.455 0.00 0.00 0.00 2.75
8016 10115 4.087892 AATCCAGCTCGCTGCCGT 62.088 61.111 13.25 0.00 44.23 5.68
8041 10140 3.501911 CGCCCCCTCCCATCCAAT 61.502 66.667 0.00 0.00 0.00 3.16
8082 10181 1.598856 CCCCTCCCTCCTCTCTCCTT 61.599 65.000 0.00 0.00 0.00 3.36
8083 10182 0.105709 CCCTCCCTCCTCTCTCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
8084 10183 0.467290 CCTCCCTCCTCTCTCCTTCG 60.467 65.000 0.00 0.00 0.00 3.79
8085 10184 1.076632 TCCCTCCTCTCTCCTTCGC 60.077 63.158 0.00 0.00 0.00 4.70
8086 10185 1.076339 CCCTCCTCTCTCCTTCGCT 60.076 63.158 0.00 0.00 0.00 4.93
8087 10186 0.686112 CCCTCCTCTCTCCTTCGCTT 60.686 60.000 0.00 0.00 0.00 4.68
8088 10187 0.744281 CCTCCTCTCTCCTTCGCTTC 59.256 60.000 0.00 0.00 0.00 3.86
8089 10188 0.744281 CTCCTCTCTCCTTCGCTTCC 59.256 60.000 0.00 0.00 0.00 3.46
8090 10189 0.684805 TCCTCTCTCCTTCGCTTCCC 60.685 60.000 0.00 0.00 0.00 3.97
8091 10190 1.681486 CCTCTCTCCTTCGCTTCCCC 61.681 65.000 0.00 0.00 0.00 4.81
8092 10191 0.686112 CTCTCTCCTTCGCTTCCCCT 60.686 60.000 0.00 0.00 0.00 4.79
8093 10192 0.684805 TCTCTCCTTCGCTTCCCCTC 60.685 60.000 0.00 0.00 0.00 4.30
8094 10193 0.686112 CTCTCCTTCGCTTCCCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
8095 10194 0.684805 TCTCCTTCGCTTCCCCTCTC 60.685 60.000 0.00 0.00 0.00 3.20
8096 10195 0.972983 CTCCTTCGCTTCCCCTCTCA 60.973 60.000 0.00 0.00 0.00 3.27
8097 10196 0.325671 TCCTTCGCTTCCCCTCTCAT 60.326 55.000 0.00 0.00 0.00 2.90
8098 10197 0.179062 CCTTCGCTTCCCCTCTCATG 60.179 60.000 0.00 0.00 0.00 3.07
8099 10198 0.813210 CTTCGCTTCCCCTCTCATGC 60.813 60.000 0.00 0.00 0.00 4.06
8100 10199 2.203126 CGCTTCCCCTCTCATGCC 60.203 66.667 0.00 0.00 0.00 4.40
8101 10200 2.203126 GCTTCCCCTCTCATGCCG 60.203 66.667 0.00 0.00 0.00 5.69
8102 10201 2.203126 CTTCCCCTCTCATGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
8103 10202 4.161295 TTCCCCTCTCATGCCGCG 62.161 66.667 0.00 0.00 0.00 6.46
8137 10236 3.282740 GACGCGATGTCGGTTACG 58.717 61.111 15.93 1.96 37.96 3.18
8138 10237 2.842582 GACGCGATGTCGGTTACGC 61.843 63.158 15.93 0.00 46.08 4.42
8140 10239 4.261495 GCGATGTCGGTTACGCGC 62.261 66.667 5.73 0.00 43.79 6.86
8141 10240 3.613702 CGATGTCGGTTACGCGCC 61.614 66.667 5.73 0.00 40.69 6.53
8142 10241 3.259751 GATGTCGGTTACGCGCCC 61.260 66.667 5.73 2.39 40.69 6.13
8143 10242 4.825252 ATGTCGGTTACGCGCCCC 62.825 66.667 5.73 1.95 40.69 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181516 CCTCGAGATAAAAAGCACTGCAC 60.182 47.826 15.71 0.00 0.00 4.57
2 3 2.352960 CCCTCGAGATAAAAAGCACTGC 59.647 50.000 15.71 0.00 0.00 4.40
3 4 2.939103 CCCCTCGAGATAAAAAGCACTG 59.061 50.000 15.71 0.00 0.00 3.66
4 5 2.681097 GCCCCTCGAGATAAAAAGCACT 60.681 50.000 15.71 0.00 0.00 4.40
5 6 1.671328 GCCCCTCGAGATAAAAAGCAC 59.329 52.381 15.71 0.00 0.00 4.40
6 7 1.559682 AGCCCCTCGAGATAAAAAGCA 59.440 47.619 15.71 0.00 0.00 3.91
7 8 2.158885 AGAGCCCCTCGAGATAAAAAGC 60.159 50.000 15.71 5.64 35.36 3.51
8 9 3.462021 CAGAGCCCCTCGAGATAAAAAG 58.538 50.000 15.71 0.00 35.36 2.27
9 10 2.420129 GCAGAGCCCCTCGAGATAAAAA 60.420 50.000 15.71 0.00 35.36 1.94
10 11 1.139058 GCAGAGCCCCTCGAGATAAAA 59.861 52.381 15.71 0.00 35.36 1.52
11 12 0.753262 GCAGAGCCCCTCGAGATAAA 59.247 55.000 15.71 0.00 35.36 1.40
12 13 0.397114 TGCAGAGCCCCTCGAGATAA 60.397 55.000 15.71 0.00 35.36 1.75
13 14 1.109920 GTGCAGAGCCCCTCGAGATA 61.110 60.000 15.71 0.00 35.36 1.98
14 15 2.042537 TGCAGAGCCCCTCGAGAT 60.043 61.111 15.71 0.00 35.36 2.75
15 16 3.071206 GTGCAGAGCCCCTCGAGA 61.071 66.667 15.71 0.00 35.36 4.04
71 72 6.715280 ACACTCACATCCAGTAAGAATCAAT 58.285 36.000 0.00 0.00 0.00 2.57
92 93 2.769376 CGGCAAATCGTTGTCATACAC 58.231 47.619 0.00 0.00 39.45 2.90
99 100 1.231221 TTACTGCGGCAAATCGTTGT 58.769 45.000 3.44 0.00 37.06 3.32
111 112 6.128553 ACAACATAAGAGACACATTTACTGCG 60.129 38.462 0.00 0.00 0.00 5.18
150 151 1.669115 CCAGCCACACTCGGTCTTG 60.669 63.158 0.00 0.00 0.00 3.02
206 207 1.208052 GAAGGCCACATCTACTGCAGA 59.792 52.381 23.35 0.00 37.79 4.26
218 219 2.297701 TCAAGAACAACAGAAGGCCAC 58.702 47.619 5.01 0.00 0.00 5.01
250 251 0.326264 ATCAACCAGCCAGACTCACC 59.674 55.000 0.00 0.00 0.00 4.02
257 258 0.322277 AGCAGTCATCAACCAGCCAG 60.322 55.000 0.00 0.00 31.59 4.85
271 272 1.474677 GCCAGCTGACATCATAGCAGT 60.475 52.381 17.39 0.00 42.29 4.40
277 278 0.917533 AGAAGGCCAGCTGACATCAT 59.082 50.000 17.39 0.00 0.00 2.45
278 279 1.483827 CTAGAAGGCCAGCTGACATCA 59.516 52.381 17.39 1.38 0.00 3.07
292 305 6.758416 TGTTGCACATACAATCTAGCTAGAAG 59.242 38.462 26.62 22.48 35.69 2.85
317 330 5.823045 GCTAATAATGCTAAAGGGAGTGTGT 59.177 40.000 0.00 0.00 0.00 3.72
319 332 5.057149 CGCTAATAATGCTAAAGGGAGTGT 58.943 41.667 0.00 0.00 0.00 3.55
320 333 4.452455 CCGCTAATAATGCTAAAGGGAGTG 59.548 45.833 0.00 0.00 0.00 3.51
323 336 3.809324 GCCCGCTAATAATGCTAAAGGGA 60.809 47.826 0.26 0.00 38.62 4.20
325 338 3.146066 TGCCCGCTAATAATGCTAAAGG 58.854 45.455 0.00 0.00 0.00 3.11
327 340 4.215399 GTCATGCCCGCTAATAATGCTAAA 59.785 41.667 0.00 0.00 0.00 1.85
328 341 3.751175 GTCATGCCCGCTAATAATGCTAA 59.249 43.478 0.00 0.00 0.00 3.09
330 343 2.154462 GTCATGCCCGCTAATAATGCT 58.846 47.619 0.00 0.00 0.00 3.79
331 344 2.095567 CAGTCATGCCCGCTAATAATGC 60.096 50.000 0.00 0.00 0.00 3.56
332 345 3.818961 CAGTCATGCCCGCTAATAATG 57.181 47.619 0.00 0.00 0.00 1.90
377 400 7.797121 TGAGAATATAATACTGGAGATGCCA 57.203 36.000 0.00 0.00 46.96 4.92
379 402 9.935241 TTCTTGAGAATATAATACTGGAGATGC 57.065 33.333 0.00 0.00 0.00 3.91
390 413 9.823647 AGACACGATGTTTCTTGAGAATATAAT 57.176 29.630 0.00 0.00 33.54 1.28
391 414 9.302345 GAGACACGATGTTTCTTGAGAATATAA 57.698 33.333 0.00 0.00 33.54 0.98
392 415 8.687242 AGAGACACGATGTTTCTTGAGAATATA 58.313 33.333 0.00 0.00 38.49 0.86
393 416 7.551585 AGAGACACGATGTTTCTTGAGAATAT 58.448 34.615 0.00 0.00 38.49 1.28
428 451 8.026607 GCATAGGCAGTGTTAAGTTTTATTCAA 58.973 33.333 0.00 0.00 40.72 2.69
430 453 7.971004 GCATAGGCAGTGTTAAGTTTTATTC 57.029 36.000 0.00 0.00 40.72 1.75
471 496 4.536090 TGGTGGAGAATACTGGACAGAAAT 59.464 41.667 6.29 0.00 0.00 2.17
472 497 3.907474 TGGTGGAGAATACTGGACAGAAA 59.093 43.478 6.29 0.00 0.00 2.52
702 838 8.133024 TCTTGGCCAAAGTATAAATGTTTGAT 57.867 30.769 20.91 0.00 37.18 2.57
777 915 7.485418 TGGAAAATTATTTCATGATGCATGC 57.515 32.000 11.82 11.82 45.53 4.06
814 952 2.124320 CCCCCGCACCAATACCAG 60.124 66.667 0.00 0.00 0.00 4.00
826 964 2.187946 CAGTGCTAGAAGCCCCCG 59.812 66.667 0.00 0.00 41.51 5.73
830 968 2.226674 GACAAAACCAGTGCTAGAAGCC 59.773 50.000 0.00 0.00 41.51 4.35
935 1073 7.553044 GCTCCAAAGTATAAGGTGTACTGATTT 59.447 37.037 0.00 0.00 32.94 2.17
942 1080 4.025360 TCCGCTCCAAAGTATAAGGTGTA 58.975 43.478 0.00 0.00 0.00 2.90
1017 1155 6.373759 AGTATCTTCCTCAAAGTTTTTGGGT 58.626 36.000 1.22 0.00 36.31 4.51
1202 1340 2.757868 GTGTAGACAGAGATCACCAGCT 59.242 50.000 0.00 0.00 0.00 4.24
1316 1454 4.202070 ACCAACGACAAAAATACAACCAGG 60.202 41.667 0.00 0.00 0.00 4.45
1364 1502 5.163311 ACCACGGATAATCAACATCTGATCA 60.163 40.000 0.00 0.00 44.43 2.92
1438 1576 1.846439 ACCCCATATCCCACACTGAAG 59.154 52.381 0.00 0.00 0.00 3.02
1558 1696 2.288030 GCACAAGAGCTTGCAACAGAAT 60.288 45.455 9.99 0.00 44.03 2.40
1586 1724 4.532126 ACACACCTGATCACCAGATTTCTA 59.468 41.667 0.00 0.00 45.78 2.10
1588 1726 3.438087 CACACACCTGATCACCAGATTTC 59.562 47.826 0.00 0.00 45.78 2.17
1590 1728 2.373169 ACACACACCTGATCACCAGATT 59.627 45.455 0.00 0.00 45.78 2.40
1591 1729 1.980765 ACACACACCTGATCACCAGAT 59.019 47.619 0.00 0.00 45.78 2.90
1593 1731 1.202687 ACACACACACCTGATCACCAG 60.203 52.381 0.00 0.00 42.55 4.00
1594 1732 0.836606 ACACACACACCTGATCACCA 59.163 50.000 0.00 0.00 0.00 4.17
1595 1733 1.229428 CACACACACACCTGATCACC 58.771 55.000 0.00 0.00 0.00 4.02
1597 1735 1.209261 ACACACACACACACCTGATCA 59.791 47.619 0.00 0.00 0.00 2.92
1598 1736 1.953559 ACACACACACACACCTGATC 58.046 50.000 0.00 0.00 0.00 2.92
1599 1737 2.169561 TGTACACACACACACACCTGAT 59.830 45.455 0.00 0.00 0.00 2.90
1600 1738 1.550976 TGTACACACACACACACCTGA 59.449 47.619 0.00 0.00 0.00 3.86
1601 1739 2.017138 TGTACACACACACACACCTG 57.983 50.000 0.00 0.00 0.00 4.00
1605 1743 2.675348 CACACATGTACACACACACACA 59.325 45.455 0.00 0.00 37.54 3.72
1607 1745 2.093447 TCCACACATGTACACACACACA 60.093 45.455 0.00 0.00 37.54 3.72
1609 1747 2.432510 TCTCCACACATGTACACACACA 59.567 45.455 0.00 0.00 37.54 3.72
1611 1749 3.323403 TCATCTCCACACATGTACACACA 59.677 43.478 0.00 0.00 39.52 3.72
1613 1751 4.040339 AGTTCATCTCCACACATGTACACA 59.960 41.667 0.00 0.00 0.00 3.72
1635 1773 2.295885 CCGGGTGTAGGTCAGTAGTAG 58.704 57.143 0.00 0.00 0.00 2.57
1638 1776 0.968901 TGCCGGGTGTAGGTCAGTAG 60.969 60.000 2.18 0.00 0.00 2.57
1639 1777 0.324923 ATGCCGGGTGTAGGTCAGTA 60.325 55.000 2.18 0.00 0.00 2.74
1640 1778 0.324923 TATGCCGGGTGTAGGTCAGT 60.325 55.000 2.18 0.00 0.00 3.41
1641 1779 0.389391 CTATGCCGGGTGTAGGTCAG 59.611 60.000 2.18 0.00 0.00 3.51
1642 1780 1.046472 CCTATGCCGGGTGTAGGTCA 61.046 60.000 2.18 0.00 32.20 4.02
1643 1781 1.047034 ACCTATGCCGGGTGTAGGTC 61.047 60.000 20.13 0.00 43.54 3.85
1644 1782 1.002533 ACCTATGCCGGGTGTAGGT 59.997 57.895 20.13 20.13 42.50 3.08
1645 1783 0.106149 GAACCTATGCCGGGTGTAGG 59.894 60.000 19.14 19.14 40.63 3.18
1646 1784 1.068741 GAGAACCTATGCCGGGTGTAG 59.931 57.143 2.18 0.00 37.13 2.74
1707 1977 0.643820 GATACGTACGCTGGCAACAC 59.356 55.000 16.72 0.00 46.17 3.32
1812 2082 9.440773 AATACTACACAATCATATGCTATGTGG 57.559 33.333 25.52 18.02 44.24 4.17
1870 2141 9.778741 GGTGATAGTAGGATTTAATGATCACAA 57.221 33.333 0.00 0.00 42.28 3.33
1948 2219 2.621338 AGCAGTGTGAACCATGATACG 58.379 47.619 0.00 0.00 0.00 3.06
2021 2292 2.564947 GGCCACACATTTGTTAATCCCA 59.435 45.455 0.00 0.00 31.66 4.37
2079 2360 5.008316 CCGTATTTAGCCTTTACCCATTGAC 59.992 44.000 0.00 0.00 0.00 3.18
2101 2382 8.353684 AGAGAGACATAATACATTCAGTAACCG 58.646 37.037 0.00 0.00 36.05 4.44
2126 2407 3.123453 TCAAAACATGAGAACGCGATGAG 59.877 43.478 15.93 0.00 33.04 2.90
2137 2418 8.597662 AAAATCCAAGTGAATCAAAACATGAG 57.402 30.769 0.00 0.00 42.53 2.90
2227 2508 4.342862 TGACCAGGAAAGAGAAGACAAG 57.657 45.455 0.00 0.00 0.00 3.16
2243 2524 6.599244 GGATTTCAACACAGATTCTATGACCA 59.401 38.462 0.00 0.00 0.00 4.02
2289 2570 8.358582 AGAAATTTTAATTGCAGTGATCCTCT 57.641 30.769 0.00 0.00 0.00 3.69
2331 2627 7.049799 TGAATAAACAGTTTTCCAGGGAAAG 57.950 36.000 12.83 5.49 43.75 2.62
2552 2848 1.663695 AACCAATCATTACCTCCGCG 58.336 50.000 0.00 0.00 0.00 6.46
2578 2874 7.819415 TCAGTATGAACAAAGTACATGGAGAAG 59.181 37.037 0.00 0.00 45.97 2.85
2739 3037 3.226347 GTGTCGCTGTAGCAATTGTTTC 58.774 45.455 7.40 0.00 42.21 2.78
2872 3170 7.335627 AGTGAACATCCTTATTGGTTTATCGA 58.664 34.615 0.00 0.00 37.07 3.59
2874 3172 9.788960 GAAAGTGAACATCCTTATTGGTTTATC 57.211 33.333 0.00 0.00 37.07 1.75
2970 4285 0.606944 GACCCCACACATAAACGCCA 60.607 55.000 0.00 0.00 0.00 5.69
3471 4793 7.999450 AGTACCCAGCTGTATAGTAATAGAC 57.001 40.000 13.81 0.00 0.00 2.59
3798 5362 4.394300 AGCATCTTTCTTCAAGACGAATGG 59.606 41.667 0.00 0.00 44.70 3.16
3982 5547 2.287644 TGTGACACTGCATTCAAGAACG 59.712 45.455 7.20 0.00 0.00 3.95
4046 5611 5.841957 AGCAATTGTAGGATTTAGCAAGG 57.158 39.130 7.40 0.00 0.00 3.61
4080 5645 7.822334 TGTACAAGACTAAAAGTATGACCCATG 59.178 37.037 0.00 0.00 0.00 3.66
4110 5675 4.724399 TCCAGGACTTGAAACATAAAGCA 58.276 39.130 0.00 0.00 0.00 3.91
4153 5720 2.747855 GACCGCAGCCTTTCCCTG 60.748 66.667 0.00 0.00 0.00 4.45
4168 5735 2.640316 ACCACTTTGGGTCTTCTGAC 57.360 50.000 0.00 0.00 43.37 3.51
4244 5823 6.121590 TGCTTTATGCCTATCAAATCTCACA 58.878 36.000 0.00 0.00 42.00 3.58
4274 5853 8.884726 CATCAAAATGCATCACATAAAATCCAA 58.115 29.630 0.00 0.00 38.34 3.53
4342 5921 3.188873 ACTCAAGAGTCTTAAGACCGACG 59.811 47.826 28.05 16.47 45.85 5.12
4345 5924 4.142425 GGGTACTCAAGAGTCTTAAGACCG 60.142 50.000 28.05 16.16 45.85 4.79
4352 5931 7.162082 CACTAATTTGGGTACTCAAGAGTCTT 58.838 38.462 8.46 0.00 42.54 3.01
4353 5932 6.270231 ACACTAATTTGGGTACTCAAGAGTCT 59.730 38.462 8.46 0.00 42.54 3.24
4391 5970 9.184523 TCTTTTGAAAAGAAAACATAGGAGACA 57.815 29.630 17.27 0.00 0.00 3.41
4861 6440 3.857157 ATGTACGTTATGGGCCATCTT 57.143 42.857 25.07 5.83 0.00 2.40
4904 6483 9.887862 ATTATGTACTAGTAGTTTTAGGGCCTA 57.112 33.333 9.81 9.81 0.00 3.93
4937 6516 5.822519 TCAGTTAACAGTTCTTTGCAGTGAT 59.177 36.000 8.61 0.00 0.00 3.06
5018 6598 6.828273 CCCTGTCCATGATGAAAATACACTTA 59.172 38.462 0.00 0.00 0.00 2.24
5019 6599 5.653769 CCCTGTCCATGATGAAAATACACTT 59.346 40.000 0.00 0.00 0.00 3.16
5090 6670 2.396955 CGCTCTTTCCCAGCAGCAG 61.397 63.158 0.00 0.00 36.61 4.24
5157 6737 6.496144 AAAATAGTAGCTTAACCCTCGGAT 57.504 37.500 0.00 0.00 0.00 4.18
5272 6852 2.912956 TGCTACCTTGAACATTCCCTCT 59.087 45.455 0.00 0.00 0.00 3.69
5293 6873 7.155328 AGAGAATCGTCAGTGACAAAAACTAT 58.845 34.615 22.66 9.30 42.67 2.12
5310 6890 5.233988 AGAAGACAGGACAAAAGAGAATCG 58.766 41.667 0.00 0.00 42.67 3.34
5322 6902 3.608316 AGCATCAGAAGAAGACAGGAC 57.392 47.619 0.00 0.00 0.00 3.85
5471 7156 2.270352 TTTCAATGCCAGTCGGAAGT 57.730 45.000 0.00 0.00 0.00 3.01
5477 7162 4.455533 TGTACACTCATTTCAATGCCAGTC 59.544 41.667 0.00 0.00 36.36 3.51
5547 7232 6.839124 TCAATGGAATGTGCTTCTTACAAT 57.161 33.333 0.00 0.00 34.08 2.71
5550 7235 8.072567 GTCATATCAATGGAATGTGCTTCTTAC 58.927 37.037 0.00 0.00 34.08 2.34
5634 7321 4.101430 TGCATTCAGATACCAGCTACATGA 59.899 41.667 0.00 0.00 0.00 3.07
5743 7430 1.815003 GCCAGTAGCTGCAATTCAACT 59.185 47.619 4.12 0.00 38.99 3.16
5868 7555 3.771577 TCCTGTCAAAGAGAAGGGTTC 57.228 47.619 0.00 0.00 0.00 3.62
6010 7697 5.011023 GGGGCAATAATCCAACCTGAAATAG 59.989 44.000 0.00 0.00 0.00 1.73
6055 7742 7.741027 ATTGCTCTCAGATAATTACCACATG 57.259 36.000 0.00 0.00 0.00 3.21
6104 8028 8.001881 ACAACATCAGGACTACACTCTAATAG 57.998 38.462 0.00 0.00 0.00 1.73
6209 8133 1.582968 GCCACATGCAAGTGACTGG 59.417 57.895 22.96 7.75 42.05 4.00
6252 8176 6.567687 TGTCAAAGACAAACAAAAGAGTCA 57.432 33.333 0.00 0.00 39.78 3.41
6283 8207 1.477700 TGATTAACCAAGCTGCATGCC 59.522 47.619 16.68 0.00 44.23 4.40
6289 8213 6.392354 ACACAAATGATGATTAACCAAGCTG 58.608 36.000 0.00 0.00 0.00 4.24
6448 8372 5.840940 AGTTACACACTTAAACTCGATGC 57.159 39.130 0.00 0.00 27.32 3.91
6465 8389 7.519002 CAAATACAGAACAGCACCTTAGTTAC 58.481 38.462 0.00 0.00 0.00 2.50
6636 8560 8.993424 ACTAGTCTTACAGGGATAATTGATTGT 58.007 33.333 0.00 0.00 0.00 2.71
6668 8592 5.414360 AGCATAATAGCTACATCGACCATG 58.586 41.667 0.00 0.00 44.50 3.66
6669 8593 5.420421 AGAGCATAATAGCTACATCGACCAT 59.580 40.000 0.00 0.00 46.75 3.55
6670 8594 4.767409 AGAGCATAATAGCTACATCGACCA 59.233 41.667 0.00 0.00 46.75 4.02
6671 8595 5.317733 AGAGCATAATAGCTACATCGACC 57.682 43.478 0.00 0.00 46.75 4.79
6672 8596 6.843208 TGTAGAGCATAATAGCTACATCGAC 58.157 40.000 0.00 0.00 46.75 4.20
6673 8597 7.631717 ATGTAGAGCATAATAGCTACATCGA 57.368 36.000 0.00 0.00 46.13 3.59
6677 8601 7.445121 AGCAAATGTAGAGCATAATAGCTACA 58.555 34.615 0.00 0.00 46.75 2.74
6678 8602 7.897575 AGCAAATGTAGAGCATAATAGCTAC 57.102 36.000 0.00 0.00 46.75 3.58
6679 8603 7.095060 GCAAGCAAATGTAGAGCATAATAGCTA 60.095 37.037 0.00 0.00 46.75 3.32
6681 8605 5.855395 GCAAGCAAATGTAGAGCATAATAGC 59.145 40.000 0.00 0.00 36.67 2.97
6720 8648 6.001449 TCCTACCATAAGCAATAAAGCACT 57.999 37.500 0.00 0.00 36.85 4.40
6747 8675 9.575783 CAGAAAGACTTTTATACAGAGGACTAC 57.424 37.037 1.12 0.00 0.00 2.73
6765 8711 6.372659 TGGCAATCAGATTTCTACAGAAAGAC 59.627 38.462 10.01 6.96 45.87 3.01
6803 8749 7.928706 AGGTTATGCTATGAGATTGTAAGACAC 59.071 37.037 0.00 0.00 0.00 3.67
6965 8911 1.607467 CAGGGAAAAGGGTGCAGGG 60.607 63.158 0.00 0.00 0.00 4.45
7243 9199 3.214328 CAACTGCTACAACTCCCAAAGT 58.786 45.455 0.00 0.00 41.10 2.66
7284 9241 6.033966 GCCCAACTTTTATATCCAAAACTCG 58.966 40.000 0.00 0.00 0.00 4.18
7387 9349 3.288809 CTGGGTCAGCTTTAGTTTTGC 57.711 47.619 0.00 0.00 0.00 3.68
7416 9378 5.168569 TCTACTTGGTGAAGAACTATTGCG 58.831 41.667 0.00 0.00 32.98 4.85
7443 9405 9.713740 GTGAAATCTGCTATCTGAAGTAAATTG 57.286 33.333 0.00 0.00 0.00 2.32
7509 9471 3.569250 TTTCTTGCAAGCGGTTTATCC 57.431 42.857 21.99 0.00 0.00 2.59
7538 9500 9.582223 CTGTTGTCTTTCTTTTCGTTTATCTAC 57.418 33.333 0.00 0.00 0.00 2.59
7539 9501 9.537192 TCTGTTGTCTTTCTTTTCGTTTATCTA 57.463 29.630 0.00 0.00 0.00 1.98
7582 9594 6.850752 TCCCTCTTTTTCTGTTGTCTTTTT 57.149 33.333 0.00 0.00 0.00 1.94
7587 9599 5.221067 GGTCTTTCCCTCTTTTTCTGTTGTC 60.221 44.000 0.00 0.00 0.00 3.18
7623 9704 4.280677 CCTCGCCATCTCTCTCTTTATCTT 59.719 45.833 0.00 0.00 0.00 2.40
7624 9705 3.826157 CCTCGCCATCTCTCTCTTTATCT 59.174 47.826 0.00 0.00 0.00 1.98
7627 9708 1.683917 GCCTCGCCATCTCTCTCTTTA 59.316 52.381 0.00 0.00 0.00 1.85
7649 9730 3.423154 GCAAGGGTTCGACGCCTG 61.423 66.667 5.34 1.88 0.00 4.85
7650 9731 4.699522 GGCAAGGGTTCGACGCCT 62.700 66.667 5.34 0.00 39.73 5.52
7659 9740 0.768221 TGACTCAAGAGGGCAAGGGT 60.768 55.000 1.73 0.00 0.00 4.34
7677 9758 5.005586 CGCTTTGAGCTTATCTCTCTCTTTG 59.994 44.000 0.00 0.00 42.38 2.77
7678 9759 5.105554 TCGCTTTGAGCTTATCTCTCTCTTT 60.106 40.000 0.00 0.00 42.38 2.52
7689 9770 1.548719 TGGCTAGTCGCTTTGAGCTTA 59.451 47.619 0.00 0.00 39.60 3.09
7694 9775 0.178068 GGGATGGCTAGTCGCTTTGA 59.822 55.000 0.00 0.00 39.13 2.69
7722 9803 9.764363 TGTCATGTACAAAATATCCTACATCTC 57.236 33.333 0.00 0.00 34.29 2.75
7727 9808 6.204882 GGCCTGTCATGTACAAAATATCCTAC 59.795 42.308 0.00 0.00 37.74 3.18
7731 9812 7.986085 ATAGGCCTGTCATGTACAAAATATC 57.014 36.000 17.99 0.00 37.74 1.63
7732 9813 8.880244 TCTATAGGCCTGTCATGTACAAAATAT 58.120 33.333 17.99 0.00 37.74 1.28
7733 9814 8.257602 TCTATAGGCCTGTCATGTACAAAATA 57.742 34.615 17.99 0.00 37.74 1.40
7734 9815 7.136822 TCTATAGGCCTGTCATGTACAAAAT 57.863 36.000 17.99 0.00 37.74 1.82
7738 9819 6.552932 AGTATCTATAGGCCTGTCATGTACA 58.447 40.000 17.99 0.00 36.42 2.90
7739 9820 8.754991 ATAGTATCTATAGGCCTGTCATGTAC 57.245 38.462 17.99 11.23 0.00 2.90
7740 9821 8.782927 AGATAGTATCTATAGGCCTGTCATGTA 58.217 37.037 17.99 0.00 38.00 2.29
7741 9822 7.647827 AGATAGTATCTATAGGCCTGTCATGT 58.352 38.462 17.99 0.00 38.00 3.21
7742 9823 9.283768 CTAGATAGTATCTATAGGCCTGTCATG 57.716 40.741 17.99 2.99 40.82 3.07
7743 9824 9.231679 TCTAGATAGTATCTATAGGCCTGTCAT 57.768 37.037 17.99 7.32 40.82 3.06
7744 9825 8.487848 GTCTAGATAGTATCTATAGGCCTGTCA 58.512 40.741 17.99 0.00 40.82 3.58
7745 9826 8.487848 TGTCTAGATAGTATCTATAGGCCTGTC 58.512 40.741 17.99 0.00 40.82 3.51
7746 9827 8.395288 TGTCTAGATAGTATCTATAGGCCTGT 57.605 38.462 17.99 12.48 40.82 4.00
7747 9828 8.710239 TCTGTCTAGATAGTATCTATAGGCCTG 58.290 40.741 17.99 0.00 40.82 4.85
7765 9846 7.953158 TGAATTTGAACTGAAGTCTGTCTAG 57.047 36.000 0.00 0.00 0.00 2.43
7767 9848 7.630242 TTTGAATTTGAACTGAAGTCTGTCT 57.370 32.000 0.00 0.00 0.00 3.41
7814 9895 2.027625 GTGGAGTTCCTCGCCGTTG 61.028 63.158 0.00 0.00 38.89 4.10
7815 9896 2.035237 TTGTGGAGTTCCTCGCCGTT 62.035 55.000 0.00 0.00 38.89 4.44
7905 9992 1.529309 GGAGTGCCTCCTCCCAATC 59.471 63.158 12.53 0.00 46.41 2.67
7906 9993 3.746957 GGAGTGCCTCCTCCCAAT 58.253 61.111 12.53 0.00 46.41 3.16
7992 10091 2.586245 CGAGCTGGATTGGCAGGA 59.414 61.111 0.00 0.00 0.00 3.86
8082 10181 2.735772 GGCATGAGAGGGGAAGCGA 61.736 63.158 0.00 0.00 0.00 4.93
8083 10182 2.203126 GGCATGAGAGGGGAAGCG 60.203 66.667 0.00 0.00 0.00 4.68
8084 10183 2.203126 CGGCATGAGAGGGGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
8085 10184 2.203126 GCGGCATGAGAGGGGAAG 60.203 66.667 0.00 0.00 0.00 3.46
8086 10185 4.161295 CGCGGCATGAGAGGGGAA 62.161 66.667 0.00 0.00 0.00 3.97
8120 10219 2.842582 GCGTAACCGACATCGCGTC 61.843 63.158 5.77 0.00 41.62 5.19
8121 10220 2.877582 GCGTAACCGACATCGCGT 60.878 61.111 5.77 0.00 39.35 6.01
8123 10222 4.261495 GCGCGTAACCGACATCGC 62.261 66.667 8.43 0.00 44.23 4.58
8124 10223 3.613702 GGCGCGTAACCGACATCG 61.614 66.667 8.43 0.00 35.95 3.84
8125 10224 3.259751 GGGCGCGTAACCGACATC 61.260 66.667 8.43 0.00 38.19 3.06
8126 10225 4.825252 GGGGCGCGTAACCGACAT 62.825 66.667 8.43 0.00 38.19 3.06


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

AutoCloner maintained by Alex Coulton.