Multiple sequence alignment - TraesCS5A01G311900

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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 TraesCS5A01G311900 chr5A 100.000 2720 0 0 1 2720 523610515 523607796 0.000000e+00 5024.0
1 TraesCS5A01G311900 chr5A 87.797 631 64 8 1055 1677 523587986 523587361 0.000000e+00 726.0
2 TraesCS5A01G311900 chr5A 82.838 606 101 1 1063 1668 523567061 523566459 8.570000e-150 540.0
3 TraesCS5A01G311900 chr5A 78.226 124 15 8 933 1044 523588147 523588024 4.860000e-08 69.4
4 TraesCS5A01G311900 chr5D 92.026 1229 69 9 550 1762 411791112 411789897 0.000000e+00 1700.0
5 TraesCS5A01G311900 chr5D 88.122 623 74 0 1055 1677 411785499 411784877 0.000000e+00 741.0
6 TraesCS5A01G311900 chr5D 83.306 617 90 7 1066 1677 411743055 411742447 8.510000e-155 556.0
7 TraesCS5A01G311900 chr5D 92.557 309 16 5 1865 2173 411789310 411789009 1.160000e-118 436.0
8 TraesCS5A01G311900 chr5D 83.333 498 51 14 1 470 411791602 411791109 5.380000e-117 431.0
9 TraesCS5A01G311900 chr5D 92.442 172 8 1 2201 2372 411789015 411788849 9.730000e-60 241.0
10 TraesCS5A01G311900 chr5D 90.566 106 8 2 1767 1871 411789825 411789721 3.650000e-29 139.0
11 TraesCS5A01G311900 chr5D 97.403 77 2 0 2368 2444 411788559 411788483 6.110000e-27 132.0
12 TraesCS5A01G311900 chr5D 81.818 154 14 6 824 967 411743318 411743169 1.710000e-22 117.0
13 TraesCS5A01G311900 chr5B 89.147 1161 58 25 628 1762 494296963 494295845 0.000000e+00 1384.0
14 TraesCS5A01G311900 chr5B 87.748 906 63 20 887 1762 494045601 494044714 0.000000e+00 1014.0
15 TraesCS5A01G311900 chr5B 87.360 625 72 6 1055 1677 494033737 494033118 0.000000e+00 710.0
16 TraesCS5A01G311900 chr5B 88.975 517 34 6 1767 2271 494044606 494044101 3.850000e-173 617.0
17 TraesCS5A01G311900 chr5B 79.758 909 123 31 821 1677 494027132 494026233 1.080000e-168 603.0
18 TraesCS5A01G311900 chr5B 89.091 165 17 1 1913 2077 494295610 494295447 1.280000e-48 204.0
19 TraesCS5A01G311900 chr5B 84.729 203 27 4 269 470 494297391 494297192 1.650000e-47 200.0
20 TraesCS5A01G311900 chr5B 89.394 132 12 1 2080 2211 494295089 494294960 6.030000e-37 165.0
21 TraesCS5A01G311900 chr5B 87.368 95 7 3 640 729 494034147 494034053 1.330000e-18 104.0
22 TraesCS5A01G311900 chr6A 86.957 92 10 2 462 553 512181927 512182016 4.790000e-18 102.0


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 TraesCS5A01G311900 chr5A 523607796 523610515 2719 True 5024.000000 5024 100.000000 1 2720 1 chr5A.!!$R2 2719
1 TraesCS5A01G311900 chr5A 523566459 523567061 602 True 540.000000 540 82.838000 1063 1668 1 chr5A.!!$R1 605
2 TraesCS5A01G311900 chr5A 523587361 523588147 786 True 397.700000 726 83.011500 933 1677 2 chr5A.!!$R3 744
3 TraesCS5A01G311900 chr5D 411784877 411791602 6725 True 545.714286 1700 90.921286 1 2444 7 chr5D.!!$R2 2443
4 TraesCS5A01G311900 chr5D 411742447 411743318 871 True 336.500000 556 82.562000 824 1677 2 chr5D.!!$R1 853
5 TraesCS5A01G311900 chr5B 494044101 494045601 1500 True 815.500000 1014 88.361500 887 2271 2 chr5B.!!$R3 1384
6 TraesCS5A01G311900 chr5B 494026233 494027132 899 True 603.000000 603 79.758000 821 1677 1 chr5B.!!$R1 856
7 TraesCS5A01G311900 chr5B 494294960 494297391 2431 True 488.250000 1384 88.090250 269 2211 4 chr5B.!!$R4 1942
8 TraesCS5A01G311900 chr5B 494033118 494034147 1029 True 407.000000 710 87.364000 640 1677 2 chr5B.!!$R2 1037

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
391 418 0.028902 GTCGGTAATTTGGCGCCATC 59.971 55.0 33.25 17.44 0.0 3.51 F
918 1142 0.101399 AGCTCAAGTATCTCGCACCG 59.899 55.0 0.00 0.00 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 1859 0.100146 GTAGTACGAGCCCAAGTCCG 59.900 60.0 0.0 0.0 0.0 4.79 R
2618 4167 0.179084 GATCGGAGGCGAAATGGTCA 60.179 55.0 0.0 0.0 0.0 4.02 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
75 76 6.297694 TGCACATTTTCATTTAAAAGGCAC 57.702 33.333 0.00 0.00 41.45 5.01
77 78 5.238214 GCACATTTTCATTTAAAAGGCACCA 59.762 36.000 0.00 0.00 41.45 4.17
135 139 1.874345 GCTCTCGTCCCGGTTTCTCA 61.874 60.000 0.00 0.00 0.00 3.27
137 141 1.204941 CTCTCGTCCCGGTTTCTCAAT 59.795 52.381 0.00 0.00 0.00 2.57
142 146 3.998341 TCGTCCCGGTTTCTCAATAAAAG 59.002 43.478 0.00 0.00 0.00 2.27
144 148 4.142966 CGTCCCGGTTTCTCAATAAAAGAC 60.143 45.833 0.00 0.00 0.00 3.01
145 149 4.758165 GTCCCGGTTTCTCAATAAAAGACA 59.242 41.667 0.00 0.00 0.00 3.41
151 175 7.346695 CGGTTTCTCAATAAAAGACAACGTTA 58.653 34.615 0.00 0.00 30.92 3.18
167 191 8.033626 AGACAACGTTAGGGAAACTTCTAATAG 58.966 37.037 0.00 0.00 35.81 1.73
197 221 4.060205 GTTGTCAACACGGTGGTAGTTAT 58.940 43.478 13.48 0.00 0.00 1.89
201 225 4.151157 GTCAACACGGTGGTAGTTATTGAC 59.849 45.833 17.16 17.16 38.30 3.18
209 233 6.650390 ACGGTGGTAGTTATTGACGTTTTATT 59.350 34.615 0.00 0.00 0.00 1.40
221 245 5.849858 TGACGTTTTATTACAATGAGTCGC 58.150 37.500 0.00 0.00 0.00 5.19
222 246 5.405873 TGACGTTTTATTACAATGAGTCGCA 59.594 36.000 0.00 0.00 0.00 5.10
223 247 5.614760 ACGTTTTATTACAATGAGTCGCAC 58.385 37.500 0.00 0.00 0.00 5.34
244 268 3.440522 ACGCCTTGCCTAATTCTTTCTTC 59.559 43.478 0.00 0.00 0.00 2.87
245 269 3.691609 CGCCTTGCCTAATTCTTTCTTCT 59.308 43.478 0.00 0.00 0.00 2.85
246 270 4.201861 CGCCTTGCCTAATTCTTTCTTCTC 60.202 45.833 0.00 0.00 0.00 2.87
250 274 7.256286 CCTTGCCTAATTCTTTCTTCTCATTG 58.744 38.462 0.00 0.00 0.00 2.82
251 275 6.199937 TGCCTAATTCTTTCTTCTCATTGC 57.800 37.500 0.00 0.00 0.00 3.56
265 289 5.862924 TCTCATTGCTTTAGTAGTTGTGC 57.137 39.130 0.00 0.00 0.00 4.57
266 290 5.304778 TCTCATTGCTTTAGTAGTTGTGCA 58.695 37.500 0.00 0.00 0.00 4.57
274 298 5.395682 TTTAGTAGTTGTGCACGTCCTAT 57.604 39.130 13.13 0.00 0.00 2.57
315 342 2.610727 GCGTTTAGCTCCTTGAGACACT 60.611 50.000 0.00 0.00 44.04 3.55
331 358 9.903682 CTTGAGACACTACAATTCAATGAAAAT 57.096 29.630 0.00 0.00 0.00 1.82
339 366 5.484715 ACAATTCAATGAAAATGCCCTCTG 58.515 37.500 0.00 0.00 0.00 3.35
340 367 3.598019 TTCAATGAAAATGCCCTCTGC 57.402 42.857 0.00 0.00 41.77 4.26
341 368 2.811410 TCAATGAAAATGCCCTCTGCT 58.189 42.857 0.00 0.00 42.00 4.24
360 387 2.800250 CTTCCTTGAGTCCCAATTGCT 58.200 47.619 0.00 0.00 33.68 3.91
364 391 1.470098 CTTGAGTCCCAATTGCTTCGG 59.530 52.381 0.00 0.00 33.68 4.30
369 396 0.331278 TCCCAATTGCTTCGGACCAT 59.669 50.000 0.00 0.00 0.00 3.55
373 400 2.951642 CCAATTGCTTCGGACCATATGT 59.048 45.455 0.00 0.00 0.00 2.29
375 402 1.934589 TTGCTTCGGACCATATGTCG 58.065 50.000 1.24 3.26 45.46 4.35
391 418 0.028902 GTCGGTAATTTGGCGCCATC 59.971 55.000 33.25 17.44 0.00 3.51
428 457 1.901948 TGTCTCTCGTGCCTTCCGT 60.902 57.895 0.00 0.00 0.00 4.69
457 486 3.933861 AACTTGGAGAAACACAGGACT 57.066 42.857 0.00 0.00 0.00 3.85
469 498 7.907389 AGAAACACAGGACTCATTCAATAGTA 58.093 34.615 0.00 0.00 0.00 1.82
470 499 7.819900 AGAAACACAGGACTCATTCAATAGTAC 59.180 37.037 0.00 0.00 0.00 2.73
471 500 6.859112 ACACAGGACTCATTCAATAGTACT 57.141 37.500 0.00 0.00 37.38 2.73
472 501 6.868622 ACACAGGACTCATTCAATAGTACTC 58.131 40.000 0.00 0.00 34.55 2.59
473 502 6.127310 ACACAGGACTCATTCAATAGTACTCC 60.127 42.308 0.00 0.00 34.55 3.85
474 503 5.364157 ACAGGACTCATTCAATAGTACTCCC 59.636 44.000 0.00 0.00 34.55 4.30
475 504 5.600484 CAGGACTCATTCAATAGTACTCCCT 59.400 44.000 0.00 0.00 34.55 4.20
476 505 5.836358 AGGACTCATTCAATAGTACTCCCTC 59.164 44.000 0.00 0.00 30.80 4.30
477 506 5.836358 GGACTCATTCAATAGTACTCCCTCT 59.164 44.000 0.00 0.00 0.00 3.69
478 507 6.239176 GGACTCATTCAATAGTACTCCCTCTG 60.239 46.154 0.00 0.00 0.00 3.35
479 508 6.198639 ACTCATTCAATAGTACTCCCTCTGT 58.801 40.000 0.00 0.00 0.00 3.41
480 509 6.322712 ACTCATTCAATAGTACTCCCTCTGTC 59.677 42.308 0.00 0.00 0.00 3.51
481 510 5.598830 TCATTCAATAGTACTCCCTCTGTCC 59.401 44.000 0.00 0.00 0.00 4.02
482 511 3.912248 TCAATAGTACTCCCTCTGTCCC 58.088 50.000 0.00 0.00 0.00 4.46
483 512 3.271225 TCAATAGTACTCCCTCTGTCCCA 59.729 47.826 0.00 0.00 0.00 4.37
484 513 4.030913 CAATAGTACTCCCTCTGTCCCAA 58.969 47.826 0.00 0.00 0.00 4.12
485 514 2.715763 AGTACTCCCTCTGTCCCAAA 57.284 50.000 0.00 0.00 0.00 3.28
486 515 2.258109 AGTACTCCCTCTGTCCCAAAC 58.742 52.381 0.00 0.00 0.00 2.93
487 516 2.158143 AGTACTCCCTCTGTCCCAAACT 60.158 50.000 0.00 0.00 0.00 2.66
488 517 2.715763 ACTCCCTCTGTCCCAAACTA 57.284 50.000 0.00 0.00 0.00 2.24
489 518 3.207044 ACTCCCTCTGTCCCAAACTAT 57.793 47.619 0.00 0.00 0.00 2.12
490 519 4.348020 ACTCCCTCTGTCCCAAACTATA 57.652 45.455 0.00 0.00 0.00 1.31
491 520 4.695606 ACTCCCTCTGTCCCAAACTATAA 58.304 43.478 0.00 0.00 0.00 0.98
492 521 5.098663 ACTCCCTCTGTCCCAAACTATAAA 58.901 41.667 0.00 0.00 0.00 1.40
493 522 5.550403 ACTCCCTCTGTCCCAAACTATAAAA 59.450 40.000 0.00 0.00 0.00 1.52
494 523 6.045106 ACTCCCTCTGTCCCAAACTATAAAAA 59.955 38.462 0.00 0.00 0.00 1.94
495 524 6.243148 TCCCTCTGTCCCAAACTATAAAAAC 58.757 40.000 0.00 0.00 0.00 2.43
496 525 5.123344 CCCTCTGTCCCAAACTATAAAAACG 59.877 44.000 0.00 0.00 0.00 3.60
497 526 5.704053 CCTCTGTCCCAAACTATAAAAACGT 59.296 40.000 0.00 0.00 0.00 3.99
498 527 6.206048 CCTCTGTCCCAAACTATAAAAACGTT 59.794 38.462 0.00 0.00 0.00 3.99
499 528 7.255346 CCTCTGTCCCAAACTATAAAAACGTTT 60.255 37.037 7.96 7.96 0.00 3.60
500 529 7.998580 TCTGTCCCAAACTATAAAAACGTTTT 58.001 30.769 20.26 20.26 0.00 2.43
501 530 8.468399 TCTGTCCCAAACTATAAAAACGTTTTT 58.532 29.630 33.94 33.94 42.51 1.94
502 531 9.733219 CTGTCCCAAACTATAAAAACGTTTTTA 57.267 29.630 35.47 35.47 44.07 1.52
540 569 9.558648 GTGTTAAAAACGTTGTTATATTAGGGG 57.441 33.333 11.64 0.00 0.00 4.79
541 570 9.512588 TGTTAAAAACGTTGTTATATTAGGGGA 57.487 29.630 11.64 0.00 0.00 4.81
542 571 9.773328 GTTAAAAACGTTGTTATATTAGGGGAC 57.227 33.333 11.64 0.68 0.00 4.46
543 572 6.667007 AAAACGTTGTTATATTAGGGGACG 57.333 37.500 0.00 0.00 35.59 4.79
544 573 4.326504 ACGTTGTTATATTAGGGGACGG 57.673 45.455 0.00 0.00 33.95 4.79
545 574 3.960102 ACGTTGTTATATTAGGGGACGGA 59.040 43.478 0.00 0.00 33.95 4.69
546 575 4.038402 ACGTTGTTATATTAGGGGACGGAG 59.962 45.833 0.00 0.00 33.95 4.63
547 576 4.313282 GTTGTTATATTAGGGGACGGAGC 58.687 47.826 0.00 0.00 0.00 4.70
548 577 2.559668 TGTTATATTAGGGGACGGAGCG 59.440 50.000 0.00 0.00 0.00 5.03
549 578 2.821969 GTTATATTAGGGGACGGAGCGA 59.178 50.000 0.00 0.00 0.00 4.93
550 579 1.546961 ATATTAGGGGACGGAGCGAG 58.453 55.000 0.00 0.00 0.00 5.03
551 580 0.184451 TATTAGGGGACGGAGCGAGT 59.816 55.000 0.00 0.00 0.00 4.18
555 584 2.345760 GGGGACGGAGCGAGTAACA 61.346 63.158 0.00 0.00 0.00 2.41
576 605 1.228894 TGTCTGTCCCTTCGAGCCT 60.229 57.895 0.00 0.00 0.00 4.58
577 606 0.832135 TGTCTGTCCCTTCGAGCCTT 60.832 55.000 0.00 0.00 0.00 4.35
578 607 0.108567 GTCTGTCCCTTCGAGCCTTC 60.109 60.000 0.00 0.00 0.00 3.46
579 608 0.541998 TCTGTCCCTTCGAGCCTTCA 60.542 55.000 0.00 0.00 0.00 3.02
580 609 0.390472 CTGTCCCTTCGAGCCTTCAC 60.390 60.000 0.00 0.00 0.00 3.18
581 610 0.832135 TGTCCCTTCGAGCCTTCACT 60.832 55.000 0.00 0.00 0.00 3.41
582 611 1.183549 GTCCCTTCGAGCCTTCACTA 58.816 55.000 0.00 0.00 0.00 2.74
583 612 1.135333 GTCCCTTCGAGCCTTCACTAG 59.865 57.143 0.00 0.00 0.00 2.57
621 650 4.722700 CCAGCCGTCCAACCCCAG 62.723 72.222 0.00 0.00 0.00 4.45
684 880 2.483583 TGTTTAACACTGCAAAGCCG 57.516 45.000 0.00 0.00 0.00 5.52
723 925 3.436015 CAGCAGGAGAAAAGTCACATGAG 59.564 47.826 0.00 0.00 28.92 2.90
729 931 5.045286 AGGAGAAAAGTCACATGAGGCTATT 60.045 40.000 0.00 0.00 0.00 1.73
820 1026 1.927174 GTCTTCAGCGCGTTCATACAT 59.073 47.619 8.43 0.00 0.00 2.29
822 1028 2.603110 TCTTCAGCGCGTTCATACATTC 59.397 45.455 8.43 0.00 0.00 2.67
844 1054 0.325933 AGCTCCAGCACAGCACATAA 59.674 50.000 0.48 0.00 45.16 1.90
855 1065 7.226523 CCAGCACAGCACATAACTATAAATACA 59.773 37.037 0.00 0.00 0.00 2.29
892 1113 2.946762 GCCAACAGCGAACACTCC 59.053 61.111 0.00 0.00 0.00 3.85
907 1131 1.071385 CACTCCCACTCAAGCTCAAGT 59.929 52.381 0.00 0.00 0.00 3.16
918 1142 0.101399 AGCTCAAGTATCTCGCACCG 59.899 55.000 0.00 0.00 0.00 4.94
919 1143 0.872021 GCTCAAGTATCTCGCACCGG 60.872 60.000 0.00 0.00 0.00 5.28
920 1144 0.738975 CTCAAGTATCTCGCACCGGA 59.261 55.000 9.46 0.00 0.00 5.14
921 1145 0.738975 TCAAGTATCTCGCACCGGAG 59.261 55.000 9.46 0.00 35.32 4.63
1022 1262 1.535685 GCATGGGCCTTGAGATCCT 59.464 57.895 22.50 0.00 0.00 3.24
1424 1703 2.358125 CATCACCGCCACCGTCAA 60.358 61.111 0.00 0.00 0.00 3.18
1464 1743 4.813526 CCTGCGGAGTCGTCGTCG 62.814 72.222 2.36 0.00 38.89 5.12
1509 1788 0.663568 AGACGTCGAAACCTTCTGCG 60.664 55.000 10.46 0.00 0.00 5.18
1515 1794 1.508088 GAAACCTTCTGCGCATGGG 59.492 57.895 12.24 15.94 0.00 4.00
1521 1800 3.884704 TTCTGCGCATGGGGCCTTT 62.885 57.895 12.24 0.00 40.86 3.11
1580 1859 1.001706 GCTTGACTTGTTCCCGGAAAC 60.002 52.381 0.73 0.00 0.00 2.78
1632 1911 4.783621 GCGCTGCTCATGGACCCA 62.784 66.667 0.00 0.00 0.00 4.51
1679 1958 2.100989 GTACTGGGATGACGGAGAGTT 58.899 52.381 0.00 0.00 0.00 3.01
1688 1973 3.441290 CGGAGAGTTCGGCGAGGT 61.441 66.667 10.46 0.27 0.00 3.85
1731 2017 1.757118 AGCTTGTAGCCGATTCTGCTA 59.243 47.619 5.77 5.77 43.77 3.49
1866 2307 3.315191 TCAAGCTGTAAAAAGGAGCACAC 59.685 43.478 0.00 0.00 35.03 3.82
1870 2311 4.159506 AGCTGTAAAAAGGAGCACACAAAA 59.840 37.500 0.00 0.00 35.03 2.44
1931 2786 2.125952 GACGGCTTTGCAATGGGC 60.126 61.111 13.62 13.72 45.13 5.36
1989 2844 0.032540 CAACAGGCAAAGCAGAACCC 59.967 55.000 0.00 0.00 0.00 4.11
1998 2853 0.894184 AAGCAGAACCCGACGAGAGA 60.894 55.000 0.00 0.00 0.00 3.10
2005 2860 2.477176 CCCGACGAGAGAGAGGCAG 61.477 68.421 0.00 0.00 0.00 4.85
2047 2913 0.452784 GTTCGCAACGAGCAATCCAC 60.453 55.000 0.00 0.00 46.13 4.02
2100 3321 3.126514 CGTCTGTCTATAACGTGTGGTCT 59.873 47.826 0.00 0.00 0.00 3.85
2134 3355 4.974721 CACGGGCCCAGCAGGTTT 62.975 66.667 24.92 0.00 38.26 3.27
2168 3423 3.506810 CTCTGAATCTTCTCGGTGTGTC 58.493 50.000 0.00 0.00 0.00 3.67
2169 3424 3.157881 TCTGAATCTTCTCGGTGTGTCT 58.842 45.455 0.00 0.00 0.00 3.41
2170 3425 3.191581 TCTGAATCTTCTCGGTGTGTCTC 59.808 47.826 0.00 0.00 0.00 3.36
2171 3426 2.231478 TGAATCTTCTCGGTGTGTCTCC 59.769 50.000 0.00 0.00 0.00 3.71
2172 3427 2.223803 ATCTTCTCGGTGTGTCTCCT 57.776 50.000 0.00 0.00 0.00 3.69
2173 3428 1.248486 TCTTCTCGGTGTGTCTCCTG 58.752 55.000 0.00 0.00 0.00 3.86
2174 3429 0.962489 CTTCTCGGTGTGTCTCCTGT 59.038 55.000 0.00 0.00 0.00 4.00
2175 3430 0.673985 TTCTCGGTGTGTCTCCTGTG 59.326 55.000 0.00 0.00 0.00 3.66
2176 3431 1.179174 TCTCGGTGTGTCTCCTGTGG 61.179 60.000 0.00 0.00 0.00 4.17
2177 3432 1.152631 TCGGTGTGTCTCCTGTGGA 60.153 57.895 0.00 0.00 0.00 4.02
2178 3433 0.757561 TCGGTGTGTCTCCTGTGGAA 60.758 55.000 0.00 0.00 0.00 3.53
2179 3434 0.105964 CGGTGTGTCTCCTGTGGAAA 59.894 55.000 0.00 0.00 0.00 3.13
2180 3435 1.270839 CGGTGTGTCTCCTGTGGAAAT 60.271 52.381 0.00 0.00 0.00 2.17
2181 3436 2.427506 GGTGTGTCTCCTGTGGAAATC 58.572 52.381 0.00 0.00 0.00 2.17
2182 3437 2.039084 GGTGTGTCTCCTGTGGAAATCT 59.961 50.000 0.00 0.00 0.00 2.40
2183 3438 3.496870 GGTGTGTCTCCTGTGGAAATCTT 60.497 47.826 0.00 0.00 0.00 2.40
2184 3439 4.137543 GTGTGTCTCCTGTGGAAATCTTT 58.862 43.478 0.00 0.00 0.00 2.52
2185 3440 4.023707 GTGTGTCTCCTGTGGAAATCTTTG 60.024 45.833 0.00 0.00 0.00 2.77
2186 3441 3.057946 GTGTCTCCTGTGGAAATCTTTGC 60.058 47.826 0.00 0.00 0.00 3.68
2187 3442 3.149196 GTCTCCTGTGGAAATCTTTGCA 58.851 45.455 0.00 0.00 36.11 4.08
2188 3443 3.190118 GTCTCCTGTGGAAATCTTTGCAG 59.810 47.826 0.00 0.00 39.20 4.41
2189 3444 1.888512 TCCTGTGGAAATCTTTGCAGC 59.111 47.619 0.00 0.00 39.20 5.25
2190 3445 1.891150 CCTGTGGAAATCTTTGCAGCT 59.109 47.619 0.00 0.00 39.20 4.24
2191 3446 2.352421 CCTGTGGAAATCTTTGCAGCTG 60.352 50.000 10.11 10.11 39.20 4.24
2192 3447 2.555325 CTGTGGAAATCTTTGCAGCTGA 59.445 45.455 20.43 0.00 39.20 4.26
2193 3448 2.555325 TGTGGAAATCTTTGCAGCTGAG 59.445 45.455 20.43 6.19 39.20 3.35
2194 3449 1.542915 TGGAAATCTTTGCAGCTGAGC 59.457 47.619 20.43 2.81 33.44 4.26
2195 3450 1.135170 GGAAATCTTTGCAGCTGAGCC 60.135 52.381 20.43 0.00 0.00 4.70
2196 3451 1.817447 GAAATCTTTGCAGCTGAGCCT 59.183 47.619 20.43 0.00 0.00 4.58
2197 3452 1.174783 AATCTTTGCAGCTGAGCCTG 58.825 50.000 20.43 2.79 35.93 4.85
2221 3476 1.609072 TCACCTTCACTCACAGACTCG 59.391 52.381 0.00 0.00 0.00 4.18
2242 3497 2.418746 GCTTTCAGCGGGACTAAGATGA 60.419 50.000 0.00 0.00 0.00 2.92
2325 3580 4.271696 TGTAGGATGTGACTTGTCCTTG 57.728 45.455 9.35 0.00 42.24 3.61
2330 3585 2.543777 TGTGACTTGTCCTTGTAGCC 57.456 50.000 0.00 0.00 0.00 3.93
2365 3620 5.163744 ACGTGTAGTGATACTTGCTGAGTAG 60.164 44.000 0.00 0.00 43.79 2.57
2397 3946 3.666001 GTGTGCACAATACGTAATTCCG 58.334 45.455 23.59 0.00 0.00 4.30
2438 3987 6.015434 GGTGTAAAGGATTTCACAGGATTTGT 60.015 38.462 0.00 0.00 40.09 2.83
2444 3993 8.877864 AAGGATTTCACAGGATTTGTATAACA 57.122 30.769 0.00 0.00 38.16 2.41
2445 3994 8.281212 AGGATTTCACAGGATTTGTATAACAC 57.719 34.615 0.00 0.00 38.16 3.32
2446 3995 8.109634 AGGATTTCACAGGATTTGTATAACACT 58.890 33.333 0.00 0.00 38.16 3.55
2447 3996 9.391006 GGATTTCACAGGATTTGTATAACACTA 57.609 33.333 0.00 0.00 38.16 2.74
2477 4026 9.985730 TTTCTTTCGTAGTACTATTTTGAAGGA 57.014 29.630 5.75 10.69 0.00 3.36
2478 4027 9.985730 TTCTTTCGTAGTACTATTTTGAAGGAA 57.014 29.630 19.15 19.15 30.70 3.36
2479 4028 9.985730 TCTTTCGTAGTACTATTTTGAAGGAAA 57.014 29.630 5.75 6.57 0.00 3.13
2482 4031 9.768662 TTCGTAGTACTATTTTGAAGGAAAACT 57.231 29.630 5.75 0.00 36.35 2.66
2509 4058 7.158099 AGGAAAATGATAACTAGCAAACACC 57.842 36.000 0.00 0.00 0.00 4.16
2510 4059 6.719370 AGGAAAATGATAACTAGCAAACACCA 59.281 34.615 0.00 0.00 0.00 4.17
2511 4060 7.029563 GGAAAATGATAACTAGCAAACACCAG 58.970 38.462 0.00 0.00 0.00 4.00
2512 4061 7.094377 GGAAAATGATAACTAGCAAACACCAGA 60.094 37.037 0.00 0.00 0.00 3.86
2513 4062 7.944729 AAATGATAACTAGCAAACACCAGAT 57.055 32.000 0.00 0.00 0.00 2.90
2514 4063 7.944729 AATGATAACTAGCAAACACCAGATT 57.055 32.000 0.00 0.00 0.00 2.40
2515 4064 7.944729 ATGATAACTAGCAAACACCAGATTT 57.055 32.000 0.00 0.00 0.00 2.17
2516 4065 7.759489 TGATAACTAGCAAACACCAGATTTT 57.241 32.000 0.00 0.00 0.00 1.82
2517 4066 8.177119 TGATAACTAGCAAACACCAGATTTTT 57.823 30.769 0.00 0.00 0.00 1.94
2532 4081 3.395210 TTTTTGGCGCTCTGAGTGA 57.605 47.368 21.63 0.00 0.00 3.41
2533 4082 1.674359 TTTTTGGCGCTCTGAGTGAA 58.326 45.000 21.63 5.40 0.00 3.18
2534 4083 0.944386 TTTTGGCGCTCTGAGTGAAC 59.056 50.000 21.63 13.22 0.00 3.18
2535 4084 1.221466 TTTGGCGCTCTGAGTGAACG 61.221 55.000 21.63 9.92 37.33 3.95
2538 4087 2.811317 CGCTCTGAGTGAACGCCC 60.811 66.667 12.80 0.00 0.00 6.13
2539 4088 2.659610 GCTCTGAGTGAACGCCCT 59.340 61.111 6.53 0.00 0.00 5.19
2540 4089 1.446966 GCTCTGAGTGAACGCCCTC 60.447 63.158 6.53 0.00 0.00 4.30
2541 4090 1.967535 CTCTGAGTGAACGCCCTCA 59.032 57.895 0.00 0.00 36.35 3.86
2542 4091 0.318441 CTCTGAGTGAACGCCCTCAA 59.682 55.000 0.00 0.00 37.27 3.02
2543 4092 0.756294 TCTGAGTGAACGCCCTCAAA 59.244 50.000 0.00 0.00 37.27 2.69
2544 4093 1.151668 CTGAGTGAACGCCCTCAAAG 58.848 55.000 0.00 0.00 37.27 2.77
2545 4094 0.884704 TGAGTGAACGCCCTCAAAGC 60.885 55.000 0.00 0.00 34.88 3.51
2546 4095 1.578206 GAGTGAACGCCCTCAAAGCC 61.578 60.000 0.00 0.00 0.00 4.35
2547 4096 2.668212 TGAACGCCCTCAAAGCCG 60.668 61.111 0.00 0.00 0.00 5.52
2548 4097 2.668550 GAACGCCCTCAAAGCCGT 60.669 61.111 0.00 0.00 35.14 5.68
2549 4098 2.668550 AACGCCCTCAAAGCCGTC 60.669 61.111 0.00 0.00 32.89 4.79
2550 4099 3.178540 AACGCCCTCAAAGCCGTCT 62.179 57.895 0.00 0.00 32.89 4.18
2551 4100 3.121030 CGCCCTCAAAGCCGTCTG 61.121 66.667 0.00 0.00 0.00 3.51
2552 4101 2.347490 GCCCTCAAAGCCGTCTGA 59.653 61.111 0.00 0.00 0.00 3.27
2553 4102 1.078143 GCCCTCAAAGCCGTCTGAT 60.078 57.895 0.00 0.00 0.00 2.90
2554 4103 1.092345 GCCCTCAAAGCCGTCTGATC 61.092 60.000 0.00 0.00 0.00 2.92
2555 4104 0.250234 CCCTCAAAGCCGTCTGATCA 59.750 55.000 0.00 0.00 0.00 2.92
2556 4105 1.134280 CCCTCAAAGCCGTCTGATCAT 60.134 52.381 0.00 0.00 0.00 2.45
2557 4106 1.938577 CCTCAAAGCCGTCTGATCATG 59.061 52.381 0.00 0.00 0.00 3.07
2558 4107 1.938577 CTCAAAGCCGTCTGATCATGG 59.061 52.381 0.00 0.00 0.00 3.66
2559 4108 1.278985 TCAAAGCCGTCTGATCATGGT 59.721 47.619 0.00 0.00 0.00 3.55
2560 4109 2.499693 TCAAAGCCGTCTGATCATGGTA 59.500 45.455 0.00 0.00 0.00 3.25
2561 4110 2.868583 CAAAGCCGTCTGATCATGGTAG 59.131 50.000 0.00 0.00 0.00 3.18
2562 4111 2.073252 AGCCGTCTGATCATGGTAGA 57.927 50.000 0.00 0.00 0.00 2.59
2563 4112 2.388735 AGCCGTCTGATCATGGTAGAA 58.611 47.619 0.00 0.00 0.00 2.10
2564 4113 2.101582 AGCCGTCTGATCATGGTAGAAC 59.898 50.000 0.00 0.00 0.00 3.01
2565 4114 2.159099 GCCGTCTGATCATGGTAGAACA 60.159 50.000 0.00 0.00 0.00 3.18
2566 4115 3.678806 GCCGTCTGATCATGGTAGAACAA 60.679 47.826 0.00 0.00 0.00 2.83
2567 4116 3.865745 CCGTCTGATCATGGTAGAACAAC 59.134 47.826 0.00 0.00 0.00 3.32
2568 4117 4.494484 CGTCTGATCATGGTAGAACAACA 58.506 43.478 0.00 0.00 0.00 3.33
2569 4118 4.564372 CGTCTGATCATGGTAGAACAACAG 59.436 45.833 0.00 0.00 0.00 3.16
2570 4119 4.331168 GTCTGATCATGGTAGAACAACAGC 59.669 45.833 0.00 0.00 0.00 4.40
2571 4120 4.020307 TCTGATCATGGTAGAACAACAGCA 60.020 41.667 0.00 0.00 0.00 4.41
2572 4121 4.650734 TGATCATGGTAGAACAACAGCAA 58.349 39.130 0.00 0.00 0.00 3.91
2573 4122 5.255687 TGATCATGGTAGAACAACAGCAAT 58.744 37.500 0.00 0.00 0.00 3.56
2574 4123 5.711506 TGATCATGGTAGAACAACAGCAATT 59.288 36.000 0.00 0.00 0.00 2.32
2575 4124 6.209192 TGATCATGGTAGAACAACAGCAATTT 59.791 34.615 0.00 0.00 0.00 1.82
2576 4125 6.403866 TCATGGTAGAACAACAGCAATTTT 57.596 33.333 0.00 0.00 0.00 1.82
2577 4126 6.815089 TCATGGTAGAACAACAGCAATTTTT 58.185 32.000 0.00 0.00 0.00 1.94
2578 4127 6.922957 TCATGGTAGAACAACAGCAATTTTTC 59.077 34.615 0.00 0.00 0.00 2.29
2579 4128 6.463995 TGGTAGAACAACAGCAATTTTTCT 57.536 33.333 6.60 6.60 0.00 2.52
2580 4129 6.272318 TGGTAGAACAACAGCAATTTTTCTG 58.728 36.000 10.16 0.00 36.45 3.02
2581 4130 6.127479 TGGTAGAACAACAGCAATTTTTCTGT 60.127 34.615 10.16 0.35 44.64 3.41
2582 4131 6.198966 GGTAGAACAACAGCAATTTTTCTGTG 59.801 38.462 10.16 4.10 42.19 3.66
2583 4132 5.964758 AGAACAACAGCAATTTTTCTGTGA 58.035 33.333 5.76 0.00 42.19 3.58
2584 4133 6.397272 AGAACAACAGCAATTTTTCTGTGAA 58.603 32.000 5.76 0.00 42.19 3.18
2585 4134 6.532657 AGAACAACAGCAATTTTTCTGTGAAG 59.467 34.615 5.76 3.36 42.19 3.02
2593 4142 3.673746 TTTTTCTGTGAAGCGTGACAG 57.326 42.857 12.70 12.70 40.89 3.51
2622 4171 1.828979 TTTTTCCCCGCTACATGACC 58.171 50.000 0.00 0.00 0.00 4.02
2623 4172 0.693622 TTTTCCCCGCTACATGACCA 59.306 50.000 0.00 0.00 0.00 4.02
2634 4183 0.744414 ACATGACCATTTCGCCTCCG 60.744 55.000 0.00 0.00 0.00 4.63
2635 4184 0.461870 CATGACCATTTCGCCTCCGA 60.462 55.000 0.00 0.00 42.66 4.55
2646 4195 1.729881 GCCTCCGATCATGGCAAAC 59.270 57.895 13.62 0.00 45.46 2.93
2649 4198 0.107017 CTCCGATCATGGCAAACCCT 60.107 55.000 0.00 0.00 33.59 4.34
2651 4200 1.134220 TCCGATCATGGCAAACCCTAC 60.134 52.381 0.00 0.00 33.59 3.18
2653 4202 2.364632 CGATCATGGCAAACCCTACAA 58.635 47.619 0.00 0.00 33.59 2.41
2664 4213 4.037446 GCAAACCCTACAAAGTTGACATGA 59.963 41.667 0.00 0.00 0.00 3.07
2666 4215 4.431416 ACCCTACAAAGTTGACATGACA 57.569 40.909 0.00 0.00 0.00 3.58
2689 4238 9.869757 GACAAATTTATTAGTAGGTTTGGCATT 57.130 29.630 0.00 0.00 35.29 3.56
2703 4254 5.505985 GGTTTGGCATTGTAAGTTTGACGTA 60.506 40.000 0.00 0.00 0.00 3.57
2704 4255 5.950758 TTGGCATTGTAAGTTTGACGTAT 57.049 34.783 0.00 0.00 0.00 3.06
2709 4260 5.390461 GCATTGTAAGTTTGACGTATGCTGA 60.390 40.000 5.57 0.00 35.89 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.006323 ACTCGGATCCAAGCACATAGATC 59.994 47.826 13.41 0.00 35.45 2.75
12 13 2.362397 GACTCGGATCCAAGCACATAGA 59.638 50.000 13.41 0.00 0.00 1.98
45 46 7.670009 TTTAAATGAAAATGTGCATGAAGGG 57.330 32.000 0.00 0.00 0.00 3.95
47 48 7.747357 GCCTTTTAAATGAAAATGTGCATGAAG 59.253 33.333 0.00 0.00 36.44 3.02
104 108 1.465387 GACGAGAGCTCTTCAGAACGA 59.535 52.381 19.36 0.00 0.00 3.85
135 139 7.812690 AGTTTCCCTAACGTTGTCTTTTATT 57.187 32.000 11.99 0.00 41.78 1.40
137 141 7.049754 AGAAGTTTCCCTAACGTTGTCTTTTA 58.950 34.615 11.99 0.00 41.78 1.52
142 146 7.816513 ACTATTAGAAGTTTCCCTAACGTTGTC 59.183 37.037 11.99 0.00 41.78 3.18
144 148 8.543862 AACTATTAGAAGTTTCCCTAACGTTG 57.456 34.615 11.99 0.68 41.78 4.10
145 149 7.543520 CGAACTATTAGAAGTTTCCCTAACGTT 59.456 37.037 5.88 5.88 39.78 3.99
151 175 6.210984 ACACTCGAACTATTAGAAGTTTCCCT 59.789 38.462 0.00 0.00 39.78 4.20
197 221 6.073711 TGCGACTCATTGTAATAAAACGTCAA 60.074 34.615 0.00 0.00 0.00 3.18
201 225 4.717299 CGTGCGACTCATTGTAATAAAACG 59.283 41.667 0.00 0.00 0.00 3.60
209 233 0.037697 AAGGCGTGCGACTCATTGTA 60.038 50.000 0.00 0.00 29.93 2.41
221 245 2.749621 AGAAAGAATTAGGCAAGGCGTG 59.250 45.455 0.00 0.00 0.00 5.34
222 246 3.073274 AGAAAGAATTAGGCAAGGCGT 57.927 42.857 0.00 0.00 0.00 5.68
223 247 3.691609 AGAAGAAAGAATTAGGCAAGGCG 59.308 43.478 0.00 0.00 0.00 5.52
244 268 5.385617 GTGCACAACTACTAAAGCAATGAG 58.614 41.667 13.17 0.00 33.37 2.90
245 269 4.084066 CGTGCACAACTACTAAAGCAATGA 60.084 41.667 18.64 0.00 33.37 2.57
246 270 4.151070 CGTGCACAACTACTAAAGCAATG 58.849 43.478 18.64 0.00 33.37 2.82
250 274 2.157085 GGACGTGCACAACTACTAAAGC 59.843 50.000 18.64 0.00 0.00 3.51
251 275 3.650139 AGGACGTGCACAACTACTAAAG 58.350 45.455 18.64 0.00 0.00 1.85
256 280 2.094390 TGGATAGGACGTGCACAACTAC 60.094 50.000 18.64 9.62 0.00 2.73
258 282 0.973632 TGGATAGGACGTGCACAACT 59.026 50.000 18.64 13.37 0.00 3.16
265 289 1.942657 CCTTTGCATGGATAGGACGTG 59.057 52.381 17.09 0.00 0.00 4.49
266 290 1.559682 ACCTTTGCATGGATAGGACGT 59.440 47.619 26.38 5.26 0.00 4.34
274 298 0.478072 ACACCTGACCTTTGCATGGA 59.522 50.000 12.48 0.00 0.00 3.41
311 335 6.014327 AGGGCATTTTCATTGAATTGTAGTGT 60.014 34.615 0.00 0.00 0.00 3.55
315 342 6.632909 CAGAGGGCATTTTCATTGAATTGTA 58.367 36.000 0.00 0.00 0.00 2.41
339 366 1.203287 GCAATTGGGACTCAAGGAAGC 59.797 52.381 7.72 0.00 38.95 3.86
340 367 2.800250 AGCAATTGGGACTCAAGGAAG 58.200 47.619 7.72 0.00 38.95 3.46
341 368 2.978156 AGCAATTGGGACTCAAGGAA 57.022 45.000 7.72 0.00 38.95 3.36
360 387 4.675976 AATTACCGACATATGGTCCGAA 57.324 40.909 7.80 0.37 43.95 4.30
364 391 3.059188 CGCCAAATTACCGACATATGGTC 60.059 47.826 7.80 1.77 40.96 4.02
369 396 1.301423 GGCGCCAAATTACCGACATA 58.699 50.000 24.80 0.00 0.00 2.29
373 400 1.433053 CGATGGCGCCAAATTACCGA 61.433 55.000 36.33 6.47 0.00 4.69
398 425 0.957395 GAGAGACACCGGTGACCGTA 60.957 60.000 40.21 0.00 46.80 4.02
409 436 1.444553 CGGAAGGCACGAGAGACAC 60.445 63.158 0.00 0.00 0.00 3.67
412 439 1.863662 GACACGGAAGGCACGAGAGA 61.864 60.000 3.38 0.00 34.93 3.10
416 443 3.220999 CTGGACACGGAAGGCACGA 62.221 63.158 3.38 0.00 34.93 4.35
428 457 5.163248 TGTGTTTCTCCAAGTTATCTGGACA 60.163 40.000 0.00 0.00 0.00 4.02
457 486 5.598830 GGACAGAGGGAGTACTATTGAATGA 59.401 44.000 0.00 0.00 0.00 2.57
469 498 2.715763 TAGTTTGGGACAGAGGGAGT 57.284 50.000 0.00 0.00 42.39 3.85
470 499 5.693769 TTTATAGTTTGGGACAGAGGGAG 57.306 43.478 0.00 0.00 42.39 4.30
471 500 6.243148 GTTTTTATAGTTTGGGACAGAGGGA 58.757 40.000 0.00 0.00 42.39 4.20
472 501 5.123344 CGTTTTTATAGTTTGGGACAGAGGG 59.877 44.000 0.00 0.00 42.39 4.30
473 502 5.704053 ACGTTTTTATAGTTTGGGACAGAGG 59.296 40.000 0.00 0.00 42.39 3.69
474 503 6.796705 ACGTTTTTATAGTTTGGGACAGAG 57.203 37.500 0.00 0.00 42.39 3.35
475 504 7.571080 AAACGTTTTTATAGTTTGGGACAGA 57.429 32.000 7.96 0.00 42.39 3.41
476 505 8.637281 AAAAACGTTTTTATAGTTTGGGACAG 57.363 30.769 31.82 0.00 37.97 3.51
514 543 9.558648 CCCCTAATATAACAACGTTTTTAACAC 57.441 33.333 10.67 0.00 0.00 3.32
515 544 9.512588 TCCCCTAATATAACAACGTTTTTAACA 57.487 29.630 10.67 3.27 0.00 2.41
516 545 9.773328 GTCCCCTAATATAACAACGTTTTTAAC 57.227 33.333 10.67 0.00 0.00 2.01
517 546 8.663911 CGTCCCCTAATATAACAACGTTTTTAA 58.336 33.333 10.67 2.24 0.00 1.52
518 547 7.279758 CCGTCCCCTAATATAACAACGTTTTTA 59.720 37.037 9.18 9.18 0.00 1.52
519 548 6.093909 CCGTCCCCTAATATAACAACGTTTTT 59.906 38.462 0.00 0.31 0.00 1.94
520 549 5.585844 CCGTCCCCTAATATAACAACGTTTT 59.414 40.000 0.00 0.00 0.00 2.43
521 550 5.104982 TCCGTCCCCTAATATAACAACGTTT 60.105 40.000 0.00 0.00 0.00 3.60
522 551 4.405358 TCCGTCCCCTAATATAACAACGTT 59.595 41.667 0.00 0.00 0.00 3.99
523 552 3.960102 TCCGTCCCCTAATATAACAACGT 59.040 43.478 0.00 0.00 0.00 3.99
524 553 4.553323 CTCCGTCCCCTAATATAACAACG 58.447 47.826 0.00 0.00 0.00 4.10
525 554 4.313282 GCTCCGTCCCCTAATATAACAAC 58.687 47.826 0.00 0.00 0.00 3.32
526 555 3.006110 CGCTCCGTCCCCTAATATAACAA 59.994 47.826 0.00 0.00 0.00 2.83
527 556 2.559668 CGCTCCGTCCCCTAATATAACA 59.440 50.000 0.00 0.00 0.00 2.41
528 557 2.821969 TCGCTCCGTCCCCTAATATAAC 59.178 50.000 0.00 0.00 0.00 1.89
529 558 3.087031 CTCGCTCCGTCCCCTAATATAA 58.913 50.000 0.00 0.00 0.00 0.98
530 559 2.040813 ACTCGCTCCGTCCCCTAATATA 59.959 50.000 0.00 0.00 0.00 0.86
531 560 1.203025 ACTCGCTCCGTCCCCTAATAT 60.203 52.381 0.00 0.00 0.00 1.28
532 561 0.184451 ACTCGCTCCGTCCCCTAATA 59.816 55.000 0.00 0.00 0.00 0.98
533 562 0.184451 TACTCGCTCCGTCCCCTAAT 59.816 55.000 0.00 0.00 0.00 1.73
534 563 0.034186 TTACTCGCTCCGTCCCCTAA 60.034 55.000 0.00 0.00 0.00 2.69
535 564 0.749454 GTTACTCGCTCCGTCCCCTA 60.749 60.000 0.00 0.00 0.00 3.53
536 565 2.050934 GTTACTCGCTCCGTCCCCT 61.051 63.158 0.00 0.00 0.00 4.79
537 566 1.880819 TTGTTACTCGCTCCGTCCCC 61.881 60.000 0.00 0.00 0.00 4.81
538 567 0.735287 GTTGTTACTCGCTCCGTCCC 60.735 60.000 0.00 0.00 0.00 4.46
539 568 0.243095 AGTTGTTACTCGCTCCGTCC 59.757 55.000 0.00 0.00 0.00 4.79
540 569 1.335689 ACAGTTGTTACTCGCTCCGTC 60.336 52.381 0.00 0.00 30.26 4.79
541 570 0.672342 ACAGTTGTTACTCGCTCCGT 59.328 50.000 0.00 0.00 30.26 4.69
542 571 1.068472 AGACAGTTGTTACTCGCTCCG 60.068 52.381 0.00 0.00 30.26 4.63
543 572 2.288273 ACAGACAGTTGTTACTCGCTCC 60.288 50.000 0.00 0.00 30.26 4.70
544 573 2.981140 GACAGACAGTTGTTACTCGCTC 59.019 50.000 0.00 0.00 30.26 5.03
545 574 2.288273 GGACAGACAGTTGTTACTCGCT 60.288 50.000 0.00 0.00 30.26 4.93
546 575 2.059541 GGACAGACAGTTGTTACTCGC 58.940 52.381 0.00 0.00 30.26 5.03
547 576 2.296471 AGGGACAGACAGTTGTTACTCG 59.704 50.000 0.00 0.00 30.26 4.18
548 577 4.308265 GAAGGGACAGACAGTTGTTACTC 58.692 47.826 0.00 0.00 30.26 2.59
549 578 3.243771 CGAAGGGACAGACAGTTGTTACT 60.244 47.826 0.00 0.00 34.00 2.24
550 579 3.057734 CGAAGGGACAGACAGTTGTTAC 58.942 50.000 0.00 0.00 0.00 2.50
551 580 2.960384 TCGAAGGGACAGACAGTTGTTA 59.040 45.455 0.00 0.00 0.00 2.41
555 584 0.318762 GCTCGAAGGGACAGACAGTT 59.681 55.000 0.00 0.00 0.00 3.16
613 642 0.693049 ACTAGTGAAGGCTGGGGTTG 59.307 55.000 0.00 0.00 0.00 3.77
621 650 3.113260 ACACAGTGAACTAGTGAAGGC 57.887 47.619 7.81 0.00 37.05 4.35
729 931 7.010367 CGTGTAGGATTAAATTAAGTGGCGTTA 59.990 37.037 0.00 0.00 0.00 3.18
751 953 2.654877 GTGACGATGGGACCGTGT 59.345 61.111 0.00 0.00 40.67 4.49
820 1026 1.669115 GCTGTGCTGGAGCTTCGAA 60.669 57.895 0.00 0.00 42.66 3.71
822 1028 2.357881 TGCTGTGCTGGAGCTTCG 60.358 61.111 0.00 0.00 42.66 3.79
844 1054 8.198109 GTGGAGTGTGTGAGATGTATTTATAGT 58.802 37.037 0.00 0.00 0.00 2.12
855 1065 2.354503 GCATCTGTGGAGTGTGTGAGAT 60.355 50.000 0.00 0.00 0.00 2.75
892 1113 3.443037 CGAGATACTTGAGCTTGAGTGG 58.557 50.000 11.84 0.00 0.00 4.00
907 1131 0.179026 AGCTACTCCGGTGCGAGATA 60.179 55.000 0.00 0.00 33.83 1.98
919 1143 2.442413 AGTGAGGAGTGTGAGCTACTC 58.558 52.381 6.58 6.58 44.68 2.59
920 1144 2.595750 AGTGAGGAGTGTGAGCTACT 57.404 50.000 0.00 0.00 31.03 2.57
921 1145 3.428316 GCTTAGTGAGGAGTGTGAGCTAC 60.428 52.174 0.00 0.00 0.00 3.58
1022 1262 2.955246 AGGAGGGGGAGGAGCTCA 60.955 66.667 17.19 0.00 31.08 4.26
1455 1734 1.132232 GTCAGACTCCGACGACGAC 59.868 63.158 9.28 0.00 42.66 4.34
1464 1743 2.105128 CCGGCATCGTCAGACTCC 59.895 66.667 0.00 0.00 33.95 3.85
1580 1859 0.100146 GTAGTACGAGCCCAAGTCCG 59.900 60.000 0.00 0.00 0.00 4.79
1669 1948 2.100603 CTCGCCGAACTCTCCGTC 59.899 66.667 0.00 0.00 0.00 4.79
1679 1958 4.680237 CAGTTGCCACCTCGCCGA 62.680 66.667 0.00 0.00 0.00 5.54
1688 1973 3.345808 GCGCGAACTCAGTTGCCA 61.346 61.111 12.10 0.00 0.00 4.92
1715 2000 3.819564 AACATAGCAGAATCGGCTACA 57.180 42.857 16.72 0.00 45.77 2.74
1792 2180 4.091549 AGAACCGGAGTATAAACAGTGGA 58.908 43.478 9.46 0.00 0.00 4.02
1830 2219 2.287915 CAGCTTGAAACTGCGTGTACTT 59.712 45.455 0.00 0.00 0.00 2.24
1870 2311 6.734137 TGTATCTGCTTCGATTTGTGTTTTT 58.266 32.000 0.00 0.00 0.00 1.94
1873 2314 4.997395 ACTGTATCTGCTTCGATTTGTGTT 59.003 37.500 0.00 0.00 0.00 3.32
1875 2316 5.807520 ACTACTGTATCTGCTTCGATTTGTG 59.192 40.000 0.00 0.00 0.00 3.33
1920 2775 1.714541 TTTCTGGAGCCCATTGCAAA 58.285 45.000 1.71 0.00 44.83 3.68
1989 2844 1.653094 AAGCTGCCTCTCTCTCGTCG 61.653 60.000 0.00 0.00 0.00 5.12
1998 2853 0.901124 ATCGACTGAAAGCTGCCTCT 59.099 50.000 0.00 0.00 37.60 3.69
2005 2860 3.335579 AGGGTTAACATCGACTGAAAGC 58.664 45.455 8.10 0.00 37.60 3.51
2047 2913 2.385013 TGACATCGGACCACATCTTG 57.615 50.000 0.00 0.00 0.00 3.02
2100 3321 0.895530 GTGACCAGATCAACCCGAGA 59.104 55.000 0.00 0.00 39.72 4.04
2168 3423 2.094854 GCTGCAAAGATTTCCACAGGAG 60.095 50.000 0.00 0.00 31.21 3.69
2169 3424 1.888512 GCTGCAAAGATTTCCACAGGA 59.111 47.619 0.00 0.00 0.00 3.86
2170 3425 1.891150 AGCTGCAAAGATTTCCACAGG 59.109 47.619 1.02 0.00 0.00 4.00
2171 3426 2.555325 TCAGCTGCAAAGATTTCCACAG 59.445 45.455 9.47 0.00 0.00 3.66
2172 3427 2.555325 CTCAGCTGCAAAGATTTCCACA 59.445 45.455 9.47 0.00 0.00 4.17
2173 3428 2.670509 GCTCAGCTGCAAAGATTTCCAC 60.671 50.000 9.47 0.00 0.00 4.02
2174 3429 1.542915 GCTCAGCTGCAAAGATTTCCA 59.457 47.619 9.47 0.00 0.00 3.53
2175 3430 1.135170 GGCTCAGCTGCAAAGATTTCC 60.135 52.381 9.47 0.00 34.04 3.13
2176 3431 1.817447 AGGCTCAGCTGCAAAGATTTC 59.183 47.619 9.47 0.00 34.04 2.17
2177 3432 1.544691 CAGGCTCAGCTGCAAAGATTT 59.455 47.619 9.47 0.00 34.04 2.17
2178 3433 1.174783 CAGGCTCAGCTGCAAAGATT 58.825 50.000 9.47 0.00 34.04 2.40
2179 3434 1.313812 GCAGGCTCAGCTGCAAAGAT 61.314 55.000 9.47 0.00 45.11 2.40
2180 3435 1.970114 GCAGGCTCAGCTGCAAAGA 60.970 57.895 9.47 0.00 45.11 2.52
2181 3436 2.567049 GCAGGCTCAGCTGCAAAG 59.433 61.111 9.47 2.20 45.11 2.77
2186 3441 4.383861 TGACGGCAGGCTCAGCTG 62.384 66.667 7.63 7.63 43.90 4.24
2187 3442 4.385405 GTGACGGCAGGCTCAGCT 62.385 66.667 0.00 0.00 0.00 4.24
2189 3444 3.245668 AAGGTGACGGCAGGCTCAG 62.246 63.158 0.00 0.00 0.00 3.35
2190 3445 3.240134 GAAGGTGACGGCAGGCTCA 62.240 63.158 0.00 0.00 0.00 4.26
2191 3446 2.435059 GAAGGTGACGGCAGGCTC 60.435 66.667 0.00 0.00 0.00 4.70
2192 3447 3.241530 TGAAGGTGACGGCAGGCT 61.242 61.111 0.00 0.00 0.00 4.58
2193 3448 3.050275 GTGAAGGTGACGGCAGGC 61.050 66.667 0.00 0.00 0.00 4.85
2194 3449 1.374758 GAGTGAAGGTGACGGCAGG 60.375 63.158 0.00 0.00 0.00 4.85
2195 3450 0.946221 GTGAGTGAAGGTGACGGCAG 60.946 60.000 0.00 0.00 0.00 4.85
2196 3451 1.069090 GTGAGTGAAGGTGACGGCA 59.931 57.895 0.00 0.00 0.00 5.69
2197 3452 0.946221 CTGTGAGTGAAGGTGACGGC 60.946 60.000 0.00 0.00 0.00 5.68
2198 3453 0.673985 TCTGTGAGTGAAGGTGACGG 59.326 55.000 0.00 0.00 0.00 4.79
2199 3454 1.338337 AGTCTGTGAGTGAAGGTGACG 59.662 52.381 0.00 0.00 0.00 4.35
2200 3455 2.605823 CGAGTCTGTGAGTGAAGGTGAC 60.606 54.545 0.00 0.00 0.00 3.67
2201 3456 1.609072 CGAGTCTGTGAGTGAAGGTGA 59.391 52.381 0.00 0.00 0.00 4.02
2242 3497 1.376942 GAGTGTGCTGCTGCCTCAT 60.377 57.895 13.47 0.00 38.71 2.90
2275 3530 4.699522 AAGAACACCCGCCGGCTC 62.700 66.667 26.68 14.27 0.00 4.70
2325 3580 6.856938 CACTACACGTCTAAATATCTGGCTAC 59.143 42.308 0.00 0.00 0.00 3.58
2365 3620 2.733218 TGCACACGCGCTAGTCAC 60.733 61.111 5.73 0.00 42.97 3.67
2451 4000 9.985730 TCCTTCAAAATAGTACTACGAAAGAAA 57.014 29.630 4.31 0.00 0.00 2.52
2452 4001 9.985730 TTCCTTCAAAATAGTACTACGAAAGAA 57.014 29.630 4.31 8.44 0.00 2.52
2453 4002 9.985730 TTTCCTTCAAAATAGTACTACGAAAGA 57.014 29.630 4.31 3.19 0.00 2.52
2456 4005 9.768662 AGTTTTCCTTCAAAATAGTACTACGAA 57.231 29.630 4.31 5.41 36.35 3.85
2483 4032 8.903820 GGTGTTTGCTAGTTATCATTTTCCTAT 58.096 33.333 0.00 0.00 0.00 2.57
2484 4033 7.885922 TGGTGTTTGCTAGTTATCATTTTCCTA 59.114 33.333 0.00 0.00 0.00 2.94
2485 4034 6.719370 TGGTGTTTGCTAGTTATCATTTTCCT 59.281 34.615 0.00 0.00 0.00 3.36
2486 4035 6.919721 TGGTGTTTGCTAGTTATCATTTTCC 58.080 36.000 0.00 0.00 0.00 3.13
2487 4036 7.816640 TCTGGTGTTTGCTAGTTATCATTTTC 58.183 34.615 0.00 0.00 0.00 2.29
2488 4037 7.759489 TCTGGTGTTTGCTAGTTATCATTTT 57.241 32.000 0.00 0.00 0.00 1.82
2489 4038 7.944729 ATCTGGTGTTTGCTAGTTATCATTT 57.055 32.000 0.00 0.00 0.00 2.32
2490 4039 7.944729 AATCTGGTGTTTGCTAGTTATCATT 57.055 32.000 0.00 0.00 0.00 2.57
2491 4040 7.944729 AAATCTGGTGTTTGCTAGTTATCAT 57.055 32.000 0.00 0.00 0.00 2.45
2492 4041 7.759489 AAAATCTGGTGTTTGCTAGTTATCA 57.241 32.000 0.00 0.00 0.00 2.15
2514 4063 1.333619 GTTCACTCAGAGCGCCAAAAA 59.666 47.619 2.29 0.00 0.00 1.94
2515 4064 0.944386 GTTCACTCAGAGCGCCAAAA 59.056 50.000 2.29 0.00 0.00 2.44
2516 4065 1.221466 CGTTCACTCAGAGCGCCAAA 61.221 55.000 2.29 0.00 43.81 3.28
2517 4066 1.664649 CGTTCACTCAGAGCGCCAA 60.665 57.895 2.29 0.00 43.81 4.52
2518 4067 2.049156 CGTTCACTCAGAGCGCCA 60.049 61.111 2.29 0.00 43.81 5.69
2522 4071 1.446966 GAGGGCGTTCACTCAGAGC 60.447 63.158 0.00 0.00 33.95 4.09
2523 4072 0.318441 TTGAGGGCGTTCACTCAGAG 59.682 55.000 0.00 0.00 43.84 3.35
2524 4073 0.756294 TTTGAGGGCGTTCACTCAGA 59.244 50.000 0.00 0.00 43.84 3.27
2525 4074 1.151668 CTTTGAGGGCGTTCACTCAG 58.848 55.000 0.00 0.00 43.84 3.35
2526 4075 0.884704 GCTTTGAGGGCGTTCACTCA 60.885 55.000 0.00 0.00 41.63 3.41
2527 4076 1.578206 GGCTTTGAGGGCGTTCACTC 61.578 60.000 0.00 0.00 0.00 3.51
2528 4077 1.600916 GGCTTTGAGGGCGTTCACT 60.601 57.895 0.00 0.00 0.00 3.41
2529 4078 2.954611 GGCTTTGAGGGCGTTCAC 59.045 61.111 0.00 0.00 0.00 3.18
2535 4084 1.078143 ATCAGACGGCTTTGAGGGC 60.078 57.895 0.00 0.00 0.00 5.19
2536 4085 0.250234 TGATCAGACGGCTTTGAGGG 59.750 55.000 0.00 0.00 0.00 4.30
2537 4086 1.938577 CATGATCAGACGGCTTTGAGG 59.061 52.381 0.09 0.00 0.00 3.86
2538 4087 1.938577 CCATGATCAGACGGCTTTGAG 59.061 52.381 0.09 0.00 0.00 3.02
2539 4088 1.278985 ACCATGATCAGACGGCTTTGA 59.721 47.619 0.09 0.00 0.00 2.69
2540 4089 1.742761 ACCATGATCAGACGGCTTTG 58.257 50.000 0.09 0.00 0.00 2.77
2541 4090 2.766263 TCTACCATGATCAGACGGCTTT 59.234 45.455 0.09 0.00 0.00 3.51
2542 4091 2.388735 TCTACCATGATCAGACGGCTT 58.611 47.619 0.09 0.00 0.00 4.35
2543 4092 2.073252 TCTACCATGATCAGACGGCT 57.927 50.000 0.09 0.00 0.00 5.52
2544 4093 2.159099 TGTTCTACCATGATCAGACGGC 60.159 50.000 0.09 0.00 0.00 5.68
2545 4094 3.801114 TGTTCTACCATGATCAGACGG 57.199 47.619 0.09 4.27 0.00 4.79
2546 4095 4.494484 TGTTGTTCTACCATGATCAGACG 58.506 43.478 0.09 0.00 0.00 4.18
2547 4096 4.331168 GCTGTTGTTCTACCATGATCAGAC 59.669 45.833 0.09 0.00 0.00 3.51
2548 4097 4.020307 TGCTGTTGTTCTACCATGATCAGA 60.020 41.667 0.09 0.00 0.00 3.27
2549 4098 4.256110 TGCTGTTGTTCTACCATGATCAG 58.744 43.478 0.09 0.00 0.00 2.90
2550 4099 4.284829 TGCTGTTGTTCTACCATGATCA 57.715 40.909 0.00 0.00 0.00 2.92
2551 4100 5.824904 ATTGCTGTTGTTCTACCATGATC 57.175 39.130 0.00 0.00 0.00 2.92
2552 4101 6.594788 AAATTGCTGTTGTTCTACCATGAT 57.405 33.333 0.00 0.00 0.00 2.45
2553 4102 6.403866 AAAATTGCTGTTGTTCTACCATGA 57.596 33.333 0.00 0.00 0.00 3.07
2554 4103 6.925165 AGAAAAATTGCTGTTGTTCTACCATG 59.075 34.615 5.58 0.00 0.00 3.66
2555 4104 6.925165 CAGAAAAATTGCTGTTGTTCTACCAT 59.075 34.615 6.72 0.00 0.00 3.55
2556 4105 6.127479 ACAGAAAAATTGCTGTTGTTCTACCA 60.127 34.615 0.72 0.00 42.33 3.25
2557 4106 6.198966 CACAGAAAAATTGCTGTTGTTCTACC 59.801 38.462 3.97 0.00 42.33 3.18
2558 4107 6.972328 TCACAGAAAAATTGCTGTTGTTCTAC 59.028 34.615 3.97 0.00 42.33 2.59
2559 4108 7.094508 TCACAGAAAAATTGCTGTTGTTCTA 57.905 32.000 3.97 0.00 42.33 2.10
2560 4109 5.964758 TCACAGAAAAATTGCTGTTGTTCT 58.035 33.333 3.97 2.42 42.33 3.01
2561 4110 6.645700 TTCACAGAAAAATTGCTGTTGTTC 57.354 33.333 3.97 0.00 42.33 3.18
2562 4111 5.063817 GCTTCACAGAAAAATTGCTGTTGTT 59.936 36.000 3.97 0.00 42.33 2.83
2563 4112 4.567959 GCTTCACAGAAAAATTGCTGTTGT 59.432 37.500 3.97 0.00 42.33 3.32
2564 4113 4.317558 CGCTTCACAGAAAAATTGCTGTTG 60.318 41.667 3.97 1.67 42.33 3.33
2565 4114 3.798337 CGCTTCACAGAAAAATTGCTGTT 59.202 39.130 3.97 0.00 42.33 3.16
2566 4115 3.181487 ACGCTTCACAGAAAAATTGCTGT 60.181 39.130 0.72 0.72 45.62 4.40
2567 4116 3.180980 CACGCTTCACAGAAAAATTGCTG 59.819 43.478 0.00 0.00 38.10 4.41
2568 4117 3.066621 TCACGCTTCACAGAAAAATTGCT 59.933 39.130 0.00 0.00 0.00 3.91
2569 4118 3.180387 GTCACGCTTCACAGAAAAATTGC 59.820 43.478 0.00 0.00 0.00 3.56
2570 4119 4.350346 TGTCACGCTTCACAGAAAAATTG 58.650 39.130 0.00 0.00 0.00 2.32
2571 4120 4.096382 ACTGTCACGCTTCACAGAAAAATT 59.904 37.500 0.07 0.00 42.37 1.82
2572 4121 3.627577 ACTGTCACGCTTCACAGAAAAAT 59.372 39.130 0.07 0.00 42.37 1.82
2573 4122 3.006940 ACTGTCACGCTTCACAGAAAAA 58.993 40.909 0.07 0.00 42.37 1.94
2574 4123 2.627945 ACTGTCACGCTTCACAGAAAA 58.372 42.857 0.07 0.00 42.37 2.29
2575 4124 2.309528 ACTGTCACGCTTCACAGAAA 57.690 45.000 0.07 0.00 42.37 2.52
2576 4125 2.309528 AACTGTCACGCTTCACAGAA 57.690 45.000 0.07 0.00 42.37 3.02
2577 4126 2.309528 AAACTGTCACGCTTCACAGA 57.690 45.000 0.07 0.00 42.37 3.41
2578 4127 2.609459 AGAAAACTGTCACGCTTCACAG 59.391 45.455 0.00 0.00 44.83 3.66
2579 4128 2.351418 CAGAAAACTGTCACGCTTCACA 59.649 45.455 0.00 0.00 0.00 3.58
2580 4129 2.351726 ACAGAAAACTGTCACGCTTCAC 59.648 45.455 0.00 0.00 30.83 3.18
2581 4130 2.627945 ACAGAAAACTGTCACGCTTCA 58.372 42.857 0.00 0.00 30.83 3.02
2582 4131 3.675467 AACAGAAAACTGTCACGCTTC 57.325 42.857 3.38 0.00 36.42 3.86
2583 4132 4.434713 AAAACAGAAAACTGTCACGCTT 57.565 36.364 3.38 0.00 36.42 4.68
2584 4133 4.434713 AAAAACAGAAAACTGTCACGCT 57.565 36.364 3.38 0.00 36.42 5.07
2608 4157 1.308998 GAAATGGTCATGTAGCGGGG 58.691 55.000 0.00 0.00 0.00 5.73
2609 4158 0.937304 CGAAATGGTCATGTAGCGGG 59.063 55.000 0.00 0.00 0.00 6.13
2611 4160 0.304705 GGCGAAATGGTCATGTAGCG 59.695 55.000 0.00 0.00 0.00 4.26
2612 4161 1.599542 GAGGCGAAATGGTCATGTAGC 59.400 52.381 0.00 0.00 0.00 3.58
2613 4162 2.213499 GGAGGCGAAATGGTCATGTAG 58.787 52.381 0.00 0.00 0.00 2.74
2614 4163 1.472552 CGGAGGCGAAATGGTCATGTA 60.473 52.381 0.00 0.00 0.00 2.29
2615 4164 0.744414 CGGAGGCGAAATGGTCATGT 60.744 55.000 0.00 0.00 0.00 3.21
2616 4165 0.461870 TCGGAGGCGAAATGGTCATG 60.462 55.000 0.00 0.00 0.00 3.07
2617 4166 0.469917 ATCGGAGGCGAAATGGTCAT 59.530 50.000 0.00 0.00 0.00 3.06
2618 4167 0.179084 GATCGGAGGCGAAATGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
2619 4168 0.179084 TGATCGGAGGCGAAATGGTC 60.179 55.000 0.00 0.00 0.00 4.02
2620 4169 0.469917 ATGATCGGAGGCGAAATGGT 59.530 50.000 0.00 0.00 0.00 3.55
2621 4170 0.870393 CATGATCGGAGGCGAAATGG 59.130 55.000 0.00 0.00 0.00 3.16
2622 4171 0.870393 CCATGATCGGAGGCGAAATG 59.130 55.000 0.00 0.00 0.00 2.32
2623 4172 0.886490 GCCATGATCGGAGGCGAAAT 60.886 55.000 7.06 0.00 38.86 2.17
2634 4183 3.763897 ACTTTGTAGGGTTTGCCATGATC 59.236 43.478 0.00 0.00 36.17 2.92
2635 4184 3.778265 ACTTTGTAGGGTTTGCCATGAT 58.222 40.909 0.00 0.00 36.17 2.45
2646 4195 5.766150 TTTGTCATGTCAACTTTGTAGGG 57.234 39.130 4.81 0.00 0.00 3.53
2664 4213 9.651913 CAATGCCAAACCTACTAATAAATTTGT 57.348 29.630 0.00 0.00 0.00 2.83
2678 4227 4.499019 CGTCAAACTTACAATGCCAAACCT 60.499 41.667 0.00 0.00 0.00 3.50
2689 4238 6.606234 TTTTCAGCATACGTCAAACTTACA 57.394 33.333 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.