Multiple sequence alignment - TraesCS2B01G276300

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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 TraesCS2B01G276300 chr2B 100.000 4735 0 0 1 4735 381920126 381915392 0.000000e+00 8745.0
1 TraesCS2B01G276300 chr2D 93.360 3976 175 38 52 3969 314081593 314077649 0.000000e+00 5797.0
2 TraesCS2B01G276300 chr2D 89.567 508 35 5 2178 2678 314047480 314046984 3.110000e-176 628.0
3 TraesCS2B01G276300 chr2D 83.651 367 35 14 4003 4364 314077555 314077209 5.910000e-84 322.0
4 TraesCS2B01G276300 chr2A 93.779 3054 119 23 936 3969 422095669 422098671 0.000000e+00 4521.0
5 TraesCS2B01G276300 chr2A 79.500 200 15 10 3966 4165 422098832 422099005 8.320000e-23 119.0
6 TraesCS2B01G276300 chr1A 76.133 662 99 47 188 801 548555133 548554483 4.630000e-75 292.0
7 TraesCS2B01G276300 chr1A 79.392 296 45 15 278 563 456447240 456446951 1.340000e-45 195.0
8 TraesCS2B01G276300 chr5D 76.569 478 83 26 237 696 342964522 342964056 7.920000e-58 235.0
9 TraesCS2B01G276300 chr7A 75.439 570 91 37 336 879 107401775 107402321 1.020000e-56 231.0
10 TraesCS2B01G276300 chr7A 78.149 389 58 24 154 524 566005607 566005986 6.170000e-54 222.0
11 TraesCS2B01G276300 chr7B 75.701 535 86 35 154 669 527959671 527960180 1.330000e-55 228.0
12 TraesCS2B01G276300 chr3A 77.311 357 66 12 154 500 35756172 35755821 3.740000e-46 196.0
13 TraesCS2B01G276300 chr5B 76.762 383 64 24 302 669 423234296 423233924 1.740000e-44 191.0
14 TraesCS2B01G276300 chr3D 77.152 302 43 19 133 420 457064657 457064946 8.210000e-33 152.0
15 TraesCS2B01G276300 chrUn 88.462 52 5 1 4560 4611 51450373 51450423 1.420000e-05 62.1


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 TraesCS2B01G276300 chr2B 381915392 381920126 4734 True 8745.0 8745 100.0000 1 4735 1 chr2B.!!$R1 4734
1 TraesCS2B01G276300 chr2D 314077209 314081593 4384 True 3059.5 5797 88.5055 52 4364 2 chr2D.!!$R2 4312
2 TraesCS2B01G276300 chr2A 422095669 422099005 3336 False 2320.0 4521 86.6395 936 4165 2 chr2A.!!$F1 3229
3 TraesCS2B01G276300 chr1A 548554483 548555133 650 True 292.0 292 76.1330 188 801 1 chr1A.!!$R2 613
4 TraesCS2B01G276300 chr7A 107401775 107402321 546 False 231.0 231 75.4390 336 879 1 chr7A.!!$F1 543
5 TraesCS2B01G276300 chr7B 527959671 527960180 509 False 228.0 228 75.7010 154 669 1 chr7B.!!$F1 515

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
941 1196 3.983420 CTGGGCCCCAAAGCAGGA 61.983 66.667 22.27 0.0 30.80 3.86 F
1367 1623 0.514691 CCGTTCAGTTTGAGCTGAGC 59.485 55.000 0.00 0.0 45.03 4.26 F
3039 3305 0.037303 CCACTGGTGACTCTTGGCAT 59.963 55.000 1.93 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2198 5.049129 GGCCTGAATAGCACATTGAAGATAC 60.049 44.0 0.0 0.0 0.0 2.24 R
3122 3388 1.191535 CCTAGTTCCACCACCATCGA 58.808 55.0 0.0 0.0 0.0 3.59 R
4454 4900 0.033090 AACGTCTCAGAACCCGAACC 59.967 55.0 0.0 0.0 0.0 3.62 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
25 26 7.977985 GTACACATTCAACATTTTTCGTACAC 58.022 34.615 0.00 0.00 0.00 2.90
26 27 6.556212 ACACATTCAACATTTTTCGTACACA 58.444 32.000 0.00 0.00 0.00 3.72
27 28 7.199766 ACACATTCAACATTTTTCGTACACAT 58.800 30.769 0.00 0.00 0.00 3.21
28 29 7.704472 ACACATTCAACATTTTTCGTACACATT 59.296 29.630 0.00 0.00 0.00 2.71
29 30 7.997658 CACATTCAACATTTTTCGTACACATTG 59.002 33.333 0.00 0.00 0.00 2.82
30 31 7.168972 ACATTCAACATTTTTCGTACACATTGG 59.831 33.333 0.00 0.00 0.00 3.16
31 32 6.378710 TCAACATTTTTCGTACACATTGGA 57.621 33.333 0.00 0.00 0.00 3.53
32 33 6.796426 TCAACATTTTTCGTACACATTGGAA 58.204 32.000 0.00 0.00 0.00 3.53
33 34 7.258441 TCAACATTTTTCGTACACATTGGAAA 58.742 30.769 0.00 0.00 0.00 3.13
34 35 7.221067 TCAACATTTTTCGTACACATTGGAAAC 59.779 33.333 0.00 0.00 0.00 2.78
35 36 6.565234 ACATTTTTCGTACACATTGGAAACA 58.435 32.000 0.00 0.00 39.83 2.83
36 37 7.206687 ACATTTTTCGTACACATTGGAAACAT 58.793 30.769 0.00 0.00 42.32 2.71
37 38 7.708752 ACATTTTTCGTACACATTGGAAACATT 59.291 29.630 0.00 0.00 42.32 2.71
38 39 8.547069 CATTTTTCGTACACATTGGAAACATTT 58.453 29.630 0.00 0.00 42.32 2.32
39 40 8.480643 TTTTTCGTACACATTGGAAACATTTT 57.519 26.923 0.00 0.00 42.32 1.82
40 41 8.480643 TTTTCGTACACATTGGAAACATTTTT 57.519 26.923 0.00 0.00 42.32 1.94
235 244 9.374838 GCTTGATCATCCTTTTTCAAATACATT 57.625 29.630 0.00 0.00 0.00 2.71
277 286 8.049117 AGACATGGTCAACACATTTCTATACAT 58.951 33.333 0.00 0.00 34.56 2.29
278 287 8.579850 ACATGGTCAACACATTTCTATACATT 57.420 30.769 0.00 0.00 0.00 2.71
279 288 9.679661 ACATGGTCAACACATTTCTATACATTA 57.320 29.630 0.00 0.00 0.00 1.90
282 291 9.898152 TGGTCAACACATTTCTATACATTATCA 57.102 29.630 0.00 0.00 0.00 2.15
532 731 7.040494 TGGTCAAATGGTTTATATGCACATTG 58.960 34.615 0.00 0.00 32.60 2.82
547 749 6.230849 TGCACATTGAATTTTGAAATGCTC 57.769 33.333 0.00 0.00 35.20 4.26
568 770 7.367285 TGCTCGATTAACATTTTTAAACAGCT 58.633 30.769 0.00 0.00 0.00 4.24
941 1196 3.983420 CTGGGCCCCAAAGCAGGA 61.983 66.667 22.27 0.00 30.80 3.86
1054 1309 2.432444 CGGCTCCAAACTTTATGTCCA 58.568 47.619 0.00 0.00 0.00 4.02
1167 1422 3.726517 CGGCTTGCCGTTGACCTG 61.727 66.667 24.03 0.00 0.00 4.00
1239 1494 2.024871 CGCGGTCTCGATGTCCTC 59.975 66.667 0.00 0.00 39.00 3.71
1258 1513 2.498078 CTCACTAACAAGGTCTCCCTCC 59.502 54.545 0.00 0.00 41.56 4.30
1295 1551 2.163509 CTCCTCTCGAACACTCCAGAA 58.836 52.381 0.00 0.00 0.00 3.02
1300 1556 0.530744 TCGAACACTCCAGAATCCCG 59.469 55.000 0.00 0.00 0.00 5.14
1317 1573 8.237267 CAGAATCCCGCCTTGTATATATTTTTC 58.763 37.037 0.00 0.00 0.00 2.29
1318 1574 8.164070 AGAATCCCGCCTTGTATATATTTTTCT 58.836 33.333 0.00 0.00 0.00 2.52
1320 1576 7.739498 TCCCGCCTTGTATATATTTTTCTTC 57.261 36.000 0.00 0.00 0.00 2.87
1321 1577 7.284074 TCCCGCCTTGTATATATTTTTCTTCA 58.716 34.615 0.00 0.00 0.00 3.02
1322 1578 7.776030 TCCCGCCTTGTATATATTTTTCTTCAA 59.224 33.333 0.00 0.00 0.00 2.69
1323 1579 8.410141 CCCGCCTTGTATATATTTTTCTTCAAA 58.590 33.333 0.00 0.00 0.00 2.69
1324 1580 9.796120 CCGCCTTGTATATATTTTTCTTCAAAA 57.204 29.630 0.00 0.00 38.76 2.44
1367 1623 0.514691 CCGTTCAGTTTGAGCTGAGC 59.485 55.000 0.00 0.00 45.03 4.26
1372 1628 2.024319 AGTTTGAGCTGAGCGACGC 61.024 57.895 13.03 13.03 0.00 5.19
1381 1637 1.457303 GCTGAGCGACGCTATATTTGG 59.543 52.381 24.55 8.76 39.88 3.28
1432 1688 2.303676 GCATCGTCGATCCTTCGGC 61.304 63.158 4.34 0.78 46.37 5.54
1449 1705 3.777925 CGGAGTTCACTTGCCGCG 61.778 66.667 0.00 0.00 37.08 6.46
1493 1749 5.220739 GCCTGTAAGCTTACATCTGATGTTG 60.221 44.000 33.45 20.34 41.63 3.33
1712 1968 7.706607 TGTTCATAGTTCAATTCTGGTCGATAG 59.293 37.037 0.00 0.00 0.00 2.08
1713 1969 6.216569 TCATAGTTCAATTCTGGTCGATAGC 58.783 40.000 0.00 0.00 0.00 2.97
1714 1970 3.798202 AGTTCAATTCTGGTCGATAGCC 58.202 45.455 0.00 0.00 0.00 3.93
1715 1971 3.452627 AGTTCAATTCTGGTCGATAGCCT 59.547 43.478 0.00 0.00 34.09 4.58
1716 1972 4.080863 AGTTCAATTCTGGTCGATAGCCTT 60.081 41.667 0.00 0.00 34.09 4.35
1717 1973 5.128827 AGTTCAATTCTGGTCGATAGCCTTA 59.871 40.000 0.00 0.00 34.09 2.69
2545 2808 0.111061 TGGGCTGCTTGATGAAGTGT 59.889 50.000 0.00 0.00 0.00 3.55
2778 3041 1.822506 GCCAAGTAAACACTCCCTCC 58.177 55.000 0.00 0.00 0.00 4.30
2999 3262 6.855836 TGATGTGTTCTTTTCCTTCATATGC 58.144 36.000 0.00 0.00 0.00 3.14
3033 3299 2.379226 ACTAGGTACCACTGGTGACTCT 59.621 50.000 15.94 5.53 36.19 3.24
3039 3305 0.037303 CCACTGGTGACTCTTGGCAT 59.963 55.000 1.93 0.00 0.00 4.40
3122 3388 5.957842 TTGGCAAGTAAAGATTGTTCGAT 57.042 34.783 0.00 0.00 0.00 3.59
3238 3504 3.317150 GTTCTGGTTATGCTTTGGTTGC 58.683 45.455 0.00 0.00 0.00 4.17
3271 3537 7.472334 AATTGGTTGAAGTATCTGATGCTTT 57.528 32.000 19.67 6.35 35.28 3.51
3282 3548 4.836125 TCTGATGCTTTCCTTTTGTCAC 57.164 40.909 0.00 0.00 0.00 3.67
3283 3549 4.206375 TCTGATGCTTTCCTTTTGTCACA 58.794 39.130 0.00 0.00 0.00 3.58
3289 3555 3.321968 GCTTTCCTTTTGTCACATCCCTT 59.678 43.478 0.00 0.00 0.00 3.95
3438 3704 1.021202 CACCGGAAAAGAACACAGCA 58.979 50.000 9.46 0.00 0.00 4.41
3547 3813 6.339587 TGGAACACCATTTAGATTGGTTTC 57.660 37.500 0.00 2.04 45.19 2.78
3625 3891 8.211629 ACACTAGTTCTGATCTTTAAAGGTGTT 58.788 33.333 15.13 0.00 0.00 3.32
3645 3911 3.921119 TTTTGTATGCTGCCTGACTTG 57.079 42.857 0.00 0.00 0.00 3.16
3655 3921 1.756538 TGCCTGACTTGATATCGCAGA 59.243 47.619 13.17 0.00 45.75 4.26
3694 3960 7.702348 GTCTTAATTTATGCCCATTCTGAACAC 59.298 37.037 0.00 0.00 0.00 3.32
3804 4070 7.528481 AAAAACAAAAGGTAAATCGTGGAAC 57.472 32.000 0.00 0.00 0.00 3.62
3806 4072 4.466827 ACAAAAGGTAAATCGTGGAACCT 58.533 39.130 0.00 0.00 44.24 3.50
3822 4093 5.008415 GTGGAACCTTAGAATGCAGATCATG 59.992 44.000 0.00 0.00 35.13 3.07
3859 4130 2.762535 ATCCAGGACGAATTCAACGT 57.237 45.000 6.22 0.00 46.58 3.99
3883 4162 1.818642 ATCAGTGAAAGCAGCAGTCC 58.181 50.000 0.00 0.00 0.00 3.85
3938 4217 1.445871 GCGGTCCAGACGGTTTTATT 58.554 50.000 7.13 0.00 34.59 1.40
3947 4226 5.099575 CCAGACGGTTTTATTATGCCAAAC 58.900 41.667 0.00 0.00 0.00 2.93
3949 4228 6.386654 CAGACGGTTTTATTATGCCAAACTT 58.613 36.000 0.00 0.00 32.09 2.66
3950 4229 7.362229 CCAGACGGTTTTATTATGCCAAACTTA 60.362 37.037 0.00 0.00 32.09 2.24
3954 4233 6.691388 CGGTTTTATTATGCCAAACTTAGCTC 59.309 38.462 0.00 0.00 32.09 4.09
3999 4442 4.692228 AGGCACTTATTTGTGTGGTTTTG 58.308 39.130 0.00 0.00 39.89 2.44
4000 4443 3.807071 GGCACTTATTTGTGTGGTTTTGG 59.193 43.478 0.00 0.00 39.89 3.28
4001 4444 4.438148 GCACTTATTTGTGTGGTTTTGGT 58.562 39.130 0.00 0.00 39.89 3.67
4002 4445 4.873259 GCACTTATTTGTGTGGTTTTGGTT 59.127 37.500 0.00 0.00 39.89 3.67
4003 4446 5.352846 GCACTTATTTGTGTGGTTTTGGTTT 59.647 36.000 0.00 0.00 39.89 3.27
4011 4454 4.275936 TGTGTGGTTTTGGTTTTGGTTTTG 59.724 37.500 0.00 0.00 0.00 2.44
4018 4461 2.716217 TGGTTTTGGTTTTGGCCTTTG 58.284 42.857 3.32 0.00 0.00 2.77
4056 4499 4.016444 TGACAATATCCACTCAAAAGCCC 58.984 43.478 0.00 0.00 0.00 5.19
4075 4518 3.681313 GCCCAAAGCCAAAGAGTCAAAAA 60.681 43.478 0.00 0.00 34.35 1.94
4076 4519 4.122046 CCCAAAGCCAAAGAGTCAAAAAG 58.878 43.478 0.00 0.00 0.00 2.27
4077 4520 3.557185 CCAAAGCCAAAGAGTCAAAAAGC 59.443 43.478 0.00 0.00 0.00 3.51
4078 4521 4.183101 CAAAGCCAAAGAGTCAAAAAGCA 58.817 39.130 0.00 0.00 0.00 3.91
4079 4522 3.443099 AGCCAAAGAGTCAAAAAGCAC 57.557 42.857 0.00 0.00 0.00 4.40
4083 4526 4.391523 GCCAAAGAGTCAAAAAGCACAAAA 59.608 37.500 0.00 0.00 0.00 2.44
4084 4527 5.106752 GCCAAAGAGTCAAAAAGCACAAAAA 60.107 36.000 0.00 0.00 0.00 1.94
4085 4528 6.403527 GCCAAAGAGTCAAAAAGCACAAAAAT 60.404 34.615 0.00 0.00 0.00 1.82
4129 4572 7.848223 AAACCAAACTTCAAAAATCAAGGAG 57.152 32.000 0.00 0.00 0.00 3.69
4135 4578 5.988287 ACTTCAAAAATCAAGGAGGCAAAA 58.012 33.333 0.00 0.00 0.00 2.44
4141 4584 1.533753 CAAGGAGGCAAAAGGGGCA 60.534 57.895 0.00 0.00 35.46 5.36
4147 4590 2.259511 GCAAAAGGGGCAAGCGAG 59.740 61.111 0.00 0.00 0.00 5.03
4154 4597 2.190578 GGGCAAGCGAGGCTGTAT 59.809 61.111 0.00 0.00 39.62 2.29
4156 4599 0.880718 GGGCAAGCGAGGCTGTATAC 60.881 60.000 0.00 0.00 39.62 1.47
4165 4608 2.031857 CGAGGCTGTATACGAGGACTTC 60.032 54.545 0.00 0.00 0.00 3.01
4203 4648 1.428370 GATGCGTCGTATGCTGGCAA 61.428 55.000 0.00 0.00 37.15 4.52
4204 4649 0.815213 ATGCGTCGTATGCTGGCAAT 60.815 50.000 0.00 0.00 37.15 3.56
4210 4655 1.202746 TCGTATGCTGGCAATGGCATA 60.203 47.619 10.64 13.91 45.74 3.14
4212 4657 1.913778 TATGCTGGCAATGGCATAGG 58.086 50.000 10.64 0.00 45.74 2.57
4213 4658 1.469335 ATGCTGGCAATGGCATAGGC 61.469 55.000 10.64 11.20 45.74 3.93
4214 4659 2.129146 GCTGGCAATGGCATAGGCA 61.129 57.895 21.03 9.81 43.71 4.75
4215 4660 2.038690 CTGGCAATGGCATAGGCAG 58.961 57.895 21.03 14.03 46.99 4.85
4216 4661 2.083835 CTGGCAATGGCATAGGCAGC 62.084 60.000 21.03 11.63 46.55 5.25
4217 4662 1.831286 GGCAATGGCATAGGCAGCT 60.831 57.895 21.03 0.00 42.43 4.24
4218 4663 1.362717 GCAATGGCATAGGCAGCTG 59.637 57.895 10.11 10.11 42.43 4.24
4219 4664 1.105167 GCAATGGCATAGGCAGCTGA 61.105 55.000 20.43 0.00 42.43 4.26
4220 4665 0.952280 CAATGGCATAGGCAGCTGAG 59.048 55.000 20.43 1.91 42.43 3.35
4221 4666 0.178998 AATGGCATAGGCAGCTGAGG 60.179 55.000 20.43 0.00 42.43 3.86
4222 4667 2.065470 ATGGCATAGGCAGCTGAGGG 62.065 60.000 20.43 2.26 42.43 4.30
4223 4668 2.446848 GGCATAGGCAGCTGAGGGA 61.447 63.158 20.43 0.00 43.71 4.20
4249 4694 2.334023 GCCATGTAAGAGGGAGAGGAT 58.666 52.381 0.00 0.00 0.00 3.24
4251 4696 2.636893 CCATGTAAGAGGGAGAGGATGG 59.363 54.545 0.00 0.00 0.00 3.51
4282 4727 2.050350 CGAGGCCGTGTAAGAGGGA 61.050 63.158 0.00 0.00 0.00 4.20
4285 4730 0.684805 AGGCCGTGTAAGAGGGAGAG 60.685 60.000 0.00 0.00 0.00 3.20
4296 4741 4.452733 GGGAGAGGACAACGGCGG 62.453 72.222 13.24 0.00 0.00 6.13
4305 4750 0.802494 GACAACGGCGGATCATTTGT 59.198 50.000 13.24 11.62 33.12 2.83
4307 4752 0.798009 CAACGGCGGATCATTTGTGC 60.798 55.000 13.24 0.00 0.00 4.57
4308 4753 1.933115 AACGGCGGATCATTTGTGCC 61.933 55.000 13.24 0.00 42.29 5.01
4309 4754 2.405805 CGGCGGATCATTTGTGCCA 61.406 57.895 0.00 0.00 46.02 4.92
4313 4758 0.386476 CGGATCATTTGTGCCATGGG 59.614 55.000 15.13 0.00 0.00 4.00
4320 4765 3.626996 TTGTGCCATGGGAGAGCGG 62.627 63.158 15.13 0.00 0.00 5.52
4326 4771 0.745845 CCATGGGAGAGCGGAACAAG 60.746 60.000 2.85 0.00 0.00 3.16
4328 4773 0.539051 ATGGGAGAGCGGAACAAGAG 59.461 55.000 0.00 0.00 0.00 2.85
4338 4784 1.540267 CGGAACAAGAGAAGTCTCCGA 59.460 52.381 4.67 0.00 43.88 4.55
4340 4786 2.352912 GGAACAAGAGAAGTCTCCGACC 60.353 54.545 4.67 3.65 43.88 4.79
4344 4790 0.114560 AGAGAAGTCTCCGACCCCAA 59.885 55.000 4.67 0.00 43.88 4.12
4348 4794 0.108019 AAGTCTCCGACCCCAACAAC 59.892 55.000 0.00 0.00 32.18 3.32
4349 4795 1.052124 AGTCTCCGACCCCAACAACA 61.052 55.000 0.00 0.00 32.18 3.33
4356 4802 1.056660 GACCCCAACAACAGAGGAGA 58.943 55.000 0.00 0.00 0.00 3.71
4360 4806 2.551071 CCCCAACAACAGAGGAGAAGTC 60.551 54.545 0.00 0.00 0.00 3.01
4369 4815 4.051932 GGAGAAGTCCGGGGACAT 57.948 61.111 19.38 7.99 46.76 3.06
4370 4816 1.823976 GGAGAAGTCCGGGGACATC 59.176 63.158 19.38 16.44 46.76 3.06
4372 4818 2.903404 AGAAGTCCGGGGACATCTC 58.097 57.895 17.41 11.61 46.16 2.75
4373 4819 1.038130 AGAAGTCCGGGGACATCTCG 61.038 60.000 17.41 0.00 46.16 4.04
4374 4820 2.630592 GAAGTCCGGGGACATCTCGC 62.631 65.000 19.38 0.00 46.76 5.03
4375 4821 4.570663 GTCCGGGGACATCTCGCG 62.571 72.222 12.90 0.00 44.02 5.87
4377 4823 3.214123 CCGGGGACATCTCGCGTA 61.214 66.667 5.77 0.00 38.60 4.42
4378 4824 2.331805 CGGGGACATCTCGCGTAG 59.668 66.667 5.77 2.22 36.13 3.51
4379 4825 2.728817 GGGGACATCTCGCGTAGG 59.271 66.667 5.77 0.00 0.00 3.18
4380 4826 2.125961 GGGGACATCTCGCGTAGGT 61.126 63.158 5.77 3.23 0.00 3.08
4381 4827 0.820891 GGGGACATCTCGCGTAGGTA 60.821 60.000 5.77 0.00 0.00 3.08
4382 4828 0.592148 GGGACATCTCGCGTAGGTAG 59.408 60.000 5.77 0.00 0.00 3.18
4383 4829 0.040246 GGACATCTCGCGTAGGTAGC 60.040 60.000 5.77 0.00 0.00 3.58
4399 4845 2.410469 GCGACCTACCGCGTGTAT 59.590 61.111 4.92 0.00 45.86 2.29
4400 4846 1.656569 GCGACCTACCGCGTGTATC 60.657 63.158 4.92 2.23 45.86 2.24
4401 4847 1.009222 CGACCTACCGCGTGTATCC 60.009 63.158 4.92 0.00 0.00 2.59
4402 4848 1.442526 CGACCTACCGCGTGTATCCT 61.443 60.000 4.92 0.00 0.00 3.24
4403 4849 0.743097 GACCTACCGCGTGTATCCTT 59.257 55.000 4.92 0.00 0.00 3.36
4404 4850 1.135721 GACCTACCGCGTGTATCCTTT 59.864 52.381 4.92 0.00 0.00 3.11
4405 4851 1.551883 ACCTACCGCGTGTATCCTTTT 59.448 47.619 4.92 0.00 0.00 2.27
4406 4852 1.931172 CCTACCGCGTGTATCCTTTTG 59.069 52.381 4.92 0.00 0.00 2.44
4407 4853 2.613691 CTACCGCGTGTATCCTTTTGT 58.386 47.619 4.92 0.00 0.00 2.83
4408 4854 1.153353 ACCGCGTGTATCCTTTTGTG 58.847 50.000 4.92 0.00 0.00 3.33
4409 4855 0.179200 CCGCGTGTATCCTTTTGTGC 60.179 55.000 4.92 0.00 0.00 4.57
4410 4856 0.518355 CGCGTGTATCCTTTTGTGCG 60.518 55.000 0.00 0.00 38.28 5.34
4411 4857 0.793104 GCGTGTATCCTTTTGTGCGC 60.793 55.000 0.00 0.00 36.97 6.09
4412 4858 0.179200 CGTGTATCCTTTTGTGCGCC 60.179 55.000 4.18 0.00 0.00 6.53
4413 4859 0.878416 GTGTATCCTTTTGTGCGCCA 59.122 50.000 4.18 0.00 0.00 5.69
4414 4860 1.472480 GTGTATCCTTTTGTGCGCCAT 59.528 47.619 4.18 0.00 0.00 4.40
4415 4861 1.472082 TGTATCCTTTTGTGCGCCATG 59.528 47.619 4.18 0.00 0.00 3.66
4416 4862 1.472480 GTATCCTTTTGTGCGCCATGT 59.528 47.619 4.18 0.00 0.00 3.21
4417 4863 0.527565 ATCCTTTTGTGCGCCATGTC 59.472 50.000 4.18 0.00 0.00 3.06
4418 4864 1.080569 CCTTTTGTGCGCCATGTCC 60.081 57.895 4.18 0.00 0.00 4.02
4419 4865 1.442520 CTTTTGTGCGCCATGTCCG 60.443 57.895 4.18 0.00 0.00 4.79
4420 4866 2.801113 CTTTTGTGCGCCATGTCCGG 62.801 60.000 4.18 0.00 0.00 5.14
4428 4874 2.597340 CCATGTCCGGCCCATTCT 59.403 61.111 0.00 0.00 0.00 2.40
4429 4875 1.836391 CCATGTCCGGCCCATTCTA 59.164 57.895 0.00 0.00 0.00 2.10
4430 4876 0.250467 CCATGTCCGGCCCATTCTAG 60.250 60.000 0.00 0.00 0.00 2.43
4431 4877 0.250467 CATGTCCGGCCCATTCTAGG 60.250 60.000 0.00 0.00 0.00 3.02
4432 4878 0.694444 ATGTCCGGCCCATTCTAGGT 60.694 55.000 0.00 0.00 0.00 3.08
4433 4879 0.912487 TGTCCGGCCCATTCTAGGTT 60.912 55.000 0.00 0.00 0.00 3.50
4434 4880 0.255033 GTCCGGCCCATTCTAGGTTT 59.745 55.000 0.00 0.00 0.00 3.27
4435 4881 0.996583 TCCGGCCCATTCTAGGTTTT 59.003 50.000 0.00 0.00 0.00 2.43
4436 4882 1.356398 TCCGGCCCATTCTAGGTTTTT 59.644 47.619 0.00 0.00 0.00 1.94
4437 4883 1.749063 CCGGCCCATTCTAGGTTTTTC 59.251 52.381 0.00 0.00 0.00 2.29
4438 4884 1.749063 CGGCCCATTCTAGGTTTTTCC 59.251 52.381 0.00 0.00 0.00 3.13
4439 4885 2.108168 GGCCCATTCTAGGTTTTTCCC 58.892 52.381 0.00 0.00 36.75 3.97
4440 4886 2.558800 GGCCCATTCTAGGTTTTTCCCA 60.559 50.000 0.00 0.00 36.75 4.37
4441 4887 3.374764 GCCCATTCTAGGTTTTTCCCAT 58.625 45.455 0.00 0.00 36.75 4.00
4442 4888 3.384789 GCCCATTCTAGGTTTTTCCCATC 59.615 47.826 0.00 0.00 36.75 3.51
4443 4889 3.632145 CCCATTCTAGGTTTTTCCCATCG 59.368 47.826 0.00 0.00 36.75 3.84
4444 4890 3.632145 CCATTCTAGGTTTTTCCCATCGG 59.368 47.826 0.00 0.00 36.75 4.18
4445 4891 4.270008 CATTCTAGGTTTTTCCCATCGGT 58.730 43.478 0.00 0.00 36.75 4.69
4446 4892 4.376225 TTCTAGGTTTTTCCCATCGGTT 57.624 40.909 0.00 0.00 36.75 4.44
4447 4893 4.376225 TCTAGGTTTTTCCCATCGGTTT 57.624 40.909 0.00 0.00 36.75 3.27
4448 4894 4.732065 TCTAGGTTTTTCCCATCGGTTTT 58.268 39.130 0.00 0.00 36.75 2.43
4449 4895 3.744238 AGGTTTTTCCCATCGGTTTTG 57.256 42.857 0.00 0.00 36.75 2.44
4450 4896 2.367241 AGGTTTTTCCCATCGGTTTTGG 59.633 45.455 0.00 0.00 36.75 3.28
4456 4902 3.356814 CCATCGGTTTTGGGAAGGT 57.643 52.632 0.00 0.00 0.00 3.50
4457 4903 1.627864 CCATCGGTTTTGGGAAGGTT 58.372 50.000 0.00 0.00 0.00 3.50
4458 4904 1.544246 CCATCGGTTTTGGGAAGGTTC 59.456 52.381 0.00 0.00 0.00 3.62
4459 4905 1.199097 CATCGGTTTTGGGAAGGTTCG 59.801 52.381 0.00 0.00 0.00 3.95
4460 4906 0.535553 TCGGTTTTGGGAAGGTTCGG 60.536 55.000 0.00 0.00 0.00 4.30
4461 4907 1.520600 CGGTTTTGGGAAGGTTCGGG 61.521 60.000 0.00 0.00 0.00 5.14
4462 4908 0.468585 GGTTTTGGGAAGGTTCGGGT 60.469 55.000 0.00 0.00 0.00 5.28
4463 4909 1.405872 GTTTTGGGAAGGTTCGGGTT 58.594 50.000 0.00 0.00 0.00 4.11
4464 4910 1.338973 GTTTTGGGAAGGTTCGGGTTC 59.661 52.381 0.00 0.00 0.00 3.62
4465 4911 0.848053 TTTGGGAAGGTTCGGGTTCT 59.152 50.000 0.00 0.00 0.00 3.01
4466 4912 0.109723 TTGGGAAGGTTCGGGTTCTG 59.890 55.000 0.00 0.00 0.00 3.02
4467 4913 0.765135 TGGGAAGGTTCGGGTTCTGA 60.765 55.000 0.00 0.00 0.00 3.27
4468 4914 0.036294 GGGAAGGTTCGGGTTCTGAG 60.036 60.000 0.00 0.00 0.00 3.35
4469 4915 0.974383 GGAAGGTTCGGGTTCTGAGA 59.026 55.000 0.00 0.00 0.00 3.27
4470 4916 1.337917 GGAAGGTTCGGGTTCTGAGAC 60.338 57.143 0.00 0.00 0.00 3.36
4471 4917 0.317479 AAGGTTCGGGTTCTGAGACG 59.683 55.000 0.00 0.00 0.00 4.18
4472 4918 0.826672 AGGTTCGGGTTCTGAGACGT 60.827 55.000 0.00 0.00 0.00 4.34
4473 4919 0.033090 GGTTCGGGTTCTGAGACGTT 59.967 55.000 0.00 0.00 0.00 3.99
4474 4920 1.539712 GGTTCGGGTTCTGAGACGTTT 60.540 52.381 0.00 0.00 0.00 3.60
4475 4921 2.207590 GTTCGGGTTCTGAGACGTTTT 58.792 47.619 0.00 0.00 0.00 2.43
4476 4922 2.607631 TCGGGTTCTGAGACGTTTTT 57.392 45.000 0.00 0.00 0.00 1.94
4580 5026 9.956720 TTTTGTGAACATTGTTTTGAAATTTGT 57.043 22.222 3.08 0.00 0.00 2.83
4581 5027 8.945758 TTGTGAACATTGTTTTGAAATTTGTG 57.054 26.923 3.08 0.00 0.00 3.33
4582 5028 7.524912 TGTGAACATTGTTTTGAAATTTGTGG 58.475 30.769 3.08 0.00 0.00 4.17
4583 5029 7.388776 TGTGAACATTGTTTTGAAATTTGTGGA 59.611 29.630 3.08 0.00 0.00 4.02
4584 5030 7.691877 GTGAACATTGTTTTGAAATTTGTGGAC 59.308 33.333 3.08 0.00 0.00 4.02
4585 5031 7.388776 TGAACATTGTTTTGAAATTTGTGGACA 59.611 29.630 3.08 0.00 0.00 4.02
4586 5032 7.678947 ACATTGTTTTGAAATTTGTGGACAA 57.321 28.000 0.00 2.59 0.00 3.18
4587 5033 8.278729 ACATTGTTTTGAAATTTGTGGACAAT 57.721 26.923 0.00 4.81 37.05 2.71
4588 5034 8.738106 ACATTGTTTTGAAATTTGTGGACAATT 58.262 25.926 12.95 6.48 35.11 2.32
4589 5035 9.570488 CATTGTTTTGAAATTTGTGGACAATTT 57.430 25.926 12.95 0.00 35.11 1.82
4591 5037 9.971922 TTGTTTTGAAATTTGTGGACAATTTTT 57.028 22.222 11.63 7.06 38.64 1.94
4592 5038 9.403110 TGTTTTGAAATTTGTGGACAATTTTTG 57.597 25.926 11.63 0.00 38.64 2.44
4593 5039 9.617975 GTTTTGAAATTTGTGGACAATTTTTGA 57.382 25.926 11.63 0.87 38.64 2.69
4597 5043 9.784680 TGAAATTTGTGGACAATTTTTGAATTG 57.215 25.926 11.63 9.61 43.77 2.32
4599 5045 9.786105 AAATTTGTGGACAATTTTTGAATTGAC 57.214 25.926 16.26 10.96 41.44 3.18
4600 5046 6.580963 TTGTGGACAATTTTTGAATTGACG 57.419 33.333 16.26 0.00 41.44 4.35
4601 5047 5.046529 TGTGGACAATTTTTGAATTGACGG 58.953 37.500 16.26 0.00 41.44 4.79
4602 5048 5.163509 TGTGGACAATTTTTGAATTGACGGA 60.164 36.000 16.26 1.47 41.44 4.69
4603 5049 5.174943 GTGGACAATTTTTGAATTGACGGAC 59.825 40.000 16.26 8.32 41.44 4.79
4604 5050 5.163509 TGGACAATTTTTGAATTGACGGACA 60.164 36.000 16.26 4.19 41.44 4.02
4605 5051 5.925969 GGACAATTTTTGAATTGACGGACAT 59.074 36.000 16.26 0.00 41.44 3.06
4606 5052 7.087639 GGACAATTTTTGAATTGACGGACATA 58.912 34.615 16.26 0.00 41.44 2.29
4607 5053 7.759433 GGACAATTTTTGAATTGACGGACATAT 59.241 33.333 16.26 0.00 41.44 1.78
4608 5054 9.139174 GACAATTTTTGAATTGACGGACATATT 57.861 29.630 16.26 0.00 41.44 1.28
4609 5055 9.487790 ACAATTTTTGAATTGACGGACATATTT 57.512 25.926 16.26 0.00 41.44 1.40
4612 5058 8.527567 TTTTTGAATTGACGGACATATTTTCC 57.472 30.769 0.00 0.00 0.00 3.13
4613 5059 6.825944 TTGAATTGACGGACATATTTTCCA 57.174 33.333 1.82 0.00 31.94 3.53
4614 5060 6.189677 TGAATTGACGGACATATTTTCCAC 57.810 37.500 1.82 0.00 31.94 4.02
4615 5061 5.707764 TGAATTGACGGACATATTTTCCACA 59.292 36.000 1.82 0.00 31.94 4.17
4616 5062 6.376864 TGAATTGACGGACATATTTTCCACAT 59.623 34.615 1.82 0.00 31.94 3.21
4617 5063 7.554476 TGAATTGACGGACATATTTTCCACATA 59.446 33.333 1.82 0.00 31.94 2.29
4618 5064 8.463930 AATTGACGGACATATTTTCCACATAT 57.536 30.769 1.82 0.00 31.94 1.78
4619 5065 6.859420 TGACGGACATATTTTCCACATATG 57.141 37.500 0.00 0.00 39.57 1.78
4620 5066 6.353323 TGACGGACATATTTTCCACATATGT 58.647 36.000 1.41 1.41 46.21 2.29
4621 5067 6.259829 TGACGGACATATTTTCCACATATGTG 59.740 38.462 26.02 26.02 44.43 3.21
4639 5085 9.352784 ACATATGTGAATGTGTTTTAAAATCCG 57.647 29.630 7.78 0.00 38.65 4.18
4640 5086 9.352784 CATATGTGAATGTGTTTTAAAATCCGT 57.647 29.630 3.52 0.00 0.00 4.69
4643 5089 9.751542 ATGTGAATGTGTTTTAAAATCCGTAAA 57.248 25.926 3.52 0.00 0.00 2.01
4644 5090 9.751542 TGTGAATGTGTTTTAAAATCCGTAAAT 57.248 25.926 3.52 0.00 0.00 1.40
4659 5105 8.994429 AATCCGTAAATATTTTTGAATGTGCA 57.006 26.923 5.91 0.00 0.00 4.57
4660 5106 8.994429 ATCCGTAAATATTTTTGAATGTGCAA 57.006 26.923 5.91 0.00 0.00 4.08
4661 5107 8.818141 TCCGTAAATATTTTTGAATGTGCAAA 57.182 26.923 5.91 0.00 36.08 3.68
4662 5108 8.704234 TCCGTAAATATTTTTGAATGTGCAAAC 58.296 29.630 5.91 0.00 37.48 2.93
4663 5109 7.682055 CCGTAAATATTTTTGAATGTGCAAACG 59.318 33.333 5.91 5.32 37.48 3.60
4664 5110 8.211181 CGTAAATATTTTTGAATGTGCAAACGT 58.789 29.630 5.91 0.00 37.48 3.99
4665 5111 9.856803 GTAAATATTTTTGAATGTGCAAACGTT 57.143 25.926 5.91 0.00 37.48 3.99
4667 5113 9.780413 AAATATTTTTGAATGTGCAAACGTTTT 57.220 22.222 11.66 0.00 37.48 2.43
4668 5114 9.780413 AATATTTTTGAATGTGCAAACGTTTTT 57.220 22.222 11.66 2.35 37.48 1.94
4680 5126 9.692749 TGTGCAAACGTTTTTATAATTTATGGA 57.307 25.926 11.66 0.00 0.00 3.41
4702 5148 9.981114 ATGGAAATTTTAAAAACTCGAGAACAT 57.019 25.926 21.68 5.13 0.00 2.71
4703 5149 9.810545 TGGAAATTTTAAAAACTCGAGAACATT 57.189 25.926 21.68 10.64 0.00 2.71
4713 5159 9.586435 AAAAACTCGAGAACATTTCTTGAAATT 57.414 25.926 21.68 0.00 46.69 1.82
4714 5160 8.788409 AAACTCGAGAACATTTCTTGAAATTC 57.212 30.769 21.68 4.18 46.69 2.17
4715 5161 7.496529 ACTCGAGAACATTTCTTGAAATTCA 57.503 32.000 21.68 0.00 46.69 2.57
4716 5162 8.103948 ACTCGAGAACATTTCTTGAAATTCAT 57.896 30.769 21.68 0.00 46.69 2.57
4717 5163 8.019669 ACTCGAGAACATTTCTTGAAATTCATG 58.980 33.333 21.68 0.00 46.69 3.07
4718 5164 8.098220 TCGAGAACATTTCTTGAAATTCATGA 57.902 30.769 7.38 7.38 45.02 3.07
4719 5165 8.567104 TCGAGAACATTTCTTGAAATTCATGAA 58.433 29.630 16.98 16.98 45.02 2.57
4720 5166 9.350357 CGAGAACATTTCTTGAAATTCATGAAT 57.650 29.630 20.17 15.36 42.69 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.640630 TGTGTACGAAAAATGTTGAATGTGTAC 59.359 33.333 0.00 0.00 0.00 2.90
2 3 6.556212 TGTGTACGAAAAATGTTGAATGTGT 58.444 32.000 0.00 0.00 0.00 3.72
3 4 7.621832 ATGTGTACGAAAAATGTTGAATGTG 57.378 32.000 0.00 0.00 0.00 3.21
4 5 7.168972 CCAATGTGTACGAAAAATGTTGAATGT 59.831 33.333 0.00 0.00 0.00 2.71
5 6 7.380870 TCCAATGTGTACGAAAAATGTTGAATG 59.619 33.333 0.00 0.00 0.00 2.67
6 7 7.429633 TCCAATGTGTACGAAAAATGTTGAAT 58.570 30.769 0.00 0.00 0.00 2.57
7 8 6.796426 TCCAATGTGTACGAAAAATGTTGAA 58.204 32.000 0.00 0.00 0.00 2.69
8 9 6.378710 TCCAATGTGTACGAAAAATGTTGA 57.621 33.333 0.00 0.00 0.00 3.18
9 10 7.009631 TGTTTCCAATGTGTACGAAAAATGTTG 59.990 33.333 0.00 0.00 0.00 3.33
10 11 7.036220 TGTTTCCAATGTGTACGAAAAATGTT 58.964 30.769 0.00 0.00 0.00 2.71
11 12 6.565234 TGTTTCCAATGTGTACGAAAAATGT 58.435 32.000 0.00 0.00 0.00 2.71
12 13 7.636259 ATGTTTCCAATGTGTACGAAAAATG 57.364 32.000 0.00 0.00 0.00 2.32
13 14 8.655651 AAATGTTTCCAATGTGTACGAAAAAT 57.344 26.923 0.00 0.00 0.00 1.82
14 15 8.480643 AAAATGTTTCCAATGTGTACGAAAAA 57.519 26.923 0.00 0.00 0.00 1.94
15 16 8.480643 AAAAATGTTTCCAATGTGTACGAAAA 57.519 26.923 0.00 0.00 0.00 2.29
252 261 7.609760 TGTATAGAAATGTGTTGACCATGTC 57.390 36.000 0.00 0.00 0.00 3.06
521 720 8.500753 AGCATTTCAAAATTCAATGTGCATAT 57.499 26.923 0.00 0.00 31.60 1.78
931 1186 1.237285 CGGGTGTTCTCCTGCTTTGG 61.237 60.000 0.00 0.00 0.00 3.28
933 1188 0.250338 GACGGGTGTTCTCCTGCTTT 60.250 55.000 0.00 0.00 37.37 3.51
941 1196 2.232452 CAGAAGAGATGACGGGTGTTCT 59.768 50.000 0.00 0.00 0.00 3.01
972 1227 3.832490 GGGCAGATTTTACAGGGTTCTTT 59.168 43.478 0.00 0.00 0.00 2.52
1045 1300 0.388778 TCGCGAGCGTTGGACATAAA 60.389 50.000 17.24 0.00 40.74 1.40
1090 1345 2.763902 CTTCCTCCGCCCCCTTTT 59.236 61.111 0.00 0.00 0.00 2.27
1197 1452 4.819761 TGCATGGAGTCGGCGCTC 62.820 66.667 18.67 18.67 34.89 5.03
1258 1513 1.470632 GGAGAGACCGTTCTGCTCATG 60.471 57.143 10.11 0.00 33.28 3.07
1295 1551 7.942341 TGAAGAAAAATATATACAAGGCGGGAT 59.058 33.333 0.00 0.00 0.00 3.85
1325 1581 7.822334 ACGGAACTGAATTTCCTTTTTCTTTTT 59.178 29.630 0.66 0.00 42.74 1.94
1326 1582 7.327975 ACGGAACTGAATTTCCTTTTTCTTTT 58.672 30.769 0.66 0.00 42.74 2.27
1327 1583 6.873997 ACGGAACTGAATTTCCTTTTTCTTT 58.126 32.000 0.66 0.00 42.74 2.52
1328 1584 6.465439 ACGGAACTGAATTTCCTTTTTCTT 57.535 33.333 0.66 0.00 42.74 2.52
1329 1585 6.096282 TGAACGGAACTGAATTTCCTTTTTCT 59.904 34.615 0.66 0.00 42.74 2.52
1330 1586 6.270064 TGAACGGAACTGAATTTCCTTTTTC 58.730 36.000 0.66 1.98 42.74 2.29
1331 1587 6.127451 ACTGAACGGAACTGAATTTCCTTTTT 60.127 34.615 0.66 0.00 42.74 1.94
1372 1628 2.545526 CCTGCAGACACGCCAAATATAG 59.454 50.000 17.39 0.00 0.00 1.31
1381 1637 2.607892 GGAACACCTGCAGACACGC 61.608 63.158 17.39 1.05 0.00 5.34
1410 1666 2.209838 GAAGGATCGACGATGCTCAA 57.790 50.000 28.69 0.00 39.73 3.02
1432 1688 3.777925 CGCGGCAAGTGAACTCCG 61.778 66.667 0.00 6.29 44.29 4.63
1449 1705 2.542411 GCAAGGCATGATCACGGAAATC 60.542 50.000 0.00 0.00 0.00 2.17
1493 1749 3.709987 ACTGAAACAAAGTTGCATCAGC 58.290 40.909 19.02 0.00 42.87 4.26
1607 1863 2.765699 AGAAGTTTGTGCCACCAACAAT 59.234 40.909 13.53 2.75 0.00 2.71
1846 2108 9.435688 TGGTTTCAATATTCACCTATATCATCG 57.564 33.333 8.71 0.00 0.00 3.84
1936 2198 5.049129 GGCCTGAATAGCACATTGAAGATAC 60.049 44.000 0.00 0.00 0.00 2.24
2198 2460 5.185454 CCTGTGGTTGCATATAACTCAAGA 58.815 41.667 0.00 0.00 0.00 3.02
2356 2618 9.927081 ATCCATATTGAAACAGGAAAGTCTAAT 57.073 29.630 0.00 0.00 31.17 1.73
2545 2808 6.054941 CGGCACCTGGATTATATATATTGCA 58.945 40.000 0.00 8.12 0.00 4.08
2948 3211 1.619654 CCAATTCAACACTCTGGGCA 58.380 50.000 0.00 0.00 0.00 5.36
3122 3388 1.191535 CCTAGTTCCACCACCATCGA 58.808 55.000 0.00 0.00 0.00 3.59
3238 3504 9.224267 CAGATACTTCAACCAATTATCATAGGG 57.776 37.037 0.00 0.00 31.76 3.53
3271 3537 3.874383 TCAAGGGATGTGACAAAAGGA 57.126 42.857 0.00 0.00 0.00 3.36
3438 3704 5.734720 TGATCTTACTCTTCCGCTTCAAAT 58.265 37.500 0.00 0.00 0.00 2.32
3625 3891 3.485394 TCAAGTCAGGCAGCATACAAAA 58.515 40.909 0.00 0.00 0.00 2.44
3645 3911 4.086025 CGAACTCGAGTTTTCTGCGATATC 60.086 45.833 30.22 13.00 43.02 1.63
3655 3921 7.955864 GCATAAATTAAGACGAACTCGAGTTTT 59.044 33.333 30.22 21.94 43.02 2.43
3694 3960 4.872691 AGCTCCATGAACAATTAGAAGACG 59.127 41.667 0.00 0.00 0.00 4.18
3799 4065 4.842531 TGATCTGCATTCTAAGGTTCCA 57.157 40.909 0.00 0.00 0.00 3.53
3800 4066 5.371526 TCATGATCTGCATTCTAAGGTTCC 58.628 41.667 0.00 0.00 34.15 3.62
3802 4068 9.584008 AAATATCATGATCTGCATTCTAAGGTT 57.416 29.630 12.53 0.00 34.15 3.50
3835 4106 5.293569 ACGTTGAATTCGTCCTGGATATTTC 59.706 40.000 0.00 4.94 36.85 2.17
3839 4110 3.517602 CACGTTGAATTCGTCCTGGATA 58.482 45.455 0.00 0.00 39.55 2.59
3845 4116 2.392933 TTTGCACGTTGAATTCGTCC 57.607 45.000 0.04 0.00 39.55 4.79
3859 4130 1.682323 TGCTGCTTTCACTGATTTGCA 59.318 42.857 0.00 0.00 0.00 4.08
3861 4132 3.562505 GACTGCTGCTTTCACTGATTTG 58.437 45.455 0.00 0.00 0.00 2.32
3883 4162 1.009829 GAATGTAGTTGGAGGCGCTG 58.990 55.000 7.64 0.00 0.00 5.18
3947 4226 7.920908 GCTTATAAGCCAAATTTGAGCTAAG 57.079 36.000 24.34 23.52 46.20 2.18
3989 4432 4.320567 CCAAAACCAAAACCAAAACCACAC 60.321 41.667 0.00 0.00 0.00 3.82
3991 4434 3.366476 GCCAAAACCAAAACCAAAACCAC 60.366 43.478 0.00 0.00 0.00 4.16
3994 4437 3.085533 AGGCCAAAACCAAAACCAAAAC 58.914 40.909 5.01 0.00 0.00 2.43
3996 4439 3.441500 AAGGCCAAAACCAAAACCAAA 57.558 38.095 5.01 0.00 0.00 3.28
3997 4440 3.084786 CAAAGGCCAAAACCAAAACCAA 58.915 40.909 5.01 0.00 0.00 3.67
3998 4441 2.619074 CCAAAGGCCAAAACCAAAACCA 60.619 45.455 5.01 0.00 0.00 3.67
3999 4442 2.020720 CCAAAGGCCAAAACCAAAACC 58.979 47.619 5.01 0.00 0.00 3.27
4000 4443 1.403679 GCCAAAGGCCAAAACCAAAAC 59.596 47.619 5.01 0.00 44.06 2.43
4001 4444 1.756430 GCCAAAGGCCAAAACCAAAA 58.244 45.000 5.01 0.00 44.06 2.44
4002 4445 3.485764 GCCAAAGGCCAAAACCAAA 57.514 47.368 5.01 0.00 44.06 3.28
4011 4454 7.572744 CACATTAAGGTGTAAGCCAAAGGCC 62.573 48.000 12.02 0.00 40.73 5.19
4018 4461 5.897377 ATTGTCACATTAAGGTGTAAGCC 57.103 39.130 18.86 5.27 39.76 4.35
4056 4499 4.033243 GTGCTTTTTGACTCTTTGGCTTTG 59.967 41.667 0.00 0.00 0.00 2.77
4110 4553 5.612725 TGCCTCCTTGATTTTTGAAGTTT 57.387 34.783 0.00 0.00 0.00 2.66
4129 4572 3.286915 CTCGCTTGCCCCTTTTGCC 62.287 63.158 0.00 0.00 0.00 4.52
4141 4584 0.669077 CCTCGTATACAGCCTCGCTT 59.331 55.000 3.32 0.00 36.40 4.68
4147 4590 2.426024 TGTGAAGTCCTCGTATACAGCC 59.574 50.000 3.32 0.00 0.00 4.85
4154 4597 3.446161 CCAACCTATGTGAAGTCCTCGTA 59.554 47.826 0.00 0.00 0.00 3.43
4156 4599 2.893637 CCAACCTATGTGAAGTCCTCG 58.106 52.381 0.00 0.00 0.00 4.63
4165 4608 0.806102 CGTCCTCGCCAACCTATGTG 60.806 60.000 0.00 0.00 0.00 3.21
4197 4642 2.038690 CTGCCTATGCCATTGCCAG 58.961 57.895 0.00 0.00 36.33 4.85
4203 4648 1.454976 CCTCAGCTGCCTATGCCAT 59.545 57.895 9.47 0.00 36.33 4.40
4204 4649 2.749584 CCCTCAGCTGCCTATGCCA 61.750 63.158 9.47 0.00 36.33 4.92
4209 4654 2.759973 CGGTCCCTCAGCTGCCTA 60.760 66.667 9.47 0.00 0.00 3.93
4210 4655 4.704103 TCGGTCCCTCAGCTGCCT 62.704 66.667 9.47 0.00 0.00 4.75
4211 4656 4.154347 CTCGGTCCCTCAGCTGCC 62.154 72.222 9.47 2.68 0.00 4.85
4212 4657 4.154347 CCTCGGTCCCTCAGCTGC 62.154 72.222 9.47 0.00 0.00 5.25
4213 4658 4.154347 GCCTCGGTCCCTCAGCTG 62.154 72.222 7.63 7.63 0.00 4.24
4216 4661 2.765807 ATGGCCTCGGTCCCTCAG 60.766 66.667 3.32 0.00 0.00 3.35
4217 4662 2.523740 TACATGGCCTCGGTCCCTCA 62.524 60.000 3.32 0.00 0.00 3.86
4218 4663 1.335132 TTACATGGCCTCGGTCCCTC 61.335 60.000 3.32 0.00 0.00 4.30
4219 4664 1.306654 TTACATGGCCTCGGTCCCT 60.307 57.895 3.32 0.00 0.00 4.20
4220 4665 1.146263 CTTACATGGCCTCGGTCCC 59.854 63.158 3.32 0.00 0.00 4.46
4221 4666 0.105039 CTCTTACATGGCCTCGGTCC 59.895 60.000 3.32 0.00 0.00 4.46
4222 4667 0.105039 CCTCTTACATGGCCTCGGTC 59.895 60.000 3.32 0.00 0.00 4.79
4223 4668 1.338136 CCCTCTTACATGGCCTCGGT 61.338 60.000 3.32 1.56 0.00 4.69
4232 4677 2.334023 GCCATCCTCTCCCTCTTACAT 58.666 52.381 0.00 0.00 0.00 2.29
4262 4707 2.202756 CTCTTACACGGCCTCGGC 60.203 66.667 0.00 0.00 41.39 5.54
4269 4714 1.104630 GTCCTCTCCCTCTTACACGG 58.895 60.000 0.00 0.00 0.00 4.94
4282 4727 1.330655 ATGATCCGCCGTTGTCCTCT 61.331 55.000 0.00 0.00 0.00 3.69
4285 4730 0.098728 CAAATGATCCGCCGTTGTCC 59.901 55.000 0.00 0.00 0.00 4.02
4305 4750 3.008517 TTCCGCTCTCCCATGGCA 61.009 61.111 6.09 0.00 0.00 4.92
4307 4752 0.745845 CTTGTTCCGCTCTCCCATGG 60.746 60.000 4.14 4.14 0.00 3.66
4308 4753 0.250234 TCTTGTTCCGCTCTCCCATG 59.750 55.000 0.00 0.00 0.00 3.66
4309 4754 0.539051 CTCTTGTTCCGCTCTCCCAT 59.461 55.000 0.00 0.00 0.00 4.00
4313 4758 2.230266 AGACTTCTCTTGTTCCGCTCTC 59.770 50.000 0.00 0.00 0.00 3.20
4338 4784 1.421646 CTTCTCCTCTGTTGTTGGGGT 59.578 52.381 0.00 0.00 0.00 4.95
4340 4786 2.551071 GGACTTCTCCTCTGTTGTTGGG 60.551 54.545 0.00 0.00 33.07 4.12
4344 4790 0.969894 CCGGACTTCTCCTCTGTTGT 59.030 55.000 0.00 0.00 33.79 3.32
4348 4794 1.000486 TCCCCGGACTTCTCCTCTG 60.000 63.158 0.73 0.00 33.79 3.35
4349 4795 1.000612 GTCCCCGGACTTCTCCTCT 59.999 63.158 0.73 0.00 41.57 3.69
4356 4802 2.722201 GCGAGATGTCCCCGGACTT 61.722 63.158 14.78 8.61 44.80 3.01
4360 4806 3.195591 CTACGCGAGATGTCCCCGG 62.196 68.421 15.93 0.00 0.00 5.73
4364 4810 0.040246 GCTACCTACGCGAGATGTCC 60.040 60.000 15.93 0.00 0.00 4.02
4365 4811 3.458388 GCTACCTACGCGAGATGTC 57.542 57.895 15.93 0.00 0.00 3.06
4383 4829 1.009222 GGATACACGCGGTAGGTCG 60.009 63.158 12.47 0.00 34.92 4.79
4384 4830 0.743097 AAGGATACACGCGGTAGGTC 59.257 55.000 12.47 5.54 34.92 3.85
4385 4831 1.188863 AAAGGATACACGCGGTAGGT 58.811 50.000 12.47 5.59 34.92 3.08
4386 4832 1.931172 CAAAAGGATACACGCGGTAGG 59.069 52.381 12.47 0.00 34.92 3.18
4387 4833 2.347452 CACAAAAGGATACACGCGGTAG 59.653 50.000 12.47 1.86 34.92 3.18
4388 4834 2.339418 CACAAAAGGATACACGCGGTA 58.661 47.619 12.47 10.58 41.41 4.02
4389 4835 1.153353 CACAAAAGGATACACGCGGT 58.847 50.000 12.47 8.38 41.41 5.68
4390 4836 0.179200 GCACAAAAGGATACACGCGG 60.179 55.000 12.47 1.27 41.41 6.46
4391 4837 0.518355 CGCACAAAAGGATACACGCG 60.518 55.000 3.53 3.53 41.41 6.01
4392 4838 0.793104 GCGCACAAAAGGATACACGC 60.793 55.000 0.30 0.00 41.41 5.34
4393 4839 0.179200 GGCGCACAAAAGGATACACG 60.179 55.000 10.83 0.00 41.41 4.49
4394 4840 0.878416 TGGCGCACAAAAGGATACAC 59.122 50.000 10.83 0.00 41.41 2.90
4395 4841 1.472082 CATGGCGCACAAAAGGATACA 59.528 47.619 10.83 0.00 41.41 2.29
4396 4842 1.472480 ACATGGCGCACAAAAGGATAC 59.528 47.619 10.83 0.00 0.00 2.24
4397 4843 1.742831 GACATGGCGCACAAAAGGATA 59.257 47.619 10.83 0.00 0.00 2.59
4398 4844 0.527565 GACATGGCGCACAAAAGGAT 59.472 50.000 10.83 0.00 0.00 3.24
4399 4845 1.523154 GGACATGGCGCACAAAAGGA 61.523 55.000 10.83 0.00 0.00 3.36
4400 4846 1.080569 GGACATGGCGCACAAAAGG 60.081 57.895 10.83 0.00 0.00 3.11
4401 4847 1.442520 CGGACATGGCGCACAAAAG 60.443 57.895 10.83 2.57 0.00 2.27
4402 4848 2.642129 CGGACATGGCGCACAAAA 59.358 55.556 10.83 0.00 0.00 2.44
4403 4849 3.361158 CCGGACATGGCGCACAAA 61.361 61.111 10.83 0.00 0.00 2.83
4411 4857 0.250467 CTAGAATGGGCCGGACATGG 60.250 60.000 11.00 0.00 0.00 3.66
4412 4858 0.250467 CCTAGAATGGGCCGGACATG 60.250 60.000 11.00 0.00 0.00 3.21
4413 4859 0.694444 ACCTAGAATGGGCCGGACAT 60.694 55.000 11.00 8.12 42.80 3.06
4414 4860 0.912487 AACCTAGAATGGGCCGGACA 60.912 55.000 11.00 5.49 42.80 4.02
4415 4861 0.255033 AAACCTAGAATGGGCCGGAC 59.745 55.000 5.05 0.00 42.80 4.79
4416 4862 0.996583 AAAACCTAGAATGGGCCGGA 59.003 50.000 5.05 0.00 42.80 5.14
4417 4863 1.749063 GAAAAACCTAGAATGGGCCGG 59.251 52.381 0.00 0.00 42.80 6.13
4418 4864 1.749063 GGAAAAACCTAGAATGGGCCG 59.251 52.381 0.00 0.00 42.80 6.13
4419 4865 2.108168 GGGAAAAACCTAGAATGGGCC 58.892 52.381 0.00 0.00 42.80 5.80
4420 4866 2.815158 TGGGAAAAACCTAGAATGGGC 58.185 47.619 0.00 0.00 42.80 5.36
4421 4867 3.632145 CGATGGGAAAAACCTAGAATGGG 59.368 47.826 0.00 0.00 45.72 4.00
4422 4868 3.632145 CCGATGGGAAAAACCTAGAATGG 59.368 47.826 0.00 0.00 38.98 3.16
4423 4869 4.270008 ACCGATGGGAAAAACCTAGAATG 58.730 43.478 0.00 0.00 38.98 2.67
4424 4870 4.586306 ACCGATGGGAAAAACCTAGAAT 57.414 40.909 0.00 0.00 38.98 2.40
4425 4871 4.376225 AACCGATGGGAAAAACCTAGAA 57.624 40.909 0.00 0.00 38.98 2.10
4426 4872 4.376225 AAACCGATGGGAAAAACCTAGA 57.624 40.909 0.00 0.00 38.98 2.43
4427 4873 4.321675 CCAAAACCGATGGGAAAAACCTAG 60.322 45.833 0.00 0.00 38.98 3.02
4428 4874 3.574826 CCAAAACCGATGGGAAAAACCTA 59.425 43.478 0.00 0.00 38.98 3.08
4429 4875 2.367241 CCAAAACCGATGGGAAAAACCT 59.633 45.455 0.00 0.00 38.98 3.50
4430 4876 2.761559 CCAAAACCGATGGGAAAAACC 58.238 47.619 0.00 0.00 36.97 3.27
4438 4884 1.544246 GAACCTTCCCAAAACCGATGG 59.456 52.381 0.00 0.00 37.71 3.51
4439 4885 1.199097 CGAACCTTCCCAAAACCGATG 59.801 52.381 0.00 0.00 0.00 3.84
4440 4886 1.530323 CGAACCTTCCCAAAACCGAT 58.470 50.000 0.00 0.00 0.00 4.18
4441 4887 0.535553 CCGAACCTTCCCAAAACCGA 60.536 55.000 0.00 0.00 0.00 4.69
4442 4888 1.520600 CCCGAACCTTCCCAAAACCG 61.521 60.000 0.00 0.00 0.00 4.44
4443 4889 0.468585 ACCCGAACCTTCCCAAAACC 60.469 55.000 0.00 0.00 0.00 3.27
4444 4890 1.338973 GAACCCGAACCTTCCCAAAAC 59.661 52.381 0.00 0.00 0.00 2.43
4445 4891 1.215924 AGAACCCGAACCTTCCCAAAA 59.784 47.619 0.00 0.00 0.00 2.44
4446 4892 0.848053 AGAACCCGAACCTTCCCAAA 59.152 50.000 0.00 0.00 0.00 3.28
4447 4893 0.109723 CAGAACCCGAACCTTCCCAA 59.890 55.000 0.00 0.00 0.00 4.12
4448 4894 0.765135 TCAGAACCCGAACCTTCCCA 60.765 55.000 0.00 0.00 0.00 4.37
4449 4895 0.036294 CTCAGAACCCGAACCTTCCC 60.036 60.000 0.00 0.00 0.00 3.97
4450 4896 0.974383 TCTCAGAACCCGAACCTTCC 59.026 55.000 0.00 0.00 0.00 3.46
4451 4897 1.669211 CGTCTCAGAACCCGAACCTTC 60.669 57.143 0.00 0.00 0.00 3.46
4452 4898 0.317479 CGTCTCAGAACCCGAACCTT 59.683 55.000 0.00 0.00 0.00 3.50
4453 4899 0.826672 ACGTCTCAGAACCCGAACCT 60.827 55.000 0.00 0.00 0.00 3.50
4454 4900 0.033090 AACGTCTCAGAACCCGAACC 59.967 55.000 0.00 0.00 0.00 3.62
4455 4901 1.861971 AAACGTCTCAGAACCCGAAC 58.138 50.000 0.00 0.00 0.00 3.95
4456 4902 2.607631 AAAACGTCTCAGAACCCGAA 57.392 45.000 0.00 0.00 0.00 4.30
4457 4903 2.607631 AAAAACGTCTCAGAACCCGA 57.392 45.000 0.00 0.00 0.00 5.14
4554 5000 9.956720 ACAAATTTCAAAACAATGTTCACAAAA 57.043 22.222 0.00 0.00 0.00 2.44
4555 5001 9.390795 CACAAATTTCAAAACAATGTTCACAAA 57.609 25.926 0.00 0.00 0.00 2.83
4556 5002 8.019669 CCACAAATTTCAAAACAATGTTCACAA 58.980 29.630 0.00 0.00 0.00 3.33
4557 5003 7.388776 TCCACAAATTTCAAAACAATGTTCACA 59.611 29.630 0.00 0.00 0.00 3.58
4558 5004 7.691877 GTCCACAAATTTCAAAACAATGTTCAC 59.308 33.333 0.00 0.00 0.00 3.18
4559 5005 7.388776 TGTCCACAAATTTCAAAACAATGTTCA 59.611 29.630 0.00 0.00 0.00 3.18
4560 5006 7.746929 TGTCCACAAATTTCAAAACAATGTTC 58.253 30.769 0.00 0.00 0.00 3.18
4561 5007 7.678947 TGTCCACAAATTTCAAAACAATGTT 57.321 28.000 0.00 0.00 0.00 2.71
4562 5008 7.678947 TTGTCCACAAATTTCAAAACAATGT 57.321 28.000 0.00 0.00 32.11 2.71
4563 5009 9.570488 AAATTGTCCACAAATTTCAAAACAATG 57.430 25.926 14.44 0.00 39.55 2.82
4565 5011 9.971922 AAAAATTGTCCACAAATTTCAAAACAA 57.028 22.222 6.05 7.69 37.81 2.83
4566 5012 9.403110 CAAAAATTGTCCACAAATTTCAAAACA 57.597 25.926 6.05 0.00 37.81 2.83
4567 5013 9.617975 TCAAAAATTGTCCACAAATTTCAAAAC 57.382 25.926 6.05 0.00 37.81 2.43
4571 5017 9.784680 CAATTCAAAAATTGTCCACAAATTTCA 57.215 25.926 6.05 0.00 44.43 2.69
4586 5032 9.150348 GGAAAATATGTCCGTCAATTCAAAAAT 57.850 29.630 0.00 0.00 0.00 1.82
4587 5033 8.144478 TGGAAAATATGTCCGTCAATTCAAAAA 58.856 29.630 2.15 0.00 38.06 1.94
4588 5034 7.596995 GTGGAAAATATGTCCGTCAATTCAAAA 59.403 33.333 2.15 0.00 38.06 2.44
4589 5035 7.087639 GTGGAAAATATGTCCGTCAATTCAAA 58.912 34.615 2.15 0.00 38.06 2.69
4590 5036 6.207614 TGTGGAAAATATGTCCGTCAATTCAA 59.792 34.615 2.15 0.00 38.06 2.69
4591 5037 5.707764 TGTGGAAAATATGTCCGTCAATTCA 59.292 36.000 2.15 0.00 38.06 2.57
4592 5038 6.189677 TGTGGAAAATATGTCCGTCAATTC 57.810 37.500 2.15 0.00 38.06 2.17
4593 5039 6.773976 ATGTGGAAAATATGTCCGTCAATT 57.226 33.333 2.15 0.00 38.06 2.32
4594 5040 7.874940 CATATGTGGAAAATATGTCCGTCAAT 58.125 34.615 0.00 0.00 39.26 2.57
4595 5041 7.258022 CATATGTGGAAAATATGTCCGTCAA 57.742 36.000 0.00 0.00 39.26 3.18
4596 5042 6.859420 CATATGTGGAAAATATGTCCGTCA 57.141 37.500 0.00 4.39 39.26 4.35
4613 5059 9.352784 CGGATTTTAAAACACATTCACATATGT 57.647 29.630 1.41 1.41 39.27 2.29
4614 5060 9.352784 ACGGATTTTAAAACACATTCACATATG 57.647 29.630 1.97 0.00 0.00 1.78
4617 5063 9.751542 TTTACGGATTTTAAAACACATTCACAT 57.248 25.926 1.97 0.00 0.00 3.21
4618 5064 9.751542 ATTTACGGATTTTAAAACACATTCACA 57.248 25.926 1.97 0.00 0.00 3.58
4633 5079 9.429359 TGCACATTCAAAAATATTTACGGATTT 57.571 25.926 0.01 0.00 0.00 2.17
4634 5080 8.994429 TGCACATTCAAAAATATTTACGGATT 57.006 26.923 0.01 0.00 0.00 3.01
4635 5081 8.994429 TTGCACATTCAAAAATATTTACGGAT 57.006 26.923 0.01 0.00 0.00 4.18
4636 5082 8.704234 GTTTGCACATTCAAAAATATTTACGGA 58.296 29.630 0.01 0.00 37.65 4.69
4637 5083 7.682055 CGTTTGCACATTCAAAAATATTTACGG 59.318 33.333 0.01 0.00 37.65 4.02
4638 5084 8.211181 ACGTTTGCACATTCAAAAATATTTACG 58.789 29.630 0.01 5.57 37.65 3.18
4639 5085 9.856803 AACGTTTGCACATTCAAAAATATTTAC 57.143 25.926 0.01 0.00 37.65 2.01
4641 5087 9.780413 AAAACGTTTGCACATTCAAAAATATTT 57.220 22.222 15.46 0.00 37.65 1.40
4642 5088 9.780413 AAAAACGTTTGCACATTCAAAAATATT 57.220 22.222 15.46 0.00 37.65 1.28
4654 5100 9.692749 TCCATAAATTATAAAAACGTTTGCACA 57.307 25.926 15.46 0.42 0.00 4.57
4676 5122 9.981114 ATGTTCTCGAGTTTTTAAAATTTCCAT 57.019 25.926 13.13 0.00 0.00 3.41
4677 5123 9.810545 AATGTTCTCGAGTTTTTAAAATTTCCA 57.189 25.926 13.13 0.00 0.00 3.53
4687 5133 9.586435 AATTTCAAGAAATGTTCTCGAGTTTTT 57.414 25.926 13.13 8.13 40.57 1.94
4688 5134 9.237846 GAATTTCAAGAAATGTTCTCGAGTTTT 57.762 29.630 13.13 8.47 40.57 2.43
4689 5135 8.405531 TGAATTTCAAGAAATGTTCTCGAGTTT 58.594 29.630 13.13 5.34 40.57 2.66
4690 5136 7.930217 TGAATTTCAAGAAATGTTCTCGAGTT 58.070 30.769 13.13 0.00 40.57 3.01
4691 5137 7.496529 TGAATTTCAAGAAATGTTCTCGAGT 57.503 32.000 13.13 0.00 40.57 4.18
4692 5138 8.232513 TCATGAATTTCAAGAAATGTTCTCGAG 58.767 33.333 5.93 5.93 40.57 4.04
4693 5139 8.098220 TCATGAATTTCAAGAAATGTTCTCGA 57.902 30.769 8.66 3.82 40.57 4.04
4694 5140 8.732413 TTCATGAATTTCAAGAAATGTTCTCG 57.268 30.769 13.14 1.96 40.57 4.04


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

AutoCloner maintained by Alex Coulton.