Multiple sequence alignment - TraesCS4A01G124800

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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 TraesCS4A01G124800 chr4A 100.000 8590 0 0 1 8590 158190555 158181966 0.000000e+00 15863.0
1 TraesCS4A01G124800 chr4A 93.750 128 6 2 4742 4868 158185688 158185814 3.170000e-44 191.0
2 TraesCS4A01G124800 chr4A 93.846 65 4 0 6387 6451 158184105 158184041 1.970000e-16 99.0
3 TraesCS4A01G124800 chr4A 93.846 65 4 0 6451 6515 158184169 158184105 1.970000e-16 99.0
4 TraesCS4A01G124800 chr4A 82.727 110 17 2 3875 3983 542605671 542605779 7.100000e-16 97.1
5 TraesCS4A01G124800 chr4B 96.106 4109 103 22 671 4744 394103918 394108004 0.000000e+00 6649.0
6 TraesCS4A01G124800 chr4B 96.277 3707 81 23 4869 8566 394108003 394111661 0.000000e+00 6028.0
7 TraesCS4A01G124800 chr4B 96.923 65 2 0 6387 6451 394109588 394109652 9.120000e-20 110.0
8 TraesCS4A01G124800 chr4B 95.385 65 3 0 6451 6515 394109524 394109588 4.240000e-18 104.0
9 TraesCS4A01G124800 chr4B 85.149 101 11 4 3878 3976 366897081 366896983 5.490000e-17 100.0
10 TraesCS4A01G124800 chr4B 97.143 35 1 0 4053 4087 28668581 28668547 9.310000e-05 60.2
11 TraesCS4A01G124800 chr4D 97.458 3737 67 15 4869 8590 316530548 316534271 0.000000e+00 6349.0
12 TraesCS4A01G124800 chr4D 96.419 3044 71 16 1725 4744 316527520 316530549 0.000000e+00 4983.0
13 TraesCS4A01G124800 chr4D 94.206 1260 49 8 476 1726 316526114 316527358 0.000000e+00 1901.0
14 TraesCS4A01G124800 chr4D 90.446 471 35 5 1 465 316525603 316526069 5.700000e-171 612.0
15 TraesCS4A01G124800 chr4D 74.227 291 66 3 163 445 49877187 49876898 7.050000e-21 113.0
16 TraesCS4A01G124800 chr4D 96.923 65 2 0 6387 6451 316532127 316532191 9.120000e-20 110.0
17 TraesCS4A01G124800 chr4D 95.385 65 3 0 6451 6515 316532063 316532127 4.240000e-18 104.0
18 TraesCS4A01G124800 chr7D 95.279 466 13 4 3542 4006 112768764 112769221 0.000000e+00 730.0
19 TraesCS4A01G124800 chr7D 77.950 322 59 10 45 359 56229123 56229439 3.170000e-44 191.0
20 TraesCS4A01G124800 chr7D 86.170 94 12 1 3886 3979 265706885 265706793 5.490000e-17 100.0
21 TraesCS4A01G124800 chr7D 87.500 80 10 0 297 376 440596167 440596246 9.180000e-15 93.5
22 TraesCS4A01G124800 chr3A 88.123 261 21 4 8208 8464 543726373 543726119 1.400000e-77 302.0
23 TraesCS4A01G124800 chr3A 90.708 226 16 1 7985 8210 543727214 543726994 6.520000e-76 296.0
24 TraesCS4A01G124800 chr3A 84.694 98 15 0 3879 3976 207243082 207243179 1.970000e-16 99.0
25 TraesCS4A01G124800 chr3A 81.897 116 21 0 164 279 610446776 610446891 1.970000e-16 99.0
26 TraesCS4A01G124800 chr3A 91.304 69 3 3 8499 8566 543726108 543726042 3.300000e-14 91.6
27 TraesCS4A01G124800 chr3B 75.350 357 76 11 25 375 716985652 716985302 2.480000e-35 161.0
28 TraesCS4A01G124800 chr2B 86.822 129 12 3 4743 4871 25018791 25018668 1.160000e-28 139.0
29 TraesCS4A01G124800 chr2B 85.606 132 11 6 4738 4867 25018666 25018791 1.950000e-26 132.0
30 TraesCS4A01G124800 chr1B 85.606 132 13 6 4739 4868 420362948 420363075 5.410000e-27 134.0
31 TraesCS4A01G124800 chr1B 85.271 129 13 6 4742 4868 420363075 420362951 2.520000e-25 128.0
32 TraesCS4A01G124800 chr1B 76.923 221 43 7 15 228 322493592 322493373 1.510000e-22 119.0
33 TraesCS4A01G124800 chr2D 73.575 386 85 13 5 375 636433155 636433538 1.950000e-26 132.0
34 TraesCS4A01G124800 chr1A 85.385 130 13 6 4743 4867 299107801 299107673 7.000000e-26 130.0
35 TraesCS4A01G124800 chr1A 76.623 231 49 4 150 375 15779829 15780059 1.170000e-23 122.0
36 TraesCS4A01G124800 chr7B 85.714 126 13 5 4743 4868 115523710 115523590 2.520000e-25 128.0
37 TraesCS4A01G124800 chr7B 85.849 106 14 1 3878 3983 246011854 246011750 2.530000e-20 111.0
38 TraesCS4A01G124800 chr5D 85.714 126 12 5 4742 4867 254839791 254839672 2.520000e-25 128.0
39 TraesCS4A01G124800 chr5D 85.039 127 12 6 4743 4867 13912948 13913069 1.170000e-23 122.0
40 TraesCS4A01G124800 chr5D 77.604 192 31 10 8 195 458785577 458785760 1.180000e-18 106.0
41 TraesCS4A01G124800 chr6D 75.325 231 52 3 150 375 391921177 391921407 1.180000e-18 106.0
42 TraesCS4A01G124800 chr7A 87.097 93 11 1 3887 3979 290925880 290925789 4.240000e-18 104.0
43 TraesCS4A01G124800 chr7A 97.059 34 1 0 1985 2018 156565693 156565660 3.350000e-04 58.4
44 TraesCS4A01G124800 chr3D 88.750 80 8 1 3897 3976 169887510 169887588 7.100000e-16 97.1


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 TraesCS4A01G124800 chr4A 158181966 158190555 8589 True 15863.000000 15863 100.00000 1 8590 1 chr4A.!!$R1 8589
1 TraesCS4A01G124800 chr4B 394103918 394111661 7743 False 3222.750000 6649 96.17275 671 8566 4 chr4B.!!$F1 7895
2 TraesCS4A01G124800 chr4D 316525603 316534271 8668 False 2343.166667 6349 95.13950 1 8590 6 chr4D.!!$F1 8589
3 TraesCS4A01G124800 chr3A 543726042 543727214 1172 True 229.866667 302 90.04500 7985 8566 3 chr3A.!!$R1 581

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
510 550 0.178990 GCCCCATACCATGTCCCTTC 60.179 60.000 0.00 0.00 0.00 3.46 F
850 900 0.248702 CCAAAACGAAACCACCCGTG 60.249 55.000 0.00 0.00 39.14 4.94 F
943 994 0.249073 AGCACGAAATCCCTCGATCG 60.249 55.000 9.36 9.36 41.44 3.69 F
1338 1389 1.200020 GATCCGGTGGTTTTGCAGAAG 59.800 52.381 0.00 0.00 0.00 2.85 F
3045 3272 1.531264 CGAGCTGCAGAAATGTGATGC 60.531 52.381 20.43 0.00 40.40 3.91 F
3587 3820 0.251165 TAGAAACAACAGCAGGGGCC 60.251 55.000 0.00 0.00 42.56 5.80 F
3667 3900 0.614979 GCAGTGAGGAGGGTAGGTGA 60.615 60.000 0.00 0.00 0.00 4.02 F
4117 4358 0.829333 ACTGAGATTCGGAGCAGCAT 59.171 50.000 0.00 0.00 31.74 3.79 F
5427 5672 1.479730 TGCAGACAGGCATCAGACTAG 59.520 52.381 0.00 0.00 39.25 2.57 F
6232 6480 1.062886 TGCTACCCTGCTCTGGAGTAT 60.063 52.381 0.00 0.00 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2605 0.038526 AACCTAAGTCACGGACTGCG 60.039 55.000 7.23 0.00 42.59 5.18 R
2501 2727 2.826725 ACAGACCTACTTGCACCTACTC 59.173 50.000 0.00 0.00 0.00 2.59 R
2886 3113 2.555325 CAGAGTGTGCCACATCAATGTT 59.445 45.455 0.00 0.00 39.39 2.71 R
3080 3307 0.036732 GGTCACCAGCAACCAGATGA 59.963 55.000 0.00 0.00 35.00 2.92 R
3855 4088 1.453155 ACGGAAATGTAGCCTTGCAG 58.547 50.000 0.00 0.00 0.00 4.41 R
4845 5090 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71 R
4846 5091 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32 R
5950 6198 2.360483 AGCATCATGTGAGTACTCCTCG 59.640 50.000 20.11 6.41 43.64 4.63 R
6492 6742 0.039618 ACTCGTCATGGGGCCAAAAT 59.960 50.000 4.39 0.00 0.00 1.82 R
8151 8415 0.031716 ACTGCAGATCCTAGAGCCCA 60.032 55.000 23.35 0.00 0.00 5.36 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
38 39 3.294214 AGGGCTCATGCTTCAATTTAGG 58.706 45.455 0.00 0.00 39.59 2.69
39 40 3.026694 GGGCTCATGCTTCAATTTAGGT 58.973 45.455 0.00 0.00 39.59 3.08
71 72 6.189133 AGTTTGTTTAGGGTTTTGTGTCCTA 58.811 36.000 0.00 0.00 32.46 2.94
121 122 7.032598 TCCCTGAGATGAAATAAGGTTCTTT 57.967 36.000 0.00 0.00 0.00 2.52
135 136 1.910580 TTCTTTCAGCCTAGCCCCCG 61.911 60.000 0.00 0.00 0.00 5.73
143 144 1.382146 CCTAGCCCCCGTCCTAACA 60.382 63.158 0.00 0.00 0.00 2.41
144 145 0.979187 CCTAGCCCCCGTCCTAACAA 60.979 60.000 0.00 0.00 0.00 2.83
146 147 0.834612 TAGCCCCCGTCCTAACAATG 59.165 55.000 0.00 0.00 0.00 2.82
154 155 2.159282 CCGTCCTAACAATGCGTCTAGT 60.159 50.000 0.00 0.00 0.00 2.57
181 182 4.250305 GGGCGTGTGGAGGTGTGT 62.250 66.667 0.00 0.00 0.00 3.72
197 198 1.002430 TGTGTCTCCTGTGGATCTTGC 59.998 52.381 0.00 0.00 0.00 4.01
216 217 0.796312 CGGGATTCAGTCGGTGTTTG 59.204 55.000 0.00 0.00 0.00 2.93
229 230 1.474498 GGTGTTTGTCTTCGGTGGACT 60.474 52.381 0.00 0.00 35.04 3.85
235 236 1.689813 TGTCTTCGGTGGACTTGCTTA 59.310 47.619 0.00 0.00 35.04 3.09
243 244 1.666189 GTGGACTTGCTTAGATTCGGC 59.334 52.381 0.00 0.00 0.00 5.54
245 246 1.406887 GGACTTGCTTAGATTCGGCCA 60.407 52.381 2.24 0.00 0.00 5.36
246 247 1.936547 GACTTGCTTAGATTCGGCCAG 59.063 52.381 2.24 0.00 0.00 4.85
247 248 1.279271 ACTTGCTTAGATTCGGCCAGT 59.721 47.619 2.24 0.00 0.00 4.00
255 256 0.872388 GATTCGGCCAGTGTTCGTTT 59.128 50.000 2.24 0.00 0.00 3.60
274 275 5.747675 TCGTTTGTGTTCGTGTTTCTACATA 59.252 36.000 0.00 0.00 36.50 2.29
285 291 6.814644 TCGTGTTTCTACATATTGGTTCGATT 59.185 34.615 0.00 0.00 36.50 3.34
295 301 8.506168 ACATATTGGTTCGATTTACACTTCAT 57.494 30.769 0.00 0.00 0.00 2.57
300 306 6.664515 TGGTTCGATTTACACTTCATTTCAC 58.335 36.000 0.00 0.00 0.00 3.18
340 346 0.755327 GTGTGCTGGTCTTTTGGGGT 60.755 55.000 0.00 0.00 0.00 4.95
357 363 1.270678 GGGTCTTAGCACGGTGACTTT 60.271 52.381 13.29 0.00 0.00 2.66
360 366 3.057033 GGTCTTAGCACGGTGACTTTCTA 60.057 47.826 13.29 0.21 0.00 2.10
383 389 8.148351 TCTAACTGTCTACTACAATGTTTGCTT 58.852 33.333 0.00 0.00 37.74 3.91
390 396 7.813148 GTCTACTACAATGTTTGCTTGACTCTA 59.187 37.037 0.00 0.00 0.00 2.43
397 403 7.665559 ACAATGTTTGCTTGACTCTAATAAGGA 59.334 33.333 0.00 0.00 0.00 3.36
410 416 8.749026 ACTCTAATAAGGAAGAGACGATAACA 57.251 34.615 6.36 0.00 41.51 2.41
434 440 2.103143 CGACTTCGGCTCGCTCAT 59.897 61.111 0.00 0.00 35.37 2.90
465 471 0.181114 CAGTGGCATAAGCAGGGCTA 59.819 55.000 0.00 0.00 44.61 3.93
466 472 0.918983 AGTGGCATAAGCAGGGCTAA 59.081 50.000 0.00 0.00 44.61 3.09
467 473 1.284785 AGTGGCATAAGCAGGGCTAAA 59.715 47.619 0.00 0.00 44.61 1.85
469 475 1.032794 GGCATAAGCAGGGCTAAACC 58.967 55.000 0.00 0.00 44.61 3.27
471 477 1.405463 GCATAAGCAGGGCTAAACCAC 59.595 52.381 0.00 0.00 38.25 4.16
472 478 2.722094 CATAAGCAGGGCTAAACCACA 58.278 47.619 0.00 0.00 38.25 4.17
473 479 3.290710 CATAAGCAGGGCTAAACCACAT 58.709 45.455 0.00 0.00 38.25 3.21
474 480 2.309136 AAGCAGGGCTAAACCACATT 57.691 45.000 0.00 0.00 38.25 2.71
489 529 9.357652 CTAAACCACATTAAAGGATTTGTCATG 57.642 33.333 0.00 0.00 39.63 3.07
494 534 0.532115 AAAGGATTTGTCATGCGCCC 59.468 50.000 4.18 0.00 36.60 6.13
501 541 2.191908 GTCATGCGCCCCATACCA 59.808 61.111 4.18 0.00 31.47 3.25
510 550 0.178990 GCCCCATACCATGTCCCTTC 60.179 60.000 0.00 0.00 0.00 3.46
511 551 1.522900 CCCCATACCATGTCCCTTCT 58.477 55.000 0.00 0.00 0.00 2.85
518 558 1.076024 ACCATGTCCCTTCTTGCATGT 59.924 47.619 0.00 0.00 37.57 3.21
522 562 0.798776 GTCCCTTCTTGCATGTGACG 59.201 55.000 0.00 0.00 0.00 4.35
538 578 3.671459 TGTGACGCTGTTTGTAGTTATCG 59.329 43.478 0.00 0.00 0.00 2.92
539 579 3.671928 GTGACGCTGTTTGTAGTTATCGT 59.328 43.478 0.00 0.00 0.00 3.73
540 580 3.916172 TGACGCTGTTTGTAGTTATCGTC 59.084 43.478 0.00 0.00 43.44 4.20
543 583 3.303495 CGCTGTTTGTAGTTATCGTCAGG 59.697 47.826 0.00 0.00 0.00 3.86
546 586 5.456548 TGTTTGTAGTTATCGTCAGGTGA 57.543 39.130 0.00 0.00 0.00 4.02
552 592 8.913487 TTGTAGTTATCGTCAGGTGATCTATA 57.087 34.615 0.00 0.00 0.00 1.31
564 604 6.210185 TCAGGTGATCTATAGACATGGATGTG 59.790 42.308 4.10 0.00 41.95 3.21
580 623 7.546667 ACATGGATGTGATTTTTATTGCTTGTC 59.453 33.333 0.00 0.00 40.03 3.18
584 627 9.638239 GGATGTGATTTTTATTGCTTGTCTTTA 57.362 29.630 0.00 0.00 0.00 1.85
634 677 2.957680 TGAATTTTGTCCTTGCTCAGCA 59.042 40.909 0.00 0.00 36.47 4.41
655 698 8.081633 TCAGCAAACATCACGAAATAGAAAAAT 58.918 29.630 0.00 0.00 0.00 1.82
657 700 9.341899 AGCAAACATCACGAAATAGAAAAATAC 57.658 29.630 0.00 0.00 0.00 1.89
660 703 9.755064 AAACATCACGAAATAGAAAAATACTCG 57.245 29.630 0.00 0.00 0.00 4.18
661 704 8.475331 ACATCACGAAATAGAAAAATACTCGT 57.525 30.769 0.00 0.00 38.48 4.18
662 705 9.577110 ACATCACGAAATAGAAAAATACTCGTA 57.423 29.630 0.00 0.00 36.38 3.43
665 708 9.630098 TCACGAAATAGAAAAATACTCGTAAGT 57.370 29.630 0.00 0.00 36.38 2.24
843 893 6.947903 TTTTACACTTTCCAAAACGAAACC 57.052 33.333 0.00 0.00 0.00 3.27
850 900 0.248702 CCAAAACGAAACCACCCGTG 60.249 55.000 0.00 0.00 39.14 4.94
943 994 0.249073 AGCACGAAATCCCTCGATCG 60.249 55.000 9.36 9.36 41.44 3.69
974 1025 2.080286 TCGAAGCTTTTCTTCCTCCG 57.920 50.000 0.00 0.00 46.60 4.63
1338 1389 1.200020 GATCCGGTGGTTTTGCAGAAG 59.800 52.381 0.00 0.00 0.00 2.85
1681 1732 6.707161 ACACGTCTACTCTATGAGATACTTCC 59.293 42.308 1.25 0.00 33.32 3.46
1704 1755 3.343617 TCAGGTTAAATGCAGTAGCCAC 58.656 45.455 13.42 0.00 41.13 5.01
1778 1992 3.519107 TCAGTGTGATGGCAGAGGAAATA 59.481 43.478 0.00 0.00 0.00 1.40
1791 2005 8.494433 TGGCAGAGGAAATATCTACAATTAGTT 58.506 33.333 0.00 0.00 0.00 2.24
2035 2261 8.837389 AGTTAAACTAGTTTGATTCAGGACAAC 58.163 33.333 27.40 18.89 34.23 3.32
2046 2272 6.601332 TGATTCAGGACAACCTTAGAACTTT 58.399 36.000 0.00 0.00 45.36 2.66
2198 2424 2.489329 TCTGCTCTGCAAGTTTATTGGC 59.511 45.455 0.00 0.00 38.41 4.52
2355 2581 3.146066 TGGAAGTTCACCATGCAGTTAC 58.854 45.455 5.01 0.00 32.03 2.50
2363 2589 2.034053 CACCATGCAGTTACGGTGTTTT 59.966 45.455 11.73 0.00 43.23 2.43
2379 2605 3.006247 TGTTTTTGTTTTGGGCTTGAGC 58.994 40.909 0.00 0.00 41.14 4.26
2501 2727 5.437289 TGCGCTCAAATAGGGATAAAATG 57.563 39.130 9.73 0.00 40.56 2.32
2520 2746 3.170991 TGAGTAGGTGCAAGTAGGTCT 57.829 47.619 0.00 0.00 0.00 3.85
2659 2885 6.402222 AGTGAGCACTGAGGTATAAGAAAAG 58.598 40.000 1.71 0.00 40.75 2.27
2878 3105 3.900855 GAGCTCACAGCACCATGG 58.099 61.111 11.19 11.19 45.56 3.66
2886 3113 2.105649 TCACAGCACCATGGTTCACTTA 59.894 45.455 16.84 0.00 0.00 2.24
2898 3125 5.703978 TGGTTCACTTAACATTGATGTGG 57.296 39.130 0.00 0.00 41.61 4.17
2998 3225 2.747460 GCTGGCAGCGATGAACCA 60.747 61.111 25.47 1.64 0.00 3.67
3034 3261 2.508887 GCTGTCCTCGAGCTGCAG 60.509 66.667 10.11 10.11 33.37 4.41
3045 3272 1.531264 CGAGCTGCAGAAATGTGATGC 60.531 52.381 20.43 0.00 40.40 3.91
3080 3307 0.839946 AATTCCCTGTAGCTGCCGAT 59.160 50.000 0.00 0.00 0.00 4.18
3182 3409 1.197721 GAAATGTCACGGAAGGCACAG 59.802 52.381 0.00 0.00 31.45 3.66
3379 3611 0.380378 GAAAACCGTGCACAGCTTGA 59.620 50.000 18.64 0.00 0.00 3.02
3427 3660 5.305644 CAGCCACCCTCTAAATAGTATGTCT 59.694 44.000 0.00 0.00 0.00 3.41
3587 3820 0.251165 TAGAAACAACAGCAGGGGCC 60.251 55.000 0.00 0.00 42.56 5.80
3632 3865 3.200825 AGAGAGAACAGGGAGAGAGAGAG 59.799 52.174 0.00 0.00 0.00 3.20
3633 3866 3.189606 AGAGAACAGGGAGAGAGAGAGA 58.810 50.000 0.00 0.00 0.00 3.10
3660 3893 1.668101 GAGGTACGCAGTGAGGAGGG 61.668 65.000 0.00 0.00 45.73 4.30
3667 3900 0.614979 GCAGTGAGGAGGGTAGGTGA 60.615 60.000 0.00 0.00 0.00 4.02
3746 3979 7.728148 TGACATGTCAACTAGGTAAACAACTA 58.272 34.615 26.02 0.00 36.53 2.24
3841 4074 5.401531 TGTACGAGGAGTTTTAAGCATCT 57.598 39.130 0.00 0.00 0.00 2.90
4095 4336 0.896226 AGAGGGAGTACGAAGTTGGC 59.104 55.000 0.00 0.00 37.78 4.52
4117 4358 0.829333 ACTGAGATTCGGAGCAGCAT 59.171 50.000 0.00 0.00 31.74 3.79
4213 4454 4.808077 AAGCGAGCAAGATATCATGTTG 57.192 40.909 9.53 4.60 36.68 3.33
4619 4864 8.981659 TGGTGTGAATCTGAATTTCTAGAGATA 58.018 33.333 0.00 0.00 0.00 1.98
4660 4905 6.071840 AGTGCTCGAGTTAATTCTGAGTAACT 60.072 38.462 15.13 12.84 46.11 2.24
4748 4993 9.847224 TCCTCAAAATAAGAAACATATACTCCC 57.153 33.333 0.00 0.00 0.00 4.30
4749 4994 9.853177 CCTCAAAATAAGAAACATATACTCCCT 57.147 33.333 0.00 0.00 0.00 4.20
4751 4996 9.847224 TCAAAATAAGAAACATATACTCCCTCC 57.153 33.333 0.00 0.00 0.00 4.30
4752 4997 8.774586 CAAAATAAGAAACATATACTCCCTCCG 58.225 37.037 0.00 0.00 0.00 4.63
4753 4998 7.613551 AATAAGAAACATATACTCCCTCCGT 57.386 36.000 0.00 0.00 0.00 4.69
4754 4999 5.952347 AAGAAACATATACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
4755 5000 5.532664 AGAAACATATACTCCCTCCGTTC 57.467 43.478 0.00 0.00 0.00 3.95
4756 5001 4.344390 AGAAACATATACTCCCTCCGTTCC 59.656 45.833 0.00 0.00 0.00 3.62
4757 5002 3.614568 ACATATACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
4758 5003 4.736611 ACATATACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
4759 5004 5.070823 ACATATACTCCCTCCGTTCCTAA 57.929 43.478 0.00 0.00 0.00 2.69
4760 5005 5.461327 ACATATACTCCCTCCGTTCCTAAA 58.539 41.667 0.00 0.00 0.00 1.85
4761 5006 6.082707 ACATATACTCCCTCCGTTCCTAAAT 58.917 40.000 0.00 0.00 0.00 1.40
4762 5007 7.243824 ACATATACTCCCTCCGTTCCTAAATA 58.756 38.462 0.00 0.00 0.00 1.40
4763 5008 7.899709 ACATATACTCCCTCCGTTCCTAAATAT 59.100 37.037 0.00 0.00 0.00 1.28
4764 5009 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
4766 5011 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4767 5012 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4768 5013 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4769 5014 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4770 5015 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4771 5016 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4772 5017 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4773 5018 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4804 5049 8.662781 TTTCAATAAGTGACTACATATGGAGC 57.337 34.615 15.30 8.47 35.39 4.70
4805 5050 7.360113 TCAATAAGTGACTACATATGGAGCA 57.640 36.000 15.30 10.95 0.00 4.26
4806 5051 7.966812 TCAATAAGTGACTACATATGGAGCAT 58.033 34.615 15.30 0.00 0.00 3.79
4807 5052 8.090831 TCAATAAGTGACTACATATGGAGCATC 58.909 37.037 15.30 6.73 0.00 3.91
4808 5053 7.789202 ATAAGTGACTACATATGGAGCATCT 57.211 36.000 15.30 7.58 33.73 2.90
4809 5054 5.465532 AGTGACTACATATGGAGCATCTG 57.534 43.478 15.30 0.00 33.73 2.90
4810 5055 4.898265 AGTGACTACATATGGAGCATCTGT 59.102 41.667 15.30 0.00 35.77 3.41
4811 5056 6.071320 AGTGACTACATATGGAGCATCTGTA 58.929 40.000 15.30 0.00 34.08 2.74
4812 5057 6.723515 AGTGACTACATATGGAGCATCTGTAT 59.276 38.462 15.30 0.00 34.54 2.29
4813 5058 6.810676 GTGACTACATATGGAGCATCTGTATG 59.189 42.308 15.30 0.00 34.54 2.39
4814 5059 6.494835 TGACTACATATGGAGCATCTGTATGT 59.505 38.462 15.30 0.00 43.06 2.29
4815 5060 7.669722 TGACTACATATGGAGCATCTGTATGTA 59.330 37.037 15.30 0.00 41.82 2.29
4817 5062 6.924913 ACATATGGAGCATCTGTATGTAGT 57.075 37.500 7.80 0.00 40.81 2.73
4818 5063 6.929625 ACATATGGAGCATCTGTATGTAGTC 58.070 40.000 7.80 0.00 40.81 2.59
4819 5064 6.494835 ACATATGGAGCATCTGTATGTAGTCA 59.505 38.462 7.80 0.00 40.81 3.41
4820 5065 4.655762 TGGAGCATCTGTATGTAGTCAC 57.344 45.455 0.00 0.00 35.38 3.67
4821 5066 4.281657 TGGAGCATCTGTATGTAGTCACT 58.718 43.478 0.00 0.00 35.38 3.41
4822 5067 4.711846 TGGAGCATCTGTATGTAGTCACTT 59.288 41.667 0.00 0.00 35.38 3.16
4823 5068 5.891551 TGGAGCATCTGTATGTAGTCACTTA 59.108 40.000 0.00 0.00 35.38 2.24
4824 5069 6.551227 TGGAGCATCTGTATGTAGTCACTTAT 59.449 38.462 0.00 0.00 35.38 1.73
4825 5070 7.069950 TGGAGCATCTGTATGTAGTCACTTATT 59.930 37.037 0.00 0.00 35.38 1.40
4826 5071 7.383572 GGAGCATCTGTATGTAGTCACTTATTG 59.616 40.741 0.00 0.00 35.38 1.90
4827 5072 8.011844 AGCATCTGTATGTAGTCACTTATTGA 57.988 34.615 0.00 0.00 35.38 2.57
4828 5073 8.478066 AGCATCTGTATGTAGTCACTTATTGAA 58.522 33.333 0.00 0.00 33.86 2.69
4829 5074 9.098355 GCATCTGTATGTAGTCACTTATTGAAA 57.902 33.333 0.00 0.00 33.86 2.69
4858 5103 9.211485 TCTAAAAAGACTTACATTTAGGAACGG 57.789 33.333 13.94 0.00 36.48 4.44
4859 5104 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
4860 5105 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
4861 5106 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
4862 5107 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
4863 5108 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4864 5109 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4865 5110 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
4866 5111 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
4867 5112 4.296056 ACATTTAGGAACGGAGGGAGTAT 58.704 43.478 0.00 0.00 0.00 2.12
4991 5236 9.031537 TCCTGTGAAATAACTACAGAGTTGATA 57.968 33.333 0.00 0.00 45.74 2.15
5152 5397 5.877564 GCCTGCTAGTTTTAAAGTCAGATCT 59.122 40.000 0.00 0.00 0.00 2.75
5292 5537 4.453136 TGTTATACCTTTGACGGCAAGTTC 59.547 41.667 2.76 0.00 35.04 3.01
5427 5672 1.479730 TGCAGACAGGCATCAGACTAG 59.520 52.381 0.00 0.00 39.25 2.57
5769 6016 7.278868 GTGTTCTCATATTGAACCTAACAGGAG 59.721 40.741 12.94 0.00 42.04 3.69
5911 6159 7.584122 TCACATAAGAGAGTACTATTGGGTC 57.416 40.000 0.00 0.00 0.00 4.46
5950 6198 7.484035 AAATGAGATTTATCGCTACAAGACC 57.516 36.000 0.00 0.00 0.00 3.85
6232 6480 1.062886 TGCTACCCTGCTCTGGAGTAT 60.063 52.381 0.00 0.00 0.00 2.12
6296 6544 7.225931 ACACGTAAGCAACTGAAAATTCTTCTA 59.774 33.333 0.00 0.00 45.62 2.10
6369 6617 4.595762 ATGCTTTGCACAAGAACTGAAT 57.404 36.364 11.34 0.00 43.04 2.57
6370 6618 3.968649 TGCTTTGCACAAGAACTGAATC 58.031 40.909 11.34 0.00 31.71 2.52
6424 6674 8.585881 TCACTTGCTTCTAACATTCTAAGTAGT 58.414 33.333 0.00 0.00 0.00 2.73
6490 6740 7.332182 ACTTGCTTCTAACATTCTAAGTAGCAC 59.668 37.037 2.88 0.00 41.45 4.40
6492 6742 8.063200 TGCTTCTAACATTCTAAGTAGCACTA 57.937 34.615 0.00 0.00 38.31 2.74
6507 6757 1.136891 GCACTATTTTGGCCCCATGAC 59.863 52.381 0.00 0.00 0.00 3.06
6510 6760 1.949525 CTATTTTGGCCCCATGACGAG 59.050 52.381 0.00 0.00 0.00 4.18
6526 6776 7.434492 CCATGACGAGTCTTTACCTATGTTAT 58.566 38.462 4.78 0.00 0.00 1.89
6527 6777 7.926555 CCATGACGAGTCTTTACCTATGTTATT 59.073 37.037 4.78 0.00 0.00 1.40
6528 6778 9.961265 CATGACGAGTCTTTACCTATGTTATTA 57.039 33.333 4.78 0.00 0.00 0.98
6532 6782 9.674824 ACGAGTCTTTACCTATGTTATTAATCG 57.325 33.333 0.00 0.00 0.00 3.34
6572 6822 5.545658 TGATCAAGTTGTATTCTTTCGGC 57.454 39.130 2.11 0.00 0.00 5.54
6616 6867 3.806949 TTGGGTATTTGAGCACTCCTT 57.193 42.857 0.00 0.00 0.00 3.36
6705 6956 6.954102 TGCTATGGCAGGTATAGATTCTCTAA 59.046 38.462 0.00 0.00 44.28 2.10
6981 7232 7.944729 TCTTAGCTCTAAAATGCTTTTGGAT 57.055 32.000 0.00 0.00 39.04 3.41
6987 7238 5.708948 TCTAAAATGCTTTTGGATTGTCCG 58.291 37.500 0.00 0.00 39.61 4.79
7202 7453 5.373222 ACACAGAAGTTGGCACTTGTAATA 58.627 37.500 6.99 0.00 43.79 0.98
7438 7691 0.751643 ACAGTGTGTTCCTGTTGCCC 60.752 55.000 0.00 0.00 40.14 5.36
7456 7709 1.730902 CCCGATATGCTGTCTCGCG 60.731 63.158 0.00 0.00 0.00 5.87
7537 7790 2.793946 GGCCAGCTAATGTGTGCG 59.206 61.111 0.00 0.00 0.00 5.34
7602 7855 6.718454 TCAAGATCTCTGAAATTGGCTTTCTT 59.282 34.615 0.00 0.00 43.14 2.52
7699 7952 7.540474 TTTCATCTCTGGAGTAGTAGTTGTT 57.460 36.000 0.00 0.00 0.00 2.83
7700 7953 6.516739 TCATCTCTGGAGTAGTAGTTGTTG 57.483 41.667 0.00 0.00 0.00 3.33
7701 7954 6.246163 TCATCTCTGGAGTAGTAGTTGTTGA 58.754 40.000 0.00 0.00 0.00 3.18
7744 7997 4.831107 ACTTGTTGTGGCTTTGAACAAAT 58.169 34.783 0.00 0.00 38.70 2.32
7847 8102 1.004440 GGTGACCACTGAGTCTGCC 60.004 63.158 0.00 0.00 37.66 4.85
7872 8127 0.790814 ACTTCTTAACGCGCTTCAGC 59.209 50.000 5.73 0.00 37.78 4.26
7893 8149 5.630680 CAGCTGCACAGGTTTTTACTTATTG 59.369 40.000 0.00 0.00 36.98 1.90
8101 8365 2.768527 TCTCCCTTGCAGACAGGAATAG 59.231 50.000 4.39 0.11 0.00 1.73
8200 8464 2.132762 CCAATCTTACGGTCATACGCC 58.867 52.381 0.00 0.00 37.37 5.68
8258 9146 1.793258 CTGTGCAGAGTTGAGGTGAG 58.207 55.000 1.91 0.00 0.00 3.51
8445 9340 6.763355 TGAATTGCTAGGATTATCCAGACTC 58.237 40.000 14.30 1.63 39.61 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.609841 CCCGAGTAGGACACAAAACCC 60.610 57.143 0.00 0.00 45.00 4.11
63 64 2.100197 CATCTTCCCGAGTAGGACACA 58.900 52.381 0.00 0.00 45.00 3.72
71 72 2.427245 CCGCCTCATCTTCCCGAGT 61.427 63.158 0.00 0.00 0.00 4.18
135 136 3.846360 ACACTAGACGCATTGTTAGGAC 58.154 45.455 0.00 0.00 0.00 3.85
139 140 5.929415 TCAAATGACACTAGACGCATTGTTA 59.071 36.000 0.00 0.00 31.86 2.41
143 144 3.935203 CCTCAAATGACACTAGACGCATT 59.065 43.478 0.00 0.00 32.75 3.56
144 145 3.525537 CCTCAAATGACACTAGACGCAT 58.474 45.455 0.00 0.00 0.00 4.73
146 147 2.271800 CCCTCAAATGACACTAGACGC 58.728 52.381 0.00 0.00 0.00 5.19
154 155 0.888736 CCACACGCCCTCAAATGACA 60.889 55.000 0.00 0.00 0.00 3.58
181 182 1.617018 CCCGCAAGATCCACAGGAGA 61.617 60.000 0.00 0.00 43.02 3.71
186 187 0.617935 TGAATCCCGCAAGATCCACA 59.382 50.000 0.00 0.00 43.02 4.17
188 189 0.911769 ACTGAATCCCGCAAGATCCA 59.088 50.000 0.00 0.00 43.02 3.41
197 198 0.796312 CAAACACCGACTGAATCCCG 59.204 55.000 0.00 0.00 0.00 5.14
216 217 2.029290 TCTAAGCAAGTCCACCGAAGAC 60.029 50.000 0.00 0.00 34.31 3.01
229 230 1.003118 ACACTGGCCGAATCTAAGCAA 59.997 47.619 0.00 0.00 0.00 3.91
235 236 0.034896 AACGAACACTGGCCGAATCT 59.965 50.000 0.00 0.00 0.00 2.40
243 244 1.395608 ACGAACACAAACGAACACTGG 59.604 47.619 0.00 0.00 0.00 4.00
245 246 2.070783 ACACGAACACAAACGAACACT 58.929 42.857 0.00 0.00 0.00 3.55
246 247 2.513964 ACACGAACACAAACGAACAC 57.486 45.000 0.00 0.00 0.00 3.32
247 248 3.186817 AGAAACACGAACACAAACGAACA 59.813 39.130 0.00 0.00 0.00 3.18
255 256 5.992829 ACCAATATGTAGAAACACGAACACA 59.007 36.000 0.00 0.00 38.78 3.72
274 275 7.807907 GTGAAATGAAGTGTAAATCGAACCAAT 59.192 33.333 0.00 0.00 0.00 3.16
285 291 1.801771 CGCCGGTGAAATGAAGTGTAA 59.198 47.619 10.20 0.00 0.00 2.41
318 324 1.110442 CCAAAAGACCAGCACACCAA 58.890 50.000 0.00 0.00 0.00 3.67
340 346 4.280174 AGTTAGAAAGTCACCGTGCTAAGA 59.720 41.667 0.00 0.00 0.00 2.10
357 363 7.667557 AGCAAACATTGTAGTAGACAGTTAGA 58.332 34.615 0.00 0.00 39.88 2.10
360 366 6.765989 TCAAGCAAACATTGTAGTAGACAGTT 59.234 34.615 0.00 0.00 39.88 3.16
383 389 8.838365 GTTATCGTCTCTTCCTTATTAGAGTCA 58.162 37.037 0.00 0.00 39.13 3.41
390 396 7.435488 CGTCATTGTTATCGTCTCTTCCTTATT 59.565 37.037 0.00 0.00 0.00 1.40
397 403 2.852413 CGCGTCATTGTTATCGTCTCTT 59.148 45.455 0.00 0.00 0.00 2.85
410 416 1.805945 GAGCCGAAGTCGCGTCATT 60.806 57.895 5.77 0.00 38.18 2.57
412 418 4.753877 CGAGCCGAAGTCGCGTCA 62.754 66.667 5.77 0.00 38.18 4.35
434 440 1.600636 GCCACTGGCTACAAGCACA 60.601 57.895 13.28 0.00 46.69 4.57
453 459 3.669939 ATGTGGTTTAGCCCTGCTTAT 57.330 42.857 0.00 0.00 40.44 1.73
456 462 3.449746 TTAATGTGGTTTAGCCCTGCT 57.550 42.857 0.00 0.00 43.41 4.24
465 471 6.650390 GCATGACAAATCCTTTAATGTGGTTT 59.350 34.615 0.00 0.00 0.00 3.27
466 472 6.165577 GCATGACAAATCCTTTAATGTGGTT 58.834 36.000 0.00 0.00 0.00 3.67
467 473 5.622007 CGCATGACAAATCCTTTAATGTGGT 60.622 40.000 0.00 0.00 0.00 4.16
469 475 4.266029 GCGCATGACAAATCCTTTAATGTG 59.734 41.667 0.30 0.00 0.00 3.21
471 477 3.798337 GGCGCATGACAAATCCTTTAATG 59.202 43.478 10.83 0.00 0.00 1.90
472 478 3.181476 GGGCGCATGACAAATCCTTTAAT 60.181 43.478 10.83 0.00 0.00 1.40
473 479 2.165437 GGGCGCATGACAAATCCTTTAA 59.835 45.455 10.83 0.00 0.00 1.52
474 480 1.748493 GGGCGCATGACAAATCCTTTA 59.252 47.619 10.83 0.00 0.00 1.85
489 529 2.594592 GGACATGGTATGGGGCGC 60.595 66.667 0.00 0.00 33.60 6.53
494 534 2.301346 GCAAGAAGGGACATGGTATGG 58.699 52.381 0.00 0.00 33.60 2.74
501 541 2.440409 GTCACATGCAAGAAGGGACAT 58.560 47.619 0.00 0.00 0.00 3.06
510 550 1.268692 ACAAACAGCGTCACATGCAAG 60.269 47.619 0.00 0.00 31.07 4.01
511 551 0.737804 ACAAACAGCGTCACATGCAA 59.262 45.000 0.00 0.00 31.07 4.08
518 558 3.904571 ACGATAACTACAAACAGCGTCA 58.095 40.909 0.00 0.00 0.00 4.35
522 562 4.091509 CACCTGACGATAACTACAAACAGC 59.908 45.833 0.00 0.00 0.00 4.40
538 578 6.210385 ACATCCATGTCTATAGATCACCTGAC 59.790 42.308 5.57 0.00 35.87 3.51
539 579 6.210185 CACATCCATGTCTATAGATCACCTGA 59.790 42.308 5.57 4.78 39.39 3.86
540 580 6.210185 TCACATCCATGTCTATAGATCACCTG 59.790 42.308 5.57 3.20 39.39 4.00
543 583 9.499479 AAAATCACATCCATGTCTATAGATCAC 57.501 33.333 5.57 0.00 39.39 3.06
552 592 7.414222 AGCAATAAAAATCACATCCATGTCT 57.586 32.000 0.00 0.00 39.39 3.41
612 655 3.384146 TGCTGAGCAAGGACAAAATTCAA 59.616 39.130 3.81 0.00 34.76 2.69
634 677 9.755064 CGAGTATTTTTCTATTTCGTGATGTTT 57.245 29.630 0.00 0.00 0.00 2.83
655 698 3.438087 GCACCACTGAGTACTTACGAGTA 59.562 47.826 0.00 0.00 37.33 2.59
657 700 2.488545 AGCACCACTGAGTACTTACGAG 59.511 50.000 0.00 0.00 0.00 4.18
669 712 1.588082 GGATTTGCCAGCACCACTG 59.412 57.895 0.00 0.00 46.77 3.66
811 861 7.690952 TTTGGAAAGTGTAAAATATAGGCGT 57.309 32.000 0.00 0.00 0.00 5.68
843 893 1.874872 ACATCGTTTTAACCACGGGTG 59.125 47.619 6.55 8.15 38.23 4.61
850 900 7.007995 GCAGTGCTTTATTACATCGTTTTAACC 59.992 37.037 8.18 0.00 0.00 2.85
943 994 2.310966 GCTTCGATCGGATTCGGGC 61.311 63.158 16.41 1.52 39.56 6.13
974 1025 1.652329 CGCGCGAGATTTGGATTGC 60.652 57.895 28.94 0.00 0.00 3.56
1338 1389 1.755783 CAGGCCCTCCAATTGCTCC 60.756 63.158 0.00 0.00 33.74 4.70
1681 1732 4.009675 TGGCTACTGCATTTAACCTGAAG 58.990 43.478 0.00 0.00 41.91 3.02
1791 2005 6.957631 TCTAGAAAGGCCATTTGTGAGATAA 58.042 36.000 5.01 0.00 0.00 1.75
2017 2243 7.311092 TCTAAGGTTGTCCTGAATCAAACTA 57.689 36.000 0.00 0.00 44.35 2.24
2046 2272 5.192121 TCCTCCCTCCGTTCCAAATTAATTA 59.808 40.000 0.01 0.00 0.00 1.40
2198 2424 1.959042 ATGCTTGCAGAGTTATCCCG 58.041 50.000 0.87 0.00 0.00 5.14
2355 2581 2.017138 AGCCCAAAACAAAAACACCG 57.983 45.000 0.00 0.00 0.00 4.94
2363 2589 1.067250 GCGCTCAAGCCCAAAACAA 59.933 52.632 0.00 0.00 37.91 2.83
2379 2605 0.038526 AACCTAAGTCACGGACTGCG 60.039 55.000 7.23 0.00 42.59 5.18
2387 2613 7.089538 GGTAAACTCACTCTAACCTAAGTCAC 58.910 42.308 0.00 0.00 0.00 3.67
2501 2727 2.826725 ACAGACCTACTTGCACCTACTC 59.173 50.000 0.00 0.00 0.00 2.59
2520 2746 4.609947 CAAATGCAACTTGTAAGCTCACA 58.390 39.130 0.00 0.00 0.00 3.58
2583 2809 9.612620 AAGCGAGAGAAAATAACACATTTTAAG 57.387 29.630 0.00 0.00 32.03 1.85
2659 2885 8.484641 TCAATTTGAGTCACAGATCAATAGAC 57.515 34.615 0.00 0.00 35.47 2.59
2878 3105 4.917415 GTGCCACATCAATGTTAAGTGAAC 59.083 41.667 0.00 0.00 39.39 3.18
2886 3113 2.555325 CAGAGTGTGCCACATCAATGTT 59.445 45.455 0.00 0.00 39.39 2.71
2898 3125 2.980233 GTGCCACCCAGAGTGTGC 60.980 66.667 0.00 0.00 45.74 4.57
3034 3261 5.565592 TGTGTTCTATGGCATCACATTTC 57.434 39.130 13.78 2.47 34.74 2.17
3045 3272 6.153340 ACAGGGAATTTCAATGTGTTCTATGG 59.847 38.462 5.28 0.00 0.00 2.74
3080 3307 0.036732 GGTCACCAGCAACCAGATGA 59.963 55.000 0.00 0.00 35.00 2.92
3182 3409 1.744741 GCTCTTGGCTCCACTGCTC 60.745 63.158 0.00 0.00 38.06 4.26
3202 3429 2.102252 AGCCTCTTACAGTGCTGCTATC 59.898 50.000 0.00 0.00 31.70 2.08
3379 3611 4.330944 TTTTGTGTCTCAGGACGTATGT 57.669 40.909 0.00 0.00 44.83 2.29
3427 3660 2.026262 GGGCCCAAGATCAGTGAACTAA 60.026 50.000 19.95 0.00 0.00 2.24
3520 3753 0.469917 TGCAGCAGCTATTACTCCCC 59.530 55.000 1.76 0.00 42.74 4.81
3587 3820 2.091055 TGATCTGGTAGGGAGAGGAAGG 60.091 54.545 0.00 0.00 0.00 3.46
3632 3865 1.305201 CTGCGTACCTCCTCTCTCTC 58.695 60.000 0.00 0.00 0.00 3.20
3633 3866 0.621609 ACTGCGTACCTCCTCTCTCT 59.378 55.000 0.00 0.00 0.00 3.10
3772 4005 6.072673 ACGTTCTTAAACAGGCCTCAAATAAG 60.073 38.462 0.00 9.86 34.93 1.73
3841 4074 5.560724 AGCCTTGCAGAAGTCAAACTATAA 58.439 37.500 0.00 0.00 0.00 0.98
3855 4088 1.453155 ACGGAAATGTAGCCTTGCAG 58.547 50.000 0.00 0.00 0.00 4.41
4095 4336 1.802136 GCTGCTCCGAATCTCAGTGAG 60.802 57.143 14.36 14.36 0.00 3.51
4117 4358 6.239217 AGGTCATAACAGCTGACATTATGA 57.761 37.500 23.95 23.95 43.85 2.15
4619 4864 3.929610 GAGCACTAAAATCGCTTCTGTCT 59.070 43.478 0.00 0.00 35.75 3.41
4742 4987 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
4743 4988 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
4744 4989 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4745 4990 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4746 4991 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4747 4992 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
4778 5023 9.277783 GCTCCATATGTAGTCACTTATTGAAAT 57.722 33.333 1.24 0.00 35.39 2.17
4779 5024 8.264347 TGCTCCATATGTAGTCACTTATTGAAA 58.736 33.333 1.24 0.00 35.39 2.69
4780 5025 7.791029 TGCTCCATATGTAGTCACTTATTGAA 58.209 34.615 1.24 0.00 35.39 2.69
4781 5026 7.360113 TGCTCCATATGTAGTCACTTATTGA 57.640 36.000 1.24 0.00 0.00 2.57
4782 5027 8.093307 AGATGCTCCATATGTAGTCACTTATTG 58.907 37.037 1.24 0.00 0.00 1.90
4783 5028 8.093307 CAGATGCTCCATATGTAGTCACTTATT 58.907 37.037 1.24 0.00 29.68 1.40
4784 5029 7.234371 ACAGATGCTCCATATGTAGTCACTTAT 59.766 37.037 3.87 0.00 43.20 1.73
4785 5030 6.551227 ACAGATGCTCCATATGTAGTCACTTA 59.449 38.462 3.87 0.00 43.20 2.24
4786 5031 5.365025 ACAGATGCTCCATATGTAGTCACTT 59.635 40.000 3.87 0.00 43.20 3.16
4787 5032 4.898265 ACAGATGCTCCATATGTAGTCACT 59.102 41.667 3.87 0.00 43.20 3.41
4788 5033 5.207110 ACAGATGCTCCATATGTAGTCAC 57.793 43.478 3.87 0.00 43.20 3.67
4789 5034 6.494835 ACATACAGATGCTCCATATGTAGTCA 59.505 38.462 15.21 0.00 46.69 3.41
4790 5035 6.929625 ACATACAGATGCTCCATATGTAGTC 58.070 40.000 15.21 0.00 46.69 2.59
4791 5036 6.924913 ACATACAGATGCTCCATATGTAGT 57.075 37.500 15.21 11.32 46.69 2.73
4792 5037 8.060931 ACTACATACAGATGCTCCATATGTAG 57.939 38.462 20.37 20.37 46.69 2.74
4794 5039 6.494835 TGACTACATACAGATGCTCCATATGT 59.505 38.462 9.94 9.94 46.08 2.29
4795 5040 6.810676 GTGACTACATACAGATGCTCCATATG 59.189 42.308 0.00 0.00 38.78 1.78
4796 5041 6.723515 AGTGACTACATACAGATGCTCCATAT 59.276 38.462 0.00 0.00 36.43 1.78
4797 5042 6.071320 AGTGACTACATACAGATGCTCCATA 58.929 40.000 0.00 0.00 36.43 2.74
4798 5043 4.898265 AGTGACTACATACAGATGCTCCAT 59.102 41.667 0.00 0.00 36.43 3.41
4799 5044 4.281657 AGTGACTACATACAGATGCTCCA 58.718 43.478 0.00 0.00 36.43 3.86
4800 5045 4.927978 AGTGACTACATACAGATGCTCC 57.072 45.455 0.00 0.00 36.43 4.70
4801 5046 8.138074 TCAATAAGTGACTACATACAGATGCTC 58.862 37.037 0.00 0.00 36.43 4.26
4802 5047 8.011844 TCAATAAGTGACTACATACAGATGCT 57.988 34.615 0.00 0.00 36.43 3.79
4803 5048 8.648557 TTCAATAAGTGACTACATACAGATGC 57.351 34.615 0.00 0.00 35.39 3.91
4832 5077 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
4833 5078 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
4834 5079 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
4835 5080 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
4836 5081 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
4837 5082 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
4838 5083 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
4839 5084 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
4840 5085 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
4841 5086 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
4842 5087 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
4843 5088 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
4844 5089 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
4845 5090 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
4846 5091 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
4847 5092 7.628501 AATAATACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
4848 5093 8.731591 ATAATAATACTCCCTCCGTTCCTAAA 57.268 34.615 0.00 0.00 0.00 1.85
4849 5094 8.731591 AATAATAATACTCCCTCCGTTCCTAA 57.268 34.615 0.00 0.00 0.00 2.69
4851 5096 8.912614 ATAATAATAATACTCCCTCCGTTCCT 57.087 34.615 0.00 0.00 0.00 3.36
4991 5236 5.815233 ATGATATCCAGGACAACGAGAAT 57.185 39.130 0.00 0.00 0.00 2.40
5152 5397 5.076182 TCATTGTTTCCATCTAAAGGCACA 58.924 37.500 0.00 0.00 0.00 4.57
5427 5672 6.459298 CCATCAGTCAAGCATAAATTCAGGAC 60.459 42.308 0.00 0.00 0.00 3.85
5769 6016 5.948992 ATAGAACAGAGCCTGTGAAAAAC 57.051 39.130 8.37 0.00 44.62 2.43
5815 6063 4.944619 TCCATCATCTGTACTGACCATC 57.055 45.455 4.39 0.00 0.00 3.51
5950 6198 2.360483 AGCATCATGTGAGTACTCCTCG 59.640 50.000 20.11 6.41 43.64 4.63
6232 6480 4.503123 CCAGTGATAATACGCCATTCCTCA 60.503 45.833 0.00 0.00 0.00 3.86
6296 6544 4.137116 ACTGAATACATACACGGCACAT 57.863 40.909 0.00 0.00 0.00 3.21
6424 6674 4.217510 CTCATCATGGGGCCAAAAGAATA 58.782 43.478 4.39 0.00 0.00 1.75
6490 6740 1.949525 CTCGTCATGGGGCCAAAATAG 59.050 52.381 4.39 0.00 0.00 1.73
6492 6742 0.039618 ACTCGTCATGGGGCCAAAAT 59.960 50.000 4.39 0.00 0.00 1.82
6507 6757 9.888878 TCGATTAATAACATAGGTAAAGACTCG 57.111 33.333 0.00 0.00 0.00 4.18
6553 6803 5.957842 AATGCCGAAAGAATACAACTTGA 57.042 34.783 0.00 0.00 0.00 3.02
6590 6841 5.163652 GGAGTGCTCAAATACCCAAACATAC 60.164 44.000 1.41 0.00 0.00 2.39
6598 6849 3.073274 ACAAGGAGTGCTCAAATACCC 57.927 47.619 1.41 0.00 0.00 3.69
6600 6851 7.617041 AATCTTACAAGGAGTGCTCAAATAC 57.383 36.000 1.41 0.00 0.00 1.89
6609 6860 6.300354 ACAACGAAAATCTTACAAGGAGTG 57.700 37.500 0.00 0.00 0.00 3.51
6616 6867 4.737765 GCAAGCAACAACGAAAATCTTACA 59.262 37.500 0.00 0.00 0.00 2.41
6705 6956 9.546428 AACATTAAGCAAAGCAAGAAAAGTTAT 57.454 25.926 0.00 0.00 0.00 1.89
6782 7033 1.270907 ACAGGCTAGGGTGAACTGAG 58.729 55.000 0.00 0.00 33.57 3.35
6981 7232 0.617935 TTGATGCCATCTCCGGACAA 59.382 50.000 0.00 0.00 0.00 3.18
6987 7238 9.399797 TCACATATTAATATTGATGCCATCTCC 57.600 33.333 6.21 0.00 0.00 3.71
7202 7453 2.845659 TGAAGTGGATACCCTGGTGAT 58.154 47.619 0.00 0.00 0.00 3.06
7290 7542 4.215965 ACACAATTGCGATTACGTGAAAC 58.784 39.130 19.11 0.00 41.98 2.78
7438 7691 1.730902 CGCGAGACAGCATATCGGG 60.731 63.158 0.00 7.49 41.82 5.14
7456 7709 3.050275 GACTCACGGGGTGCAAGC 61.050 66.667 0.00 0.00 32.98 4.01
7602 7855 1.670674 CGTGTTAAAGAGGGCGCAGTA 60.671 52.381 10.83 0.00 0.00 2.74
7696 7949 7.062749 ACAGTAGAAACTAGAACCATCAACA 57.937 36.000 0.00 0.00 33.48 3.33
7699 7952 8.418597 AGTTACAGTAGAAACTAGAACCATCA 57.581 34.615 0.00 0.00 34.23 3.07
7700 7953 9.141400 CAAGTTACAGTAGAAACTAGAACCATC 57.859 37.037 0.00 0.00 34.91 3.51
7701 7954 8.648693 ACAAGTTACAGTAGAAACTAGAACCAT 58.351 33.333 0.00 0.00 34.91 3.55
7744 7997 3.838565 AGTTCAAGAGACTGAGTCTGGA 58.161 45.455 21.45 11.59 43.53 3.86
7847 8102 1.787847 CGCGTTAAGAAGTGGCCAG 59.212 57.895 5.11 0.00 0.00 4.85
7872 8127 4.616802 CGCAATAAGTAAAAACCTGTGCAG 59.383 41.667 0.00 0.00 0.00 4.41
7893 8149 4.541085 AACAGTAACAAAACACCTACGC 57.459 40.909 0.00 0.00 0.00 4.42
7996 8259 2.110213 GGGTGGTTGCGTCTGTGA 59.890 61.111 0.00 0.00 0.00 3.58
8151 8415 0.031716 ACTGCAGATCCTAGAGCCCA 60.032 55.000 23.35 0.00 0.00 5.36
8258 9146 4.269523 TGCCCTGGACCACTGTGC 62.270 66.667 1.29 0.00 0.00 4.57
8418 9313 8.538701 AGTCTGGATAATCCTAGCAATTCATAG 58.461 37.037 0.00 0.00 37.46 2.23
8445 9340 4.159857 GCTAAGCTCGGTATACTGATTCG 58.840 47.826 14.78 5.09 0.00 3.34


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

AutoCloner maintained by Alex Coulton.