Multiple sequence alignment - TraesCS3B01G244000

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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 TraesCS3B01G244000 chr3B 100.000 5105 0 0 1 5105 385467831 385462727 0.000000e+00 9428.0
1 TraesCS3B01G244000 chr3A 94.911 4775 127 37 362 5103 387295677 387300368 0.000000e+00 7365.0
2 TraesCS3B01G244000 chr3A 88.441 372 30 3 1 362 387292595 387292963 2.180000e-118 436.0
3 TraesCS3B01G244000 chr3D 94.726 4797 124 30 361 5105 292030572 292025853 0.000000e+00 7337.0
4 TraesCS3B01G244000 chr3D 88.889 261 29 0 102 362 292033629 292033369 6.380000e-84 322.0
5 TraesCS3B01G244000 chr2A 74.085 683 167 8 2515 3195 38966787 38967461 6.510000e-69 272.0
6 TraesCS3B01G244000 chr2D 73.043 690 165 15 2515 3195 35782822 35783499 1.850000e-54 224.0
7 TraesCS3B01G244000 chr1D 97.297 37 1 0 3456 3492 18429087 18429123 4.270000e-06 63.9


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 TraesCS3B01G244000 chr3B 385462727 385467831 5104 True 9428.0 9428 100.0000 1 5105 1 chr3B.!!$R1 5104
1 TraesCS3B01G244000 chr3A 387292595 387300368 7773 False 3900.5 7365 91.6760 1 5103 2 chr3A.!!$F1 5102
2 TraesCS3B01G244000 chr3D 292025853 292033629 7776 True 3829.5 7337 91.8075 102 5105 2 chr3D.!!$R1 5003
3 TraesCS3B01G244000 chr2A 38966787 38967461 674 False 272.0 272 74.0850 2515 3195 1 chr2A.!!$F1 680
4 TraesCS3B01G244000 chr2D 35782822 35783499 677 False 224.0 224 73.0430 2515 3195 1 chr2D.!!$F1 680

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
107 116 0.473755 TGGGACAGCAGAAGCAAAGA 59.526 50.0 0.00 0.0 45.49 2.52 F
1553 4409 0.611896 GTACCAAAGCAGGCACCCAT 60.612 55.0 0.00 0.0 0.00 4.00 F
1576 4432 0.107831 AAAGCAGGCGACAGTACCAA 59.892 50.0 0.00 0.0 0.00 3.67 F
1577 4433 0.107831 AAGCAGGCGACAGTACCAAA 59.892 50.0 0.00 0.0 0.00 3.28 F
1578 4434 0.320771 AGCAGGCGACAGTACCAAAG 60.321 55.0 0.00 0.0 0.00 2.77 F
1581 4437 0.320771 AGGCGACAGTACCAAAGCAG 60.321 55.0 0.00 0.0 0.00 4.24 F
1586 4442 0.537371 ACAGTACCAAAGCAGGCACC 60.537 55.0 0.00 0.0 0.00 5.01 F
2363 5228 0.806868 AATGTTGCTCGTGCTGATGG 59.193 50.0 11.19 0.0 40.48 3.51 F
2838 5706 0.881796 GCAAAAGAGGGTGTGCCTAC 59.118 55.0 0.00 0.0 34.45 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 4413 0.107831 TTGGTACTGTCGCCTGCTTT 59.892 50.000 0.00 0.0 0.00 3.51 R
2972 5840 0.315251 GGGAAAAACAGCAGCTCCAC 59.685 55.000 0.00 0.0 0.00 4.02 R
3125 5993 2.927201 AAACCCACCTGCCACACCAG 62.927 60.000 0.00 0.0 0.00 4.00 R
3403 6271 4.530553 TGTTGCAATAGTACTTGGAGAGGA 59.469 41.667 0.59 0.0 0.00 3.71 R
3438 6306 7.094762 CGCCCTTCTTCAAAGTTATAAAACTCT 60.095 37.037 0.00 0.0 45.37 3.24 R
3631 6499 2.695666 AGCTCACAGGTATATCACGCTT 59.304 45.455 0.00 0.0 0.00 4.68 R
3750 6618 1.404986 CCTACTCGCGGGTGAATTTCA 60.405 52.381 24.75 0.0 0.00 2.69 R
3795 6663 2.047844 CAGTCAGGTGCCCAGTCG 60.048 66.667 0.00 0.0 0.00 4.18 R
4783 7704 0.172578 GGTATTCTTTTGGCGCACCC 59.827 55.000 10.83 0.0 33.59 4.61 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
36 37 3.842923 ACGATCGGCCAGCCAGAG 61.843 66.667 20.98 0.00 35.37 3.35
56 57 2.124151 GGCCGAGCATTGGACCAT 60.124 61.111 0.00 0.00 44.53 3.55
69 70 4.424711 ACCATCGCACCGGCCATT 62.425 61.111 0.00 0.00 36.38 3.16
76 77 1.153086 GCACCGGCCATTGAGATCT 60.153 57.895 0.00 0.00 0.00 2.75
104 113 1.597854 CGTGGGACAGCAGAAGCAA 60.598 57.895 0.00 0.00 45.49 3.91
107 116 0.473755 TGGGACAGCAGAAGCAAAGA 59.526 50.000 0.00 0.00 45.49 2.52
223 235 3.386237 GCCCGAGTCAGCTGACCT 61.386 66.667 37.09 26.00 45.85 3.85
236 248 2.202892 GACCTTCGTCGCATCCCC 60.203 66.667 0.00 0.00 0.00 4.81
239 251 2.721167 CCTTCGTCGCATCCCCAGA 61.721 63.158 0.00 0.00 0.00 3.86
247 259 2.665000 CATCCCCAGACGCACACT 59.335 61.111 0.00 0.00 0.00 3.55
443 3291 6.048732 TGTTCTATACAATCTGACAGGCAA 57.951 37.500 1.81 0.00 32.64 4.52
445 3293 6.539826 TGTTCTATACAATCTGACAGGCAATG 59.460 38.462 1.81 0.00 32.64 2.82
446 3294 5.059161 TCTATACAATCTGACAGGCAATGC 58.941 41.667 1.81 0.00 0.00 3.56
533 3381 9.489084 TGCATATATGGACTTAAATGTGACTAC 57.511 33.333 14.51 0.00 0.00 2.73
541 3389 7.048512 GGACTTAAATGTGACTACTAGCCATT 58.951 38.462 0.00 0.00 0.00 3.16
559 3407 4.860022 CCATTGTTAGACCCTCCAAATCT 58.140 43.478 0.00 0.00 0.00 2.40
679 3535 6.767902 ACTCAAGTGATTGCTACTGAGAAAAA 59.232 34.615 4.02 0.00 32.56 1.94
892 3748 5.928264 GGTCCCAAATTTGAGATTGTTTGAG 59.072 40.000 19.86 0.00 34.38 3.02
1278 4134 1.068954 CGGAAGCTTGCCTTTTCACTC 60.069 52.381 12.80 0.00 32.78 3.51
1459 4315 0.670162 CACAGGACCAAAGCAAGGTG 59.330 55.000 0.00 0.00 40.09 4.00
1548 4404 1.603455 GGCAGTACCAAAGCAGGCA 60.603 57.895 0.00 0.00 38.86 4.75
1549 4405 1.581447 GCAGTACCAAAGCAGGCAC 59.419 57.895 0.00 0.00 0.00 5.01
1551 4407 1.074951 AGTACCAAAGCAGGCACCC 59.925 57.895 0.00 0.00 0.00 4.61
1552 4408 1.228429 GTACCAAAGCAGGCACCCA 60.228 57.895 0.00 0.00 0.00 4.51
1553 4409 0.611896 GTACCAAAGCAGGCACCCAT 60.612 55.000 0.00 0.00 0.00 4.00
1554 4410 0.995803 TACCAAAGCAGGCACCCATA 59.004 50.000 0.00 0.00 0.00 2.74
1555 4411 0.611896 ACCAAAGCAGGCACCCATAC 60.612 55.000 0.00 0.00 0.00 2.39
1556 4412 1.322538 CCAAAGCAGGCACCCATACC 61.323 60.000 0.00 0.00 0.00 2.73
1557 4413 0.611618 CAAAGCAGGCACCCATACCA 60.612 55.000 0.00 0.00 0.00 3.25
1558 4414 0.114168 AAAGCAGGCACCCATACCAA 59.886 50.000 0.00 0.00 0.00 3.67
1559 4415 0.114168 AAGCAGGCACCCATACCAAA 59.886 50.000 0.00 0.00 0.00 3.28
1560 4416 0.323725 AGCAGGCACCCATACCAAAG 60.324 55.000 0.00 0.00 0.00 2.77
1561 4417 1.948721 GCAGGCACCCATACCAAAGC 61.949 60.000 0.00 0.00 0.00 3.51
1562 4418 0.611618 CAGGCACCCATACCAAAGCA 60.612 55.000 0.00 0.00 0.00 3.91
1563 4419 0.323725 AGGCACCCATACCAAAGCAG 60.324 55.000 0.00 0.00 0.00 4.24
1564 4420 1.322538 GGCACCCATACCAAAGCAGG 61.323 60.000 0.00 0.00 0.00 4.85
1565 4421 1.948721 GCACCCATACCAAAGCAGGC 61.949 60.000 0.00 0.00 0.00 4.85
1566 4422 1.378514 ACCCATACCAAAGCAGGCG 60.379 57.895 0.00 0.00 0.00 5.52
1567 4423 1.077787 CCCATACCAAAGCAGGCGA 60.078 57.895 0.00 0.00 0.00 5.54
1568 4424 1.376609 CCCATACCAAAGCAGGCGAC 61.377 60.000 0.00 0.00 0.00 5.19
1569 4425 0.676466 CCATACCAAAGCAGGCGACA 60.676 55.000 0.00 0.00 0.00 4.35
1570 4426 0.729116 CATACCAAAGCAGGCGACAG 59.271 55.000 0.00 0.00 0.00 3.51
1571 4427 0.324943 ATACCAAAGCAGGCGACAGT 59.675 50.000 0.00 0.00 0.00 3.55
1572 4428 0.970640 TACCAAAGCAGGCGACAGTA 59.029 50.000 0.00 0.00 0.00 2.74
1573 4429 0.602905 ACCAAAGCAGGCGACAGTAC 60.603 55.000 0.00 0.00 0.00 2.73
1574 4430 1.298859 CCAAAGCAGGCGACAGTACC 61.299 60.000 0.00 0.00 0.00 3.34
1575 4431 0.602638 CAAAGCAGGCGACAGTACCA 60.603 55.000 0.00 0.00 0.00 3.25
1576 4432 0.107831 AAAGCAGGCGACAGTACCAA 59.892 50.000 0.00 0.00 0.00 3.67
1577 4433 0.107831 AAGCAGGCGACAGTACCAAA 59.892 50.000 0.00 0.00 0.00 3.28
1578 4434 0.320771 AGCAGGCGACAGTACCAAAG 60.321 55.000 0.00 0.00 0.00 2.77
1579 4435 1.912371 GCAGGCGACAGTACCAAAGC 61.912 60.000 0.00 0.00 0.00 3.51
1580 4436 0.602638 CAGGCGACAGTACCAAAGCA 60.603 55.000 0.00 0.00 0.00 3.91
1581 4437 0.320771 AGGCGACAGTACCAAAGCAG 60.321 55.000 0.00 0.00 0.00 4.24
1582 4438 1.298859 GGCGACAGTACCAAAGCAGG 61.299 60.000 0.00 0.00 0.00 4.85
1583 4439 1.912371 GCGACAGTACCAAAGCAGGC 61.912 60.000 0.00 0.00 0.00 4.85
1584 4440 0.602638 CGACAGTACCAAAGCAGGCA 60.603 55.000 0.00 0.00 0.00 4.75
1585 4441 0.875059 GACAGTACCAAAGCAGGCAC 59.125 55.000 0.00 0.00 0.00 5.01
1586 4442 0.537371 ACAGTACCAAAGCAGGCACC 60.537 55.000 0.00 0.00 0.00 5.01
1587 4443 1.074951 AGTACCAAAGCAGGCACCC 59.925 57.895 0.00 0.00 0.00 4.61
1700 4556 1.494721 ACCAGTTCCATCAACCACTGT 59.505 47.619 0.00 0.00 35.79 3.55
1860 4716 6.127647 TGCCTTCTGTATTCACATCAAATTCC 60.128 38.462 0.00 0.00 33.14 3.01
1865 4721 8.578448 TCTGTATTCACATCAAATTCCATCAA 57.422 30.769 0.00 0.00 33.14 2.57
2011 4873 2.584391 GCGGGTGGTGAGGAGAAGT 61.584 63.158 0.00 0.00 0.00 3.01
2226 5088 1.228925 CCCTAGTCCCCGGAGATCC 60.229 68.421 0.73 0.00 0.00 3.36
2280 5142 1.173913 CGGTTCCCCCTAGCAAAAAG 58.826 55.000 0.00 0.00 0.00 2.27
2298 5160 5.419760 AAAAGAGGCGAACACTAAAAGAC 57.580 39.130 0.00 0.00 0.00 3.01
2341 5206 9.950680 ACACTAGTTGTAAGAAAATGTTTGATG 57.049 29.630 0.00 0.00 36.32 3.07
2363 5228 0.806868 AATGTTGCTCGTGCTGATGG 59.193 50.000 11.19 0.00 40.48 3.51
2411 5276 3.252701 AGCAAAGCACACAATGAAGAGAG 59.747 43.478 0.00 0.00 0.00 3.20
2459 5324 7.898014 ACCAGGAAAGTGTTAAGAAAGAATT 57.102 32.000 0.00 0.00 0.00 2.17
2763 5628 7.921745 TGTGGGAAGTTTAATTTAGGAAAAACG 59.078 33.333 0.00 0.00 37.02 3.60
2838 5706 0.881796 GCAAAAGAGGGTGTGCCTAC 59.118 55.000 0.00 0.00 34.45 3.18
2972 5840 3.743521 TGTCAGACTTCACAATGGAAGG 58.256 45.455 13.34 0.69 46.73 3.46
3125 5993 4.960938 AGGACAAAAGGAAATGAAAAGGC 58.039 39.130 0.00 0.00 0.00 4.35
3403 6271 3.027412 TCTTCTTCTCAGCTATTCCGCT 58.973 45.455 0.00 0.00 41.90 5.52
3435 6303 7.663081 CCAAGTACTATTGCAACATATCCAGAT 59.337 37.037 0.00 0.00 0.00 2.90
3438 6306 8.432013 AGTACTATTGCAACATATCCAGATTCA 58.568 33.333 0.00 0.00 0.00 2.57
3631 6499 3.557898 GGAGCAAGAGAAGATGTGGTTGA 60.558 47.826 0.00 0.00 0.00 3.18
3750 6618 3.723260 CCAAGTTAATGGGCAACGTTTT 58.277 40.909 0.00 0.00 36.79 2.43
3795 6663 5.529060 TGAAATTTGGGCCATTTACAACAAC 59.471 36.000 7.26 0.00 0.00 3.32
3796 6664 2.802787 TTGGGCCATTTACAACAACG 57.197 45.000 7.26 0.00 0.00 4.10
3882 6750 3.075998 CGCACTGAAGCTAGCACG 58.924 61.111 18.83 9.29 0.00 5.34
4014 6882 5.450171 CATATACCTTCTTACCGTCTGACG 58.550 45.833 22.49 22.49 42.11 4.35
4092 6960 1.915078 ATGCTTTCCTGGTCCGAGGG 61.915 60.000 7.32 0.00 33.41 4.30
4164 7032 5.808366 TCAAGTCAAGTAGTCATCTGGTT 57.192 39.130 0.00 0.00 0.00 3.67
4184 7052 4.572389 GGTTGCTACTGTGATCTGGTTATG 59.428 45.833 0.00 0.00 0.00 1.90
4189 7057 6.098838 TGCTACTGTGATCTGGTTATGAATCT 59.901 38.462 0.00 0.00 0.00 2.40
4224 7092 0.034670 ATCTGCAGGGGAGAGCAAAC 60.035 55.000 15.13 0.00 40.73 2.93
4313 7182 4.766891 CCATTTCTGTTGTGGACCTTATGT 59.233 41.667 0.00 0.00 34.94 2.29
4328 7197 4.161754 ACCTTATGTAAGCTAGGTGTGGAC 59.838 45.833 2.72 0.00 39.47 4.02
4332 7201 9.724337 CCTTATGTAAGCTAGGTGTGGACCTTC 62.724 48.148 0.00 0.00 41.27 3.46
4366 7258 3.009033 TGTGGACCTTATGAAAGACTGGG 59.991 47.826 0.00 0.00 34.37 4.45
4564 7463 3.612472 TTGCTTAACGTTTGCTACCAC 57.388 42.857 20.93 0.84 0.00 4.16
4597 7496 4.059511 TCGGAGAGTAGAAGCTAAGATCG 58.940 47.826 0.00 0.00 0.00 3.69
4733 7648 6.856426 GGTTTTAAAGGATCGTGAAAACTGAG 59.144 38.462 23.94 0.00 39.08 3.35
4742 7657 4.380531 TCGTGAAAACTGAGATTGCTCTT 58.619 39.130 0.00 0.00 41.84 2.85
4783 7704 7.646526 CACATGATTCCATAATAGCAGTGTTTG 59.353 37.037 0.00 0.00 0.00 2.93
4795 7716 1.153549 GTGTTTGGGTGCGCCAAAA 60.154 52.632 19.98 17.47 38.61 2.44
4994 7915 2.356135 ACGGAATTAGACACATGGCAC 58.644 47.619 0.00 0.00 0.00 5.01
5075 7996 0.027979 CATTAATGGTGCAGACGCGG 59.972 55.000 12.47 0.00 42.97 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.301558 CATCTCTGGCTGGCCGATC 60.302 63.158 7.14 0.00 39.42 3.69
36 37 2.189499 GGTCCAATGCTCGGCCATC 61.189 63.158 2.24 0.00 0.00 3.51
40 41 2.537560 CGATGGTCCAATGCTCGGC 61.538 63.158 0.00 0.00 0.00 5.54
41 42 2.537560 GCGATGGTCCAATGCTCGG 61.538 63.158 13.14 0.00 0.00 4.63
56 57 2.923426 GATCTCAATGGCCGGTGCGA 62.923 60.000 1.90 0.00 38.85 5.10
69 70 2.993008 GGCTGGTGGCAGATCTCA 59.007 61.111 0.00 0.00 44.01 3.27
104 113 0.250338 GTGGTTGTCTCGCCCTTCTT 60.250 55.000 0.00 0.00 0.00 2.52
107 116 2.397413 CTGGTGGTTGTCTCGCCCTT 62.397 60.000 0.00 0.00 34.09 3.95
218 230 2.577059 GGGATGCGACGAAGGTCA 59.423 61.111 0.00 0.00 43.61 4.02
223 235 2.577059 GTCTGGGGATGCGACGAA 59.423 61.111 0.00 0.00 0.00 3.85
335 347 4.537433 CTCTGGCTAGGGCGTGGC 62.537 72.222 7.02 7.02 39.81 5.01
357 371 1.271840 AATAGGGTCAGCGAAGGCCA 61.272 55.000 5.01 0.00 41.24 5.36
366 3214 5.163301 ACCACTAATGTGCTAATAGGGTCAG 60.163 44.000 0.00 0.00 42.54 3.51
443 3291 7.118723 TGGAATCTAAAGTCAAAGTATGGCAT 58.881 34.615 4.88 4.88 35.54 4.40
445 3293 7.255277 GGATGGAATCTAAAGTCAAAGTATGGC 60.255 40.741 0.00 0.00 44.71 4.40
446 3294 7.775093 TGGATGGAATCTAAAGTCAAAGTATGG 59.225 37.037 0.00 0.00 44.71 2.74
447 3295 8.737168 TGGATGGAATCTAAAGTCAAAGTATG 57.263 34.615 0.00 0.00 44.71 2.39
448 3296 9.347240 CATGGATGGAATCTAAAGTCAAAGTAT 57.653 33.333 0.00 0.00 44.71 2.12
449 3297 7.283127 GCATGGATGGAATCTAAAGTCAAAGTA 59.717 37.037 0.00 0.00 44.71 2.24
450 3298 6.096001 GCATGGATGGAATCTAAAGTCAAAGT 59.904 38.462 0.00 0.00 44.71 2.66
451 3299 6.095860 TGCATGGATGGAATCTAAAGTCAAAG 59.904 38.462 0.00 0.00 44.71 2.77
533 3381 2.771943 TGGAGGGTCTAACAATGGCTAG 59.228 50.000 0.00 0.00 0.00 3.42
541 3389 5.576563 TTTGAGATTTGGAGGGTCTAACA 57.423 39.130 0.00 0.00 0.00 2.41
679 3535 6.600822 CAGATTGGATAGATCAACAAACACCT 59.399 38.462 0.00 0.00 0.00 4.00
892 3748 5.397142 AAATTTGATTTGAGTCTCCCTGC 57.603 39.130 0.00 0.00 0.00 4.85
1278 4134 6.546034 CAGGGTAACTATTTTTATCAGGGTGG 59.454 42.308 0.00 0.00 0.00 4.61
1459 4315 1.606313 TAGCCTGCTTTGGTTGGGC 60.606 57.895 0.00 0.00 42.74 5.36
1548 4404 1.378514 CGCCTGCTTTGGTATGGGT 60.379 57.895 0.00 0.00 0.00 4.51
1549 4405 1.077787 TCGCCTGCTTTGGTATGGG 60.078 57.895 0.00 0.00 0.00 4.00
1551 4407 0.729116 CTGTCGCCTGCTTTGGTATG 59.271 55.000 0.00 0.00 0.00 2.39
1552 4408 0.324943 ACTGTCGCCTGCTTTGGTAT 59.675 50.000 0.00 0.00 0.00 2.73
1553 4409 0.970640 TACTGTCGCCTGCTTTGGTA 59.029 50.000 0.00 0.00 0.00 3.25
1554 4410 0.602905 GTACTGTCGCCTGCTTTGGT 60.603 55.000 0.00 0.00 0.00 3.67
1555 4411 1.298859 GGTACTGTCGCCTGCTTTGG 61.299 60.000 0.00 0.00 0.00 3.28
1556 4412 0.602638 TGGTACTGTCGCCTGCTTTG 60.603 55.000 0.00 0.00 0.00 2.77
1557 4413 0.107831 TTGGTACTGTCGCCTGCTTT 59.892 50.000 0.00 0.00 0.00 3.51
1558 4414 0.107831 TTTGGTACTGTCGCCTGCTT 59.892 50.000 0.00 0.00 0.00 3.91
1559 4415 0.320771 CTTTGGTACTGTCGCCTGCT 60.321 55.000 0.00 0.00 0.00 4.24
1560 4416 1.912371 GCTTTGGTACTGTCGCCTGC 61.912 60.000 0.00 2.50 0.00 4.85
1561 4417 0.602638 TGCTTTGGTACTGTCGCCTG 60.603 55.000 0.00 0.00 0.00 4.85
1562 4418 0.320771 CTGCTTTGGTACTGTCGCCT 60.321 55.000 0.00 0.00 0.00 5.52
1563 4419 1.298859 CCTGCTTTGGTACTGTCGCC 61.299 60.000 0.00 0.00 0.00 5.54
1564 4420 1.912371 GCCTGCTTTGGTACTGTCGC 61.912 60.000 0.00 0.00 0.00 5.19
1565 4421 0.602638 TGCCTGCTTTGGTACTGTCG 60.603 55.000 0.00 0.00 0.00 4.35
1566 4422 0.875059 GTGCCTGCTTTGGTACTGTC 59.125 55.000 0.00 0.00 39.21 3.51
1567 4423 0.537371 GGTGCCTGCTTTGGTACTGT 60.537 55.000 10.56 0.00 41.50 3.55
1568 4424 1.244019 GGGTGCCTGCTTTGGTACTG 61.244 60.000 10.56 0.00 41.50 2.74
1569 4425 1.074951 GGGTGCCTGCTTTGGTACT 59.925 57.895 10.56 0.00 41.50 2.73
1570 4426 0.611896 ATGGGTGCCTGCTTTGGTAC 60.612 55.000 4.29 4.29 41.13 3.34
1571 4427 0.995803 TATGGGTGCCTGCTTTGGTA 59.004 50.000 0.00 0.00 0.00 3.25
1572 4428 0.611896 GTATGGGTGCCTGCTTTGGT 60.612 55.000 0.00 0.00 0.00 3.67
1573 4429 1.322538 GGTATGGGTGCCTGCTTTGG 61.323 60.000 0.00 0.00 0.00 3.28
1574 4430 0.611618 TGGTATGGGTGCCTGCTTTG 60.612 55.000 0.00 0.00 0.00 2.77
1575 4431 0.114168 TTGGTATGGGTGCCTGCTTT 59.886 50.000 0.00 0.00 0.00 3.51
1576 4432 0.114168 TTTGGTATGGGTGCCTGCTT 59.886 50.000 0.00 0.00 0.00 3.91
1577 4433 0.323725 CTTTGGTATGGGTGCCTGCT 60.324 55.000 0.00 0.00 0.00 4.24
1578 4434 1.948721 GCTTTGGTATGGGTGCCTGC 61.949 60.000 0.00 0.00 0.00 4.85
1579 4435 0.611618 TGCTTTGGTATGGGTGCCTG 60.612 55.000 0.00 0.00 0.00 4.85
1580 4436 0.323725 CTGCTTTGGTATGGGTGCCT 60.324 55.000 0.00 0.00 0.00 4.75
1581 4437 1.322538 CCTGCTTTGGTATGGGTGCC 61.323 60.000 0.00 0.00 0.00 5.01
1582 4438 1.948721 GCCTGCTTTGGTATGGGTGC 61.949 60.000 0.00 0.00 0.00 5.01
1583 4439 1.656818 CGCCTGCTTTGGTATGGGTG 61.657 60.000 0.00 0.00 0.00 4.61
1584 4440 1.378514 CGCCTGCTTTGGTATGGGT 60.379 57.895 0.00 0.00 0.00 4.51
1585 4441 2.120909 CCGCCTGCTTTGGTATGGG 61.121 63.158 0.00 0.00 0.00 4.00
1586 4442 2.774799 GCCGCCTGCTTTGGTATGG 61.775 63.158 0.00 0.00 36.87 2.74
1587 4443 1.996786 CTGCCGCCTGCTTTGGTATG 61.997 60.000 0.00 0.00 42.00 2.39
1700 4556 1.638070 TGGTCCATATTGCCTGTCCAA 59.362 47.619 0.00 0.00 0.00 3.53
1826 4682 7.787786 TGTGAATACAGAAGGCACATCATGTG 61.788 42.308 13.93 13.93 40.53 3.21
1830 4686 4.284829 TGTGAATACAGAAGGCACATCA 57.715 40.909 0.00 0.00 34.85 3.07
1860 4716 3.631686 TCTGTTGTCCAACACCTTTGATG 59.368 43.478 8.71 0.00 45.42 3.07
1865 4721 2.643551 CACTCTGTTGTCCAACACCTT 58.356 47.619 8.71 0.00 45.42 3.50
2064 4926 6.595326 CACTTGGTGCAGAAGATTTAGACATA 59.405 38.462 11.53 0.00 0.00 2.29
2093 4955 0.108585 TCTTCCACCTGCCTTGTCAC 59.891 55.000 0.00 0.00 0.00 3.67
2226 5088 1.087501 GGTTTGCCTTTCTCCTAGCG 58.912 55.000 0.00 0.00 0.00 4.26
2280 5142 2.737252 CCAGTCTTTTAGTGTTCGCCTC 59.263 50.000 0.00 0.00 0.00 4.70
2298 5160 4.311816 AGTGTCAGCATTTGAAAACCAG 57.688 40.909 0.00 0.00 37.61 4.00
2341 5206 0.867746 TCAGCACGAGCAACATTGTC 59.132 50.000 7.77 0.00 45.49 3.18
2342 5207 1.198408 CATCAGCACGAGCAACATTGT 59.802 47.619 7.77 0.00 45.49 2.71
2343 5208 1.466866 CCATCAGCACGAGCAACATTG 60.467 52.381 7.77 0.00 45.49 2.82
2363 5228 4.540824 GACATGAGCTTCACCAGTTTTTC 58.459 43.478 0.00 0.00 0.00 2.29
2411 5276 1.538950 CTTCTTTGGCAGTGCTTCCTC 59.461 52.381 16.11 0.00 0.00 3.71
2485 5350 1.372582 TGTGCAGAATCGCAAGGATC 58.627 50.000 1.80 0.00 45.14 3.36
2763 5628 3.478540 GGCACCTTGTGATACCTCC 57.521 57.895 0.00 0.00 35.23 4.30
2972 5840 0.315251 GGGAAAAACAGCAGCTCCAC 59.685 55.000 0.00 0.00 0.00 4.02
3125 5993 2.927201 AAACCCACCTGCCACACCAG 62.927 60.000 0.00 0.00 0.00 4.00
3403 6271 4.530553 TGTTGCAATAGTACTTGGAGAGGA 59.469 41.667 0.59 0.00 0.00 3.71
3438 6306 7.094762 CGCCCTTCTTCAAAGTTATAAAACTCT 60.095 37.037 0.00 0.00 45.37 3.24
3631 6499 2.695666 AGCTCACAGGTATATCACGCTT 59.304 45.455 0.00 0.00 0.00 4.68
3750 6618 1.404986 CCTACTCGCGGGTGAATTTCA 60.405 52.381 24.75 0.00 0.00 2.69
3795 6663 2.047844 CAGTCAGGTGCCCAGTCG 60.048 66.667 0.00 0.00 0.00 4.18
3796 6664 2.348998 CCAGTCAGGTGCCCAGTC 59.651 66.667 0.00 0.00 0.00 3.51
3882 6750 3.978687 TGGAGTCAGAAACGAGAACTTC 58.021 45.455 0.00 0.00 0.00 3.01
4164 7032 5.675684 TTCATAACCAGATCACAGTAGCA 57.324 39.130 0.00 0.00 0.00 3.49
4224 7092 5.446143 AATACAGAGAGCCTAACTGATCG 57.554 43.478 0.00 0.00 35.85 3.69
4328 7197 2.303022 TCCACACCTAGCTTTCAGAAGG 59.697 50.000 0.00 0.00 33.34 3.46
4332 7201 2.100605 GGTCCACACCTAGCTTTCAG 57.899 55.000 0.00 0.00 40.00 3.02
4553 7445 5.972382 CGATCTCTTAGTAGTGGTAGCAAAC 59.028 44.000 0.00 0.00 0.00 2.93
4554 7446 5.067413 CCGATCTCTTAGTAGTGGTAGCAAA 59.933 44.000 0.00 0.00 0.00 3.68
4564 7463 6.367969 GCTTCTACTCTCCGATCTCTTAGTAG 59.632 46.154 12.45 12.45 38.38 2.57
4597 7496 1.686052 TGTGGTTGTGCTGGGAAATTC 59.314 47.619 0.00 0.00 0.00 2.17
4733 7648 5.391416 GCTTTCAGTTCCTACAAGAGCAATC 60.391 44.000 0.00 0.00 0.00 2.67
4742 7657 4.350368 TCATGTGCTTTCAGTTCCTACA 57.650 40.909 0.00 0.00 0.00 2.74
4783 7704 0.172578 GGTATTCTTTTGGCGCACCC 59.827 55.000 10.83 0.00 33.59 4.61
4795 7716 6.589907 GCAATTCCGAAAAACAATGGTATTCT 59.410 34.615 0.00 0.00 0.00 2.40
4857 7778 1.529226 TTGTGATTGTTGTAGGGCCG 58.471 50.000 0.00 0.00 0.00 6.13
4911 7832 5.560953 GCGTCAAGAATTTTGCAAGTCTACT 60.561 40.000 0.00 0.00 36.29 2.57
4973 7894 3.527533 GTGCCATGTGTCTAATTCCGTA 58.472 45.455 0.00 0.00 0.00 4.02
5051 7972 3.546815 GCGTCTGCACCATTAATGATGTC 60.547 47.826 17.23 7.10 42.15 3.06


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

AutoCloner maintained by Alex Coulton.