Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008603.1 Hibiscus syriacus cultivar Beakdansim tig00111558_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 555603
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:219549 original size:16 final size:16
Alignment explanation
Indices: 219530--219560 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
219520 GGATAATTTA
219530 ATAGAATTAAAGCTAG
1 ATAGAATTAAAGCTAG
219546 ATAGAATTAAAGCTA
1 ATAGAATTAAAGCTA
219561 TTTTCGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (16 bp):
ATAGAATTAAAGCTAG
Found at i:219732 original size:19 final size:19
Alignment explanation
Indices: 219708--219748 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
219698 AAAATGTTTT
219708 ATATTATATACGTTATATG
1 ATATTATATACGTTATATG
*
219727 ATATTATATATGTTATATG
1 ATATTATATACGTTATATG
219746 ATA
1 ATA
219749 CGACACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATTATATACGTTATATG
Found at i:220294 original size:185 final size:184
Alignment explanation
Indices: 219989--220341 Score: 573
Period size: 185 Copynumber: 1.9 Consensus size: 184
219979 TCAAAAAAAG
*
219989 TTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAACTTTTTTAATTAAT
1 TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAACTTTTTTAATTAAT
220054 TAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGG
66 TAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGG
* * *
220119 GTTTAACCCATATGTTATATATAATATATATAATATTTTTTAATTAAAATTTTT
131 GCTGAACCCATATGTTATATATAATATATATAAAATTTTTTAATTAAAATTTTT
* *
220173 TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTTATATAA-TTTTTTAAATTA
1 TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA-TTTCAGATAACTTTTTT-AATTA
* * *
220237 ATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTT
64 ATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTT
* * *
220302 GGGCTGAGCTCATATGTTATATATAATATATTTAAAATTT
129 GGGCTGAACCCATATGTTATATATAATATATATAAAATTT
220342 AAAATTTAAT
Statistics
Matches: 155, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
184 46 0.30
185 109 0.70
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (184 bp):
TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAACTTTTTTAATTAAT
TAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGG
GCTGAACCCATATGTTATATATAATATATATAAAATTTTTTAATTAAAATTTTT
Found at i:228319 original size:18 final size:18
Alignment explanation
Indices: 228296--228332 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
228286 GTTTCGGTTT
228296 AAAAAAAACTGATTTTTA
1 AAAAAAAACTGATTTTTA
228314 AAAAAAAACTGATTTTTA
1 AAAAAAAACTGATTTTTA
228332 A
1 A
228333 TCCGATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAAAAACTGATTTTTA
Found at i:232793 original size:26 final size:25
Alignment explanation
Indices: 232763--232818 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
232753 TTTCTCAGTA
232763 TTATTCTTAATCACCAAATTATTTT
1 TTATTCTTAATCACCAAATTATTTT
* * **
232788 TCTATTTTTAATTATTAAATTATTTT
1 T-TATTCTTAATCACCAAATTATTTT
232814 TTATT
1 TTATT
232819 AAAATACCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTCTTAATCACCAAATTATTTT
Found at i:233644 original size:28 final size:27
Alignment explanation
Indices: 233601--233656 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 27
233591 AAAAAGAGAA
233601 ACAATGAAAGAATGTTACACAGAAGTT
1 ACAATGAAAGAATGTTACACAGAAGTT
233628 ACAATGAAGAGAATGTTACACAGAAGTT
1 ACAATGAA-AGAATGTTACACAGAAGTT
233656 A
1 A
233657 ACGATAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (27 bp):
ACAATGAAAGAATGTTACACAGAAGTT
Found at i:239016 original size:35 final size:35
Alignment explanation
Indices: 238962--239050 Score: 169
Period size: 35 Copynumber: 2.5 Consensus size: 35
238952 TAAAAACAAG
238962 AAAATTAATAATCACCGACAGTCGATAATCAACATT
1 AAAATTAAT-ATCACCGACAGTCGATAATCAACATT
238998 AAAATTAATATCACCGACAGTCGATAATCAACATT
1 AAAATTAATATCACCGACAGTCGATAATCAACATT
239033 AAAATTAATATCACCGAC
1 AAAATTAATATCACCGAC
239051 GACCATACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 44 0.83
36 9 0.17
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (35 bp):
AAAATTAATATCACCGACAGTCGATAATCAACATT
Found at i:243721 original size:30 final size:32
Alignment explanation
Indices: 243662--243722 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
243652 TAGTGTAAAC
*
243662 TATGTGTTTAGTATTTAAGCTATCAATTTTGA
1 TATGTGTTTAGTATTTAAACTATCAATTTTGA
* *
243694 TATGT-TTTAGTATTTAAACTTTCATTTTT
1 TATGTGTTTAGTATTTAAACTATCAATTTT
243723 TTTAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (32 bp):
TATGTGTTTAGTATTTAAACTATCAATTTTGA
Found at i:245745 original size:34 final size:36
Alignment explanation
Indices: 245703--245782 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 36
245693 TTTATTTCTT
* * * *
245703 TAATTATTTATTTTTTCTTCATGGAAAAA-ATAAAA
1 TAATTATTTATTTATTCTTCACGAAAAAAGACAAAA
*
245738 T-ATTATTTCTTTATTCTTCACGAAAAAAGACAAAA
1 TAATTATTTATTTATTCTTCACGAAAAAAGACAAAA
245773 TAATTATTTA
1 TAATTATTTA
245783 AAAAGAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 23 0.62
35 7 0.19
36 7 0.19
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (36 bp):
TAATTATTTATTTATTCTTCACGAAAAAAGACAAAA
Found at i:247288 original size:42 final size:41
Alignment explanation
Indices: 247242--247341 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
247232 CTCAAACCAA
*
247242 ACCCGA-TCTGACCCAAATCAACTTAACCCCGAAAGTATTCCG
1 ACCCGATTC-GACCCAAATCAACCTAA-CCCGAAAGTATTCCG
*
247284 ACCCGATTCGACTCAAATCAACCTAACCCGAAAGTATTCCG
1 ACCCGATTCGACCCAAATCAACCTAACCCGAAAGTATTCCG
* * *
247325 ACCTGAATCGATCCAAA
1 ACCCGATTCGACCCAAA
247342 AGGCTCCTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 28 0.55
42 21 0.41
43 2 0.04
ACGTcount: A:0.35, C:0.34, G:0.12, T:0.19
Consensus pattern (41 bp):
ACCCGATTCGACCCAAATCAACCTAACCCGAAAGTATTCCG
Found at i:247326 original size:41 final size:42
Alignment explanation
Indices: 247242--247327 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
247232 CTCAAACCAA
*
247242 ACCCGATCTGACCCAAATCAACTTAACCCCGAAAGTATTCCG
1 ACCCGATCTGACCCAAATCAACCTAACCCCGAAAGTATTCCG
*
247284 ACCCGAT-TCGACTCAAATCAACCTAA-CCCGAAAGTATTCCG
1 ACCCGATCT-GACCCAAATCAACCTAACCCCGAAAGTATTCCG
247325 ACC
1 ACC
247328 TGAATCGATC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 19 0.46
42 22 0.54
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.19
Consensus pattern (42 bp):
ACCCGATCTGACCCAAATCAACCTAACCCCGAAAGTATTCCG
Found at i:247630 original size:23 final size:23
Alignment explanation
Indices: 247602--247647 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
247592 TAAAAGGAAA
247602 AAGAAAGAAAGACTATCGATTGT
1 AAGAAAGAAAGACTATCGATTGT
*
247625 AAGAAAGAAAGACTATCTATTGT
1 AAGAAAGAAAGACTATCGATTGT
247648 GTTATGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (23 bp):
AAGAAAGAAAGACTATCGATTGT
Found at i:249940 original size:18 final size:18
Alignment explanation
Indices: 249919--249953 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
249909 AAATGTTCCA
249919 GCCTATACAACTGCTCCG
1 GCCTATACAACTGCTCCG
249937 GCCTATACAACTGCTCC
1 GCCTATACAACTGCTCC
249954 TCAAACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (18 bp):
GCCTATACAACTGCTCCG
Found at i:261610 original size:93 final size:93
Alignment explanation
Indices: 261504--261689 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
261494 CACTTGATGG
261504 GTTCCATCATCCACATCCCGAAGTTCACCATTCTCAATTCCAGGCATAGAATTACTGGATGCAGG
1 GTTCCATCATCCACATCCCGAAGTTCACCATTCTCAATTCCAGGCATAGAATTACTGGATGCAGG
*
261569 AAAGGTAATTAAATCCTGACCTTCTACA
66 AAAGGTAATTAAAACCTGACCTTCTACA
*
261597 GTTCCATCATCCACATCCCGAAGTTCACCATTCTCAGTTCCAGGCATAGAATTACTGGATGCAGG
1 GTTCCATCATCCACATCCCGAAGTTCACCATTCTCAATTCCAGGCATAGAATTACTGGATGCAGG
261662 AAAGGTAATTAAAACCTGACCTTCTACA
66 AAAGGTAATTAAAACCTGACCTTCTACA
261690 ATTTCATTGC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (93 bp):
GTTCCATCATCCACATCCCGAAGTTCACCATTCTCAATTCCAGGCATAGAATTACTGGATGCAGG
AAAGGTAATTAAAACCTGACCTTCTACA
Found at i:262877 original size:11 final size:12
Alignment explanation
Indices: 262860--262888 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
262850 TCATGTTTGA
262860 ATAAATATATTT
1 ATAAATATATTT
262872 -TAAATATATTT
1 ATAAATATATTT
262883 ATAAAT
1 ATAAAT
262889 GACATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAAATATATTT
Found at i:262974 original size:23 final size:24
Alignment explanation
Indices: 262948--263001 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
262938 TAAAAATAGA
*
262948 TATTTTTATA-TGTAAAAATAACT
1 TATTTATATAGTGTAAAAATAACT
* *
262971 TATTTATGTAGTGTAAAAATAAGT
1 TATTTATATAGTGTAAAAATAACT
262995 TATTTAT
1 TATTTAT
263002 GGGGTTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (24 bp):
TATTTATATAGTGTAAAAATAACT
Found at i:271796 original size:39 final size:39
Alignment explanation
Indices: 271753--271829 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
271743 CGTCGATTCT
271753 TTTTAAAACT-TATATCATGTAATTTATTATACATTAAAA
1 TTTTAAAACTATATATCAT-TAATTTATTATACATTAAAA
* * * * *
271792 TTTTATATCTATTTATTATTAATTTATTATATATTAAA
1 TTTTAAAACTATATATCATTAATTTATTATACATTAAA
271830 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 26 0.81
40 6 0.19
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.53
Consensus pattern (39 bp):
TTTTAAAACTATATATCATTAATTTATTATACATTAAAA
Found at i:276390 original size:8 final size:8
Alignment explanation
Indices: 276358--276388 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
276348 ATTTAAACTA
276358 TTTAAAAT
1 TTTAAAAT
276366 TTTAAAAT
1 TTTAAAAT
276374 TTTAAAAT
1 TTTAAAAT
276382 TTATAAA
1 TT-TAAA
276389 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:291713 original size:20 final size:20
Alignment explanation
Indices: 291688--291756 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
291678 CCAGATTCGT
291688 AACGCGATTATGACTATCGC
1 AACGCGATTATGACTATCGC
* *
291708 AACGCGATAAT-ACAAAATCGC
1 AACGCGATTATGAC--TATCGC
* *
291729 AACTCGA-TACTGACTTTCGC
1 AACGCGATTA-TGACTATCGC
291749 AACGCGAT
1 AACGCGAT
291757 ACTTAATTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
19 2 0.05
20 21 0.57
21 12 0.32
22 2 0.05
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
AACGCGATTATGACTATCGC
Found at i:291757 original size:20 final size:20
Alignment explanation
Indices: 291725--291797 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
291715 TAATACAAAA
*
291725 TCGCAACTCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
291745 TCGCAACGCGATACTTAATT
1 TCGCAACGCGATACTGACTT
*
291765 TCGCAACGCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
291785 TCGCAACGAGATA
1 TCGCAACGCGATA
291798 ATACATAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:291780 original size:40 final size:41
Alignment explanation
Indices: 291698--291811 Score: 140
Period size: 40 Copynumber: 2.8 Consensus size: 41
291688 AACGCGATTA
* * *
291698 TGACTATCGCAACGCGATAATACAAAATCGCAACTCGATAC
1 TGACTTTCGCAACGCGATAATACAAAATCGCAACGCAATAC
* * **
291739 TGACTTTCGCAACGCGATACT-TAATTTCGCAACGCAATAC
1 TGACTTTCGCAACGCGATAATACAAAATCGCAACGCAATAC
* *
291779 TGACTTTCGCAACGAGATAATACATAATCGCAA
1 TGACTTTCGCAACGCGATAATACAAAATCGCAA
291812 TGCGATTTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
40 33 0.56
41 26 0.44
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (41 bp):
TGACTTTCGCAACGCGATAATACAAAATCGCAACGCAATAC
Found at i:292012 original size:22 final size:22
Alignment explanation
Indices: 291984--292027 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
291974 CACTCTCTCA
*
291984 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
292006 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
292028 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:292334 original size:20 final size:20
Alignment explanation
Indices: 292311--292348 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
292301 TCAAATTTGC
292311 GTTGCGATTGTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
* *
292331 GTTGTGATTTTCATTTTC
1 GTTGCGATTGTCATTTTC
292349 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (20 bp):
GTTGCGATTGTCATTTTCGT
Found at i:292539 original size:25 final size:24
Alignment explanation
Indices: 292485--292539 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
292475 TGTTTATTAT
* *
292485 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
292509 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
292535 TGTTT
1 TGTTT
292540 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:294021 original size:42 final size:42
Alignment explanation
Indices: 293975--294054 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
293965 CGATGACAGT
* *
293975 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTGAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
294017 GGCCTCTTTAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTGAACGATAGGAGGGGACTCTCGAGGAATGA
294055 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:294451 original size:91 final size:90
Alignment explanation
Indices: 294276--294460 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
294266 ATTTCAAACT
* *
294276 TTCAGCCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAACAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
294341 AGAATTGGCAGTAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
294369 TTCAACCAAAAGACAAAACAAAAAGACAAATGCTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
294433 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
294460 T
1 T
294461 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 41 0.48
93 18 0.21
95 26 0.31
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:296192 original size:40 final size:38
Alignment explanation
Indices: 296148--296293 Score: 132
Period size: 33 Copynumber: 4.1 Consensus size: 38
296138 TCTTTTGGTT
**
296148 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGACTATCGCAACGAGA-AATGAAAATCGCAACGC
296187 GGAAATGACTATCGCAACGAG--A-G--AATCGCAACGC
1 -GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* *
296221 GAAATGACTATCGCAACGCGAAATGAAAATCGTAA--C
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* * * *
296257 GAGA-GA--ATCGCAACGCGAAATAAAAATCGCAATGC
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
296292 GA
1 GA
296294 TTTTGGTTTC
Statistics
Matches: 92, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
33 43 0.47
34 11 0.12
35 6 0.07
36 6 0.07
37 1 0.01
38 7 0.08
40 18 0.20
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (38 bp):
GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:296235 original size:19 final size:19
Alignment explanation
Indices: 296157--296246 Score: 91
Period size: 20 Copynumber: 4.9 Consensus size: 19
296147 TGAAATGAAA
* **
296157 ATCGCAACGAGATAATGAAA
1 ATCGCAACGCGA-AATGACT
296177 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
296197 ATCGCAA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
296211 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
296230 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
296247 AAATCGTAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.12
16 6 0.10
17 5 0.08
18 1 0.02
19 17 0.29
20 21 0.36
21 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:296252 original size:19 final size:19
Alignment explanation
Indices: 296148--296293 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
296138 TCTTTTGGTT
*
296148 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
296167 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
296187 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
296205 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
296221 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
296240 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
296257 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
296273 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
296292 GA
1 GA
296294 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 18 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 40 0.40
20 28 0.28
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:296262 original size:52 final size:53
Alignment explanation
Indices: 296156--296288 Score: 187
Period size: 52 Copynumber: 2.5 Consensus size: 53
296146 TTGAAATGAA
* **
296156 AATCGCAACGAGATAATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
** *
296210 AATCGCAACGCGAAATGACTATCGCAACGC-GAAATGAAAATCGTAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
*
296262 AATCGCAACGCGAAATAAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
296289 TGCGATTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
52 43 0.61
53 15 0.21
54 12 0.17
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
Found at i:296925 original size:20 final size:20
Alignment explanation
Indices: 296902--296995 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
296892 CAATAGTAAG
* *
296902 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACTT
* *
296922 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGA-TTTACTT
296943 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* *
296963 AATCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
296983 ATTCGCATTGCGA
1 ATTCGCATTGCGA
296996 ATTGGGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 46 0.73
21 17 0.27
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:296956 original size:41 final size:40
Alignment explanation
Indices: 296902--296995 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
296892 CAATAGTAAG
* * *
296902 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACTA
* * *
296943 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACTA
296983 ATTCGCATTGCGA
1 ATTCGCATTGCGA
296996 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 18 0.38
41 29 0.62
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACTA
Found at i:297037 original size:21 final size:22
Alignment explanation
Indices: 296986--297037 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
296976 TTTACTTATT
*
296986 CGCATTGCG-AATTGGGAAAAT
1 CGCATTGCGAAATTGGGAAAAC
**
297007 CGCAACGCGAAATT-GGAAAAC
1 CGCATTGCGAAATTGGGAAAAC
297028 CGCATTGCGA
1 CGCATTGCGA
297038 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (22 bp):
CGCATTGCGAAATTGGGAAAAC
Found at i:300577 original size:14 final size:13
Alignment explanation
Indices: 300492--300580 Score: 80
Period size: 14 Copynumber: 7.0 Consensus size: 13
300482 TTCATTTTAC
300492 TTAAATTATTATTA
1 TTAAA-TATTATTA
**
300506 TTAAA-ATTAAAA
1 TTAAATATTATTA
*
300518 TT-ATTATTATTA
1 TTAAATATTATTA
300530 -TAAATATTATTA
1 TTAAATATTATTA
300542 TT--ATATTATTA
1 TTAAATATTATTA
*
300553 TTATTATATTATTA
1 TTA-AATATTATTA
300567 TTAAATAATTATTA
1 TTAAAT-ATTATTA
300581 CAAACCCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 13 0.21
12 21 0.34
13 3 0.05
14 24 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATATTATTA
Found at i:300580 original size:3 final size:3
Alignment explanation
Indices: 300496--300569 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
300486 TTTTACTTAA
** ** * *
300496 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
300544 A-T ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
300570 AATAATTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:301295 original size:13 final size:13
Alignment explanation
Indices: 301277--301305 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
301267 ACCACCGTTA
301277 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
301290 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
301303 CGG
1 CGG
301306 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:302013 original size:13 final size:13
Alignment explanation
Indices: 301995--302033 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
301985 GTAATTAAAT
301995 TTTTAAATATTTA
1 TTTTAAATATTTA
*
302008 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
302022 TTTT-AATATTTA
1 TTTTAAATATTTA
302034 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:309933 original size:75 final size:75
Alignment explanation
Indices: 309773--309942 Score: 182
Period size: 75 Copynumber: 2.3 Consensus size: 75
309763 AACAAGAAGC
* ** * *
309773 AAATATTGGGGCATGCTGAAAACCTTTTTTCAAACAGAATCAAAAATGTTGAAATATTCTGAATA
1 AAATGTTGGGGCATGCTGAAAACCTCATTTCAAACAGAATCAAAAATGTTGAAACATTCTGAACA
309838 TTTATCAGCA
66 TTTATCAGCA
* * * * ** *
309848 AAATGCTGGGGCATGCTGAAAACC-CATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACA
1 AAATGTTGGGGCATGCTGAAAACCTCATTTCAAACAGAATCAAAAATGTTGAAACATTCTGAACA
*
309912 CTTGTATTAGC-
66 -TT-TATCAGCA
*
309923 CAATGTTGGGGCATGCTGAA
1 AAATGTTGGGGCATGCTGAA
309943 GGCCCACAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
74 30 0.38
75 42 0.54
76 6 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAACCTCATTTCAAACAGAATCAAAAATGTTGAAACATTCTGAACA
TTTATCAGCA
Found at i:311347 original size:22 final size:22
Alignment explanation
Indices: 311279--311358 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
311269 TACATCTGCA
* *
311279 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
311301 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
311323 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
311345 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
311359 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:312261 original size:76 final size:76
Alignment explanation
Indices: 312028--312669 Score: 1149
Period size: 76 Copynumber: 8.4 Consensus size: 76
312018 CTATTTCTCA
*
312028 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
312093 AAATCCTTCGGGT
64 AAAGCCTTCGGGT
*
312106 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGTAGCTTTTTGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
312171 AAAGCCTTCGGGT
64 AAAGCCTTCGGGT
*
312184 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
312249 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
312260 CATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
312325 AGCCTTCGGGT
66 AGCCTTCGGGT
*
312336 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
312401 AGCCTTCGGGT
66 AGCCTTCGGGT
312412 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
312477 AGCCTTCGGGT
66 AGCCTTCGGGT
*
312488 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
312553 AGCCTTCGGGT
66 AGCCTTCGGGT
312564 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
312629 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
312640 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTT
312670 TTAAGACCTC
Statistics
Matches: 549, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
76 442 0.81
78 107 0.19
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:312904 original size:14 final size:13
Alignment explanation
Indices: 312819--312907 Score: 80
Period size: 14 Copynumber: 7.0 Consensus size: 13
312809 TTCATTTTAC
312819 TTAAATTATTATTA
1 TTAAA-TATTATTA
**
312833 TTAAA-ATTAAAA
1 TTAAATATTATTA
*
312845 TT-ATTATTATTA
1 TTAAATATTATTA
312857 -TAAATATTATTA
1 TTAAATATTATTA
312869 TT--ATATTATTA
1 TTAAATATTATTA
*
312880 TTATTATATTATTA
1 TTA-AATATTATTA
312894 TTAAATAATTATTA
1 TTAAAT-ATTATTA
312908 CAAACCCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 13 0.21
12 21 0.34
13 3 0.05
14 24 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATATTATTA
Found at i:312907 original size:3 final size:3
Alignment explanation
Indices: 312823--312896 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
312813 TTTTACTTAA
** ** * *
312823 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
312871 A-T ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
312897 AATAATTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:313347 original size:12 final size:12
Alignment explanation
Indices: 313330--313354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
313320 GAGAACGACA
313330 AGAAAAAAAAAC
1 AGAAAAAAAAAC
313342 AGAAAAAAAAAC
1 AGAAAAAAAAAC
313354 A
1 A
313355 AAGCAAGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAC
Found at i:313622 original size:13 final size:13
Alignment explanation
Indices: 313604--313632 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
313594 ACCACCGTTA
313604 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
313617 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
313630 CGG
1 CGG
313633 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:314339 original size:13 final size:13
Alignment explanation
Indices: 314321--314359 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
314311 GTAATTAAAT
314321 TTTTAAATATTTA
1 TTTTAAATATTTA
*
314334 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
314348 TTTT-AATATTTA
1 TTTTAAATATTTA
314360 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:333655 original size:2 final size:2
Alignment explanation
Indices: 333648--333675 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
333638 CCCGCGCTCA
333648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
333676 GGAGGGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:347448 original size:16 final size:18
Alignment explanation
Indices: 347427--347471 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
347417 ACATTCCCAG
347427 TAATCTTATTC-C-CTGA
1 TAATCTTATTCTCACTGA
347443 TAATCTTACATTCTCACTGA
1 TAATCTT--ATTCTCACTGA
347463 TAATCTTAT
1 TAATCTTAT
347472 ATTTCGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.28
18 6 0.24
19 1 0.04
20 11 0.44
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.44
Consensus pattern (18 bp):
TAATCTTATTCTCACTGA
Found at i:354582 original size:20 final size:20
Alignment explanation
Indices: 354537--354589 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
354527 ACGAATTTGT
*
354537 AATTCATAACACAGAAGTCA
1 AATTCGTAACACAGAAGTCA
*
354557 AATTCGTAACACATAAGTCA
1 AATTCGTAACACAGAAGTCA
*
354577 AATTCGCAACACA
1 AATTCGTAACACA
354590 AATTCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (20 bp):
AATTCGTAACACAGAAGTCA
Found at i:354651 original size:21 final size:21
Alignment explanation
Indices: 354632--354828 Score: 259
Period size: 21 Copynumber: 9.4 Consensus size: 21
354622 CAATACATTA
* *
354632 CGATTTTGGAGAACCACATTG
1 CGATTTTGGAGAACCGCGTTG
* *
354653 CGATTTTAGAGAACCGCGTTA
1 CGATTTTGGAGAACCGCGTTG
* * *
354674 CGAATTTGGAGAATCACGTTG
1 CGATTTTGGAGAACCGCGTTG
354695 CGATTTTGGAGAACCGCGTTG
1 CGATTTTGGAGAACCGCGTTG
*
354716 TGATTTTGGAGAACCGCGTTG
1 CGATTTTGGAGAACCGCGTTG
*
354737 CGATTTTGGAGAACCGCGTTA
1 CGATTTTGGAGAACCGCGTTG
*
354758 CGATTTTGGAGAATCGCGTTG
1 CGATTTTGGAGAACCGCGTTG
* *
354779 CGAATTTGGAGAACCGCGTTA
1 CGATTTTGGAGAACCGCGTTG
* **
354800 CGATTTTGGAGAATCGTATTG
1 CGATTTTGGAGAACCGCGTTG
354821 CGATTTTG
1 CGATTTTG
354829 AAAACTGTGT
Statistics
Matches: 151, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 151 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (21 bp):
CGATTTTGGAGAACCGCGTTG
Found at i:354676 original size:42 final size:42
Alignment explanation
Indices: 354629--354828 Score: 292
Period size: 42 Copynumber: 4.8 Consensus size: 42
354619 TCGCAATACA
* * * *
354629 TTACGATTTTGGAGAACCACATTGCGATTTTAGAGAACCGCG
1 TTACGATTTTGGAGAATCGCGTTGCGATTTTGGAGAACCGCG
* *
354671 TTACGAATTTGGAGAATCACGTTGCGATTTTGGAGAACCGCG
1 TTACGATTTTGGAGAATCGCGTTGCGATTTTGGAGAACCGCG
** *
354713 TTGTGATTTTGGAGAACCGCGTTGCGATTTTGGAGAACCGCG
1 TTACGATTTTGGAGAATCGCGTTGCGATTTTGGAGAACCGCG
*
354755 TTACGATTTTGGAGAATCGCGTTGCGAATTTGGAGAACCGCG
1 TTACGATTTTGGAGAATCGCGTTGCGATTTTGGAGAACCGCG
**
354797 TTACGATTTTGGAGAATCGTATTGCGATTTTG
1 TTACGATTTTGGAGAATCGCGTTGCGATTTTG
354829 AAAACTGTGT
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (42 bp):
TTACGATTTTGGAGAATCGCGTTGCGATTTTGGAGAACCGCG
Found at i:359488 original size:19 final size:19
Alignment explanation
Indices: 359464--359510 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
359454 CGGCCACCGT
359464 GAATAGTGATCGATGATCG
1 GAATAGTGATCGATGATCG
359483 GAATAGTGATCGATGATCG
1 GAATAGTGATCGATGATCG
359502 GAATAGTGA
1 GAATAGTGA
359511 CCGACGGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.32, T:0.26
Consensus pattern (19 bp):
GAATAGTGATCGATGATCG
Found at i:361022 original size:3 final size:3
Alignment explanation
Indices: 361014--361039 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
361004 GAATAGAGTT
361014 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
361040 TTCCACCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:363724 original size:2 final size:2
Alignment explanation
Indices: 363719--363761 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
363709 TTTATATAGA
363719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
363761 A
1 A
363762 AAATTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:364146 original size:19 final size:20
Alignment explanation
Indices: 364095--364146 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
364085 TAAAAATATT
**
364095 TATTTTAAATAACGAAATTAA
1 TATTTTAAATAAC-AAAAAAA
**
364116 TATTTTTGATAA-AAAAAAA
1 TATTTTAAATAACAAAAAAA
364135 TATTTTAAATAA
1 TATTTTAAATAA
364147 TATTTTATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
TATTTTAAATAACAAAAAAA
Found at i:366647 original size:33 final size:34
Alignment explanation
Indices: 366605--366674 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
366595 TTCATGTTCA
366605 AAATTCCAAAACAC-TTAA-TACATTCTAAACTCC
1 AAATTCCAAAACACTTTAATTACATTCTAAAC-CC
*
366638 AAATTCCAAAATACTTTAATTACATTCTAAACCC
1 AAATTCCAAAACACTTTAATTACATTCTAAACCC
366672 AAA
1 AAA
366675 ATTAAAGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 13 0.38
34 9 0.26
35 12 0.35
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (34 bp):
AAATTCCAAAACACTTTAATTACATTCTAAACCC
Found at i:366677 original size:35 final size:34
Alignment explanation
Indices: 366603--366677 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 34
366593 AATTCATGTT
366603 CAAAATTCCAAAACACTTAATACATTCTAAACTC
1 CAAAATTCCAAAACACTTAATACATTCTAAACTC
*
366637 C-AAATTCCAAAATACTTTAATTACATTCTAAAC-C
1 CAAAATTCCAAAACAC-TTAA-TACATTCTAAACTC
366671 CAAAATT
1 CAAAATT
366678 AAAGTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 13 0.35
34 7 0.19
35 17 0.46
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (34 bp):
CAAAATTCCAAAACACTTAATACATTCTAAACTC
Found at i:366721 original size:35 final size:35
Alignment explanation
Indices: 366673--366747 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
366663 TCTAAACCCA
366673 AAATTAAAGTATTTTAGAATTTGAGGTTTAAAATG
1 AAATTAAAGTATTTTAGAATTTGAGGTTTAAAATG
* * *
366708 TAATTAAATTATTTTAGAATTTGGGGTTTAAAATG
1 AAATTAAAGTATTTTAGAATTTGAGGTTTAAAATG
366743 AAATT
1 AAATT
366748 GAGGAATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (35 bp):
AAATTAAAGTATTTTAGAATTTGAGGTTTAAAATG
Found at i:369096 original size:2 final size:2
Alignment explanation
Indices: 369089--369114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
369079 TTTGTACTGA
369089 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
369115 TATGATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:369735 original size:10 final size:10
Alignment explanation
Indices: 369720--369744 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
369710 AAACCTTTTT
369720 AATATATAAA
1 AATATATAAA
369730 AATATATAAA
1 AATATATAAA
369740 AATAT
1 AATAT
369745 TTTTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATATATAAA
Found at i:374294 original size:19 final size:16
Alignment explanation
Indices: 374260--374290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
374250 TATAAAATCT
374260 AATAATCCATAATATA
1 AATAATCCATAATATA
*
374276 AATAATCCATTATAT
1 AATAATCCATAATAT
374291 TATATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATCCATAATATA
Found at i:381003 original size:2 final size:2
Alignment explanation
Indices: 380996--381042 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
380986 TACCTAGCTT
380996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
381038 TA TA T
1 TA TA T
381043 TATGAGATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:394959 original size:23 final size:23
Alignment explanation
Indices: 394900--394959 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
394890 CTCGGCTTCC
* *
394900 CTCGGATTCCCTCACATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
394923 CTCGGATGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
394946 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
394960 GATGCCCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.13, C:0.37, G:0.25, T:0.25
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:396863 original size:2 final size:2
Alignment explanation
Indices: 396858--396899 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
396848 TTTTTTGTTT
* *
396858 TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
396900 ACTCAAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.05, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:399788 original size:8 final size:8
Alignment explanation
Indices: 399777--399819 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
399767 TGTTATTATT
399777 TTATTTAA
1 TTATTTAA
399785 TTATTTAAA
1 TTATTT-AA
399794 TTATTTAA
1 TTATTTAA
*
399802 -TATTTTAT
1 TTA-TTTAA
399810 TTATTTAA
1 TTATTTAA
399818 TT
1 TT
399820 TTTTGCAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 18 0.60
9 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATTTAA
Found at i:399814 original size:9 final size:9
Alignment explanation
Indices: 399776--399820 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
399766 TTGTTATTAT
399776 TTTATTTAA
1 TTTATTTAA
399785 -TTATTTAA
1 TTTATTTAA
*
399793 ATTATTTAA
1 TTTATTTAA
*
399802 --TATTTTA
1 TTTATTTAA
399809 TTTATTTAA
1 TTTATTTAA
399818 TTT
1 TTT
399821 TTTGCAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 6 0.19
8 8 0.26
9 17 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATTTAA
Found at i:404271 original size:28 final size:29
Alignment explanation
Indices: 404240--404295 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
404230 CCGTTTTCGC
*
404240 GTCGTGAACAATGACATA-CATATTTTTT
1 GTCGGGAACAATGACATACCATATTTTTT
* *
404268 GTCGGGAACAGTGTCATACCCATATTTT
1 GTCGGGAACAATGACATA-CCATATTTT
404296 CGCTTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
30 8 0.35
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (29 bp):
GTCGGGAACAATGACATACCATATTTTTT
Found at i:406004 original size:15 final size:13
Alignment explanation
Indices: 405970--405996 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
405960 ATCATATATA
405970 ATTATAAAAAATT
1 ATTATAAAAAATT
405983 ATTATAAAAAATT
1 ATTATAAAAAATT
405996 A
1 A
405997 CCTTATAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTATAAAAAATT
Found at i:410343 original size:20 final size:20
Alignment explanation
Indices: 410318--410408 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
410308 TTCTAAACTT
* *
410318 AAAATCGTAACATGAAAATG
1 AAAATCGCAACACGAAAATG
410338 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
410358 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
410379 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
410398 AAAATCGCAAC
1 AAAATCGCAAC
410409 GAGATAATCG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.26
20 29 0.48
21 16 0.26
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:410397 original size:19 final size:19
Alignment explanation
Indices: 410333--410409 Score: 91
Period size: 19 Copynumber: 3.9 Consensus size: 19
410323 CGTAACATGA
*
410333 AAATGAAAATCGCAACACG
1 AAATGAAAATCGCAACGCG
** *
410352 AAAATGACTATCGCAACGAGAG
1 -AAATGAAAATCGCAAC--GCG
410374 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
410393 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
410410 AGATAATCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 19 0.40
20 14 0.29
21 14 0.29
22 1 0.02
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:410408 original size:40 final size:41
Alignment explanation
Indices: 410333--410412 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
410323 CGTAACATGA
**
410333 AAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACACGAAAATGAAAATCGCAACGAGAG
*
410374 AAATGAAAATCGCAACGCG-AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACACGAAAATGAAAATCGCAACGAGA
410413 TAATCGTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 18 0.50
41 18 0.50
ACGTcount: A:0.50, C:0.19, G:0.20, T:0.11
Consensus pattern (41 bp):
AAATGAAAATCGCAACACGAAAATGAAAATCGCAACGAGAG
Found at i:410512 original size:20 final size:19
Alignment explanation
Indices: 410435--410505 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
410425 GAAACCAAAA
* **
410435 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
410454 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
410473 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATAGTCATT
*
410493 CTCTCGTTGCGAT
1 -TCGCGTTGCGAT
410506 TTTCATTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.39
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:412364 original size:94 final size:94
Alignment explanation
Indices: 412203--412417 Score: 378
Period size: 94 Copynumber: 2.3 Consensus size: 94
412193 TAGATTGCTT
* *
412203 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
412268 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
412297 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
412362 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
412391 AGTAAATTTGTTCAGTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
412418 GAAACTTGAA
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 20 0.17
94 96 0.83
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:414275 original size:14 final size:14
Alignment explanation
Indices: 414256--414291 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
414246 ATTGTTTAAT
414256 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
414270 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
414284 TGATTTGT
1 TGATTTGT
414292 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:414414 original size:19 final size:17
Alignment explanation
Indices: 414398--414448 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
414388 AAAAATGACT
414398 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
414417 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
414431 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
414448 A
1 A
414449 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:414440 original size:33 final size:33
Alignment explanation
Indices: 414398--414491 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
414388 AAAAATGACT
* *
414398 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
414431 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
414464 ATCACAACGCGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
414492 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:414454 original size:19 final size:19
Alignment explanation
Indices: 414398--414456 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
414388 AAAAATGACT
414398 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
414417 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
414431 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
414450 ATCGCAA
1 ATCGCAA
414457 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:414513 original size:19 final size:19
Alignment explanation
Indices: 414430--414507 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
414420 GCAACGAGAG
*
414430 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
414449 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
414463 AATCACAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
414482 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
414501 ATTCGCA
1 AATCGCA
414508 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 34 0.68
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:414524 original size:19 final size:19
Alignment explanation
Indices: 414502--414673 Score: 113
Period size: 19 Copynumber: 9.7 Consensus size: 19
414492 CGAAACTAAA
414502 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
414521 TTCGCTTTGTGA--TTC--
1 TTCGCATTGCGATTTTCAT
* *
414536 -CCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
414554 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
414570 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
414587 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
* * *
414606 TTCCGCGTTGCAATATTCAT
1 TT-CGCATTGCGATTTTCAT
*
414626 ATTCGCGTTGCGATTTTCA-
1 -TTCGCATTGCGATTTTCAT
414645 --CG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
414660 TTCACATTGCGATT
1 TTCGCATTGCGATT
414674 CTCTCGTTGC
Statistics
Matches: 118, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
14 25 0.21
16 12 0.10
17 11 0.09
19 40 0.34
20 28 0.24
21 2 0.02
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:414625 original size:20 final size:19
Alignment explanation
Indices: 414572--414644 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
414562 GCGATTCTCT
*
414572 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
414591 CATTGCGATAGTCATTTCCG
1 CGTTGCGATATTCATTT-CG
*
414611 CGTTGCAATATTCATATTCG
1 CGTTGCGATATTCAT-TTCG
*
414631 CGTTGCGATTTTCA
1 CGTTGCGATATTCA
414645 CGTTGCGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 14 0.32
20 28 0.64
21 2 0.05
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:414650 original size:14 final size:14
Alignment explanation
Indices: 414631--414658 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
414621 TTCATATTCG
414631 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
414645 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
414659 TTTCACATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:414695 original size:33 final size:33
Alignment explanation
Indices: 414508--414706 Score: 173
Period size: 33 Copynumber: 5.8 Consensus size: 33
414498 TAAATTCGCA
* * * * *
414508 TTGCGATTTTCATTTCGCTTTGTGATTCCCTCA
1 TTGCGATATTCATTTCGCATTGCGATTCTCTCG
*
414541 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATATTCATTTCGCATTGCGATTCTCTCG
* *
414574 TTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCG
1 TTGCGATATTCATTTCGCATTGCGAT--TC---T-CTCG
* * * *
414613 TTGCAATATTCATATTCGCGTTGCGATTTTCACG
1 TTGCGATATTCAT-TTCGCATTGCGATTCTCTCG
* *
414647 TTGCGATTTTCATTTCACATTGCGATTCTCTCG
1 TTGCGATATTCATTTCGCATTGCGATTCTCTCG
* * *
414680 TTGCGATAGTAATTTCCGCGTTGCGAT
1 TTGCGATATTCATTT-CGCATTGCGAT
414707 AGACATTAAG
Statistics
Matches: 137, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
33 83 0.61
34 23 0.17
35 3 0.02
38 2 0.01
39 14 0.10
40 12 0.09
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
TTGCGATATTCATTTCGCATTGCGATTCTCTCG
Found at i:414752 original size:20 final size:20
Alignment explanation
Indices: 414679--414752 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
414669 CGATTCTCTC
* *
414679 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
414699 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
414719 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
414740 GTTGCGATAGTCA
1 GTTGCGATAGTCA
414753 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:418153 original size:21 final size:21
Alignment explanation
Indices: 418129--418169 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
418119 TATTCGCGTT
418129 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
418150 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
418170 TGCCATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:421639 original size:2 final size:2
Alignment explanation
Indices: 421632--421658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
421622 AAGCAACGGT
421632 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
421659 GCATTTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:422984 original size:21 final size:21
Alignment explanation
Indices: 422940--422984 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
422930 AGTTAACACG
* *
422940 TTTAGTACATAAATTATCAGT
1 TTTAGTACATAAACTATCAAT
* *
422961 TTTAGTATATAAACTATTAAT
1 TTTAGTACATAAACTATCAAT
422982 TTT
1 TTT
422985 TTCAAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACATAAACTATCAAT
Found at i:430505 original size:31 final size:32
Alignment explanation
Indices: 430470--430538 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
430460 ATTGTTTTTT
* *
430470 TTAATTCAAAAC-TTAAATTTTAAATAAAATA
1 TTAATTCAAAACATAAAATTTAAAATAAAATA
* ** *
430501 TTAATTTAATTCATAAAATTTAAAATTAAATA
1 TTAATTCAAAACATAAAATTTAAAATAAAATA
430533 TTAATT
1 TTAATT
430539 TAATCGTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (32 bp):
TTAATTCAAAACATAAAATTTAAAATAAAATA
Found at i:436639 original size:43 final size:45
Alignment explanation
Indices: 436558--436648 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 45
436548 CATGGTTATC
*
436558 ATACTGGTTTCTTATTATTATTTAATATTATGTGGGAAATTAATTG
1 ATACTGGTTTCTTATTATTATTT-ATATTATGTCGGAAATTAATTG
436604 ATACTGGTTTC-TATTATTATTT-TATTATGTCGGAAATTAATTG
1 ATACTGGTTTCTTATTATTATTTATATTATGTCGGAAATTAATTG
436647 AT
1 AT
436649 TCGGATCGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 22 0.50
45 11 0.25
46 11 0.25
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (45 bp):
ATACTGGTTTCTTATTATTATTTATATTATGTCGGAAATTAATTG
Found at i:439733 original size:21 final size:21
Alignment explanation
Indices: 439708--439748 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
439698 AACATGGATC
439708 ATTTTCATTTATATTTAATTT
1 ATTTTCATTTATATTTAATTT
*
439729 ATTTTCATTTTTATTTAATT
1 ATTTTCATTTATATTTAATT
439749 AAGATGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTCATTTATATTTAATTT
Found at i:440457 original size:13 final size:14
Alignment explanation
Indices: 440424--440457 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
440414 CTTTAATTGC
*
440424 AAAAATTAAGAATT
1 AAAATTTAAGAATT
440438 AAAATTTAA-AATT
1 AAAATTTAAGAATT
440451 AAAATTT
1 AAAATTT
440458 TGATTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAATTTAAGAATT
Found at i:440602 original size:40 final size:36
Alignment explanation
Indices: 440530--440616 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 36
440520 GAAGAGATAT
*
440530 TAAATAAAAGAGAAAAAGAAATTAATATAATAATAA
1 TAAATAAAAGAGAAAAAGAAATGAATATAATAATAA
440566 TAAATCAAAAGGAGAGAAAA-AAATGAATAT--T-A-AA
1 TAAAT-AAAA-GAGA-AAAAGAAATGAATATAATAATAA
*
440600 TAAATTAAAGAGAAAAA
1 TAAATAAAAGAGAAAAA
440617 TAAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 4 0.09
32 4 0.09
33 3 0.07
34 7 0.15
35 1 0.02
36 6 0.13
37 4 0.09
38 13 0.28
39 4 0.09
ACGTcount: A:0.68, C:0.01, G:0.11, T:0.20
Consensus pattern (36 bp):
TAAATAAAAGAGAAAAAGAAATGAATATAATAATAA
Found at i:440699 original size:24 final size:23
Alignment explanation
Indices: 440656--440721 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
440646 TAAGTCAAAG
*
440656 GAAT-AAATA-AAAATAGAAAAA
1 GAATAAAATATAAAATAAAAAAA
*
440677 -AATATAATTAATAAAATAAAAAAA
1 GAATA-AAAT-ATAAAATAAAAAAA
440701 TGAATAAAATATAAAATAAAA
1 -GAATAAAATATAAAATAAAA
440722 TTTAGTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.08
22 3 0.08
23 1 0.03
24 22 0.61
25 3 0.08
26 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (23 bp):
GAATAAAATATAAAATAAAAAAA
Found at i:441777 original size:29 final size:29
Alignment explanation
Indices: 441734--441796 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
441724 TACCTTGGTA
441734 TGGTTTTTTTAGTTTACTCGTGGGTTCTG
1 TGGTTTTTTTAGTTTACTCGTGGGTTCTG
*
441763 TTGGTTTTTTT-GTTTACTCGTGGGTTTTG
1 -TGGTTTTTTTAGTTTACTCGTGGGTTCTG
441792 TGGTT
1 TGGTT
441797 CTCGATCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 5 0.16
29 17 0.53
30 10 0.31
ACGTcount: A:0.05, C:0.08, G:0.29, T:0.59
Consensus pattern (29 bp):
TGGTTTTTTTAGTTTACTCGTGGGTTCTG
Found at i:442272 original size:2 final size:2
Alignment explanation
Indices: 442265--442295 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
442255 TATTTCCAAA
442265 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
442296 TTTTCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:442366 original size:35 final size:36
Alignment explanation
Indices: 442280--442591 Score: 140
Period size: 38 Copynumber: 8.3 Consensus size: 36
442270 TATATATATA
* *
442280 TATATATATATAATATTTTTCTAAAATGATTTTTAAAC
1 TATATAT-TAT-ATATTTTTCCAAAATGATTTTAAAAC
442318 TATATATTATATATATTTTCCAAAAT-ATTTTGAAAAC
1 TATATATTATATAT-TTTTCCAAAATGATTTT-AAAAC
* * * * *
442355 TATATTTTATATGTATCTT-CAAAATGTTTTTCAAAAA
1 TATATATTATATAT-TTTTCCAAAATGATTTT-AAAAC
* *
442392 TCATATAGTATATATTTTT--AAAATGTTTTTTTTTCAAAATC
1 T-ATATATTATATATTTTTCCAAAATG----ATTTT-AAAA-C
* * * *
442433 TATATAATATATA-TATTCTCAAAATGTTTTTGAAAAAA
1 TATATATTATATATTTTTC-CAAAATGATTTT--AAAAC
442471 TATATATTACATATATATTTT-CAAAATG-TTTTAAAAAC
1 TATATATT--ATATAT-TTTTCCAAAATGATTTT-AAAAC
* * * *
442509 CATATATTATATGTAAGTTTTCAAAAAT-ATTTAAAAAC
1 TATATATTATA--T-ATTTTTCCAAAATGATTTTAAAAC
* * ** *
442547 CATATATTATATA-ATTTCTGAAATGA-TTTCAAAC
1 TATATATTATATATTTTTCCAAAATGATTTTAAAAC
*
442581 TATATAATATA
1 TATATATTATA
442592 CATACTTTAA
Statistics
Matches: 220, Mismatches: 31, Indels: 50
0.73 0.10 0.17
Matches are distributed among these distances:
34 23 0.10
35 2 0.01
36 25 0.11
37 45 0.20
38 62 0.28
39 20 0.09
40 33 0.15
41 1 0.00
42 9 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATATTATATATTTTTCCAAAATGATTTTAAAAC
Found at i:442459 original size:42 final size:41
Alignment explanation
Indices: 442381--442502 Score: 119
Period size: 40 Copynumber: 3.0 Consensus size: 41
442371 CTTCAAAATG
* *
442381 TTTTTCAAAAATC-ATATAGTATATAT-TTTTAAAATGTTTT
1 TTTTTC-AAAATCTATATAATATATATATTTCAAAATGTTTT
442421 TTTTTCAAAATCTATATAATATATATATTCTCAAAATG--TT
1 TTTTTCAAAATCTATATAATATATATATT-TCAAAATGTTTT
*** *
442461 TTTGAAAAAATATATATTACATATATAT-TTTCAAAATGTTTT
1 TTTTTCAAAATCTATA-TA-ATATATATATTTCAAAATGTTTT
442503 AAAAACCATA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
39 6 0.09
40 40 0.58
41 6 0.09
42 17 0.25
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (41 bp):
TTTTTCAAAATCTATATAATATATATATTTCAAAATGTTTT
Found at i:442507 original size:38 final size:39
Alignment explanation
Indices: 442275--442559 Score: 182
Period size: 38 Copynumber: 7.4 Consensus size: 39
442265 ATATATATAT
442275 ATATATATATATATATAATATTTTTCTAAAATGATTTTT--AAA
1 ATATATAT-TATATAT-ATA-TTTTC-AAAATG-TTTTTAAAAA
* * * *
442317 CTATATATTATATATAT-TTTCCAAAAT-ATTTTGAAAA
1 ATATATATTATATATATATTTTCAAAATGTTTTTAAAAA
* * * *
442354 CTATAT-TT-TATATGTATCTTCAAAATGTTTTTCAAAA
1 ATATATATTATATATATATTTTCAAAATGTTTTTAAAAA
* **
442391 ATCATATA--GTATATAT-TTTT-AAAATGTTTTTTTTTCAAA
1 AT-ATATATTATATATATATTTTCAAAATG---TTTTTAAAAA
* * *
442430 ATCTATATAATATATATATTCTCAAAATGTTTTTGAAAAA
1 ATATATATTATATATATATTTTCAAAATGTTTTT-AAAAA
*
442470 ATATATATTACATATATATTTTCAAAATG-TTTTAAAAA
1 ATATATATTATATATATATTTTCAAAATGTTTTTAAAAA
** * * *
442508 CCATATATTATATGTA-AGTTTTCAAAA-ATATTTAAAAA
1 ATATATATTATATATATA-TTTTCAAAATGTTTTTAAAAA
**
442546 CCATATATTATATA
1 ATATATATTATATA
442560 ATTTCTGAAA
Statistics
Matches: 197, Mismatches: 29, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
35 10 0.05
36 16 0.08
37 27 0.14
38 65 0.33
39 19 0.10
40 37 0.19
41 10 0.05
42 13 0.07
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (39 bp):
ATATATATTATATATATATTTTCAAAATGTTTTTAAAAA
Found at i:451612 original size:10 final size:10
Alignment explanation
Indices: 451593--451639 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
451583 CGTTTAAATG
*
451593 ATAAATGAAC
1 ATAAACGAAC
451603 ATAAACGAAC
1 ATAAACGAAC
* *
451613 ACAAACGAAT
1 ATAAACGAAC
*
451623 GTAAACGAAC
1 ATAAACGAAC
451633 ATAAACG
1 ATAAACG
451640 GACGAAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:451875 original size:24 final size:24
Alignment explanation
Indices: 451827--451876 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
451817 CGAGTCTGGA
* *
451827 GAATATAAATGAACATAAACGAAC
1 GAATATAAATAAACATAAACAAAC
*
451851 GAATATAAATAAACATAAATAAAC
1 GAATATAAATAAACATAAACAAAC
451875 GA
1 GA
451877 GCATAAACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (24 bp):
GAATATAAATAAACATAAACAAAC
Found at i:451882 original size:24 final size:24
Alignment explanation
Indices: 451831--451883 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
451821 TCTGGAGAAT
* * *
451831 ATAAATGAACATAAACGAACGAAT
1 ATAAATAAACATAAACAAACGAAC
* *
451855 ATAAATAAACATAAATAAACGAGC
1 ATAAATAAACATAAACAAACGAAC
451879 ATAAA
1 ATAAA
451884 CGAACGAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.17
Consensus pattern (24 bp):
ATAAATAAACATAAACAAACGAAC
Found at i:453111 original size:128 final size:128
Alignment explanation
Indices: 452932--453258 Score: 645
Period size: 128 Copynumber: 2.6 Consensus size: 128
452922 CTTATTGAAA
452932 ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAT
1 ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAT
452997 ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATT
66 ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATT
453060 ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAT
1 ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAT
453125 ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATT
66 ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATT
*
453188 ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT
1 ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAT
453253 ATATCA
66 ATATCA
453259 ATTTGAATAA
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 198 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAT
ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATT
Found at i:453710 original size:33 final size:34
Alignment explanation
Indices: 453649--453748 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
453639 AAATTTAATG
*
453649 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
453683 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
453716 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
453749 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:454333 original size:21 final size:21
Alignment explanation
Indices: 454266--454338 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
454256 TATGGTATAA
*
454266 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
454287 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
454308 AACCCTGTGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
454329 AACCCTGCGG
1 AACCCTGCGG
454339 AGATGACATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:456152 original size:26 final size:29
Alignment explanation
Indices: 456123--456189 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
456113 AATAATAATT
456123 ATATAAATATT-AT-T-TTAATAAAAAAA
1 ATATAAATATTAATATATTAATAAAAAAA
** *
456149 ATATTTATATTAATATATTAATATAAAAA
1 ATATAAATATTAATATATTAATAAAAAAA
*
456178 ATAATAACTATT
1 AT-ATAAATATT
456190 TAAAAAAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 9 0.29
27 2 0.06
28 1 0.03
29 13 0.42
30 6 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAAATATTAATATATTAATAAAAAAA
Found at i:456158 original size:32 final size:29
Alignment explanation
Indices: 456107--456182 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 29
456097 TTAATAATTC
456107 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAA-AATAATTATATAAATA-TA--TTAA
* *
456141 TAAAAAAAATATTTATATTAATATATTAA
1 TAAAAAAAATAATTATATAAATATATTAA
*
456170 TATAAAAAATAAT
1 TAAAAAAAATAAT
456183 AACTATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 15 0.39
31 2 0.05
32 14 0.37
33 3 0.08
34 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAAAAAAATAATTATATAAATATATTAA
Found at i:456177 original size:29 final size:31
Alignment explanation
Indices: 456110--456182 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
456100 ATAATTCTAA
*
456110 ATAAATAATAATTATATAAATATTATTTTAAT
1 ATAAAAAATAATTATATAAATATTA-TTTAAT
* * *
456142 AAAAAAAATATTTATATTAATA-TA-TTAAT
1 ATAAAAAATAATTATATAAATATTATTTAAT
456171 ATAAAAAATAAT
1 ATAAAAAATAAT
456183 AACTATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 15 0.43
31 2 0.06
32 18 0.51
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
ATAAAAAATAATTATATAAATATTATTTAAT
Found at i:462338 original size:25 final size:25
Alignment explanation
Indices: 462300--462347 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
462290 GTTCGGTAAA
*
462300 TTATTTGTGATTCATTTATATAAAAT
1 TTATTTATGATTCATTTAT-TAAAAT
462326 TTATTTATG-TTCATTTATTAAA
1 TTATTTATGATTCATTTATTAAA
462348 TTAGATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
TTATTTATGATTCATTTATTAAAAT
Found at i:462373 original size:40 final size:40
Alignment explanation
Indices: 462323--462429 Score: 178
Period size: 40 Copynumber: 2.6 Consensus size: 40
462313 ATTTATATAA
* *
462323 AATTTATTTATGTTCATTTATTAAATTAGATAAATGAGTAT
1 AATTT-TTTATCTTCATTTAATAAATTAGATAAATGAGTAT
462364 AATTTTTTATCTTCATTTAATAAATTAGATAAATGAGTAT
1 AATTTTTTATCTTCATTTAATAAATTAGATAAATGAGTAT
462404 AATTTTTTTATCTTCATTTAATAAAT
1 AA-TTTTTTATCTTCATTTAATAAAT
462430 GAATGAACAC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 35 0.56
41 28 0.44
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (40 bp):
AATTTTTTATCTTCATTTAATAAATTAGATAAATGAGTAT
Found at i:462523 original size:24 final size:24
Alignment explanation
Indices: 462496--462547 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
462486 TATTGACTTA
462496 TTTATAGACCCAAT-TATAAGCTTG
1 TTTATAGACCC-ATCTATAAGCTTG
* * *
462520 TTTATCGACTCGTCTATAAGCTTG
1 TTTATAGACCCATCTATAAGCTTG
462544 TTTA
1 TTTA
462548 CTTGATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (24 bp):
TTTATAGACCCATCTATAAGCTTG
Found at i:462800 original size:23 final size:23
Alignment explanation
Indices: 462734--462800 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
462724 CGAATATTTC
462734 ACGAATGTTAAATGAACATGTTT
1 ACGAATGTTAAATGAACATGTTT
* * *
462757 -CAAATGTTAAACGAATATGTTT
1 ACGAATGTTAAATGAACATGTTT
* *
462779 ACGAACGTTAAATGAACGTGTT
1 ACGAATGTTAAATGAACATGTT
462801 CGTGAACATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (23 bp):
ACGAATGTTAAATGAACATGTTT
Found at i:467172 original size:3 final size:3
Alignment explanation
Indices: 467164--467193 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
467154 TAATCAAAAT
467164 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
467194 ATATTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:467515 original size:23 final size:23
Alignment explanation
Indices: 467483--467527 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
467473 AATTTATAAA
467483 ATAATAATTAAAATTTTTGAATG
1 ATAATAATTAAAATTTTTGAATG
* *
467506 ATAATTATTAAATTTTTTGAAT
1 ATAATAATTAAAATTTTTGAAT
467528 TGTTACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
ATAATAATTAAAATTTTTGAATG
Found at i:469031 original size:143 final size:143
Alignment explanation
Indices: 468822--469158 Score: 489
Period size: 143 Copynumber: 2.4 Consensus size: 143
468812 AAAAGTTTGT
* * *
468822 GAACTGAAAAGTTTCTGTCATGGTGTATTATTTTACGTATGAGAAATGCACGTTTTTATGATATG
1 GAACTGAAAAGTTTCTGTCATGGTGCATTATTTTACATATGAGAAATGCACATTTTTATGATATG
* * * * * *
468887 AAGTGATATGTCA-CTACTGAAAAAATTTCTAAAATGTGTTGATATATCATTGAAAAATTGTTGA
66 AAGTGATATGTAATC-ACTGAAAAAATTTCTAAAATGAGTTGATATATAACTGAAAAATTGCTAA
468951 AGATGATTAATTGG
130 AGATGATTAATTGG
* * * * *
468965 GCACTGAAAAGTTTATGCCATGGTGCATTATTTCT-CATATGAGAAATGTACATTTTTCTGATAT
1 GAACTGAAAAGTTTCTGTCATGGTGCATTATTT-TACATATGAGAAATGCACATTTTTATGATAT
469029 GAAGTGATATGTAATCACTGAAAAAATTTCTAAAATGAGTTGATATATAACTGAAAAATTGCTAA
65 GAAGTGATATGTAATCACTGAAAAAATTTCTAAAATGAGTTGATATATAACTGAAAAATTGCTAA
469094 AGATGATTAATTGG
130 AGATGATTAATTGG
* * *
469108 GAATTGAAAAGTTTCTGTCATGGTACATTATTTTACCTATGAGAAATGCAC
1 GAACTGAAAAGTTTCTGTCATGGTGCATTATTTTACATATGAGAAATGCAC
469159 GTTTCACTGA
Statistics
Matches: 170, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
142 1 0.01
143 167 0.98
144 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (143 bp):
GAACTGAAAAGTTTCTGTCATGGTGCATTATTTTACATATGAGAAATGCACATTTTTATGATATG
AAGTGATATGTAATCACTGAAAAAATTTCTAAAATGAGTTGATATATAACTGAAAAATTGCTAAA
GATGATTAATTGG
Found at i:479721 original size:20 final size:20
Alignment explanation
Indices: 479627--479995 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
479617 GATTTTCCAT
* ** *
479627 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
479647 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
479667 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
479687 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
479707 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
479727 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
479747 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
479767 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
479787 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
479807 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
479827 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
479847 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
479867 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
479887 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
479907 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
479927 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
479947 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
479967 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
479987 AATCACAAC
1 AATCGCAAC
479996 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:480708 original size:24 final size:24
Alignment explanation
Indices: 480669--480715 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
480659 AAATTTGGTC
480669 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
480693 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
480716 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:480907 original size:12 final size:12
Alignment explanation
Indices: 480890--480914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
480880 ATATAATCCT
480890 GAAGAAGAAAAA
1 GAAGAAGAAAAA
480902 GAAGAAGAAAAA
1 GAAGAAGAAAAA
480914 G
1 G
480915 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:483238 original size:19 final size:19
Alignment explanation
Indices: 483216--483522 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
483206 CGGAAAATAC
*
483216 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483235 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
483249 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
483269 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
483283 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
483302 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483321 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
483335 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483354 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
483368 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483387 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
483406 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
483425 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
483444 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
483463 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
483477 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
483496 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
483515 AATCGCAA
1 AATCGCAA
483523 CGAGATAATC
Statistics
Matches: 250, Mismatches: 12, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 50 0.20
15 3 0.01
16 13 0.05
17 12 0.05
18 4 0.02
19 155 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:483303 original size:33 final size:34
Alignment explanation
Indices: 483216--483544 Score: 244
Period size: 33 Copynumber: 9.5 Consensus size: 34
483206 CGGAAAATAC
* *
483216 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
483249 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
483283 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
483321 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
483354 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
483387 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--ATGAA
483425 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
483463 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
483496 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
483529 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
483545 TATAAACGCA
Statistics
Matches: 266, Mismatches: 9, Indels: 42
0.84 0.03 0.13
Matches are distributed among these distances:
33 133 0.50
34 31 0.12
35 11 0.04
36 11 0.04
37 3 0.01
38 75 0.28
39 1 0.00
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:483331 original size:52 final size:52
Alignment explanation
Indices: 483244--483522 Score: 299
Period size: 52 Copynumber: 5.2 Consensus size: 52
483234 AAATCCCAAC
*
483244 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
483297 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
483349 ATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
* *
483401 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
483458 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
483510 ATGAAAATCGCAA
1 ATGAAAATCGCAA
483523 CGAGATAATC
Statistics
Matches: 211, Mismatches: 5, Indels: 21
0.89 0.02 0.09
Matches are distributed among these distances:
47 10 0.05
48 1 0.00
49 2 0.01
50 2 0.01
51 1 0.00
52 123 0.58
53 16 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 47 0.22
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:483340 original size:14 final size:14
Alignment explanation
Indices: 483321--483375 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
483311 GCGAAATGAA
483321 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
483335 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
483354 AATCGCAACGAGAG
1 AATCGCAACGAGAG
483368 AATCGCAA
1 AATCGCAA
483376 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:483523 original size:52 final size:52
Alignment explanation
Indices: 483283--483544 Score: 354
Period size: 52 Copynumber: 4.9 Consensus size: 52
483273 GCAACGAGAG
*
483283 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
483335 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
483387 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACGAAA-G--AATCGCAATGCGAAATGAA
483444 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
483496 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
483545 TATAAACGCA
Statistics
Matches: 193, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 3 0.02
50 4 0.02
51 1 0.01
52 119 0.62
53 1 0.01
54 6 0.03
55 7 0.04
56 1 0.01
57 43 0.22
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Done.