Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 55
Found at i:4013403 original size:40 final size:40
Alignment explanation
Indices: 4013324--4013409 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 40
4013314 TGGGTTTTGT
*
4013324 AATAATAATAATAATTATTATTATTATATAATATAATGAA
1 AATAATAATAATAATTAATATTATTATATAATATAATGAA
*
4013364 TATAATAAT-ATAA-TAATATTATTATATAAGTCCAT-ATGAA
1 AATAATAATAATAATTAATATTATTATATAA-T--ATAATGAA
4013404 AATAAT
1 AATAAT
4013410 TGTCGATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 15 0.38
39 5 0.12
40 18 0.45
41 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (40 bp):
AATAATAATAATAATTAATATTATTATATAATATAATGAA
Found at i:4013609 original size:35 final size:34
Alignment explanation
Indices: 4013563--4013858 Score: 259
Period size: 35 Copynumber: 8.4 Consensus size: 34
4013553 TCTGTTCCTT
*
4013563 CTTCACTACTCTTTCATGAAGGCTGGATTGCATTA
1 CTTCACTACTCTTCCATGAAGGCTGGATTG-ATTA
* * *
4013598 CTTCACTACTCTTCCGTGAAGGCTAAGAATGATTTA
1 CTTCACTACTCTTCCATGAAGGCT-GGATTGA-TTA
* ** * *
4013634 CTTCACTACTCTTCCGTGAAGGCTAAATTATATTG
1 CTTCACTACTCTTCCATGAAGGCTGGATT-GATTA
* * *
4013669 TTTCACTACTCTTCCATGAATGCTGAGAATGATTTA
1 CTTCACTACTCTTCCATGAAGGCTG-GATTGA-TTA
* * * * *
4013705 CTTCATTACTATTCCATGAAGGTTGGGTTGTTTTA
1 CTTCACTACTCTTCCATGAAGGCTGGATTG-ATTA
* * * *
4013740 CTTAACTACTCTTCCAGGAAGGCTAAGAATGATTTA
1 CTTCACTACTCTTCCATGAAGGCT-GGATTGA-TTA
* * * *
4013776 CTTCACTACTCTTCCGTGAAGGCTGAATTACATTG
1 CTTCACTACTCTTCCATGAAGGCTGGATT-GATTA
*
4013811 CTTCACTACTCTTCCATGAAGGCTGGATTGCATTG
1 CTTCACTACTCTTCCATGAAGGCTGGATTG-ATTA
4013846 CTTCACTACTCTT
1 CTTCACTACTCTT
4013859 TCACGAACGA
Statistics
Matches: 207, Mismatches: 44, Indels: 20
0.76 0.16 0.07
Matches are distributed among these distances:
35 123 0.59
36 84 0.41
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (34 bp):
CTTCACTACTCTTCCATGAAGGCTGGATTGATTA
Found at i:4013679 original size:71 final size:71
Alignment explanation
Indices: 4013563--4013834 Score: 337
Period size: 71 Copynumber: 3.8 Consensus size: 71
4013553 TCTGTTCCTT
* * * *
4013563 CTTCACTACTCTTTCATGAAGGCTGGATTGCATTACTTCACTACTCTTCCGTGAAGGCTAAGAAT
1 CTTCACTACTCTTCCATGAAGGCTGAATTACATTACTTCACTACTCTTCCATGAAGGCTAAGAAT
4013628 GATTTA
66 GATTTA
* * * ** * *
4013634 CTTCACTACTCTTCCGTGAAGGCTAAATTATATTGTTTCACTACTCTTCCATGAATGCTGAGAAT
1 CTTCACTACTCTTCCATGAAGGCTGAATTACATTACTTCACTACTCTTCCATGAAGGCTAAGAAT
4013699 GATTTA
66 GATTTA
* * * ** *** * *
4013705 CTTCATTACTATTCCATGAAGGTTGGGTTGTTTTACTTAACTACTCTTCCAGGAAGGCTAAGAAT
1 CTTCACTACTCTTCCATGAAGGCTGAATTACATTACTTCACTACTCTTCCATGAAGGCTAAGAAT
4013770 GATTTA
66 GATTTA
* *
4013776 CTTCACTACTCTTCCGTGAAGGCTGAATTACATTGCTTCACTACTCTTCCATGAAGGCT
1 CTTCACTACTCTTCCATGAAGGCTGAATTACATTACTTCACTACTCTTCCATGAAGGCT
4013835 GGATTGCATT
Statistics
Matches: 163, Mismatches: 38, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
71 163 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (71 bp):
CTTCACTACTCTTCCATGAAGGCTGAATTACATTACTTCACTACTCTTCCATGAAGGCTAAGAAT
GATTTA
Found at i:4013819 original size:142 final size:142
Alignment explanation
Indices: 4013563--4013835 Score: 422
Period size: 142 Copynumber: 1.9 Consensus size: 142
4013553 TCTGTTCCTT
* * *
4013563 CTTCACTACTCTTTCATGAAGGCTGGATTGCATTACTTCACTACTCTTCCGTGAAGGCTAAGAAT
1 CTTCACTACTATTCCATGAAGGCTGGATTGCATTACTTAACTACTCTTCCGTGAAGGCTAAGAAT
* * *
4013628 GATTTACTTCACTACTCTTCCGTGAAGGCTAAATTATATTGTTTCACTACTCTTCCATGAATGCT
66 GATTTACTTCACTACTCTTCCGTGAAGGCTAAATTACATTGCTTCACTACTCTTCCATGAAGGCT
4013693 GAGAATGATTTA
131 GAGAATGATTTA
* * * **
4013705 CTTCATTACTATTCCATGAAGGTTGGGTTGTTTTACTTAACTACTCTTCCAG-GAAGGCTAAGAA
1 CTTCACTACTATTCCATGAAGGCTGGATTGCATTACTTAACTACTCTTCC-GTGAAGGCTAAGAA
*
4013769 TGATTTACTTCACTACTCTTCCGTGAAGGCTGAATTACATTGCTTCACTACTCTTCCATGAAGGC
65 TGATTTACTTCACTACTCTTCCGTGAAGGCTAAATTACATTGCTTCACTACTCTTCCATGAAGGC
4013834 TG
130 TG
4013836 GATTGCATTG
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
142 117 0.99
143 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (142 bp):
CTTCACTACTATTCCATGAAGGCTGGATTGCATTACTTAACTACTCTTCCGTGAAGGCTAAGAAT
GATTTACTTCACTACTCTTCCGTGAAGGCTAAATTACATTGCTTCACTACTCTTCCATGAAGGCT
GAGAATGATTTA
Found at i:4013882 original size:142 final size:142
Alignment explanation
Indices: 4013595--4013865 Score: 368
Period size: 142 Copynumber: 1.9 Consensus size: 142
4013585 CTGGATTGCA
*
4013595 TTACTTCACTACTCTTCCGTGAAGGCTAAGAATGATTTACTTCACTACTCTTCCGTGAAGGCTAA
1 TTACTTAACTACTCTTCCGTGAAGGCTAAGAATGATTTACTTCACTACTCTTCCGTGAAGGCTAA
* * * * *
4013660 ATTATATTGTTTCACTACTCTTCCATGAATGCTGAGAATGATTTACTTCATTACTATTCCATGAA
66 ATTACATTGCTTCACTACTCTTCCATGAAGGCTGAGAATGATTTACTTCACTACTATTCCACGAA
* ** *
4013725 GGTTGGGTTGTT
131 GATTGAATTGAT
*
4013737 TTACTTAACTACTCTTCCAG-GAAGGCTAAGAATGATTTACTTCACTACTCTTCCGTGAAGGCTG
1 TTACTTAACTACTCTTCC-GTGAAGGCTAAGAATGATTTACTTCACTACTCTTCCGTGAAGGCTA
* * * *
4013801 AATTACATTGCTTCACTACTCTTCCATGAAGGCTG-GATTGCA-TTGCTTCACTACTCTTTCACG
65 AATTACATTGCTTCACTACTCTTCCATGAAGGCTGAGAATG-ATTTACTTCACTACTATTCCACG
4013864 AA
129 AA
4013866 CGATAATAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
141 22 0.19
142 93 0.80
143 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (142 bp):
TTACTTAACTACTCTTCCGTGAAGGCTAAGAATGATTTACTTCACTACTCTTCCGTGAAGGCTAA
ATTACATTGCTTCACTACTCTTCCATGAAGGCTGAGAATGATTTACTTCACTACTATTCCACGAA
GATTGAATTGAT
Found at i:4014201 original size:62 final size:62
Alignment explanation
Indices: 4014059--4014586 Score: 608
Period size: 62 Copynumber: 8.6 Consensus size: 62
4014049 AATATGCAAT
* * *
4014059 GTTGACTTCTCTTCACAAGGAAGTCAAGGATTGGCTCTACT-AGGAAGTCAG--A-AA-AAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGG-AGTCAGAAATAACAAAA
*
4014117 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAACAAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGAAATAACAAAA
* * * * *
4014179 ATTGACTTCTCTTCATGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAATAAAG
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGAAATAACAAAA
* * * * *
4014241 GGTGACTTCTCTTCACGAGGAAGTCAAAAATTTACTATACTGAGGAGTCAGAAATAACAAAG
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGAAATAACAAAA
* *
4014303 GTTGACTTCTCTTCATGAGGAAGTCAAAGATTAACTCTACTGAGGAGTCAGAAATAAC-AAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGAAATAACAAAA
* * * * * * *
4014364 GTTGACTTCTCTTTATGAGGAAGTAAAAGATTGACTCAACTGGGGAGTCAAAAATACCAAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGAAATAACAAAA
* * * *
4014426 GTTGATTTCTCTTCACGATGAAGTCAAAGATTGACTATACTGAGGAGTC-GAGAATGAC-AAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA-AATAACAAAA
* * * * * *
4014487 GTTTGACTTGTCTTTACGAGGAAGTCAAGGATTGACTCCACTGAGGAGCCTAG-AATGAC-AAA
1 G-TTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTC-AGAAATAACAAAA
* * **
4014549 GCTTGTCTTCTCTTTACGAGGAAGTCATGGATTGACTC
1 G-TTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTC
4014587 AAGGAAACAA
Statistics
Matches: 408, Mismatches: 52, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
58 44 0.11
59 2 0.00
60 1 0.00
61 60 0.15
62 300 0.74
64 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (62 bp):
GTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGAAATAACAAAA
Found at i:4014508 original size:247 final size:244
Alignment explanation
Indices: 4014059--4014575 Score: 662
Period size: 247 Copynumber: 2.1 Consensus size: 244
4014049 AATATGCAAT
* * **
4014059 GTTGACTTCTCTTCACAAGGAAGTCAAGGATTGGCTCTACTAGGAAGTCAGAAAAAAAGTTGACT
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTACTAGGAAGTCAGAAAAAAAGTTGACT
* * *
4014124 TCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAACAAAAATTGACTTCT
66 TCTCTTCACGAGGAAGTAAAAGATTGACTCAACTGGGGAGTCAAAAATAACAAAAATTGACTTCT
* * * *
4014189 CTTCATGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAATAAAGGGTGACTTCTCTT
131 CTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAGAAATAACAAAGGGTGACTTCTCTT
* * *
4014254 CACGAGGAAGTCAAAAATTTACTATACTGAGGAGTC-AGAAATAACAAAG
196 CACGAGGAAGTCAAAAATTGACTACACTGAGGAGCCTAG-AATAACAAAG
*
4014303 GTTGACTTCTCTTCATGAGGAAGTCAAAGATTAACTCTACTGAGG-AGTCAGAAATAACAAAGTT
1 GTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTACT-AGGAAGTCAG-AA-AA-AAAGTT
* * * * *
4014367 GACTTCTCTTTATGAGGAAGTAAAAGATTGACTCAACTGGGGAGTCAAAAATACCAAAAGTTGAT
62 GACTTCTCTTCACGAGGAAGTAAAAGATTGACTCAACTGGGGAGTCAAAAATAACAAAAATTGAC
* * **
4014432 TTCTCTTCACGATGAAGTCAAAGATTGACTATACTGAGGAGTC-GAGAATGACAAAGTTTGACTT
127 TTCTCTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAGA-AATAACAAAGGGTGACTT
* * ** * *
4014496 GTCTTTACGAGGAAGTCAAGGATTGACTCCACTGAGGAGCCTAGAATGACAAAG
191 CTCTTCACGAGGAAGTCAAAAATTGACTACACTGAGGAGCCTAGAATAACAAAG
* * *
4014550 CTTGTCTTCTCTTTACGAGGAAGTCA
1 GTTGACTTCTCTTCACGAGGAAGTCA
4014576 TGGATTGACT
Statistics
Matches: 233, Mismatches: 34, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
244 42 0.18
245 5 0.02
246 4 0.02
247 180 0.77
248 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (244 bp):
GTTGACTTCTCTTCACGAGGAAGTCAAAGATTAACTCTACTAGGAAGTCAGAAAAAAAGTTGACT
TCTCTTCACGAGGAAGTAAAAGATTGACTCAACTGGGGAGTCAAAAATAACAAAAATTGACTTCT
CTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAGAAATAACAAAGGGTGACTTCTCTT
CACGAGGAAGTCAAAAATTGACTACACTGAGGAGCCTAGAATAACAAAG
Found at i:4023020 original size:26 final size:25
Alignment explanation
Indices: 4022991--4023039 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4022981 TGGGTTGGAC
*
4022991 TTGTAAAATGGGCTTTCGGGTTTTTG
1 TTGT-AAATGGGCCTTCGGGTTTTTG
*
4023017 TTGTAATTGGGCCTTCGGGTTTT
1 TTGTAAATGGGCCTTCGGGTTTT
4023040 GTAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.12, C:0.10, G:0.31, T:0.47
Consensus pattern (25 bp):
TTGTAAATGGGCCTTCGGGTTTTTG
Found at i:4023047 original size:24 final size:25
Alignment explanation
Indices: 4022991--4023047 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
4022981 TGGGTTGGAC
*
4022991 TTGTAA-AA-TGGGCTTTCGGGTTT
1 TTGTAATAATTGGGCCTTCGGGTTT
**
4023014 TTGTTGTAATTGGGCCTTCGGG-TT
1 TTGTAATAATTGGGCCTTCGGGTTT
4023038 TTGTAATAAT
1 TTGTAATAAT
4023048 AATATAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 4 0.15
24 12 0.44
25 11 0.41
ACGTcount: A:0.18, C:0.09, G:0.28, T:0.46
Consensus pattern (25 bp):
TTGTAATAATTGGGCCTTCGGGTTT
Found at i:4023056 original size:5 final size:5
Alignment explanation
Indices: 4023041--4023096 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
4023031 TCGGGTTTTG
*
4023041 TAATAA TAATA TAATA TAATA TAATA T-ATAA TGAATA TAATAA TATTA
1 TAAT-A TAATA TAATA TAATA TAATA TAAT-A T-AATA TAAT-A TAATA
*
4023089 TTATA TAA
1 TAATA TAA
4023097 GTCTGGACGA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
4 2 0.05
5 28 0.67
6 10 0.24
7 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:4026563 original size:130 final size:131
Alignment explanation
Indices: 4026405--4026640 Score: 352
Period size: 130 Copynumber: 1.8 Consensus size: 131
4026395 ATAATTTTAA
* * * *
4026405 GAGTGAAAAGGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGT-GCATAAAACA
1 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATAGCATAAAACA
*
4026469 ATCATTTATTACTCCA-ATTGAAAT-AAAGATATATTACTATTTCGTCTTAAAATCCAATAGTGA
66 ATCATTTATTACT-CATATCGAAATGAAA-ATATATTACTATTTCGTCTTAAAATCCAATAGTGA
4026532 TTT
129 TTT
* * *
4026535 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATATCTTAAAGCA
1 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATAGCATAAAACA
*
4026600 ATCATTTATTACTCATATCGAAATGAAAATATATTATTATT
66 ATCATTTATTACTCATATCGAAATGAAAATATATTACTATT
4026641 CTCAATATCG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
130 52 0.55
131 39 0.41
132 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (131 bp):
GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATAGCATAAAACA
ATCATTTATTACTCATATCGAAATGAAAATATATTACTATTTCGTCTTAAAATCCAATAGTGATT
T
Found at i:4029859 original size:232 final size:231
Alignment explanation
Indices: 4029330--4029985 Score: 936
Period size: 232 Copynumber: 2.8 Consensus size: 231
4029320 AAAATATCCC
* * * * **
4029330 GCCCGAAGGACTTATCATCTTGCTTGAGAGGCTTATAGTTGACCCGAAATATTTAAGCATCATGC
1 GCCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGC
* * *
4029395 TCAAAAGAATTACTGATGGCCCAAAGGACTTACCAAATTTGAAAATAGTTTACTAGGTAAGAAAC
66 TCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTG-AAATAGTTTACTAGGTAAGAAAC
**
4029460 TTTTCTTACTTTTCAAAAATTTCAATTTTTATATTTAAATGAGAGACCTTTCTCATTTTTCAACA
130 TTTTCTTACTTTTCAAAAATTTCAATTTTTATATTTAAATGAGA-AAATTTCTCATTTTTCAACA
4029525 GACATGTGAAAACATCCTACCCGAAGGTCTTATGGACT
194 GACATGTGAAAACATCCTACCCGAAGGTCTTATGGACT
* ** * *
4029563 GCCCAAAGGACTTATCATCTTGCTCAAAATACTTACAGATGACCCGAAGGATTTAAGAATCATGC
1 GCCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGC
**
4029628 TCGAAAGACTTACTGATGGCCCAAAGGACTTACCGAATTTTGAAATAACTTACTAGGTAAGAAAC
66 TCGAAAGACTTACTGATGGCCCAAAGGACTTACC-AATTTTGAAATAGTTTACTAGGTAAGAAAC
* ** *
4029693 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAATTTCTCATTTTTTGAGAG
130 TTTTCTTACTTTTCAAAAATTTCAATTTTTATATTTAAATGAGAAAATTTCTCATTTTTCAACAG
* *
4029758 ACATGTGAAAACATCTTGCCCGAAGGTCTTATGGA-T
195 ACATGTGAAAACATCCTACCCGAAGGTCTTATGGACT
* **
4029794 GGCCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGGTGATACGAAGGATTTAAGCATCATG
1 -GCCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATG
* ** *
4029859 CTCGAAAGACTTACTAATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAAAAA
65 CTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTT-GAAATAGTTTACTAGGTAAGAAA
* * * *
4029924 CTTTGCTTACTTTTCAAAAATTTCAATTTTTAGATTTAAAAGAGAAAATTTTCTTATTTTTC
129 CTTTTCTTACTTTTCAAAAATTTCAATTTTTATATTTAAATGAGAAAA-TTTCTCATTTTTC
4029986 GACTTATAAA
Statistics
Matches: 375, Mismatches: 44, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
231 7 0.02
232 201 0.54
233 161 0.43
234 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (231 bp):
GCCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGC
TCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGAAATAGTTTACTAGGTAAGAAACT
TTTCTTACTTTTCAAAAATTTCAATTTTTATATTTAAATGAGAAAATTTCTCATTTTTCAACAGA
CATGTGAAAACATCCTACCCGAAGGTCTTATGGACT
Found at i:4040267 original size:131 final size:131
Alignment explanation
Indices: 4040119--4040383 Score: 408
Period size: 131 Copynumber: 2.0 Consensus size: 131
4040109 TGAATTTTAA
* *
4040119 GAGAGAGAACGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATG-CTTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTC-TTAAAGC
* ** * *
4040183 AGTCATTTATTACTCCAATTGAAATAAAGAGATATTAAC-ATTTCGTCCTAAAATTTAATATTGA
65 AATCATTTATTACTCCAATCAAAATAAAGAGATATT-ACTATTTCGTCCTAAAATTCAATATTAA
4040247 TTC
129 TTC
*
4040250 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACTTCTCATGTCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCA
* *
4040315 ATCATTTATTACTTCAATCAAAATGAAGAGATATTACTATTTCGTCCTAAAATTCAATATTAATT
66 ATCATTTATTACTCCAATCAAAATAAAGAGATATTACTATTTCGTCCTAAAATTCAATATTAATT
4040380 C
131 C
4040381 GAG
1 GAG
4040384 TGTTATTTAT
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
130 2 0.02
131 119 0.98
132 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCA
ATCATTTATTACTCCAATCAAAATAAAGAGATATTACTATTTCGTCCTAAAATTCAATATTAATT
C
Found at i:4041348 original size:110 final size:110
Alignment explanation
Indices: 4041193--4041447 Score: 313
Period size: 110 Copynumber: 2.3 Consensus size: 110
4041183 ATACTTCACA
* *
4041193 TGACCAAAATGCAAAAACACACCTAAA-TA-A-GGGGACTAAACAACAAATATTCCAAAAAATAC
1 TGACCAAAATGCAAAAACAC-GCTAAACTATAGGGGGACTAAACAACAAATATCCCAAAAAATAC
* * *
4041255 ATAAAATACATGAAAACAGGTAAATAACAACTTTGGTCCCTATATG
65 ATAAAATACATAAAAACAGGTAAATAACAACTTTGGTCCCTACAGG
* * * * *
4041301 TGACCAATATGCAAAAGCACGCTAAACTATAGGGGGACTAAAGAACAAATATCCCATAAAATATA
1 TGACCAAAATGCAAAAACACGCTAAACTATAGGGGGACTAAACAACAAATATCCCAAAAAATACA
* * * * *
4041366 TAACATGCATAAAAACGGGTAAATAACAACTTTGGTCCTTGCAGG
66 TAAAATACATAAAAACAGGTAAATAACAACTTTGGTCCCTACAGG
*
4041411 TGACCAACATGCAAAAACACGACT-AACT-TAGGGGGAC
1 TGACCAAAATGCAAAAACACG-CTAAACTATAGGGGGAC
4041448 CTATGCATGA
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
107 5 0.04
108 20 0.16
109 10 0.08
110 89 0.71
111 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19
Consensus pattern (110 bp):
TGACCAAAATGCAAAAACACGCTAAACTATAGGGGGACTAAACAACAAATATCCCAAAAAATACA
TAAAATACATAAAAACAGGTAAATAACAACTTTGGTCCCTACAGG
Found at i:4042192 original size:23 final size:23
Alignment explanation
Indices: 4042166--4042213 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4042156 TAGATTTCAA
*
4042166 TTTGGACCCGGGTTTGGGTTTGG
1 TTTGGACCCGGGTCTGGGTTTGG
*
4042189 TTTGGACTCGGGTCTGGGTTTGG
1 TTTGGACCCGGGTCTGGGTTTGG
4042212 TT
1 TT
4042214 AGGGCTCGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.04, C:0.12, G:0.42, T:0.42
Consensus pattern (23 bp):
TTTGGACCCGGGTCTGGGTTTGG
Found at i:4042221 original size:23 final size:23
Alignment explanation
Indices: 4042169--4042227 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
4042159 ATTTCAATTT
* * *
4042169 GGACCCGGGTTTGGGTTTGGTTT
1 GGACTCGGGTCTGGGTTTGGTTA
4042192 GGACTCGGGTCTGGGTTTGGTTA
1 GGACTCGGGTCTGGGTTTGGTTA
* *
4042215 GGGCTCGGCTCTG
1 GGACTCGGGTCTG
4042228 TAAATGGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.05, C:0.17, G:0.44, T:0.34
Consensus pattern (23 bp):
GGACTCGGGTCTGGGTTTGGTTA
Found at i:4042235 original size:29 final size:29
Alignment explanation
Indices: 4042203--4042268 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
4042193 GACTCGGGTC
*
4042203 TGGGTTTGGTTAGGG-CTCGGCTCTGTAAA
1 TGGGTTTGATTAGGGTC-CGGCTCTGTAAA
* * *
4042232 TGGGTTTGATTTGGGTCCGGTTTTGTAAA
1 TGGGTTTGATTAGGGTCCGGCTCTGTAAA
4042261 TGGGTTTG
1 TGGGTTTG
4042269 TAAATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.12, C:0.09, G:0.38, T:0.41
Consensus pattern (29 bp):
TGGGTTTGATTAGGGTCCGGCTCTGTAAA
Found at i:4042704 original size:132 final size:132
Alignment explanation
Indices: 4042552--4042989 Score: 499
Period size: 133 Copynumber: 3.3 Consensus size: 132
4042542 TCTGCAAGTG
*
4042552 TTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGTAGACTTATTCCA-TGCTACTCAG
1 TTGATTCATTCCACTATTCTTC-AGGAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAG
* * * *
4042616 GGAAGATCAAATATGGAAAAAGAGGATCTACTCCGCTGCTTCTTCAGTGTAGATCAGATCTAGAA
65 GGAAGATCAAATCTGGAAAAAGAGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAA
4042681 ACT
130 ACT
* * *
4042684 TTGATTCACTCCACTGTTCTTCAGGAAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAC
1 TTGATTCATTCCACTATTCTTCAGG-AAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAG
* * * * *
4042749 GGAAGATCAAATCTGGAAAAAGGGGATCTACTCCACTACTTTTTTAGGGTGGAAT-AGATCTGGA
65 GGAAGATCAAATCTGGAAAAAGAGGATCTACTCCGCTACTTCTTCAGGGTAG-ATCAGATCTGGA
4042813 AA-T
129 AACT
* * * * * * * *
4042816 GTTGATTCATTTCACTATTCTTCTGAAAAATTAAATCGAGGCA-AGCTTGTTCCACTACTTATTC
1 -TTGATTCATTCCACTATTCTTCAGGAAGATTGAATCGAGGTAGA-CTTGTTCCACTGC-TACTC
* * *
4042880 AGGGAATATCAAATCTGGAAAAAGAAAGGGGATCTGC-CCTGCTACTTCTTCAGGGTAAATCAGA
63 AGGGAAGATCAAATCTGGAAAAAG--A--GGATCTACTCC-GCTACTTCTTCAGGGTAGATCAGA
* *
4042944 TCCGGAAACA
123 TCTGGAAACT
4042954 TTGATTCATTCCACTATTCTTCATGGAAGATTGAAT
1 TTGATTCATTCCACTATTCTTCA-GGAAGATTGAAT
4042990 TGAGTTTATT
Statistics
Matches: 253, Mismatches: 39, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
131 4 0.02
132 74 0.29
133 109 0.43
134 2 0.01
136 4 0.02
137 51 0.20
138 9 0.04
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (132 bp):
TTGATTCATTCCACTATTCTTCAGGAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAGG
GAAGATCAAATCTGGAAAAAGAGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAAA
CT
Found at i:4042821 original size:133 final size:133
Alignment explanation
Indices: 4042493--4042989 Score: 489
Period size: 133 Copynumber: 3.7 Consensus size: 133
4042483 ATTTTTAAAT
* * * * * * *
4042493 ATCAAATCT-GAAAAA-GGG-TCTGCTCTACTTC-TCTTTAGGGTAGATTATATCTGCAAGTGTT
1 ATCAAATCTGGAAAAAGGGGATCTACTCCACTACTTCTTTAGGGTAGAATAGATCTGGAAATGTT
*
4042554 GATTCATTCCACTATTCTTCAAGG-AAGATTGAATCGAGGTAGACTTATTCCA-TGCTACTCAGG
66 GATTCATTCCACTATTCTTC-AGGAAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAGG
4042617 GAAG
130 GAAG
* * * * * * *
4042621 ATCAAATATGGAAAAAGAGGATCTACTCCGCTGCTTCTTCAGTGTAG-ATCAGATCTAGAAACT-
1 ATCAAATCTGGAAAAAGGGGATCTACTCCACTACTTCTTTAGGGTAGAAT-AGATCTGGAAA-TG
* * *
4042684 TTGATTCACTCCACTGTTCTTCAGGAAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAC
64 TTGATTCATTCCACTATTCTTCAGGAAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAG
4042749 GGAAG
129 GGAAG
* *
4042754 ATCAAATCTGGAAAAAGGGGATCTACTCCACTACTTTTTTAGGGTGGAATAGATCTGGAAATGTT
1 ATCAAATCTGGAAAAAGGGGATCTACTCCACTACTTCTTTAGGGTAGAATAGATCTGGAAATGTT
* * * * * * *
4042819 GATTCATTTCACTATTCTTC-TGAAAAATTAAATCGAGGCA-AGCTTGTTCCACTACTTATTCAG
66 GATTCATTCCACTATTCTTCAGGAAAGATTGAATCGAGGTAGA-CTTGTTCCACTGC-TACTCAG
*
4042882 GGAAT
129 GGAAG
* * * *
4042887 ATCAAATCTGGAAAAAGAAAGGGGATCTGC-CCTGCTACTTCTTCAGGGTA-AATCAGATCCGGA
1 ATCAAATCTGG---AA-AAAGGGGATCTACTCC-ACTACTTCTTTAGGGTAGAAT-AGATCTGGA
**
4042950 AACATTGATTCATTCCACTATTCTTCATGG-AAGATTGAAT
60 AATGTTGATTCATTCCACTATTCTTCA-GGAAAGATTGAAT
4042990 TGAGTTTATT
Statistics
Matches: 300, Mismatches: 49, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
128 8 0.03
129 6 0.02
130 2 0.01
131 14 0.05
132 93 0.31
133 103 0.34
134 2 0.01
136 7 0.02
137 56 0.19
138 8 0.03
139 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (133 bp):
ATCAAATCTGGAAAAAGGGGATCTACTCCACTACTTCTTTAGGGTAGAATAGATCTGGAAATGTT
GATTCATTCCACTATTCTTCAGGAAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAGGG
AAG
Found at i:4066970 original size:44 final size:45
Alignment explanation
Indices: 4066908--4067023 Score: 105
Period size: 43 Copynumber: 2.6 Consensus size: 45
4066898 GCTGAAAAAT
* * **
4066908 AAGGGACAT-AAATAAAATATCAGAAAATTAAAGCA-AATAAAATTT-
1 AAGGGA-ATAAAATTAAATA-CAGAAAAATAAAAAAGAAT-AAATTTA
*
4066953 AA-GGAATAAAATTAAATAAAGAAAAATAAAAAAGAATAAATTTA
1 AAGGGAATAAAATTAAATACAGAAAAATAAAAAAGAATAAATTTA
*
4066997 AAGGGGCATAAAATTAAATAACAGAAA
1 AA-GGGAATAAAATTAAAT-ACAGAAA
4067024 TAAAAAGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
43 19 0.33
44 17 0.29
45 2 0.03
46 14 0.24
47 6 0.10
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (45 bp):
AAGGGAATAAAATTAAATACAGAAAAATAAAAAAGAATAAATTTA
Found at i:4068875 original size:3 final size:3
Alignment explanation
Indices: 4068867--4068901 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4068857 AACTCTTACC
*
4068867 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4068902 CAAAATACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4072029 original size:31 final size:31
Alignment explanation
Indices: 4071991--4072055 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
4071981 TTTTGAAAAA
*
4071991 AACTACTCCCCCTTAGTCTAACACTTACTCT
1 AACTACTCCCCCTTACTCTAACACTTACTCT
4072022 AACTACTCCCCCTTACTCTAACACTTACTCT
1 AACTACTCCCCCTTACTCTAACACTTACTCT
4072053 AAC
1 AAC
4072056 ACTTTTCCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.40, G:0.02, T:0.31
Consensus pattern (31 bp):
AACTACTCCCCCTTACTCTAACACTTACTCT
Found at i:4072050 original size:12 final size:12
Alignment explanation
Indices: 4072033--4072059 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4072023 ACTACTCCCC
4072033 CTTACTCTAACA
1 CTTACTCTAACA
4072045 CTTACTCTAACA
1 CTTACTCTAACA
4072057 CTT
1 CTT
4072060 TTCCCCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (12 bp):
CTTACTCTAACA
Found at i:4074277 original size:21 final size:22
Alignment explanation
Indices: 4074252--4074305 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
4074242 CATGGAGGGT
4074252 ATCAGTTCCC-TC-AAGAGGGGA
1 ATCAGTTCCCATCAAAG-GGGGA
4074273 ATCAGTTCCCATTCAAAGGGGGA
1 ATCAGTTCCCA-TCAAAGGGGGA
*
4074296 ATCGGTTCCC
1 ATCAGTTCCC
4074306 CTGCAAGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 10 0.34
23 16 0.55
24 3 0.10
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (22 bp):
ATCAGTTCCCATCAAAGGGGGA
Found at i:4074316 original size:23 final size:22
Alignment explanation
Indices: 4074259--4074333 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
4074249 GGTATCAGTT
*
4074259 CCCT-CAAGAGGGGAATCAGTTC
1 CCCTGCAAG-GGGGAATCGGTTC
* *
4074281 CCATTCAAAGGGGGAATCGGTTC
1 CCCTGC-AAGGGGGAATCGGTTC
* *
4074304 CCCTGCAAGGGGGTATCGATTC
1 CCCTGCAAGGGGGAATCGGTTC
4074326 CTCCTGCA
1 C-CCTGCA
4074334 CTAAAATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.21
Consensus pattern (22 bp):
CCCTGCAAGGGGGAATCGGTTC
Found at i:4080491 original size:2 final size:2
Alignment explanation
Indices: 4080484--4080519 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4080474 ACTTTGTATG
4080484 AT AT AT AT 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 AT AT AT AT
4080520 CACATATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4085984 original size:17 final size:15
Alignment explanation
Indices: 4085949--4086014 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
4085939 TTTTTAATTA
4085949 AATTTAATTATTATT
1 AATTTAATTATTATT
*
4085964 AATTTAGATTACTTTTT
1 AATTTA-ATTA-TTATT
*
4085981 AATTTAA--A-TAAT
1 AATTTAATTATTATT
4085993 AATTTAATTATTATT
1 AATTTAATTATTATT
*
4086008 TATTTAA
1 AATTTAA
4086015 AATTCTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 9 0.22
14 2 0.05
15 15 0.37
16 5 0.12
17 10 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTAATTATTATT
Found at i:4086023 original size:44 final size:43
Alignment explanation
Indices: 4085949--4086041 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
4085939 TTTTTAATTA
* **
4085949 AATTTAATTATTATTAATTTAGATTACTTTTTAATTTAAATAAT
1 AATTTAATTATTATTAATTTAAATTAC-TTTTAAAATAAATAAT
* *
4085993 AATTTAATTATTATTTATTTAAAATT-CTTTTAAAATAAATAGT
1 AATTTAATTATTATTAATTT-AAATTACTTTTAAAATAAATAAT
4086036 AATTTA
1 AATTTA
4086042 GACAAATCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 19 0.44
44 20 0.47
45 4 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (43 bp):
AATTTAATTATTATTAATTTAAATTACTTTTAAAATAAATAAT
Found at i:4087563 original size:29 final size:28
Alignment explanation
Indices: 4087500--4087563 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
4087490 CCATATTAAT
** *
4087500 AAAAAAAATTATGCAAATAAAAATTTGA
1 AAAAAAAATTATAAAAATAAAAATATGA
4087528 AACAAAAAATTATAAAAATTATAAAA-ATGA
1 AA-AAAAAATTATAAAAA-TA-AAAATATGA
4087558 AAAAAA
1 AAAAAA
4087564 TAGAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 2 0.07
29 17 0.57
30 7 0.23
31 4 0.13
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (28 bp):
AAAAAAAATTATAAAAATAAAAATATGA
Found at i:4092498 original size:29 final size:29
Alignment explanation
Indices: 4092456--4092514 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
4092446 ATTTTCACCT
4092456 AACTAAATTGATGTAACCAATGACATCAA
1 AACTAAATTGATGTAACCAATGACATCAA
* *
4092485 AACTAAATTGATGTAAGCAATGCCATCAA
1 AACTAAATTGATGTAACCAATGACATCAA
4092514 A
1 A
4092515 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAACCAATGACATCAA
Found at i:4097185 original size:29 final size:29
Alignment explanation
Indices: 4097143--4097201 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
4097133 ATTTTCGCCT
4097143 AACTAAATTGATGTAACCAATGACACCAA
1 AACTAAATTGATGTAACCAATGACACCAA
* *
4097172 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAACCAATGACACCAA
4097201 A
1 A
4097202 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (29 bp):
AACTAAATTGATGTAACCAATGACACCAA
Found at i:4112271 original size:18 final size:19
Alignment explanation
Indices: 4112250--4112285 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4112240 AAAATTGCCT
*
4112250 TTTATTTAATC-TATTTTC
1 TTTACTTAATCGTATTTTC
4112268 TTTACTTAATCGTATTTT
1 TTTACTTAATCGTATTTT
4112286 ACCAAACCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTACTTAATCGTATTTTC
Found at i:4117649 original size:22 final size:21
Alignment explanation
Indices: 4117621--4117669 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4117611 GGGATTTTGG
*
4117621 TAAAAATATATTTAAA-TAATAA
1 TAAAAAT-GATTTAAAGTAA-AA
4117643 TAAAAATGATTTAAAGTAAAA
1 TAAAAATGATTTAAAGTAAAA
4117664 TAAAAA
1 TAAAAA
4117670 AAAGATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAAAATGATTTAAAGTAAAA
Found at i:4117654 original size:21 final size:22
Alignment explanation
Indices: 4117621--4117683 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
4117611 GGGATTTTGG
*
4117621 TAAAAATATATTTAAA-TAATAA
1 TAAAAATAGATTTAAAGTAA-AA
4117643 TAAAAAT-GATTTAAAGTAAAA
1 TAAAAATAGATTTAAAGTAAAA
*
4117664 TAAAAAAAAGATTTTAAAGT
1 T-AAAAATAGA-TTTAAAGT
4117684 TGAAATTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 10 0.29
22 15 0.43
23 2 0.06
24 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (22 bp):
TAAAAATAGATTTAAAGTAAAA
Found at i:4117670 original size:23 final size:25
Alignment explanation
Indices: 4117638--4117683 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
4117628 ATATTTAAAT
*
4117638 AATAATAAAAATGA-TTTAAAGTAA
1 AATAATAAAAAAGATTTTAAAGTAA
4117662 AATAA-AAAAAAGATTTTAAAGT
1 AATAATAAAAAAGATTTTAAAGT
4117684 TGAAATTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (25 bp):
AATAATAAAAAAGATTTTAAAGTAA
Found at i:4122115 original size:24 final size:23
Alignment explanation
Indices: 4122087--4122246 Score: 133
Period size: 23 Copynumber: 6.7 Consensus size: 23
4122077 AAAATTTCAA
*
4122087 GAGCTCGATTGAAACTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-ACTC
*
4122111 GAGCTCGATTGAAACTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-ACTC
* *
4122135 GAGCTCAAGACTCG-AGCTCAAGACTC
1 GAGCTC--GA-TTGAAGCTCGA-ACTC
* ** *
4122161 AAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTC
** *
4122184 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTC
** *
4122207 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTC
4122230 GAGCTCGATTGAAGCTC
1 GAGCTCGATTGAAGCTC
4122247 AATTTTGAGC
Statistics
Matches: 122, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
23 65 0.53
24 38 0.31
26 17 0.14
27 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGAACTC
Found at i:4122147 original size:13 final size:13
Alignment explanation
Indices: 4122129--4122166 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4122119 TTGAAACTCG
4122129 AGACTCGAGCTCA
1 AGACTCGAGCTCA
4122142 AGACTCGAGCTCA
1 AGACTCGAGCTCA
*
4122155 AGACTCAAGCTC
1 AGACTCGAGCTC
4122167 GATTGAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (13 bp):
AGACTCGAGCTCA
Found at i:4122177 original size:11 final size:11
Alignment explanation
Indices: 4122161--4122246 Score: 97
Period size: 11 Copynumber: 7.5 Consensus size: 11
4122151 CTCAAGACTC
4122161 AAGCTCGATTG
1 AAGCTCGATTG
4122172 AAGCTCGATTTTG
1 AAGCTCGA--TTG
4122185 -AGCTCGATTG
1 AAGCTCGATTG
4122195 AAGCTCGATTTTG
1 AAGCTCGA--TTG
4122208 -AGCTCGATTG
1 AAGCTCGATTG
4122218 AAGCTCGATTTTG
1 AAGCTCGA--TTG
4122231 -AGCTCGATTG
1 AAGCTCGATTG
4122241 AAGCTC
1 AAGCTC
4122247 AATTTTGAGC
Statistics
Matches: 66, Mismatches: 0, Indels: 18
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.14
11 27 0.41
12 21 0.32
13 9 0.14
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (11 bp):
AAGCTCGATTG
Found at i:4122189 original size:23 final size:23
Alignment explanation
Indices: 4122162--4122271 Score: 193
Period size: 23 Copynumber: 4.8 Consensus size: 23
4122152 TCAAGACTCA
4122162 AGCTCGATTGAAGCTCGATTTTG
1 AGCTCGATTGAAGCTCGATTTTG
4122185 AGCTCGATTGAAGCTCGATTTTG
1 AGCTCGATTGAAGCTCGATTTTG
4122208 AGCTCGATTGAAGCTCGATTTTG
1 AGCTCGATTGAAGCTCGATTTTG
*
4122231 AGCTCGATTGAAGCTCAATTTTG
1 AGCTCGATTGAAGCTCGATTTTG
* *
4122254 AGCTTGATTCAAGCTCGA
1 AGCTCGATTGAAGCTCGA
4122272 CGGGTTTTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (23 bp):
AGCTCGATTGAAGCTCGATTTTG
Found at i:4122190 original size:12 final size:12
Alignment explanation
Indices: 4122173--4122262 Score: 93
Period size: 12 Copynumber: 7.8 Consensus size: 12
4122163 GCTCGATTGA
4122173 AGCTCGATTTTG
1 AGCTCGATTTTG
4122185 AGCTCGA--TTG
1 AGCTCGATTTTG
4122195 AAGCTCGATTTTG
1 -AGCTCGATTTTG
4122208 AGCTCGA--TTG
1 AGCTCGATTTTG
4122218 AAGCTCGATTTTG
1 -AGCTCGATTTTG
4122231 AGCTCGA--TTG
1 AGCTCGATTTTG
*
4122241 AAGCTCAATTTTG
1 -AGCTCGATTTTG
*
4122254 AGCTTGATT
1 AGCTCGATT
4122263 CAAGCTCGAC
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
10 9 0.14
11 20 0.30
12 28 0.42
13 9 0.14
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:4124608 original size:11 final size:11
Alignment explanation
Indices: 4124592--4124654 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
4124582 GTATTGTAGA
4124592 ATTTTTAATAT
1 ATTTTTAATAT
4124603 ATTTTTTAA-AT
1 A-TTTTTAATAT
*
4124614 -TTTATAAT-T
1 ATTTTTAATAT
*** *
4124623 ATCAATAATGT
1 ATTTTTAATAT
4124634 ATTTTTAATAT
1 ATTTTTAATAT
4124645 ATTTTTAATA
1 ATTTTTAATA
4124655 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 7 0.17
10 6 0.15
11 21 0.51
12 7 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:4129108 original size:25 final size:25
Alignment explanation
Indices: 4129080--4129131 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4129070 CGGAGTAGTT
4129080 ATATGCGAGGAACTAATGTATGTAA
1 ATATGCGAGGAACTAATGTATGTAA
4129105 ATATGCGAGGAACTAATGTATGTAA
1 ATATGCGAGGAACTAATGTATGTAA
4129130 AT
1 AT
4129132 GACAACTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (25 bp):
ATATGCGAGGAACTAATGTATGTAA
Found at i:4133332 original size:25 final size:24
Alignment explanation
Indices: 4133304--4133358 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
4133294 TGTAAAATAA
4133304 ATATATAATACATAAAACATAAAAC
1 ATATATAAT-CATAAAACATAAAAC
* ** *
4133329 ATATTTAATGGTACAACATAAAAC
1 ATATATAATCATAAAACATAAAAC
4133353 A-ATATA
1 ATATATA
4133359 CATGTGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 4 0.16
24 13 0.52
25 8 0.32
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (24 bp):
ATATATAATCATAAAACATAAAAC
Found at i:4133839 original size:39 final size:40
Alignment explanation
Indices: 4133796--4133894 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
4133786 AGGTTGAACA
* *
4133796 AGTTCTTCTCATTATGAACTTTTTCTCCC-CCATTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCCATCGGATG
*
4133835 AGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCCATCGGATG
*
4133875 AGTTATTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
4133895 CTCCATTTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
39 28 0.51
40 27 0.49
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.43
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCCTCCATCGGATG
Found at i:4134586 original size:51 final size:53
Alignment explanation
Indices: 4134531--4134634 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 53
4134521 ATTTATAGTT
* * *
4134531 ATCAAGTAACCCCT-AAAATTAGGCTTAGCTTCT-AAAAGTTCATTTAAAAAC
1 ATCAAGAAACCCCTAAAAATTAGACTTAGCTTCTAAAAAGCTCATTTAAAAAC
*
4134582 ATCAAGAAACCCCTAAAAATTAGACTTAGTTTCTAAAAAAGCTCATTTAAAAA
1 ATCAAGAAACCCCTAAAAATTAGACTTAGCTTCT-AAAAAGCTCATTTAAAAA
4134635 ATAATCAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 13 0.28
52 17 0.37
54 16 0.35
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (53 bp):
ATCAAGAAACCCCTAAAAATTAGACTTAGCTTCTAAAAAGCTCATTTAAAAAC
Found at i:4134794 original size:55 final size:55
Alignment explanation
Indices: 4134705--4134977 Score: 260
Period size: 55 Copynumber: 4.8 Consensus size: 55
4134695 TAAAATACTT
* * * *
4134705 ATTTGAAAATCATCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAGCTC
1 ATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTC
* * *
4134760 ATTTAAAAATCATCAGGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGTTC
1 ATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTC
* * * * *
4134815 ATTTAAAAAATAATTAAGAAACTTCTGAAAATCAAACTTAATTTTTTTATAAAAAAAAAACTC
1 ATTT-AAAAATAATCAAGAAACTTCTGAAAATCAGACTT-AGTTTCTT-T-----AAAAGCTC
* ** * * * *
4134878 ATTTGAAAATTGTCAAGAAACTTCTGAAAATCAAATTTAGTTTATTTGAAAGCTC
1 ATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTC
* * *
4134933 ATTTAAAAATAACCAA-AGAACCTCTGAAAATTAGACTTAGTTTCT
1 ATTTAAAAATAATCAAGA-AACTTCTGAAAATCAGACTTAGTTTCT
4134978 AAAAAAACAC
Statistics
Matches: 178, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
54 1 0.01
55 94 0.53
56 30 0.17
57 6 0.03
58 1 0.01
60 1 0.01
61 6 0.03
62 29 0.16
63 10 0.06
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (55 bp):
ATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTC
Found at i:4136836 original size:11 final size:10
Alignment explanation
Indices: 4136819--4136947 Score: 64
Period size: 9 Copynumber: 13.4 Consensus size: 10
4136809 ATTTGATCGG
4136819 TTTTCTTTCT
1 TTTTCTTTCT
4136829 TATTTCTTCTCT
1 T-TTTCTT-TCT
4136841 TTTTCTTT-T
1 TTTTCTTTCT
* *
4136850 GTCTCTCTT-T
1 TTTTCT-TTCT
4136860 TTTTC-TTCTT
1 TTTTCTTTC-T
4136870 TTTTCTTTC-
1 TTTTCTTTCT
*
4136879 TTTT-TTCCT
1 TTTTCTTTCT
* *
4136888 TTTTTTTTGT
1 TTTTCTTTCT
* *
4136898 TTTT-TCTCC
1 TTTTCTTTCT
4136907 TTTT-TTTC-
1 TTTTCTTTCT
4136915 -TTTCTTTC-
1 TTTTCTTTCT
4136923 TTTTCTATAT-T
1 TTTTCT-T-TCT
4136934 TTTTCTTTCT
1 TTTTCTTTCT
4136944 TTTT
1 TTTT
4136948 TTGGCTATAT
Statistics
Matches: 94, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
7 3 0.03
8 9 0.10
9 28 0.30
10 28 0.30
11 22 0.23
12 4 0.04
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:4136874 original size:51 final size:52
Alignment explanation
Indices: 4136819--4136947 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 52
4136809 ATTTGATCGG
*
4136819 TTTTCTTTCTTATTTCTTCTCTTTTTCTTTTGTCTCTCTTTTTTTC-TTC-TT-
1 TTTTCTTTCTTTTTTCTT-TCTTTTTCTTTTGTCTC-CTTTTTTTCTTTCTTTC
* * *
4136870 TTTTCTTTCTTTTTTCCTTTTTTTTTGTTTTTTCTCCTTTTTTTCTTTCTTTC
1 TTTTCTTTCTTTTTT-CTTTCTTTTTCTTTTGTCTCCTTTTTTTCTTTCTTTC
* *
4136923 TTTTCTATATTTTTTCTTTCTTTTT
1 TTTTCTTTCTTTTTTCTTTCTTTTT
4136948 TTGGCTATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
50 9 0.13
51 31 0.46
52 14 0.21
53 13 0.19
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (52 bp):
TTTTCTTTCTTTTTTCTTTCTTTTTCTTTTGTCTCCTTTTTTTCTTTCTTTC
Found at i:4136948 original size:11 final size:11
Alignment explanation
Indices: 4136820--4136948 Score: 83
Period size: 11 Copynumber: 11.9 Consensus size: 11
4136810 TTTGATCGGT
* *
4136820 TTTCTTTCTTA
1 TTTCTTTTTTC
*
4136831 TTTCTTCTCTT-
1 TTTCTT-TTTTC
*
4136842 TTTCTTTTGTC
1 TTTCTTTTTTC
*
4136853 TCTCTTTTTT-
1 TTTCTTTTTTC
4136863 TCTTCTTTTTTC
1 T-TTCTTTTTTC
4136875 TTTCTTTTTTC
1 TTTCTTTTTTC
4136886 ---CTTTTTT-
1 TTTCTTTTTTC
*
4136893 TTTGTTTTTTC
1 TTTCTTTTTTC
*
4136904 -TCCTTTTTTTC
1 TTTC-TTTTTTC
4136915 TTTCTTTCTTTTC
1 TTTC-TT-TTTTC
* *
4136928 TATATTTTTTC
1 TTTCTTTTTTC
4136939 TTTCTTTTTT
1 TTTCTTTTTT
4136949 TGGCTATATC
Statistics
Matches: 94, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
8 7 0.07
10 10 0.11
11 58 0.62
12 12 0.13
13 7 0.07
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:4136955 original size:25 final size:24
Alignment explanation
Indices: 4136908--4136971 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
4136898 TTTTTCTCCT
4136908 TTTTTTCTTTCTTTCTTTTCTATA
1 TTTTTTCTTTCTTTCTTTTCTATA
4136932 TTTTTTCTTTCTTT-TTTTGGCTATA
1 TTTTTTCTTTCTTTCTTTT--CTATA
*
4136957 TCTTTTC-TTCTTTCT
1 TTTTTTCTTTCTTTCT
4136972 CTCTGTGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 4 0.11
24 20 0.56
25 12 0.33
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTTTTCTTTCTTTCTTTTCTATA
Found at i:4141375 original size:16 final size:17
Alignment explanation
Indices: 4141332--4141377 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
4141322 TTTTTTAAAA
*
4141332 TTCAAAAATATATTTAAT
1 TTCAAAATTATA-TTAAT
*
4141350 TT-ATAATTATATT-AT
1 TTCAAAATTATATTAAT
4141365 TTCAAAATTATAT
1 TTCAAAATTATAT
4141378 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 11 0.46
17 7 0.29
18 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCAAAATTATATTAAT
Found at i:4143058 original size:3 final size:3
Alignment explanation
Indices: 4143050--4143153 Score: 127
Period size: 3 Copynumber: 34.0 Consensus size: 3
4143040 TTATTTATTA
* *
4143050 AAT AAT AAT AAT ATAT AAT AAT AAT AAAT AAT AAT AAT TAT TAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* * * **
4143097 AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT AAT AAT AAT AAT TTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4143145 AAT AAT AAT
1 AAT AAT AAT
4143154 TTTAAATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
3 81 0.93
4 6 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:4143097 original size:15 final size:15
Alignment explanation
Indices: 4143044--4143162 Score: 81
Period size: 15 Copynumber: 7.8 Consensus size: 15
4143034 TTGTAATTAT
4143044 TTATTA-AATAATAA
1 TTATTATAATAATAA
*
4143058 TAATATATAATAATAA
1 TTAT-TATAATAATAA
*
4143074 -TA-AATAATAATAA
1 TTATTATAATAATAA
4143087 TTATTATAATAATAA
1 TTATTATAATAATAA
4143102 TAATACTAATACTAATAATAA
1 T--TA-T--TA-TAATAATAA
*
4143123 -TACTAATAATAATAA
1 TTA-TTATAATAATAA
4143138 TT-TTAATAATAATAA
1 TTATT-ATAATAATAA
4143153 TT-TTA-AATAA
1 TTATTATAATAA
4143163 AAAAATTGAT
Statistics
Matches: 87, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
13 15 0.17
14 7 0.08
15 37 0.43
16 10 0.11
17 2 0.02
18 5 0.06
20 2 0.02
21 9 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
TTATTATAATAATAA
Found at i:4143169 original size:15 final size:15
Alignment explanation
Indices: 4143126--4143169 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4143116 ATAATAATAC
*
4143126 TAATAATAATAATTT
1 TAATAATAAAAATTT
*
4143141 TAATAATAATAATTT
1 TAATAATAAAAATTT
4143156 TAAATAA-AAAAATT
1 T-AATAATAAAAATT
4143170 GATGTCTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAAAAATTT
Found at i:4143530 original size:76 final size:76
Alignment explanation
Indices: 4143284--4144840 Score: 2835
Period size: 76 Copynumber: 20.4 Consensus size: 76
4143274 GAAATGTTGA
4143284 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143349 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
4143360 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
*
4143425 AATGCTTTTTGG
65 AAGGCTTTTTGG
*
4143437 AAACATCATGCACTGAAGGACTTACAGATGACCCGAATGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143502 AGGCTTTTTGG
66 AGGCTTTTTGG
4143513 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143578 AGGCTTTTTGG
66 AGGCTTTTTGG
4143589 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143654 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
4143665 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4143730 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
4143742 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143807 AGGCTTTTTGG
66 AGGCTTTTTGG
4143818 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143883 AGGCTTTTTGG
66 AGGCTTTTTGG
4143894 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4143959 AGGCTTTTTGG
66 AGGCTTTTTGG
4143970 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144035 AGGCTTTTTGG
66 AGGCTTTTTGG
4144046 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144111 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4144122 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144187 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
4144198 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144263 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
4144275 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144340 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4144351 AAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144416 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
4144427 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144492 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
4144504 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144569 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4144580 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4144645 AGGCTTTTTTGG
66 AGGC-TTTTTGG
* * *
4144657 AAACATCATACACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144722 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
4144734 AAACATCATGTACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144799 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
4144811 AAACATCATGCATTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
4144841 GGGGAAATAG
Statistics
Matches: 1442, Mismatches: 33, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
76 963 0.67
77 452 0.31
78 27 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:4143717 original size:229 final size:228
Alignment explanation
Indices: 4143284--4144840 Score: 2853
Period size: 229 Copynumber: 6.8 Consensus size: 228
4143274 GAAATGTTGA
*
4143284 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4143349 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCA
* *
4143414 AAAAGCTCCCGAATGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAATGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
4143479 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
4143513 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4143578 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
4143643 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TT
*
4143708 TGTAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
4143742 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4143807 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
4143872 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
4143937 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
4143970 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4144035 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
4144100 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
4144165 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
4144198 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144263 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
*
4144328 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
4144393 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
4144427 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144492 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
*
4144557 AAAATCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
*
4144622 TGAAAACATCAAAAAGTTCCCGAAGGCTTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGG
* *
4144657 AAACATCATACACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCG
* *
4144722 AAGGCTTTTTGGAAACATCATGTACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATC
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATC
*
4144787 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGAAGGACTTACAGATG
129 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
4144841 GGGGAAATAG
Statistics
Matches: 1300, Mismatches: 24, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
228 372 0.29
229 743 0.57
230 122 0.09
231 63 0.05
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (228 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:4143835 original size:305 final size:304
Alignment explanation
Indices: 4143284--4144840 Score: 2853
Period size: 305 Copynumber: 5.1 Consensus size: 304
4143274 GAAATGTTGA
4143284 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4143349 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCA
* *
4143414 AAAAGCTCCCGAATGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAATGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
4143479 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
*
4143544 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
260 CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
4143589 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4143654 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCA
*
4143719 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
4143784 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
*
4143849 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
260 CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
4143894 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4143959 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
4144024 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
4144089 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
4144154 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
261 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* *
4144198 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
4144263 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
*
4144328 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
4144393 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
*
4144458 CCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
260 CCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* *
4144504 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4144569 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
* * *
4144634 AAAGTTCCCGAAGGCTTTTTTGGAAACATCATACACTGAAGGACTTACAGATGACCCTAAGGCTT
131 AAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-T
* *
4144699 TTGTAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGTACTGAAGGACTTACAGATG
194 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
*
4144764 ACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
259 ACCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
4144811 AAACATCATGCATTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
4144841 GGGGAAATAG
Statistics
Matches: 1226, Mismatches: 22, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
304 224 0.18
305 743 0.61
306 119 0.10
307 140 0.11
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (304 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:4146030 original size:54 final size:54
Alignment explanation
Indices: 4145885--4146097 Score: 293
Period size: 54 Copynumber: 3.9 Consensus size: 54
4145875 ATAATCACTG
* * * *
4145885 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGCTT-GGATT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTG-TTCAGA-T
* * *
4145940 ATTGGTCAAGTAGCATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTTCAGAT
1 GTTCGT-AA--AACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTTCAGAT
*
4145997 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTTCAGAT
*
4146051 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTG
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTG
4146098 CCAAGATTTC
Statistics
Matches: 141, Mismatches: 13, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
54 89 0.63
55 4 0.03
56 4 0.03
57 7 0.05
58 37 0.26
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTTCAGAT
Found at i:4155048 original size:9 final size:9
Alignment explanation
Indices: 4155028--4155070 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
4155018 AATACTTGAA
4155028 AATAAA-AT
1 AATAAATAT
4155036 AATAAATAT
1 AATAAATAT
4155045 AATAAATAT
1 AATAAATAT
*
4155054 TATGAAA-AT
1 AAT-AAATAT
4155063 AATAAATA
1 AATAAATA
4155071 ATAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 9 0.30
9 18 0.60
10 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AATAAATAT
Found at i:4155087 original size:18 final size:17
Alignment explanation
Indices: 4155065--4155107 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4155055 ATGAAAATAA
4155065 TAAATAATAA-AAAAAAT
1 TAAATAA-AAGAAAAAAT
4155082 TGAAATAAAAGAAAAAAT
1 T-AAATAAAAGAAAAAAT
4155100 TAAATAAA
1 TAAATAAA
4155108 TGATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAATAAAAGAAAAAAT
Found at i:4155823 original size:18 final size:18
Alignment explanation
Indices: 4155791--4155825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4155781 TTTGAAATAA
* *
4155791 ATATTTATTATTATATAT
1 ATATTTATGACTATATAT
4155809 ATATTTATGACTATATA
1 ATATTTATGACTATATA
4155826 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
ATATTTATGACTATATAT
Found at i:4157137 original size:3 final size:3
Alignment explanation
Indices: 4157129--4157232 Score: 118
Period size: 3 Copynumber: 34.0 Consensus size: 3
4157119 TTATTTATTA
* * *
4157129 AAT AAT AAT AAT ATAT AAT AAT AAT AAAT AAT AAT TAT TAT TAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* * * **
4157176 AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT AAT AAT AAT AAT TTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4157224 AAT AAT AAT
1 AAT AAT AAT
4157233 TTTAAATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
3 81 0.93
4 6 0.07
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:4157248 original size:15 final size:15
Alignment explanation
Indices: 4157205--4157248 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4157195 ATAATAATAC
*
4157205 TAATAATAATAATTT
1 TAATAATAAAAATTT
*
4157220 TAATAATAATAATTT
1 TAATAATAAAAATTT
4157235 TAAATAA-AAAAATT
1 T-AATAATAAAAATT
4157249 GATGTCTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAAAAATTT
Found at i:4179785 original size:24 final size:24
Alignment explanation
Indices: 4179758--4179809 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4179748 CGTTCATTTA
*
4179758 CGTTT-GTGAACGTTCGGTTATGTT
1 CGTTTGGT-AACGTTCGCTTATGTT
* *
4179782 CGTTTGGTTATGTTCGCTTATGTT
1 CGTTTGGTAACGTTCGCTTATGTT
4179806 CGTT
1 CGTT
4179810 CGATTATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.50
Consensus pattern (24 bp):
CGTTTGGTAACGTTCGCTTATGTT
Found at i:4179790 original size:14 final size:14
Alignment explanation
Indices: 4179768--4179823 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
4179758 CGTTTGTGAA
4179768 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
4179782 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
4179796 CG--C--TTATGTT
1 CGTTCGGTTATGTT
*
4179806 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
4179820 CGTT
1 CGTT
4179824 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:4179816 original size:24 final size:24
Alignment explanation
Indices: 4179769--4179843 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
4179759 GTTTGTGAAC
* * *
4179769 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGCTTATGTTCGTTCGATTAT
4179793 GTTCGCTTATGTTCGTTCGATTAT
1 GTTCGCTTATGTTCGTTCGATTAT
* *
4179817 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGCTTATGTTCGTTCGA-TTAT
4179841 GTT
1 GTT
4179844 TAACACAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 44 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTCGCTTATGTTCGTTCGATTAT
Found at i:4180590 original size:16 final size:16
Alignment explanation
Indices: 4180569--4180635 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
4180559 GTCTCCAACG
4180569 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
4180585 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
4180601 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
4180617 TTTATATTCGT-TT-A
1 TTTATGTTCGTGTTCA
4180631 TTTAT
1 TTTAT
4180636 TAAATGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:4180608 original size:32 final size:32
Alignment explanation
Indices: 4180567--4180627 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
4180557 GGGTCTCCAA
*
4180567 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATATTCGTGTT
*
4180599 CGTTTATGTTCGTGTTCGTTTATATTCGT
1 CGTTTATGTTCGTGTTCATTTATATTCGT
4180628 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATATTCGTGTT
Found at i:4180718 original size:16 final size:16
Alignment explanation
Indices: 4180697--4180729 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4180687 AAAAAAAATT
4180697 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4180713 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4180729 T
1 T
4180730 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4181980 original size:22 final size:22
Alignment explanation
Indices: 4181955--4182041 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
4181945 CACGCTCTCC
4181955 ACATGAGCTACGCTCCATGTGT
1 ACATGAGCTACGCTCCATGTGT
4181977 ACATGAGCTACGCTCCATGTGT
1 ACATGAGCTACGCTCCATGTGT
4181999 ACATGAGCTACGCTCCATGTGT
1 ACATGAGCTACGCTCCATGTGT
4182021 ACATGAGCTACGCTCCATGTG
1 ACATGAGCTACGCTCCATGTG
4182042 GCTTTTTCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (22 bp):
ACATGAGCTACGCTCCATGTGT
Found at i:4184269 original size:2 final size:2
Alignment explanation
Indices: 4184262--4184297 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4184252 ACTAAAAATA
4184262 AT AT AT AT 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 AT AT AT AT
4184298 CCTTTTGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4198418 original size:11 final size:11
Alignment explanation
Indices: 4198404--4198433 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4198394 TAATATTGGG
4198404 GTAACGTAATT
1 GTAACGTAATT
*
4198415 GTAACGTCATT
1 GTAACGTAATT
4198426 GTAACGTA
1 GTAACGTA
4198434 TTTTACCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (11 bp):
GTAACGTAATT
Found at i:4201628 original size:30 final size:28
Alignment explanation
Indices: 4201592--4201675 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 28
4201582 AGAGAGGGTG
4201592 AAGCTTAGAAAAGCTTAGGAATATGAGGAA
1 AAGCTTAGAAAAGCTTAGGAATATGA-G-A
* *
4201622 AAGCTTAGAAAAGCTAGAGAGAATTTGAGA
1 AAGCTTAGAAAAGCT-TAG-GAATATGAGA
* *
4201652 GAGCTTAGCAAAGCTTA-GAATATG
1 AAGCTTAGAAAAGCTTAGGAATATG
4201676 GTGATTGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 6 0.13
29 1 0.02
30 29 0.63
31 3 0.07
32 7 0.15
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.21
Consensus pattern (28 bp):
AAGCTTAGAAAAGCTTAGGAATATGAGA
Found at i:4203469 original size:21 final size:20
Alignment explanation
Indices: 4203443--4203509 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
4203433 AACAGACGGA
4203443 AAAAATATTGGTCGAGGCAAG
1 AAAAAT-TTGGTCGAGGCAAG
4203464 AAAAATTGTGAAGT-G-GGC-AG
1 AAAAATT-TG--GTCGAGGCAAG
* *
4203484 AAAAGTTTTGTCGAGGCAAG
1 AAAAATTTGGTCGAGGCAAG
4203504 AAAAAT
1 AAAAAT
4203510 ATGCAAAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
17 2 0.05
18 1 0.03
19 4 0.11
20 16 0.43
21 11 0.30
22 1 0.03
23 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.28, T:0.21
Consensus pattern (20 bp):
AAAAATTTGGTCGAGGCAAG
Found at i:4213591 original size:284 final size:284
Alignment explanation
Indices: 4213074--4213647 Score: 1015
Period size: 284 Copynumber: 2.0 Consensus size: 284
4213064 AAATAAGATG
* **
4213074 TTAAATGACATATTTGACCTTATTATTTTCATAATTACAACCTTGCCATAAAACCTAATATAATG
1 TTAAATAACATATTTGACCTTATTATTCCCATAATTACAACCTTGCCATAAAACCTAATATAATG
*
4213139 AAATAGCCTCCATTTTATTTTCAATGAAGTTGTGTAAAATGAATTTTATGCAACGTCTAATGATG
66 AAATAGCCTCCATTTTATTTTCAATGAAGTTGTGTAAAATGAATTTTATGCAACGTCTAATAATG
4213204 AATTAGTGAAATTTTATTTTATTATTCTATTTTTTTAGTTGTAGATTCTCAAATATATTTTAGTT
131 AATTAGTGAAATTTTATTTTATTATTCTATTTTTTTAGTTGTAGATTCTCAAATATATTTTAGTT
4213269 AAGAAAATATAGCAAAACATGAAAGTAAAAAAATATTTATACAAGGTTAATAGTATGCATCAATC
196 AAGAAAATATAGCAAAACATGAAAGTAAAAAAATATTTATACAAGGTTAATAGTATGCATCAATC
* *
4213334 TCACAATGTTAATATTTGTATATA
261 TCACAAGGTTAATATTTGTAAATA
* *
4213358 TTAAATAACATATTTGACCTTATTATTCCCATAATTACAACCTTGTCATAAAACCTAATCTAATG
1 TTAAATAACATATTTGACCTTATTATTCCCATAATTACAACCTTGCCATAAAACCTAATATAATG
* *
4213423 AAATAGTCTCCATTTTATTTTCATTGAAGTTGTGTAAAATGAATTTTATGCAACGTCTAATAATG
66 AAATAGCCTCCATTTTATTTTCAATGAAGTTGTGTAAAATGAATTTTATGCAACGTCTAATAATG
4213488 AATTAGTGAAATTTTATTTTATTATTCTA-TTTTTTAGTTGTAGATTCTCAAATATATTTTAGTT
131 AATTAGTGAAATTTTATTTTATTATTCTATTTTTTTAGTTGTAGATTCTCAAATATATTTTAGTT
* * *
4213552 AAGAAAATATAGCAAAATATGAATGTAAAAAAAATATTTATACAGGGTTAATAGTATGCATCAAT
196 AAGAAAATATAGCAAAACATGAAAGT-AAAAAAATATTTATACAAGGTTAATAGTATGCATCAAT
4213617 CTCACAAGGTTAATATTTGTAAATA
260 CTCACAAGGTTAATATTTGTAAATA
4213642 TTAAAT
1 TTAAAT
4213648 TTAAAAAAAT
Statistics
Matches: 276, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
283 59 0.21
284 217 0.79
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (284 bp):
TTAAATAACATATTTGACCTTATTATTCCCATAATTACAACCTTGCCATAAAACCTAATATAATG
AAATAGCCTCCATTTTATTTTCAATGAAGTTGTGTAAAATGAATTTTATGCAACGTCTAATAATG
AATTAGTGAAATTTTATTTTATTATTCTATTTTTTTAGTTGTAGATTCTCAAATATATTTTAGTT
AAGAAAATATAGCAAAACATGAAAGTAAAAAAATATTTATACAAGGTTAATAGTATGCATCAATC
TCACAAGGTTAATATTTGTAAATA
Found at i:4215102 original size:15 final size:15
Alignment explanation
Indices: 4215082--4215113 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4215072 AGAGACACTT
4215082 CTTGCGACGCTCTTA
1 CTTGCGACGCTCTTA
4215097 CTTGCGACGCTCTTA
1 CTTGCGACGCTCTTA
4215112 CT
1 CT
4215114 AGCGTCGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.34, G:0.19, T:0.34
Consensus pattern (15 bp):
CTTGCGACGCTCTTA
Found at i:4215808 original size:18 final size:18
Alignment explanation
Indices: 4215785--4215821 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4215775 ATTTCATTAC
4215785 ATAGTTATATTAAATATT
1 ATAGTTATATTAAATATT
4215803 ATAGTTATATTAAATATT
1 ATAGTTATATTAAATATT
4215821 A
1 A
4215822 ATTTAACATA
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:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATAGTTATATTAAATATT
Found at i:4242151 original size:3 final size:3
Alignment explanation
Indices: 4242143--4242174 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4242133 ACAGTAGGAA
4242143 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
4242175 AGCAAATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4248033 original size:21 final size:22
Alignment explanation
Indices: 4248000--4248040 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
4247990 TTAAAAATAA
4248000 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTATCGATACTCAT
4248022 TAAAGG-AGTATCGATACTC
1 TAAAGGAAGTATCGATACTC
4248041 CATGTACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTATCGATACTCAT
Found at i:4248717 original size:19 final size:20
Alignment explanation
Indices: 4248667--4248719 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
4248657 ACTCAAAAAA
4248667 AATATTATTTT-ATACTTTT
1 AATATTATTTTAATACTTTT
* **
4248686 AATATGAAATTAATA-TTTT
1 AATATTATTTTAATACTTTT
4248705 AATATTATTTTAATA
1 AATATTATTTTAATA
4248720 AAAAAATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 24 0.89
20 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
AATATTATTTTAATACTTTT
Found at i:4248881 original size:17 final size:17
Alignment explanation
Indices: 4248859--4248896 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4248849 ATTTATCTAT
4248859 TATTTTTATAAATA-TAA
1 TATTTTTA-AAATATTAA
*
4248876 TATTTTTAAATTATTAA
1 TATTTTTAAAATATTAA
4248893 TATT
1 TATT
4248897 GAGTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTTAAAATATTAA
Found at i:4248944 original size:19 final size:19
Alignment explanation
Indices: 4248902--4248945 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4248892 ATATTGAGTA
* *
4248902 ATATTAATTTATATATTTT
1 ATATTAATATATATAATTT
4248921 ATATTAATATA-ATAATTT
1 ATATTAATATATATAATTT
4248939 AGTATTA
1 A-TATTA
4248946 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATATTAATATATATAATTT
Found at i:4248946 original size:57 final size:56
Alignment explanation
Indices: 4248819--4248954 Score: 134
Period size: 57 Copynumber: 2.4 Consensus size: 56
4248809 ATTATATTTT
* * *
4248819 TAATTTAGTAATATGTAATAAATTGTTAATATTTATCTATTATTTTTATAAATATAA
1 TAATTTAGTATTATGTAAT-AATTGGTAATATTAATCTATTATTTTTATAAATATAA
* * * *
4248876 TATTTTTA-AATTAT-TAAT-ATTGAGTAATATTAATTTATATATTTTATATTAATATAA
1 TA-ATTTAGTATTATGTAATAATTG-GTAATATTAATCTAT-TATTTT-TATAAATATAA
4248933 TAATTTAGTATTATGTTAATAA
1 TAATTTAGTATTATG-TAATAA
4248955 AATACTAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
54 4 0.06
55 12 0.19
56 14 0.23
57 23 0.37
58 4 0.06
59 4 0.06
60 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (56 bp):
TAATTTAGTATTATGTAATAATTGGTAATATTAATCTATTATTTTTATAAATATAA
Found at i:4249267 original size:29 final size:29
Alignment explanation
Indices: 4249225--4249329 Score: 129
Period size: 29 Copynumber: 3.5 Consensus size: 29
4249215 CTTAGAAAAT
*
4249225 GTAATTAATTTTACATAAAACAGTTTTAG
1 GTAATTCATTTTACATAAAACAGTTTTAG
* *
4249254 GTAATTCATTTTACGTAAAACAGTTTTCAT
1 GTAATTCATTTTACATAAAACAGTTTT-AG
* *
4249284 GTAATTCATTTTTACGTAATACAGTTTTTAG
1 GTAATTCA-TTTTACATAAAACAG-TTTTAG
*
4249315 GTAATTCGTTTTACA
1 GTAATTCATTTTACA
4249330 CAAACTATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.38
30 15 0.23
31 22 0.33
32 4 0.06
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (29 bp):
GTAATTCATTTTACATAAAACAGTTTTAG
Found at i:4249300 original size:31 final size:30
Alignment explanation
Indices: 4249225--4249326 Score: 127
Period size: 31 Copynumber: 3.4 Consensus size: 30
4249215 CTTAGAAAAT
* *
4249225 GTAATT-AATTTTACATAAAACAGTTTTAG
1 GTAATTCATTTTTACGTAAAACAGTTTTAG
*
4249254 GTAATTCA-TTTTACGTAAAACAGTTTTCAT
1 GTAATTCATTTTTACGTAAAACAGTTTT-AG
*
4249284 GTAATTCATTTTTACGTAATACAGTTTTTAG
1 GTAATTCATTTTTACGTAAAACAG-TTTTAG
*
4249315 GTAATTCGTTTT
1 GTAATTCATTTT
4249327 ACACAAACTA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 24 0.38
30 10 0.16
31 26 0.41
32 4 0.06
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (30 bp):
GTAATTCATTTTTACGTAAAACAGTTTTAG
Found at i:4249302 original size:15 final size:15
Alignment explanation
Indices: 4249248--4249326 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 15
4249238 CATAAAACAG
*
4249248 TTTTAGGTAATTCA-
1 TTTTACGTAATTCAT
**
4249262 TTTTACGTAAAACAGT
1 TTTTACGTAATTCA-T
* *
4249278 TTTCATGTAATTCAT
1 TTTTACGTAATTCAT
*
4249293 TTTTACGTAATACAGT
1 TTTTACGTAATTCA-T
* *
4249309 TTTTAGGTAATTCGT
1 TTTTACGTAATTCAT
4249324 TTT
1 TTT
4249327 ACACAAACTA
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
14 11 0.22
15 16 0.33
16 22 0.45
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (15 bp):
TTTTACGTAATTCAT
Found at i:4250592 original size:18 final size:19
Alignment explanation
Indices: 4250564--4250611 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
4250554 TCTTAAATTT
* *
4250564 TTAATATTAAATTCATGTA
1 TTAACATTAAATTCATATA
*
4250583 TTAA-ATTAAATTCATATC
1 TTAACATTAAATTCATATA
4250601 TTAACATTAAA
1 TTAACATTAAA
4250612 AAATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (19 bp):
TTAACATTAAATTCATATA
Found at i:4250634 original size:31 final size:30
Alignment explanation
Indices: 4250599--4250658 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4250589 TAAATTCATA
4250599 TCTTAACATTAAAAAATATATTTTATTTTTT
1 TCTTAAC-TTAAAAAATATATTTTATTTTTT
**
4250630 TCTTAACTTATTAAATATATTTTATTTTT
1 TCTTAACTTAAAAAATATATTTTATTTTT
4250659 AACTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (30 bp):
TCTTAACTTAAAAAATATATTTTATTTTTT
Found at i:4252840 original size:17 final size:17
Alignment explanation
Indices: 4252818--4252858 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4252808 ACGGTTGACT
*
4252818 GTTGACCGTTGACCTGC
1 GTTGACCGTTGACCGGC
*
4252835 GTTGACCGTTTACCGGC
1 GTTGACCGTTGACCGGC
4252852 GTTGACC
1 GTTGACC
4252859 ACTGTTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.29
Consensus pattern (17 bp):
GTTGACCGTTGACCGGC
Found at i:4255390 original size:24 final size:24
Alignment explanation
Indices: 4255362--4255418 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
4255352 AAATATTTTA
* *
4255362 TCTGATTTCCGACTTGAATTTTGT
1 TCTGATTTCCGACCTGAATTATGT
* **
4255386 TCTGATATATGACCTGAATTATGT
1 TCTGATTTCCGACCTGAATTATGT
4255410 TCTGATTTC
1 TCTGATTTC
4255419 TGATTTCTGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (24 bp):
TCTGATTTCCGACCTGAATTATGT
Found at i:4255442 original size:55 final size:55
Alignment explanation
Indices: 4255362--4255477 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 55
4255352 AAATATTTTA
*
4255362 TCTGATTTCCGACTTGAATTTTGTTCTGATATATGACCTGAATTATGTTCTGATT
1 TCTGATTTCCGACTTGAATTATGTTCTGATATATGACCTGAATTATGTTCTGATT
* * * * ** * *
4255417 TCTGATTTCTGATTTGGATTATGTTCTGATATTTGTTCTGAATTCTGTTTTGATT
1 TCTGATTTCCGACTTGAATTATGTTCTGATATATGACCTGAATTATGTTCTGATT
4255472 TCTGAT
1 TCTGAT
4255478 ATCTCTGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (55 bp):
TCTGATTTCCGACTTGAATTATGTTCTGATATATGACCTGAATTATGTTCTGATT
Found at i:4255443 original size:24 final size:25
Alignment explanation
Indices: 4255416--4255477 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
4255406 ATGTTCTGAT
*
4255416 TTCTGATTTCTGATT-TGGATTATG
1 TTCTGATTTCTGATTCTGAATTATG
*
4255440 TTCTGATATT-TG-TTCTGAATTCTG
1 TTCTGAT-TTCTGATTCTGAATTATG
*
4255464 TTTTGATTTCTGAT
1 TTCTGATTTCTGAT
4255478 ATCTCTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 4 0.13
24 24 0.77
25 3 0.10
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (25 bp):
TTCTGATTTCTGATTCTGAATTATG
Found at i:4257053 original size:17 final size:18
Alignment explanation
Indices: 4257032--4257076 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4257022 AATATTTCTC
4257032 TTAAAAA-AT-ATATTAA
1 TTAAAAATATGATATTAA
*
4257048 TATAAAAATATGATATTTA
1 T-TAAAAATATGATATTAA
4257067 TTAAAAATAT
1 TTAAAAATAT
4257077 CAGAAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 6 0.24
18 11 0.44
19 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TTAAAAATATGATATTAA
Found at i:4257203 original size:8 final size:8
Alignment explanation
Indices: 4257192--4257219 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4257182 TAAATAGAAT
4257192 AAAAAATA
1 AAAAAATA
4257200 AAAAAATA
1 AAAAAATA
4257208 AAAAAATA
1 AAAAAATA
4257216 AAAA
1 AAAA
4257220 TTATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:4258698 original size:3 final size:3
Alignment explanation
Indices: 4258692--4258776 Score: 95
Period size: 3 Copynumber: 29.0 Consensus size: 3
4258682 GTCCTATTTG
* *
4258692 TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA T-A TAA TAA TAA TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
4258738 TAAA TAA -AA TAA TAA TAA TAA TAA AAA TAT TAA AAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4258777 AAACAAATGG
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 5 0.07
3 61 0.90
4 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4259368 original size:122 final size:120
Alignment explanation
Indices: 4259148--4259585 Score: 560
Period size: 122 Copynumber: 3.7 Consensus size: 120
4259138 GAATTAAGGC
* * * *
4259148 AAGGTTGAACAAATTCTTCTCATTATTAACTTCTTC-TCTTTCTTCATATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTA
* *
4259212 TGAACTCTTCTGGAAATGTTGATGTTGATATATCTCCTTCTGTGATAGCA-TCGAGCAA
65 TGAACTCTTCTGGAAA--TTAATGTTGATCTATCTCCTTCTGTGATAG-AGTCGAGCAA
*
4259270 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGCTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
4259335 GAACTCTTCTGGAAAAATTAATGCTGATCTATCTCCTTCTGTGATAGAGTC-ATGCAA
66 GAACTCTTCTGG--AAATTAATGTTGATCTATCTCCTTCTGTGATAGAGTCGA-GCAA
4259392 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * ** *
4259457 GAACTCTACCTGG----CAATGTTGATCCA--T-C--AAGTGAT-GAATTCGAGCAA
66 GAACTCT-TCTGGAAATTAATGTTGATCTATCTCCTTCTGTGATAG-AGTCGAGCAA
*
4259504 AAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
4259569 TGAACTCTTCTGGAAAT
65 TGAACTCTTCTGGAAAT
4259586 GTTGATCCAT
Statistics
Matches: 285, Mismatches: 18, Indels: 32
0.85 0.05 0.10
Matches are distributed among these distances:
111 1 0.00
112 55 0.19
113 33 0.12
114 1 0.00
115 1 0.00
117 10 0.04
121 2 0.01
122 173 0.61
123 6 0.02
124 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (120 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCTGGAAATTAATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
Found at i:4259906 original size:22 final size:22
Alignment explanation
Indices: 4259881--4259969 Score: 108
Period size: 22 Copynumber: 4.0 Consensus size: 22
4259871 AAATCCAATA
* *
4259881 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
*
4259903 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
* *
4259925 AATCTGTCATCTTTGAAGAA-AA
1 AATCTATCATCTTTGAA-AAGAG
*
4259947 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
4259969 A
1 A
4259970 TGTAGATAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.02
22 54 0.96
23 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:4259951 original size:44 final size:44
Alignment explanation
Indices: 4259881--4259969 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
4259871 AAATCCAATA
* * *
4259881 AATCTTTCTTCTTTGAAAAGAGAATCTATCATCTTTGAAGAGAG
1 AATCTGTCATCTTTGAAAAGAAAATCTATCATCTTTGAAGAGAG
4259925 AATCTGTCATCTTTGAAGAA-AAAATCTATCATCTTTGAAGAGAG
1 AATCTGTCATCTTTGAA-AAGAAAATCTATCATCTTTGAAGAGAG
4259969 A
1 A
4259970 TGTAGATAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 39 0.95
45 2 0.05
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (44 bp):
AATCTGTCATCTTTGAAAAGAAAATCTATCATCTTTGAAGAGAG
Found at i:4260621 original size:18 final size:18
Alignment explanation
Indices: 4260584--4260621 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4260574 TATATGAAAG
* *
4260584 AATAAATTTAATTTCGAA
1 AATAAATTGAATTTCAAA
4260602 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
4260620 AA
1 AA
4260622 GATAAACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:4265495 original size:14 final size:15
Alignment explanation
Indices: 4265476--4265504 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4265466 TTATTTTTCA
4265476 AATTTTA-CTTAATG
1 AATTTTATCTTAATG
4265490 AATTTTATCTTAATG
1 AATTTTATCTTAATG
4265505 TAAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
AATTTTATCTTAATG
Found at i:4269730 original size:3 final size:3
Alignment explanation
Indices: 4269722--4269759 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4269712 ATATGACTAC
4269722 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4269760 TAAATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4271180 original size:3 final size:3
Alignment explanation
Indices: 4271174--4271290 Score: 116
Period size: 3 Copynumber: 40.0 Consensus size: 3
4271164 GGCTTGTTTG
* *
4271174 TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
4271222 T-A TAA TAA -AA AAA TGA TAA TAA TAG T-A TAAA TAA -AA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * *
4271264 TAA TAA TAT TAA TAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
4271291 AAGCAAATGG
Statistics
Matches: 92, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
2 7 0.08
3 83 0.90
4 2 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4271750 original size:83 final size:83
Alignment explanation
Indices: 4271611--4271776 Score: 296
Period size: 83 Copynumber: 2.0 Consensus size: 83
4271601 CATATTATGA
* *
4271611 GGGTTGATAGCTAGTAAGAAGGCTTTGTGATGCTCAGGGTATTAGACTGTCTAATAAAGATGACG
1 GGGTTGATAGCTAGTAAGAAGGCTTTGTGATGCTCAGGGAATTAGACTGTCTAATAAAGACGACG
4271676 GTGTGCAATGGGAGGATT
66 GTGTGCAATGGGAGGATT
* *
4271694 GGGTTGATAGTTAGTGAGAAGGCTTTGTGATGCTCAGGGAATTAGACTGTCTAATAAAGACGACG
1 GGGTTGATAGCTAGTAAGAAGGCTTTGTGATGCTCAGGGAATTAGACTGTCTAATAAAGACGACG
4271759 GTGTGCAATGGGAGGATT
66 GTGTGCAATGGGAGGATT
4271777 AGGTGATTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (83 bp):
GGGTTGATAGCTAGTAAGAAGGCTTTGTGATGCTCAGGGAATTAGACTGTCTAATAAAGACGACG
GTGTGCAATGGGAGGATT
Found at i:4284981 original size:81 final size:83
Alignment explanation
Indices: 4284879--4285054 Score: 198
Period size: 84 Copynumber: 2.1 Consensus size: 83
4284869 ATTGTAACTT
* * *
4284879 TAGTGGCGTTTTTATTCAAAC-A-CCGCGACAGAGTTGTAGTTTAGCAGCGTTTGTATA-AAAAC
1 TAGTGGCATTTTTATTCAAACAAGCCGCAACAGAGTTGTACTTTAGCAGCGTTTGTATACAAAA-
* * *
4284941 GTCGCCATAGGGTCATCTA
65 GCCGCAATAGGGTCATCCA
* * *
4284960 TAGTGGCATTTTT-TTCAAAACAATGCCGCAAGAGAGTTGTACTTTAGCGGCGTTTTTATACAAA
1 TAGTGGCATTTTTATTC-AAACAA-GCCGCAACAGAGTTGTACTTTAGCAGCGTTTGTATACAAA
*
4285024 AGCCGCAATAGGTTCATCCA
64 AGCCGCAATAGGGTCATCCA
*
4285044 TAGTGGTATTT
1 TAGTGGCATTT
4285055 CTCAATAACC
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
80 3 0.04
81 16 0.20
82 1 0.01
84 55 0.70
85 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (83 bp):
TAGTGGCATTTTTATTCAAACAAGCCGCAACAGAGTTGTACTTTAGCAGCGTTTGTATACAAAAG
CCGCAATAGGGTCATCCA
Found at i:4285169 original size:81 final size:82
Alignment explanation
Indices: 4285077--4285237 Score: 213
Period size: 81 Copynumber: 2.0 Consensus size: 82
4285067 CGTGACAGAG
* *
4285077 TATTACTTTAGCGACGTTTATATAAAACA-GTCGTAATAGGTTTTGA-CTATAGTTG-TGGTTTT
1 TATTACTTTAGCGACGTTTATATAAAA-ATGTCGTAATAGG-GTTCATCTATAG-TGATGGTTTT
4285139 TCAACAAACGCCGCAAAAGT
63 TCAACAAACGCCGCAAAAGT
** * *
4285159 TATTAC-TTAGCGGTGTTTGTATAAAAATGTCGTAATAGGGTTCATCTATAGTGATGTTTTTTCA
1 TATTACTTTAGCGACGTTTATATAAAAATGTCGTAATAGGGTTCATCTATAGTGATGGTTTTTCA
4285223 ACAAACGCCGCAAAA
66 ACAAACGCCGCAAAA
4285238 ACGCGTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
80 6 0.09
81 58 0.83
82 6 0.09
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (82 bp):
TATTACTTTAGCGACGTTTATATAAAAATGTCGTAATAGGGTTCATCTATAGTGATGGTTTTTCA
ACAAACGCCGCAAAAGT
Found at i:4285491 original size:21 final size:21
Alignment explanation
Indices: 4285466--4285525 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
4285456 CGGCGCCTGG
* *
4285466 TCACCAACGTCGCTCCTCCGC
1 TCACCATCGTCGCTCCTCCGA
*
4285487 TCACCATCATCGCTCCTCCGA
1 TCACCATCGTCGCTCCTCCGA
*
4285508 TCACCATCGTCTCTCCTC
1 TCACCATCGTCGCTCCTC
4285526 AAGGCTCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.50, G:0.10, T:0.25
Consensus pattern (21 bp):
TCACCATCGTCGCTCCTCCGA
Found at i:4288569 original size:43 final size:42
Alignment explanation
Indices: 4288389--4288691 Score: 356
Period size: 42 Copynumber: 7.1 Consensus size: 42
4288379 AAGGTAATTA
* * *
4288389 GCGGCATTTGTATCTAAAAACGTCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
4288432 GCGGCATTTGTTCCAAAAACGCCGCTATAGATCTGACGTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
** * * *
4288474 GCTTCGTTTGTTCCAAAAATGCCTCTATAGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
*
4288516 GCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
4288559 GCGGCGTTTGTTCC-GAAACACCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * * * * *
4288601 TCTGCATTTGTTCTAAAAACGCCACTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* *
4288644 GCGTCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
4288687 GCGGC
1 GCGGC
4288692 ATTTTTTGTT
Statistics
Matches: 221, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
42 126 0.57
43 94 0.43
44 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:4288613 original size:85 final size:83
Alignment explanation
Indices: 4288412--4288695 Score: 354
Period size: 85 Copynumber: 3.3 Consensus size: 83
4288402 CTAAAAACGT
* *
4288412 CGCTATAGATCTGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCT-GACGTTTTGC
1 CGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGC
* *
4288476 TTCGTTTGTTCCAAAAATGC
66 GTCGTTTGTTCCAAACA--C
* **
4288496 CTCTATAGATATGACCTTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGC
1 CGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGC
*
4288561 GGCGTTTGTTCCGAAACAC
66 GTCGTTTGTTCC-AAACAC
* * * * *
4288580 CGCTATAGATATCGACCTTTTTCTGCATTTGTTCTAAAAACGCCACTATAGATATCGACCTTTTG
1 CGCTATAGATAT-GACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
*
4288645 CGTCGTTTGTTCCAAAAACGC
65 CGTCGTTTGTTCC--AAACAC
* *
4288666 CGCTATAGATCTTGACCTATTGCGGCATTT
1 CGCTATAGAT-ATGACCTTTTGCGGCATTT
4288696 TTTGTTCTCA
Statistics
Matches: 172, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
84 62 0.36
85 76 0.44
86 33 0.19
87 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (83 bp):
CGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGC
GTCGTTTGTTCCAAACAC
Found at i:4290588 original size:16 final size:16
Alignment explanation
Indices: 4290569--4290600 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4290559 AGGAGAAAAT
4290569 GAGATTATATAGGAAC
1 GAGATTATATAGGAAC
4290585 GAGATTATATAGGAAC
1 GAGATTATATAGGAAC
4290601 ATGACAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
GAGATTATATAGGAAC
Found at i:4290910 original size:22 final size:22
Alignment explanation
Indices: 4290883--4290934 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
4290873 TCAATAGATA
4290883 AATAATTTTATTATTATTTAAT
1 AATAATTTTATTATTATTTAAT
4290905 AATAATTTTATTATTATTTAAT
1 AATAATTTTATTATTATTTAAT
4290927 AATAATTT
1 AATAATTT
4290935 CGTTTATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATAATTTTATTATTATTTAAT
Found at i:4293383 original size:13 final size:13
Alignment explanation
Indices: 4293365--4293395 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4293355 CAAAACAAAT
4293365 GATAATTCCTAAA
1 GATAATTCCTAAA
4293378 GATAATTCCTAAA
1 GATAATTCCTAAA
*
4293391 AATAA
1 GATAA
4293396 CATTAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (13 bp):
GATAATTCCTAAA
Found at i:4295212 original size:217 final size:217
Alignment explanation
Indices: 4294837--4295273 Score: 739
Period size: 217 Copynumber: 2.0 Consensus size: 217
4294827 CGCTCATTGT
* * *
4294837 ATGGTGTAATCGAACCGAGAGGGACAATGTATGGTGCACTGGGAGTTCTGGCAAGCAGTCTGATC
1 ATGGTGTAATCGAACCAAGAGGGACAACGTATGGTGCACTGGGAGTTCCGGCAAGCAGTCTGATC
*
4294902 GAGTCCAAACACCTAGAATCAAAAGGATCAATTTCAAAAGTATAAGTAAATTGATTAGAATAAAA
66 GAGTCCAAACACCTAGAATCAAAAGGATCAATTTCAAAAGCATAAGTAAATTGATTAGAATAAAA
*
4294967 TGTAAACGGAAATAAACGAGATGCAAGGCGAGTAATGTAGGGTATGAGAATTAGTGGGCGATCGA
131 TGTAAACAGAAATAAACGAGATGCAAGGCGAGTAATGTAGGGTATGAGAATTAGTGGGCGATCGA
*
4295032 AACACATAACACACTCAAAGGC
196 AACACACAACACACTCAAAGGC
* * * *
4295054 ATGGTGTAATCGAGCCAAGAGGGACAACGTATGTTTCACTGGGAGTTCCGGCGAGCAGTCTGATC
1 ATGGTGTAATCGAACCAAGAGGGACAACGTATGGTGCACTGGGAGTTCCGGCAAGCAGTCTGATC
*
4295119 GAGTCCAAACACCTAGAATCCAAAGGATCAATTTCAAAAGCATAAGTAAATTGATTAGAATAAAA
66 GAGTCCAAACACCTAGAATCAAAAGGATCAATTTCAAAAGCATAAGTAAATTGATTAGAATAAAA
* *
4295184 TGTAAACAGAAATAAATGAGATGCAAGGCGAGTAATGTAGGGTATGAGAATTAGTGGGCGATCGG
131 TGTAAACAGAAATAAACGAGATGCAAGGCGAGTAATGTAGGGTATGAGAATTAGTGGGCGATCGA
* *
4295249 AACGCACAACACGCTCAAAGGC
196 AACACACAACACACTCAAAGGC
4295271 ATG
1 ATG
4295274 CGCGAACCAA
Statistics
Matches: 205, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 205 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.21
Consensus pattern (217 bp):
ATGGTGTAATCGAACCAAGAGGGACAACGTATGGTGCACTGGGAGTTCCGGCAAGCAGTCTGATC
GAGTCCAAACACCTAGAATCAAAAGGATCAATTTCAAAAGCATAAGTAAATTGATTAGAATAAAA
TGTAAACAGAAATAAACGAGATGCAAGGCGAGTAATGTAGGGTATGAGAATTAGTGGGCGATCGA
AACACACAACACACTCAAAGGC
Found at i:4295698 original size:12 final size:12
Alignment explanation
Indices: 4295681--4295707 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4295671 TTAGTTACGA
4295681 AAATTAAAATTT
1 AAATTAAAATTT
4295693 AAATTAAAATTT
1 AAATTAAAATTT
4295705 AAA
1 AAA
4295708 ACATTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:4298391 original size:124 final size:124
Alignment explanation
Indices: 4298064--4298566 Score: 613
Period size: 124 Copynumber: 4.0 Consensus size: 124
4298054 GGCTTTGATG
* * * * * *
4298064 TGAATTCCAATCTAGAGATGGATGTTTCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATT
1 TGAAATCCAATCTAAAGATGAATGTTACTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATC
* * * * * * * *
4298129 GTAGATGGCTCATTCATTGTGAAGTTGAGCTTTTAATTGGATATCATTCGTTGTGAAGT
66 GTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTATGAAGT
* * *
4298188 TGAAA-CCTAATCTAGAG-TTATAT-TT-CTGTTTGTGGGCACGATATCCTTCGTCATGAAGTTG
1 TGAAATCC-AATCTAAAGATGA-ATGTTACTG---GTGGGCACGATATCCTTCGTCGTGAAGTTG
* *
4298249 AAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTCGTTGTGAAGT
61 AAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTATGAAGT
*
4298313 TGAAATCCAATCTAAAGATGAATGTTACTGGTGGGCACGATATCCTTCTTCGTGAAGTTGAAATC
1 TGAAATCCAATCTAAAGATGAATGTTACTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATC
*
4298378 GTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGT
66 GTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTATGAAGT
* * * * *
4298437 TGAAATCCAATCTAAAGATGAAGGATGA-TGGTGGGCACAATATCATTCGTTGTGAAGTTGAAAT
1 TGAAATCCAATCTAAAGATGAATG-TTACTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAAT
* ** * * *
4298501 CATGGATAACCCCTTTG-TGTTGAAGTTGAGCTTTGAATTGGATATCCTTCATTATGAAGT
65 CGTGGATGGCCCCTTCGTTG-TGAAGTTGAGCCTTGAATTGGATATCCTTCGTTATGAAGT
4298561 TGAAAT
1 TGAAAT
4298567 TATGGATGGC
Statistics
Matches: 334, Mismatches: 34, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
122 2 0.01
123 7 0.02
124 215 0.64
125 101 0.30
126 6 0.02
127 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (124 bp):
TGAAATCCAATCTAAAGATGAATGTTACTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATC
GTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTATGAAGT
Found at i:4298547 original size:190 final size:190
Alignment explanation
Indices: 4298351--4298757 Score: 532
Period size: 190 Copynumber: 2.1 Consensus size: 190
4298341 TGGTGGGCAC
* ** *
4298351 GATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATT
1 GATATCCTTCTTCGTGAAGTTGAAATCATGGATGGCCCCTTCGTTACGAAGTTAAGCCTTGAATT
* * *
4298416 GGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAAGGATGATGGTGGGCACAATA-T
66 GGATATCCTTCATCATGAAGTTGAAATCCAATCTAAAGATGAAGGATGATAGTGGACACAATATT
* * * * *
4298480 CATTCGTTGTGAAGTTGAAATCATGGATAACCCCTTTG-TGTTGAAGTTGAGCTTTGAATTG
131 C-TTCGTCGTAAAGTTGAAATCATGAATAACCCCTTCGTTG-TGAAGTTGAGCCTTGAATTG
* *
4298541 GATATCCTTCATT-ATGAAGTTGAAATTATGGATGGCCCCTTCGTTACGAAGTTAAGCCTTGAAT
1 GATATCCTTC-TTCGTGAAGTTGAAATCATGGATGGCCCCTTCGTTACGAAGTTAAGCCTTGAAT
** * * * *
4298605 TGGATATCCTTCATTGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTAGTGGACACGATAT
65 TGGATATCCTTCATCATGAAGTTGAAATCCAATCTAAAGATGAAGGATGATAGTGGACACAATAT
* ** * *
4298670 TCTTCGTCGTAAAGTTGAAATCGTGAATGGCTCGTTCGTTGTGAAGTTGAGCCTTGAATTG
130 TCTTCGTCGTAAAGTTGAAATCATGAATAACCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
*
4298731 GATATCCTTCGTCGTGAAGTTGAAATC
1 GATATCCTTCTTCGTGAAGTTGAAATC
4298758 CAATCTTGAG
Statistics
Matches: 185, Mismatches: 28, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
189 1 0.01
190 178 0.96
191 6 0.03
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (190 bp):
GATATCCTTCTTCGTGAAGTTGAAATCATGGATGGCCCCTTCGTTACGAAGTTAAGCCTTGAATT
GGATATCCTTCATCATGAAGTTGAAATCCAATCTAAAGATGAAGGATGATAGTGGACACAATATT
CTTCGTCGTAAAGTTGAAATCATGAATAACCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
Found at i:4298561 original size:34 final size:34
Alignment explanation
Indices: 4298521--4298629 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 34
4298511 CCCTTTGTGT
4298521 TGAAGTTGAGCTTTGAATTGGATATCCTTCATTA
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCATTA
** * ** *
4298555 TGAAGTTGAAATTATGGA-TGG--CCCCTTCGTTA
1 TGAAGTTGAGCTT-TGAATTGGATATCCTTCATTA
* * * *
4298587 CGAAGTTAAGCCTTGAATTGGATATCCTTCATTG
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCATTA
4298621 TGAAGTTGA
1 TGAAGTTGA
4298630 AATCCAATCT
Statistics
Matches: 53, Mismatches: 18, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
31 3 0.06
32 19 0.36
34 28 0.53
35 3 0.06
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (34 bp):
TGAAGTTGAGCTTTGAATTGGATATCCTTCATTA
Found at i:4298561 original size:66 final size:66
Alignment explanation
Indices: 4298489--4298633 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 66
4298479 TCATTCGTTG
* * * *
4298489 TGAAGTTGAAATCATGGATAACCCCTTTGTGT-TGAAGTTGAGCTTTGAATTGGATATCCTTCAT
1 TGAAGTTGAAATCATGGATAACCCCTTCGT-TACGAAGTTAAGCCTTGAATTGGATATCCTTCAT
4298553 TA
65 TA
* **
4298555 TGAAGTTGAAATTATGGATGGCCCCTTCGTTACGAAGTTAAGCCTTGAATTGGATATCCTTCATT
1 TGAAGTTGAAATCATGGATAACCCCTTCGTTACGAAGTTAAGCCTTGAATTGGATATCCTTCATT
*
4298620 G
66 A
4298621 TGAAGTTGAAATC
1 TGAAGTTGAAATC
4298634 CAATCTAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.01
66 68 0.99
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (66 bp):
TGAAGTTGAAATCATGGATAACCCCTTCGTTACGAAGTTAAGCCTTGAATTGGATATCCTTCATT
A
Found at i:4301610 original size:3 final size:3
Alignment explanation
Indices: 4301604--4301629 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4301594 AAAAATATTA
4301604 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4301630 ATATTTTTTA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4302890 original size:14 final size:13
Alignment explanation
Indices: 4302866--4302899 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4302856 CGAAAATAAC
*
4302866 AAATGAAAATTGA
1 AAATAAAAATTGA
4302879 AAACTAAAAATTGA
1 AAA-TAAAAATTGA
4302893 AAATAAA
1 AAATAAA
4302900 TTAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (13 bp):
AAATAAAAATTGA
Found at i:4302895 original size:21 final size:20
Alignment explanation
Indices: 4302857--4302896 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
4302847 ATAAATGAAC
4302857 GAAAATAACAAATGAAAATT
1 GAAAATAACAAATGAAAATT
4302877 GAAAACTAA-AAATTGAAAAT
1 GAAAA-TAACAAA-TGAAAAT
4302897 AAATTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.20
Consensus pattern (20 bp):
GAAAATAACAAATGAAAATT
Done.