Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1853635 original size:6 final size:6
Alignment explanation
Indices: 1853624--1853654 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1853614 AAATCATCTG
1853624 CATTTA CATTTA CATTTA CATTTA CATTTA C
1 CATTTA CATTTA CATTTA CATTTA CATTTA C
1853655 TTTTCATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTTA
Found at i:1854317 original size:15 final size:15
Alignment explanation
Indices: 1854297--1854326 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1854287 TAAATTTTAA
1854297 ATTTTTAACTCATTT
1 ATTTTTAACTCATTT
*
1854312 ATTTTTAGCTCATTT
1 ATTTTTAACTCATTT
1854327 CATAGTAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTTAACTCATTT
Found at i:1860985 original size:288 final size:288
Alignment explanation
Indices: 1860467--1861332 Score: 1633
Period size: 288 Copynumber: 3.0 Consensus size: 288
1860457 ACCGTACTAC
*
1860467 AAGGATGAAAAACATTGTGTTTGATGTCTCACCTTCTGTCATGTCAGTGTCAGTTGTACTTGATT
1 AAGGATGAAAAACATTGTGTTTGATGTCTCATCTTCTGTCATGTCAGTGTCAGTTGTACTTGATT
* **
1860532 GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGTTATGGCATTATGATCCAGTCTTTTGGA
66 GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGATATGGCATTATGATCCAGTCTTTTCAA
**
1860597 TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTCGTGTT
131 TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTTATGTT
*
1860662 TTGTCGTTATTGTATACCAGCGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
196 TTGTCGTTATTGTATACCAGTGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
1860727 TGGCAGCATTGCATTCTGACCTAACCTT
261 TGGCAGCATTGCATTCTGACCTAACCTT
* *
1860755 ATGGATGAAAAACATTGTGTTTGATGTCTCATCTTCTGTCATGTCAGAGTCAGTTGTACTTGATT
1 AAGGATGAAAAACATTGTGTTTGATGTCTCATCTTCTGTCATGTCAGTGTCAGTTGTACTTGATT
1860820 GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGATATGGCATTATGATCCAGTCTTTTCAA
66 GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGATATGGCATTATGATCCAGTCTTTTCAA
1860885 TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTTATGTT
131 TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTTATGTT
*
1860950 TTGTCGTTATTGTATATCAGTGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
196 TTGTCGTTATTGTATACCAGTGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
1861015 TGGCAGCATTGCATTCTGACCTAACCTT
261 TGGCAGCATTGCATTCTGACCTAACCTT
1861043 AAGGATGAAAAACATTGTGTTTGATGTCTCATCTTCTGTCATGTCAGTGTCAGTTGTACTTGATT
1 AAGGATGAAAAACATTGTGTTTGATGTCTCATCTTCTGTCATGTCAGTGTCAGTTGTACTTGATT
*
1861108 GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGATATGGCATTTTGATCCAGTCTTTTCAA
66 GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGATATGGCATTATGATCCAGTCTTTTCAA
1861173 TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTTATGTT
131 TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTTATGTT
1861238 TTGTCGTTATTGTATACCAGTGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
196 TTGTCGTTATTGTATACCAGTGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
1861303 TGGCAGCATTGCATTCTGACCTAACCTT
261 TGGCAGCATTGCATTCTGACCTAACCTT
1861331 AA
1 AA
1861333 TTTTGACTCT
Statistics
Matches: 564, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
288 564 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (288 bp):
AAGGATGAAAAACATTGTGTTTGATGTCTCATCTTCTGTCATGTCAGTGTCAGTTGTACTTGATT
GATACTTTTCTTGCCATGGACTGAATAATTTATCTTGATATGGCATTATGATCCAGTCTTTTCAA
TTTTATCGTGACATGTGGTTTCATTTTATTGAAATTTAATGCAAGATGTAAACTCTCCTTATGTT
TTGTCGTTATTGTATACCAGTGTGGCAGCCTGTTTATTACCCAATATATACATACATACACACCC
TGGCAGCATTGCATTCTGACCTAACCTT
Found at i:1874009 original size:102 final size:102
Alignment explanation
Indices: 1873833--1874026 Score: 264
Period size: 102 Copynumber: 1.9 Consensus size: 102
1873823 AGTCAGTATA
* * * * * *
1873833 TTTTGGTGAAAGTAGTCTATTGGTATCTTAGCTTATTCTTTTTGCTGTAAGATAATGACTAGTGT
1 TTTTGGTGAAAGTAGTCTACTGATATCTTAGCTCATTCTGTTTCCTATAAGATAATGACTAGTGT
* *
1873898 CTCATATATGCTTGGTCGCAGGTTATTTCTTCAGATT
66 CTCAAATATGCTTGGTCGCAGGATATTTCTTCAGATT
* *
1873935 TTTTGGTTAAATTAGTCTACTGATATCTTAGCTCATTCTGTTTCCTATAAGATAATGACT-GTTG
1 TTTTGGTGAAAGTAGTCTACTGATATCTTAGCTCATTCTGTTTCCTATAAGATAATGACTAG-TG
* *
1873999 TCTCAAATATGTTTGGTTGCAGGATATT
65 TCTCAAATATGCTTGGTCGCAGGATATT
1874027 CATACTTCCT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 1 0.01
102 78 0.99
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (102 bp):
TTTTGGTGAAAGTAGTCTACTGATATCTTAGCTCATTCTGTTTCCTATAAGATAATGACTAGTGT
CTCAAATATGCTTGGTCGCAGGATATTTCTTCAGATT
Found at i:1887360 original size:102 final size:102
Alignment explanation
Indices: 1887176--1887369 Score: 271
Period size: 102 Copynumber: 1.9 Consensus size: 102
1887166 GTTCAGTCTA
* * * * * *
1887176 TTTTGGTTAAAATATTCTATTGGTATCTTAGCTTATTCTATTTCCTGTAAGATAATGACTAGTGT
1 TTTTGGTTAAAATAGTCTATTGGAATCCTAGCTTATTCTATGTCCTATAAGATAATGACTAATGT
* *
1887241 CTCAAATGTGTTTGGTTGCAGGATATTTCTTCTCATT
66 CTCAAATATGTTGGGTTGCAGGATATTTCTTCTCATT
* * * *
1887278 TTTTGGTTAAAATGGTCTCTTGGAATCCTAGCTTATTCTATGTCGTATAAGATAATGGCTAATGT
1 TTTTGGTTAAAATAGTCTATTGGAATCCTAGCTTATTCTATGTCCTATAAGATAATGACTAATGT
*
1887343 CTCAAATATGTTGGGTTGCTGGATATT
66 CTCAAATATGTTGGGTTGCAGGATATT
1887370 CATACTTCCT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.44
Consensus pattern (102 bp):
TTTTGGTTAAAATAGTCTATTGGAATCCTAGCTTATTCTATGTCCTATAAGATAATGACTAATGT
CTCAAATATGTTGGGTTGCAGGATATTTCTTCTCATT
Found at i:1887722 original size:55 final size:56
Alignment explanation
Indices: 1887638--1887754 Score: 182
Period size: 55 Copynumber: 2.1 Consensus size: 56
1887628 TGAATTTGAG
* *
1887638 AACTGGTTTAGGGATCAAAACTTTGAGGTAA-TTTCTTGTTTCTTTTCTGGTTATT
1 AACTGGTTTAGGGATCAAAACTTCGAGGTAATTTTCTTGTTTCTTTTCAGGTTATT
* *
1887693 AACTGGTTTAGGGATCCAAACTTCGAGGTAATTTTCTTGTTTCTTTTCAGTTTATT
1 AACTGGTTTAGGGATCAAAACTTCGAGGTAATTTTCTTGTTTCTTTTCAGGTTATT
*
1887749 AGCTGG
1 AACTGG
1887755 ATTGATCAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 29 0.52
56 27 0.48
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (56 bp):
AACTGGTTTAGGGATCAAAACTTCGAGGTAATTTTCTTGTTTCTTTTCAGGTTATT
Found at i:1891358 original size:137 final size:137
Alignment explanation
Indices: 1891112--1891386 Score: 460
Period size: 137 Copynumber: 2.0 Consensus size: 137
1891102 CGCTTTAGGC
* * **
1891112 TGGCAATAGCTACCTTAGTTTTCTTATTTTTGAAATTTTTGGTATACTACCCCTAATGTGCAGAA
1 TGGCAATAGCGACCTTAGTTTTCTCATTTTTGAAATTTTTGGTATACTACCCCTAATGCACAGAA
* *
1891177 AAAGTATTTCATCTGTGGATTTGTGTGTTTATGATGGAGCAGTTTTATTTGAAAATAGTTTGGAC
66 AAACTATTTCATCTGAGGATTTGTGTGTTTATGATGGAGCAGTTTTATTTGAAAATAGTTTGGAC
1891242 TGATGTT
131 TGATGTT
* *
1891249 TGGCAATAGCGGCCTTAGTTTTCTCATTTTTGAACTTTTTGGTATACTACCCCTAATGCACAGAA
1 TGGCAATAGCGACCTTAGTTTTCTCATTTTTGAAATTTTTGGTATACTACCCCTAATGCACAGAA
* *
1891314 AAACTATTTCATCTGAGGATTTGTGTTTTTATGATGGAGCAGTTTTATTTGAAAATAGTTTTGAC
66 AAACTATTTCATCTGAGGATTTGTGTGTTTATGATGGAGCAGTTTTATTTGAAAATAGTTTGGAC
1891379 TGATGTT
131 TGATGTT
1891386 T
1 T
1891387 CTTTTCCCCT
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 128 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (137 bp):
TGGCAATAGCGACCTTAGTTTTCTCATTTTTGAAATTTTTGGTATACTACCCCTAATGCACAGAA
AAACTATTTCATCTGAGGATTTGTGTGTTTATGATGGAGCAGTTTTATTTGAAAATAGTTTGGAC
TGATGTT
Found at i:1894851 original size:204 final size:204
Alignment explanation
Indices: 1894501--1894906 Score: 742
Period size: 204 Copynumber: 2.0 Consensus size: 204
1894491 TGTAAGTGAC
*
1894501 TAGTGTGATTCTTGCAGTTTTATGATGAAAAGTGAGCTTTCGTTGAGATTCATAGTTCTTTGCAT
1 TAGTGTGATTCTTGCAGTTATATGATGAAAAGTGAGCTTTCGTTGAGATTCATAGTTCTTTGCAT
*
1894566 ATATCTGAGATAAGAATAGCTTGGTCCATTAAGTGCAATGATCCTGTTAACTTGATTGGTGAAAC
66 ATATCTGAGATAAGAATAGCTTGATCCATTAAGTGCAATGATCCTGTTAACTTGATTGGTGAAAC
* *
1894631 TGGCACTGGGAAGACAACACTTGTTCGGAGTCTGGCTACGTGGATGCATCAAAGACTTAGTGTTC
131 TGGCACTGGGAAGACAACACTTGTTCGGAGTCTGGCCACGTGGATGCATAAAAGACTTAGTGTTC
1894696 TGGTATGAT
196 TGGTATGAT
1894705 TAGTGTGATTCTTGCAGTTATATGATGAAAAGTGAGCTTTCGTTGAGATTCATAGTTCTTTGCAT
1 TAGTGTGATTCTTGCAGTTATATGATGAAAAGTGAGCTTTCGTTGAGATTCATAGTTCTTTGCAT
*
1894770 ATA-CTTGAGATAAGAATAGCTTGATCCATTAAGTGCAGTGATCCTGTTAACTTGATTGGTGAAA
66 ATATC-TGAGATAAGAATAGCTTGATCCATTAAGTGCAATGATCCTGTTAACTTGATTGGTGAAA
*
1894834 CTGGCACTGGGAAGACAACACTTGTTCGGAGTCTGGCCACGTGGATGGATAAAAGACTTAGTGTT
130 CTGGCACTGGGAAGACAACACTTGTTCGGAGTCTGGCCACGTGGATGCATAAAAGACTTAGTGTT
1894899 CTGGTATG
195 CTGGTATG
1894907 CTTGGTGAGT
Statistics
Matches: 195, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
203 1 0.01
204 194 0.99
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (204 bp):
TAGTGTGATTCTTGCAGTTATATGATGAAAAGTGAGCTTTCGTTGAGATTCATAGTTCTTTGCAT
ATATCTGAGATAAGAATAGCTTGATCCATTAAGTGCAATGATCCTGTTAACTTGATTGGTGAAAC
TGGCACTGGGAAGACAACACTTGTTCGGAGTCTGGCCACGTGGATGCATAAAAGACTTAGTGTTC
TGGTATGAT
Found at i:1897659 original size:13 final size:13
Alignment explanation
Indices: 1897643--1897669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1897633 GTGTTCTGGA
1897643 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
1897656 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
1897669 T
1 T
1897670 AATTTTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:1907681 original size:69 final size:69
Alignment explanation
Indices: 1907596--1907732 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
1907586 ATTTTTGGTT
1907596 TTTATCTAATGCTGCAGATCTTCAATGTC-GCACCTCTTGGTTTACTTTTTGAAATTTGAGTTTG
1 TTTATCTAATGCTGCAGATCTTCAATG-CAGCACCTCTTGGTTTACTTTTTGAAATTTGAGTTTG
1907660 TTGGC
65 TTGGC
*
1907665 TTTATCTAATGCTGCAGATCTTCAATGCAGCACCTCTTGTTTTACTTTTTGAAATTTGAGTTTGT
1 TTTATCTAATGCTGCAGATCTTCAATGCAGCACCTCTTGGTTTACTTTTTGAAATTTGAGTTTGT
1907730 TGG
66 TGG
1907733 TTTTTCATTT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 1 0.02
69 65 0.98
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (69 bp):
TTTATCTAATGCTGCAGATCTTCAATGCAGCACCTCTTGGTTTACTTTTTGAAATTTGAGTTTGT
TGGC
Found at i:1912171 original size:16 final size:16
Alignment explanation
Indices: 1912150--1912182 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1912140 TTATTTTAGA
*
1912150 TTGAGAACATCCTGGT
1 TTGAGAAAATCCTGGT
1912166 TTGAGAAAATCCTGGT
1 TTGAGAAAATCCTGGT
1912182 T
1 T
1912183 ACGCTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (16 bp):
TTGAGAAAATCCTGGT
Found at i:1912731 original size:204 final size:204
Alignment explanation
Indices: 1912381--1912792 Score: 788
Period size: 204 Copynumber: 2.0 Consensus size: 204
1912371 GTGCTAACAG
1912381 TATTTGCTCCCATCCCTCCCCCCACCAAAAAAATAATTGAAAATAAAGAATATATAAACTAACTT
1 TATTTGCTCCCATCCCTCCCCCCACCAAAAAAATAATTGAAAATAAAGAATATATAAACTAACTT
*
1912446 GCCTTATGTTTCTGTTTGCTCTTAACAATGAGTGCTTCCTAGATGTTGTTCTTACTATGGAGAAT
66 GCCTTATGTTTCTGTTTGCTCTTAACAATGAGTGCTTCCTAGATGTTGTTCTTACTATCGAGAAT
1912511 AACATTACAATTGCAAAGATATTTCAGGTATTTCAATTTAGTCAAAAAAATCTGTTCTTTGTTCA
131 AACATTACAATTGCAAAGATATTTCAGGTATTTCAATTTAGTCAAAAAAATCTGTTCTTTGTTCA
1912576 TTCAAGTTC
196 TTCAAGTTC
*
1912585 TATTTGCTCCCATCCCTCCCCCTACCAAAAAAATAATTGAAAATAAAGAATATATAAACTAACTT
1 TATTTGCTCCCATCCCTCCCCCCACCAAAAAAATAATTGAAAATAAAGAATATATAAACTAACTT
*
1912650 GCCTTATGTTTCTGTTTGTTCTTAACAATGAGTGCTTCCTAGATGTTGTTCTTACTATCGAGAAT
66 GCCTTATGTTTCTGTTTGCTCTTAACAATGAGTGCTTCCTAGATGTTGTTCTTACTATCGAGAAT
*
1912715 AACATTACAATTGCAAAGATATTTCAGGTATTTCAATTTAGTCAAAAAAATCTGTTCTTTGTTCG
131 AACATTACAATTGCAAAGATATTTCAGGTATTTCAATTTAGTCAAAAAAATCTGTTCTTTGTTCA
1912780 TTCAAGTTC
196 TTCAAGTTC
1912789 TATT
1 TATT
1912793 AGTGGTTGAA
Statistics
Matches: 204, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
204 204 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (204 bp):
TATTTGCTCCCATCCCTCCCCCCACCAAAAAAATAATTGAAAATAAAGAATATATAAACTAACTT
GCCTTATGTTTCTGTTTGCTCTTAACAATGAGTGCTTCCTAGATGTTGTTCTTACTATCGAGAAT
AACATTACAATTGCAAAGATATTTCAGGTATTTCAATTTAGTCAAAAAAATCTGTTCTTTGTTCA
TTCAAGTTC
Found at i:1924403 original size:24 final size:24
Alignment explanation
Indices: 1924376--1924423 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1924366 TTTGCATTGA
* *
1924376 AAATTTTCTGATTAGTCTCTCCTT
1 AAATTATCTGATTACTCTCTCCTT
1924400 AAATTATCTGATTACTCTCTCCTT
1 AAATTATCTGATTACTCTCTCCTT
1924424 TTAGTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTATCTGATTACTCTCTCCTT
Found at i:1925115 original size:25 final size:23
Alignment explanation
Indices: 1925087--1925133 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1925077 CCATTGAGGT
* *
1925087 ATTTTTGTTATCTGTAATGTTGATA
1 ATTTCTGTGATCTG-AAT-TTGATA
1925112 ATTTCTGTGATCTGAATTTGAT
1 ATTTCTGTGATCTGAATTTGAT
1925134 TTCTGGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.53
Consensus pattern (23 bp):
ATTTCTGTGATCTGAATTTGATA
Found at i:1928339 original size:14 final size:14
Alignment explanation
Indices: 1928320--1928353 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1928310 ATATATAAAT
1928320 TTATATCTTAATAA
1 TTATATCTTAATAA
*
1928334 TTATATATTAATAA
1 TTATATCTTAATAA
1928348 -TATATC
1 TTATATC
1928354 AAATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATATCTTAATAA
Found at i:1931893 original size:2 final size:2
Alignment explanation
Indices: 1931886--1931917 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1931876 TTTATGGATA
1931886 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
1931918 TCAAATATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1932578 original size:2 final size:2
Alignment explanation
Indices: 1932571--1932600 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1932561 ATTTTAACTC
1932571 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
1932601 CTTCAATCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1933047 original size:3 final size:3
Alignment explanation
Indices: 1933039--1933094 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1933029 TCGAGTTAAT
1933039 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1933087 GAA GAA GA
1 GAA GAA GA
1933095 TTTCATTGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1934382 original size:18 final size:18
Alignment explanation
Indices: 1934360--1934400 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1934350 ATAATATATT
1934360 TATATATAAAAATAATAAAA
1 TATA-ATAAAAAT-ATAAAA
*
1934380 TATAATATAAATATAAAA
1 TATAATAAAAATATAAAA
1934398 TAT
1 TAT
1934401 TTTAAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAATAAAAATATAAAA
Found at i:1934487 original size:18 final size:18
Alignment explanation
Indices: 1934456--1934505 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1934446 TAAATATTAA
* *
1934456 ATAAATTTATAATACAAT
1 ATAAATATAAAATACAAT
1934474 A-AAATATATAAATACAAT
1 ATAAATATA-AAATACAAT
1934492 ATAAATATAAAATA
1 ATAAATATAAAATA
1934506 TATTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.21
18 15 0.54
19 7 0.25
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATATAAAATACAAT
Found at i:1934492 original size:13 final size:13
Alignment explanation
Indices: 1934447--1934508 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
1934437 AATTTTATAT
1934447 AAATAT-TAAATA
1 AAATATATAAATA
*
1934459 AATTTATAATACAATA
1 AA-ATAT-ATA-AATA
1934475 AAATATATAAATA
1 AAATATATAAATA
*
1934488 CAATATA-AATATA
1 AAATATATAA-ATA
1934501 AAATATAT
1 AAATATAT
1934509 TTTTATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 4 0.10
13 22 0.55
14 3 0.08
15 5 0.12
16 6 0.15
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATATAAATA
Found at i:1935378 original size:11 final size:12
Alignment explanation
Indices: 1935356--1935391 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
1935346 ATTTTCATGA
1935356 ATAAATTTATTT
1 ATAAATTTATTT
1935368 ATAAA-TTATTT
1 ATAAATTTATTT
1935379 A-AAATTTATTT
1 ATAAATTTATTT
1935390 AT
1 AT
1935392 TATTTGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.14
11 14 0.64
12 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATTTATTT
Found at i:1935407 original size:15 final size:16
Alignment explanation
Indices: 1935389--1935426 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1935379 AAAATTTATT
1935389 TATTATTTGATA-TAA
1 TATTATTTGATATTAA
*
1935404 TATTA-TTGATATTAT
1 TATTATTTGATATTAA
1935419 TATTATTT
1 TATTATTT
1935427 ATGTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 12 0.60
16 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TATTATTTGATATTAA
Found at i:1935595 original size:20 final size:20
Alignment explanation
Indices: 1935548--1935610 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
1935538 AGATTTATTT
*
1935548 ATTT-ATTATTCATAAATAA
1 ATTTAATTAATCATAAATAA
*
1935567 ATTTTTAATTAATCATGAATAA
1 A--TTTAATTAATCATAAATAA
*
1935589 ATTTAATTATAT-ATTAATAA
1 ATTTAATTA-ATCATAAATAA
1935609 AT
1 AT
1935611 ATATTCATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.03
20 17 0.46
21 5 0.14
22 14 0.38
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTAATTAATCATAAATAA
Found at i:1935628 original size:23 final size:23
Alignment explanation
Indices: 1935599--1935650 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1935589 ATTTAATTAT
*
1935599 ATATTAATAAATATATTCATTTA
1 ATATTAACAAATATATTCATTTA
*
1935622 ATATTAACAAATATATTTATTTA
1 ATATTAACAAATATATTCATTTA
1935645 AT-TTAA
1 ATATTAA
1935651 ATGAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTAACAAATATATTCATTTA
Found at i:1937806 original size:20 final size:21
Alignment explanation
Indices: 1937764--1937807 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1937754 TGTATCTGAT
*
1937764 AAATAAATATAACAACAATAA
1 AAATAAATATAACAACAAAAA
1937785 AAATAAATA-AATC-ACAAAAA
1 AAATAAATATAA-CAACAAAAA
1937805 AAA
1 AAA
1937808 GGGGGGAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (21 bp):
AAATAAATATAACAACAAAAA
Found at i:1939068 original size:20 final size:20
Alignment explanation
Indices: 1939046--1939084 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1939036 ATATCTAAAC
*
1939046 TTTAATAAATAATTCTTAACT
1 TTTAA-AAATAATTATTAACT
1939067 TTTAAAAATAATTATTAA
1 TTTAAAAATAATTATTAA
1939085 TTATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAAAAATAATTATTAACT
Found at i:1939439 original size:12 final size:12
Alignment explanation
Indices: 1939433--1939470 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1939423 AATTTATATT
1939433 TATATTTAAATA
1 TATATTTAAATA
1939445 TATA-TTAAATA
1 TATATTTAAATA
*
1939456 TAAAATTTAAATA
1 T-ATATTTAAATA
1939469 TA
1 TA
1939471 AATACTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 8 0.35
12 7 0.30
13 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:1939461 original size:18 final size:19
Alignment explanation
Indices: 1939404--1939461 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
1939394 TTAAATTTTT
1939404 TATATAATTAAAATATTAAAA
1 TATAT-ATT-AAATATTAAAA
* * *
1939425 TTTATATT-TATATTTAAA
1 TATATATTAAATATTAAAA
1939443 TATATATTAAATA-TAAAA
1 TATATATTAAATATTAAAA
1939461 T
1 T
1939462 TTAAATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 20 0.67
19 3 0.10
20 3 0.10
21 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATATTAAATATTAAAA
Found at i:1941261 original size:2 final size:2
Alignment explanation
Indices: 1941254--1941282 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1941244 GACCGTCCAC
1941254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1941283 TACAAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1942102 original size:2 final size:2
Alignment explanation
Indices: 1942095--1942123 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1942085 TATACAAAAT
1942095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1942124 CTTGTTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1950956 original size:20 final size:20
Alignment explanation
Indices: 1950928--1950987 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1950918 ATTTTTATGT
1950928 AAATTTAATTATAAAATATA
1 AAATTTAATTATAAAATATA
* *
1950948 AAATATAA-TATAAATAAATA
1 AAATTTAATTATAAA-ATATA
1950968 AAATTTAAATTTATAAAATA
1 AAATTT-AA-TTATAAAATA
1950988 AATTGAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.19
20 16 0.50
21 2 0.06
22 2 0.06
23 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTTAATTATAAAATATA
Found at i:1950990 original size:28 final size:26
Alignment explanation
Indices: 1950938--1951018 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 26
1950928 AAATTTAATT
* *
1950938 ATAAAATATAAAATATAATATAAATAA
1 ATAAAAT-TTAAATATAAAATAAATAA
*
1950965 ATAAAATTTAAATTTATAAAATAAATTGA
1 ATAAAATTTAAA--TATAAAATAAA-TAA
1950994 ATAAAA-TTAAATATAAATATAAATA
1 ATAAAATTTAAATATAAA-ATAAATA
1951019 TAATTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
26 11 0.24
27 12 0.26
28 15 0.33
29 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (26 bp):
ATAAAATTTAAATATAAAATAAATAA
Found at i:1951010 original size:6 final size:6
Alignment explanation
Indices: 1950927--1951021 Score: 62
Period size: 6 Copynumber: 16.5 Consensus size: 6
1950917 TATTTTTATG
* * *
1950927 TAAATT TAATTA TAAAATA TAAA-A TATAATA T-AA-A TAAATA -AAATT
1 TAAATA TAAATA T-AAATA TAAATA TA-AATA TAAATA TAAATA TAAATA
*
1950973 TAAATTTA TAAA-A TAAAT- TGAATA -AAAT- TAAATA TAAATA TAAATA
1 TAAA--TA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1951019 TAA
1 TAA
1951022 TTTTAAAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
4 2 0.03
5 27 0.39
6 29 0.41
7 7 0.10
8 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:1954798 original size:14 final size:14
Alignment explanation
Indices: 1954779--1954824 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1954769 TTTTTATAAA
*
1954779 AAAAATTATAATTT
1 AAAAATTAAAATTT
*
1954793 AAAAATAAAAATATT
1 AAAAATTAAAAT-TT
*
1954808 AAATATTAAAATTT
1 AAAAATTAAAATTT
1954822 AAA
1 AAA
1954825 CTCTTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAATTAAAATTT
Found at i:1954808 original size:22 final size:22
Alignment explanation
Indices: 1954777--1954818 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1954767 TTTTTTTATA
1954777 AAAAAAATTATAAT-TTAAAAAT
1 AAAAAAATTA-AATATTAAAAAT
*
1954799 AAAAATATTAAATATTAAAA
1 AAAAAAATTAAATATTAAAA
1954819 TTTAAACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAAATTAAATATTAAAAAT
Found at i:1967545 original size:27 final size:27
Alignment explanation
Indices: 1967507--1967560 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1967497 AAAGAAAATT
1967507 CCCATTTACGGTTTATTTATTTATTTA
1 CCCATTTACGGTTTATTTATTTATTTA
1967534 CCCATTTACGGTTTATTTATTTATTTA
1 CCCATTTACGGTTTATTTATTTATTTA
1967561 TTATCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (27 bp):
CCCATTTACGGTTTATTTATTTATTTA
Found at i:1967828 original size:15 final size:15
Alignment explanation
Indices: 1967804--1967843 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1967794 ACACTATCAA
*
1967804 AAATAAAATTTCATG
1 AAATATAATTTCATG
1967819 AAATATAATTTCATG
1 AAATATAATTTCATG
*
1967834 AACTATAATT
1 AAATATAATT
1967844 ACGTGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (15 bp):
AAATATAATTTCATG
Found at i:1973360 original size:23 final size:21
Alignment explanation
Indices: 1973300--1973360 Score: 52
Period size: 23 Copynumber: 2.8 Consensus size: 21
1973290 TCTAATTGAA
*
1973300 TTAA-TTTAAATAATTTAATT
1 TTAATTTTAAATAATTAAATT
* *
1973320 TTTATTTTATATAAAATTAAATT
1 TTAATTTTA-A-ATAATTAAATT
1973343 TTAAATTTTAAATCAATT
1 TT-AATTTTAAAT-AATT
1973361 TTAAACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 2 0.06
23 16 0.52
24 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATTTTAAATAATTAAATT
Found at i:1973372 original size:17 final size:18
Alignment explanation
Indices: 1973339--1973372 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1973329 TATAAAATTA
*
1973339 AATTTTAAATTTTAAATC
1 AATTTTAAATCTTAAATC
1973357 AATTTTAAA-CTTAAAT
1 AATTTTAAATCTTAAAT
1973373 TTATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTTAAATCTTAAATC
Found at i:1973750 original size:16 final size:16
Alignment explanation
Indices: 1973729--1973760 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1973719 AATTATATTT
1973729 GGTTCTGATTTAAATC
1 GGTTCTGATTTAAATC
1973745 GGTTCTGATTTAAATC
1 GGTTCTGATTTAAATC
1973761 TTTCCTTTAT
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:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
GGTTCTGATTTAAATC
Found at i:1977511 original size:14 final size:14
Alignment explanation
Indices: 1977492--1977521 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1977482 CATTTTTAGT
1977492 ACACACACACCCAC
1 ACACACACACCCAC
1977506 ACACACACACCCAC
1 ACACACACACCCAC
1977520 AC
1 AC
1977522 CTATAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.57, G:0.00, T:0.00
Consensus pattern (14 bp):
ACACACACACCCAC
Found at i:1979395 original size:20 final size:22
Alignment explanation
Indices: 1979372--1979422 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1979362 ATTTTTAAAA
1979372 ATATTAA-AAATAT-TATTTTT
1 ATATTAATAAATATATATTTTT
**
1979392 ATATTAATATTTATATATTTTT
1 ATATTAATAAATATATATTTTT
1979414 ATAATTAAT
1 AT-ATTAAT
1979423 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 4 0.15
22 9 0.35
23 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTAATAAATATATATTTTT
Found at i:1982098 original size:25 final size:24
Alignment explanation
Indices: 1982070--1982122 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
1982060 TCTGTTAATA
1982070 TTTAATATTATAAT-TGATTTATATT
1 TTTAATATTATAATAT-ATTT-TATT
* *
1982095 TTTAATTTTGTAATATATTTTATT
1 TTTAATATTATAATATATTTTATT
1982119 TTTA
1 TTTA
1982123 TATAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 16 0.64
26 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTAATATTATAATATATTTTATT
Found at i:1987230 original size:49 final size:50
Alignment explanation
Indices: 1987158--1987258 Score: 177
Period size: 49 Copynumber: 2.0 Consensus size: 50
1987148 ATTGAGAATA
1987158 TCTGTGACAAAGAACACCTGTATAAAGCTGCCA-TTTGTAAAACCTTTCT
1 TCTGTGACAAAGAACACCTGTATAAAGCTGCCATTTTGTAAAACCTTTCT
* *
1987207 TCTGTGACAGAGAACACTTGTATAAAGCTGCCATTTTGTAAAACCTTTCT
1 TCTGTGACAAAGAACACCTGTATAAAGCTGCCATTTTGTAAAACCTTTCT
1987257 TC
1 TC
1987259 CCATCATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 31 0.63
50 18 0.37
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (50 bp):
TCTGTGACAAAGAACACCTGTATAAAGCTGCCATTTTGTAAAACCTTTCT
Found at i:1992067 original size:2 final size:2
Alignment explanation
Indices: 1992060--1992092 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1992050 AACAGCTGCT
1992060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1992093 GTCCTGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1997779 original size:15 final size:14
Alignment explanation
Indices: 1997752--1997809 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
1997742 TCGTCGCTAA
1997752 TTTATATACTTATAT
1 TTTATATA-TTATAT
1997767 TTTATTATATTATAT
1 TTTA-TATATTATAT
* **
1997782 TTATATTTAAAATAT
1 TT-TATATATTATAT
1997797 TTTATAT-TTATAT
1 TTTATATATTATAT
1997810 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 21 0.60
16 6 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATATATTATAT
Found at i:1997788 original size:16 final size:16
Alignment explanation
Indices: 1997756--1997841 Score: 54
Period size: 16 Copynumber: 5.3 Consensus size: 16
1997746 CGCTAATTTA
1997756 TATACTTATATTT-TAT
1 TATA-TTATATTTATAT
1997772 TATATTATATTTATAT
1 TATATTATATTTATAT
**
1997788 T-TAAAATATTTTATAT
1 TATATTATA-TTTATAT
* *
1997804 T-TATATAAATTTA-AA
1 TATAT-TATATTTATAT
*
1997819 TATATTAATAATTTATTT
1 TATATT-AT-ATTTATAT
1997837 TATAT
1 TATAT
1997842 AAATTTTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
15 16 0.30
16 26 0.48
17 7 0.13
18 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTATATTTATAT
Found at i:1997839 original size:32 final size:33
Alignment explanation
Indices: 1997792--1997856 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1997782 TTATATTTAA
*
1997792 AATATTTTATATTTATATAAA-TTTAAATATATT
1 AATAATTTATATTTATATAAATTTTAAA-ATATT
1997825 AATAATTTAT-TTTATATAAATTTTAAAATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
1997857 TATTATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAAAATATT
Found at i:1998917 original size:15 final size:14
Alignment explanation
Indices: 1998897--1998977 Score: 55
Period size: 15 Copynumber: 5.9 Consensus size: 14
1998887 TATATAAATT
1998897 TTTATATATTAATAA
1 TTTATATATT-ATAA
*
1998912 TTTATATATTTATGA
1 TTTATATA-TTATAA
*
1998927 TATATTATATTAT-A
1 TTTA-TATATTATAA
1998941 TTT-TATATTAT-A
1 TTTATATATTATAA
* *
1998953 TTCATAAAATTAT-A
1 TTTAT-ATATTATAA
1998967 TTTA-ATATTAT
1 TTTATATATTAT
1998978 TATATTTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 17 0.31
13 1 0.02
14 13 0.24
15 18 0.33
16 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (14 bp):
TTTATATATTATAA
Found at i:1998946 original size:12 final size:12
Alignment explanation
Indices: 1998913--1998977 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1998903 TATTAATAAT
*
1998913 TTATATATT-TA
1 TTATATTTTATA
* *
1998924 TGATATATTATA
1 TTATATTTTATA
1998936 TTATATTTTATA
1 TTATATTTTATA
* *
1998948 TTATATTCATAAAA
1 TTATATT--TTATA
*
1998962 TTATATTTAATA
1 TTATATTTTATA
1998974 TTAT
1 TTAT
1998978 TATATTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
11 8 0.18
12 27 0.60
14 10 0.22
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:1998981 original size:15 final size:15
Alignment explanation
Indices: 1998853--1998987 Score: 62
Period size: 17 Copynumber: 8.4 Consensus size: 15
1998843 GTGTTTTTTT
*
1998853 TTTATTATTATTATCA
1 TTTAATATTATTAT-A
1998869 TTTAAAATATT-TTATA
1 TTT--AATATTATTATA
*
1998885 TTTATATAAATTTTTATA
1 TTTA-AT--ATTATTATA
1998903 TATTAATAATT-TATATA
1 T-TTAAT-ATTAT-TATA
1998920 TTT-ATGATATATTATA
1 TTTAAT-AT-TATTATA
* *
1998936 TTATATTTTATATTATA
1 TT-TAATAT-TATTATA
* **
1998953 -TTCATAAAATTATA
1 TTTAATATTATTATA
1998967 TTTAATATTATTATA
1 TTTAATATTATTATA
1998982 TTTAAT
1 TTTAAT
1998988 TTTTTTTAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.07
15 25 0.27
16 18 0.19
17 27 0.29
18 14 0.15
19 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (15 bp):
TTTAATATTATTATA
Found at i:2000038 original size:20 final size:19
Alignment explanation
Indices: 2000023--2000068 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 19
2000013 GATATTTTTA
2000023 TTAAATTAATTTTATTTATT
1 TTAAA-TAATTTTATTTATT
2000043 TTAAATAATTATTTATTTAATT
1 TTAAATAA-T-TTTATTT-ATT
2000065 TTAA
1 TTAA
2000069 TTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.13
20 6 0.26
21 7 0.30
22 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATAATTTTATTTATT
Found at i:2000284 original size:20 final size:20
Alignment explanation
Indices: 2000261--2000298 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2000251 TAATAAAATT
*
2000261 TTTAA-AAATATATTTATAAA
1 TTTAATAAA-ATATGTATAAA
2000281 TTTAATAAAATATGTATA
1 TTTAATAAAATATGTATA
2000299 TTTACATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTAATAAAATATGTATAAA
Found at i:2000289 original size:32 final size:34
Alignment explanation
Indices: 2000229--2000291 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
2000219 ATTTTTTAAA
*
2000229 TAAAAATTTATCTGATAAATTATAATAAAATTTT
1 TAAAAATATATCTGATAAATTATAATAAAATTTT
*
2000263 TAAAAATATAT-TTATAAATT-TAATAAAAT
1 TAAAAATATATCTGATAAATTATAATAAAAT
2000292 ATGTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 9 0.33
33 8 0.30
34 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (34 bp):
TAAAAATATATCTGATAAATTATAATAAAATTTT
Found at i:2000747 original size:17 final size:19
Alignment explanation
Indices: 2000725--2000759 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2000715 GTAGTTTACT
2000725 CCAAAA-AAA-AAAAAATC
1 CCAAAATAAATAAAAAATC
2000742 CCAAAATAAATAAAAAAT
1 CCAAAATAAATAAAAAAT
2000760 TAAATATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.11
Consensus pattern (19 bp):
CCAAAATAAATAAAAAATC
Found at i:2000913 original size:44 final size:45
Alignment explanation
Indices: 2000863--2000948 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
2000853 ATTTCAAGTT
2000863 TTTATATGAACAAA-GCCCTTTAAAGATCAAAGGCC-ATTGTTTAA
1 TTTATATGAACAAAGGCCCTTTAAAGATCAAA-GCCTATTGTTTAA
2000907 TTTATATGAACAAAGGCCCTTTAAAGATCAAAGCCTATTGTT
1 TTTATATGAACAAAGGCCCTTTAAAGATCAAAGCCTATTGTT
2000949 GGAAAGGCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
44 17 0.43
45 23 0.57
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (45 bp):
TTTATATGAACAAAGGCCCTTTAAAGATCAAAGCCTATTGTTTAA
Found at i:2011059 original size:14 final size:16
Alignment explanation
Indices: 2011042--2011078 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2011032 TCTTTTTTGG
2011042 TTCTTTT-TT-TTCTC
1 TTCTTTTCTTCTTCTC
2011056 TTCTTATTCTTCTTCTC
1 TTCTT-TTCTTCTTCTC
2011073 TTCTTT
1 TTCTTT
2011079 AAGTCCGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 2 0.10
16 3 0.15
17 10 0.50
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTTCTTCTTCTC
Found at i:2015960 original size:2 final size:2
Alignment explanation
Indices: 2015953--2015993 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2015943 TTTAATCCAT
2015953 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2015994 AAGTAGCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2018259 original size:20 final size:20
Alignment explanation
Indices: 2018236--2018274 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2018226 TGTTACAAAC
2018236 AAAAATAATATAAATATATT
1 AAAAATAATATAAATATATT
* *
2018256 AAAATTTATATAAATATAT
1 AAAAATAATATAAATATAT
2018275 AATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATAATATAAATATATT
Found at i:2018270 original size:10 final size:10
Alignment explanation
Indices: 2018238--2018318 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 10
2018228 TTACAAACAA
2018238 AAATA-ATAT
1 AAATATATAT
2018247 AAATATAT-T
1 AAATATATAT
*
2018256 AAA-ATTTAT
1 AAATATATAT
2018265 ATAA-ATATAT
1 A-AATATATAT
*
2018275 -AATAT-TTT
1 AAATATATAT
2018283 AAATATA-ATT
1 AAATATATA-T
*
2018293 ATAATATATAA
1 A-AATATATAT
2018304 AAATATTATAT
1 AAATA-TATAT
2018315 AAAT
1 AAAT
2018319 TACCATCGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
8 7 0.12
9 18 0.32
10 15 0.27
11 15 0.27
12 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATATATAT
Found at i:2018283 original size:20 final size:20
Alignment explanation
Indices: 2018243--2018299 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2018233 AACAAAAATA
*
2018243 ATATAAATATATTAA-AATTT
1 ATATAAATATA-TAATATTTT
2018263 ATATAAATATATAATATTTT
1 ATATAAATATATAATATTTT
*
2018283 AAATATAAT-TATAATAT
1 ATATA-AATATATAATAT
2018300 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATAAATATATAATATTTT
Found at i:2018315 original size:20 final size:19
Alignment explanation
Indices: 2018270--2018320 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
2018260 TTTATATAAA
**
2018270 TATATAATATTTTAAATAT
1 TATATAATATTAAAAATAT
*
2018289 AATTATAATATATAAAAATAT
1 TA-TATAATAT-TAAAAATAT
2018310 TATATAA-ATTA
1 TATATAATATTA
2018321 CCATCGTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 13 0.50
21 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATAATATTAAAAATAT
Found at i:2027290 original size:17 final size:17
Alignment explanation
Indices: 2027229--2027290 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 17
2027219 ATATTCTTTT
*
2027229 AAAT-AAAATAAATGTTC
1 AAATAAAAAAAAAT-TTC
2027246 AAATAAAAAAATAATTATAC
1 AAATAAAAAAA-AATT-T-C
2027266 TTAAATAAAAAAAAATTTC
1 --AAATAAAAAAAAATTTC
2027285 AAATAA
1 AAATAA
2027291 TTAATCATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
17 10 0.26
18 6 0.16
19 5 0.13
20 2 0.05
21 4 0.11
22 11 0.29
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAAAAAAAAATTTC
Found at i:2027393 original size:18 final size:18
Alignment explanation
Indices: 2027360--2027407 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
2027350 ATTTTAAATA
2027360 AAATTTTAATTAATTTAATT
1 AAATTTTAA-TAATTT-ATT
*
2027380 TAA-TTTAATAATTTATT
1 AAATTTTAATAATTTATT
2027397 AAATTTTAATA
1 AAATTTTAATA
2027408 TTATTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 5 0.20
18 13 0.52
19 5 0.20
20 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTTTAATAATTTATT
Found at i:2027453 original size:15 final size:16
Alignment explanation
Indices: 2027428--2027457 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2027418 ATAAAATTTT
2027428 AAATTATTTTAAATTA
1 AAATTATTTTAAATTA
2027444 AAATTA-TTTAAATT
1 AAATTATTTTAAATT
2027458 TGAGAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTATTTTAAATTA
Found at i:2027991 original size:26 final size:25
Alignment explanation
Indices: 2027962--2028036 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 25
2027952 TTTATGTAAT
2027962 TAAATTTTAAAAATAATAATTTTTAA
1 TAAATTTTAAAAATAAT-ATTTTTAA
** **
2027988 TAAA-TTTAATATTTAATATTTATTTT
1 TAAATTTTAA-AAATAATATTT-TTAA
2028014 TAAATTTTAAAAAT-ATGATTTTT
1 TAAATTTTAAAAATAAT-ATTTTT
2028037 TTAAACTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
25 13 0.33
26 21 0.54
27 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAATTTTAAAAATAATATTTTTAA
Found at i:2030997 original size:22 final size:20
Alignment explanation
Indices: 2030968--2031038 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 20
2030958 ATTTGATTTG
2030968 ATTTATTTATTTAAGTTAAAA
1 ATTTATTTATTTAA-TTAAAA
* *
2030989 TTATTATTTATTTTATTAAAA
1 AT-TTATTTATTTAATTAAAA
*
2031010 ATTTA-TT-TTTAATT-AAT
1 ATTTATTTATTTAATTAAAA
*
2031027 ATTTATATATTT
1 ATTTATTTATTT
2031039 TATATTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
19 5 0.12
20 3 0.07
21 8 0.20
22 11 0.27
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (20 bp):
ATTTATTTATTTAATTAAAA
Found at i:2031038 original size:21 final size:21
Alignment explanation
Indices: 2031013--2031052 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2031003 ATTAAAAATT
2031013 TATTTT-TAATTAATATTTATA
1 TATTTTATAATTAAT-TTTATA
*
2031034 TATTTTATATTTAATTTTA
1 TATTTTATAATTAATTTTA
2031053 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTATAATTAATTTTATA
Found at i:2031095 original size:20 final size:21
Alignment explanation
Indices: 2031047--2031098 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2031037 TTTATATTTA
*
2031047 ATTTTAAA-TAAAAATATGTT
1 ATTTTAAATTAAAAATATATT
*
2031067 ATTTT-AATTTAAAAT-TATT
1 ATTTTAAATTAAAAATATATT
2031086 ATTTTAAATTAAA
1 ATTTTAAATTAAA
2031099 CTGAATCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTTAAATTAAAAATATATT
Found at i:2031796 original size:28 final size:28
Alignment explanation
Indices: 2031755--2031810 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2031745 ATATTGAGAA
*
2031755 TTTAATTTAAATATAT-TAAATATTATAT
1 TTTAATATAAATATATAT-AATATTATAT
*
2031783 TTTAATATATATATATATAATATTATAT
1 TTTAATATAAATATATATAATATTATAT
2031811 ACATTCTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAATATAAATATATATAATATTATAT
Found at i:2031800 original size:23 final size:22
Alignment explanation
Indices: 2031759--2031806 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2031749 TGAGAATTTA
*
2031759 ATTTAAATATATTAAATATTAT
1 ATTTAAATATATTAAATATAAT
* *
2031781 ATTTTAATATATATATATATAAT
1 ATTTAAATATAT-TAAATATAAT
2031804 ATT
1 ATT
2031807 ATATACATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTAAATATATTAAATATAAT
Found at i:2032302 original size:25 final size:25
Alignment explanation
Indices: 2032272--2032321 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2032262 ATATGACAAA
*
2032272 TAAAAAGACACGTGCTAATATTTTAT
1 TAAAAA-ACACGTGATAATATTTTAT
* *
2032298 TAAAAAATATGTGATAATATTTTA
1 TAAAAAACACGTGATAATATTTTA
2032322 ATATTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (25 bp):
TAAAAAACACGTGATAATATTTTAT
Found at i:2033127 original size:22 final size:22
Alignment explanation
Indices: 2033095--2033150 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2033085 TATGGTGATA
*
2033095 TTTAAATAAATTAT-TTTTAAAAT
1 TTTAAA-AAATTATATATT-AAAT
*
2033118 TTTAAAAAATAATATATTAAAT
1 TTTAAAAAATTATATATTAAAT
*
2033140 ATTAAAAAATT
1 TTTAAAAAATT
2033151 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAAAATTATATATTAAAT
Found at i:2038141 original size:2 final size:2
Alignment explanation
Indices: 2038134--2038163 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2038124 ATTTAAATAC
2038134 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
2038164 TTACTTCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2040229 original size:18 final size:18
Alignment explanation
Indices: 2040180--2040231 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2040170 AATATAATTT
2040180 TTAATTTTAATAATATAATA
1 TTAATTTTAAT-AT-TAATA
*
2040200 TT-ATTTAAATATTAATA
1 TTAATTTTAATATTAATA
*
2040217 TTAATTTTTATATTA
1 TTAATTTTAATATTA
2040232 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.25
18 12 0.43
19 7 0.25
20 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTTTAATATTAATA
Found at i:2040235 original size:21 final size:21
Alignment explanation
Indices: 2040157--2040235 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
2040147 TTAATATGCC
*
2040157 TTTTTAT-TATATCAATA-TAA
1 TTTTTATAT-TATTAATATTAA
* * *
2040177 TTTTTAATTTTAATAATATAATA
1 TTTTT-ATATTATTAATATTA-A
*
2040200 TTATTTA-AATATTAATATTAA
1 TT-TTTATATTATTAATATTAA
2040221 TTTTTATATTATTAA
1 TTTTTATATTATTAA
2040236 AAATTACGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
20 9 0.20
21 18 0.40
22 11 0.24
23 4 0.09
24 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTATATTATTAATATTAA
Found at i:2040587 original size:3 final size:3
Alignment explanation
Indices: 2040579--2040604 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2040569 CCATTTATTC
2040579 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
2040605 CGTTGGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2041581 original size:2 final size:2
Alignment explanation
Indices: 2041576--2041602 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2041566 TCTCTCTCTC
2041576 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2041603 CTGCCATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2049666 original size:2 final size:2
Alignment explanation
Indices: 2049661--2049711 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
2049651 ATAATGTGTG
* * *
2049661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2049703 TA CA TA TA T
1 TA TA TA TA T
2049712 TAAAAAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2059062 original size:2 final size:2
Alignment explanation
Indices: 2059055--2059085 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2059045 TGTAGCAGTG
2059055 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2059086 CCCCCTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2059720 original size:20 final size:21
Alignment explanation
Indices: 2059687--2059734 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
2059677 TTGGTAAATG
*
2059687 TTTTTAATTATTTAAATT-TTA
1 TTTTTTATTATTT-AATTATTA
2059708 TTTTTTATT-TTTAATTATTA
1 TTTTTTATTATTTAATTATTA
2059728 TTTTTTA
1 TTTTTTA
2059735 AATAAAACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTATTATTTAATTATTA
Found at i:2060390 original size:3 final size:3
Alignment explanation
Indices: 2060382--2060408 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2060372 AGGCATACCA
2060382 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2060409 TTGGCAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2060663 original size:13 final size:13
Alignment explanation
Indices: 2060645--2060669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2060635 TAAATTTAGA
2060645 TAAAAATTATTTT
1 TAAAAATTATTTT
2060658 TAAAAATTATTT
1 TAAAAATTATTT
2060670 ATTTATCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAAATTATTTT
Found at i:2064273 original size:2 final size:2
Alignment explanation
Indices: 2064266--2064300 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2064256 TAAACCCTCA
2064266 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2064301 ACTGTCGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2072556 original size:2 final size:2
Alignment explanation
Indices: 2072549--2072586 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
2072539 GCATACATGC
2072549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
2072587 AACTACAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2078356 original size:30 final size:30
Alignment explanation
Indices: 2078300--2078356 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2078290 TTTAGATTAG
*
2078300 ATTAATAAATTTATTTTATTATTTAAAAAT
1 ATTAATAAATTTATTTTATTAATTAAAAAT
2078330 ATTAA-AAATATTATTTT-TATAATTAAA
1 ATTAATAAAT-TTATTTTAT-TAATTAAA
2078357 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTAATAAATTTATTTTATTAATTAAAAAT
Found at i:2080638 original size:21 final size:21
Alignment explanation
Indices: 2080612--2080653 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2080602 AAGAAGTAGA
2080612 AGTAGAAGGATTACTTCCCTT
1 AGTAGAAGGATTACTTCCCTT
2080633 AGTAGAAGGATTACTTCCCTT
1 AGTAGAAGGATTACTTCCCTT
2080654 GAAGATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
AGTAGAAGGATTACTTCCCTT
Found at i:2081946 original size:13 final size:13
Alignment explanation
Indices: 2081928--2081952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2081918 AATTTTTTTA
2081928 AAAAAATTATATC
1 AAAAAATTATATC
2081941 AAAAAATTATAT
1 AAAAAATTATAT
2081953 TTTCATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTATATC
Found at i:2085680 original size:27 final size:27
Alignment explanation
Indices: 2085642--2085693 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2085632 TTTTAAGACT
*
2085642 GCACATAGATGACGAAATTGTATTATA
1 GCACATAGATGACGAAATTGCATTATA
*
2085669 GCACATAGATGATGAAATTGCATTA
1 GCACATAGATGACGAAATTGCATTA
2085694 ATTTTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (27 bp):
GCACATAGATGACGAAATTGCATTATA
Found at i:2086184 original size:23 final size:23
Alignment explanation
Indices: 2086110--2086185 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
2086100 TGAATTAATT
2086110 TAAAATTT-TATATTATAATTTAAAA
1 TAAAATTTATA-ATTA-AATTT-AAA
* * * * *
2086135 TAATATTAAAAATT-ATTTTATAT
1 TAAAATTTATAATTAAATTTA-AA
2086158 TAAAATTTATAATTAAATTTAAA
1 TAAAATTTATAATTAAATTTAAA
2086181 TAAAA
1 TAAAA
2086186 ATATTTTTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 1 0.03
23 22 0.58
24 5 0.13
25 9 0.24
26 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAATTTATAATTAAATTTAAA
Found at i:2086194 original size:40 final size:40
Alignment explanation
Indices: 2086141--2086221 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
2086131 AAAATAATAT
2086141 TAAAAATTATTTTA-TAT-TAAAATTTATAATTAAATTTAAA
1 TAAAAATTATTTTATTATATAAAA--TATAATTAAATTTAAA
*
2086181 TAAAAA-TATTTTTATTATATAAAATATAATTTAATTTAAA
1 TAAAAATTA-TTTTATTATATAAAATATAATTAAATTTAAA
2086221 T
1 T
2086222 TATTAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
39 2 0.05
40 27 0.73
41 3 0.08
42 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
TAAAAATTATTTTATTATATAAAATATAATTAAATTTAAA
Found at i:2086234 original size:40 final size:40
Alignment explanation
Indices: 2086136--2086245 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 40
2086126 AATTTAAAAT
2086136 AATATTAAAAATTATT-TTATATTAAAATTTATAATTAAATTTA
1 AATATT-AAAATT-TTATTATA-TAAAA-TTATAATTAAATTTA
* *
2086179 AATA-AAAATATTTTTATTATATAAAA-TATAATTTAATTTA
1 AATATTAAA-A-TTTTATTATATAAAATTATAATTAAATTTA
2086219 AATTATTAAAATTTTATTTAATATAAA
1 AA-TATTAAAATTTTA-TT-ATATAAA
2086246 TTAGATGTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
40 20 0.35
41 8 0.14
42 18 0.32
43 11 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
AATATTAAAATTTTATTATATAAAATTATAATTAAATTTA
Found at i:2086237 original size:25 final size:26
Alignment explanation
Indices: 2086194--2086248 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
2086184 AAATATTTTT
*
2086194 ATTATATAAAATATAATTTAATTTAA
1 ATTATATAAAATATAATTTAATATAA
* *
2086220 ATTAT-TAAAATTTTATTTAATATAA
1 ATTATATAAAATATAATTTAATATAA
2086245 ATTA
1 ATTA
2086249 GATGTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTATATAAAATATAATTTAATATAA
Found at i:2090641 original size:2 final size:2
Alignment explanation
Indices: 2090634--2090665 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2090624 CCAAAAGTTT
2090634 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2090666 AATTCCAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2091491 original size:13 final size:13
Alignment explanation
Indices: 2091475--2091516 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2091465 CTTTTATGTA
2091475 TTTATATTATTTT
1 TTTATATTATTTT
2091488 TTTATATTATATATT
1 TTTATATTAT-T-TT
2091503 TTTA-ATTATTTT
1 TTTATATTATTTT
2091515 TT
1 TT
2091517 AAAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 11 0.41
14 6 0.22
15 6 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATATTATTTT
Found at i:2091502 original size:26 final size:27
Alignment explanation
Indices: 2091468--2091526 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2091458 CTTTAACCTT
* * *
2091468 TTATGTATTTAT-ATTATTTTTTTATA
1 TTATATATTTATAATTATTTTTTAAAA
*
2091494 TTATATATTTTTAATTATTTTTTAAAA
1 TTATATATTTATAATTATTTTTTAAAA
2091521 TTATAT
1 TTATAT
2091527 TTATATGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTATATATTTATAATTATTTTTTAAAA
Found at i:2092075 original size:23 final size:22
Alignment explanation
Indices: 2092049--2092100 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2092039 TAAAAACTAA
2092049 ATTTTAAATAAAACAATTTTATT
1 ATTTTAAATAAAA-AATTTTATT
** *
2092072 ATTTTTAAATTTAAATTTTTATT
1 A-TTTTAAATAAAAAATTTTATT
2092095 ATTTTA
1 ATTTTA
2092101 GATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 5 0.20
23 10 0.40
24 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAAATAAAAAATTTTATT
Found at i:2096869 original size:13 final size:15
Alignment explanation
Indices: 2096846--2096879 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2096836 ACTTACTTAT
2096846 AATTATTTA-TTTAA
1 AATTATTTATTTTAA
2096860 AATT-TTTATTTTAA
1 AATTATTTATTTTAA
2096874 AATTAT
1 AATTAT
2096880 AACGATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 13 0.72
15 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTTATTTTAA
Found at i:2097410 original size:18 final size:18
Alignment explanation
Indices: 2097387--2097433 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2097377 ATAAAACATG
2097387 ATATAA-AAAATAATATAA
1 ATATAATAAAATAA-ATAA
*
2097405 ATATAATACAATAAATAA
1 ATATAATAAAATAAATAA
*
2097423 ATATATTAAAA
1 ATATAATAAAA
2097434 CTAATAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATATAATAAAATAAATAA
Found at i:2097582 original size:21 final size:23
Alignment explanation
Indices: 2097556--2097600 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2097546 AATTTTTTAA
2097556 ATAAAAT-TTT-TATAATAAATT
1 ATAAAATATTTATATAATAAATT
*
2097577 ATAAAATATTTATATTATAAATT
1 ATAAAATATTTATATAATAAATT
2097600 A
1 A
2097601 AGATATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAAATATTTATATAATAAATT
Found at i:2097708 original size:18 final size:17
Alignment explanation
Indices: 2097676--2097709 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2097666 ACTTAATTAA
*
2097676 AAATAATATAAAATAAC
1 AAATAATAAAAAATAAC
2097693 AAATATATAAAAAATAA
1 AAATA-ATAAAAAATAA
2097710 ATTATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAATAAAAAATAAC
Found at i:2100513 original size:3 final size:3
Alignment explanation
Indices: 2100507--2100544 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2100497 ATAACAATCT
2100507 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2100545 GTATGATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2100557 original size:14 final size:14
Alignment explanation
Indices: 2100540--2100593 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
2100530 TAATAATAAT
*
2100540 AATAAGTATGATTA
1 AATAAGTATAATTA
*
2100554 AATAAATATAATATA
1 AATAAGTATAAT-TA
*
2100569 AATAA-AATAATTA
1 AATAAGTATAATTA
2100582 AATATAGTATAA
1 AATA-AGTATAA
2100594 ATATATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 6 0.18
14 16 0.48
15 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (14 bp):
AATAAGTATAATTA
Found at i:2100571 original size:11 final size:11
Alignment explanation
Indices: 2100555--2100598 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2100545 GTATGATTAA
2100555 ATAAATATAAT
1 ATAAATATAAT
*
2100566 ATAAATAAAAT
1 ATAAATATAAT
*
2100577 AATTAAATATAGT
1 -A-TAAATATAAT
2100590 ATAAATATA
1 ATAAATATA
2100599 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 18 0.64
12 2 0.07
13 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2100615 original size:29 final size:31
Alignment explanation
Indices: 2100583--2100655 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
2100573 AAATAATTAA
* *
2100583 ATATAGTATAAA-TATATATTT-TAAAATTT
1 ATATAATATAAATTATAAATTTATAAAATTT
2100612 ATATAATATAAATTATAAATTTATAAAATTT
1 ATATAATATAAATTATAAATTTATAAAATTT
2100643 ATATAAATATAAA
1 ATAT-AATATAAA
2100656 ATATTTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 11 0.28
30 8 0.21
31 12 0.31
32 8 0.21
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATAATATAAATTATAAATTTATAAAATTT
Found at i:2100631 original size:22 final size:22
Alignment explanation
Indices: 2100589--2100638 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2100579 TTAAATATAG
* *
2100589 TATAAATATATATTTTAAAATT
1 TATAAATATAAATTATAAAATT
2100611 TATATAATATAAATTAT-AAATT
1 TATA-AATATAAATTATAAAATT
2100633 TATAAA
1 TATAAA
2100639 ATTTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 13 0.52
23 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAAATATAAATTATAAAATT
Found at i:2100649 original size:19 final size:21
Alignment explanation
Indices: 2100625--2100674 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2100615 TAATATAAAT
2100625 TATAAATTTATAAA-A-TTTA
1 TATAAATTTATAAATATTTTA
*
2100644 TATAAATATA-AAATATTTTA
1 TATAAATTTATAAATATTTTA
*
2100664 TATAAAATTAT
1 TATAAATTTAT
2100675 GATATAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 10 0.40
20 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAAATTTATAAATATTTTA
Found at i:2100653 original size:17 final size:17
Alignment explanation
Indices: 2100604--2100657 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
2100594 ATATATATTT
2100604 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
2100620 T-AAA-TTATA-AATTTA
1 TAAAATTTATATAA-ATA
2100635 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
2100652 TAAAAT
1 TAAAAT
2100658 ATTTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
16 4 0.13
17 13 0.42
18 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:2100668 original size:31 final size:31
Alignment explanation
Indices: 2100589--2100681 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 31
2100579 TTAAATATAG
*
2100589 TATAAATATATATTT-TAAAATTTATAT-AA
1 TATAAATATAAATTTATAAAATTTATATAAA
2100618 TATAAATTATAAATTTATAAAATTTATATAAA
1 TATAAA-TATAAATTTATAAAATTTATATAAA
**
2100650 TATAAA-ATATTTTATATAAAATTATGATATAA
1 TATAAATATAAATT-TATAAAATT-T-ATATAA
2100682 TCAAATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
29 6 0.11
30 13 0.24
31 21 0.38
32 9 0.16
33 6 0.11
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
TATAAATATAAATTTATAAAATTTATATAAA
Found at i:2109157 original size:16 final size:16
Alignment explanation
Indices: 2109136--2109202 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
2109126 TAGATTTGGA
2109136 TCATTTC-AGGTTCGGG
1 TCATTTCGA-GTTCGGG
*
2109152 TCATTTCGAGTTCGAG
1 TCATTTCGAGTTCGGG
* * * *
2109168 TTATTTCGAATTTGGA
1 TCATTTCGAGTTCGGG
*
2109184 TCATTTCAAGTTCGGG
1 TCATTTCGAGTTCGGG
2109200 TCA
1 TCA
2109203 ATCGAGATTT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
16 38 0.97
17 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.40
Consensus pattern (16 bp):
TCATTTCGAGTTCGGG
Found at i:2109174 original size:32 final size:31
Alignment explanation
Indices: 2109069--2109174 Score: 79
Period size: 32 Copynumber: 3.3 Consensus size: 31
2109059 AAAATTTTTA
* * * *
2109069 GATTATTTTCAGGTTTGAGTTATTTTGAGTTC
1 GATTA-TTTCAGGTTCGGGTCATTTAGAGTTC
* * *
2109101 GAATTATTTC-GGATTCGGGCCACTTTAGATTTG
1 G-ATTATTTCAGG-TTCGGGTCA-TTTAGAGTTC
* *
2109134 GATCATTTCAGGTTCGGGTCATTTCGAGTTC
1 GATTATTTCAGGTTCGGGTCATTTAGAGTTC
2109165 GAGTTATTTC
1 GA-TTATTTC
2109175 GAATTTGGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
31 11 0.20
32 31 0.55
33 14 0.25
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (31 bp):
GATTATTTCAGGTTCGGGTCATTTAGAGTTC
Found at i:2110224 original size:20 final size:20
Alignment explanation
Indices: 2110177--2110229 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
2110167 ATATAATCAC
*
2110177 ATATTATATAATTAATTTAAA
1 ATATTATATTA-TAATTTAAA
* *
2110198 ATTTTATATTATAATTTATA
1 ATATTATATTATAATTTAAA
* *
2110218 GTATTATTTTAT
1 ATATTATATTAT
2110230 TAACTTGATG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATTATATTATAATTTAAA
Found at i:2110408 original size:48 final size:48
Alignment explanation
Indices: 2110299--2110408 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
2110289 ATTATTCAGG
* * **
2110299 TCATTTCGAGTTCGAGTCATTTTCGATTTGGATTATTTCGGATTCGGA
1 TCATTTCGAGTTCGAGTCATTTTCGATTTGAATAATTTCGGATTCAAA
* *
2110347 TGATTTC-AGGTTCGTGTCATTTT-GAATTTGAATAATTTC-GAGTTCAAA
1 TCATTTCGA-GTTCGAGTCATTTTCG-ATTTGAATAATTTCGGA-TTCAAA
2110395 TCATTTCGAGTTCG
1 TCATTTCGAGTTCG
2110409 GATCAATTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
47 4 0.08
48 46 0.90
49 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.44
Consensus pattern (48 bp):
TCATTTCGAGTTCGAGTCATTTTCGATTTGAATAATTTCGGATTCAAA
Found at i:2110413 original size:16 final size:16
Alignment explanation
Indices: 2110299--2110413 Score: 60
Period size: 16 Copynumber: 7.2 Consensus size: 16
2110289 ATTATTCAGG
2110299 TCATTTCGAGTTC-GA
1 TCATTTCGAGTTCGGA
*
2110314 GTCATTTTCGA-TTTGGA
1 -TCA-TTTCGAGTTCGGA
*
2110331 TTATTTCG-GATTCGGA
1 TCATTTCGAG-TTCGGA
*
2110347 TGATTTC-AGGTTCGTG-
1 TCATTTCGA-GTTCG-GA
* * * *
2110363 TCATTTTGAATTTGAA
1 TCATTTCGAGTTCGGA
* **
2110379 TAATTTCGAGTTCAAA
1 TCATTTCGAGTTCGGA
2110395 TCATTTCGAGTTCGGA
1 TCATTTCGAGTTCGGA
2110411 TCA
1 TCA
2110414 ATTCAGATTA
Statistics
Matches: 73, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
15 5 0.07
16 57 0.78
17 11 0.15
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.43
Consensus pattern (16 bp):
TCATTTCGAGTTCGGA
Found at i:2111566 original size:16 final size:16
Alignment explanation
Indices: 2111545--2111581 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2111535 TTTAAAACTT
*
2111545 AATATATAATAAATAA
1 AATATAAAATAAATAA
*
2111561 AATATAAAATATATAA
1 AATATAAAATAAATAA
2111577 AATAT
1 AATAT
2111582 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATATAAAATAAATAA
Found at i:2111622 original size:58 final size:55
Alignment explanation
Indices: 2111512--2111622 Score: 134
Period size: 57 Copynumber: 2.0 Consensus size: 55
2111502 TATATTAAAT
* * *
2111512 AAATAATTAAATATTTAAATTTATTTAAAACTTAATATATAATAAATAAAATATA
1 AAATAATAAAATATTTAAATTTAATTAAAACTTAACATATAATAAATAAAATATA
* *
2111567 AAATATATAAAATATTTTTAATTTAATTAAAA-TTCAACATGTACATAAATAAAATA
1 AAATA-ATAAAATA-TTTAAATTTAATTAAAACTT-AACATATA-ATAAATAAAATA
2111623 CAAATTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 5 0.11
56 9 0.19
57 21 0.45
58 12 0.26
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (55 bp):
AAATAATAAAATATTTAAATTTAATTAAAACTTAACATATAATAAATAAAATATA
Found at i:2118144 original size:28 final size:29
Alignment explanation
Indices: 2118112--2118198 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 29
2118102 GTTTTAAATA
2118112 AATTTATATTTAAATAAATTTTTTATTTT
1 AATTTATATTTAAATAAATTTTTTATTTT
* * *
2118141 -ATTTAAATTCAAATAAGTTTTTATATTTT
1 AATTTATATTTAAATAAATTTTT-TATTTT
* *
2118170 AATAATAAATATTTAAATAATTTTTTTAT
1 AAT--T-TATATTTAAATAAATTTTTTAT
2118199 AAGTTAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
28 19 0.41
29 6 0.13
30 2 0.04
32 4 0.09
33 15 0.33
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
AATTTATATTTAAATAAATTTTTTATTTT
Found at i:2119260 original size:17 final size:17
Alignment explanation
Indices: 2119238--2119272 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2119228 GTGAAGTTGG
2119238 TTTATAAAGTAAAGTAT
1 TTTATAAAGTAAAGTAT
2119255 TTTATAAAGTAAAGTAT
1 TTTATAAAGTAAAGTAT
2119272 T
1 T
2119273 ATAATAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTTATAAAGTAAAGTAT
Found at i:2124988 original size:2 final size:2
Alignment explanation
Indices: 2124981--2125012 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2124971 ACTAAGTATT
2124981 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2125013 GGTGAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.