Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 6 of 126
Found at i:1818124 original size:16 final size:15
Alignment explanation
Indices: 1818103--1818153 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1818093 ATGCAGAATT
1818103 AAAAAATAATGAAATA
1 AAAAAATAAT-AAATA
*
1818119 AAAAAATCATAAATA
1 AAAAAATAATAAATA
*
1818134 ATTAAAAACAAT-AATA
1 A--AAAAATAATAAATA
1818150 AAAA
1 AAAA
1818154 TATTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.10
15 6 0.20
16 14 0.47
17 7 0.23
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAAAATAATAAATA
Found at i:1829592 original size:76 final size:76
Alignment explanation
Indices: 1829466--1829620 Score: 256
Period size: 76 Copynumber: 2.0 Consensus size: 76
1829456 TGATTGGTCC
* * * *
1829466 ATTATGAAGGGTGGTGCTGCTAATGGAAACGGCGGCATAGAGATTTACTGTTCAAAACAAGTTAT
1 ATTATGAAAGGTAGTGCCGCTAATGAAAACGGCGGCATAGAGATTTACTGTTCAAAACAAGTTAT
1829531 TTTCGTACATA
66 TTTCGTACATA
**
1829542 ATTATGAAAGGTAGTGCCGCTAATGAAAATTGCGGCATAGAGATTTACTGTTCAAAACAAGTTAT
1 ATTATGAAAGGTAGTGCCGCTAATGAAAACGGCGGCATAGAGATTTACTGTTCAAAACAAGTTAT
1829607 TTTCGTACATA
66 TTTCGTACATA
1829618 ATT
1 ATT
1829621 TTGCAAGTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (76 bp):
ATTATGAAAGGTAGTGCCGCTAATGAAAACGGCGGCATAGAGATTTACTGTTCAAAACAAGTTAT
TTTCGTACATA
Found at i:1840928 original size:28 final size:27
Alignment explanation
Indices: 1840897--1840952 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1840887 TTTCGCATTA
*
1840897 TACTGTCTTTCCTTTTCCTTTTTTTCTT
1 TACTGTCTTTCATTTTCC-TTTTTTCTT
* * *
1840925 TACTTTGTTTTATTTTCCTTTTTTCTT
1 TACTGTCTTTCATTTTCCTTTTTTCTT
1840952 T
1 T
1840953 CTTTTTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.05, C:0.20, G:0.04, T:0.71
Consensus pattern (27 bp):
TACTGTCTTTCATTTTCCTTTTTTCTT
Found at i:1840956 original size:26 final size:26
Alignment explanation
Indices: 1840909--1840988 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 26
1840899 CTGTCTTTCC
1840909 TTTTCCTTTTTTTCTTTACTTTGTT-TTA
1 TTTTCC-TTTTTTCTTT-CTTT-TTCTTA
1840937 TTTTCCTTTTTTCTTTCTTTTTCTTA
1 TTTTCCTTTTTTCTTTCTTTTTCTTA
* *
1840963 TCTT-CTTTTCCTCTTTCTTCTTTCTT
1 TTTTCCTTTT-TTCTTTCTT-TTTCTT
1840989 TTTCTTCTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.15
26 18 0.38
27 16 0.34
28 6 0.13
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (26 bp):
TTTTCCTTTTTTCTTTCTTTTTCTTA
Found at i:1840959 original size:10 final size:10
Alignment explanation
Indices: 1840944--1840994 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
1840934 TTATTTTCCT
1840944 TTTTTCTTTC
1 TTTTTCTTTC
1840954 TTTTTCTTATC
1 TTTTTCTT-TC
*
1840965 TTCTTT-TCCTC
1 TT-TTTCT-TTC
1840976 TTTCTTCTTTC
1 TTT-TTCTTTC
1840987 TTTTTCTT
1 TTTTTCTT
1840995 CTACACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 14 0.41
11 16 0.47
12 4 0.12
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:1840970 original size:14 final size:14
Alignment explanation
Indices: 1840946--1840996 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1840936 ATTTTCCTTT
1840946 TTTCTTTCTTTT-TC
1 TTTC-TTCTTTTCTC
1840960 TTATCTTCTTTTCCTC
1 TT-TCTTCTTTT-CTC
*
1840976 TTTCTTC-TTTCTT
1 TTTCTTCTTTTCTC
1840989 TTTCTTCT
1 TTTCTTCT
1840997 ACACAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 9 0.28
14 12 0.38
15 7 0.22
16 4 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTCTTCTTTTCTC
Found at i:1843496 original size:57 final size:57
Alignment explanation
Indices: 1843435--1843551 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 57
1843425 ATACTACTCT
* *
1843435 AATGTA-AATATTAAAATAATATTAAGATAACTAT-ATA-AAAAATTTTAATAAATAAAA
1 AATGTATAAAATTAAAA-AATATTAAAATAA-TATAATATAAAAATTTT-ATAAATAAAA
** * *
1843492 AATGTATAAAATTATTAAATATTAAAATAATATAATATAAATATTTTTTAAATAAAA
1 AATGTATAAAATTAAAAAATATTAAAATAATATAATATAAAAATTTTATAAATAAAA
1843549 AAT
1 AAT
1843552 AATATGAACA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
56 3 0.06
57 33 0.65
58 15 0.29
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (57 bp):
AATGTATAAAATTAAAAAATATTAAAATAATATAATATAAAAATTTTATAAATAAAA
Found at i:1843979 original size:13 final size:13
Alignment explanation
Indices: 1843961--1843985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1843951 TCACGAACTC
1843961 AAATAAATAAAAT
1 AAATAAATAAAAT
1843974 AAATAAATAAAA
1 AAATAAATAAAA
1843986 AGAGAAGAGA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:1860935 original size:23 final size:22
Alignment explanation
Indices: 1860908--1860962 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
1860898 CATGACATTT
*
1860908 TTAATTAAATAAAAATATTTTAA
1 TTAATTAAATAAAAATATTCT-A
* **
1860931 TTAATTTAATTTTAAATATTCTA
1 TTAA-TTAAATAAAAATATTCTA
1860954 TTAATTAAA
1 TTAATTAAA
1860963 AAAGACATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATTAAATAAAAATATTCTA
Found at i:1874079 original size:18 final size:19
Alignment explanation
Indices: 1874056--1874091 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1874046 AGGATGTTCG
1874056 ATCAAG-CTCGAGTTGAGT
1 ATCAAGTCTCGAGTTGAGT
*
1874074 ATCAAGTTTCGAGTTGAG
1 ATCAAGTCTCGAGTTGAG
1874092 CTCGAGCTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (19 bp):
ATCAAGTCTCGAGTTGAGT
Found at i:1876849 original size:19 final size:19
Alignment explanation
Indices: 1876833--1876870 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1876823 TAACTTTTTC
*
1876833 ATATATTATTATATTTTAA
1 ATATATTATCATATTTTAA
1876852 ATATATTATCATATTTTAA
1 ATATATTATCATATTTTAA
1876871 CATACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTATCATATTTTAA
Found at i:1877053 original size:26 final size:26
Alignment explanation
Indices: 1877014--1877069 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
1877004 ATTTTATATT
* *
1877014 AAAAATATTGTTATAGTTTCTACTAA
1 AAAAATATTGTTATAATTTATACTAA
* * *
1877040 AAAAATGTTTTTATAATTTATATTAA
1 AAAAATATTGTTATAATTTATACTAA
1877066 AAAA
1 AAAA
1877070 GTTAAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (26 bp):
AAAAATATTGTTATAATTTATACTAA
Found at i:1882376 original size:16 final size:16
Alignment explanation
Indices: 1882355--1882409 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1882345 AAAATTAGAA
1882355 ATACTATATTTTAAAT
1 ATACTATATTTTAAAT
* ** * *
1882371 ATACTAAAAAATGAGAT
1 ATACT-ATATTTTAAAT
1882388 ATACTATATTTTAAAT
1 ATACTATATTTTAAAT
1882404 ATACTA
1 ATACTA
1882410 AAAATGAGAT
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (16 bp):
ATACTATATTTTAAAT
Found at i:1882418 original size:32 final size:33
Alignment explanation
Indices: 1882345--1882419 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
1882335 TCTTGAACTT
* *
1882345 AAAATTAGAAATACTATATTTTAAATATACTAA
1 AAAATGAGATATACTATATTTTAAATATACTAA
1882378 AAAATGAGATATACTATATTTTAAATATACT-A
1 AAAATGAGATATACTATATTTTAAATATACTAA
1882410 AAAATGAGAT
1 AAAATGAGAT
1882420 TGGAAGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 11 0.28
33 29 0.73
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (33 bp):
AAAATGAGATATACTATATTTTAAATATACTAA
Found at i:1886496 original size:197 final size:198
Alignment explanation
Indices: 1886150--1886587 Score: 727
Period size: 197 Copynumber: 2.2 Consensus size: 198
1886140 TTCTATGCAG
* **
1886150 TAGTTTCGAACATGTATGATCCGACAATTATATGAAAAAAAAAAACTCAAAAAAAGTTAAAAATT
1 TAGTTTAGAACATGTATGATCCTCCAATTATATG---AAAAAAAACTCAAAAAAAGTTAAAAATT
*
1886215 GAGCACACCAGTGTCAAGTACATGCACCTAACATATCCAACACCAACATTCGAGTCCAATAGCAG
63 GAGCACACCAGTGTCAAATACATGCACCTAACATATCCAACACCAACATTCGAGTCCAATAGCAG
1886280 ACAGCATACTACGGTAGTCTTTACCTATGTTACTCAAACTCTTCATTTTT-TAAAGTATCAATGC
128 ACAGCATACTACGGTAGTCTTTACCTATGTTACTCAAACTCTTCATTTTTCTAAAGTATC-ATGC
1886344 TAGACAC
192 TAGACAC
* *
1886351 TAGTTTAGAACATGAATGATCCTCCAATTATATGAAAAATAACTC-AAAAAAGTTAAAAATTGAG
1 TAGTTTAGAACATGTATGATCCTCCAATTATATGAAAAAAAACTCAAAAAAAGTTAAAAATTGAG
1886415 CACACCAGTGTCAAATACATGCACCTAACATATCCAACACCAACATTCGAGTCCAATAGCAGACA
66 CACACCAGTGTCAAATACATGCACCTAACATATCCAACACCAACATTCGAGTCCAATAGCAGACA
* * *
1886480 GCATACTACGGTAGTCTTTACCTATGTTATTCGAACTCTTCATTTTTCTAAAGTATCATGCTTGA
131 GCATACTACGGTAGTCTTTACCTATGTTACTCAAACTCTTCATTTTTCTAAAGTATCATGCTAGA
*
1886545 CGC
196 CAC
*
1886548 TAGTTTAGAACATGTATGATCCTCCGATTATATGAAAAAA
1 TAGTTTAGAACATGTATGATCCTCCAATTATATGAAAAAA
1886588 CAAAAAAACA
Statistics
Matches: 223, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
197 174 0.78
198 19 0.09
201 30 0.13
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (198 bp):
TAGTTTAGAACATGTATGATCCTCCAATTATATGAAAAAAAACTCAAAAAAAGTTAAAAATTGAG
CACACCAGTGTCAAATACATGCACCTAACATATCCAACACCAACATTCGAGTCCAATAGCAGACA
GCATACTACGGTAGTCTTTACCTATGTTACTCAAACTCTTCATTTTTCTAAAGTATCATGCTAGA
CAC
Found at i:1898093 original size:2 final size:2
Alignment explanation
Indices: 1898082--1898114 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1898072 CTGCTTCCCT
1898082 AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1898115 GTTCCTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1899207 original size:197 final size:197
Alignment explanation
Indices: 1898872--1899262 Score: 568
Period size: 197 Copynumber: 2.0 Consensus size: 197
1898862 GATTATGATA
* * *
1898872 GTGGTATGCTTTTGGATCACTATCGTCTTTGGTTGAATGCTCTTTATTCTTTCGAGCATATATTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTCGAGCATATATTT
* * * ** * *
1898937 GAATGTCTGTGTCTTCTCAATCGTTATATTGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CAATGTCAGTGTATTCTCAATCGTTATAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATAT
** * *
1899002 TAAATCCAACATTGTCTCCAAAAACAATGAGTGATTAAATTGAATGG-CATGGTAAGAAGATTGG
131 TAAATCCAACATTACCTCCAAAAACAATGAGTGATTAAATGGAATGGTC-TGATAAGAAGATTGG
1899066 GTT
195 GTT
* * *
1899069 GTGGTATGCTTTTAGATCACTTTCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATGTTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTCGAGCATATATTT
* * * *
1899134 CTATGTCAGTGTATTCTCAATTGTTGTAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATGT
66 CAATGTCAGTGTATTCTCAATCGTTATAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATAT
*
1899199 TAAATCCAACATTACCTCCAAAAACAGTGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTACCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
1899263 ATTGCATTTA
Statistics
Matches: 171, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
197 170 0.99
198 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (197 bp):
GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTCGAGCATATATTT
CAATGTCAGTGTATTCTCAATCGTTATAAAGTCTATCGAGGATGTAGGTTGAATCCTTTATATAT
TAAATCCAACATTACCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:1910990 original size:23 final size:23
Alignment explanation
Indices: 1910964--1911049 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
1910954 ACATTGTTTA
*
1910964 TGAACATGTTTGTTTAATGTTCG
1 TGAACATGTTTATTTAATGTTCG
* * * **
1910987 TGAACATATTCAATTAA-GTTAAA
1 TGAACATGTTTATTTAATGTT-CG
1911010 TGAACATGTTTATTTAATGTTCG
1 TGAACATGTTTATTTAATGTTCG
*
1911033 TGAACATGTTCATTTAA
1 TGAACATGTTTATTTAA
1911050 CATATTCAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
22 3 0.06
23 43 0.88
24 3 0.06
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (23 bp):
TGAACATGTTTATTTAATGTTCG
Found at i:1913934 original size:30 final size:31
Alignment explanation
Indices: 1913867--1913936 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1913857 AATACTAATG
*
1913867 AGTGATTGATTTGTCACTTTTCGATAATGTT
1 AGTGACTGATTTGTCACTTTTCGATAATGTT
* * *
1913898 AGTGACTGATTTGTTATTTTTTGA-AA-GTT
1 AGTGACTGATTTGTCACTTTTCGATAATGTT
1913927 AAGTGACTGA
1 -AGTGACTGA
1913937 ATTGAAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 20 0.59
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (31 bp):
AGTGACTGATTTGTCACTTTTCGATAATGTT
Found at i:1914097 original size:154 final size:153
Alignment explanation
Indices: 1913813--1914097 Score: 367
Period size: 153 Copynumber: 1.9 Consensus size: 153
1913803 TACATTAGCT
* * * * * *
1913813 AGTTAACTGGCCACATCACCTGTCCCGTTAGGACAGTAACGAAAAATACTAATGAGTGATTGATT
1 AGTTAACTAGCCACATCACCTGTCCCGTTAAGACAATAACGAAAAATACTAATAAGTGACTGATC
* *
1913878 TGTCACTTTTCGATAATGTTAGTGACTGATTTGTTATTTTTTGAAAGTTAAGTGACTGAATTGAA
66 TGTCACTTTTCGATAACGTTAGTGACTGATTTGTTATTTTTTGAAAGTTAAGTGACTGAAATGAA
1913943 ACTTTGTCTCGTCCAACATGGCA
131 ACTTTGTCTCGTCCAACATGGCA
** * * **
1913966 AGTTAACTAGCCATGTCACTTGTTCCGTTAAGACAATAAC-AGAAAATGTTAATAAGTGACTGAT
1 AGTTAACTAGCCACATCACCTGTCCCGTTAAGACAATAACGA-AAAATACTAATAAGTGACTGAT
** * *
1914030 CTGTCACTTTTTTTATAACGTTAGTGACTGTTTTGTTATTTTTCT-AAAGTTGAGTGACTGAAAT
65 CTGTCAC-TTTTCGATAACGTTAGTGACTGATTTGTTATTTTT-TGAAAGTTAAGTGACTGAAAT
1914094 GAAA
128 GAAA
1914098 TAAAGATGAT
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
152 1 0.01
153 57 0.51
154 52 0.47
155 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (153 bp):
AGTTAACTAGCCACATCACCTGTCCCGTTAAGACAATAACGAAAAATACTAATAAGTGACTGATC
TGTCACTTTTCGATAACGTTAGTGACTGATTTGTTATTTTTTGAAAGTTAAGTGACTGAAATGAA
ACTTTGTCTCGTCCAACATGGCA
Found at i:1915069 original size:2 final size:2
Alignment explanation
Indices: 1915062--1915095 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1915052 CTTACAGAGA
1915062 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
1915096 TATTTTGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1930179 original size:16 final size:16
Alignment explanation
Indices: 1930160--1930193 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1930150 ACTTAGTACT
1930160 ATCCATATAAAGTATA
1 ATCCATATAAAGTATA
1930176 ATCCATATAAAGTATA
1 ATCCATATAAAGTATA
1930192 AT
1 AT
1930194 TATAATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (16 bp):
ATCCATATAAAGTATA
Found at i:1948166 original size:15 final size:14
Alignment explanation
Indices: 1948145--1948175 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1948135 TATGAAAAGT
*
1948145 ATTAATTTAAAAAA
1 ATTAAATTAAAAAA
1948159 ATTAAATTAAAAAA
1 ATTAAATTAAAAAA
1948173 ATT
1 ATT
1948176 CAAGAGATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAAATTAAAAAA
Found at i:1952642 original size:24 final size:24
Alignment explanation
Indices: 1952612--1952658 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1952602 TGTTTCCATG
1952612 AAAGAGGGTGACATATTCTTTGGT
1 AAAGAGGGTGACATATTCTTTGGT
1952636 AAAGAGGGTGACATATTCTTTGG
1 AAAGAGGGTGACATATTCTTTGG
1952659 ACAGTGCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (24 bp):
AAAGAGGGTGACATATTCTTTGGT
Found at i:1955378 original size:21 final size:22
Alignment explanation
Indices: 1955340--1955380 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1955330 GGTTACACTC
1955340 ATAATAATATAAACATTTATGT
1 ATAATAATATAAACATTTATGT
* *
1955362 ATAAT-ATTTAAATATTTAT
1 ATAATAATATAAACATTTAT
1955381 ACTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAATAATATAAACATTTATGT
Found at i:1963115 original size:2 final size:2
Alignment explanation
Indices: 1963108--1963134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1963098 TAAAAATTTG
1963108 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1963135 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1963139 original size:2 final size:2
Alignment explanation
Indices: 1963134--1963170 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1963124 ATATATATAT
1963134 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1963171 AATAACTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1963957 original size:23 final size:25
Alignment explanation
Indices: 1963931--1963976 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1963921 CCAATTAGGG
1963931 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
1963954 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
1963977 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:1965860 original size:23 final size:23
Alignment explanation
Indices: 1965815--1965863 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1965805 CAGTTATAAA
**
1965815 TTTAAAATTTAATCCTTTTATTT
1 TTTAAAATTTAATAATTTTATTT
*
1965838 TTTAAAATTTAA-AATTTTAATT
1 TTTAAAATTTAATAATTTTATTT
1965860 TTTA
1 TTTA
1965864 CTTAAACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAAAATTTAATAATTTTATTT
Found at i:1966643 original size:2 final size:2
Alignment explanation
Indices: 1966636--1966661 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1966626 AAATCAGTAC
1966636 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
1966662 GAAGGAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1968200 original size:19 final size:20
Alignment explanation
Indices: 1968163--1968200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1968153 ATAAAATTAA
**
1968163 AATAAAAATAAATTGAACAC
1 AATAAAAATAAATCCAACAC
1968183 AATAAAAATAAA-CCAACA
1 AATAAAAATAAATCCAACA
1968201 AAGTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.68, C:0.13, G:0.03, T:0.16
Consensus pattern (20 bp):
AATAAAAATAAATCCAACAC
Found at i:1972107 original size:22 final size:21
Alignment explanation
Indices: 1972082--1972144 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1972072 CTGATTGACC
*
1972082 TAATAAATTTAATATATATTTT
1 TAATAAATTTAA-ATATATTTA
*
1972104 TAATTTAATTTAAATATATTTA
1 TAA-TAAATTTAAATATATTTA
* *
1972126 TAATATATGATAAATATAT
1 TAATAAAT-TTAAATATAT
1972145 AACGTATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.09
22 23 0.68
23 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATAAATTTAAATATATTTA
Found at i:1983188 original size:158 final size:158
Alignment explanation
Indices: 1982900--1983212 Score: 464
Period size: 158 Copynumber: 2.0 Consensus size: 158
1982890 ATCATGCAGC
* * *
1982900 GCTCACATGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAGATGTTATGCTACACGA
1 GCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCAAGATGTTAGGCTACACGA
* ** ** * * * *
1982965 TGCTGCTCACACGAGCTGTGGAGAATCTGCAACGTATGCTGGACCTTAGTCATCGATAGTACATC
66 TGCTGCTCACACGAGCTATGGAGAATCCACAACACATGCTAGACCTCAGCCATCGATAGAACATC
1983030 TAGGACCAGCACCCATATAACATGTGAT
131 TAGGACCAGCACCCATATAACATGTGAT
* *
1983058 GCTCACACGAGCTGTGAAGTGGGTCTGCTCACACGAGCTGTGGGTCAAGATGTTAGGCTACATGA
1 GCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCAAGATGTTAGGCTACACGA
* * *
1983123 TGTTGCTCACACGAGCTATGGAGAATCCACAACACATGCTAGATCTCAGCCATCTATAGAACATC
66 TGCTGCTCACACGAGCTATGGAGAATCCACAACACATGCTAGACCTCAGCCATCGATAGAACATC
*
1983188 TAGGACCAGCACTCATATAACATGT
131 TAGGACCAGCACCCATATAACATGT
1983213 AAATCTTAGT
Statistics
Matches: 137, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
158 137 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (158 bp):
GCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCAAGATGTTAGGCTACACGA
TGCTGCTCACACGAGCTATGGAGAATCCACAACACATGCTAGACCTCAGCCATCGATAGAACATC
TAGGACCAGCACCCATATAACATGTGAT
Found at i:1984061 original size:20 final size:20
Alignment explanation
Indices: 1984033--1984071 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1984023 CAAAAGCCAA
1984033 ATTTCATTTCTATT-TTTCTT
1 ATTTCATTT-TATTATTTCTT
*
1984053 ATTTTATTTTATTATTTCT
1 ATTTCATTTTATTATTTCT
1984072 AATAGCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTCATTTTATTATTTCTT
Found at i:1986323 original size:43 final size:43
Alignment explanation
Indices: 1986262--1986363 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
1986252 TAAATTAAGT
* *
1986262 GGCGTTTGTGTGAAAAGCGCCACTAAAGACCATTTTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTTTAGC
* * * *
1986305 GGCGTTTATGGGAAAAGCGTCGCTAAAGACTATGTTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTTTAGC
*
1986348 GGTGTTTGTGAGGAAA
1 GGCGTTTGTG-GGAAA
1986364 GCTTCTTTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
43 45 0.90
44 5 0.10
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTTTAGC
Found at i:1988207 original size:43 final size:43
Alignment explanation
Indices: 1988143--1988241 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
1988133 ATCTGTTAAA
* * * *
1988143 TTTAGCGGCATTTGTGTGAAAAGCGCCACTAAAGACCATTTTC
1 TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
* * *
1988186 TTTAGCGGCGTTTATGGGAAAAGCGTCGCTAAAGACTATGTTC
1 TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
*
1988229 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
1988242 GTTAGGAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
Found at i:1990092 original size:43 final size:43
Alignment explanation
Indices: 1990028--1990126 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
1990018 ATCTGTTAAA
* * * *
1990028 TTTAGCGGCATTTGTGTGAAAAGCGCCACTAAAGACCATTTTC
1 TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
* * *
1990071 TTTAGCGGCGTTTATGGGAAAAGCGTCGCTAAAGACTATGTTC
1 TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
*
1990114 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
1990127 GTTAGGAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
Found at i:1991979 original size:43 final size:43
Alignment explanation
Indices: 1991915--1992013 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
1991905 ATCTGTTAAA
* * * *
1991915 TTTAGCGGCATTTGTGTGAAAAGCGCCACTAAAGACCATTTTC
1 TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
* * *
1991958 TTTAGCGGCGTTTATGGGAAAAGCGTCGCTAAAGACTATGTTC
1 TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
*
1992001 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
1992014 GTTAGGAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTATGGGAAAAGCGCCACTAAAGACCATGTTC
Found at i:1993707 original size:17 final size:16
Alignment explanation
Indices: 1993684--1993724 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1993674 ATAGTAAAAA
1993684 TATAATTTTAT-TATT
1 TATAATTTTATATATT
1993699 T-TAATAATTTATATATT
1 TATAAT--TTTATATATT
1993716 TATAATTTT
1 TATAATTTT
1993725 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.18
15 1 0.05
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:1993837 original size:82 final size:85
Alignment explanation
Indices: 1993675--1993828 Score: 219
Period size: 82 Copynumber: 1.8 Consensus size: 85
1993665 ATTTTTATGA
* * *
1993675 TAGTAAAAATATAATTTTATTATTTTAATAATTTATATATTTATAATTTTTAAAAAATTAAATTA
1 TAGTAAAAATATAATTTTATTATTTTAATAATTTAAATATTTAAAAATTTTAAAAAATTAAATTA
1993740 AATTTTTATCATATTTAAAT
66 AATTTTTATCATATTTAAAT
*
1993760 TAGT-AAAATATAATTTTA-T-TTTTACTAATTTAAA-ATTTTAAAAATTTTAAAAAATCT-AAT
1 TAGTAAAAATATAATTTTATTATTTTAATAATTTAAATA-TTTAAAAATTTTAAAAAAT-TAAAT
1993820 TAAATTTTT
64 TAAATTTTT
1993829 TTTTTATTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
81 1 0.02
82 42 0.67
83 2 0.03
84 14 0.22
85 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (85 bp):
TAGTAAAAATATAATTTTATTATTTTAATAATTTAAATATTTAAAAATTTTAAAAAATTAAATTA
AATTTTTATCATATTTAAAT
Found at i:1995840 original size:16 final size:16
Alignment explanation
Indices: 1995799--1995843 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1995789 TTTTAAAGCT
1995799 TTTTTAA-TAAAT--A
1 TTTTTAAGTAAATAAA
1995812 TTTCTTAAG-AAATAAA
1 TTT-TTAAGTAAATAAA
1995828 TTTTTAAGTAAATAAA
1 TTTTTAAGTAAATAAA
1995844 AAATATAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.11
14 8 0.30
15 5 0.19
16 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (16 bp):
TTTTTAAGTAAATAAA
Found at i:1996647 original size:43 final size:43
Alignment explanation
Indices: 1996600--1996806 Score: 143
Period size: 43 Copynumber: 4.8 Consensus size: 43
1996590 AAAGAAAGAA
* * * *
1996600 ACTGGTACACATAGTGCATCATCGGGCAAGCCGAATCAATTAT
1 ACTGGCACACATAGTGCATCATCGGACAAACCGAAGCAATTAT
* * * *
1996643 ACTGGCACACA-AGGTGTATTATCTGATAAACCGAAGCAATTAT
1 ACTGGCACACATA-GTGCATCATCGGACAAACCGAAGCAATTAT
* * * **
1996686 ATTGGCACACCTAGTGCATCATCGGATAAATTGAAGCAATTAT
1 ACTGGCACACATAGTGCATCATCGGACAAACCGAAGCAATTAT
* * ** * * * *
1996729 AAC-GACACACGTAGTGCATCATCAAATAAACCAAAGTAATCAT
1 -ACTGGCACACATAGTGCATCATCGGACAAACCGAAGCAATTAT
* * *
1996772 ACT-GC-CACATAAATGCATCATCGGATAAACTGAAG
1 ACTGGCACACAT-AGTGCATCATCGGACAAACCGAAG
1996807 TATAAACCTA
Statistics
Matches: 127, Mismatches: 32, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
41 4 0.03
42 23 0.18
43 98 0.77
44 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (43 bp):
ACTGGCACACATAGTGCATCATCGGACAAACCGAAGCAATTAT
Found at i:1998495 original size:23 final size:23
Alignment explanation
Indices: 1998467--1998511 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1998457 ATTGGACATA
*
1998467 TAATTATACTTGTC-TTGTACTTG
1 TAATTATA-TTGTCATTCTACTTG
1998490 TAATTATATTGTCATTCTACTT
1 TAATTATATTGTCATTCTACTT
1998512 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.53
Consensus pattern (23 bp):
TAATTATATTGTCATTCTACTTG
Found at i:1999545 original size:5 final size:5
Alignment explanation
Indices: 1999535--1999561 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1999525 CATATTTCAA
1999535 TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TA
1999562 AGATTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1999743 original size:30 final size:29
Alignment explanation
Indices: 1999707--1999773 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1999697 AATTAACAAA
1999707 AATAAAA-TTACATTTTAATTATCTAAAAAT
1 AATAAAATTTA-A-TTTAATTATCTAAAAAT
* *
1999737 AATAAAAATTTAATTTAATTTTTTAAAAAT
1 AAT-AAAATTTAATTTAATTATCTAAAAAT
*
1999767 TATAAAA
1 AATAAAA
1999774 ATATAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.12
30 20 0.62
31 5 0.16
32 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAAAATTTAATTTAATTATCTAAAAAT
Found at i:1999829 original size:82 final size:82
Alignment explanation
Indices: 1999675--1999834 Score: 191
Period size: 82 Copynumber: 2.0 Consensus size: 82
1999665 ATATAAATCC
** * *
1999675 TTTTAAATTTTATAAAAATTTAAATTAACAAAAATAAAATTACATTTTAATTATCTAAAAATAAT
1 TTTTAAAAATTATAAAAATTAAAATTAACAAAAATAAAATTACATTTTAATTATATAAAAATAAT
1999740 AAAAATTTAATTTAATT
66 AAAAATTTAATTTAATT
* ** *
1999757 TTTTAAAAATTATAAAAATATAAATATTAA-AATAATAAAATTATTTTTTTATTATTATAAAAAT
1 TTTTAAAAATTATAAAAAT-TAAA-ATTAACAAAAATAAAATTACATTTTAATTA-TATAAAAAT
*
1999821 -AT-ACAATTTAATTT
63 AATAAAAATTTAATTT
1999835 CTATCCTATT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
82 28 0.42
83 25 0.38
84 13 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (82 bp):
TTTTAAAAATTATAAAAATTAAAATTAACAAAAATAAAATTACATTTTAATTATATAAAAATAAT
AAAAATTTAATTTAATT
Found at i:2015580 original size:18 final size:17
Alignment explanation
Indices: 2015557--2015599 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
2015547 GGATAGGTTT
*
2015557 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTAAA
2015575 TTAATTGAAAAAATTAAA
1 TTAATT-AAAAAATTAAA
2015593 TTAATTA
1 TTAATTA
2015600 CACATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAATTAAAAAATTAAA
Found at i:2019461 original size:14 final size:14
Alignment explanation
Indices: 2019414--2019463 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2019404 GTTTAATGAC
2019414 TTAAATAAAAACTT
1 TTAAATAAAAACTT
* *
2019428 TTGAATAATTCAAC-T
1 TTAAATAA--AAACTT
2019443 TTAAATAAAAACTT
1 TTAAATAAAAACTT
2019457 TTAAATA
1 TTAAATA
2019464 GTTTAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 15 0.52
15 8 0.28
16 3 0.10
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (14 bp):
TTAAATAAAAACTT
Found at i:2027544 original size:32 final size:32
Alignment explanation
Indices: 2027508--2027570 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2027498 ACATGGATCC
*
2027508 TTTGTTCAATCATTGTCAATGTAAAGTCTCTT
1 TTTGTTCAATCATTGCCAATGTAAAGTCTCTT
*
2027540 TTTGTTCAATCATTGCCAATGTAAATTCTCT
1 TTTGTTCAATCATTGCCAATGTAAAGTCTCT
2027571 CTCTCTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (32 bp):
TTTGTTCAATCATTGCCAATGTAAAGTCTCTT
Found at i:2031813 original size:3 final size:3
Alignment explanation
Indices: 2031807--2031832 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2031797 AAAAAAAAAA
2031807 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2031833 AAATTTGTAT
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:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2034765 original size:143 final size:142
Alignment explanation
Indices: 2034499--2034774 Score: 326
Period size: 143 Copynumber: 1.9 Consensus size: 142
2034489 TTGTGTCATC
* **
2034499 TGTGCGTGTAGCATCGAGAAATGTCTTCTTTTTCTTTGGGGGGGGGGTAGGCGGGTGAGTTTTTG
1 TGTGCGTGTAGCATCGAGAAATGTCTTCTTTTTCTTT-GGAGGGGGGTAGGCGGGCAAGTTTTTG
* ** **
2034564 TGTGTTGTCATAAATGAAACGGAAATCAAGTAAATGCTTGATCAAGGATTTTTTTTTTGTCATAT
65 CGTGTCCTCATAAATGAAACACAAATCAAGTAAATGCTTGATCAAGGATTTTTTTTTTGTCATAT
2034629 GTGTGTGCATGTA
130 GTGTGTGCATGTA
*
2034642 TGTGTGTGTAGCATCGAGAAATGTCTTCTTTTTC-TT-GAGGGGGGTA-GCGGGCAAGTTTTTGC
1 TGTGCGTGTAGCATCGAGAAATGTCTTCTTTTTCTTTGGAGGGGGGTAGGCGGGCAAGTTTTTGC
* * * ** *
2034704 GTGATCCTCGTAAATGATACACAATTCGTGTAAATGCTT-AGTCATGGATGTTTATTGTTTTGTC
66 GTG-TCCTCATAAATGAAACACAAATCAAGTAAATGCTTGA-TCAAGGAT-TTT-TT-TTTTGTC
*
2034768 TTATGTG
126 ATATGTG
2034775 CGTACAAGGT
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
139 17 0.15
140 42 0.38
141 3 0.03
142 4 0.04
143 46 0.41
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (142 bp):
TGTGCGTGTAGCATCGAGAAATGTCTTCTTTTTCTTTGGAGGGGGGTAGGCGGGCAAGTTTTTGC
GTGTCCTCATAAATGAAACACAAATCAAGTAAATGCTTGATCAAGGATTTTTTTTTTGTCATATG
TGTGTGCATGTA
Found at i:2038406 original size:24 final size:20
Alignment explanation
Indices: 2038359--2038407 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
2038349 CATTAAATAA
2038359 AAAAATTTATTTTTTTATTG
1 AAAAATTTATTTTTTTATTG
2038379 -AAAATTTCATTCATTTTTATTG
1 AAAAATTT-ATT--TTTTTATTG
2038401 TAAAAAT
1 -AAAAAT
2038408 CGACATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
22 9 0.38
24 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
AAAAATTTATTTTTTTATTG
Found at i:2045470 original size:21 final size:20
Alignment explanation
Indices: 2045436--2045474 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2045426 GAATTGTACT
2045436 AAAACAAAACCAGACAATTAA
1 AAAACAAAACCAGA-AATTAA
* *
2045457 AAAACATAATCAGAAATT
1 AAAACAAAACCAGAAATT
2045475 CATGTTCGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAACAAAACCAGAAATTAA
Found at i:2048181 original size:8 final size:10
Alignment explanation
Indices: 2048146--2048183 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2048136 TTGTCTAAAT
*
2048146 TTTCTTTCAC
1 TTTCTCTCAC
2048156 TTTCTCTCAC
1 TTTCTCTCAC
*
2048166 TTTCTCTCAT
1 TTTCTCTCAC
2048176 TTTCTCTC
1 TTTCTCTC
2048184 TCTGCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.08, C:0.34, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTCTCTCAC
Found at i:2060270 original size:16 final size:17
Alignment explanation
Indices: 2060246--2060283 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2060236 CATATATTTG
*
2060246 TTTATTGAG-AATTTTT
1 TTTACTGAGTAATTTTT
2060262 TTTACTGAGTTAATTTTT
1 TTTACTGAG-TAATTTTT
2060280 TTTA
1 TTTA
2060284 AATATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTACTGAGTAATTTTT
Found at i:2068561 original size:52 final size:51
Alignment explanation
Indices: 2068485--2068584 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 51
2068475 CACATTCTAA
** *
2068485 TAATTTGATCTTAATTTAGTAAATTTAAC-CAGCAACATTTACACATTTTTGT
1 TAATTTGATCTTAATTTAACAAATTTAACTC-GCAACAATT-CACATTTTTGT
*
2068537 TAATTTGGATC-TAATTTAACAAATTTAGCTCGCAACAATTCACATTTT
1 TAATTT-GATCTTAATTTAACAAATTTAACTCGCAACAATTCACATTTT
2068585 ATCAACATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 8 0.19
52 29 0.69
53 5 0.12
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (51 bp):
TAATTTGATCTTAATTTAACAAATTTAACTCGCAACAATTCACATTTTTGT
Found at i:2072976 original size:6 final size:6
Alignment explanation
Indices: 2072965--2073017 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
2072955 AGAGAAGATT
2072965 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
2073013 GAGAG
1 GAGAG
2073018 AACAAGGTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:2084174 original size:2 final size:2
Alignment explanation
Indices: 2084167--2084191 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2084157 ATTATAGTTC
2084167 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2084192 ACTTGAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2088413 original size:12 final size:12
Alignment explanation
Indices: 2088396--2088421 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2088386 GTGGGTTATA
2088396 AGAGAGACTATG
1 AGAGAGACTATG
2088408 AGAGAGACTATG
1 AGAGAGACTATG
2088420 AG
1 AG
2088422 CAATCTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (12 bp):
AGAGAGACTATG
Found at i:2097699 original size:17 final size:17
Alignment explanation
Indices: 2097669--2097702 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2097659 TTGGATGAAC
*
2097669 TTATATTATAATTTTAT
1 TTATAATATAATTTTAT
*
2097686 TTATAATATTATTTTAT
1 TTATAATATAATTTTAT
2097703 ATCTTGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATATAATTTTAT
Found at i:2097746 original size:7 final size:7
Alignment explanation
Indices: 2097734--2097759 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2097724 ATTGTAATTG
2097734 TTTTTAA
1 TTTTTAA
2097741 TTTTTAA
1 TTTTTAA
2097748 TTTTTAA
1 TTTTTAA
2097755 TTTTT
1 TTTTT
2097760 TGGGTGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:2099585 original size:23 final size:24
Alignment explanation
Indices: 2099539--2099589 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2099529 AACTTAATAT
* *
2099539 AAAATATTAATTTTAAATATTTTA
1 AAAAAATTAATATTAAATATTTTA
*
2099563 AAAAAATTAATATTAATTA-TTTA
1 AAAAAATTAATATTAAATATTTTA
2099586 AAAA
1 AAAA
2099590 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAATTAATATTAAATATTTTA
Found at i:2104889 original size:15 final size:16
Alignment explanation
Indices: 2104862--2104892 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2104852 ATGCTCATTG
2104862 TTAATTAAATATAATT
1 TTAATTAAATATAATT
2104878 TTAATT-AATATAATT
1 TTAATTAAATATAATT
2104893 ATAAATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATTAAATATAATT
Found at i:2111756 original size:2 final size:2
Alignment explanation
Indices: 2111749--2111775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2111739 TATAATGTTC
2111749 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
2111776 TCCAAAGTTT
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:2119592 original size:22 final size:18
Alignment explanation
Indices: 2119552--2119587 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2119542 TCGTTAACCA
2119552 ATTAATTGAATTTTTAGT
1 ATTAATTGAATTTTTAGT
2119570 ATTAATTGAATTTTTAGT
1 ATTAATTGAATTTTTAGT
2119588 GAGTAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTAATTGAATTTTTAGT
Found at i:2119594 original size:19 final size:18
Alignment explanation
Indices: 2119554--2119594 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
2119544 GTTAACCAAT
*
2119554 TAATTGAATTTTTAGTAT
1 TAATTGAATTTTTAGTAG
2119572 TAATTGAATTTTTAGTGAG
1 TAATTGAATTTTTAGT-AG
2119591 TAAT
1 TAAT
2119595 ATGTGGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (18 bp):
TAATTGAATTTTTAGTAG
Found at i:2120013 original size:32 final size:32
Alignment explanation
Indices: 2119972--2120033 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2119962 TAGGCTAAAT
*
2119972 AACTTATTTACACAATTTTTTAATCTAATTTA
1 AACTTATTTAAACAATTTTTTAATCTAATTTA
*
2120004 AACTTATTTAAACTATTTTTTAATCTAATT
1 AACTTATTTAAACAATTTTTTAATCTAATT
2120034 CAATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (32 bp):
AACTTATTTAAACAATTTTTTAATCTAATTTA
Found at i:2120284 original size:14 final size:15
Alignment explanation
Indices: 2120241--2120318 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 15
2120231 TTAATTGTAC
2120241 AATTATTTTATATGTTT
1 AATT-TTTTATAT-TTT
* *
2120258 AA-TTATAATA-TTT
1 AATTTTTTATATTTT
2120271 AATTTTTTATATTTTT
1 AATTTTTTATA-TTTT
*
2120287 AA--TTATATATTTT
1 AATTTTTTATATTTT
*
2120300 AATTTTTTA-AGTTT
1 AATTTTTTATATTTT
2120314 AATTT
1 AATTT
2120319 ATAAAAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
13 11 0.22
14 21 0.43
15 9 0.18
16 6 0.12
17 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
AATTTTTTATATTTT
Found at i:2120287 original size:29 final size:29
Alignment explanation
Indices: 2120241--2120321 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
2120231 TTAATTGTAC
2120241 AATTATTTTATATGTTTAATTATA-ATATTT
1 AATT-TTTTATATGTTTAATTATATAT-TTT
*
2120271 AATTTTTTATATTTTTAATTATATATTTT
1 AATTTTTTATATGTTTAATTATATATTTT
2120300 AATTTTTTA-A-GTTTAATT-TATA
1 AATTTTTTATATGTTTAATTATATA
2120322 AAAATTAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.08
27 7 0.15
28 1 0.02
29 30 0.62
30 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
AATTTTTTATATGTTTAATTATATATTTT
Found at i:2120301 original size:13 final size:14
Alignment explanation
Indices: 2120249--2120303 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
2120239 ACAATTATTT
*
2120249 TATATGTTTAATTA
1 TATATATTTAATTA
*
2120263 TA-ATATTTAATTTTT
1 TATATATTTAA--TTA
*
2120278 TATATTTTTAATTA
1 TATATATTTAATTA
2120292 TATAT-TTTAATT
1 TATATATTTAATT
2120304 TTTTAAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 14 0.41
14 9 0.26
15 4 0.12
16 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TATATATTTAATTA
Found at i:2125703 original size:34 final size:34
Alignment explanation
Indices: 2125625--2125712 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
2125615 GTTTGCTTGG
** *
2125625 TTTGTCTTTTCATTAGCTGTAAATATTTTATTTATT
1 TTTGTCTTTTCATTAGC--TAAATATTTTACCTACT
* *
2125661 TTTATCTTTTCATTAGCTAAATATTTTACCTGCT
1 TTTGTCTTTTCATTAGCTAAATATTTTACCTACT
*
2125695 TTTGTCTTTTCAATAGCT
1 TTTGTCTTTTCATTAGCT
2125713 TGTAACAAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 29 0.64
36 16 0.36
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.57
Consensus pattern (34 bp):
TTTGTCTTTTCATTAGCTAAATATTTTACCTACT
Found at i:2126983 original size:22 final size:21
Alignment explanation
Indices: 2126958--2127004 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2126948 TTTCTATTTC
*
2126958 TTTTAATTCTATTTTGTTTTAT
1 TTTTAATTCTA-TTTCTTTTAT
*
2126980 TTTTTATTCTATTTCTTTTAT
1 TTTTAATTCTATTTCTTTTAT
2127001 TTTT
1 TTTT
2127005 CCTTAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTAATTCTATTTCTTTTAT
Found at i:2126998 original size:21 final size:22
Alignment explanation
Indices: 2126944--2127004 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
2126934 TTCGACTTCC
*
2126944 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTATTTTTAATT
* *
2126966 CTATTTTGTTTTATTTTTTATT
1 CTATTTTCTTTTATTTTTAATT
2126988 CTA-TTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
2127005 CCTTAGATCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:2127286 original size:19 final size:19
Alignment explanation
Indices: 2127262--2127316 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2127252 AAAATAAAAT
*
2127262 AATTCAGAATAATTT-TAAA
1 AATTCAAAAT-ATTTATAAA
2127281 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
2127300 AATTTCAAAA-ATTTATA
1 AA-TTCAAAATATTTATA
2127317 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 4 0.12
19 22 0.67
20 7 0.21
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:2128893 original size:24 final size:26
Alignment explanation
Indices: 2128859--2128913 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
2128849 TGTATACATT
*
2128859 TTAATACATAT-ATTATTTTT-TATG
1 TTAATAAATATAATTATTTTTGTATG
*
2128883 TTAATAAATATAATTGTTTTTGTATG
1 TTAATAAATATAATTATTTTTGTATG
2128909 -TAATA
1 TTAATA
2128914 TGTAAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 10 0.37
25 13 0.48
26 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (26 bp):
TTAATAAATATAATTATTTTTGTATG
Found at i:2142670 original size:15 final size:17
Alignment explanation
Indices: 2142646--2142678 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2142636 TTATATAAAG
2142646 AGCTTAGATAT-GAATA
1 AGCTTAGATATCGAATA
2142662 AGCTT-GATATCGAATA
1 AGCTTAGATATCGAATA
2142678 A
1 A
2142679 CTAGATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (17 bp):
AGCTTAGATATCGAATA
Found at i:2144974 original size:8 final size:9
Alignment explanation
Indices: 2144958--2144982 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2144948 ATAATATAAT
2144958 TTAAAAAAA
1 TTAAAAAAA
2144967 TTAAAAAAA
1 TTAAAAAAA
2144976 TTAAAAA
1 TTAAAAA
2144983 TAATATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:2152679 original size:5 final size:5
Alignment explanation
Indices: 2152669--2152693 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2152659 AATTTTTTAT
2152669 TGGGG TGGGG TGGGG TGGGG TGGGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG
2152694 GGCTAAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
TGGGG
Found at i:2153665 original size:16 final size:15
Alignment explanation
Indices: 2153626--2153668 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2153616 TTTTAAAATG
2153626 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
*
2153641 A-AATTATTTATAATTT
1 ATAA-AATTT-TAATTT
2153657 ATAAAATTTTAA
1 ATAAAATTTTAA
2153669 ATTAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 8 0.35
16 11 0.48
17 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:2153721 original size:28 final size:30
Alignment explanation
Indices: 2153672--2153742 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 30
2153662 ATTTTAAATT
2153672 AATAATGATAAAAATATATTTTAA-TCTC-AA
1 AATAAT-A-AAAAATATATTTTAACTCTCTAA
2153702 AATAATAAAAAAT-TAATTTTAACTCTCTAA
1 AATAATAAAAAATAT-ATTTTAACTCTCTAA
*
2153732 AA-ATTAAAAAA
1 AATAATAAAAAA
2153743 CATAAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 1 0.03
28 13 0.35
29 13 0.35
30 10 0.27
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (30 bp):
AATAATAAAAAATATATTTTAACTCTCTAA
Found at i:2158878 original size:45 final size:45
Alignment explanation
Indices: 2158824--2158911 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
2158814 ATTAAGAGTC
2158824 TATTTGGACAACACAAAGTAATTGAATGAGACTATAATTAACGTT
1 TATTTGGACAACACAAAGTAATTGAATGAGACTATAATTAACGTT
* * *
2158869 TATTTGGACAGCACAAAGTAATTGGATGAGATTATAATTAACG
1 TATTTGGACAACACAAAGTAATTGAATGAGACTATAATTAACG
2158912 CTCTCTTGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (45 bp):
TATTTGGACAACACAAAGTAATTGAATGAGACTATAATTAACGTT
Found at i:2159096 original size:19 final size:19
Alignment explanation
Indices: 2159056--2159099 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2159046 ATTATAAATT
* *
2159056 TAAAAAATATTAATTACTA
1 TAAAAAATATTAAGTACAA
2159075 TAAAAAATTATT-AGTACAA
1 TAAAAAA-TATTAAGTACAA
2159094 TAAAAA
1 TAAAAA
2159100 TAATTTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAAAATATTAAGTACAA
Found at i:2161497 original size:30 final size:30
Alignment explanation
Indices: 2161461--2161518 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2161451 TAGTTTATAG
* * *
2161461 ATTTTTTATATTTAAAAATTTAATTTCATT
1 ATTTTTTAAATTTAAAAATCTAAGTTCATT
*
2161491 ATTTTTTAAATTTTAAAATCTAAGTTCA
1 ATTTTTTAAATTTAAAAATCTAAGTTCA
2161519 ATGGTTAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTTTTAAATTTAAAAATCTAAGTTCATT
Found at i:2175609 original size:29 final size:29
Alignment explanation
Indices: 2175569--2175628 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
2175559 TATAATTTAT
2175569 AAAATTACATTTTAATCACA-AAAAATATA
1 AAAATTACA-TTTAATCACATAAAAATATA
**
2175598 AAAATTTA-ATTTAATCTTATAAAAATATA
1 AAAA-TTACATTTAATCACATAAAAATATA
2175627 AA
1 AA
2175629 TTATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.30
29 16 0.59
30 3 0.11
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTAATCACATAAAAATATA
Found at i:2176670 original size:16 final size:16
Alignment explanation
Indices: 2176649--2176683 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2176639 ACTTCACCAA
2176649 ATAAACAATAAATAAT
1 ATAAACAATAAATAAT
2176665 ATAAACAATAAATAAT
1 ATAAACAATAAATAAT
2176681 ATA
1 ATA
2176684 CAGATCCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAACAATAAATAAT
Found at i:2180809 original size:137 final size:138
Alignment explanation
Indices: 2180603--2180886 Score: 326
Period size: 139 Copynumber: 2.0 Consensus size: 138
2180593 GAAACCTCAT
* * * *
2180603 ACTCAATGATGTAATCGTAATTATCTAATCATATAAAGGAAAGAGCTAATATGCTAAAAATATTA
1 ACTCAATGATGTAATCGTAACTATCTAACCATATAAACGAAAGAACTAATATGCTAAAAATATTA
2180668 ATT-AAA-AAAAAGCTTGATGAAGCAACATAAAATAAAAAAATACAAATGTGAATAGTAA-AGAA
66 ATTAAAATAAAAAGC-T--TGAAGCAACATAAAATAAAAAAATACAAATGTGAATAG-AAGAGAA
*
2180730 ATCAAACTCAAG
127 ATCAAACCCAAG
* * * * * * *
2180742 ACTCAATGATGTAATTG-AACTCTCTAACCATCT-AACGAAAGAATTAATATGTTAAAAATTTTG
1 ACTCAATGATGTAATCGTAACTATCTAACCATATAAACGAAAGAACTAATATGCTAAAAATATTA
* *
2180805 ATTAAAAAATTAAAAAGCTTGAAGTAACATGAAATAAAAAAATACAAATGTGAATAGAAGAGAAA
66 ATT--AAAA-TAAAAAGCTTGAAGCAACATAAAATAAAAAAATACAAATGTGAATAGAAGAGAAA
* *
2180870 TCGAACCCGAG
128 TCAAACCCAAG
2180881 ACTCAA
1 ACTCAA
2180887 AGATAAAAAC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
137 27 0.22
138 14 0.11
139 71 0.58
140 3 0.02
141 1 0.01
142 7 0.06
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (138 bp):
ACTCAATGATGTAATCGTAACTATCTAACCATATAAACGAAAGAACTAATATGCTAAAAATATTA
ATTAAAATAAAAAGCTTGAAGCAACATAAAATAAAAAAATACAAATGTGAATAGAAGAGAAATCA
AACCCAAG
Found at i:2191634 original size:13 final size:13
Alignment explanation
Indices: 2191573--2191639 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
2191563 CAAAAAAATT
*
2191573 ATTTTAAAATAT-
1 ATTTTAAAATTTA
2191585 ATTTT-AAATTTA
1 ATTTTAAAATTTA
* **
2191597 AATTTATTATTT-
1 ATTTTAAAATTTA
2191609 ATTTGTAAAAATTTA
1 ATTT-T-AAAATTTA
*
2191624 ATTTTAAAATTAA
1 ATTTTAAAATTTA
2191637 ATT
1 ATT
2191640 ATTTTTTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
11 5 0.12
12 12 0.29
13 15 0.36
14 6 0.14
15 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (13 bp):
ATTTTAAAATTTA
Found at i:2193889 original size:22 final size:23
Alignment explanation
Indices: 2193831--2193889 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
2193821 TTGTTTATTG
* *
2193831 CTATTATGTTGTTATTTTGCTAA
1 CTATTTTGTTGTTATATTGCTAA
* * *
2193854 C-ATTTCGATATTATATTGCT-A
1 CTATTTTGTTGTTATATTGCTAA
2193875 CTATTTTGTTGTTAT
1 CTATTTTGTTGTTAT
2193890 TGTTTAGATA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (23 bp):
CTATTTTGTTGTTATATTGCTAA
Found at i:2194483 original size:45 final size:45
Alignment explanation
Indices: 2194419--2194510 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
2194409 ATAGTATAAA
*
2194419 ATGTTACGAAAGAGTGTAAAACTACTTTAATTTCACATGTTTTAT
1 ATGTTACGAAAGAGTGTAAAACTACTTCAATTTCACATGTTTTAT
*
2194464 ATGTTACGAAAGGGTGTAAAACTACTTCAATTTCACATGTTTTAT
1 ATGTTACGAAAGAGTGTAAAACTACTTCAATTTCACATGTTTTAT
2194509 AT
1 AT
2194511 TGGTATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (45 bp):
ATGTTACGAAAGAGTGTAAAACTACTTCAATTTCACATGTTTTAT
Found at i:2194727 original size:2 final size:2
Alignment explanation
Indices: 2194722--2194763 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2194712 AAGAAAAAGT
* *
2194722 TA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2194764 CTTAAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2205493 original size:21 final size:22
Alignment explanation
Indices: 2205467--2205521 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
2205457 ATTTAACCAA
*
2205467 ATTTAATATATAT-TATTATTT
1 ATTTAATATAAATATATTATTT
*
2205488 ATTTAATTTAAATATATTA-TT
1 ATTTAATATAAATATATTATTT
*
2205509 ATATAA-ATAAATA
1 ATTTAATATAAATA
2205522 ATTTAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 18 0.62
22 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTAATATAAATATATTATTT
Found at i:2205899 original size:12 final size:12
Alignment explanation
Indices: 2205882--2205907 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2205872 GCAGTTTTCC
2205882 TTCTTTTCTTCT
1 TTCTTTTCTTCT
2205894 TTCTTTTCTTCT
1 TTCTTTTCTTCT
2205906 TT
1 TT
2205908 GTCCTGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:2214780 original size:13 final size:13
Alignment explanation
Indices: 2214762--2214790 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2214752 TTATAATTTA
2214762 GTAACTAAGGTTT
1 GTAACTAAGGTTT
2214775 GTAACTAAGGTTT
1 GTAACTAAGGTTT
2214788 GTA
1 GTA
2214791 GTTTACCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (13 bp):
GTAACTAAGGTTT
Found at i:2221836 original size:31 final size:31
Alignment explanation
Indices: 2221793--2221859 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2221783 TAAATTAATA
* *
2221793 TTATTATATGCTTTATATTGTAATTAAACCT
1 TTATTATATGCTTTATACTGTAATTAAACAT
* *
2221824 TTATTATGTGCTTTATACTGTAGTTAAACAT
1 TTATTATATGCTTTATACTGTAATTAAACAT
2221855 TTATT
1 TTATT
2221860 GAACTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (31 bp):
TTATTATATGCTTTATACTGTAATTAAACAT
Found at i:2221926 original size:17 final size:18
Alignment explanation
Indices: 2221896--2221931 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2221886 AAAATATATT
*
2221896 AATTTATTTTTATTTTTA
1 AATTTATTTATATTTTTA
2221914 AATTT-TTTATATTTTTA
1 AATTTATTTATATTTTTA
2221931 A
1 A
2221932 TAATATGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTTATTTATATTTTTA
Found at i:2223035 original size:22 final size:21
Alignment explanation
Indices: 2222994--2223042 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2222984 AACTATGTAG
* *
2222994 AATAATATAAAATGTTAAATT
1 AATAATATAAAATGTAAAATA
2223015 AATAATACTAAAAT-TAAAAATA
1 AATAATA-TAAAATGT-AAAATA
2223037 AATAAT
1 AATAAT
2223043 CTGTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAATATAAAATGTAAAATA
Found at i:2223918 original size:21 final size:21
Alignment explanation
Indices: 2223886--2223927 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2223876 TTGAATGATT
* *
2223886 TAACAAATAACACAAATTTAA
1 TAACAAATAACAAAAAATTAA
2223907 TAACTAAA-AACAAAAAATTAA
1 TAAC-AAATAACAAAAAATTAA
2223928 ATAAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (21 bp):
TAACAAATAACAAAAAATTAA
Found at i:2224830 original size:9 final size:9
Alignment explanation
Indices: 2224802--2224832 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2224792 TAAATTGTGC
2224802 ATATTAAAA
1 ATATTAAAA
2224811 ATATATAAAA
1 ATAT-TAAAA
2224821 ATATTAAAA
1 ATATTAAAA
2224830 ATA
1 ATA
2224833 AGTCATGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATATTAAAA
Found at i:2224981 original size:16 final size:15
Alignment explanation
Indices: 2224942--2224984 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2224932 CCCTAAAATG
2224942 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
*
2224957 A-AATCATTTATAATTT
1 ATAA-AATTT-TAATTT
2224973 ATAAAATTTTAA
1 ATAAAATTTTAA
2224985 ATTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 8 0.35
16 11 0.48
17 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:2225037 original size:15 final size:15
Alignment explanation
Indices: 2225017--2225045 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2225007 ATTGATCTTA
2225017 AAAATATAAATTATT
1 AAAATATAAATTATT
2225032 AAAATATAAATTAT
1 AAAATATAAATTAT
2225046 ATTTATACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATAAATTATT
Found at i:2235453 original size:99 final size:99
Alignment explanation
Indices: 2235190--2235554 Score: 408
Period size: 99 Copynumber: 3.6 Consensus size: 99
2235180 CTGTTTGAAT
* * * *
2235190 AATTTTTTTCTTTTCGTTGCGTGTTTAAGAAACTGTTTAAATTGAATTCGCACTAGAATTTTCTG
1 AATTCTTTT-TTTTCGTTGCGTGGTTAAGAAAATGTTTAATTTGAATTCGCACTAGAATTTTCTG
* *
2235255 TTTGCTTGCTGAGAAACACTCTGAGAAAAACTGTTTG
65 ATTGTTTGCTGAG-AA-ACTCTGAGAAAAACTGTTTG
* * * * * * * * *
2235292 AATTCCTATTTTTGGTCGCGTGGATAAGAAAATGTTTGATTCGAATTCGCATTAGAGTTTTCTGA
1 AATTCTTTTTTTTCGTTGCGTGGTTAAGAAAATGTTTAATTTGAATTCGCACTAGAATTTTCTGA
* *
2235357 TTGTTTGCTGAGAAACTGTGAGAAGAACTGTTTG
66 TTGTTTGCTGAGAAACTCTGAGAAAAACTGTTTG
* * * * *
2235391 AATTCTTTTATTTTCGTTTCGCGGTTAAGAAAATG-TTAATTTTAATTAGCACTAGAAATTTCTG
1 AATTCTTTT-TTTTCGTTGCGTGGTTAAGAAAATGTTTAATTTGAATTCGCACTAGAATTTTCTG
* ** * *
2235455 ATTGTTTGCTGAGAAACACAAAGAAAAATTCTTTG
65 ATTGTTTGCTGAGAAACTCTGAGAAAAACTGTTTG
* * *
2235490 AATTTTTTTTATTTCGTTGCGTGGTTAAGAAATTGTTTAATTTGAACTCGCACTAGAATTTTCTG
1 AATTCTTTTT-TTTCGTTGCGTGGTTAAGAAAATGTTTAATTTGAATTCGCACTAGAATTTTCTG
2235555 TTTCTGGTCG
Statistics
Matches: 214, Mismatches: 46, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
98 1 0.00
99 104 0.49
100 47 0.22
101 56 0.26
102 6 0.03
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (99 bp):
AATTCTTTTTTTTCGTTGCGTGGTTAAGAAAATGTTTAATTTGAATTCGCACTAGAATTTTCTGA
TTGTTTGCTGAGAAACTCTGAGAAAAACTGTTTG
Found at i:2235551 original size:56 final size:56
Alignment explanation
Indices: 2235503--2235610 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
2235493 TTTTTTTATT
* *
2235503 TCGTTGCGTGGTTAAGAAATTGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTC
1 TCGTCGCGTGGTTAAGAAAATGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTC
* * * *
2235559 TGGTCGCGTGGTTAATAAAATGTTTAATTTGAATTCGCATTAGAATTTTCTG
1 TCGTCGCGTGGTTAAGAAAATGTTTAATTTGAACTCGCACTAGAATTTTCTG
2235611 ATTGTTTCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (56 bp):
TCGTCGCGTGGTTAAGAAAATGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTC
Found at i:2254568 original size:12 final size:12
Alignment explanation
Indices: 2254553--2254619 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
2254543 GGAAGAGGAA
2254553 GACGACGATGAT
1 GACGACGATGAT
*
2254565 GACGACGAGGAT
1 GACGACGATGAT
* * *
2254577 GAGGATGATGAA
1 GACGACGATGAT
* *
2254589 GGCGAAGATGAT
1 GACGACGATGAT
* * *
2254601 GATGACGACGAC
1 GACGACGATGAT
2254613 GACGACG
1 GACGACG
2254620 GAGAGGAGGA
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.34, C:0.15, G:0.39, T:0.12
Consensus pattern (12 bp):
GACGACGATGAT
Found at i:2254584 original size:21 final size:21
Alignment explanation
Indices: 2254550--2254614 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
2254540 AGCGGAAGAG
* *
2254550 GAAGACGACGATGATGACGAC
1 GAAGATGAGGATGATGACGAC
* * *
2254571 GAGGATGAGGATGATGAAGGC
1 GAAGATGAGGATGATGACGAC
* *
2254592 GAAGATGATGATGACGACGAC
1 GAAGATGAGGATGATGACGAC
2254613 GA
1 GA
2254615 CGACGGAGAG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.38, T:0.12
Consensus pattern (21 bp):
GAAGATGAGGATGATGACGAC
Found at i:2254596 original size:48 final size:48
Alignment explanation
Indices: 2254544--2254635 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
2254534 TGGCGAAGCG
* * *
2254544 GAAGAGGAAGACGACGATGATGACGAC-GAGGATGAGGATGATGAAGGC
1 GAAGAGGAAGACGACGACGACGACGACGGA-GAGGAGGATGATGAAGGC
* * *
2254592 GAAGATGATGATGACGACGACGACGACGGAGAGGAGGATGATGA
1 GAAGAGGAAGACGACGACGACGACGACGGAGAGGAGGATGATGA
2254636 CGATGACGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
48 35 0.95
49 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.41, T:0.11
Consensus pattern (48 bp):
GAAGAGGAAGACGACGACGACGACGACGGAGAGGAGGATGATGAAGGC
Found at i:2254745 original size:24 final size:25
Alignment explanation
Indices: 2254694--2254790 Score: 69
Period size: 24 Copynumber: 4.0 Consensus size: 25
2254684 GTCAGTTGAT
*
2254694 GACGACGAGGACGA-GGATGATGAA
1 GACGACGAGGACGACGGATGAAGAA
**
2254718 GACGACGAGGACGACGG-TGAAGGC
1 GACGACGAGGACGACGGATGAAGAA
* * * * *
2254742 GACGGCGATGACGAC-GACGACGAT
1 GACGACGAGGACGACGGATGAAGAA
*
2254766 GACGAC-AGTGATGAC-GATGAAGAA
1 GACGACGAG-GACGACGGATGAAGAA
2254790 G
1 G
2254791 GTGAAGAAGA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.40, T:0.08
Consensus pattern (25 bp):
GACGACGAGGACGACGGATGAAGAA
Found at i:2254759 original size:15 final size:15
Alignment explanation
Indices: 2254721--2254771 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
2254711 TGATGAAGAC
* *
2254721 GACGAGGACGACGGT
1 GACGACGACGACGAT
* * *
2254736 GAAGGCGACGGCGAT
1 GACGACGACGACGAT
2254751 GACGACGACGACGAT
1 GACGACGACGACGAT
2254766 GACGAC
1 GACGAC
2254772 AGTGATGACG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.41, T:0.06
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:2255548 original size:12 final size:12
Alignment explanation
Indices: 2255533--2255572 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2255523 TGGTGAAGAG
*
2255533 GAAGAAGAGGAA
1 GAAGAAGATGAA
*
2255545 GAAGAAGATGAT
1 GAAGAAGATGAA
*
2255557 GAAGACGATGAA
1 GAAGAAGATGAA
2255569 GAAG
1 GAAG
2255573 GTAGTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.07
Consensus pattern (12 bp):
GAAGAAGATGAA
Found at i:2255813 original size:3 final size:3
Alignment explanation
Indices: 2255807--2255842 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2255797 TAGAAAGGAT
*
2255807 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ACG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2255843 GGATGGATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:2258039 original size:17 final size:16
Alignment explanation
Indices: 2258014--2258049 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2258004 AATATATAAC
2258014 TTTTGAAATTACAAATT
1 TTTTGAAATT-CAAATT
*
2258031 TTTTTAAATTCAAATT
1 TTTTGAAATTCAAATT
2258047 TTT
1 TTT
2258050 AACTCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTGAAATTCAAATT
Found at i:2261497 original size:15 final size:15
Alignment explanation
Indices: 2261477--2261507 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2261467 CAAGAAGAAT
*
2261477 ACAAATTATCGTACA
1 ACAAATTATCATACA
2261492 ACAAATTATCATACA
1 ACAAATTATCATACA
2261507 A
1 A
2261508 TAAAGCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (15 bp):
ACAAATTATCATACA
Found at i:2263081 original size:30 final size:30
Alignment explanation
Indices: 2263041--2263106 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2263031 TGGGTACTTT
* *
2263041 AACTTCTAAATAGCTCAATTACTTAATTG-A
1 AACTTTTAAATAGCTCAATGACTTAA-TGAA
*
2263071 AACTTTTAAATAGTTCAATGACTTAATGAA
1 AACTTTTAAATAGCTCAATGACTTAATGAA
2263101 AACTTT
1 AACTTT
2263107 CGAATAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTTAAATAGCTCAATGACTTAATGAA
Found at i:2263113 original size:30 final size:30
Alignment explanation
Indices: 2263048--2263115 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2263038 TTTAACTTCT
* * *
2263048 AAATAGCTCAATTACTTAATTGAAACTTTT
1 AAATAGTTCAATGACTTAATTGAAACTTTC
2263078 AAATAGTTCAATGACTTAA-TGAAAACTTTC
1 AAATAGTTCAATGACTTAATTG-AAACTTTC
*
2263108 GAATAGTT
1 AAATAGTT
2263116 TAGTGATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (30 bp):
AAATAGTTCAATGACTTAATTGAAACTTTC
Found at i:2263624 original size:8 final size:8
Alignment explanation
Indices: 2263607--2263638 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
2263597 TAATTTTACA
2263607 TTTAATAAT
1 TTTAA-AAT
2263616 TTTAAAAT
1 TTTAAAAT
2263624 TTTAAAAT
1 TTTAAAAT
2263632 TTTAAAA
1 TTTAAAA
2263639 GGCCTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:2269439 original size:7 final size:7
Alignment explanation
Indices: 2269429--2269454 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2269419 AATTAAAAAT
2269429 TCAATAC
1 TCAATAC
2269436 TCAATAC
1 TCAATAC
2269443 TCAATAC
1 TCAATAC
2269450 TCAAT
1 TCAAT
2269455 TTTTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (7 bp):
TCAATAC
Found at i:2271316 original size:15 final size:15
Alignment explanation
Indices: 2271296--2271356 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
2271286 ATTATTTTTA
*
2271296 AAAAATAAAATATAT
1 AAAAATAAAATAAAT
2271311 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
** *
2271326 AAATTTTAAAAAAAAT
1 AAA-AATAAAATAAAT
2271342 AATAAATGAAAATAA
1 AA-AAAT-AAAATAA
2271357 TATATTCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 17 0.47
16 12 0.33
17 7 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:2271355 original size:33 final size:29
Alignment explanation
Indices: 2271311--2271376 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
2271301 TAAAATATAT
*
2271311 AAAAAT-A-AAAT-AAATAA-ATTTTAAA
1 AAAAATAATAAATAAAATAATATATTAAA
*
2271336 AAAAATAATAAATGAAAATAATATATTCAA
1 AAAAATAATAAAT-AAAATAATATATTAAA
2271366 AAAAATAATAA
1 AAAAATAATAA
2271377 GGAGAATACG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 1 0.03
27 4 0.12
29 6 0.18
30 17 0.50
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAAATAATAAATAAAATAATATATTAAA
Found at i:2271504 original size:13 final size:13
Alignment explanation
Indices: 2271488--2271513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2271478 TACCATTAGC
2271488 TTTTATGTTATTG
1 TTTTATGTTATTG
2271501 TTTTATGTTATTG
1 TTTTATGTTATTG
2271514 AAATTTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (13 bp):
TTTTATGTTATTG
Found at i:2280896 original size:19 final size:21
Alignment explanation
Indices: 2280872--2280917 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2280862 ACCAGCTATG
*
2280872 TTATATA-TAT-TCATTTATA
1 TTATATATTATGTAATTTATA
2280891 TTATATATTATGTAATTTATA
1 TTATATATTATGTAATTTATA
2280912 TTATAT
1 TTATAT
2280918 GAAACCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 14 0.58
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATATATTATGTAATTTATA
Found at i:2281095 original size:17 final size:17
Alignment explanation
Indices: 2281073--2281107 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2281063 TATATTAATA
2281073 CCATAAACTCCTCTACT
1 CCATAAACTCCTCTACT
2281090 CCATAAACTCCTCTACT
1 CCATAAACTCCTCTACT
2281107 C
1 C
2281108 ATGGGTGGAT
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:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (17 bp):
CCATAAACTCCTCTACT
Done.