Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 121 of 208
Found at i:39912106 original size:35 final size:35
Alignment explanation
Indices: 39912054--39912176 Score: 183
Period size: 35 Copynumber: 3.5 Consensus size: 35
39912044 TCCACAGTTA
* *
39912054 ACCATTCAGCACACCAGATGTTCATAAGAGCTAGT
1 ACCATCCAGCACACCAGATGCTCATAAGAGCTAGT
* * *
39912089 ACCACCCAGCACACCAGATGCTCACAAGAGTTAGT
1 ACCATCCAGCACACCAGATGCTCATAAGAGCTAGT
* *
39912124 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
1 ACCATCCAGCACACCAGATGCTCATAAGAGCTAGT
39912159 ACCATCCAGCACACCAGA
1 ACCATCCAGCACACCAGA
39912177 AACACTGTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 77 1.00
ACGTcount: A:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (35 bp):
ACCATCCAGCACACCAGATGCTCATAAGAGCTAGT
Found at i:39915889 original size:29 final size:29
Alignment explanation
Indices: 39915826--39915893 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
39915816 TAATCAACCG
*
39915826 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39915855 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39915884 CGCACACTTA
1 CGCACACTTA
39915894 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39916005 original size:174 final size:174
Alignment explanation
Indices: 39915715--39916216 Score: 941
Period size: 174 Copynumber: 2.9 Consensus size: 174
39915705 AACTCAAGGT
* *
39915715 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
39915780 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
39915845 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
39915889 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
39915954 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
39916019 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
39916063 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTCAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
39916128 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
39916193 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
39916217 TGTACAATTT
Statistics
Matches: 319, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 319 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:39916063 original size:29 final size:29
Alignment explanation
Indices: 39916000--39916067 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
39915990 TAATCAACCG
39916000 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39916029 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39916058 CGCACACTTA
1 CGCACACTTA
39916068 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39916208 original size:29 final size:30
Alignment explanation
Indices: 39916169--39916247 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
39916159 CTTAATAATC
39916169 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
39916199 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
39916228 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39916248 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:39924881 original size:80 final size:81
Alignment explanation
Indices: 39924765--39924950 Score: 222
Period size: 80 Copynumber: 2.3 Consensus size: 81
39924755 AGTAACTCAT
* ** *
39924765 ACAATGCCTTCGGGACTTAACCCGG-ATTTTTAAACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 ACAAAGCCTTCGGGACTTAACCCGGAATTAATAAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
39924828 GGA-ATTAGT-A-TCTCGC
65 GGATA-TAGTCACT-TAGC
**
39924844 ACAAAGGCCTTCGGGACTTAACCCGGAATTAAT-AACTCGCACAAATGCCTTCGGATCTTATTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGAATTAATAAACTCGCACAAATGCCTTCGGATCTTAACCC
39924908 GGATATAGTCACTTAGC
65 GGATATAGTCACTTAGC
*
39924925 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
39924951 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 7 0.08
80 71 0.76
81 14 0.15
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (81 bp):
ACAAAGCCTTCGGGACTTAACCCGGAATTAATAAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTCACTTAGC
Found at i:39924910 original size:40 final size:40
Alignment explanation
Indices: 39924767--39924950 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
39924757 TAACTCATAC
** *
39924767 AATGCCTTCGGGACTTAACCCGG-ATTTTTAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGAATTAAT-AACTCGCACA
* *
39924807 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
39924847 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
39924887 AATGCCTTC-GGATCTTATTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
39924928 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39924951 CAGCATTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.04
40 103 0.84
41 15 0.12
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:39927353 original size:29 final size:29
Alignment explanation
Indices: 39927290--39927357 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
39927280 TAATCAACCA
*
39927290 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39927319 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39927348 CGCACACTTA
1 CGCACACTTA
39927358 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39927527 original size:29 final size:29
Alignment explanation
Indices: 39927464--39927531 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
39927454 TAATCAACCG
39927464 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39927493 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39927522 CGCACACTTA
1 CGCACACTTA
39927532 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39927672 original size:29 final size:30
Alignment explanation
Indices: 39927633--39927711 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
39927623 CTTAATAATC
39927633 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
39927663 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
39927692 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39927712 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:39927705 original size:174 final size:174
Alignment explanation
Indices: 39927179--39927680 Score: 941
Period size: 174 Copynumber: 2.9 Consensus size: 174
39927169 AACTCAAGGT
* *
39927179 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
39927244 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
39927309 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
39927353 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
39927418 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
39927483 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
39927527 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
39927592 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
39927657 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
39927681 TGTACAATTT
Statistics
Matches: 319, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 319 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:39931481 original size:35 final size:36
Alignment explanation
Indices: 39931442--39931552 Score: 120
Period size: 35 Copynumber: 3.0 Consensus size: 36
39931432 TCCTCCCTTC
*
39931442 TCTCTCTTTC-CCTCTTTTATTC-TCTGTTGGCTGAA
1 TCTCTCTTTCTCCTCTCTTATTCTTCT-TTGGCTGAA
* *
39931477 TCTCTC-TTCTCTTCTCTTCTTCTTCTTTGGCTGAA
1 TCTCTCTTTCTCCTCTCTTATTCTTCTTTGGCTGAA
*
39931512 TCTCTCTTCTCTTCTCTTCTCTTCTTCTTCTTTGGCTGAA
1 TCTCTCTT-TC-TC-C-TCTCTTATTCTTCTTTGGCTGAA
39931552 T
1 T
39931553 AACTTCTTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
34 3 0.05
35 30 0.46
36 4 0.06
37 2 0.03
38 2 0.03
40 24 0.37
ACGTcount: A:0.06, C:0.31, G:0.09, T:0.54
Consensus pattern (36 bp):
TCTCTCTTTCTCCTCTCTTATTCTTCTTTGGCTGAA
Found at i:39931489 original size:5 final size:5
Alignment explanation
Indices: 39931479--39931542 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
39931469 TGGCTGAATC
** **
39931479 TCTCT TCTCT TCTCT TCTTCT TCT-T TGGCT GAATC- TCTCT TCTCT TCTCT
1 TCTCT TCTCT TCTCT TC-TCT TCTCT TCTCT -TCTCT TCTCT TCTCT TCTCT
39931529 TCTCT TCTTCT TCT
1 TCTCT TC-TCT TCT
39931543 TTGGCTGAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.09
5 32 0.68
6 11 0.23
ACGTcount: A:0.03, C:0.34, G:0.05, T:0.58
Consensus pattern (5 bp):
TCTCT
Found at i:39932129 original size:27 final size:27
Alignment explanation
Indices: 39932071--39932187 Score: 92
Period size: 27 Copynumber: 4.3 Consensus size: 27
39932061 TCATGGGCAG
**
39932071 ATGACCGAAATACCTCCATAAAGGGTAAA
1 ATGACCGAAATACC-CC-CGAAGGGTAAA
39932100 ATGACCGAAATACCCCCGAAGGGTAAA
1 ATGACCGAAATACCCCCGAAGGGTAAA
*** **** *
39932127 ATGATTAAAATTTTGCC-AATGGTTAAA
1 ATGACCGAAATACCCCCGAA-GGGTAAA
* *
39932154 ATGACCGAAATACCCTCGAAAGGTAAA
1 ATGACCGAAATACCCCCGAAGGGTAAA
39932181 ATGACCG
1 ATGACCG
39932188 GCACTAATAT
Statistics
Matches: 66, Mismatches: 20, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
26 2 0.03
27 46 0.70
28 4 0.06
29 14 0.21
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (27 bp):
ATGACCGAAATACCCCCGAAGGGTAAA
Found at i:39932262 original size:28 final size:28
Alignment explanation
Indices: 39932230--39932298 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
39932220 GTTACATTAT
* *
39932230 CACACTGTTATTGTATTAG-GCTAAGGCC
1 CACACTGTTACTATA-TAGAGCTAAGGCC
* *
39932258 CACACTATTACTATATCGAGCTAAGGCC
1 CACACTGTTACTATATAGAGCTAAGGCC
39932286 CACACTG-TACTAT
1 CACACTGTTACTAT
39932299 TACTGCATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (28 bp):
CACACTGTTACTATATAGAGCTAAGGCC
Found at i:39935661 original size:15 final size:15
Alignment explanation
Indices: 39935643--39935671 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39935633 TTCTGGAAGT
39935643 TGGCTAAACTGTATG
1 TGGCTAAACTGTATG
39935658 TGGCTAAACTGTAT
1 TGGCTAAACTGTAT
39935672 CTACCCATTT
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:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (15 bp):
TGGCTAAACTGTATG
Found at i:39938043 original size:27 final size:27
Alignment explanation
Indices: 39938008--39938110 Score: 125
Period size: 27 Copynumber: 3.8 Consensus size: 27
39937998 TCATGGGTAG
39938008 ATGACCGAAATACCCCTGAAGGGTAAA
1 ATGACCGAAATACCCCTGAAGGGTAAA
* *
39938035 ATGGCCGAAATACCCCCGAAGGGTAAA
1 ATGACCGAAATACCCCTGAAGGGTAAA
* * * *
39938062 ATGATCAAAATACCCCTAAAAGGTAAA
1 ATGACCGAAATACCCCTGAAGGGTAAA
**
39938089 ATGACCGTTATACCCCTAGAAG
1 ATGACCGAAATACCCCT-GAAG
39938111 TCGAAATGAC
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
27 59 0.97
28 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (27 bp):
ATGACCGAAATACCCCTGAAGGGTAAA
Found at i:39938469 original size:33 final size:32
Alignment explanation
Indices: 39938405--39938469 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
39938395 ACATTATCAC
* * * *
39938405 ACTATTACTGTTTGGGCTAAGGGCCACACTGT
1 ACTATTACTGATAGGGCTAAGGCCCAAACTGT
*
39938437 ACTATTACTGCATAGGGCTCAGGCCCAAACTGT
1 ACTATTACTG-ATAGGGCTAAGGCCCAAACTGT
39938470 TACTGCATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (32 bp):
ACTATTACTGATAGGGCTAAGGCCCAAACTGT
Found at i:39946885 original size:21 final size:22
Alignment explanation
Indices: 39946856--39946902 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
39946846 CAGAAGGAGT
*
39946856 GAGTAGTACTTCACAGCAAGTG
1 GAGTAGTACTCCACAGCAAGTG
* *
39946878 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAAGTG
39946899 GAGT
1 GAGT
39946903 TTGAGCAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAAGTG
Found at i:39954367 original size:39 final size:39
Alignment explanation
Indices: 39954310--39954409 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
39954300 ATGTAATCAA
** *
39954310 GGCACGTAACTGCAAATCAGGGGTACCGAAGTACAACAAG
1 GGCACGTATGTGC-AATCAGGGGTACCAAAGTACAACAAG
* *
39954350 GGCACGTATGTGCAATCAAGGGTACCAAAGTACAACAGG
1 GGCACGTATGTGCAATCAGGGGTACCAAAGTACAACAAG
* *
39954389 GGCACGTATGTACGATCAGGG
1 GGCACGTATGTGCAATCAGGG
39954410 AATACTTACA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 41 0.79
40 11 0.21
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.15
Consensus pattern (39 bp):
GGCACGTATGTGCAATCAGGGGTACCAAAGTACAACAAG
Found at i:39955192 original size:14 final size:14
Alignment explanation
Indices: 39955175--39955201 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39955165 TTTTACTTAG
39955175 TTTATTTATTAAAA
1 TTTATTTATTAAAA
39955189 TTTATTTATTAAA
1 TTTATTTATTAAA
39955202 CTACAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTTATTAAAA
Found at i:39958062 original size:33 final size:33
Alignment explanation
Indices: 39958011--39958364 Score: 143
Period size: 33 Copynumber: 10.4 Consensus size: 33
39958001 CATATAAAGG
**
39958011 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
39958044 GGTTACTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T----GGT
*
39958087 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
**
39958114 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
39958147 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T----GGT
*
39958190 GGTTGCTAAGTGCTAATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTC-ATTGGT
* *
39958217 GGTTGCTAAGTGCTAATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
39958250 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AT-T--CAT-T---GGT
*
39958292 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
**
39958319 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
39958352 GGTTGCTAAGTGC
1 GGTTGCTAAGTGC
39958365 GGAATCCACT
Statistics
Matches: 244, Mismatches: 28, Indels: 98
0.66 0.08 0.26
Matches are distributed among these distances:
27 62 0.25
28 6 0.02
30 1 0.00
31 5 0.02
32 6 0.02
33 66 0.27
34 9 0.04
35 5 0.02
36 1 0.00
37 4 0.02
38 6 0.02
39 3 0.01
41 2 0.01
42 26 0.11
43 42 0.17
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:39958346 original size:102 final size:103
Alignment explanation
Indices: 39958007--39958373 Score: 619
Period size: 103 Copynumber: 3.6 Consensus size: 103
39957997 ATTGCATATA
*
39958007 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTACTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
39958072 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
39958110 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
39958175 TTAAATGTGAAAGGGGGTTGCTAAGTGCTAATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * * *
39958213 GAGGGGTTGCTAAGTGCTAATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
39958278 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
39958315 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCGGAATCCAC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCAC
39958374 TGATAACGGT
Statistics
Matches: 246, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
102 79 0.32
103 167 0.68
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:39961190 original size:21 final size:21
Alignment explanation
Indices: 39961164--39961206 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39961154 GGTTCGCTGT
*
39961164 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
39961185 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
39961206 A
1 A
39961207 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:39961206 original size:16 final size:16
Alignment explanation
Indices: 39961187--39961219 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39961177 TGTATTGGAT
*
39961187 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
39961203 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
39961219 T
1 T
39961220 AGCAAATCAA
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:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:39961264 original size:45 final size:44
Alignment explanation
Indices: 39961198--39961292 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
39961188 GGATTAGAGG
* *
39961198 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTATGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTATGGTTGAA
* ** *
39961243 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTATGGTTGAA
39961287 TGTAAT
1 TGTAAT
39961293 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 17 0.39
45 27 0.61
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTATGGTTGAA
Found at i:39961475 original size:18 final size:17
Alignment explanation
Indices: 39961454--39961488 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39961444 TTATTATTTA
*
39961454 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39961472 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39961489 GGTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39961482 original size:28 final size:27
Alignment explanation
Indices: 39961412--39961484 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
39961402 TTTATTATCA
*
39961412 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
39961440 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
39961467 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
39961485 AAATGGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:39961601 original size:144 final size:147
Alignment explanation
Indices: 39961373--39961644 Score: 460
Period size: 144 Copynumber: 1.9 Consensus size: 147
39961363 ATGATTATTG
*
39961373 TTATTGTTATTTGAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
39961438 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGGTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
39961503 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
39961522 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
39961584 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTA
39961645 ATATTCTTAT
Statistics
Matches: 118, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
144 90 0.76
145 1 0.01
148 22 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:39961619 original size:18 final size:17
Alignment explanation
Indices: 39961598--39961632 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39961588 TTATTATTAA
*
39961598 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39961616 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39961633 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39965531 original size:12 final size:12
Alignment explanation
Indices: 39965514--39965543 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39965504 GGACACATGG
39965514 CCGTGTCCCAAC
1 CCGTGTCCCAAC
*
39965526 CCGTGTCCCAGC
1 CCGTGTCCCAAC
39965538 CCGTGT
1 CCGTGT
39965544 AACTCACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.47, G:0.23, T:0.20
Consensus pattern (12 bp):
CCGTGTCCCAAC
Found at i:39971466 original size:75 final size:75
Alignment explanation
Indices: 39971325--39971466 Score: 164
Period size: 75 Copynumber: 1.9 Consensus size: 75
39971315 GTAAAAGAAT
* * * *
39971325 TATTTTTTATAATTTTTAAATTTTTTATTACATTTAAATTATCTGTGATTTTATTGTTATTTAAT
1 TATTTTTTATAAGTTTTAAATTTTTTATTACATTTAAATTATCTGTGATTTAATTGTTACTCAAT
39971390 GTTTCAAATA
66 GTTTCAAATA
* * * *
39971400 TATTTTTTA-ATAGTTTTAAATTTTATTGTTATATTTTAATTATTTGTGA-TTAATT-TCTACTC
1 TATTTTTTATA-AGTTTTAAATTTT-TTATTACATTTAAATTATCTGTGATTTAATTGT-TACTC
39971462 AATGT
63 AATGT
39971467 CCAAACAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
74 2 0.04
75 34 0.61
76 20 0.36
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (75 bp):
TATTTTTTATAAGTTTTAAATTTTTTATTACATTTAAATTATCTGTGATTTAATTGTTACTCAAT
GTTTCAAATA
Found at i:39973204 original size:68 final size:68
Alignment explanation
Indices: 39973093--39973228 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
39973083 CTGAACTAAT
* *
39973093 TGTTTTAACACCCTTAACTCTTTGCCCAAAGGTGAATGAGAGATAGAGAGAAACTATTTTCAACC
1 TGTTTGAACACCCTTAACTCTTTGCCCAAAGCTGAATGAGAGATAGAGAGAAACTATTTTCAACC
39973158 AAC
66 AAC
* *
39973161 TGTTTGAACACCCTTAACTCTTTGCCCAAAGCTGAATGGGAGATAGAGAGAATCTATTTTCAACC
1 TGTTTGAACACCCTTAACTCTTTGCCCAAAGCTGAATGAGAGATAGAGAGAAACTATTTTCAACC
39973226 AAC
66 AAC
39973229 AATTGAAGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (68 bp):
TGTTTGAACACCCTTAACTCTTTGCCCAAAGCTGAATGAGAGATAGAGAGAAACTATTTTCAACC
AAC
Found at i:39994318 original size:184 final size:181
Alignment explanation
Indices: 39994090--39994451 Score: 562
Period size: 182 Copynumber: 2.0 Consensus size: 181
39994080 ATCTAATTAG
* * *
39994090 TACTTTAAATAAATAATATTATGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAGA
1 TACTTTAAATAAATAAGAATACGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAG-
* *
39994155 AAATAAAAATCGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATTTAAGC
65 AAA-AAAAATAGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATCTAAGC
* *
39994220 ATGGGTGATTAGCTCGCTTTGATGAGCATAACTAATTCCTATTTTGGGTTTTAA
129 ATGGGAGATTAGCTCACTTTGATGAGC-TAACTAATTCCTATTTTGGGTTTTAA
*
39994274 TACTTTAAATAAATAAGAATACGATAAAACATAAATAGAAGATTTTTGGGTTTTTATAATAAAGA
1 TACTTTAAATAAATAAGAATACGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAGA
* ** * *
39994339 AAAAAAATAGCGAAAATAAAGTGAACTTTGGGTGAATGAGTTCTCACTTAATCAAATCTAAGCAT
66 AAAAAAATAGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATCTAAGCAT
* *
39994404 GGGAGATTAGCTCACTTTGGTGATCTAACTAATTCCTATTTTGGGTTT
131 GGGAGATTAGCTCACTTTGATGAGCTAACTAATTCCTATTTTGGGTTT
39994452 CCACTCAATC
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
181 23 0.14
182 77 0.47
183 3 0.02
184 60 0.37
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (181 bp):
TACTTTAAATAAATAAGAATACGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAGA
AAAAAAATAGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATCTAAGCAT
GGGAGATTAGCTCACTTTGATGAGCTAACTAATTCCTATTTTGGGTTTTAA
Found at i:39994893 original size:21 final size:20
Alignment explanation
Indices: 39994863--39994901 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39994853 CTATCATTAT
*
39994863 TAAGTCTCTATTTCTGTGGC
1 TAAGTCTCTATTTATGTGGC
39994883 TAAGTACTCTATTTATGTG
1 TAAGT-CTCTATTTATGTG
39994902 TTTGAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (20 bp):
TAAGTCTCTATTTATGTGGC
Found at i:39995776 original size:17 final size:17
Alignment explanation
Indices: 39995754--39995822 Score: 102
Period size: 17 Copynumber: 4.1 Consensus size: 17
39995744 CACATGGCCG
*
39995754 TGTGGCTCAGACGGCTA
1 TGTGGCTCACACGGCTA
**
39995771 TGTGGCTCACACGGCCG
1 TGTGGCTCACACGGCTA
39995788 TGTGGCTCACACGGCTA
1 TGTGGCTCACACGGCTA
*
39995805 TGTGGCTCACATGGCTA
1 TGTGGCTCACACGGCTA
39995822 T
1 T
39995823 TTGCCAGTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.25
Consensus pattern (17 bp):
TGTGGCTCACACGGCTA
Found at i:39995787 original size:34 final size:34
Alignment explanation
Indices: 39995743--39995815 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
39995733 ATTGTCGACG
* *
39995743 TCACATGGCCGTGTGGCTCAGACGGCTATGTGGC
1 TCACACGGCCGTGTGGCTCACACGGCTATGTGGC
39995777 TCACACGGCCGTGTGGCTCACACGGCTATGTGGC
1 TCACACGGCCGTGTGGCTCACACGGCTATGTGGC
39995811 TCACA
1 TCACA
39995816 TGGCTATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (34 bp):
TCACACGGCCGTGTGGCTCACACGGCTATGTGGC
Found at i:39996026 original size:42 final size:42
Alignment explanation
Indices: 39995946--39996038 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
39995936 AATGACATGA
* *
39995946 GCGTGTGTCTAGACTATGTAACTCCCTAGCTTGTGTCACACGG
1 GCGTGTGTCTAGACCATGTAACTCCCTAGCTTGGGTCACAC-G
* *
39995989 GCGTGTGTC-AGACCGTGTAACTCTCT-GACTTGGGTCACACG
1 GCGTGTGTCTAGACCATGTAACTCCCTAG-CTTGGGTCACACG
39996030 GCTGTGTGT
1 GC-GTGTGT
39996039 TAAGTTATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 4 0.09
42 31 0.70
43 9 0.20
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (42 bp):
GCGTGTGTCTAGACCATGTAACTCCCTAGCTTGGGTCACACG
Found at i:39997554 original size:22 final size:22
Alignment explanation
Indices: 39997526--39997574 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
39997516 ATAGCAATTC
* *
39997526 TGACATTCAGCTCCCTATGTTG
1 TGACATTCAACTCCCCATGTTG
* *
39997548 TGACATTGAACTCCCCGTGTTG
1 TGACATTCAACTCCCCATGTTG
39997570 TGACA
1 TGACA
39997575 CAGTAACCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (22 bp):
TGACATTCAACTCCCCATGTTG
Found at i:39999509 original size:25 final size:25
Alignment explanation
Indices: 39999481--39999539 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
39999471 AACTTTTCGA
* *
39999481 TATTCAGCTCGCATGAGCTTCCTGT
1 TATTCAGCTCACATGAGCTTCCCGT
*
39999506 TATTCAGCACACATGAGCTTCCCGT
1 TATTCAGCTCACATGAGCTTCCCGT
39999531 TATTCAGCT
1 TATTCAGCT
39999540 TGGAAGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (25 bp):
TATTCAGCTCACATGAGCTTCCCGT
Found at i:40000859 original size:16 final size:16
Alignment explanation
Indices: 40000834--40000874 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
40000824 TTTCGATTGA
40000834 TTTTTTATATG-AATG
1 TTTTTTATATGAAATG
40000849 TTTTGTTATATGAAATG
1 TTTT-TTATATGAAATG
40000866 TTTATTTAT
1 TTT-TTTAT
40000875 TTGATTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 7 0.30
17 11 0.48
18 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (16 bp):
TTTTTTATATGAAATG
Found at i:40002737 original size:36 final size:35
Alignment explanation
Indices: 40002697--40002774 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
40002687 AGAACATCGA
*
40002697 TAATCTAGCCAAAACACACGAGATGCTCATAAGAGC
1 TAATCTAGCCAAAACACACCA-ATGCTCATAAGAGC
* * * *
40002733 TAATCCATCCGAAACACACCAATGCTCATAAGAGT
1 TAATCTAGCCAAAACACACCAATGCTCATAAGAGC
40002768 TAATCTA
1 TAATCTA
40002775 TTTGAAACAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21
Consensus pattern (35 bp):
TAATCTAGCCAAAACACACCAATGCTCATAAGAGC
Found at i:40002765 original size:35 final size:35
Alignment explanation
Indices: 40002708--40002789 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
40002698 AATCTAGCCA
*
40002708 AAACACACGAGATGCTCATAAGAGCTAATCCATCCG
1 AAACACACCA-ATGCTCATAAGAGCTAATCCATCCG
* * **
40002744 AAACACACCAATGCTCATAAGAGTTAATCTATTTG
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCG
40002779 AAACACACCAA
1 AAACACACCAA
40002790 AACAGAGAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 32 0.78
36 9 0.22
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.20
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCATCCG
Found at i:40006416 original size:31 final size:31
Alignment explanation
Indices: 40006375--40006441 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
40006365 TACAAATTGA
* *
40006375 TCACTGAATTATTCGAA-AGTTTTCATTTAAG
1 TCACTAAATTATTCGAATA-TTTTCATATAAG
*
40006406 TCACTAAATTATTCGAATATTTTTATATAAG
1 TCACTAAATTATTCGAATATTTTCATATAAG
40006437 TCACT
1 TCACT
40006442 CGACTGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (31 bp):
TCACTAAATTATTCGAATATTTTCATATAAG
Found at i:40008072 original size:17 final size:17
Alignment explanation
Indices: 40008050--40008083 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40008040 TTCGAAGTTG
40008050 ATCTTCTCAATAAAATT
1 ATCTTCTCAATAAAATT
*
40008067 ATCTTCTTAATAAAATT
1 ATCTTCTCAATAAAATT
40008084 GTCTCAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCTTCTCAATAAAATT
Found at i:40010158 original size:21 final size:20
Alignment explanation
Indices: 40010134--40010184 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
40010124 ATTCATAACA
*
40010134 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
40010155 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTGC
*
40010176 TATACAAAT
1 TATTCAAAT
40010185 AGTTTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:40010161 original size:22 final size:21
Alignment explanation
Indices: 40010136--40010178 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
40010126 TCATAACATA
*
40010136 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
40010158 TTCAAATCTCATACTTGCTAT
1 TTCAAATCTCATACTTGCTAT
40010179 ACAAATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:40010399 original size:40 final size:40
Alignment explanation
Indices: 40010344--40010476 Score: 112
Period size: 37 Copynumber: 3.4 Consensus size: 40
40010334 CCAATTTGGT
* *
40010344 ACCCAGTACCTCATCGGATAATTCGAAGTAATAAATTGAC
1 ACCCAGTGCCTCATCGGATAATACGAAGTAATAAATTGAC
* * *
40010384 ACCCAGTGTCTCATCGGCTAA-ACTGAAG---TAAATTGGC
1 ACCCAGTGCCTCATCGGATAATAC-GAAGTAATAAATTGAC
* * * * *
40010421 ACCCAATGCCTCATCGAATTAGTCCGAAGTAATAAATTAAC
1 ACCCAGTGCCTCATCGGA-TAATACGAAGTAATAAATTGAC
* *
40010462 ACCTAGTGTCTCATC
1 ACCCAGTGCCTCATC
40010477 AACTCAAAGT
Statistics
Matches: 71, Mismatches: 16, Indels: 11
0.72 0.16 0.11
Matches are distributed among these distances:
37 22 0.31
38 6 0.08
39 2 0.03
40 22 0.31
41 19 0.27
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (40 bp):
ACCCAGTGCCTCATCGGATAATACGAAGTAATAAATTGAC
Found at i:40011416 original size:5 final size:5
Alignment explanation
Indices: 40011406--40011468 Score: 119
Period size: 5 Copynumber: 12.8 Consensus size: 5
40011396 TTTGTTTTAT
40011406 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
40011456 TATAA TAT-A TATA
1 TATAA TATAA TATA
40011469 CTTAAATCTT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.07
5 53 0.93
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:40013993 original size:49 final size:49
Alignment explanation
Indices: 40013940--40014037 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
40013930 AAGTTGTAAG
* * * *
40013940 TCAATTGTATATCATGCTAGAGTTATATGTTTATTTACACTATCTTGTT
1 TCAATTCTATATCATGCTAGAGTCATATGCTTATTTACAATATCTTGTT
* *
40013989 TCAATTCTATATCATTCTAGAGTCGTATGCTTATTTACAATATCTTGTT
1 TCAATTCTATATCATGCTAGAGTCATATGCTTATTTACAATATCTTGTT
40014038 AATATAATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (49 bp):
TCAATTCTATATCATGCTAGAGTCATATGCTTATTTACAATATCTTGTT
Found at i:40014932 original size:19 final size:22
Alignment explanation
Indices: 40014894--40014934 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
40014884 TATCAATGAG
40014894 TATTCTCTTTAATCTTATATTT
1 TATTCTCTTTAATCTTATATTT
40014916 TATTCT-TTT-AT-TTATATTT
1 TATTCTCTTTAATCTTATATTT
40014935 CGTTAGCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 3 0.16
22 6 0.32
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTCTCTTTAATCTTATATTT
Found at i:40021441 original size:40 final size:40
Alignment explanation
Indices: 40021385--40021612 Score: 402
Period size: 40 Copynumber: 5.7 Consensus size: 40
40021375 GAGCATTGGA
*
40021385 ATATATCCGGGGTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
40021425 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
40021465 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
40021505 ATATATCCGGGCTAAGACCCGAACGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
40021545 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
40021585 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
40021613 ATGTGTTTGC
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 180 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:40029831 original size:40 final size:40
Alignment explanation
Indices: 40029776--40030003 Score: 420
Period size: 40 Copynumber: 5.7 Consensus size: 40
40029766 GAGCATTGGA
40029776 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
40029816 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
40029856 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
40029896 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
40029936 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
40029976 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
40030004 ATGTGTTTGC
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 183 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:40037196 original size:63 final size:62
Alignment explanation
Indices: 40037124--40037282 Score: 196
Period size: 63 Copynumber: 2.5 Consensus size: 62
40037114 CTTTAGGGAC
* *
40037124 CACAAGGGCAAGAGACACAGGATTGTGTCCAGGTCGTGTGACTCACTGTTTGCCATCAAGGAT
1 CACATGGGCAAGAGACACAGGA-TGTGTCCAGGTCGTGTGACTCACTGTTTGCCATCAAGGAG
* * * * *
40037187 CACATGGGCAAGAGACACGGGCATGTGTCCAGGTCGTGTGTCTCACTGTTTGCTATTATGGAG
1 CACATGGGCAAGAGACACAGG-ATGTGTCCAGGTCGTGTGACTCACTGTTTGCCATCAAGGAG
40037250 CACATGGGCCAA-AGACACATGCG-TGTGTCCAGG
1 CACATGGG-CAAGAGACACA-G-GATGTGTCCAGG
40037283 CTATGTGACC
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 78 0.93
64 5 0.06
65 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (62 bp):
CACATGGGCAAGAGACACAGGATGTGTCCAGGTCGTGTGACTCACTGTTTGCCATCAAGGAG
Found at i:40044971 original size:50 final size:50
Alignment explanation
Indices: 40044875--40044973 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
40044865 CATTGAGGTT
* *
40044875 ATGAGAGGTCCCATGTAAGACCATGTCTTGGACATGGCGCTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTTGGACATGGCGATGGCACCGAG
* *
40044925 ATGAGAGGTCCCCCGTAAGACCATGT-TTGGGATATGGC-ATGAGCACCGA
1 ATGAGAGGTCCCACGTAAGACCATGTCTT-GGACATGGCGATG-GCACCGA
40044974 TACGAGAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 4 0.09
50 39 0.91
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTTGGACATGGCGATGGCACCGAG
Found at i:40047134 original size:14 final size:14
Alignment explanation
Indices: 40047115--40047143 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40047105 TTACTGAGTA
40047115 TGAACGTGAATTTG
1 TGAACGTGAATTTG
40047129 TGAACGTGAATTTG
1 TGAACGTGAATTTG
40047143 T
1 T
40047144 CAGGCTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (14 bp):
TGAACGTGAATTTG
Found at i:40063929 original size:16 final size:15
Alignment explanation
Indices: 40063904--40063937 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40063894 AAAGTTGATA
*
40063904 ATAATTAATATACATT
1 ATAATAAATATA-ATT
40063920 ATAATAAATATAATT
1 ATAATAAATATAATT
40063935 ATA
1 ATA
40063938 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:40064061 original size:29 final size:30
Alignment explanation
Indices: 40064003--40064062 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40063993 GTCTTTTAAA
* * *
40064003 ATATTTACAAAAAGAGGCATCTAATTTTTG
1 ATATTTACAAAAAGAGGCAACCAAATTTTG
40064033 ATATTTACAAAAAGA-GCAACCAAATTTTG
1 ATATTTACAAAAAGAGGCAACCAAATTTTG
40064062 A
1 A
40064063 AAATAGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (30 bp):
ATATTTACAAAAAGAGGCAACCAAATTTTG
Found at i:40075808 original size:13 final size:13
Alignment explanation
Indices: 40075792--40075826 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
40075782 AATAGCCAAA
40075792 TAAAATCATTCTT
1 TAAAATCATTCTT
40075805 TAAAATCATTCTT
1 TAAAATCATTCTT
*
40075818 TGAAATCAT
1 TAAAATCAT
40075827 CATTTTTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (13 bp):
TAAAATCATTCTT
Found at i:40089359 original size:13 final size:12
Alignment explanation
Indices: 40089324--40089384 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
40089314 AATATTGCTG
*
40089324 TTGAGAAGTGTT
1 TTGAAAAGTGTT
*
40089336 TTTAAAGAGTGTT
1 TTGAAA-AGTGTT
40089349 TTGGAAAAGTGATT
1 TT-GAAAAGTG-TT
* *
40089363 TTGAGAAGTATTT
1 TTGAAAAGT-GTT
40089376 TTGAAAAGT
1 TTGAAAAGT
40089385 TTGGTTTAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
12 4 0.10
13 28 0.72
14 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (12 bp):
TTGAAAAGTGTT
Found at i:40099152 original size:89 final size:88
Alignment explanation
Indices: 40099020--40099451 Score: 474
Period size: 89 Copynumber: 4.9 Consensus size: 88
40099010 TCATGGTGAG
* * * * * * * *
40099020 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGTA
1 TCTTATCTCCCTGAAATTGCAGTGAAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
*
40099085 GTGGAACAAATTGAAGATAGCAAA
66 GTGGAGCAAATTGAAGATA-CAAA
* *
40099109 TCTTATCCCCCTGAAATTGCAGTGAAGTAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAATTGCAGTGAAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
* *
40099174 GTGGAGCAGATTGAATATAGCAAA
66 GTGGAGCAAATTGAAGATA-CAAA
* * * * * *
40099198 TCTTATCTCTCTGAAGTTGCAGT-AGAGCAGATTAAAGCTACAAACCTTATCCCCCCTGAAATTG
1 TCTTATCTCCCTGAAATTGCAGTGA-AGCAGATTGAAGCTACAAATCTTAT-CTCCCTGAAGTTG
* * *
40099262 CAGTGAAGCAGATTGAAGCTACAAA
64 CAGTGGAGCAAATTGAAGATACAAA
* * * *
40099287 TCTTATCTCCCT-AAAGTTGTAGT-AGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCTGAAA-TTGCAGTGA-AGCAGATTGAAGCTA-CAAATCTTATCTCCCTGAAGTT
* * * *
40099350 GCAGTAGAGCATATTAAAGCTACAAA
63 GCAGTGGAGCAAATTGAAGATACAAA
* * * *
40099376 CCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAATTGCAGTGAAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
40099441 GTGGAGCAAAT
66 GTGGAGCAAAT
40099452 GGAAACAACA
Statistics
Matches: 292, Mismatches: 45, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
88 37 0.13
89 214 0.73
90 41 0.14
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAAATTGCAGTGAAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAAATTGAAGATACAAA
Found at i:40099277 original size:134 final size:133
Alignment explanation
Indices: 40099020--40099504 Score: 618
Period size: 134 Copynumber: 3.6 Consensus size: 133
40099010 TCATGGTGAG
* * * * * * *
40099020 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCA-CAAACCTTATCTCCCTAAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAATCTTATCTCTCTGAAGTTGC
* * * * * * *
40099084 AGTGGAACAAATTGAAGATAGCAAATCTTATCCCCCTGAAATTGCAGTGAAGTAGATTGAAGCTA
66 AGTAGAGCAGATTAAAGCTA-CAAACCTTATCCCCCTGAAATTGCAGTGAAGCAGATTGAAGCTA
40099149 CAAA
130 CAAA
* *
40099153 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAATCTTATCTCTCTGAAGTTGC
40099218 AGTAGAGCAGATTAAAGCTACAAACCTTATCCCCCCTGAAATTGCAGTGAAGCAGATTGAAGCTA
66 AGTAGAGCAGATTAAAGCTACAAACCTTAT-CCCCCTGAAATTGCAGTGAAGCAGATTGAAGCTA
40099283 CAAA
130 CAAA
* * * * *
40099287 TCTTATCTCCCTAAAGTTGTAGTAGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAATCTTATCTCTCTGAAGTTGC
* * * *
40099352 AGTAGAGCATATTAAAGCTACAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGTTAC
66 AGTAGAGCAGATTAAAGCTACAAACCTTATCCCCCTGAAATTGCAGTGAAGCAGATTGAAGCTAC
40099417 AAA
131 AAA
* * * * **
40099420 TCTTATCTCTCTGAAGTTGCAGTGGAGCAAATGGAA-ACAACAAATCCAATAC-CTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAATCTTAT-CTCTCTGAAGTTG
*
40099483 CAGTAG-GTCAGATTAAATCTAC
65 CAGTAGAG-CAGATTAAAGCTAC
40099505 CATAGCAAGT
Statistics
Matches: 310, Mismatches: 38, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
131 1 0.00
132 39 0.13
133 109 0.35
134 161 0.52
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGCAAATCTTATCTCTCTGAAGTTGC
AGTAGAGCAGATTAAAGCTACAAACCTTATCCCCCTGAAATTGCAGTGAAGCAGATTGAAGCTAC
AAA
Found at i:40099463 original size:44 final size:44
Alignment explanation
Indices: 40099020--40099634 Score: 467
Period size: 44 Copynumber: 13.6 Consensus size: 44
40099010 TCATGGTGAG
* *
40099020 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATT-AAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-CTACAAA
* * * * *
40099064 CCTTATCTCCCTAAAGTTGTAGTGGAACAAATTGAAGA-TAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ACTA-CAAA
* * * * *
40099109 TCTTATCCCCCTGAAATTGCAGTGAAGTAGATTGAAGCTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAA
40099153 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATA-TAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ACTA-CAAA
* *
40099198 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT-AAAGCTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-CTACAAA
* * * * *
40099242 CCTTATCCCCCCTGAAATTGCAGTGAAGCAGATTGAAGCTACAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAA
* * * *
40099287 TCTTATCTCCCTAAAGTTGTAGTAGAGTAGATTGAAGA-TAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ACTA-CAAA
* * *
40099332 TCTTATCTCTCTGAAGTTGCAGTAGAGCATATT-AAAGCTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-CTACAAA
* * **
40099376 CCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAA
* * * *
40099420 TCTTATCTCTCTGAAGTTGCAGTGGAGCAAATGGAAACAACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAA
** * *
40099464 TCCAATAC-CTCTGAAGTTGCAGTAGG-TCAGATT-AAATCTACCATAGCAA
1 TCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAA-CTA-C--A--AA
* ** * *
40099513 GTCTTATCTCCCTGAAGTTGCAATGGAATAGACTAAAGCTACAAGATAACAAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T--TG--A-AA-CT-ACAAA
* * *
40099566 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATTACAAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAA
* * *
40099610 TCCTATAC-CCTTGAAGTTGTAGTGG
1 TCTTAT-CTCCCTGAAGTTGCAGTGG
40099635 GTTGGAATGA
Statistics
Matches: 455, Mismatches: 81, Indels: 70
0.75 0.13 0.12
Matches are distributed among these distances:
43 5 0.01
44 229 0.50
45 148 0.33
46 5 0.01
47 2 0.00
49 6 0.01
50 20 0.04
51 2 0.00
52 29 0.06
53 2 0.00
55 1 0.00
56 1 0.00
57 4 0.01
58 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAA
Found at i:40100385 original size:47 final size:47
Alignment explanation
Indices: 40100298--40100391 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
40100288 TTGGGCTTAA
* ** *
40100298 GTTTTAGATGCCAAAACGACGTCGTTTTGGCTGACCCGATCCGACCT
1 GTTTTAGATGCCAAAACGACATCGTTTTGGCCAACCCGATCCAACCT
* *
40100345 GTTTTAGATGCCAAAACGACATTGTTTTGGCCAACTCGATCCAACCT
1 GTTTTAGATGCCAAAACGACATCGTTTTGGCCAACCCGATCCAACCT
40100392 AAACCACTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (47 bp):
GTTTTAGATGCCAAAACGACATCGTTTTGGCCAACCCGATCCAACCT
Found at i:40110065 original size:20 final size:20
Alignment explanation
Indices: 40110040--40110107 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 20
40110030 TGTCACAACC
40110040 TAAAAATTATTAAATTTTAA
1 TAAAAATTATTAAATTTTAA
* *
40110060 TAAAAAATATTTAAATTTTAT
1 TAAAAATTA-TTAAATTTTAA
** *
40110081 TAAAAATTAGAAAAATTT-A
1 TAAAAATTATTAAATTTTAA
40110100 TAAAAATT
1 TAAAAATT
40110108 GTAAAAACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 8 0.20
20 14 0.35
21 18 0.45
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
TAAAAATTATTAAATTTTAA
Found at i:40110103 original size:19 final size:20
Alignment explanation
Indices: 40110040--40110127 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
40110030 TGTCACAACC
* *
40110040 TAAAAATTA-TTAAATTTTAA
1 TAAAAATTAGTAAAAATTT-A
* * * *
40110060 TAAAAAATATTTAAATTTTA
1 TAAAAATTAGTAAAAATTTA
40110080 TTAAAAATTAG-AAAAATTTA
1 -TAAAAATTAGTAAAAATTTA
*
40110100 TAAAAATT-GTAAAAACTTA
1 TAAAAATTAGTAAAAATTTA
40110119 TAAAAATTA
1 TAAAAATTA
40110128 TCGTATCGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.02
19 24 0.41
20 16 0.28
21 17 0.29
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAAAATTAGTAAAAATTTA
Found at i:40110106 original size:10 final size:10
Alignment explanation
Indices: 40110076--40110126 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
40110066 ATATTTAAAT
40110076 TTTATTAAAAA
1 TTTA-TAAAAA
*
40110087 -TTAGAAAAA
1 TTTATAAAAA
40110096 TTTATAAAAA
1 TTTATAAAAA
*
40110106 -TTGTAAAAA
1 TTTATAAAAA
*
40110115 CTTATAAAAA
1 TTTATAAAAA
40110125 TT
1 TT
40110127 ATCGTATCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
9 13 0.39
10 20 0.61
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:40110128 original size:9 final size:9
Alignment explanation
Indices: 40110081--40110128 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
40110071 TAAATTTTAT
40110081 TAAAAATTA
1 TAAAAATTA
*
40110090 GAAAAATTTA
1 TAAAAA-TTA
*
40110100 TAAAAATTG
1 TAAAAATTA
40110109 TAAAAACTTA
1 TAAAAA-TTA
40110119 TAAAAATTA
1 TAAAAATTA
40110128 T
1 T
40110129 CGTATCGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:40110324 original size:10 final size:10
Alignment explanation
Indices: 40110311--40110381 Score: 58
Period size: 10 Copynumber: 7.2 Consensus size: 10
40110301 TTTTGAGACA
40110311 TTTTATAATT
1 TTTTATAATT
*
40110321 TTTTATGA-T
1 TTTTATAATT
*
40110330 TTTTATAA-A
1 TTTTATAATT
* *
40110339 TATTACAA-T
1 TTTTATAATT
40110348 TTTTATAAATTT
1 TTTTAT-AA-TT
40110360 TTTTATAATT
1 TTTTATAATT
*
40110370 TTTAATAATT
1 TTTTATAATT
40110380 TT
1 TT
40110382 AAATATATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 18 0.37
10 22 0.45
11 2 0.04
12 7 0.14
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:40110441 original size:29 final size:28
Alignment explanation
Indices: 40110359--40110441 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
40110349 TTTATAAATT
* *
40110359 TTTTTATAATTTTTAATAATTTTAAATA
1 TTTTTATAATTTTTATTAATTTTTAATA
**
40110387 TATTTT-TACATTTTTATTAAAATTTAATA
1 T-TTTTATA-ATTTTTATTAATTTTTAATA
*
40110416 GTTTTTATAATTTTTATTGATTTTTA
1 -TTTTTATAATTTTTATTAATTTTTA
40110442 TTTTTTGTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTATAATTTTTATTAATTTTTAATA
Found at i:40116965 original size:19 final size:19
Alignment explanation
Indices: 40116941--40116977 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40116931 CAAAAACATG
40116941 CTTTATACATATAGTATAC
1 CTTTATACATATAGTATAC
40116960 CTTTATACATATAGTATA
1 CTTTATACATATAGTATA
40116978 ACCACACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (19 bp):
CTTTATACATATAGTATAC
Found at i:40118545 original size:24 final size:24
Alignment explanation
Indices: 40118488--40118575 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 24
40118478 ATATATGTAT
* *
40118488 GCTCATACGAGCTCTGAATCGGTAT
1 GCTCATACGAGCTGT-AATCGGTAA
* **
40118513 GTTTTTACGAGCTGTAATCGGTAA
1 GCTCATACGAGCTGTAATCGGTAA
40118537 GCTCATACGAGCTGAGTAA-CGGTAA
1 GCTCATACGAGCT--GTAATCGGTAA
*
40118562 GCTCATATGAGCTG
1 GCTCATACGAGCTG
40118576 AGTAACGATA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.02
24 18 0.35
25 29 0.56
26 4 0.08
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (24 bp):
GCTCATACGAGCTGTAATCGGTAA
Found at i:40118564 original size:25 final size:25
Alignment explanation
Indices: 40118518--40118590 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
40118508 GGTATGTTTT
40118518 TACGAGCT--GTAATCGGTAAGCTCA
1 TACGAGCTGAGTAA-CGGTAAGCTCA
40118542 TACGAGCTGAGTAACGGTAAGCTCA
1 TACGAGCTGAGTAACGGTAAGCTCA
* *
40118567 TATGAGCTGAGTAACGATAAGCTC
1 TACGAGCTGAGTAACGGTAAGCTC
40118591 TCTCAAGCTG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
24 8 0.18
25 33 0.73
26 4 0.09
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
TACGAGCTGAGTAACGGTAAGCTCA
Found at i:40124520 original size:24 final size:25
Alignment explanation
Indices: 40124473--40124560 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
40124463 ATACATGTAT
*
40124473 GCTCATACGAGCTCTGAATCGGTACA
1 GCTCATACGAGCTGTGAATCGGTA-A
*
40124499 -CTCTTACGAGCTGT-AATCGGTAA
1 GCTCATACGAGCTGTGAATCGGTAA
*
40124522 GCTCATACGAGCTGAGTAA-CGGTAA
1 GCTCATACGAGCTGTG-AATCGGTAA
* *
40124547 CCTCATACAAGCTG
1 GCTCATACGAGCTG
40124561 AATAACAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.02
24 20 0.38
25 30 0.57
26 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAATCGGTAA
Found at i:40130135 original size:7 final size:7
Alignment explanation
Indices: 40130123--40130167 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
40130113 TAAAAAAAAT
40130123 TAAACCC
1 TAAACCC
40130130 TAAACCC
1 TAAACCC
*
40130137 TAAGCCC
1 TAAACCC
*
40130144 TAAGCCC
1 TAAACCC
*
40130151 TAGACCC
1 TAAACCC
*
40130158 TAAACTC
1 TAAACCC
40130165 TAA
1 TAA
40130168 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.38, C:0.38, G:0.07, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:40135729 original size:14 final size:14
Alignment explanation
Indices: 40135710--40135743 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
40135700 TGACCTCGTA
40135710 AATATTAAATAAAT
1 AATATTAAATAAAT
40135724 AATATTAAATAAAT
1 AATATTAAATAAAT
40135738 AATATT
1 AATATT
40135744 TATAGACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAAATAAAT
Found at i:40144682 original size:25 final size:25
Alignment explanation
Indices: 40144648--40144697 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40144638 ATAATAAAAC
40144648 AATAATAATAAAATATTCAACCAAT
1 AATAATAATAAAATATTCAACCAAT
40144673 AATAATAATAAAATATTCAACCAAT
1 AATAATAATAAAATATTCAACCAAT
40144698 CATATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (25 bp):
AATAATAATAAAATATTCAACCAAT
Found at i:40145810 original size:16 final size:16
Alignment explanation
Indices: 40145789--40145856 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
40145779 TTTGGTTCGC
40145789 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40145805 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40145821 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40145837 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
40145853 TGTA
1 TGTA
40145857 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40145896 original size:45 final size:41
Alignment explanation
Indices: 40145837--40145946 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
40145827 GGATTAGAGG
*
40145837 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
40145879 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
40145922 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
40145947 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:40146109 original size:16 final size:16
Alignment explanation
Indices: 40146072--40146113 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40146062 TTAATCATAT
*
40146072 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40146088 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40146103 TTAAAATATAT
1 TTAAAATATAT
40146114 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40146120 original size:14 final size:15
Alignment explanation
Indices: 40146081--40146122 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40146071 TTTAAACATA
*
40146081 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40146096 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40146110 A-TATAATTTAATA
1 ATTATAATTAAATA
40146123 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40151571 original size:21 final size:21
Alignment explanation
Indices: 40151547--40151586 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40151537 TTTTCTAAAA
* *
40151547 TTAAAAGTCAAAACTATTAAG
1 TTAAAAGGCAAAACCATTAAG
40151568 TTAAAAGGCAAAACCATTA
1 TTAAAAGGCAAAACCATTA
40151587 TATTGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (21 bp):
TTAAAAGGCAAAACCATTAAG
Found at i:40152649 original size:19 final size:20
Alignment explanation
Indices: 40152617--40152654 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
40152607 CAAGCTGATT
40152617 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
40152637 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
40152655 AACCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:40155467 original size:36 final size:36
Alignment explanation
Indices: 40155415--40155612 Score: 279
Period size: 36 Copynumber: 5.5 Consensus size: 36
40155405 ATATCAATAT
* *
40155415 TCCAACCGAAGCACACCAGATGCTCATAAGAGCTAA
1 TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
40155451 TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
1 TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
* * * **
40155487 TCCATCCGAAGCACGCCGGATGCTCATAAGATTTAA
1 TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
* *
40155523 TCCATTCGAAACACACCAGATGTTCATAAGAGCTAA
1 TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
* * *
40155559 TCCATCCGAAATAGACCAGATGCTTATAAGAGCTAA
1 TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
*
40155595 TCCATTCGAAACACACCA
1 TCCATCCGAAACACACCA
40155613 AAATAGGGAG
Statistics
Matches: 140, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 140 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.19
Consensus pattern (36 bp):
TCCATCCGAAACACACCAGATGCTCATAAGAGCTAA
Found at i:40156537 original size:21 final size:21
Alignment explanation
Indices: 40156496--40156537 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40156486 AAAATAAGAA
* *
40156496 TGTTTTAATCTTTCTTTAATT
1 TGTTTTAATATTTCTTAAATT
40156517 TGTTTTAA-ATTTCATTAAATT
1 TGTTTTAATATTTC-TTAAATT
40156538 ACAAAATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (21 bp):
TGTTTTAATATTTCTTAAATT
Found at i:40160634 original size:21 final size:21
Alignment explanation
Indices: 40160610--40160651 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40160600 CACGATTATT
40160610 ACTGGTGCAGGAATCGATAAG
1 ACTGGTGCAGGAATCGATAAG
40160631 ACTGGTGCAGGAATCGATAAG
1 ACTGGTGCAGGAATCGATAAG
40160652 GGCTTCAAGG
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:0.33, C:0.14, G:0.33, T:0.19
Consensus pattern (21 bp):
ACTGGTGCAGGAATCGATAAG
Found at i:40162284 original size:58 final size:58
Alignment explanation
Indices: 40162146--40162375 Score: 250
Period size: 58 Copynumber: 4.0 Consensus size: 58
40162136 ATAAAACGAA
* * * * * *
40162146 GATGTGAATCCGTGAGCTGTTTCACACTT-TAGAAAATTTTGAAAGATAA--AACTGGG
1 GATGTGAATCCATGAGTTATTTTATACTTGT-GAAAATTTTGAAAGATAATCAGCTGGG
* * * * * *
40162202 GATTTAAATCCATAAGTTGTTTTATACTAGTGGAAATTTTGAAAGATAATCAGCTGGG
1 GATGTGAATCCATGAGTTATTTTATACTTGTGAAAATTTTGAAAGATAATCAGCTGGG
* * *
40162260 GATGTGAATCCACGAGTTACTTTATACTTGTGAAAATTTTGAAAGATAATCAGCTGTG
1 GATGTGAATCCATGAGTTATTTTATACTTGTGAAAATTTTGAAAGATAATCAGCTGGG
* * ** *
40162318 GATGTGAATCCGTGAGTTTTTTTATACTTGCAAAAATTTTGAAAGATAATTAGCTGGG
1 GATGTGAATCCATGAGTTATTTTATACTTGTGAAAATTTTGAAAGATAATCAGCTGGG
40162376 AGTTTTCAAC
Statistics
Matches: 144, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
56 38 0.26
57 1 0.01
58 105 0.73
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (58 bp):
GATGTGAATCCATGAGTTATTTTATACTTGTGAAAATTTTGAAAGATAATCAGCTGGG
Found at i:40162499 original size:69 final size:68
Alignment explanation
Indices: 40162385--40162549 Score: 231
Period size: 69 Copynumber: 2.4 Consensus size: 68
40162375 GAGTTTTCAA
* * *
40162385 CTCTCACTAACTGTGTTAGAGGCTGCAGGTCTTCGCCTACAAGCCTTAATATGACAATTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTAC-GGTCTTCGCCTACAAGCCTTAATATGACAATTGGGAGC
40162450 TTTG
65 TTTG
* * *
40162454 CTCTCGCTAACTGTGTTGGAGGCTACGGCTCTTCGCCTGCGAGCCTTAATATGACAGTTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTACGG-TCTTCGCCTACAAGCCTTAATATGACAATTGGGAGC
40162519 TTTG
65 TTTG
* **
40162523 CTCTTGCTAACTGTACTGGAGGCTACG
1 CTCTCGCTAACTGTGTTGGAGGCTACG
40162550 TGATACGAGT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 2 0.02
69 84 0.98
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.30
Consensus pattern (68 bp):
CTCTCGCTAACTGTGTTGGAGGCTACGGTCTTCGCCTACAAGCCTTAATATGACAATTGGGAGCT
TTG
Found at i:40171097 original size:40 final size:40
Alignment explanation
Indices: 40171041--40171284 Score: 355
Period size: 40 Copynumber: 6.1 Consensus size: 40
40171031 TAATTATTGG
*
40171041 TGAATGCACATACGTGCCCCTGTTTTTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
40171081 CGAATGCACATACGTGCCCCTTTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
40171121 TAAATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCA
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
*
40171161 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
40171201 TGAATGCACATACGTGCCCCTGATTGTACTTTGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * **
40171241 TGAATGCACATACCTG-CCCTATTTGTACTTTGGTAATCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
40171280 TGAAT
1 TGAAT
40171285 TAAATAATAT
Statistics
Matches: 184, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 24 0.13
40 160 0.87
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:40174335 original size:12 final size:13
Alignment explanation
Indices: 40174311--40174339 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40174301 ACTTAATTAG
40174311 TTTTAGATTTTTA
1 TTTTAGATTTTTA
40174324 TTTTAG-TTTTTA
1 TTTTAGATTTTTA
40174336 TTTT
1 TTTT
40174340 CTTTCAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTAGATTTTTA
Found at i:40174886 original size:35 final size:36
Alignment explanation
Indices: 40174834--40174901 Score: 129
Period size: 35 Copynumber: 1.9 Consensus size: 36
40174824 TATAGGTCGA
40174834 TTAATTAATTAGTTAAAGGTGAGAGGTAATAACTGG
1 TTAATTAATTAGTTAAAGGTGAGAGGTAATAACTGG
40174870 TTAATTAA-TAGTTAAAGGTGAGAGGTAATAAC
1 TTAATTAATTAGTTAAAGGTGAGAGGTAATAAC
40174902 ATTGAAGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 24 0.75
36 8 0.25
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (36 bp):
TTAATTAATTAGTTAAAGGTGAGAGGTAATAACTGG
Found at i:40181727 original size:75 final size:75
Alignment explanation
Indices: 40181646--40181941 Score: 315
Period size: 75 Copynumber: 3.9 Consensus size: 75
40181636 CTAGTCGGGG
* * * * *
40181646 AAACCAACATATATAATGATGTTCCGAGCACTAGTCAGATAAACTGATGGAAGTTGTGGCCAATG
1 AAACCAACAAATATAATGATGTGCCCAGCACTAGTCAGATAAACTGATGAAAGTTGTGGCCAACG
40181711 CTAGTCAAAT
66 CTAGTCAAAT
* * * * * *
40181721 AAACCAATAGATATAATGATATGCCCAGCACTAGTTATATAAACTGATGAAAGTTGT-GCCTAGC
1 AAACCAACAAATATAATGATGTGCCCAGCACTAGTCAGATAAACTGATGAAAGTTGTGGCC-AAC
*
40181785 GCTAGTCAGAT
65 GCTAGTCAAAT
* * * * * ** *
40181796 AAATCAACAAATATAATGGTGTGCCCAACACTAATTAGATAAACTGACCAAAGTTGTGCCCAACG
1 AAACCAACAAATATAATGATGTGCCCAGCACTAGTCAGATAAACTGATGAAAGTTGTGGCCAACG
40181861 CTAGTCAAAT
66 CTAGTCAAAT
* * * * * * * * *
40181871 GAACCAACAAATATAAAGGTGTGCCAAGCACTAGTCACATAAACTGACGAAAATTTTGGCCAGCG
1 AAACCAACAAATATAATGATGTGCCCAGCACTAGTCAGATAAACTGATGAAAGTTGTGGCCAACG
40181936 CTAGTC
66 CTAGTC
40181942 GCATAAACTG
Statistics
Matches: 182, Mismatches: 37, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
74 3 0.02
75 177 0.97
76 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (75 bp):
AAACCAACAAATATAATGATGTGCCCAGCACTAGTCAGATAAACTGATGAAAGTTGTGGCCAACG
CTAGTCAAAT
Found at i:40181948 original size:150 final size:150
Alignment explanation
Indices: 40181650--40181941 Score: 352
Period size: 150 Copynumber: 1.9 Consensus size: 150
40181640 TCGGGGAAAC
* * * * * *** * *
40181650 CAACATATATAATGATGTTCCGAGCACTAGTCAGATAAACTGATGGAAGTTGTGGCCAATGCTAG
1 CAACAAATATAATGATGTGCCCAACACTAATCAGATAAACTGACCAAAGTTGTGCCCAACGCTAG
* * * * * * * *
40181715 TCAAATAAACCAATAGATATAATGATATGCCCAGCACTAGTTATATAAACTGATGAAAGTTGTGC
66 TCAAATAAACCAACAAATATAAAGATATGCCAAGCACTAGTCACATAAACTGACGAAAATTGTGC
40181780 CTAGCGCTAGTCAGATAAAT
131 CTAGCGCTAGTCAGATAAAT
* *
40181800 CAACAAATATAATGGTGTGCCCAACACTAATTAGATAAACTGACCAAAGTTGTGCCCAACGCTAG
1 CAACAAATATAATGATGTGCCCAACACTAATCAGATAAACTGACCAAAGTTGTGCCCAACGCTAG
* * * *
40181865 TCAAATGAACCAACAAATATAAAGGTGTGCCAAGCACTAGTCACATAAACTGACGAAAATTTTGG
66 TCAAATAAACCAACAAATATAAAGATATGCCAAGCACTAGTCACATAAACTGACGAAAATTGT-G
40181930 CC-AGCGCTAGTC
130 CCTAGCGCTAGTC
40181942 GCATAAACTG
Statistics
Matches: 117, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
150 114 0.97
151 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (150 bp):
CAACAAATATAATGATGTGCCCAACACTAATCAGATAAACTGACCAAAGTTGTGCCCAACGCTAG
TCAAATAAACCAACAAATATAAAGATATGCCAAGCACTAGTCACATAAACTGACGAAAATTGTGC
CTAGCGCTAGTCAGATAAAT
Found at i:40207206 original size:47 final size:47
Alignment explanation
Indices: 40207125--40207669 Score: 761
Period size: 47 Copynumber: 11.6 Consensus size: 47
40207115 TAATTGAATA
*
40207125 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
* * *
40207173 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
40207220 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
40207267 AAAGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40207314 AAAGTGAACATGTGTATGTGTGATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
40207361 AAAGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40207408 AAAGTGAACATGTGTATGTGTGATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40207455 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
40207502 AATGTGAACATGTATATGTGTGATAAGGTCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * * * *
40207549 AAAGTGAATAGGTGTATGTGTGATAAGGTCGAGTGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
40207596 AATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
**
40207643 AATGTGAA-AGTGTATAAATGTGATAAG
1 AATGTGAACA-TGTATATGTGTGATAAG
40207670 TCCCGAAGGG
Statistics
Matches: 446, Mismatches: 49, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
46 1 0.00
47 427 0.96
48 17 0.04
49 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.26
Consensus pattern (47 bp):
AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40207547 original size:22 final size:22
Alignment explanation
Indices: 40207520--40207594 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
40207510 CATGTATATG
40207520 TGTGATAAGGTCGAATGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
* ** *
40207542 TGTGATGAAAGT-GAATAGGTGTATG
1 TGTGAT-AAGGTCGAAT-GG-CCA-A
*
40207567 TGTGATAAGGTCGAGTGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
40207589 TGTGAT
1 TGTGAT
40207595 GAATGTGAGC
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
22 16 0.41
23 7 0.18
24 7 0.18
25 9 0.23
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.28
Consensus pattern (22 bp):
TGTGATAAGGTCGAATGGCCAA
Found at i:40207844 original size:37 final size:37
Alignment explanation
Indices: 40207788--40207867 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
40207778 CCGGGCTATA
* * *
40207788 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
40207825 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
40207862 AAGACT
1 AAGACT
40207868 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:40211202 original size:23 final size:24
Alignment explanation
Indices: 40211158--40211202 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
40211148 AAAATCCTAC
*
40211158 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
40211182 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
40211203 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:40214478 original size:26 final size:26
Alignment explanation
Indices: 40214449--40214529 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
40214439 TTTGATCACG
40214449 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
40214475 TGTGTA--CCGGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
40214500 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
40214526 TGTG
1 TGTG
40214530 AACCGAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:40214528 original size:51 final size:50
Alignment explanation
Indices: 40214339--40214534 Score: 227
Period size: 51 Copynumber: 3.9 Consensus size: 50
40214329 AGTGAAAGTG
* * *
40214339 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTATA-CGAGA-ACG-
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG-GATA-GT
* * *
40214388 ATAGGTCGCATGTGTAGTACTACGTGCAGGCTACTATGCGTACCGGATAGTT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG-T
* * * *
40214440 TTGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
*
40214490 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
40214535 AATATCATTG
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.02
50 37 0.30
51 84 0.68
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
Found at i:40214546 original size:102 final size:101
Alignment explanation
Indices: 40214343--40214546 Score: 261
Period size: 102 Copynumber: 2.0 Consensus size: 101
40214333 AAAGTGATGG
*
40214343 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTATACGAGAACGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTATACGAGAACGATAGGTCACATGTGTAGTAC
* * *
40214408 TACGTGCAGGCTACTATGCGTACCGGATAGTTTTGA
66 TACGTGCAGGCTACTATGCGAACCGAATAGTATTGA
* * * *
40214444 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCG-G-ATGGTAATGGTCACATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTATA-CGAGAACGAT-A-GGTCACATGTGTAG
* *
40214507 TACTATGTGCAGGCTACTATGTGAACCGAATA-TCATTGA
63 TACTACGTGCAGGCTACTATGCGAACCGAATAGT-ATTGA
40214546 T
1 T
40214547 TAGTAAGGTG
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
100 3 0.03
101 38 0.43
102 48 0.54
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTATACGAGAACGATAGGTCACATGTGTAGTAC
TACGTGCAGGCTACTATGCGAACCGAATAGTATTGA
Found at i:40214589 original size:45 final size:45
Alignment explanation
Indices: 40214538--40214624 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
40214528 TGAACCGAAT
* * *
40214538 ATCATTGATTAGTAAGGTGGTTGTTATGTGCTGATTCCACCGGAC
1 ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGGAC
40214583 ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
40214625 AGTATCTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (45 bp):
ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGGAC
Found at i:40221062 original size:9 final size:10
Alignment explanation
Indices: 40221047--40221108 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
40221037 ATTTAAAAAT
40221047 AATTTTTTTA
1 AATTTTTTTA
40221057 AATTTTTTTA
1 AATTTTTTTA
*
40221067 AATTTTGTT-
1 AATTTTTTTA
**
40221076 AATAATTTT-
1 AATTTTTTTA
*
40221085 AATGATTTTTA
1 AAT-TTTTTTA
*
40221096 ATTTTTTTTA
1 AATTTTTTTA
40221106 AAT
1 AAT
40221109 AATTCTTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 9 0.21
10 31 0.74
11 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:40222569 original size:2 final size:2
Alignment explanation
Indices: 40222564--40222589 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40222554 GAAGCAAATA
40222564 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
40222590 TGCGGAAGAA
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:40223690 original size:16 final size:15
Alignment explanation
Indices: 40223665--40223713 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
40223655 TTTTCGTTAT
40223665 TTTTTATTAAGTTAAAA
1 TTTTT-TTAA-TTAAAA
*
40223682 TTTTTTTAATTTAAA
1 TTTTTTTAATTAAAA
*
40223697 TTTTTTTCATTACAAA
1 TTTTTTTAATTA-AAA
40223713 T
1 T
40223714 AGGCGGATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 15 0.54
16 8 0.29
17 5 0.18
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTTTTAATTAAAA
Found at i:40225826 original size:22 final size:23
Alignment explanation
Indices: 40225788--40225831 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
40225778 TAGCAATTGT
*
40225788 GTAATTTTTGAAGTTAGGTAATG
1 GTAATTTTTGAAGTTAGCTAATG
40225811 GTAA-TTTTGTAA-TTAGCTAAT
1 GTAATTTTTG-AAGTTAGCTAAT
40225832 TTTGTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (23 bp):
GTAATTTTTGAAGTTAGCTAATG
Found at i:40225833 original size:16 final size:16
Alignment explanation
Indices: 40225812--40225848 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
40225802 TAGGTAATGG
40225812 TAATTTTGTAATTAGC
1 TAATTTTGTAATTAGC
*
40225828 TAATTTTGTAATTAGG
1 TAATTTTGTAATTAGC
40225844 TAATT
1 TAATT
40225849 AGTGTAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (16 bp):
TAATTTTGTAATTAGC
Found at i:40228126 original size:24 final size:24
Alignment explanation
Indices: 40228099--40228144 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
40228089 AAGCTCATGT
*
40228099 GAGCCAATAACGAGTAGCTCCGTA
1 GAGCCAATAACGAGAAGCTCCGTA
* * *
40228123 GAGCTATTAACGGGAAGCTCCG
1 GAGCCAATAACGAGAAGCTCCG
40228145 GATAGCCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.17
Consensus pattern (24 bp):
GAGCCAATAACGAGAAGCTCCGTA
Found at i:40228187 original size:48 final size:49
Alignment explanation
Indices: 40228135--40228227 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
40228125 GCTATTAACG
* * *
40228135 GGAAGCTCCGGATAGCCATATAT-AGAGAAGTTCA-AGAGAGCCAATATA
1 GGAAGCTCCGGAGAGCCATATATCAG-GAAGCTCACAAAGAGCCAATATA
**
40228183 GGAAGCTTTGGAGAGCCATATATCAGGAAGCTCACAAAGAGCCAA
1 GGAAGCTCCGGAGAGCCATATATCAGGAAGCTCACAAAGAGCCAA
40228228 CCAATGGGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
48 27 0.71
49 11 0.29
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (49 bp):
GGAAGCTCCGGAGAGCCATATATCAGGAAGCTCACAAAGAGCCAATATA
Found at i:40228261 original size:26 final size:26
Alignment explanation
Indices: 40228194--40228262 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
40228184 GAAGCTTTGG
**
40228194 AGAGCCATATATCAGGAAGCTCACAA
1 AGAGCCATATATTGGGAAGCTCACAA
* *
40228220 AGAGCCA-ACCAATGGGAAGCTCACAA
1 AGAGCCATA-TATTGGGAAGCTCACAA
*
40228246 ATAGCCATATATTGGGA
1 AGAGCCATATATTGGGA
40228263 CGCTAATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
25 1 0.03
26 32 0.94
27 1 0.03
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAGCCATATATTGGGAAGCTCACAA
Found at i:40232447 original size:33 final size:33
Alignment explanation
Indices: 40232409--40232476 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
40232399 TTTTAACATC
* *
40232409 ATTAATATACATCT-TTAATTAATGTCATGCATT
1 ATTAATATACATCTCTTAACT-ATGACATGCATT
*
40232442 ATTAATCTACATCTCTTAACTATGACATGCATT
1 ATTAATATACATCTCTTAACTATGACATGCATT
40232475 AT
1 AT
40232477 GTAACTTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (33 bp):
ATTAATATACATCTCTTAACTATGACATGCATT
Found at i:40235482 original size:39 final size:40
Alignment explanation
Indices: 40235437--40235700 Score: 302
Period size: 40 Copynumber: 6.7 Consensus size: 40
40235427 GCTCCTCGTT
* * * * *
40235437 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
40235477 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
40235516 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
40235556 CGAATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
40235595 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* ** * * * *
40235635 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
40235676 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40235701 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
39 75 0.38
40 111 0.56
41 11 0.06
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:40235648 original size:79 final size:78
Alignment explanation
Indices: 40235437--40235700 Score: 325
Period size: 79 Copynumber: 3.3 Consensus size: 78
40235427 GCTCCTCGTT
* * * * *
40235437 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTC-GGACTTAACCCGGA
40235502 TTTAACAACTCGCA
65 TTTAACAACTCGCA
*
40235516 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGACTTAACCCGGA
40235581 TTTAACAACTCGCA
65 TTTAACAACTCGCA
* * * **
40235595 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGA-CTTAACCCGG
* * *
40235660 ATATATTC-ACTTAGCA
64 ATTTA-ACAAC-TCGCA
*
40235676 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40235701 CAGCATTCAA
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
79 112 0.69
80 43 0.26
81 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGACTTAACCCGGAT
TTAACAACTCGCA
Found at i:40235684 original size:119 final size:118
Alignment explanation
Indices: 40235437--40235700 Score: 307
Period size: 119 Copynumber: 2.2 Consensus size: 118
40235427 GCTCCTCGTT
* * **
40235437 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACATAACCCGGA
* * *
40235502 TTTAACAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * *
40235556 CGAATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACATAACCCGG
** * ** * *
40235620 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
40235676 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
40235701 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
118 26 0.22
119 74 0.62
120 20 0.17
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:40235709 original size:41 final size:41
Alignment explanation
Indices: 40235632--40235709 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40235622 TTAGTATCTC
* * *
40235632 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40235673 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40235710 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40252822 original size:20 final size:20
Alignment explanation
Indices: 40252799--40252872 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
40252789 TAAAATATAA
40252799 AAAAAATTTATAAAAATCGT
1 AAAAAATTTATAAAAATCGT
* * *
40252819 AAAAAATATAAAAAAAATTGT
1 AAAAAAT-TTATAAAAATCGT
*
40252840 --AAAATTTATAAAAATCAT
1 AAAAAATTTATAAAAATCGT
* *
40252858 AGAAAAGTTATAAAA
1 AAAAAATTTATAAAA
40252873 TGCATCAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
18 9 0.21
19 5 0.12
20 19 0.44
21 10 0.23
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAAATTTATAAAAATCGT
Found at i:40252834 original size:21 final size:21
Alignment explanation
Indices: 40252810--40252853 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40252800 AAAAATTTAT
40252810 AAAAATCGTAAAAAATATAAA
1 AAAAATCGTAAAAAATATAAA
* **
40252831 AAAAATTGTAAAATTTATAAA
1 AAAAATCGTAAAAAATATAAA
40252852 AA
1 AA
40252854 TCATAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAATCGTAAAAAATATAAA
Found at i:40252907 original size:13 final size:13
Alignment explanation
Indices: 40252889--40252913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40252879 AAAAAGGCCA
40252889 TTTAACCATTAAT
1 TTTAACCATTAAT
40252902 TTTAACCATTAA
1 TTTAACCATTAA
40252914 CTGTTAAAGT
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAACCATTAAT
Found at i:40253143 original size:12 final size:10
Alignment explanation
Indices: 40253089--40253182 Score: 63
Period size: 10 Copynumber: 9.7 Consensus size: 10
40253079 ATTTCTTTAC
40253089 ATTTTTTATA
1 ATTTTTTATA
* *
40253099 ATTTTGTATG
1 ATTTTTTATA
40253109 A--TTTTATA
1 ATTTTTTATA
**
40253117 AAATTTTATA
1 ATTTTTTATA
40253127 ATTTTTTATA
1 ATTTTTTATA
40253137 TATTTTTT-T-
1 -ATTTTTTATA
*
40253146 ATGATTTTATA
1 AT-TTTTTATA
** *
40253157 AAATTTTACA
1 ATTTTTTATA
40253167 ATTTTTT-TA
1 ATTTTTTATA
40253176 ATTTTTT
1 ATTTTTT
40253183 TCTTCTAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
8 8 0.12
9 12 0.18
10 38 0.58
11 8 0.12
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:40253154 original size:40 final size:39
Alignment explanation
Indices: 40253084--40253183 Score: 152
Period size: 40 Copynumber: 2.6 Consensus size: 39
40253074 TGTATATTTC
*
40253084 TTTAC-ATTTTTTATAA-TTTTGTATGATTTTATAAAAT
1 TTTACAATTTTTTATAATTTTTTTATGATTTTATAAAAT
*
40253121 TTTATAATTTTTTATATATTTTTTTATGATTTTATAAAAT
1 TTTACAATTTTTTATA-ATTTTTTTATGATTTTATAAAAT
40253161 TTTACAATTTTTT-TAATTTTTTT
1 TTTACAATTTTTTATAATTTTTTT
40253184 CTTCTAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
37 4 0.07
38 18 0.32
39 3 0.05
40 32 0.56
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (39 bp):
TTTACAATTTTTTATAATTTTTTTATGATTTTATAAAAT
Found at i:40253155 original size:30 final size:29
Alignment explanation
Indices: 40253119--40253175 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
40253109 ATTTTATAAA
** *
40253119 ATTTTATAATTTTTTATATATTTTTTTATG
1 ATTTTATAAAATTTTACA-ATTTTTTTATG
40253149 ATTTTATAAAATTTTACAATTTTTTTA
1 ATTTTATAAAATTTTACAATTTTTTTA
40253176 ATTTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTATAAAATTTTACAATTTTTTTATG
Done.