Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 25
Found at i:2136308 original size:4 final size:4
Alignment explanation
Indices: 2136299--2136331 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2136289 AAATTAATGA
2136299 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
2136332 CTGCAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2136993 original size:17 final size:14
Alignment explanation
Indices: 2136944--2136995 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
2136934 AGCATTGTGA
2136944 AAAGAAAAT-AATG
1 AAAGAAAATAAATG
2136957 AAAGAAAATAAA-G
1 AAAGAAAATAAATG
*
2136970 AATGAAATATGGAAATG
1 AAAGAAA-AT--AAATG
2136987 AAAGAAAAT
1 AAAGAAAAT
2136996 TAGAACTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 16 0.50
14 4 0.12
16 5 0.16
17 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (14 bp):
AAAGAAAATAAATG
Found at i:2137185 original size:20 final size:20
Alignment explanation
Indices: 2137143--2137183 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2137133 TAAGAGTTCT
*
2137143 AATAAAATAACTAATTCTTA
1 AATAAAATAACTAATACTTA
*
2137163 AATAAAATAATTAA-ACTTA
1 AATAAAATAACTAATACTTA
2137182 AA
1 AA
2137184 ATCCTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAATAACTAATACTTA
Found at i:2144889 original size:2 final size:2
Alignment explanation
Indices: 2144884--2144922 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2144874 TAGAGTAAGC
2144884 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
2144923 AAATTTTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2147016 original size:2 final size:2
Alignment explanation
Indices: 2147009--2147053 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2146999 TATACAGTAA
2147009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2147051 AT A
1 AT A
2147054 CACACAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2148606 original size:2 final size:2
Alignment explanation
Indices: 2148599--2148631 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2148589 TAAGTAGACC
2148599 AT AT AT 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 AT AT AT A
2148632 GGACAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2153040 original size:11 final size:11
Alignment explanation
Indices: 2153024--2153056 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2153014 TACGAATTGC
2153024 TGAAAGTAACA
1 TGAAAGTAACA
2153035 TGAAAGTAACA
1 TGAAAGTAACA
*
2153046 TGAAATTAACA
1 TGAAAGTAACA
2153057 AAATTTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.21
Consensus pattern (11 bp):
TGAAAGTAACA
Found at i:2153542 original size:23 final size:23
Alignment explanation
Indices: 2153480--2153542 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
2153470 ATTAAGTTTT
*
2153480 TGTCTTTGTGACAAG-TTATCTA
1 TGTCTTTGTGGCAAGTTTATCTA
* * * *
2153502 TGTCTTTATGGTACGTTTATCTC
1 TGTCTTTGTGGCAAGTTTATCTA
*
2153525 TGTCTTTGTGGCATGTTT
1 TGTCTTTGTGGCAAGTTT
2153543 TTATTTGCCT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (23 bp):
TGTCTTTGTGGCAAGTTTATCTA
Found at i:2157076 original size:16 final size:16
Alignment explanation
Indices: 2157055--2157087 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2157045 TAATAAATAG
2157055 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2157071 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2157087 A
1 A
2157088 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2157168 original size:10 final size:10
Alignment explanation
Indices: 2157153--2157227 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2157143 CATTTAATAA
2157153 ATAAACGAAC
1 ATAAACGAAC
2157163 ATAAACGAAC
1 ATAAACGAAC
2157173 ----ACGAAC
1 ATAAACGAAC
2157179 ATAAACGAAC
1 ATAAACGAAC
** *
2157189 ACGAAC-ATAA
1 ATAAACGA-AC
2157199 ATGAACACGAAC
1 AT-AA-ACGAAC
2157211 ATAAACGAAC
1 ATAAACGAAC
2157221 ATAAACG
1 ATAAACG
2157228 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2157178 original size:16 final size:16
Alignment explanation
Indices: 2157157--2157221 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
2157147 TAATAAATAA
2157157 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2157173 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2157189 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2157205 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2157221 A
1 A
2157222 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2157992 original size:14 final size:14
Alignment explanation
Indices: 2157975--2158030 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2157965 AATGAACATA
*
2157975 AACGAACATAATCG
1 AACGAACATAACCG
2157989 AACGAACAT-A---
1 AACGAACATAACCG
2157999 AACGAACATAACCG
1 AACGAACATAACCG
2158013 AACGAACATAACCG
1 AACGAACATAACCG
2158027 AACG
1 AACG
2158031 TTCACGAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2157995 original size:24 final size:24
Alignment explanation
Indices: 2157955--2158029 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
2157945 GATTGGGTTA
*
2157955 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
2157979 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
2158003 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
2158027 AAC
1 AAC
2158030 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:2158029 original size:10 final size:10
Alignment explanation
Indices: 2157968--2158015 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
2157958 ATAAATGAAT
2157968 GAACATAAAC
1 GAACATAAAC
2157978 GAACATAATCGAAC
1 GAACAT-A---AAC
2157992 GAACATAAAC
1 GAACATAAAC
*
2158002 GAACATAACC
1 GAACATAAAC
2158012 GAAC
1 GAAC
2158016 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:2160370 original size:17 final size:17
Alignment explanation
Indices: 2160348--2160382 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2160338 GAAATCAGAG
*
2160348 ACCTTGCTAAGGAAAGA
1 ACCTTGCGAAGGAAAGA
*
2160365 ACCTTGCGAATGAAAGA
1 ACCTTGCGAAGGAAAGA
2160382 A
1 A
2160383 ATTCTTTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (17 bp):
ACCTTGCGAAGGAAAGA
Found at i:2160545 original size:2 final size:2
Alignment explanation
Indices: 2160538--2160562 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2160528 TACATTTTCT
2160538 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 T
2160563 TATTCATATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2173167 original size:23 final size:23
Alignment explanation
Indices: 2173137--2173184 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
2173127 CAAATGTCAA
2173137 ACCTTTATTGAGATTTTATGGTG
1 ACCTTTATTGAGATTTTATGGTG
*
2173160 ACCTTTATTGAGATTTTCTGGTG
1 ACCTTTATTGAGATTTTATGGTG
2173183 AC
1 AC
2173185 GGTGAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (23 bp):
ACCTTTATTGAGATTTTATGGTG
Found at i:2173409 original size:22 final size:23
Alignment explanation
Indices: 2173371--2173426 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 23
2173361 TCATAACATT
*
2173371 AATTAATA-AATACATTTCAA-A
1 AATTAAAATAATACATTTCAATA
* * *
2173392 AATTAAAATAATATATTTGAATC
1 AATTAAAATAATACATTTCAATA
2173415 AA-TAAAATAATA
1 AATTAAAATAATA
2173427 AAAGGGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.24
22 20 0.69
23 2 0.07
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (23 bp):
AATTAAAATAATACATTTCAATA
Found at i:2176481 original size:231 final size:231
Alignment explanation
Indices: 2176217--2176913 Score: 1146
Period size: 232 Copynumber: 3.0 Consensus size: 231
2176207 GCAGAGGAAG
* * * *
2176217 AAGAAGAAGAAATAATGGATAAAAGAGAATAAATTATATGAGAGGAAGAAGAA-AAGGTGCACAC
1 AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAA-ATGCACAC
* * * *
2176281 TGGTGAATATGGGTTTTTTATTATTTTAAAATTATCATGTCACACATCTGTTAATGAGTTAATGG
65 TGGTGAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGG
*
2176346 AGGTTAACGTCTGAAGGACTTAAATCGGACATATCGATAACATAAGGGACCAAGAGCACTTAATT
130 AGGTTAACGTCTGAAGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAATT
*
2176411 AAAAAATCGGTGACCAAAGTCGGTCAAACCGAACACA
195 AAAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
* * *
2176448 AAGAAGAATAAATAATGGATAAAGGAGAATAAATGAGATTAGAGGAGGAAGAAGAAATGCACACT
1 AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAAATGCACACT
*
2176513 GGTGAATGTGGGTTTTTTTATTAATTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGG
66 GGTGAATGTGGG-TTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGG
*
2176578 AGGTTAACGTCT-AAGGGACTTAAATCGGACAGATCGATAACATAAGGGACCAAGAGCACTTAAT
130 AGGTTAACGTCTGAA-GGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAAT
*
2176642 TAAAAAACCGGTGACCAAAGTCGGTCAGACCGAACACA
194 TAAAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
* * *
2176680 AATAAGAAGAAATAATAGATAAAGGAGAATAAATGAGATGAGAGGAAAAAGAAGAAATGCACACT
1 AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAAATGCACACT
*
2176745 GGTAAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGGA
66 GGTGAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGGA
* * *
2176810 GGTTAACGTCCGAGGGACTTAAATCGGACAAATCGATAACATAAGAGACCAAGAGCACTTAATTA
131 GGTTAACGTCTGAAGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAATTA
2176875 AAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
196 AAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
2176911 AAG
1 AAG
2176914 GGGACTATTG
Statistics
Matches: 433, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
231 216 0.50
232 217 0.50
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (231 bp):
AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAAATGCACACT
GGTGAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGGA
GGTTAACGTCTGAAGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAATTA
AAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
Found at i:2176622 original size:232 final size:231
Alignment explanation
Indices: 2176217--2176913 Score: 1146
Period size: 231 Copynumber: 3.0 Consensus size: 231
2176207 GCAGAGGAAG
* * * *
2176217 AAGAAGAAGAAATAATGGATAAAAGAGAATAAATTATATGAGAGGAAGAAGAA-AAGGTGCACAC
1 AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAA-ATGCACAC
* * * *
2176281 TGGTGAATATGGGTTTTTTATTATTTTAAAATTATCATGTCACACATCTGTTAATGAGTTAATGG
65 TGGTGAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGG
*
2176346 AGGTTAACGTCTGAA-GGACTTAAATCGGACATATCGATAACATAAGGGACCAAGAGCACTTAAT
130 AGGTTAACGTCT-AAGGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAAT
*
2176410 TAAAAAATCGGTGACCAAAGTCGGTCAAACCGAACACA
194 TAAAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
* * *
2176448 AAGAAGAATAAATAATGGATAAAGGAGAATAAATGAGATTAGAGGAGGAAGAAGAAATGCACACT
1 AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAAATGCACACT
*
2176513 GGTGAATGTGGGTTTTTTTATTAATTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGG
66 GGTGAATGTGGG-TTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGG
*
2176578 AGGTTAACGTCTAAGGGACTTAAATCGGACAGATCGATAACATAAGGGACCAAGAGCACTTAATT
130 AGGTTAACGTCTAAGGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAATT
*
2176643 AAAAAACCGGTGACCAAAGTCGGTCAGACCGAACACA
195 AAAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
* * *
2176680 AATAAGAAGAAATAATAGATAAAGGAGAATAAATGAGATGAGAGGAAAAAGAAGAAATGCACACT
1 AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAAATGCACACT
*
2176745 GGTAAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGGA
66 GGTGAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGGA
** *
2176810 GGTTAACGTCCGAGGGACTTAAATCGGACAAATCGATAACATAAGAGACCAAGAGCACTTAATTA
131 GGTTAACGTCTAAGGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAATTA
2176875 AAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
196 AAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
2176911 AAG
1 AAG
2176914 GGGACTATTG
Statistics
Matches: 434, Mismatches: 29, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
231 218 0.50
232 216 0.50
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (231 bp):
AAGAAGAAGAAATAATGGATAAAGGAGAATAAATGAGATGAGAGGAAGAAGAAGAAATGCACACT
GGTGAATGTGGGTTTTTTATTATTTTAAAATTGTCATGTCACACATCTATTAATGAGTTAACGGA
GGTTAACGTCTAAGGGACTTAAATCGGACAAATCGATAACATAAGGGACCAAGAGCACTTAATTA
AAAAATCGGTGACCAAAGTCGGTCAGACCGAACACA
Found at i:2180848 original size:16 final size:16
Alignment explanation
Indices: 2180829--2180859 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2180819 TTTAATGAAT
*
2180829 TAAAAATTTAAATATG
1 TAAAAAATTAAATATG
2180845 TAAAAAATTAAATAT
1 TAAAAAATTAAATAT
2180860 TGAATTCTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAAAAATTAAATATG
Found at i:2182432 original size:157 final size:156
Alignment explanation
Indices: 2182211--2182558 Score: 495
Period size: 157 Copynumber: 2.2 Consensus size: 156
2182201 TATATGAACT
* * * *
2182211 TGTGGTTCAAATTTAGTAAAAAATGACTTAAAATAAATCACAACTTAAAGGAATAAGGAGATTAT
1 TGTGGATCAAATTTGGT-AAAAATGACTTAAAATAAATCACAACTTAAAGAAATAAGAAGATTAT
2182276 GAAAAATTGAAGGACTAAATTGAAAAATGAAAAAATTTGTTATC-AAAAGAGGAATTGAAAGTAC
65 GAAAAATTGAAGGACTAAATTGAAAAAT-AAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAC
2182340 ACATGTATTCTACTATGGTTTAGGAGCA
129 ACATGTATTCTACTATGGTTTAGGAGCA
* * * * * *
2182368 TGTGGCTCATATTTGGTAAAAATGGACTTAAAATAAATGACGAA-TTGAAGAAATGAGAATATTA
1 TGTGGATCAAATTTGGTAAAAAT-GACTTAAAATAAATCAC-AACTTAAAGAAATAAGAAGATTA
* *
2182432 TGAAAATTTGAAGGACTAATTTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAC
64 TGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAC
*
2182497 ACATGTATTCTACTATGGTTTAGGAGTA
129 ACATGTATTCTACTATGGTTTAGGAGCA
*
2182525 TGT-AATCCAAATTTGGTAAAAATAGACTTAAAAT
1 TGTGGAT-CAAATTTGGTAAAAAT-GACTTAAAAT
2182559 GAAGGAGGGA
Statistics
Matches: 171, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
156 22 0.13
157 147 0.86
158 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (156 bp):
TGTGGATCAAATTTGGTAAAAATGACTTAAAATAAATCACAACTTAAAGAAATAAGAAGATTATG
AAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACAC
ATGTATTCTACTATGGTTTAGGAGCA
Found at i:2183375 original size:2 final size:2
Alignment explanation
Indices: 2183364--2183395 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2183354 TTAAGGTTAC
2183364 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2183396 GATAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2186479 original size:15 final size:16
Alignment explanation
Indices: 2186459--2186488 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2186449 TTTAAAGTAT
2186459 ATATTTT-AAATTAAA
1 ATATTTTAAAATTAAA
2186474 ATATTTTAAAATTAA
1 ATATTTTAAAATTAA
2186489 GATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTTAAAATTAAA
Found at i:2186594 original size:27 final size:25
Alignment explanation
Indices: 2186564--2186618 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
2186554 TTTAAACAAA
* *
2186564 AATAAAATATCTTTAAATTAAGTTAAT
1 AATAAAACATATTT-AA-TAAGTTAAT
*
2186591 AATAAAACATATTTAATATGTTAAT
1 AATAAAACATATTTAATAAGTTAAT
2186616 AAT
1 AAT
2186619 GAATTTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 2 0.08
27 12 0.48
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
AATAAAACATATTTAATAAGTTAAT
Found at i:2187158 original size:199 final size:198
Alignment explanation
Indices: 2186808--2187175 Score: 522
Period size: 199 Copynumber: 1.9 Consensus size: 198
2186798 ATTCGATTGT
* **
2186808 AGGATTAAATTTATTTTAATTTATTAAAATAAGACTAAATTGAGAGAATATGTAAATGACAAAGA
1 AGGATTAAATATATTTTAATTTATTAAAATAAGACTAAATTGAGAGAATATGTAAAAAACAAAGA
* * * * * * *
2186873 CCAAATATCTGATTATACCAAAATATCATGTCGCTTAATATGTTAATCGTTAATAATAGTTAACT
66 CCAAATATCTGATTATACCAAAATATCACGTCACCTAATATGTTAATCGTTAACAACAATTAACC
* *
2186938 TGTGGTGGTCACATCTTAATTAAATAAAAACAAAAGTGATAATATATCATGTGACATCATTTAAT
131 CGTGGTGATCACATCTTAATTAAATAAAAACAAAAGTGATAATATATCATGTGACATCATTTAAT
2187003 TAG
196 TAG
* *
2187006 AGGATTAAATATATTTTAATTTATTAAAAGTATGACTAAATTGAGAGAATATGTAAAAAACAGAG
1 AGGATTAAATATATTTTAATTTATTAAAA-TAAGACTAAATTGAGAGAATATGTAAAAAACAAAG
* * * *
2187071 ACCAAATGTTTGATTATACCCAAATATCACGTCACCTAATATGTTAATCGTTAACGACAATTAAC
65 ACCAAATATCTGATTATACCAAAATATCACGTCACCTAATATGTTAATCGTTAACAACAATTAAC
* **
2187136 CCGTGGTGAAT-ACATGTTAATTAAATAAAAATGAAAGTGA
130 CCGTGGTG-ATCACATCTTAATTAAATAAAAACAAAAGTGA
2187176 CTATATCTTA
Statistics
Matches: 147, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
198 28 0.19
199 118 0.80
200 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (198 bp):
AGGATTAAATATATTTTAATTTATTAAAATAAGACTAAATTGAGAGAATATGTAAAAAACAAAGA
CCAAATATCTGATTATACCAAAATATCACGTCACCTAATATGTTAATCGTTAACAACAATTAACC
CGTGGTGATCACATCTTAATTAAATAAAAACAAAAGTGATAATATATCATGTGACATCATTTAAT
TAG
Found at i:2187919 original size:13 final size:13
Alignment explanation
Indices: 2187896--2187957 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
2187886 CAAATATTGA
2187896 ATAAT-AAAATA-
1 ATAATAAAAATAT
2187907 ATAAGTAAAAATAT
1 ATAA-TAAAAATAT
2187921 ATAATAAAAATAT
1 ATAATAAAAATAT
* *
2187934 ACATAAGAAAGATAT
1 --ATAATAAAAATAT
2187949 ATAATAAAA
1 ATAATAAAA
2187958 TAAATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.10
12 1 0.02
13 22 0.52
14 4 0.10
15 11 0.26
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:2187926 original size:28 final size:28
Alignment explanation
Indices: 2187865--2187957 Score: 93
Period size: 28 Copynumber: 3.2 Consensus size: 28
2187855 AAAAAAAACG
* *
2187865 AATAAATATATACATAATAACCAAATAT-T
1 AATAAAAATATACATAAGAA--AAATATAT
2187894 GAATAATAAA-ATA-ATAAGTAAAAATATAT
1 -AATAA-AAATATACATAAG-AAAAATATAT
*
2187923 AATAAAAATATACATAAGAAAGATATAT
1 AATAAAAATATACATAAGAAAAATATAT
2187951 AATAAAA
1 AATAAAA
2187958 TAAATATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
27 3 0.05
28 30 0.55
29 10 0.18
30 10 0.18
31 2 0.04
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (28 bp):
AATAAAAATATACATAAGAAAAATATAT
Found at i:2188078 original size:36 final size:36
Alignment explanation
Indices: 2187949--2188078 Score: 89
Period size: 34 Copynumber: 3.7 Consensus size: 36
2187939 AGAAAGATAT
* *
2187949 ATAATAAAATAAATATATATAT-ATGT-A-ATGAGAA-
1 ATAA-AAAATAAATATATATATAATATAACAT-AAAAG
*
2187983 ATAACAAA-AAATATA-ATATAATATAACATAAAAG
1 ATAAAAAATAAATATATATATAATATAACATAAAAG
* * * *
2188017 ATAAAAGATCAATA-ATAGAGAA-ATATA-ATAAATAG
1 ATAAAAAATAAATATATATATAATATA-ACATAAA-AG
2188052 ATAAAAAATTAAATATATATATAATAT
1 ATAAAAAA-TAAATATATATATAATAT
2188079 GTAATAATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
31 4 0.05
32 10 0.14
33 7 0.10
34 21 0.29
35 18 0.25
36 5 0.07
37 6 0.08
38 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.28
Consensus pattern (36 bp):
ATAAAAAATAAATATATATATAATATAACATAAAAG
Found at i:2189962 original size:105 final size:105
Alignment explanation
Indices: 2189764--2190539 Score: 1231
Period size: 105 Copynumber: 7.4 Consensus size: 105
2189754 GTATCGTTCC
* ** **
2189764 GAGTCCAATATCC-TC-TACTGTGAAGTTGAAATTGGTTCTGGAGCTGGA-AAATTGTTTATTGA
1 GAGTCCAATATCCTTCGT--TGTGAAGTTGAAATTGGCTCT-GAATTGGAGAAA-TGTTTGGTGA
* * * * *
2189826 CAACCAACGGTCCCCTCATCGTGAAGCTGAACTTGCGTTGCCTG
62 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2189870 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
*
2189935 CAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2189975 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
*
2190040 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2190080 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
2190145 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2190185 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
*
2190250 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2190290 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAGATATTT-GTCGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGT-GACA
*
2190353 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2190395 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACAA
* *
2190459 CCAGCGATCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2190500 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
2190540 GGTAAAACCT
Statistics
Matches: 636, Mismatches: 28, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
104 2 0.00
105 591 0.93
106 40 0.06
107 2 0.00
108 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2201428 original size:23 final size:23
Alignment explanation
Indices: 2201393--2201455 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
2201383 ATAAAAAAAT
* *
2201393 TGAAAGTGA-AATAAATAATGGA
1 TGAAAGTAACAATAAATAAAGGA
2201415 TGAAAGTAACAATAAATAAAGGA
1 TGAAAGTAACAATAAATAAAGGA
**
2201438 T-AAAAAAACGAATAAATA
1 TGAAAGTAAC-AATAAATA
2201456 TATACATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (23 bp):
TGAAAGTAACAATAAATAAAGGA
Found at i:2201504 original size:29 final size:25
Alignment explanation
Indices: 2201470--2201544 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 25
2201460 CATAATAACC
2201470 AAATAT-TGAATAATAAATAATAAGTAA
1 AAATATAT-AATAA-AAATAATAAG-AA
2201497 AAATATATAATAAAAATATACATAAGAA
1 AAATATATAAT-AAAA-ATA-ATAAGAA
*
2201525 AGATATAATAATAAAAATAA
1 AAATAT-ATAATAAAAATAA
2201545 ATATATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
26 1 0.02
27 14 0.33
28 17 0.40
29 10 0.24
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (25 bp):
AAATATATAATAAAAATAATAAGAA
Found at i:2201510 original size:13 final size:14
Alignment explanation
Indices: 2201448--2201547 Score: 75
Period size: 15 Copynumber: 7.1 Consensus size: 14
2201438 TAAAAAAACG
*
2201448 AATAAATATATACAT
1 AATAAAAATATA-AT
2201463 AATAACCAAATAT--T
1 AATAA--AAATATAAT
*
2201477 GAATAATAA-ATAAT
1 -AATAAAAATATAAT
2201491 AAGTAAAAATAT-AT
1 AA-TAAAAATATAAT
2201505 AATAAAAATATACAT
1 AATAAAAATATA-AT
* *
2201520 AAGAAAGATATAAT
1 AATAAAAATATAAT
2201534 AATAAAAATA-AAT
1 AATAAAAATATAAT
2201547 A
1 A
2201548 TATATATAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
12 2 0.03
13 17 0.25
14 21 0.30
15 24 0.35
17 5 0.07
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:2208029 original size:97 final size:97
Alignment explanation
Indices: 2207863--2208057 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
2207853 GGCGGAGGCA
2207863 AGAACGACAGCTGAACGGGGAGATCTAGCAAGTGCTGTTTCAATACTTGAAAACTGTAGAAGATT
1 AGAACGACAGCTGAACGGGGAGATCTAGCAAGTGCTGTTTCAATACTTGAAAACTGTAGAAGATT
2207928 GTTGTCCGAGACCGTTTCGGCCAAAGCTCATG
66 GTTGTCCGAGACCGTTTCGGCCAAAGCTCATG
2207960 AGAACGACAGCTGAACGGGGAGATCTAGCAAGTGCTGTTTCAATACTTGAAAACTGTAGAAGATT
1 AGAACGACAGCTGAACGGGGAGATCTAGCAAGTGCTGTTTCAATACTTGAAAACTGTAGAAGATT
2208025 GTTGTCCGAGACCGTTTCGGCCAAAGCTCATG
66 GTTGTCCGAGACCGTTTCGGCCAAAGCTCATG
2208057 A
1 A
2208058 CCGACTTTGT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (97 bp):
AGAACGACAGCTGAACGGGGAGATCTAGCAAGTGCTGTTTCAATACTTGAAAACTGTAGAAGATT
GTTGTCCGAGACCGTTTCGGCCAAAGCTCATG
Found at i:2232683 original size:16 final size:16
Alignment explanation
Indices: 2232662--2232695 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2232652 AGATTTCATT
*
2232662 AAAATTAGAAAGAATC
1 AAAATTACAAAGAATC
*
2232678 AAAATTACAAAGCATC
1 AAAATTACAAAGAATC
2232694 AA
1 AA
2232696 TACGTAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAATTACAAAGAATC
Found at i:2234493 original size:51 final size:49
Alignment explanation
Indices: 2234386--2234493 Score: 114
Period size: 51 Copynumber: 2.2 Consensus size: 49
2234376 TTAAATAGTT
*
2234386 ATTATATTTTATATTAATATATTTATGTAAATATTATTTTTTTATTAAA
1 ATTATATTTTATATTAATATATTTATGTAAATATTAATTTTTTATTAAA
* * *
2234435 ATAATATTTATATAATTAATATTTATTTA-G-AATTATTAATTTTTT-TTACTA
1 ATTATATTT-TAT-ATTAATA--TATTTATGTAAATATTAATTTTTTATTA-AA
2234486 ATTATATT
1 ATTATATT
2234494 GTTTTGTCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
49 8 0.16
50 6 0.12
51 28 0.57
52 1 0.02
53 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (49 bp):
ATTATATTTTATATTAATATATTTATGTAAATATTAATTTTTTATTAAA
Found at i:2238317 original size:6 final size:6
Alignment explanation
Indices: 2238306--2238353 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
2238296 TAGAGCATTT
2238306 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG
2238354 GGGTATAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:2240765 original size:35 final size:35
Alignment explanation
Indices: 2240683--2240754 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
2240673 GAACGATTTA
*
2240683 AAGTCTTTAAATAA-ATATTATCTTGTATTCACTAT
1 AAGTCTTTAAA-AATATATTATATTGTATTCACTAT
*
2240718 AAGTCTTTAAAAATATATTATATTGTATTGACT-T
1 AAGTCTTTAAAAATATATTATATTGTATTCACTAT
2240752 AAG
1 AAG
2240755 ATTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (35 bp):
AAGTCTTTAAAAATATATTATATTGTATTCACTAT
Found at i:2249846 original size:5 final size:5
Alignment explanation
Indices: 2249836--2249892 Score: 60
Period size: 5 Copynumber: 10.2 Consensus size: 5
2249826 GACCGGTCAT
2249836 GACCC GACCC GACCC GACCC GTTTACCC GACCC GTTGACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC G---ACCC GACCC ---GACCC GACCC GACCC
2249887 GACCC G
1 GACCC G
2249893 TTAACAGGCG
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 36 0.78
8 10 0.22
ACGTcount: A:0.18, C:0.53, G:0.21, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:2249865 original size:13 final size:12
Alignment explanation
Indices: 2249837--2249895 Score: 72
Period size: 10 Copynumber: 5.1 Consensus size: 12
2249827 ACCGGTCATG
2249837 ACCCGACCCG--
1 ACCCGACCCGTT
2249847 ACCCGACCCGTTT
1 ACCCGACCCG-TT
2249860 ACCCGACCCGTT
1 ACCCGACCCGTT
2249872 GACCCGACCCG--
1 -ACCCGACCCGTT
2249883 ACCCGACCCGTT
1 ACCCGACCCGTT
2249895 A
1 A
2249896 ACAGGCGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
10 20 0.47
12 3 0.07
13 20 0.47
ACGTcount: A:0.19, C:0.51, G:0.19, T:0.12
Consensus pattern (12 bp):
ACCCGACCCGTT
Found at i:2251353 original size:26 final size:26
Alignment explanation
Indices: 2251330--2251387 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2251320 AGAATATCAC
2251330 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGGAATGATTGGATATCCT
2251356 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGGAATGATTGGATATCCT
*
2251382 CGAGCT
1 CAAGCT
2251388 CTGAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (26 bp):
CAAGCTTAGGAATGATTGGATATCCT
Found at i:2251395 original size:26 final size:26
Alignment explanation
Indices: 2251330--2251401 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
2251320 AGAATATCAC
*
2251330 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGAAATGATTGGATATCCT
*
2251356 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGAAATGATTGGATATCCT
* *
2251382 CGAGCTCT-GAAATGAATGGA
1 CAAGCT-TAGAAATGATTGGA
2251402 ATAAAACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
26 41 0.98
27 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (26 bp):
CAAGCTTAGAAATGATTGGATATCCT
Found at i:2252406 original size:24 final size:24
Alignment explanation
Indices: 2252379--2252494 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
2252369 TTCGATTTGA
2252379 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* **
2252403 ATTCTGATATGATA-TCTGACATAT
1 ATTCTGATCTGATACT-TGACATGG
*
2252427 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
2252451 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
2252475 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
2252495 TTGATTTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.01
24 76 0.95
25 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:2254640 original size:13 final size:13
Alignment explanation
Indices: 2254622--2254665 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
2254612 TGACCGATCA
2254622 TGACCCGACCCGT
1 TGACCCGACCCGT
2254635 TGACCCGACCCGT
1 TGACCCGACCCGT
*
2254648 TGACTCGACCCGT
1 TGACCCGACCCGT
2254661 TGACC
1 TGACC
2254666 TATTGACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.43, G:0.23, T:0.18
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:2256150 original size:26 final size:26
Alignment explanation
Indices: 2256127--2256184 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2256117 AGAATATCAC
2256127 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGGAATGATTGGATATCCT
2256153 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGGAATGATTGGATATCCT
*
2256179 CGAGCT
1 CAAGCT
2256185 CTGAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (26 bp):
CAAGCTTAGGAATGATTGGATATCCT
Found at i:2256192 original size:26 final size:26
Alignment explanation
Indices: 2256127--2256198 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
2256117 AGAATATCAC
*
2256127 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGAAATGATTGGATATCCT
*
2256153 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGAAATGATTGGATATCCT
* *
2256179 CGAGCTCT-GAAATGAATGGA
1 CAAGCT-TAGAAATGATTGGA
2256199 ATAAAACTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
26 41 0.98
27 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (26 bp):
CAAGCTTAGAAATGATTGGATATCCT
Found at i:2257294 original size:24 final size:24
Alignment explanation
Indices: 2257176--2257291 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
2257166 TTCGATTTGA
2257176 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* * *
2257200 ATTTTGATCTGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
*
2257224 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
2257248 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
2257272 AGTT-TGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
2257292 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.01
24 75 0.95
25 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:2257510 original size:2 final size:2
Alignment explanation
Indices: 2257503--2257537 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2257493 TGGATGGGGG
2257503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2257538 GTTTTAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2261992 original size:2 final size:2
Alignment explanation
Indices: 2261987--2262012 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2261977 ATCAACACAC
2261987 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
2262013 GAAAGAGTGT
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:2263611 original size:22 final size:22
Alignment explanation
Indices: 2263581--2263631 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2263571 ATCACCACAG
* *
2263581 TTGTATAAATCTGATGTTGTAT
1 TTGTGTAAACCTGATGTTGTAT
2263603 TTGTGTAAACCTGATGTTGTAT
1 TTGTGTAAACCTGATGTTGTAT
2263625 TTGTGTA
1 TTGTGTA
2263632 TGAGAAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.49
Consensus pattern (22 bp):
TTGTGTAAACCTGATGTTGTAT
Found at i:2264936 original size:2 final size:2
Alignment explanation
Indices: 2264929--2264957 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2264919 AATCAAATAC
2264929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2264958 CTAAGGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2265619 original size:27 final size:27
Alignment explanation
Indices: 2265589--2265640 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2265579 TTGAAATATA
*
2265589 ATTTACACTAA-AATAATTAAATACTTC
1 ATTT-CACTAATAAAAATTAAATACTTC
2265616 ATTTCACTAATAAAAATTAAATACT
1 ATTTCACTAATAAAAATTAAATACT
2265641 AAATTATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTTCACTAATAAAAATTAAATACTTC
Found at i:2267817 original size:14 final size:14
Alignment explanation
Indices: 2267794--2267827 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2267784 CAAAAATCGG
*
2267794 ATGACTGATTTTTC
1 ATGACAGATTTTTC
2267808 ATGACAGATTTTTC
1 ATGACAGATTTTTC
2267822 ATGACA
1 ATGACA
2267828 TTTTTAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
ATGACAGATTTTTC
Found at i:2276114 original size:19 final size:19
Alignment explanation
Indices: 2276092--2276148 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
2276082 TTATATAATA
2276092 ATATATTTTTATTATAGTT
1 ATATATTTTTATTATAGTT
* *
2276111 ATAT-TTTTTATTTGTATTT
1 ATATATTTTTA-TTATAGTT
*
2276130 TTATATTTTTATTATAGTT
1 ATATATTTTTATTATAGTT
2276149 TAAATTGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 6 0.19
19 19 0.61
20 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
ATATATTTTTATTATAGTT
Found at i:2281012 original size:24 final size:24
Alignment explanation
Indices: 2280975--2281069 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
2280965 TCCGATTTGA
* * * *
2280975 ATTCTGTTACGATACCTGACATGG
1 ATTCTGATATGATACTTGACCTGG
*
2280999 ATTCTGATTTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
2281023 ATTCTGATCTGATACTTGACCCGG
1 ATTCTGATATGATACTTGACCTGG
2281047 ATTCTGATATGATACTTGACCTG
1 ATTCTGATATGATACTTGACCTG
2281070 AATTATGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:2281083 original size:24 final size:24
Alignment explanation
Indices: 2280985--2281083 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
2280975 ATTCTGTTAC
* *
2280985 GATACCTGACATGGATTCTGATTT
1 GATACTTGACCTGGATTCTGATTT
*
2281009 GATACTTGACCTGGATTCTGATCT
1 GATACTTGACCTGGATTCTGATTT
* *
2281033 GATACTTGACCCGGATTCTGATAT
1 GATACTTGACCTGGATTCTGATTT
* * *
2281057 GATACTTGACCTGAATTATGTTTT
1 GATACTTGACCTGGATTCTGATTT
2281081 GAT
1 GAT
2281084 TTTTGATATA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
GATACTTGACCTGGATTCTGATTT
Found at i:2282166 original size:69 final size:69
Alignment explanation
Indices: 2282020--2282182 Score: 159
Period size: 69 Copynumber: 2.4 Consensus size: 69
2282010 GTTCTCATCT
* * * * *
2282020 GAGACACCCATAATGATCATGATTAGGTGCTCCAGTGCAAGACACTCTAACTTTCTAGGACTCCC
1 GAGACACCCAAAATCATCATGATTAGGCGCTCCAGTGCAAGACACTCTAACCTTCTAGGAATCCC
*
2282085 GTGC
66 GTAC
* * * * *
2282089 AAGTCACCCAAAATACAT-ATGATTAGGCGCTCCCGTGCAAGTCGCTCTAATCCTTC-AGGAATC
1 GAGACACCCAAAAT-CATCATGATTAGGCGCTCCAGTGCAAGACACTCTAA-CCTTCTAGGAATC
*
2282152 TCGTAC
64 CCGTAC
* * *
2282158 GAGACACCCGAAATGATTATGATTA
1 GAGACACCCAAAATCATCATGATTA
2282183 TTCACACAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
68 2 0.03
69 67 0.89
70 6 0.08
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (69 bp):
GAGACACCCAAAATCATCATGATTAGGCGCTCCAGTGCAAGACACTCTAACCTTCTAGGAATCCC
GTAC
Found at i:2283346 original size:22 final size:22
Alignment explanation
Indices: 2283318--2283362 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2283308 GAACTCAGCT
2283318 AAACAACTCACTTAGTTAAGGG
1 AAACAACTCACTTAGTTAAGGG
2283340 AAACAACTCACTTAGTTAAGGG
1 AAACAACTCACTTAGTTAAGGG
2283362 A
1 A
2283363 CTATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (22 bp):
AAACAACTCACTTAGTTAAGGG
Found at i:2284925 original size:18 final size:18
Alignment explanation
Indices: 2284902--2284952 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
2284892 TCCTGCCTTT
2284902 AATTTAAAGTAAACATGA
1 AATTTAAAGTAAACATGA
* *
2284920 AATTTAAAATAAA-ATGT
1 AATTTAAAGTAAACATGA
* *
2284937 TATATAAAGTAAACAT
1 AATTTAAAGTAAACAT
2284953 TCAACTTGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (18 bp):
AATTTAAAGTAAACATGA
Found at i:2288421 original size:2 final size:2
Alignment explanation
Indices: 2288414--2288452 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2288404 TTTGATAATC
* * *
2288414 CT CT CT CT CT CT CT CT CT CT TT CT CT TT AT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2288453 ATATGATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:2289100 original size:183 final size:183
Alignment explanation
Indices: 2288779--2289144 Score: 700
Period size: 183 Copynumber: 2.0 Consensus size: 183
2288769 TTGCCGCGAA
2288779 CATTCCCTGGTCATCCCGCTCTGGATGGTGATGGTAGAAATGCTTTGAGACGGTTACTTACAGCC
1 CATTCCCTGGTCATCCCGCTCTGGATGGTGATGGTAGAAATGCTTTGAGACGGTTACTTACAGCC
2288844 TATGCGACATAACCCCTCGGTGGGATACTGCCAGGTACTAGGTTCAGAAATATGTTAGCTATGAT
66 TATGCGACATAACCCCTCGGTGGGATACTGCCAGGTACTAGGTTCAGAAATATGTTAGCTATGAT
2288909 CGTGGTTGCAGTGTTTTGGTTTTTTGGTTTAAGTG-TTTCTC-TGCAGGCCAT
131 CGTGGTTGCAGTGTTTTGGTTTTTTGGTTTAAGTGTTTTCTCATGCAGGCCAT
2288960 CATTCCCTGGTCATCCCGCTCTGGATGGTGATGGTAGAAATGCTTTGAGACGGTTACTTACAGCC
1 CATTCCCTGGTCATCCCGCTCTGGATGGTGATGGTAGAAATGCTTTGAGACGGTTACTTACAGCC
2289025 TATGCTCGACATAACCCCTCGGTGGGATACTGCCAGGTACTAGGTTCAGAAATATGTTAGCTATG
66 TATG--CGACATAACCCCTCGGTGGGATACTGCCAGGTACTAGGTTCAGAAATATGTTAGCTATG
2289090 ATCGTGGTTGCAGTGTTTTGGTTTTTTGGTTTAAGTGTTTTCTCATGCAGGCCAT
129 ATCGTGGTTGCAGTGTTTTGGTTTTTTGGTTTAAGTGTTTTCTCATGCAGGCCAT
2289145 GAATTTCTTT
Statistics
Matches: 181, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
181 69 0.38
183 96 0.53
184 6 0.03
185 10 0.06
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (183 bp):
CATTCCCTGGTCATCCCGCTCTGGATGGTGATGGTAGAAATGCTTTGAGACGGTTACTTACAGCC
TATGCGACATAACCCCTCGGTGGGATACTGCCAGGTACTAGGTTCAGAAATATGTTAGCTATGAT
CGTGGTTGCAGTGTTTTGGTTTTTTGGTTTAAGTGTTTTCTCATGCAGGCCAT
Found at i:2294568 original size:22 final size:22
Alignment explanation
Indices: 2294542--2294592 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2294532 GATTGCAGAG
2294542 TATTTAAACTTTTATTATCAAA
1 TATTTAAACTTTTATTATCAAA
*
2294564 TATTTAAACTTTTATTATTAAA
1 TATTTAAACTTTTATTATCAAA
*
2294586 TAATTAA
1 TATTTAA
2294593 GAGTCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTAAACTTTTATTATCAAA
Found at i:2297823 original size:16 final size:16
Alignment explanation
Indices: 2297802--2297835 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2297792 TACATCATGC
2297802 TGCAGTTCTTGAATAT
1 TGCAGTTCTTGAATAT
2297818 TGCAGTTCTTGAATAT
1 TGCAGTTCTTGAATAT
2297834 TG
1 TG
2297836 ATGGAATCCG
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:0.24, C:0.12, G:0.21, T:0.44
Consensus pattern (16 bp):
TGCAGTTCTTGAATAT
Found at i:2299739 original size:3 final size:3
Alignment explanation
Indices: 2299733--2299803 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
2299723 ATTTTTTTAA
* *
2299733 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAA TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2299778 TAT TTT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2299804 CACCAGGCCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2301408 original size:12 final size:12
Alignment explanation
Indices: 2301376--2301408 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2301366 TATTATAAAA
*
2301376 AAATTATAATTT
1 AAATTATTATTT
2301388 AAATT-TTATTT
1 AAATTATTATTT
2301399 AAATTATTAT
1 AAATTATTAT
2301409 AATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAATTATTATTT
Found at i:2313062 original size:16 final size:17
Alignment explanation
Indices: 2313043--2313091 Score: 73
Period size: 16 Copynumber: 2.8 Consensus size: 17
2313033 TATTTTCTCT
2313043 AAATTCAATTTATTTG-
1 AAATTCAATTTATTTGA
2313059 AAATTCAATTTATTTTTGA
1 AAATTCAATTTA--TTTGA
2313078 AAATTCAATTTATT
1 AAATTCAATTTATT
2313092 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.40
17 2 0.07
18 4 0.13
19 12 0.40
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (17 bp):
AAATTCAATTTATTTGA
Found at i:2313083 original size:19 final size:18
Alignment explanation
Indices: 2313043--2313091 Score: 75
Period size: 19 Copynumber: 2.8 Consensus size: 18
2313033 TATTTTCTCT
2313043 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
2313059 AAATTCAATTTATTTTTG
1 AAATTCAATTTATTTTTG
2313077 AAAATTCAATTTATT
1 -AAATTCAATTTATT
2313092 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.40
18 4 0.13
19 14 0.47
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:2313591 original size:114 final size:114
Alignment explanation
Indices: 2313386--2313609 Score: 333
Period size: 114 Copynumber: 2.0 Consensus size: 114
2313376 GTGCTACGTT
* *
2313386 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATATG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATATCTGATATG
* * * * *
2313451 ATTTGGTATGAACCCCAGAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTCGGTAAGAACCACAGAATCAATCATTGGAATTAAAAGATGAATTTG
* * *
2313500 CTCATAGTAGAAATAAGGAGACCCAATAGCCTCTTCTGGAAGTGTTCTTTGAGATATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATATCTGATATG
*
2313565 GTTCGGTAAGAACCACAGAA-CAAATCATTGGAATTAAAAGATGAA
66 ATTCGGTAAGAACCACAGAATC-AATCATTGGAATTAAAAGATGAA
2313610 CTGCATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
113 1 0.01
114 97 0.99
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATATCTGATATG
ATTCGGTAAGAACCACAGAATCAATCATTGGAATTAAAAGATGAATTTG
Found at i:2314535 original size:113 final size:112
Alignment explanation
Indices: 2314302--2315205 Score: 1012
Period size: 113 Copynumber: 8.0 Consensus size: 112
2314292 TAGCAAAGAT
* * * * ** *
2314302 TTAAATCCATCATTTAATGGATCAACATTTTCAGTTAGAGTTCATAATGAGAAGAACTCATCT--
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2314365 -GAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
2314411 TAAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2314476 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
2314524 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCAT
* *
2314588 CTGAAGAATAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTAC
62 CTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
2314636 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2314701 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
2314749 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCAT
* *
2314813 CTGAAGAAGAAG-A-AA-TTCATAATGAGAGGAATTTGTTCAACCTTTTAC
62 CTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
2314861 TCAAATCCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAA
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2314926 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
2314974 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCACAATGAGAAGAACTCA--T-
1 TTAAATTCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * **
2315035 ATGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
2315083 AT-AATTCTATCACAGAAGGATATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAA
1 TTAAATTC-ATCAC-------T-T-GA-T-GGATCAACATTTCCAGAGAAAGTTCATAATGAGAA
* ** *
2315147 GAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAATAGCTTATTCAACCTTTTG
54 GAACTCATCTGAAGAAG-AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
2315206 AAAAACTCTA
Statistics
Matches: 676, Mismatches: 79, Indels: 65
0.82 0.10 0.08
Matches are distributed among these distances:
108 5 0.01
109 121 0.18
110 13 0.02
111 3 0.00
112 164 0.24
113 250 0.37
114 2 0.00
115 9 0.01
116 25 0.04
117 1 0.00
118 2 0.00
119 1 0.00
120 35 0.05
121 1 0.00
122 1 0.00
123 5 0.01
124 38 0.06
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (112 bp):
TTAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2314697 original size:225 final size:222
Alignment explanation
Indices: 2314309--2315205 Score: 1382
Period size: 225 Copynumber: 4.0 Consensus size: 222
2314299 GATTTAAATC
* ** *
2314309 CATCATTTAATGGATCAACATTTTCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* * *
2314374 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTAAAATCCATCACTTGATGGATCAGCTT
66 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTT
2314439 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
131 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
2314504 GAATTTGTTCAACCTTTTGTTTGAATT
196 GAATTTGTTCAACCTTTTGTTTGAATT
2314531 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
*
2314596 TAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAA
63 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAA
2314661 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
128 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
2314726 GAAGAATTTGTTCAACCTTTTGTTTGAATT
193 GAAGAATTTGTTCAACCTTTTGTTTGAATT
2314756 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
2314821 GAAGAAATTCATAATGAGAGGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAT
63 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAA
*
2314886 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGA
128 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
2314951 GAAGAATTTGTTCAACCTTTTGTTTGAATT
193 GAAGAATTTGTTCAACCTTTTGTTTGAATT
* *
2314981 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCACAATGAGAAGAACTCATATGAAGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* * ** * * *
2315046 GAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGATATAGAT
66 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC-TCAAATCCATCAC-------T-T-GA-
* * *
2315110 TAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
120 T-GGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* ** *
2315175 TCATAATGAGAATAGCTTATTCAACCTTTTG
184 TCATAATGAGAAGAATTTGTTCAACCTTTTG
2315206 AAAAACTCTA
Statistics
Matches: 629, Mismatches: 31, Indels: 19
0.93 0.05 0.03
Matches are distributed among these distances:
222 99 0.16
223 2 0.00
224 1 0.00
225 437 0.69
229 1 0.00
230 1 0.00
231 2 0.00
232 1 0.00
233 85 0.14
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (222 bp):
CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTT
TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAATTTGTTCAACCTTTTGTTTGAATT
Found at i:2315216 original size:124 final size:122
Alignment explanation
Indices: 2315012--2315293 Score: 351
Period size: 124 Copynumber: 2.3 Consensus size: 122
2315002 TGCCAGGTAG
* * *
2315012 AGTTCACAATGAGAAGAACTCA--T-ATGAAG-AAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTATTC
* * * * * *
2315073 AACCTTTTGCATAATTCTATCACAGAAGGATATAGATTAGCATCAACCTTTCCAG-AGAA
66 AACCTTTTGAAAAACTCTATCACAGAAGGAAATAGATCAACATCAACC---CCAGCAGAA
* *
2315132 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAATAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTATTC
* * * *
2315197 AACCTTTTGAAAAACTCTATCACATAAGGAAATAGGTCAACATCATCCCCAGCGGAA
66 AACCTTTTGAAAAACTCTATCACAGAAGGAAATAGATCAACATCAACCCCAGCAGAA
*
2315254 AGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
2315294 TTTATTCAAC
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
120 21 0.15
121 12 0.09
122 35 0.25
123 5 0.04
124 68 0.48
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTATTC
AACCTTTTGAAAAACTCTATCACAGAAGGAAATAGATCAACATCAACCCCAGCAGAA
Found at i:2315444 original size:3 final size:3
Alignment explanation
Indices: 2315438--2315509 Score: 78
Period size: 3 Copynumber: 24.7 Consensus size: 3
2315428 ATTTTTTTAA
* * *
2315438 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAA TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2315483 TAT T-T T-T TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2315510 CACCAGGCCC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 5 0.09
3 52 0.90
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2317139 original size:12 final size:12
Alignment explanation
Indices: 2317107--2317139 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2317097 ATATTATAAA
*
2317107 AAATTATAATTT
1 AAATTATTATTT
2317119 AAATT-TTATTT
1 AAATTATTATTT
2317130 AAATTATTAT
1 AAATTATTAT
2317140 AATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAATTATTATTT
Found at i:2318344 original size:3 final size:3
Alignment explanation
Indices: 2318336--2318373 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2318326 TTTTTAGATG
2318336 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2318374 TTTTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2318700 original size:16 final size:16
Alignment explanation
Indices: 2318670--2318719 Score: 82
Period size: 16 Copynumber: 3.0 Consensus size: 16
2318660 CTTGAATTTG
2318670 ACTTCAATATATTTTGGT
1 ACTTCAA-AT-TTTTGGT
2318688 ACTTCAAATTTTTGGT
1 ACTTCAAATTTTTGGT
2318704 ACTTCAAATTTTTGGT
1 ACTTCAAATTTTTGGT
2318720 TCAATTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 23 0.72
17 2 0.06
18 7 0.22
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
ACTTCAAATTTTTGGT
Found at i:2322325 original size:21 final size:21
Alignment explanation
Indices: 2322299--2322356 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2322289 CAGAACCCCA
*
2322299 GGGGGGTATCGATTCCCCTGT
1 GGGGGGTATCGATTCCCCTAT
* * * *
2322320 GGGGGGAATCGGTTCTCTTAT
1 GGGGGGTATCGATTCCCCTAT
2322341 -GGGGGTATCGATTCCC
1 GGGGGGTATCGATTCCC
2322357 TCTGCACCAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.12, C:0.21, G:0.38, T:0.29
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCCTAT
Found at i:2329944 original size:18 final size:18
Alignment explanation
Indices: 2329921--2329956 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2329911 ATTGAAAAAC
2329921 TTATAATGTTTTTT-ATAA
1 TTATAAT-TTTTTTGATAA
2329939 TTATAATTTTTTTGATAA
1 TTATAATTTTTTTGATAA
2329957 GATGGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TTATAATTTTTTTGATAA
Found at i:2334629 original size:33 final size:33
Alignment explanation
Indices: 2334589--2334683 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
2334579 TCTTCAGGCG
*
2334589 TTGCCACAAGCATGTATGAGGAGACAATGTCCA
1 TTGCCACAAGCATGTATGAGGAGACAATGCCCA
* * * *
2334622 TTTCCACAAGCATGTTTGAGGATACATTGCCCA
1 TTGCCACAAGCATGTATGAGGAGACAATGCCCA
2334655 TTGCCACAAGCATGTATGAGG-GAGCAATG
1 TTGCCACAAGCATGTATGAGGAGA-CAATG
2334684 GATGTTTCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 51 0.98
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (33 bp):
TTGCCACAAGCATGTATGAGGAGACAATGCCCA
Found at i:2335090 original size:60 final size:60
Alignment explanation
Indices: 2334985--2335388 Score: 302
Period size: 60 Copynumber: 6.8 Consensus size: 60
2334975 AATCCTGTGA
* * * * ** * *
2334985 CCTTGGCAGAAGAAATCCATACTACTCCCAGAACCTCAGGTGAAGAAACTCGAGTTATTT
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACTCCAGTTATTT
* * * **
2335045 CCTTGGCTGAAGAAACCCCTAGTCTTCCCAGATCCTTGGGAGAAGAAACTCCAGCCATTT
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACTCCAGTTATTT
* * * * *
2335105 -CTGTGGCAGAAGAAACCCTTAGTATTCCCACAACCTTGGGTGAAGAAACTCCTGTTATTC
1 CCT-TGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACTCCAGTTATTT
* * * ** ** * ** *
2335165 CCTTGGCCGAAGCAACCCCTAGTATTCCCAGAACCATGGCCGAAGACGCGCCAACTATTC
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACTCCAGTTATTT
* * * * * ** *
2335225 CCCTGGCAGAAGAAACCCCTAGTATTCACAGAACCTT-GGATGAAAAAACACCGGCCATTA
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGA-GAAGAAACTCCAGTTATTT
* * * * * **
2335285 CCCTGACAGAAGAAACCCATAGTATTCCCAGGA-----GCA-AAGAAACTCCAGCCATTT
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACTCCAGTTATTT
* * * *
2335339 CCTTGGCAGAAGAAACCCCTAATATTCCAAGAACCTTAGGCGAAGAAACT
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACT
2335389 TCAGCCATTC
Statistics
Matches: 267, Mismatches: 68, Indels: 18
0.76 0.19 0.05
Matches are distributed among these distances:
54 41 0.15
56 2 0.01
59 4 0.01
60 218 0.82
61 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (60 bp):
CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTTGGGAGAAGAAACTCCAGTTATTT
Found at i:2335419 original size:33 final size:33
Alignment explanation
Indices: 2335395--2335531 Score: 150
Period size: 33 Copynumber: 4.2 Consensus size: 33
2335385 AACTTCAGCC
*
2335395 ATTCCTGAAACCTCAAGTGGAGAAACTCCTACA
1 ATTCCTCAAACCTCAAGTGGAGAAACTCCTACA
** *
2335428 ATTCCTCCCACCTCAAGTGGAGAAACTCCTACT
1 ATTCCTCAAACCTCAAGTGGAGAAACTCCTACA
* *
2335461 ACTACT-ACAACCTCAAGTGGAGAAACTCCTACA
1 ATTCCTCA-AACCTCAAGTGGAGAAACTCCTACA
* * * * * *
2335494 ATTCCTCCAACTTCCAGCGAAGAAACTCCTACC
1 ATTCCTCAAACCTCAAGTGGAGAAACTCCTACA
2335527 ATTCC
1 ATTCC
2335532 CATACCCTTG
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.22
Consensus pattern (33 bp):
ATTCCTCAAACCTCAAGTGGAGAAACTCCTACA
Found at i:2337298 original size:2 final size:2
Alignment explanation
Indices: 2337291--2337320 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2337281 CACCTATTAT
2337291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2337321 AATGTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2337541 original size:2 final size:2
Alignment explanation
Indices: 2337534--2337602 Score: 99
Period size: 2 Copynumber: 36.0 Consensus size: 2
2337524 CCACCTATTA
2337534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2337575 AT AT -T AG AT AT AT -T AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2337603 TAAAAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2337948 original size:17 final size:17
Alignment explanation
Indices: 2337899--2337948 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2337889 TTGTTCATGT
2337899 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
2337916 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
2337930 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
2337947 TT
1 TT
2337949 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:2338593 original size:25 final size:24
Alignment explanation
Indices: 2338547--2338593 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2338537 TTTGAACTAA
* *
2338547 TTTTTATTGATATTTGAGCATTAT
1 TTTTTATTCATATTTAAGCATTAT
*
2338571 TTTTTATTCACTATTTAATCATT
1 TTTTTATTCA-TATTTAAGCATT
2338594 TTGAACGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTTATTCATATTTAAGCATTAT
Found at i:2343547 original size:20 final size:19
Alignment explanation
Indices: 2343465--2343554 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 19
2343455 AAATGACCAA
* *
2343465 CAAAATCGCAATGCGAACT
1 CAAAATCGCAACGCGATCT
* *
2343484 CTAATTCGCAACGCGATCT
1 CAAAATCGCAACGCGATCT
* * * * *
2343503 CAAATTTCTCAACTCAATTT
1 CAAA-ATCGCAACGCGATCT
2343523 CCAAAATCGCAACGCGATTCT
1 -CAAAATCGCAACGCGA-TCT
2343544 CAAAAATCGCA
1 C-AAAATCGCA
2343555 TTGCGATAGT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 18 0.34
20 20 0.38
21 15 0.28
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAAATCGCAACGCGATCT
Found at i:2343551 original size:21 final size:21
Alignment explanation
Indices: 2343489--2343554 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
2343479 GAACTCTAAT
**
2343489 TCGCAACGCGA-TCTCAAATT
1 TCGCAACGCGATTCTCAAAAA
* * * *
2343509 TCTCAACTCAATT-TCCAAAA
1 TCGCAACGCGATTCTCAAAAA
2343529 TCGCAACGCGATTCTCAAAAA
1 TCGCAACGCGATTCTCAAAAA
2343550 TCGCA
1 TCGCA
2343555 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (21 bp):
TCGCAACGCGATTCTCAAAAA
Found at i:2343577 original size:21 final size:21
Alignment explanation
Indices: 2343553--2343603 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2343543 TCAAAAATCG
*
2343553 CATTGCGATAGTACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
*
2343574 CATTGCGATAGCACTGTTCAT
1 CATTGCGATAGCACTGTTCAC
2343595 CATTGCGAT
1 CATTGCGAT
2343604 TTTACATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
CATTGCGATAGCACTGTTCAC
Found at i:2343600 original size:42 final size:42
Alignment explanation
Indices: 2343553--2343743 Score: 140
Period size: 42 Copynumber: 4.6 Consensus size: 42
2343543 TCAAAAATCG
*
2343553 CATTGCGATAGTACTGTTCACCATTGCGATAGCACTGTTCAT
1 CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCAT
** * * *
2343595 CATTGCGATTTTACAT-TTC-GCGTTGCGATAGTCTACAG-T-GT
1 CATTGCGATAGTAC-TGTTCACCGTTGCGATAG-C-ACTGTTCAT
* ** **** *
2343636 CGTTGCGATTCTCAAAAATC-GCGTTGCGATAGCACTGTTCAT
1 CATTGCGATAGT-ACTGTTCACCGTTGCGATAGCACTGTTCAT
* * *
2343678 CGTTGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCAC
1 CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCAT
* *
2343720 CTTTGCGATAGCACTGTTCACCGT
1 CATTGCGATAGTACTGTTCACCGT
2343744 ATATATTTTG
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
40 3 0.03
41 26 0.22
42 85 0.72
43 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (42 bp):
CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCAT
Found at i:2343681 original size:21 final size:21
Alignment explanation
Indices: 2343657--2343743 Score: 156
Period size: 21 Copynumber: 4.1 Consensus size: 21
2343647 TCAAAAATCG
*
2343657 CGTTGCGATAGCACTGTTCAT
1 CGTTGCGATAGCACTGTTCAC
2343678 CGTTGCGATAGCACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
2343699 CGTTGCGATAGCACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
*
2343720 CTTTGCGATAGCACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
2343741 CGT
1 CGT
2343744 ATATATTTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (21 bp):
CGTTGCGATAGCACTGTTCAC
Found at i:2344150 original size:2 final size:2
Alignment explanation
Indices: 2344143--2344169 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2344133 AAGTTAATAA
2344143 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
2344170 ATAGTCAGAT
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:2344550 original size:21 final size:21
Alignment explanation
Indices: 2344526--2344654 Score: 222
Period size: 21 Copynumber: 6.1 Consensus size: 21
2344516 CAAAATATAT
2344526 ACGGTGAACAGTGCTATCGCA
1 ACGGTGAACAGTGCTATCGCA
*
2344547 ACGGTGAACAGTGTTATCGCA
1 ACGGTGAACAGTGCTATCGCA
*
2344568 ACGGTGAACAGTACTATCGCA
1 ACGGTGAACAGTGCTATCGCA
*
2344589 ACGGTGAACAGTACTATCGCA
1 ACGGTGAACAGTGCTATCGCA
2344610 ACGGTGAACAGTGCTATCGCA
1 ACGGTGAACAGTGCTATCGCA
*
2344631 ACGATGAACAGTGCTATCGCA
1 ACGGTGAACAGTGCTATCGCA
2344652 ACG
1 ACG
2344655 CGATTTTTGA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 103 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.19
Consensus pattern (21 bp):
ACGGTGAACAGTGCTATCGCA
Found at i:2344730 original size:41 final size:41
Alignment explanation
Indices: 2344666--2344758 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
2344656 GATTTTTGAG
*
2344666 AATCGCAACGACACTGTACACTATCGCAACGTGAAATGGAA
1 AATCGCAACGACACTGTACACTATCGCAACGCGAAATGGAA
* * * *
2344707 AATCGCAATGACATTGTAGACTATCGCAACGCGAAATGTAA
1 AATCGCAACGACACTGTACACTATCGCAACGCGAAATGGAA
*
2344748 AATCACAACGA
1 AATCGCAACGA
2344759 TGAACAGTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (41 bp):
AATCGCAACGACACTGTACACTATCGCAACGCGAAATGGAA
Found at i:2344783 original size:21 final size:21
Alignment explanation
Indices: 2344753--2344818 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
2344743 TGTAAAATCA
*
2344753 CAACGATGAACAGTGCTATCG
1 CAACGGTGAACAGTGCTATCG
2344774 CAACGGTGAACAGTGCTATCG
1 CAACGGTGAACAGTGCTATCG
*
2344795 CAACGGTGAACAGTACTATCG
1 CAACGGTGAACAGTGCTATCG
2344816 CAA
1 CAA
2344819 TGCGATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (21 bp):
CAACGGTGAACAGTGCTATCG
Found at i:2344861 original size:20 final size:21
Alignment explanation
Indices: 2344819--2344884 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 21
2344809 ACTATCGCAA
* *
2344819 TGCGATTTTTGAGAATCGCGT
1 TGCGATTTTGGAGAATCGAGT
*
2344840 TGCGATTTTGGA-AATTGAGT
1 TGCGATTTTGGAGAATCGAGT
* ** *
2344860 TGAGAAATTGGAG-ATCGCGT
1 TGCGATTTTGGAGAATCGAGT
2344880 TGCGA
1 TGCGA
2344885 ATTAGAGTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
20 24 0.69
21 11 0.31
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (21 bp):
TGCGATTTTGGAGAATCGAGT
Found at i:2346335 original size:5 final size:5
Alignment explanation
Indices: 2346325--2346349 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2346315 TTTGTCTATA
2346325 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
2346350 ACATATGTAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:2346501 original size:36 final size:35
Alignment explanation
Indices: 2346410--2346616 Score: 218
Period size: 36 Copynumber: 5.7 Consensus size: 35
2346400 GAAAAATATG
* *
2346410 TATATAATATATGATTTCTAAAAATATATTTTGAAAATG
1 TATATAATATAT-ATTT-TTAAAA-ATATTTTGAAAA-C
*
2346449 TATATAATATA-GTTTTTAAAAATACTTTTGAAAAC
1 TATATAATATATATTTTTAAAAATA-TTTTGAAAAC
*
2346484 TATATAATATATATTTTTTAAAATATTTTAGAAAAC
1 TATATAATATATATTTTTAAAAATATTTT-GAAAAC
* **
2346520 ATATATAATATATAGTTTTAAAACCATTTTGAAAAC
1 -TATATAATATATATTTTTAAAAATATTTTGAAAAC
* ** *
2346556 TAATATAATATATAATTTTAAAACCATTTTGAAATC
1 T-ATATAATATATATTTTTAAAAATATTTTGAAAAC
2346592 TATATAATATATAGTTTTTTAAAAA
1 TATATAATATATA--TTTTTAAAAA
2346617 AAATATAATA
Statistics
Matches: 148, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
35 31 0.21
36 70 0.47
37 36 0.24
39 11 0.07
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (35 bp):
TATATAATATATATTTTTAAAAATATTTTGAAAAC
Found at i:2347579 original size:2 final size:2
Alignment explanation
Indices: 2347574--2347606 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2347564 TATATATATA
*
2347574 TG TG TG TG TG TC TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2347607 AAAATGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2347919 original size:2 final size:2
Alignment explanation
Indices: 2347912--2347948 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2347902 TCCACTTTAT
*
2347912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2347949 GTTTTTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2348003 original size:41 final size:40
Alignment explanation
Indices: 2347940--2348016 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 40
2347930 TATATATATA
**
2347940 CATATATATGTTTTTACTATTTA-TTTCTATATTTTTCCTT
1 CATATATATGTTTTTAAAATTTAGTTT-TATATTTTTCCTT
* *
2347980 CATATATATTTATTTTAAAATTTAGTTTTTTATTTTT
1 CATATATATGT-TTTTAAAATTTAGTTTTATATTTTT
2348017 ATTTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
40 10 0.32
41 18 0.58
42 3 0.10
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (40 bp):
CATATATATGTTTTTAAAATTTAGTTTTATATTTTTCCTT
Found at i:2353702 original size:165 final size:162
Alignment explanation
Indices: 2353428--2354400 Score: 1005
Period size: 165 Copynumber: 5.9 Consensus size: 162
2353418 GCTCAAGGCC
* * * *
2353428 AGAAGGGTTATCTGCTACC-AAGACCTTCGAGTTCGATTACGCTCCGCTCCAAGGCATATCATTT
1 AGAAGGGTTATCTG--ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
* *
2353492 GCAGCATAACTTAAGTTCGAGAAGGGTTATCTGCCAACCAAAGAC-CTTCGAGTTTGACTACACT
64 GCAGCATAACTTAAG-TCGAGAAGGGTTATCTG----CCAAAGACTC-TCGAGTTCGATTACACT
*
2353556 CAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
123 CAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * * * * * * * *
2353595 AGAAGGGTTATCTG-CTAAAGACCCTCGAGTTGGATTGCACTCAGCTTCGAGGGTACATCATTTA
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTG
* * * * * *
2353659 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGAC-CTTTGAGTTTGATTACGCTCA
65 CAGCATAACTTAAGTCGAGAAGGGTTATCTG---CC-AAAGACTC-TCGAGTTCGATTACACTCA
*
2353723 GC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCG
125 GCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
2353760 AGAAGGGTTATCTGCCAACCAAAGACATTCGAGTTTAACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* * *
2353825 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
63 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
* * *
2353890 TCGAGGGCACATCATTTGCAGCATAACTTAAGCCG
128 TCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
2353925 AGAAGGGTTATCTGCCAACCAAAGACCTTTGGGTTTGACTACGCTTAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* * *
2353990 TGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAACTCTCGAGTTCGATTACACTAAGCT
63 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
* * * *
2354055 TCGAGGGCACATCATTTACAGTATAACTTAAGTCG
128 TCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * *
2354090 AGAAGGGTTATCTACCAACCAAAAACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCT---GACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* *
2354155 TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
63 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
* *
2354220 TCGAGGGCACATCATTTGCAGCATAACTTAAG-CTG
128 TCCAAGGCACATCATTTGCAGCATAACTTAAGTC-G
* * * **
2354255 AAAAGGGTTAGCTGCCAACCAAAGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * * * * *
2354320 TAC-G-ATATAGCTCAAGGCTAGAACGGCTATCTGCCAAAGACAT-TCGAGTTCGACTACGCTAA
63 TGCAGCATA-A-CTTAAGTCGAGAAGGGTTATCTGCCAAAGAC-TCTCGAGTTCGATTACACTCA
*
2354382 GC-TCCAAGGCGCATCATTT
125 GCTTCCAAGGCACATCATTT
2354401 ATAGCATAGC
Statistics
Matches: 703, Mismatches: 84, Indels: 41
0.85 0.10 0.05
Matches are distributed among these distances:
163 3 0.00
164 46 0.07
165 551 0.78
166 27 0.04
167 14 0.02
168 39 0.06
169 23 0.03
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (162 bp):
AGAAGGGTTATCTGACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGC
AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCTTCC
AAGGCACATCATTTGCAGCATAACTTAAGTCG
Found at i:2353843 original size:249 final size:248
Alignment explanation
Indices: 2353406--2354429 Score: 1115
Period size: 249 Copynumber: 4.1 Consensus size: 248
2353396 TAAACAAACT
* * *
2353406 ATTTACAGCTTAGCTCAAGGCCAGAAGGGTTATCTGCTACC-AAGACCTTCGAGTTCGATTACGC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCTACCAAAGACCTTCGAGTTCGATTACGC
* *
2353470 TCCGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG-TCGAGAAGGGTTATCTGCCAACCAAAG
** * *
2353535 ACCTTCGAGTTTGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
130 ACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGTCGAGAAG
* * * * *
2353600 GGTTATCTGCTAAAGACCCTCGAGTTGGATTGCACTCAGCTTCGAGGGTACATC
195 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * *
2353654 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TAACCAAAAGACCTTTGAGTTTGATTAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCT-ACC-AAAGACCTTCGAGTTCGATTAC
*
2353718 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
64 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * * * *
2353783 GACATTCGAGTTTAACTACGCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAA
129 GACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGTCGAGAA
*
2353848 GGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
194 GGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * * * * *
2353903 ATTTGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGGGTTTGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG-CTACCAAAGACCTTCGAGTTCGATTACG
* *
2353968 CTTAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCC-A--AAA-
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
* * * * * *
2354029 A-CTCTCGAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAGTATAACTTAAGTCGAGA
130 ACCT-TCGAGTTCAACTACACTCAGC-TCCAAGGCACATCATTTACAGTATAGCTTAAGTCGAGA
* * * * * * * * *
2354093 AGGGTTATCTACCAACCAAAAACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
193 AGGGCTATCT----GCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * * *
2354152 ATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTG---CCAAAGA-CTCTCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCTACCAAAGACCT-TCGAGTTCGATTACG
* * * *
2354213 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAG-CTGAAAAGGGTTAGCTGCCAACCAA
65 CTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC-GAGAAGGGTTATCTGCCAACCAA
* * * * *
2354277 AGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTAC-GATATAGCTCAAGGCTAG
128 AGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTACAG-TATAGCTTAAGTCGAG
* ** * * * * * *
2354341 AACGGCTATCTGCCAAAGACATTCGAGTTCGACTACGCTAAGC-TCCAAGGCGCATC
192 AAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * *
2354397 ATTTATAGCATAGCCCTAGGCAAGAAGGGTTAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTAT
2354430 ATGTCAATAA
Statistics
Matches: 666, Mismatches: 90, Indels: 43
0.83 0.11 0.05
Matches are distributed among these distances:
244 3 0.00
245 102 0.15
246 90 0.14
247 2 0.00
248 38 0.06
249 327 0.49
250 102 0.15
251 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (248 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCTACCAAAGACCTTCGAGTTCGATTACGC
TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
CCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGTCGAGAAGG
GCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:2354071 original size:330 final size:330
Alignment explanation
Indices: 2353428--2354408 Score: 1223
Period size: 330 Copynumber: 3.0 Consensus size: 330
2353418 GCTCAAGGCC
* * * *
2353428 AGAAGGGTTATCTG-CTACC-AAGACCTTCGAGTTCGATTACGCTCCGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
2353491 TGCAGCATAACTTAAGTTCGAGAAGGGTTATCTGCCAACCAAAGAC-CTTCGAGTTTGACTACAC
66 TGCAGTATAACTTAAG-TCGAGAAGGGCTATCTG----CCAAAGACTC-TCGAGTTCGATTACAC
* * * * *
2353555 TCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CTAAAG
125 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAG
* * * * * * * * * *
2353615 ACCCTCGAGTTGGATTGCACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCTAGAA
190 ACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGTATAACTCAAGGCTAGAA
* * * * *
2353680 GGGTTATCTGTAACCAAAAGAC-CTTTGAGTTTGATTACGCTCAGC-TCCAAGGCATATCATTTG
254 GGGTTATCTG---CCAAAA-ACTC-TCGAGTTCGATTACGCTAAGCTTCCAAGGCACATCATTTA
2353743 CAGCATAACTTAAGTCG
314 CAGCATAACTTAAGTCG
* ** *
2353760 AGAAGGGTTATCTGCCAACCAAAGACATTCGAGTTTAACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
2353825 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
66 TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
2353890 TCGAGGGCACATCATTTGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTT
131 TCGAGGGCACATCATTTGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTT
* * * * * * *
2353955 GGGTTTGACTACGCTTAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTAT
196 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTAT
* * * *
2354020 CTGCCAAAAACTCTCGAGTTCGATTACACTAAGCTTCGAGGGCACATCATTTACAGTATAACTTA
261 CTGCCAAAAACTCTCGAGTTCGATTACGCTAAGCTTCCAAGGCACATCATTTACAGCATAACTTA
2354085 AGTCG
326 AGTCG
* * *
2354090 AGAAGGGTTATCTACCAACCAAAAACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
2354155 TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
66 TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
* * *
2354220 TCGAGGGCACATCATTTGCAGCATAACTTAAGCTGAAAAGGGTTAGCTGCCAACCAAAGACCTTT
131 TCGAGGGCACATCATTTGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTT
* * * *
2354285 GAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTAC-GATATAGCTCAAGGCTAGAACGGCTA
196 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAG-TATAACTCAAGGCTAGAAGGGTTA
* * * *
2354349 TCTGCCAAAGACAT-TCGAGTTCGACTACGCTAAGC-TCCAAGGCGCATCATTTATAGCATA
260 TCTGCCAAAAAC-TCTCGAGTTCGATTACGCTAAGCTTCCAAGGCACATCATTTACAGCATA
2354409 GCCCTAGGCA
Statistics
Matches: 564, Mismatches: 73, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
329 67 0.12
330 348 0.62
331 1 0.00
332 14 0.02
333 61 0.11
334 73 0.13
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (330 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTT
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTAT
CTGCCAAAAACTCTCGAGTTCGATTACGCTAAGCTTCCAAGGCACATCATTTACAGCATAACTTA
AGTCG
Found at i:2354934 original size:15 final size:15
Alignment explanation
Indices: 2354898--2354936 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2354888 ATACATATAT
*
2354898 AATATATGATTTTTAA
1 AATATAT-ATTTTGAA
2354914 AA-ATATATTTTGAA
1 AATATATATTTTGAA
2354928 AATATATAT
1 AATATATAT
2354937 AATATAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 10 0.48
16 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
AATATATATTTTGAA
Found at i:2354948 original size:37 final size:36
Alignment explanation
Indices: 2354892--2355203 Score: 180
Period size: 36 Copynumber: 8.7 Consensus size: 36
2354882 TGAAAAATAC
*
2354892 ATATATAATATATGATTTTTAAAAATATATTTTGAAAAT
1 ATATATAATATA-G-TTTTT-AAAATACATTTTGAAAAT
*
2354931 ATATATAATATAGTTTTTAAAAATAC-CTTTGAAAACT
1 ATATATAATATAGTTTTT-AAAATACATTTTGAAAA-T
*
2354968 ATATA-ATATATAGTTTTT-AAA-ACATTTTAGAAAAC
1 ATATATA-ATATAGTTTTTAAAATACATTTT-GAAAAT
2355003 ATATATAATATA-TAGTTTTAAAAT-CATTTTGAAAACT
1 ATATATAATATAGT--TTTTAAAATACATTTTGAAAA-T
*
2355040 -TATATAATATA-TAATTTTAAAA-CCATTTTG-AAAT
1 ATATATAATATAGT--TTTTAAAATACATTTTGAAAAT
* *
2355074 CTATATAATATATAGTTTTTAAAAAAACCATTTTTG-AAA-
1 ATATAT-A-ATATAGTTTTT-AAAATA-CA-TTTTGAAAAT
* * **
2355113 ACATATAATATA-ATTTTAAAAT-GTTTTTGAAAACT
1 ATATATAATATAGTTTTTAAAATACATTTTGAAAA-T
*
2355148 -TCA-AT-ATATAG--TTTGAAA-ACATTTTGAAAAT
1 AT-ATATAATATAGTTTTTAAAATACATTTTGAAAAT
*
2355179 -TATATAATATATGGTTTTGAAAATA
1 ATATATAATATA--GTTTTTAAAATA
2355204 TCTTTAAAAC
Statistics
Matches: 222, Mismatches: 19, Indels: 66
0.72 0.06 0.21
Matches are distributed among these distances:
30 1 0.00
31 4 0.02
32 25 0.11
33 8 0.04
34 7 0.03
35 29 0.13
36 66 0.30
37 53 0.24
38 3 0.01
39 18 0.08
40 8 0.04
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (36 bp):
ATATATAATATAGTTTTTAAAATACATTTTGAAAAT
Found at i:2355044 original size:108 final size:106
Alignment explanation
Indices: 2354890--2355201 Score: 313
Period size: 108 Copynumber: 2.9 Consensus size: 106
2354880 TTTGAAAAAT
*
2354890 ACATATATAATATATGATTTTTAAAAATATATTTTGAAAA-TATATATAATATAGTTTTTAAAAA
1 ACATATATAATATAT-A-TTTT-AAAAT-CATTTTGAAAACT-TATATAATATAGTTTTTAAAAA
2354954 TACCTTTGAAAACTATATAATATATAGTTTTTAAAA-CATTTTAGAAA
61 TA--TTTGAAAACTATATAATATATAGTTTTTAAAACCATTTTAGAAA
2355001 ACATATATAATATATAGTTTTAAAATCATTTTGAAAACTTATATAATATA-TAATTTTAAAACCA
1 ACATATATAATATATA-TTTTAAAATCATTTTGAAAACTTATATAATATAGT--TTTTAAAA--A
* *
2355065 T-TTTGAAATCTATATAATATATAGTTTTTAAAAAAACCATTTTTGAAA
61 TATTTGAAAACTATATAATATATAGTTTTT---AAAACCATTTTAGAAA
** *
2355113 AC--ATATAATATA-ATTTTAAAATGTTTTTGAAAACTTCA-AT-ATATAG-TTTGAAAACAT-T
1 ACATATATAATATATATTTTAAAATCATTTTGAAAACTT-ATATAATATAGTTTTTAAAA-ATAT
* * *
2355171 TTGAAAATTATATAATATATGGTTTTGAAAA
64 TTGAAAACTATATAATATATAGTTTTTAAAA
2355202 TATCTTTAAA
Statistics
Matches: 179, Mismatches: 11, Indels: 32
0.81 0.05 0.14
Matches are distributed among these distances:
101 4 0.02
104 27 0.15
105 7 0.04
107 6 0.03
108 71 0.40
109 16 0.09
110 15 0.08
111 21 0.12
112 12 0.07
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (106 bp):
ACATATATAATATATATTTTAAAATCATTTTGAAAACTTATATAATATAGTTTTTAAAAATATTT
GAAAACTATATAATATATAGTTTTTAAAACCATTTTAGAAA
Found at i:2355058 original size:72 final size:73
Alignment explanation
Indices: 2354893--2355190 Score: 277
Period size: 72 Copynumber: 4.2 Consensus size: 73
2354883 GAAAAATACA
* *
2354893 TATATAATATATGATTTTTAAAAATATATTTTGAAAA-TATAT-ATAATATAGTTTTTAAAAAT-
1 TATATAATATAT-AATTTT-AAAACAT-TTTTGAAAACTATATAAT-ATATAGTTTTTAAAAATC
*
2354955 ACCTTTGAAAAC
62 ACTTTTGAAAAC
* *
2354967 TATATAATATATAGTTTTTAAAACATTTTAGAAAACATATATAATATATAG-TTTT-AAAATCA-
1 TATATAATATATA-ATTTTAAAACATTTTTGAAAAC-TATATAATATATAGTTTTTAAAAATCAC
2355029 TTTTGAAAAC
64 TTTTGAAAAC
* *
2355039 TTATATAATATATAATTTTAAAACCA-TTTTGAAATCTATATAATATATAGTTTTTAAAAAAACC
1 -TATATAATATATAATTTTAAAA-CATTTTTGAAAACTATATAATATATAGTTTTT--AAAAATC
*
2355103 ATTTTTGAAAAC
62 ACTTTTGAAAAC
** * *
2355115 -ATAT-A-ATATAATTTTAAAATGTTTTTGAAAACT-T-CAATATATAG--TTTGAAAA-CA-TT
1 TATATAATATATAATTTTAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAAATCACTT
*
2355171 TTGAAAAT
66 TTGAAAAC
2355179 TATATAATATAT
1 TATATAATATAT
2355191 GGTTTTGAAA
Statistics
Matches: 195, Mismatches: 13, Indels: 39
0.79 0.05 0.16
Matches are distributed among these distances:
64 9 0.05
65 6 0.03
66 5 0.03
67 4 0.02
68 3 0.02
70 9 0.05
71 15 0.08
72 66 0.34
73 28 0.14
74 32 0.16
75 8 0.04
76 10 0.05
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (73 bp):
TATATAATATATAATTTTAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAAATCACTT
TTGAAAAC
Found at i:2356102 original size:2 final size:2
Alignment explanation
Indices: 2356095--2356172 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
2356085 TCTTTAAAAC
2356095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356173 GTAAAACGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2356640 original size:4 final size:4
Alignment explanation
Indices: 2356631--2356684 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
2356621 TTTTACAATA
** * *
2356631 TATT TATT TATT T-TT TCCT GATT TATT TTTT TATT TATT T-TT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
2356677 T-TT TATT T
1 TATT TATT T
2356685 TTTCTGTCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
3 9 0.22
4 31 0.77
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.78
Consensus pattern (4 bp):
TATT
Found at i:2356685 original size:12 final size:12
Alignment explanation
Indices: 2356633--2356677 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 12
2356623 TTACAATATA
2356633 TTTATTTATTTT
1 TTTATTTATTTT
2356645 TTCCTGATTTATTTT
1 TT--T-ATTTATTTT
2356660 TTTATTTA-TTT
1 TTTATTTATTTT
2356671 TTTATTT
1 TTTATTT
2356678 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.33
12 7 0.23
13 1 0.03
14 1 0.03
15 11 0.37
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:2356686 original size:27 final size:27
Alignment explanation
Indices: 2356633--2356687 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2356623 TTACAATATA
*
2356633 TTTATTTATTTTTTCCTGATTTATTTT
1 TTTATTTATTTTTTCATGATTTATTTT
**
2356660 TTTATTTATTTTTT-ATTTTTTATTTT
1 TTTATTTATTTTTTCATGATTTATTTT
2356686 TT
1 TT
2356688 CTGTCTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (27 bp):
TTTATTTATTTTTTCATGATTTATTTT
Found at i:2357471 original size:24 final size:24
Alignment explanation
Indices: 2357443--2357494 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
2357433 AAATAAATAT
2357443 TAAATAAATCAAAGAAA-GAGAAAA
1 TAAATAAAT-AAAGAAATGAGAAAA
*
2357467 TAAATAAATAAATAAATTGAGAAAA
1 TAAATAAATAAAGAAA-TGAGAAAA
2357492 TAA
1 TAA
2357495 CAACAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 9 0.36
25 10 0.40
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (24 bp):
TAAATAAATAAAGAAATGAGAAAA
Found at i:2357583 original size:2 final size:2
Alignment explanation
Indices: 2357576--2357605 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2357566 AAAGAGTGTA
2357576 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
2357606 GAAACAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2357829 original size:40 final size:41
Alignment explanation
Indices: 2357780--2357861 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
2357770 CAAATGAATG
*
2357780 TTTTTTTCTAAACACATAGATCCTATACATATATATA-ATA
1 TTTTATTCTAAACACATAGATCCTATACATATATATATATA
* * * *
2357820 TTTTATTCTAACCCCATGGATCCTATCCATATATATATATA
1 TTTTATTCTAAACACATAGATCCTATACATATATATATATA
2357861 T
1 T
2357862 AATATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (41 bp):
TTTTATTCTAAACACATAGATCCTATACATATATATATATA
Found at i:2359615 original size:84 final size:84
Alignment explanation
Indices: 2359368--2360319 Score: 1116
Period size: 84 Copynumber: 11.4 Consensus size: 84
2359358 TGACATATAG
* * * * *
2359368 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTCGG-GCTGAGTGTAATCAAAATCGAA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCGAA
*
2359432 GGTC---T-TTGGCAGATAA
65 GGTCTTTTGTTGGAAGATAA
* * * * * *
2359448 TCCTTCTTGCCTTGAGCTATGCTGCAAATTATGGTGCCTTTGAGCTGAGTGGAATCGAACTCGAA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * *
2359513 GGTCTTTTGTTAGCAGATAG
65 GGTCTTTTGTTGGAAGATAA
* * * * ** * * * * *
2359533 CCCTTCTCGCCTTAAGCTATGATGCAAATGATATGTTTTTGAGCTAAGTGTAATCAAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
2359598 GTCTTTTGTTGGAAGATAA
66 GTCTTTTGTTGGAAGATAA
* * *
2359617 CCCTT-TTAGCCTTGAGTTATGCTGTAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAA
1 CCCTTCTT-GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
2359681 GGTCTTTTGTTGGCAA-ATAA
65 GGTCTTTTGTTGG-AAGATAA
* * *
2359701 CCCTTCTTGCCTTGAGCTATGTTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * *
2359766 GTCTTTAGGTGGCAGATAA
66 GTCTTTTGTTGGAAGATAA
* * * * * * * *
2359785 CCCTTCTAGCCTTGAGTTATGCTGAAAATAATATGCCTTTGAGTTGAGCATAGTCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
2359850 GTCTTTTGTTGGCAA-ATAA
66 GTCTTTTGTTGG-AAGATAA
* * * * * * *
2359869 CCCTTATTTCCTTGAGTTATGTTGCAAATGATGTACCTTAGAGTTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
2359934 GTCTTTTGTTGGCAA-ATAG
66 GTCTTTTGTTGG-AAGATAA
*
2359953 CCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
2360018 GTATTTTTTTGGCAA-ATAA
66 GTCTTTTGTTGG-AAGATAA
* * * *
2360037 TCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
2360102 GTGTTTTGTTGGCAGATAA
66 GTCTTTTGTTGGAAGATAA
* * * * *
2360121 TCCTTCTAGCCTTGAGTTATGCTGAAAATGATGTGCCTTGGAGCTGAGCGTTGTCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
2360186 GTCTTTTGTTGGCAGATAA
66 GTCTTTTGTTGGAAGATAA
* *
2360205 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
2360270 GTATTTTGTTGGTAA-ATAA
66 GTCTTTTGTTGG-AAGATAA
* *
2360289 CCCTTCTTGCCTTGAGCTATGTTACAAATGA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGA
2360320 ACACGATATC
Statistics
Matches: 758, Mismatches: 101, Indels: 22
0.86 0.11 0.02
Matches are distributed among these distances:
80 31 0.04
81 29 0.04
83 3 0.00
84 653 0.86
85 42 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTTGTTGGAAGATAA
Found at i:2360625 original size:124 final size:124
Alignment explanation
Indices: 2360393--2360917 Score: 764
Period size: 124 Copynumber: 4.2 Consensus size: 124
2360383 CCTTTGAAAT
* * * * *
2360393 CGTGGAGGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTCGTAAAATTGAAA
1 CGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAA
* * * *
2360458 TCCAATCTGAAGATGAATGTTGCTGGTGGGCATGATTCCCTTCTTCGTGAAGTTAAAAC
66 TCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCTTCGTGAAGTTAAAAC
* * * *
2360517 CGTTGATGGCCCATTCGTTGTGAAATTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAA
1 CGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAA
* *
2360582 TCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCTCTTCTTCGTGAAGTTGAAAC
66 TCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCTTCGTGAAGTTAAAAC
* * *
2360641 TGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTTGATATCCTTCGTCGTGAAGTTTAAA
1 CGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAA
* * * *
2360706 TCCAATCTAAAGATGATTATTACTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAAC
66 TCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCTTCGTGAAGTTAAAAC
* *
2360765 CGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAA
1 CGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAA
* ** *
2360830 TCCAATCTAAATATGAATGTTGTTGGTGAGCACGATCCCCTT-TGTCGTGAAGTTAAAAC
66 TCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCT-TCGTGAAGTTAAAAC
* *
2360889 CATGGATGACCCATTCGTTGTGAAGTTGA
1 CGTGGATGACCCCTTCGTTGTGAAGTTGA
2360918 AATCCAAGCT
Statistics
Matches: 361, Mismatches: 39, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
124 361 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (124 bp):
CGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAA
TCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCTTCGTGAAGTTAAAAC
Found at i:2363729 original size:22 final size:21
Alignment explanation
Indices: 2363689--2363729 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2363679 AAATAAAAAA
* *
2363689 TCCTACCCCACATGCTTTAAT
1 TCCTACCCAACATGATTTAAT
2363710 TCCTACCCTAACATGATTTA
1 TCCTACCC-AACATGATTTA
2363730 TATCCCACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.27, C:0.34, G:0.05, T:0.34
Consensus pattern (21 bp):
TCCTACCCAACATGATTTAAT
Found at i:2364730 original size:21 final size:20
Alignment explanation
Indices: 2364688--2364734 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
2364678 GATAAATATT
2364688 AAATAAATCAAATAAAGAGA
1 AAATAAATCAAATAAAGAGA
2364708 AAATAAAT-AAATAAATTGAGA
1 AAATAAATCAAATAAA--GAGA
2364729 AAATAA
1 AAATAA
2364735 CAACAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.28
20 8 0.32
21 10 0.40
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (20 bp):
AAATAAATCAAATAAAGAGA
Found at i:2364755 original size:24 final size:23
Alignment explanation
Indices: 2364726--2364780 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
2364716 AAATAAATTG
*
2364726 AGAAAATAACAACA-AAAAATATT
1 AGAAAATAACAAAATAAAAATA-T
*
2364749 AAGAAAAATAAGAAAATAAAAATAT
1 -AG-AAAATAACAAAATAAAAATAT
2364774 AGAAAAT
1 AGAAAAT
2364781 GTTCAGTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 4 0.15
25 11 0.41
26 7 0.26
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (23 bp):
AGAAAATAACAAAATAAAAATAT
Found at i:2364769 original size:14 final size:15
Alignment explanation
Indices: 2364752--2364780 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2364742 AAATATTAAG
2364752 AAAAATA-AGAAAAT
1 AAAAATATAGAAAAT
2364766 AAAAATATAGAAAAT
1 AAAAATATAGAAAAT
2364781 GTTCAGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAATATAGAAAAT
Found at i:2364924 original size:25 final size:25
Alignment explanation
Indices: 2364870--2364950 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
2364860 TTTTTAAAAG
*
2364870 AAAAG-AATAAAATAAAGAT-AAAATA
1 AAAAGCAATAAAA-AAA-ATAAAAATT
* *
2364895 AAAAACAA-AAAAAACATATTAAAATT
1 AAAAGCAATAAAAAA-A-ATAAAAATT
2364921 AAAAGCAATAAAAAAAATAAAAATT
1 AAAAGCAATAAAAAAAATAAAAATT
2364946 AAAAG
1 AAAAG
2364951 GATCAAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 2 0.04
25 24 0.51
26 15 0.32
27 6 0.13
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (25 bp):
AAAAGCAATAAAAAAAATAAAAATT
Done.