Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 7 of 26
Found at i:1227491 original size:6 final size:5
Alignment explanation
Indices: 1227405--1227484 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
1227395 ACCATTTACG
* * * * *
1227405 TATAA TATTAG TATAA AAT-A TAAAA TATAA TTAAAA TATAA TATTA TATAA
1 TATAA TA-TAA TATAA TATAA TATAA TATAA -TATAA TATAA TATAA TATAA
1227456 -A-AA TATAA TATTAA TATAA TATTAA TATA
1 TATAA TATAA TA-TAA TATAA TA-TAA TATA
1227485 TGAATATATT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
3 2 0.03
4 4 0.07
5 34 0.59
6 18 0.31
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:1227493 original size:40 final size:42
Alignment explanation
Indices: 1227449--1227549 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 42
1227439 AATATAATAT
1227449 TATATAAAAATATAATATTAATAT-AA-TATTAATATA-TGA-A
1 TATATAAAAAT-TAATA-TAATATGAATTATTAATATATTGATA
* * *
1227489 TATATTAAAATTTATATAATATGAATTATTGATATATTGATA
1 TATATAAAAATTAATATAATATGAATTATTAATATATTGATA
*
1227531 TAAATAAAAATTAA-ATAAT
1 TATATAAAAATTAATATAAT
1227550 TTAAATATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
38 6 0.12
39 6 0.12
40 19 0.37
41 8 0.16
42 12 0.24
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (42 bp):
TATATAAAAATTAATATAATATGAATTATTAATATATTGATA
Found at i:1227915 original size:18 final size:18
Alignment explanation
Indices: 1227887--1227932 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1227877 GTATAATATT
* *
1227887 TATAA-AAATAAAATTCA
1 TATAATAAATAAAAATAA
1227904 TATAATAAATAAAAATAA
1 TATAATAAATAAAAATAA
1227922 TATAATAAATA
1 TATAATAAATA
1227933 TTATAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TATAATAAATAAAAATAA
Found at i:1227928 original size:5 final size:5
Alignment explanation
Indices: 1227903--1227965 Score: 57
Period size: 5 Copynumber: 13.8 Consensus size: 5
1227893 AATAAAATTC
* * *
1227903 ATATA ATA-A ATA-A AAATA ATATA ATA-A ATAT- -TATA ATATA TTTTA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1227948 ATATA AT-TA ATATA ATAT
1 ATATA ATATA ATATA ATAT
1227966 TTTTAATAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
3 3 0.06
4 15 0.32
5 29 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:1227933 original size:27 final size:28
Alignment explanation
Indices: 1227903--1227964 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 28
1227893 AATAAAATTC
1227903 ATATAATAAATA-AAAATAATATAATAA
1 ATATAATAAATATAAAATAATATAATAA
* *** *
1227930 ATATTAT-AATATATTTTAATATAATTA
1 ATATAATAAATATAAAATAATATAATAA
1227957 ATATAATA
1 ATATAATA
1227965 TTTTTAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAATAAATATAAAATAATATAATAA
Found at i:1227949 original size:22 final size:22
Alignment explanation
Indices: 1227924--1227991 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
1227914 AAAAATAATA
1227924 TAATAAATATTATAATATATTT
1 TAATAAATATTATAATATATTT
*
1227946 TAATATAATTAATATAATAT-TTT
1 TAATA-AA-TATTATAATATATTT
1227969 TAATAAGTATATTAT-ATATATTT
1 TAATAA--ATATTATAATATATTT
1227992 ATTATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 10 0.26
23 18 0.46
24 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TAATAAATATTATAATATATTT
Found at i:1228016 original size:8 final size:9
Alignment explanation
Indices: 1227930--1228028 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 9
1227920 AATATAATAA
1227930 ATATTATAAT
1 ATATT-TAAT
1227940 ATATTTTAAT
1 ATA-TTTAAT
*
1227950 ATAATT-A-
1 ATATTTAAT
1227957 ATA--TAAT
1 ATATTTAAT
*
1227964 ATTTTTAAT
1 ATATTTAAT
1227973 AAGTATATTATAT
1 -A-TAT-TTA-AT
*
1227986 ATATTTATT
1 ATATTTAAT
1227995 AT-TTTAAT
1 ATATTTAAT
1228003 ATATTTAAT
1 ATATTTAAT
* *
1228012 AATTTTTATT
1 -ATATTTAAT
1228022 ATATTTA
1 ATATTTA
1228029 TATCTATACA
Statistics
Matches: 70, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
5 1 0.01
6 1 0.01
7 5 0.07
8 8 0.11
9 21 0.30
10 21 0.30
11 7 0.10
12 4 0.06
13 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
ATATTTAAT
Found at i:1228018 original size:19 final size:19
Alignment explanation
Indices: 1227960--1228028 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
1227950 ATAATTAATA
* *
1227960 TAATATTTTTAATAAGTATAT
1 TAATATATTTAATAA-T-TTT
*
1227981 TATATATATTT-ATTA-TTT
1 TA-ATATATTTAATAATTTT
1227999 TAATATATTTAATAATTTT
1 TAATATATTTAATAATTTT
*
1228018 TATTATATTTA
1 TAATATATTTA
1228029 TATCTATACA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 8 0.20
18 7 0.17
19 13 0.32
21 5 0.12
22 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TAATATATTTAATAATTTT
Found at i:1228262 original size:14 final size:14
Alignment explanation
Indices: 1228219--1228277 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
1228209 TCAATTTATA
1228219 TATTCATATTATATT
1 TATT-ATATTATATT
* *
1228234 TA-TATTTTTTATT
1 TATTATATTATATT
1228247 TATTATATTATATT
1 TATTATATTATATT
**
1228261 TAAAATATTATATT
1 TATTATATTATATT
1228275 TAT
1 TAT
1228278 ATAATTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.28
14 24 0.67
15 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:1228275 original size:28 final size:27
Alignment explanation
Indices: 1228211--1228302 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 27
1228201 GAGATATATC
*
1228211 AATTTATA--TATTCATATTATATTTAT
1 AATTTATATTTATT-ATATTATATTTAA
* *
1228237 ATTTTTTATTTATTATATTATATTTAA
1 AATTTATATTTATTATATTATATTTAA
* *
1228264 AATATTATATTTA-TATAATTTTAATTAA
1 AAT-TTATATTTATTAT-ATTATATTTAA
1228292 TAATTTATATT
1 -AATTTATATT
1228303 ATATAAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 6 0.11
27 17 0.31
28 28 0.52
29 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
AATTTATATTTATTATATTATATTTAA
Found at i:1228280 original size:22 final size:22
Alignment explanation
Indices: 1228224--1228311 Score: 58
Period size: 22 Copynumber: 4.1 Consensus size: 22
1228214 TTATATATTC
* * *
1228224 ATATTATATTTATATTTTTTAT
1 ATATTATATTTATATATTTAAA
*
1228246 TTATTATA--T-TATATTTAAA
1 ATATTATATTTATATATTTAAA
*
1228265 ATATTATATTTATATAATTTTAA
1 ATATTATATTTATAT-ATTTAAA
* * *
1228288 TTAATA-ATTTATATTATATAAA
1 ATATTATATTTATA-TATTTAAA
1228310 AT
1 AT
1228312 TAAACATAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
19 14 0.28
20 1 0.02
21 1 0.02
22 23 0.46
23 11 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTATATTTATATATTTAAA
Found at i:1228314 original size:27 final size:28
Alignment explanation
Indices: 1228260--1228314 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1228250 TATATTATAT
**
1228260 TTAAAATATTATATTTATATAATTTTAA
1 TTAAAATATTATATTTATATAAAATTAA
1228288 TTAATAAT-TTATA-TTATATAAAATTAA
1 TTAA-AATATTATATTTATATAAAATTAA
1228315 ACATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 9 0.38
29 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAAAATATTATATTTATATAAAATTAA
Found at i:1228416 original size:24 final size:23
Alignment explanation
Indices: 1228383--1228427 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1228373 ATTTTTATTT
* *
1228383 AACATTTAAATTTATCAAATTAAA
1 AACATATAAATATAT-AAATTAAA
1228407 AACATATAAATATATAAATTA
1 AACATATAAATATATAAATTA
1228428 TTAACCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (23 bp):
AACATATAAATATATAAATTAAA
Found at i:1231987 original size:39 final size:39
Alignment explanation
Indices: 1231914--1231992 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
1231904 AATTGATTTG
* *
1231914 AAAATTTATTTTATTATTCAAAATAATATTAAAAAAATT
1 AAAATTTATTTTATAATTCAAAATAATATAAAAAAAATT
* *
1231953 AAAATTTATATTTATAATT-AAATTTAA-ATAAAAAATATT
1 AAAATTTAT-TTTATAATTCAAA-ATAATATAAAAAAAATT
1231992 A
1 A
1231993 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
39 23 0.68
40 11 0.32
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (39 bp):
AAAATTTATTTTATAATTCAAAATAATATAAAAAAAATT
Found at i:1236235 original size:15 final size:15
Alignment explanation
Indices: 1236217--1236246 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1236207 ACGTATATTC
1236217 TAAAAATAATAATTT
1 TAAAAATAATAATTT
1236232 TAAAAATAATAATTT
1 TAAAAATAATAATTT
1236247 ATAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAAATAATAATTT
Found at i:1237948 original size:11 final size:11
Alignment explanation
Indices: 1237917--1237993 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
1237907 AAAAATTTTG
1237917 TATAAAATAAA
1 TATAAAATAAA
1237928 TTATTAAAATAAA
1 -TA-TAAAATAAA
*
1237941 TATAAAATATA
1 TATAAAATAAA
***
1237952 -ATAAAATTTT
1 TATAAAATAAA
1237962 TATAAAATAAA
1 TATAAAATAAA
* *
1237973 TATAATATAAT
1 TATAAAATAAA
1237984 TATATAAATA
1 TATA-AAATA
1237994 CATTAATAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
10 8 0.15
11 28 0.53
12 8 0.15
13 9 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAAATAAA
Found at i:1237969 original size:45 final size:45
Alignment explanation
Indices: 1237908--1238024 Score: 130
Period size: 45 Copynumber: 2.6 Consensus size: 45
1237898 ACCGTACTTA
*
1237908 AAAATTTTGTATAAAATAAATTATTAAAATAAATATA-AAATATAAT
1 AAAATTTT-TATAAAATAAA-TATTAAAATAAATATATAAATACAAT
* * *
1237954 AAAATTTTTATAAAATAAATA-TAATATAATTATATAAATACATT
1 AAAATTTTTATAAAATAAATATTAAAATAAATATATAAATACAAT
* *
1237998 AATAATTTATATAATATAAAATATTAA
1 AA-AATTTTTATAAAAT-AAATATTAA
1238025 TATATTAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
43 11 0.18
44 11 0.18
45 23 0.38
46 13 0.21
47 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (45 bp):
AAAATTTTTATAAAATAAATATTAAAATAAATATATAAATACAAT
Found at i:1238013 original size:34 final size:33
Alignment explanation
Indices: 1237972--1238052 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
1237962 TATAAAATAA
1237972 ATATAATATAATTATATAAATACATTAATAATTT
1 ATATAATATAATTATATAAATACATTAA-AATTT
* * *
1238006 ATATAATATAA-AATATTAATATATTAAAATTT
1 ATATAATATAATTATATAAATACATTAAAATTT
1238038 ATAT-ATAT-ATTATAT
1 ATATAATATAATTATAT
1238053 TTTAAATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 8 0.19
32 9 0.21
33 13 0.31
34 11 0.26
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAATTATATAAATACATTAAAATTT
Found at i:1238040 original size:25 final size:25
Alignment explanation
Indices: 1237946--1238058 Score: 63
Period size: 25 Copynumber: 4.4 Consensus size: 25
1237936 ATAAATATAA
*
1237946 AATATAATAAAATTTTTATAAAATA--
1 AATATATTAAAA--TTTATAAAATATT
* * *
1237971 AATATAATATAATTATATAAATACATT
1 AATATATTAAAATT-TATAAA-ATATT
* * *
1237998 AATA-ATTTATATAATATAAAATATT
1 AATATATTAAAAT-TTATAAAATATT
*
1238023 AATATATTAAAATTTATATATATATT
1 AATATATTAAAATTTATA-AAATATT
*
1238049 -ATATTTTAAA
1 AATATATTAAA
1238059 TATAATTATC
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
23 2 0.03
24 6 0.09
25 34 0.50
26 22 0.32
27 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATATTAAAATTTATAAAATATT
Found at i:1238045 original size:18 final size:18
Alignment explanation
Indices: 1237981--1238049 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 18
1237971 AATATAATAT
* *
1237981 AATTATATAAATACATTAA
1 AATT-TATATATATATTAA
1238000 TAATTTATATA-ATA-TAA
1 -AATTTATATATATATTAA
*
1238017 AATAT-TA-ATATATTAA
1 AATTTATATATATATTAA
1238033 AATTTATATATATATTA
1 AATTTATATATATATTA
1238050 TATTTTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.02
15 5 0.12
16 11 0.27
17 5 0.12
18 10 0.24
19 5 0.12
20 4 0.10
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTATATATATATTAA
Found at i:1238056 original size:18 final size:18
Alignment explanation
Indices: 1238024--1238067 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1238014 TAAAATATTA
* *
1238024 ATATATTAAAATTTATAT
1 ATATATTATAATTTAAAT
*
1238042 ATATATTATATTTTAAAT
1 ATATATTATAATTTAAAT
1238060 ATA-ATTAT
1 ATATATTAT
1238068 CACACATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATATTATAATTTAAAT
Found at i:1238061 original size:16 final size:17
Alignment explanation
Indices: 1237968--1238100 Score: 51
Period size: 19 Copynumber: 7.5 Consensus size: 17
1237958 TTTTTATAAA
*
1237968 ATAAATATAATATAATTAT
1 ATAAATATATTAT-ATT-T
*
1237987 ATAAATACATTAATAATTT
1 ATAAATATATT-AT-ATTT
*
1238006 ATATAATATA--A-A-AT
1 ATA-AATATATTATATTT
* *
1238020 ATTAATATATTAAAATTT
1 ATAAATATATT-ATATTT
*
1238038 ATATATATATTATATTT
1 ATAAATATATTATATTT
***
1238055 -TAAATATAATTATCACAC
1 ATAAATAT-ATTAT-ATTT
1238073 ATAAAATATATTAATTATTT
1 AT-AAATATATT-A-TATTT
1238093 ATAAATAT
1 ATAAATAT
1238101 TCTTTTTAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
13 6 0.07
14 3 0.04
15 1 0.01
16 7 0.08
17 12 0.14
18 11 0.13
19 23 0.27
20 21 0.25
21 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATATATTATATTT
Found at i:1239147 original size:25 final size:25
Alignment explanation
Indices: 1239117--1239179 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1239107 AAATGTATTA
**
1239117 AAAATAATAATTTT-TTTTTAAATT
1 AAAATAATAATTTTATAATTAAATT
* *
1239141 AATAATATTTATTTTATAATTAAATT
1 AA-AATAATAATTTTATAATTAAATT
*
1239167 TAAATAATAATTT
1 AAAATAATAATTT
1239180 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 2 0.07
25 19 0.63
26 9 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AAAATAATAATTTTATAATTAAATT
Found at i:1239155 original size:21 final size:22
Alignment explanation
Indices: 1239119--1239163 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1239109 ATGTATTAAA
*
1239119 AATAATAATTT-TTTTTTAAATT
1 AATAATAATTTATTTTAT-AATT
1239141 AATAAT-ATTTATTTTATAATT
1 AATAATAATTTATTTTATAATT
1239162 AA
1 AA
1239164 ATTTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATAATAATTTATTTTATAATT
Found at i:1240012 original size:14 final size:14
Alignment explanation
Indices: 1239995--1240056 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
1239985 ATAATTCGAT
1239995 TAATATAATAAATA
1 TAATATAATAAATA
* *
1240009 TAATATAATATATT
1 TAATATAATAAATA
1240023 TAAATATAATTAAA-A
1 T-AATATAA-TAAATA
*
1240038 TAATAT-AT-AATT
1 TAATATAATAAATA
1240050 TAATATA
1 TAATATA
1240057 TATTATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.05
12 7 0.18
13 1 0.03
14 18 0.46
15 8 0.21
16 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATATAATAAATA
Found at i:1240013 original size:5 final size:5
Alignment explanation
Indices: 1239995--1240044 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
1239985 ATAATTCGAT
* *
1239995 TAATA TAATA -AATA TAATA TAATA T-ATT TAAATA TAAT- TAAAA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA T-AATA TAATA TAATA TAATA
1240043 TA
1 TA
1240045 TAATTTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 10 0.27
5 24 0.65
6 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:1240152 original size:23 final size:22
Alignment explanation
Indices: 1240091--1240167 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 22
1240081 TAATTTATAT
*
1240091 TATATTTATA-ATTAATAAAAAA
1 TATATTTATATATTAAT-ATAAA
1240113 TATAATTTATATA--AATATAAA
1 TAT-ATTTATATATTAATATAAA
1240134 TATATTTATATATTTAATAGTAATA
1 TATATTTATATA-TTAATA-TAA-A
*
1240159 TATAATTAT
1 TATATTTAT
1240168 GATTAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 9 0.20
21 7 0.15
22 6 0.13
23 11 0.24
24 4 0.09
25 9 0.20
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
TATATTTATATATTAATATAAA
Found at i:1240205 original size:18 final size:17
Alignment explanation
Indices: 1240182--1240242 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
1240172 AAAATATTAT
1240182 TATTTATATACATTTTAA
1 TATTTATATA-ATTTTAA
*
1240200 TATTTAAATAA-TTT-A
1 TATTTATATAATTTTAA
1240215 TA-TTATATAAATTTTAAA
1 TATTTATAT-AATTTT-AA
*
1240233 TATTTGTATA
1 TATTTATATA
1240243 TTTAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 5 0.14
15 5 0.14
16 6 0.17
17 1 0.03
18 13 0.37
19 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TATTTATATAATTTTAA
Found at i:1240777 original size:23 final size:23
Alignment explanation
Indices: 1240732--1240777 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1240722 TATATTAATA
* *
1240732 AAATAAATTATTAATTTATATTT
1 AAATAAATTATTAATATAAATTT
*
1240755 AAATAAATTTTTAATATAAATTT
1 AAATAAATTATTAATATAAATTT
1240778 CTATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATAAATTATTAATATAAATTT
Found at i:1241621 original size:3 final size:3
Alignment explanation
Indices: 1241615--1241643 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1241605 TTTAATGTTG
1241615 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1241644 TTTGCCGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1242122 original size:21 final size:22
Alignment explanation
Indices: 1242098--1242156 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1242088 CATTTAAGTC
* *
1242098 AAATTAATTAAAATTGAT-CAA
1 AAATTAATAAAAATTGATAAAA
*
1242119 AAATT-ATCATAAATTGATAAAAA
1 AAATTAAT-AAAAATTGAT-AAAA
1242142 AAATTAATAAAAATT
1 AAATTAATAAAAATT
1242157 TAATGTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 13 0.43
23 13 0.43
24 2 0.07
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (22 bp):
AAATTAATAAAAATTGATAAAA
Found at i:1242689 original size:36 final size:36
Alignment explanation
Indices: 1242637--1242710 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
1242627 ATCGATTAAA
*
1242637 TTAAACAATGCCATGGCTCTCTTCATCCCGTCCGCT
1 TTAAACAATGCCATGGCTCTCTTCATCCAGTCCGCT
*
1242673 TTAATCAATGCCATGGCTCTCTTCATCCAGTCCGCT
1 TTAAACAATGCCATGGCTCTCTTCATCCAGTCCGCT
1242709 TT
1 TT
1242711 TTCTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.34
Consensus pattern (36 bp):
TTAAACAATGCCATGGCTCTCTTCATCCAGTCCGCT
Found at i:1242830 original size:2 final size:2
Alignment explanation
Indices: 1242823--1242853 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1242813 ACCACCTTTT
1242823 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 T
1242854 TTGCAACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1243025 original size:19 final size:19
Alignment explanation
Indices: 1242981--1243025 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1242971 TATGAAATAT
* *
1242981 AATATTTTAAATATATAAA
1 AATATTTTAAAAAAATAAA
*
1243000 AAAATTTTAAAAAAATAAA
1 AATATTTTAAAAAAATAAA
*
1243019 TATATTT
1 AATATTT
1243026 ATATTAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTTTAAAAAAATAAA
Found at i:1243318 original size:2 final size:2
Alignment explanation
Indices: 1243313--1243340 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1243303 TTAGCCAATA
1243313 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
1243341 TGAATGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1245599 original size:20 final size:20
Alignment explanation
Indices: 1245558--1245615 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1245548 CAATTTGTTT
* **
1245558 ATATAATTATTTTAAATTTA
1 ATATATTTATTTTAAAAATA
* *
1245578 ATTTTTTTATTTTAAAAATA
1 ATATATTTATTTTAAAAATA
*
1245598 ATATATATATTTTAAAAA
1 ATATATTTATTTTAAAAA
1245616 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTTATTTTAAAAATA
Found at i:1250874 original size:21 final size:21
Alignment explanation
Indices: 1250850--1250899 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1250840 AATTTAATTA
1250850 TAATAATA-TATAATAATATTT
1 TAATAATATTATAAT-ATATTT
*
1250871 TAAT-ATATTTTAATATATTT
1 TAATAATATTATAATATATTT
1250891 TAAATAATA
1 T-AATAATA
1250900 AAATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 10 0.40
21 12 0.48
22 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATAATATTATAATATATTT
Found at i:1250878 original size:10 final size:10
Alignment explanation
Indices: 1250860--1250893 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
1250850 TAATAATATA
1250860 TAATAATATTT
1 TAAT-ATATTT
1250871 TAATATATTT
1 TAATATATTT
1250881 TAATATATTT
1 TAATATATTT
1250891 TAA
1 TAA
1250894 ATAATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TAATATATTT
Found at i:1251632 original size:11 final size:11
Alignment explanation
Indices: 1251583--1251634 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
1251573 CCAACTAATT
*
1251583 TATAAATATGA
1 TATAAATATAA
* *
1251594 TAAAAATTTAA
1 TATAAATATAA
1251605 TATAAA-A-AA
1 TATAAATATAA
*
1251614 TATGAATATAA
1 TATAAATATAA
1251625 TATAAATATA
1 TATAAATATA
1251635 TAAATATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 7 0.22
10 1 0.03
11 24 0.75
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
TATAAATATAA
Found at i:1251647 original size:17 final size:19
Alignment explanation
Indices: 1251583--1251662 Score: 58
Period size: 19 Copynumber: 4.1 Consensus size: 19
1251573 CCAACTAATT
*
1251583 TATAAATATGATAAAAATTTAA
1 TATAAATAT-AT--AAATATAA
* *
1251605 TATAAAAAATATGAATATAA
1 TAT-AAATATATAAATATAA
1251625 TATAAATATATAAATAT-A
1 TATAAATATATAAATATAA
*
1251643 T-TAAATA-ATTAATATTAA
1 TATAAATATATAAATA-TAA
1251661 TA
1 TA
1251663 CATTAACAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.12
17 7 0.15
18 4 0.08
19 12 0.25
20 9 0.19
22 5 0.10
23 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATAAATATATAAATATAA
Found at i:1251654 original size:8 final size:9
Alignment explanation
Indices: 1251602--1251651 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
1251592 GATAAAAATT
1251602 TAATATAAA
1 TAATATAAA
*
1251611 AAATATGAATA
1 TAATAT-AA-A
1251622 TAATATAAA
1 TAATATAAA
1251631 T-ATATAAA
1 TAATATAAA
1251639 T-ATATTAAA
1 TAATA-TAAA
1251648 TAAT
1 TAAT
1251652 TAATATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 11 0.31
9 12 0.34
10 6 0.17
11 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (9 bp):
TAATATAAA
Found at i:1251716 original size:24 final size:23
Alignment explanation
Indices: 1251689--1251736 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1251679 TTTTAAAAAA
1251689 TTTAA-TACATATTTTATTTATATT
1 TTTAATTA-ATATTTTA-TTATATT
*
1251713 TTTAATTAATTTTTTATTATATT
1 TTTAATTAATATTTTATTATATT
1251736 T
1 T
1251737 AAAATATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 12 0.55
25 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATTAATATTTTATTATATT
Found at i:1252612 original size:2 final size:2
Alignment explanation
Indices: 1252607--1252631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1252597 TTTATAAGTT
1252607 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
1252632 TAAAGTTTTG
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:1256973 original size:16 final size:16
Alignment explanation
Indices: 1256954--1257014 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
1256944 AAATAATTAA
1256954 AATATAATATAAATAT
1 AATATAATATAAATAT
*
1256970 AATATTATATAAATAT
1 AATATAATATAAATAT
* * * *
1256986 GATAGATTAAAAAT-T
1 AATATAATATAAATAT
*
1257001 TATATAATATAAAT
1 AATATAATATAAAT
1257015 TATTAATGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 11 0.31
16 24 0.69
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AATATAATATAAATAT
Found at i:1257090 original size:11 final size:11
Alignment explanation
Indices: 1257062--1257096 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1257052 TTAAATAATT
1257062 TATGATAAAAA
1 TATGATAAAAA
*
1257073 -ATAATAAAAA
1 TATGATAAAAA
1257083 TATGATAAAAA
1 TATGATAAAAA
1257094 TAT
1 TAT
1257097 ATATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (11 bp):
TATGATAAAAA
Found at i:1257199 original size:40 final size:40
Alignment explanation
Indices: 1257126--1257205 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
1257116 CTCATACAGG
** *
1257126 ATATAAATATAAAAATATAATTATTTAAATATATATATAT
1 ATATAAATATAAAAATATAAAAAATTAAATATATATATAT
* * * *
1257166 ATATAAATATTAAAATTTAAAAAATTAAGTATATTTATAT
1 ATATAAATATAAAAATATAAAAAATTAAATATATATATAT
1257206 TAAACACTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (40 bp):
ATATAAATATAAAAATATAAAAAATTAAATATATATATAT
Found at i:1262659 original size:26 final size:23
Alignment explanation
Indices: 1262625--1262686 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
1262615 GTAATATAAA
1262625 TTATTATATATTTTAAATTAATAATT
1 TTATTATAT-TTTTAAATT--TAATT
** *
1262651 TTATTATATTTAAAAATTTTATT
1 TTATTATATTTTTAAATTTAATT
1262674 TTATTATATTTTT
1 TTATTATATTTTT
1262687 TATTTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 15 0.48
25 7 0.23
26 9 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATTATATTTTTAAATTTAATT
Found at i:1262668 original size:18 final size:18
Alignment explanation
Indices: 1262642--1262678 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1262632 ATATTTTAAA
*
1262642 TTAATAATTTTATTATAT
1 TTAAAAATTTTATTATAT
*
1262660 TTAAAAATTTTATTTTAT
1 TTAAAAATTTTATTATAT
1262678 T
1 T
1262679 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAAAATTTTATTATAT
Found at i:1262692 original size:16 final size:17
Alignment explanation
Indices: 1262667--1262700 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1262657 TATTTAAAAA
*
1262667 TTTTATTTTATTATATT
1 TTTTATTTTATTAAATT
1262684 TTTTA-TTTATTAAATT
1 TTTTATTTTATTAAATT
1262700 T
1 T
1262701 ATCATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTTATTAAATT
Found at i:1262792 original size:58 final size:58
Alignment explanation
Indices: 1262728--1262838 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
1262718 TTTCATATTT
* *
1262728 AAAATTAA-TAAATTTATATTTATATTA-TATTATTAT-AAAAATGATTAAATTTAATATC
1 AAAATTAAGTAAATTTA-ATTT-TATTATTAAT-TTATAAAAAATAATTAAATTTAATATC
* *
1262786 AAAATTAAGTAATTTTAATTTTATTGTTAATTTATAAAAAATAATTAAATTTA
1 AAAATTAAGTAAATTTAATTTTATTATTAATTTATAAAAAATAATTAAATTTA
1262839 TAATATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 8 0.17
58 31 0.67
59 7 0.15
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (58 bp):
AAAATTAAGTAAATTTAATTTTATTATTAATTTATAAAAAATAATTAAATTTAATATC
Found at i:1263443 original size:35 final size:36
Alignment explanation
Indices: 1263404--1263472 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
1263394 ATTTATTTTT
* *
1263404 ATTAAATATGTAATA-TTATT-TAAATTTAAATTTCA
1 ATTAAATA-ATAATATTTATTAAAAATTTAAATTTCA
*
1263439 ATTAAATAATATTATTTATTAAAAATTTAAATTT
1 ATTAAATAATAATATTTATTAAAAATTTAAATTT
1263473 ATAAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.14
35 13 0.45
36 12 0.41
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTAAATAATAATATTTATTAAAAATTTAAATTTCA
Found at i:1263472 original size:17 final size:17
Alignment explanation
Indices: 1263425--1263488 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
1263415 AATATTATTT
1263425 AAATTTAAATTTCAATTAA
1 AAATTTAAATTT--ATTAA
1263444 ATAATATT--ATTTATTAA
1 A-AAT-TTAAATTTATTAA
1263461 AAATTTAAATTTA-TAA
1 AAATTTAAATTTATTAA
1263477 AATATTTAAATT
1 AA-ATTTAAATT
1263489 CAATAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
16 8 0.20
17 20 0.50
19 5 0.12
20 3 0.08
21 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTTAAATTTATTAA
Found at i:1263538 original size:26 final size:23
Alignment explanation
Indices: 1263491--1263552 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 23
1263481 TTTAAATTCA
1263491 ATAAATAAAATTTAAATTTTTACT
1 ATAAATAAAATTTAAATTTTTA-T
*
1263515 -TAAATATAAATTTTTAATATTTTAT
1 ATAAATA-AAA-TTTAAAT-TTTTAT
1263540 ATAAAT-AAATTTA
1 ATAAATAAAATTTA
1263553 TTACCTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
23 9 0.28
24 6 0.19
25 7 0.22
26 10 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAATAAAATTTAAATTTTTAT
Found at i:1270663 original size:20 final size:21
Alignment explanation
Indices: 1270613--1270665 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1270603 TGTCATAATT
* *
1270613 TATATACATATATAATATATTA
1 TATATAAAT-TATAATATATAA
*
1270635 AATAT-AATTATAATATA-AA
1 TATATAAATTATAATATATAA
1270654 TATATAAATTAT
1 TATATAAATTAT
1270666 GAAGTTGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.19
20 15 0.58
21 2 0.08
22 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAAATTATAATATATAA
Found at i:1270690 original size:2 final size:2
Alignment explanation
Indices: 1270685--1270714 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1270675 TTTTTTCGCT
1270685 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1270715 TTCAGCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1271366 original size:20 final size:18
Alignment explanation
Indices: 1271343--1271381 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1271333 GTATATTAAA
*
1271343 ATATTTTTACATTAATATTT
1 ATATATTTA-ATTAA-ATTT
1271363 ATATATTTAATTAAATTT
1 ATATATTTAATTAAATTT
1271381 A
1 A
1271382 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATATTTAATTAAATTT
Found at i:1271972 original size:29 final size:29
Alignment explanation
Indices: 1271939--1271996 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1271929 TAAACGAGCA
*
1271939 TTAAATAATTTTTTAT-ATATTAATTATAT
1 TTAAAT-ATATTTTATCATATTAATTATAT
*
1271968 TTAAATATATTTTATCATATTTATTATAT
1 TTAAATATATTTTATCATATTAATTATAT
1271997 AATTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TTAAATATATTTTATCATATTAATTATAT
Found at i:1271987 original size:20 final size:19
Alignment explanation
Indices: 1271962--1272026 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
1271952 TATATATTAA
1271962 TTATATTTA-AATATATTT
1 TTATATTTATAATATATTT
*
1271980 TATCATATTTATTATATAATTT
1 T-T-ATATTTATAATAT-ATTT
*
1272002 TTATATTTATATTATATTT
1 TTATATTTATAATATATTT
1272021 TTATAT
1 TTATAT
1272027 CATACTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.28
20 18 0.45
21 5 0.12
22 5 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATATTTATAATATATTT
Found at i:1272019 original size:11 final size:11
Alignment explanation
Indices: 1271951--1272020 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 11
1271941 AAATAATTTT
1271951 TTATATATTA-A
1 TTATAT-TTATA
1271962 TTATATTTA-A
1 TTATATTTATA
*
1271972 ATATATTT-TA
1 TTATATTTATA
*
1271982 TCATATTTAT-
1 TTATATTTATA
*
1271992 TATATAATT-T-
1 T-TATATTTATA
1272002 TTATATTTATA
1 TTATATTTATA
1272013 TTATATTT
1 TTATATTT
1272021 TTATATCATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 6 0.12
10 22 0.46
11 20 0.42
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1273195 original size:18 final size:18
Alignment explanation
Indices: 1273140--1273196 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
1273130 CTTAATTTAT
*
1273140 AAATTTATTTTATAAATTAA
1 AAATATATTTTAT-AATT-A
*
1273160 AAATATATTTTAT-TTTA
1 AAATATATTTTATAATTA
*
1273177 ATATATATTTTATAATTA
1 AAATATATTTTATAATTA
1273195 AA
1 AA
1273197 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 13 0.42
18 6 0.19
20 12 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATATATTTTATAATTA
Found at i:1273205 original size:14 final size:13
Alignment explanation
Indices: 1273183--1273239 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
1273173 TTTAATATAT
*
1273183 ATTTTATAATTAA
1 ATTTAATAATTAA
*
1273196 ATTTAAATAAAATAA
1 ATTT-AAT-AATTAA
*
1273211 A-TTAATATTTAA
1 ATTTAATAATTAA
1273223 TATTTAATAATTAA
1 -ATTTAATAATTAA
1273237 ATT
1 ATT
1273240 AACTTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.11
13 11 0.31
14 14 0.40
15 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAATAATTAA
Found at i:1273246 original size:10 final size:10
Alignment explanation
Indices: 1273233--1273260 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1273223 TATTTAATAA
1273233 TTAAATTAAC
1 TTAAATTAAC
1273243 TTAAATTAAC
1 TTAAATTAAC
1273253 TTAAATTA
1 TTAAATTA
1273261 TTAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAAATTAAC
Found at i:1273598 original size:18 final size:17
Alignment explanation
Indices: 1273564--1273601 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1273554 GATTATTATT
*
1273564 ATTATTTTTAATTTTAA
1 ATTAATTTTAATTTTAA
1273581 ATTAATTTTAATTATTAA
1 ATTAATTTTAATT-TTAA
1273599 ATT
1 ATT
1273602 TAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTAATTTTAATTTTAA
Found at i:1273752 original size:19 final size:17
Alignment explanation
Indices: 1273725--1273766 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
1273715 TTTTTATTTT
1273725 AAATAAAATTTGAATTTAA
1 AAATAAAATTT-AA-TTAA
*
1273744 AAATTAAATTTAATTAA
1 AAATAAAATTTAATTAA
1273761 AAATAA
1 AAATAA
1273767 TATATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 2 0.10
19 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATAAAATTTAATTAA
Found at i:1274480 original size:19 final size:20
Alignment explanation
Indices: 1274458--1274507 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1274448 ATATATTGTA
*
1274458 TTTATATATTTTAT-TATAT
1 TTTATATATTTTATATAAAT
1274477 TTTA-ATTATATTTATATAAAT
1 TTTATA-TAT-TTTATATAAAT
*
1274498 TTAATATATT
1 TTTATATATT
1274508 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 1 0.04
19 7 0.28
20 6 0.24
21 10 0.40
22 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATATTTTATATAAAT
Found at i:1274531 original size:6 final size:6
Alignment explanation
Indices: 1274520--1274557 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1274510 AAATTTTAAA
*
1274520 ATATTT ATATTT ATATTT TTATGTT ATATTT A-ATTT AT
1 ATATTT ATATTT ATATTT ATAT-TT ATATTT ATATTT AT
1274558 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:1274857 original size:20 final size:20
Alignment explanation
Indices: 1274788--1274857 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1274778 TACATAAGAT
1274788 ATAAA-ATACAAAATATTTA
1 ATAAATATACAAAATATTTA
* *
1274807 ATAAATTTA-AAAATAATATA
1 ATAAATATACAAAAT-ATTTA
*
1274827 ATAAACTTATACAATATATTTA
1 ATAAA--TATACAAAATATTTA
1274849 ATAAATATA
1 ATAAATATA
1274858 TCATACTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.24
20 15 0.37
22 12 0.29
23 4 0.10
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATATACAAAATATTTA
Found at i:1275349 original size:21 final size:21
Alignment explanation
Indices: 1275325--1275366 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1275315 TATTTATCAT
*
1275325 TATTATTATT-ATATTCTTTTA
1 TATTAATATTAATA-TCTTTTA
1275346 TATTAATATTAATATCTTTTA
1 TATTAATATTAATATCTTTTA
1275367 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTAATATTAATATCTTTTA
Found at i:1275583 original size:17 final size:15
Alignment explanation
Indices: 1275563--1275601 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
1275553 AATAATACTC
1275563 ATTTTAATTATATATA
1 ATTTTAATTA-ATATA
1275579 TATTTTAAATTAATATA
1 -ATTTT-AATTAATATA
1275596 ATTTTA
1 ATTTTA
1275602 TTTGTGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 5 0.24
17 10 0.48
18 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTAATTAATATA
Found at i:1276191 original size:2 final size:2
Alignment explanation
Indices: 1276186--1276212 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1276176 GAGAAAAAAA
1276186 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1276213 AAATAAGAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1284059 original size:17 final size:16
Alignment explanation
Indices: 1284028--1284070 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
1284018 ATTCATTTTG
*
1284028 ATTTAAATTATTATTT
1 ATTTAAATAATTATTT
1284044 ATTTAATATAATTATTTTT
1 ATTTAA-ATAATTA--TTT
1284063 ATTTAAAT
1 ATTTAAAT
1284071 TTAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 6 0.26
17 6 0.26
18 2 0.09
19 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTAAATAATTATTT
Found at i:1284075 original size:20 final size:20
Alignment explanation
Indices: 1284028--1284076 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
1284018 ATTCATTTTG
1284028 ATTTAAATTATTATTTATTTA
1 ATTT-AATTATTATTTATTTA
*
1284049 ATATAATTATT-TTTATTTAA
1 ATTTAATTATTATTTATTT-A
1284069 ATTTAATT
1 ATTTAATT
1284077 TATAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 15 0.60
21 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATTATTATTTATTTA
Found at i:1284689 original size:2 final size:2
Alignment explanation
Indices: 1284684--1284722 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1284674 AATCATATGA
1284684 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
1284723 ATCAAAGGAA
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:1288504 original size:5 final size:5
Alignment explanation
Indices: 1288494--1288556 Score: 63
Period size: 5 Copynumber: 11.4 Consensus size: 5
1288484 AAATTTATAG
1288494 TATTT TATTT TATTAAAT TATTAT TATTAT TATTT TATTT TATTT TAATTT
1 TATTT TATTT TATT---T TATT-T TATT-T TATTT TATTT TATTT T-ATTT
*
1288545 TATTT CATTT TA
1 TATTT TATTT TA
1288557 ATAAACTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
5 30 0.58
6 17 0.33
8 5 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:1288544 original size:16 final size:16
Alignment explanation
Indices: 1288495--1288558 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1288485 AATTTATAGT
1288495 ATTTTATTTTA--TTA
1 ATTTTATTTTATTTTA
*
1288509 A-ATTATTATTATTATT-
1 ATTTTATT-TTATT-TTA
1288525 ATTTTATTTTATTTTA
1 ATTTTATTTTATTTTA
*
1288541 ATTTTATTTCATTTTA
1 ATTTTATTTTATTTTA
1288557 AT
1 AT
1288559 AAACTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
13 5 0.12
14 4 0.10
15 2 0.05
16 23 0.56
17 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTATTTTATTTTA
Found at i:1289769 original size:19 final size:18
Alignment explanation
Indices: 1289728--1289769 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1289718 ATAGCATAAT
1289728 ATAATA-TATAAAAATTA
1 ATAATATTATAAAAATTA
*
1289745 AT-ATATTATAATAAATTG
1 ATAATATTATAA-AAATTA
1289763 ATAATAT
1 ATAATAT
1289770 AATTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 7 0.33
19 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATATTATAAAAATTA
Found at i:1289792 original size:8 final size:8
Alignment explanation
Indices: 1289779--1289824 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1289769 TAATTAAATT
1289779 TATATAAA
1 TATATAAA
1289787 TATAT-AA
1 TATATAAA
1289794 TAT-TAAAA
1 TATAT-AAA
1289802 TATATAAA
1 TATATAAA
1289810 TATAATAAA
1 TAT-ATAAA
*
1289819 AATATA
1 TATATA
1289825 TTTATAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
6 1 0.03
7 5 0.15
8 19 0.58
9 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TATATAAA
Found at i:1289793 original size:27 final size:29
Alignment explanation
Indices: 1289726--1289796 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 29
1289716 ATATAGCATA
1289726 ATAT-AATATATAA-A-AATTAATATATT
1 ATATAAATATATAATATAATTAATATATT
1289752 ATAATAAAT-TGATAATATAATTAA-AT-TT
1 AT-ATAAATAT-ATAATATAATTAATATATT
1289780 ATATAAATATATAATAT
1 ATATAAATATATAATAT
1289797 TAAAATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
26 2 0.05
27 16 0.41
28 12 0.31
29 3 0.08
30 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
ATATAAATATATAATATAATTAATATATT
Found at i:1289812 original size:21 final size:21
Alignment explanation
Indices: 1289779--1289825 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 21
1289769 TAATTAAATT
1289779 TATATAAATATATAATATTAAAA
1 TATATAAATATATAATA--AAAA
1289802 TATAT-AA-ATATAATAAAAA
1 TATATAAATATATAATAAAAA
1289821 TATAT
1 TATAT
1289826 TTATAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.38
21 8 0.33
22 2 0.08
23 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAAA
Found at i:1289822 original size:19 final size:20
Alignment explanation
Indices: 1289765--1289825 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
1289755 ATAAATTGAT
**
1289765 AATATAATTAAATTTATATAA
1 AATATAA-TAAAAATATATAA
1289786 ATATATAATATTAAAATATAT-A
1 A-ATATAATA--AAAATATATAA
1289808 AATATAATAAAAATATAT
1 AATATAATAAAAATATAT
1289826 TTATAGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 9 0.26
21 11 0.31
22 8 0.23
23 7 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAATAAAAATATATAA
Found at i:1300948 original size:3 final size:3
Alignment explanation
Indices: 1300940--1300976 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1300930 TGATATTCAG
1300940 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1300977 GATTGTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1307300 original size:22 final size:22
Alignment explanation
Indices: 1307274--1307342 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1307264 TTTTATCATC
1307274 AATAAGATTTATTTAATTTATA
1 AATAAGATTTATTTAATTTATA
*
1307296 AATAA-AATT-TTTAATTCCGT-TA
1 AATAAGATTTATTTAATT---TATA
*
1307318 AAT-AGATTTATTTAA-TCATA
1 AATAAGATTTATTTAATTTATA
1307338 AATAA
1 AATAA
1307343 AAATAGTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 15
0.67 0.05 0.27
Matches are distributed among these distances:
20 12 0.32
21 5 0.14
22 14 0.38
23 6 0.16
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
AATAAGATTTATTTAATTTATA
Found at i:1307985 original size:2 final size:2
Alignment explanation
Indices: 1307978--1308002 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1307968 ATCGTTATCT
1307978 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
1308003 TTAATTATAG
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:1312587 original size:3 final size:3
Alignment explanation
Indices: 1312579--1312609 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1312569 CAAGGCTTTC
1312579 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1312610 ATAAAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1313881 original size:11 final size:13
Alignment explanation
Indices: 1313852--1313886 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1313842 CTCAAAAATA
1313852 TATTTATATATAT
1 TATTTATATATAT
1313865 TATTTATAT-TAT
1 TATTTATATATAT
1313877 T-TTTATATAT
1 TATTTATATAT
1313887 TATAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 5 0.24
13 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTATATATAT
Found at i:1313883 original size:22 final size:23
Alignment explanation
Indices: 1313852--1313898 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
1313842 CTCAAAAATA
1313852 TATTTATATATATTAT-TTATAT
1 TATTTATATATATTATATTATAT
*
1313874 TATTTTTATATATTATAATTATAT
1 TATTTATATATATTAT-ATTATAT
1313898 T
1 T
1313899 TAAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
24 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTATATATATTATATTATAT
Found at i:1313916 original size:21 final size:22
Alignment explanation
Indices: 1313850--1313959 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 22
1313840 CTCTCAAAAA
*
1313850 TATATTTATATATATT-AT-TT
1 TATATTTAAATATATTAATATT
** *
1313870 ATATTATTTTTATATATT-ATAAT
1 -TA-TATTTAAATATATTAATATT
1313893 TATATTTAAA-ATATTAATATT
1 TATATTTAAATATATTAATATT
***
1313914 TATAAAAAAATATATTAA-ATT
1 TATATTTAAATATATTAATATT
*
1313935 TATATTTTAATATATATAAATATT
1 TATA-TTTAA-ATATATTAATATT
1313959 T
1 T
1313960 TTTAATATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
20 5 0.07
21 26 0.37
22 26 0.37
23 9 0.13
24 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATTTAAATATATTAATATT
Found at i:1313988 original size:21 final size:22
Alignment explanation
Indices: 1313955--1314015 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
1313945 TATATATAAA
1313955 TATTTTTTA--ATATT-TATTT
1 TATTTTTTATTATATTATATTT
1313974 TATTTTTTATTATATTATATTT
1 TATTTTTTATTATATTATATTT
* *
1313996 AATTATTT-TTATATTATATT
1 TATTTTTTATTATATTATATT
1314016 CGTTGAATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.24
21 17 0.46
22 11 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTTATTATATTATATTT
Found at i:1313993 original size:26 final size:26
Alignment explanation
Indices: 1313964--1314015 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1313954 ATATTTTTTA
*
1313964 ATATTTATTTTATTTTT-TATTATATT
1 ATATTTA-ATTATTTTTATATTATATT
1313990 ATATTTAATTATTTTTATATTATATT
1 ATATTTAATTATTTTTATATTATATT
1314016 CGTTGAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
ATATTTAATTATTTTTATATTATATT
Found at i:1314006 original size:10 final size:11
Alignment explanation
Indices: 1313850--1314015 Score: 56
Period size: 10 Copynumber: 15.5 Consensus size: 11
1313840 CTCTCAAAAA
1313850 TATATTTATAT
1 TATATTTATAT
1313861 ATATTATTTATAT
1 -TA-TATTTATAT
1313874 TAT-TTT-TA-
1 TATATTTATAT
1313882 TATA-TTATAAT
1 TATATTTAT-AT
1313893 TATATTTAAAATAT
1 TATATTT---ATAT
1313907 TAATATTTATA-
1 T-ATATTTATAT
* * **
1313918 AAAAAATATAT
1 TATATTTATAT
*
1313929 TAAATTTATAT
1 TATATTTATAT
* *
1313940 TTTAATATATAT
1 TAT-ATTTATAT
*
1313952 AAATATTT-T-T
1 -TATATTTATAT
1313962 TAATATTTAT-T
1 T-ATATTTATAT
1313973 T-TA-TT-T-T
1 TATATTTATAT
1313980 T-TA-TTATAT
1 TATATTTATAT
1313989 TATATTTA-AT
1 TATATTTATAT
*
1313999 TATTTTTATAT
1 TATATTTATAT
1314010 TATATT
1 TATATT
1314016 CGTTGAATGT
Statistics
Matches: 118, Mismatches: 16, Indels: 41
0.67 0.09 0.23
Matches are distributed among these distances:
7 7 0.06
8 8 0.07
9 7 0.06
10 28 0.24
11 28 0.24
12 19 0.16
13 10 0.08
14 3 0.03
15 8 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1315464 original size:2 final size:2
Alignment explanation
Indices: 1315457--1315481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1315447 CTCAATGATT
1315457 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
1315482 TTCATGATTC
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:1316008 original size:19 final size:19
Alignment explanation
Indices: 1315982--1316023 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1315972 ATGTGTAAAA
*
1315982 TATTTATATATT-T-ATAT
1 TATTTTTATATTATAATAT
1315999 TATTTTTATATTATAATAT
1 TATTTTTATATTATAATAT
1316018 TATTTT
1 TATTTT
1316024 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTTATATTATAATAT
Found at i:1316017 original size:27 final size:24
Alignment explanation
Indices: 1315987--1316046 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 24
1315977 TAAAATATTT
* *
1315987 ATATATTTATATTATTTTTATATTATA
1 ATATATTT-TATAATTTTT-TA-TAAA
1316014 ATATTATTTTATAATTTTTTATAAA
1 ATA-TATTTTATAATTTTTTATAAA
1316039 ATATATTT
1 ATATATTT
1316047 GGATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.17
25 6 0.20
26 2 0.07
27 12 0.40
28 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATATTTTATAATTTTTTATAAA
Found at i:1317236 original size:17 final size:17
Alignment explanation
Indices: 1317202--1317235 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1317192 AATTAGATTG
1317202 ATTTTTTATAAAATAAA
1 ATTTTTTATAAAATAAA
*
1317219 ATTTTTTA-AAATTAAA
1 ATTTTTTATAAAATAAA
1317235 A
1 A
1317236 AATTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTTTATAAAATAAA
Found at i:1317587 original size:19 final size:21
Alignment explanation
Indices: 1317563--1317609 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1317553 TAATTTATGA
1317563 TTTAAATTG-AATAAAAAT-T
1 TTTAAATTGTAATAAAAATAT
*
1317582 TTTAAA-TGTAATATAAATAT
1 TTTAAATTGTAATAAAAATAT
1317602 TTTAAATT
1 TTTAAATT
1317610 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 14 0.58
20 7 0.29
21 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAAATTGTAATAAAAATAT
Found at i:1317616 original size:21 final size:19
Alignment explanation
Indices: 1317563--1317615 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1317553 TAATTTATGA
* *
1317563 TTTAAATTGAATAAAAATT
1 TTTAAATTTAATATAAATT
*
1317582 TTTAAATGTAATATAAATAT
1 TTTAAATTTAATATAAAT-T
1317602 TTTAAATTT-ATATA
1 TTTAAATTTAATATA
1317616 TTTAATTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TTTAAATTTAATATAAATT
Found at i:1317713 original size:20 final size:20
Alignment explanation
Indices: 1317690--1317737 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1317680 TTATATTATT
1317690 TTTAAATTTA-TA-TAATTAAA
1 TTTAAATTTATTATTAA-T-AA
*
1317710 TTTAAAATTATTATTAATAA
1 TTTAAATTTATTATTAATAA
1317730 TTTAAATT
1 TTTAAATT
1317738 AAATCAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.75
21 3 0.12
22 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAAATTTATTATTAATAA
Found at i:1318852 original size:12 final size:12
Alignment explanation
Indices: 1318835--1318868 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1318825 TAATATAGTT
1318835 ATTTTTAATTAA
1 ATTTTTAATTAA
*
1318847 ATTTTTAAGTAA
1 ATTTTTAATTAA
1318859 ATTTATTAAT
1 ATTT-TTAAT
1318869 CAAGTGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
ATTTTTAATTAA
Found at i:1318948 original size:152 final size:153
Alignment explanation
Indices: 1318680--1318958 Score: 380
Period size: 152 Copynumber: 1.8 Consensus size: 153
1318670 CCTAACTTAA
* * ***
1318680 TTATTTATAATTAAATTTTTAAGTAAATTTATCAATCGAGTCGGTAAAAATTAAATTGTGATGTC
1 TTATTTATAATTAAATTTTTAAGTAAATTTATCAATCAAGTCGGTAAAAATTAAATTATGACACC
* ** * * * * *
1318745 AAATCCAATTAGTTTTTTTATAATACTATAGATAAAAATGATAAAATGTTTCAAGAACTAAAAAA
66 AAATCCAATCAACTATTTTATAATACTATAAATAAAAATAATAAAAGGTTTCAACAACTAAAAAA
1318810 GTATATAATTAACCCTAATATAG
131 GTATATAATTAACCCTAATATAG
* * *
1318833 TTATTTTTAATTAAATTTTTAAGTAAATTTATTAATCAAGT-GGTGAAAATTAAATTATGACACC
1 TTATTTATAATTAAATTTTTAAGTAAATTTATCAATCAAGTCGGTAAAAATTAAATTATGACACC
** *
1318897 AAATGTAATCAACTATTTTATAATAGTATAAATAAAAATAATAAAAGGTTTCAACAACTAAA
66 AAATCCAATCAACTATTTTATAATACTATAAATAAAAATAATAAAAGGTTTCAACAACTAAA
1318959 TCTGATGGAT
Statistics
Matches: 107, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
152 69 0.64
153 38 0.36
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (153 bp):
TTATTTATAATTAAATTTTTAAGTAAATTTATCAATCAAGTCGGTAAAAATTAAATTATGACACC
AAATCCAATCAACTATTTTATAATACTATAAATAAAAATAATAAAAGGTTTCAACAACTAAAAAA
GTATATAATTAACCCTAATATAG
Found at i:1320531 original size:2 final size:2
Alignment explanation
Indices: 1320524--1320556 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1320514 AATAATGGAT
*
1320524 AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1320557 TTATTTTGAA
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:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1322985 original size:12 final size:13
Alignment explanation
Indices: 1322958--1322987 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1322948 ACTTTAAATT
1322958 AATTATTTTATAA
1 AATTATTTTATAA
1322971 AATTATTTT-TAA
1 AATTATTTTATAA
1322983 AATTA
1 AATTA
1322988 ATATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTATTTTATAA
Found at i:1325000 original size:25 final size:24
Alignment explanation
Indices: 1324943--1325001 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1324933 ATATTTTAAA
1324943 ATTATTTTTAATATAATTATATAT
1 ATTATTTTTAATATAATTATATAT
* *
1324967 ATTAATTTTGATATTAA-TATATTAT
1 ATTATTTTTAATA-TAATTATA-TAT
*
1324992 GTTATTTTTA
1 ATTATTTTTA
1325002 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (24 bp):
ATTATTTTTAATATAATTATATAT
Found at i:1325521 original size:14 final size:14
Alignment explanation
Indices: 1325502--1325529 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1325492 TATTTAAAAT
1325502 TAACTTAAAAATAA
1 TAACTTAAAAATAA
1325516 TAACTTAAAAATAA
1 TAACTTAAAAATAA
1325530 ATGTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
TAACTTAAAAATAA
Found at i:1329118 original size:2 final size:2
Alignment explanation
Indices: 1329111--1329137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1329101 TTGTTCCTTT
1329111 TG TG TG 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 T
1329138 TTCTTGATTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1330042 original size:15 final size:13
Alignment explanation
Indices: 1330009--1330038 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1329999 TATTTTTTAA
*
1330009 ATATTTATGTTTG
1 ATATTTATATTTG
1330022 ATATTTATATTTG
1 ATATTTATATTTG
1330035 ATAT
1 ATAT
1330039 ATTTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:1349457 original size:42 final size:42
Alignment explanation
Indices: 1349398--1349482 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1349388 ATGATCAGAC
1349398 AATCTTAGACATAGATTATGCTTACCTTTATCATTAAGTGGG
1 AATCTTAGACATAGATTATGCTTACCTTTATCATTAAGTGGG
1349440 AATCTTAGACATAGATTATGCTTACCTTTATCATTAAGTGGG
1 AATCTTAGACATAGATTATGCTTACCTTTATCATTAAGTGGG
1349482 A
1 A
1349483 CCCATCTCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (42 bp):
AATCTTAGACATAGATTATGCTTACCTTTATCATTAAGTGGG
Found at i:1349772 original size:34 final size:34
Alignment explanation
Indices: 1349705--1349890 Score: 266
Period size: 34 Copynumber: 5.5 Consensus size: 34
1349695 CATAGATGCA
* *
1349705 CATTGTTGATTAAAT-GGTGATTTGGTAGTTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* *
1349738 CATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
1349772 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * * *
1349806 CATTATTGATTAAATGGGTGATTTGGTGGTTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * *
1349840 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
1349874 CATTGTTGATTAAATGG
1 CATTGTTGATTAAATGG
1349891 TGGTTTTTAC
Statistics
Matches: 135, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 14 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
Found at i:1349843 original size:102 final size:101
Alignment explanation
Indices: 1349705--1349890 Score: 318
Period size: 102 Copynumber: 1.8 Consensus size: 101
1349695 CATAGATGCA
*
1349705 CATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
1 CATTATTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
1349770 ACCATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
66 ACCATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * *
1349806 CATTATTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGT
1 CATTATTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCT
*
1349871 TGCCATTGTTGATTAAATGG
65 TACCATTGTTGATTAAATGG
1349891 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
CATTATTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
ACCATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
Found at i:1350251 original size:19 final size:19
Alignment explanation
Indices: 1350195--1350257 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1350185 TGGTTGTCGA
**
1350195 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1350214 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1350233 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1350252 GTTACT
1 GGTACT
1350258 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1354369 original size:33 final size:33
Alignment explanation
Indices: 1354323--1354411 Score: 135
Period size: 34 Copynumber: 2.7 Consensus size: 33
1354313 AAGTGGGAGA
*
1354323 ATTGTTGATTAAATGGTG-ATTTGGTAGTTTACC
1 ATTGTTGATTAAATGG-GAATTTGGTAGCTTACC
*
1354356 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGG-AATTTGGTAGCTTACC
1354390 ATTGTTGATTAAATGGGAATTT
1 ATTGTTGATTAAATGGGAATTT
1354412 CATAAACATA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 1 0.02
33 20 0.39
34 30 0.59
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (33 bp):
ATTGTTGATTAAATGGGAATTTGGTAGCTTACC
Found at i:1356961 original size:21 final size:20
Alignment explanation
Indices: 1356935--1356996 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
1356925 AAAAAGACTG
1356935 TATTAAATAAAAAATATTTT
1 TATTAAATAAAAAATATTTT
** * *
1356955 TATTTAAATTTAATATA-ATT
1 TA-TTAAATAAAAAATATTTT
1356975 TATTAAATAAAAAATATTTT
1 TATTAAATAAAAAATATTTT
1356995 TA
1 TA
1356997 ATTCAATCTC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 11 0.34
20 10 0.31
21 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTAAATAAAAAATATTTT
Found at i:1359746 original size:2 final size:2
Alignment explanation
Indices: 1359739--1359774 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1359729 GCAAGAACCA
1359739 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1359775 CAACATGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1361710 original size:24 final size:24
Alignment explanation
Indices: 1361665--1361714 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1361655 TCCTCCACCA
*
1361665 CCGCCGCTTCCGCCAAATTTGTCT
1 CCGCCGCTTCCGCCAAAGTTGTCT
**
1361689 CCGCCGCTTCCGCTGAAGTTGTCT
1 CCGCCGCTTCCGCCAAAGTTGTCT
1361713 CC
1 CC
1361715 ACCTCCTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.42, G:0.20, T:0.28
Consensus pattern (24 bp):
CCGCCGCTTCCGCCAAAGTTGTCT
Found at i:1361728 original size:24 final size:24
Alignment explanation
Indices: 1361683--1361728 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1361673 TCCGCCAAAT
* * *
1361683 TTGTCTCCGCCGCTTCCGCTGAAG
1 TTGTCTCCACCGCCTCCACTGAAG
*
1361707 TTGTCTCCACCTCCTCCACTGA
1 TTGTCTCCACCGCCTCCACTGA
1361729 GAAGGGTGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.11, C:0.41, G:0.17, T:0.30
Consensus pattern (24 bp):
TTGTCTCCACCGCCTCCACTGAAG
Found at i:1374041 original size:40 final size:42
Alignment explanation
Indices: 1373967--1374075 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 42
1373957 ATTTGTATTT
* * * *
1373967 TATATTTATA-TTAATATATAT-GTAAAT-ATAAATATAAGA
1 TATATTTATATTTAATATTTATAATAAATAAAAAATATAAAA
1374006 TATAATTT-T-TTATAA-ATTTATAA-AAATAAAAAATATAAAA
1 TAT-ATTTATATT-TAATATTTATAATAAATAAAAAATATAAAA
1374046 TATATTTATATTTAATATTTATAATAAATA
1 TATATTTATATTTAATATTTATAATAAATA
1374076 TTTAATCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
39 18 0.32
40 24 0.42
41 10 0.18
42 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (42 bp):
TATATTTATATTTAATATTTATAATAAATAAAAAATATAAAA
Found at i:1381950 original size:22 final size:22
Alignment explanation
Indices: 1381924--1381972 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
1381914 TTTAATACAA
*
1381924 ATATTTTTTAAAATTT-TA-TT
1 ATATTTTTAAAAATTTATATTT
*
1381944 ATATATTTAAAAATTTATATTT
1 ATATTTTTAAAAATTTATATTT
1381966 ATATTTT
1 ATATTTT
1381973 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.58
21 2 0.08
22 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTTTAAAAATTTATATTT
Found at i:1381954 original size:19 final size:19
Alignment explanation
Indices: 1381930--1381995 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
1381920 ACAAATATTT
1381930 TTTAAAATTTTATTATATA
1 TTTAAAATTTTATTATATA
1381949 TTTAAAAATTTATATT-TATA
1 TTT-AAAATTT-TATTATATA
* * * *
1381969 TTTTATATTTAAATATATA
1 TTTAAAATTTTATTATATA
*
1381988 TTAAAAAT
1 TTTAAAAT
1381996 AAATAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 17 0.46
20 14 0.38
21 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTTATTATATA
Found at i:1381982 original size:25 final size:25
Alignment explanation
Indices: 1381936--1381989 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
1381926 ATTTTTTAAA
*
1381936 ATTTTATTATATATTTAAAAATTTAT
1 ATTTTATTATATATTT-AAAATATAT
*
1381962 ATTTATATTTTATATTT-AAATATAT
1 ATTT-TATTATATATTTAAAATATAT
1381987 ATT
1 ATT
1381990 AAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 4 0.16
27 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTATTATATATTTAAAATATAT
Found at i:1382638 original size:259 final size:260
Alignment explanation
Indices: 1382169--1382676 Score: 964
Period size: 259 Copynumber: 2.0 Consensus size: 260
1382159 TACTCTCTGA
*
1382169 TTCTTTGCCTTTTTTTTGGATAGACTTTTGTAATGATTTAAAAGGTTCGAATTTTTAATAAATAC
1 TTCTTTACCTTTTTTTTGGATAGACTTTTGTAATGATTTAAAAGGTTCGAATTTTTAATAAATAC
*
1382234 TGATTTTCTTTGGGGGGAAAGTAGGCCATGTGATGACATCAGCTTTCCATAATAATGTAGAAAAT
66 TGATTTTCTTTGGGGGGAAAGTAGGCCATGTGATGACATCAGCTTTCCATAATAATGTAAAAAAT
* *
1382299 ACTGTGAGAATTCAGTGGCTGCATTAATATTGTATTTGAAAATTTAATCAGATTGATTAGAACTA
131 ACTGTGAGAATTCAGTGGCTGCACTAATATTGTATTTGAAAATTTAATCAGATTGATTAGAAATA
*
1382364 ATAAAGTTTTGACAGTGACACATAAAAAATGCAATGAAACAAATAAATTATTTCTAATGATTTTC
196 ATAAAGTTTTGACAGTGACACATAAAAAATGCAATGAAAAAAATAAATTATTTCTAATGATTTTC
1382429 TTCTTTACC-TTTTTTTGGATAGACTTTTGTAATGATTTAAAAGGTTCGAATTTTTAATAAATAC
1 TTCTTTACCTTTTTTTTGGATAGACTTTTGTAATGATTTAAAAGGTTCGAATTTTTAATAAATAC
1382493 TGATTTTCTTTGGGGGGAAAGTAGGCCATGTGATGACATCAGCTTTCCATAATAATGTAAAAAAT
66 TGATTTTCTTTGGGGGGAAAGTAGGCCATGTGATGACATCAGCTTTCCATAATAATGTAAAAAAT
1382558 ACTGTGAGAATTCAGTGGCTGCACTAATATTGTATTTGAAAATTTAATCAGATTGATTAGAAATA
131 ACTGTGAGAATTCAGTGGCTGCACTAATATTGTATTTGAAAATTTAATCAGATTGATTAGAAATA
1382623 ATAAAGTTTTGACAGTGACACATAAAAAATGCAATGAAAAAAATAAATTATTTC
196 ATAAAGTTTTGACAGTGACACATAAAAAATGCAATGAAAAAAATAAATTATTTC
1382677 ATGCTTCATG
Statistics
Matches: 243, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
259 235 0.97
260 8 0.03
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (260 bp):
TTCTTTACCTTTTTTTTGGATAGACTTTTGTAATGATTTAAAAGGTTCGAATTTTTAATAAATAC
TGATTTTCTTTGGGGGGAAAGTAGGCCATGTGATGACATCAGCTTTCCATAATAATGTAAAAAAT
ACTGTGAGAATTCAGTGGCTGCACTAATATTGTATTTGAAAATTTAATCAGATTGATTAGAAATA
ATAAAGTTTTGACAGTGACACATAAAAAATGCAATGAAAAAAATAAATTATTTCTAATGATTTTC
Found at i:1382889 original size:14 final size:14
Alignment explanation
Indices: 1382855--1382889 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1382845 TGAATATGTA
1382855 TTAAAA-ATAAATT
1 TTAAAATATAAATT
1382868 TT-AAATATAAATT
1 TTAAAATATAAATT
1382881 TTAAAATAT
1 TTAAAATAT
1382890 TTTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 11 0.55
14 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAATATAAATT
Done.