Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 18 of 19
Found at i:2287730 original size:22 final size:23
Alignment explanation
Indices: 2287692--2287750 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2287682 ATAATAAATA
2287692 TATTTATATTATTAAAT-TTAAT
1 TATTTATATTATTAAATGTTAAT
2287714 TATTTAT-TTATTAAAATGTTAAT
1 TATTTATATTATT-AAATGTTAAT
* * *
2287737 GATATATAATATTA
1 TATTTATATTATTA
2287751 TAAAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 5 0.16
22 11 0.35
23 11 0.35
24 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (23 bp):
TATTTATATTATTAAATGTTAAT
Found at i:2289372 original size:20 final size:20
Alignment explanation
Indices: 2289344--2289392 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
2289334 TAGTGTTGGC
*
2289344 TTTCCCTTTGTGGTGATACA
1 TTTCTCTTTGTGGTGATACA
2289364 TTTCTC-TT-TGGTGATACA
1 TTTCTCTTTGTGGTGATACA
2289382 TTTCTCTTTGT
1 TTTCTCTTTGT
2289393 CCTTGACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 16 0.62
19 4 0.15
20 6 0.23
ACGTcount: A:0.12, C:0.18, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTCTCTTTGTGGTGATACA
Found at i:2289377 original size:18 final size:18
Alignment explanation
Indices: 2289354--2289391 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2289344 TTTCCCTTTG
2289354 TGGTGATACATTTCTCTT
1 TGGTGATACATTTCTCTT
2289372 TGGTGATACATTTCTCTT
1 TGGTGATACATTTCTCTT
2289390 TG
1 TG
2289392 TCCTTGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (18 bp):
TGGTGATACATTTCTCTT
Found at i:2298507 original size:45 final size:45
Alignment explanation
Indices: 2298458--2298548 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
2298448 ATCACATTAG
2298458 GTATAATTATTTTAAAATTAAGTCGGGTTAAATCTTAAACGAAAA
1 GTATAATTATTTTAAAATTAAGTCGGGTTAAATCTTAAACGAAAA
2298503 GTATAATTATTTTAAAATTAAGTCGGGTTAAATCTTAAACGAAAA
1 GTATAATTATTTTAAAATTAAGTCGGGTTAAATCTTAAACGAAAA
2298548 G
1 G
2298549 AAAAGTTTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (45 bp):
GTATAATTATTTTAAAATTAAGTCGGGTTAAATCTTAAACGAAAA
Found at i:2299289 original size:2 final size:2
Alignment explanation
Indices: 2299282--2299344 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
2299272 GAGCTAATTT
*
2299282 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2299324 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2299345 GAATGTGTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2300579 original size:21 final size:21
Alignment explanation
Indices: 2300542--2300594 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2300532 TAAATTAAGT
2300542 AATAAATT-AACACAAAATTA
1 AATAAATTCAACACAAAATTA
* *
2300562 AATAAATTCAACATAAAATTG
1 AATAAATTCAACACAAAATTA
2300583 AATCAAATTCAA
1 AAT-AAATTCAA
2300595 ACACTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 8 0.28
21 13 0.45
22 8 0.28
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAAATTCAACACAAAATTA
Found at i:2301019 original size:17 final size:17
Alignment explanation
Indices: 2300999--2301031 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2300989 TTGAAAAATC
2300999 TTAAAAAAGATATTTAA
1 TTAAAAAAGATATTTAA
*
2301016 TTAAAAATGATATTTA
1 TTAAAAAAGATATTTA
2301032 TTTTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TTAAAAAAGATATTTAA
Found at i:2301921 original size:3 final size:3
Alignment explanation
Indices: 2301913--2301960 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2301903 TGAGATAACC
2301913 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2301961 ATTTCATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2302196 original size:22 final size:24
Alignment explanation
Indices: 2302158--2302201 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2302148 AAATTAATAA
2302158 TTTTATAATTAATCTCA-TTAATT
1 TTTTATAATTAATCTCACTTAATT
*
2302181 TTTTATATTTAA-CTCACTTAA
1 TTTTATAATTAATCTCACTTAA
2302202 AAAATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATAATTAATCTCACTTAATT
Found at i:2304293 original size:2 final size:2
Alignment explanation
Indices: 2304286--2304310 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2304276 AAATAAATAA
2304286 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2304311 CTTGAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2304406 original size:23 final size:22
Alignment explanation
Indices: 2304354--2304413 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
2304344 AGATTAAATC
2304354 TAAATTATTATTT--ATTTAATA
1 TAAA-TATTATTTAAATTTAATA
* *
2304375 AAAAAATTATTTAAATTTAATTA
1 TAAATATTATTTAAATTTAA-TA
2304398 TAAATATTAATTTAAA
1 TAAATATT-ATTTAAA
2304414 AATAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 7 0.23
21 3 0.10
22 6 0.19
23 8 0.26
24 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATATTATTTAAATTTAATA
Found at i:2308014 original size:15 final size:15
Alignment explanation
Indices: 2307971--2308016 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2307961 AAAACTTACA
* *
2307971 TTTAATAATTTTATT
1 TTTAATAATTATAAT
*
2307986 TTTAA-ATTTA-AAT
1 TTTAATAATTATAAT
2307999 TTTAATAATTATAAT
1 TTTAATAATTATAAT
2308014 TTT
1 TTT
2308017 TTATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.28
14 7 0.28
15 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATAATTATAAT
Found at i:2308025 original size:28 final size:28
Alignment explanation
Indices: 2307971--2308025 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2307961 AAAACTTACA
* *
2307971 TTTAATAATTTTATTTTTAAATTTAAAT
1 TTTAATAATTTAATTTTTAAATATAAAT
*
2307999 TTTAATAATTATAATTTTT-TATATAAA
1 TTTAATAATT-TAATTTTTAAATATAAA
2308026 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAATAATTTAATTTTTAAATATAAAT
Found at i:2308807 original size:11 final size:12
Alignment explanation
Indices: 2308791--2308819 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2308781 TATTTACATA
2308791 TTTTTTCATT-C
1 TTTTTTCATTCC
2308802 TTTTTTCATTCC
1 TTTTTTCATTCC
2308814 TTTTTT
1 TTTTTT
2308820 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTCATTCC
Found at i:2313731 original size:3 final size:3
Alignment explanation
Indices: 2313725--2313780 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
2313715 GTTATTATTT
* *
2313725 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- TTA ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
2313772 ATT ATA ATA
1 ATA ATA ATA
2313781 TCAAAATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 1 0.02
3 45 0.98
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:2313855 original size:22 final size:23
Alignment explanation
Indices: 2313818--2313902 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 23
2313808 CATCATTTTA
2313818 TAAAATATGAATATTAAAAAAAT
1 TAAAATATGAATATTAAAAAAAT
2313841 TAAAATAT-AATATTAAATAAAA-
1 TAAAATATGAATATTAAA-AAAAT
*
2313863 -ATAATATGAAT-TTAATAAAAAT
1 TAAAATATGAATATTAA-AAAAAT
*
2313885 ATATAATAT-AATTATTAA
1 -TAAAATATGAA-TATTAA
2313903 TTTATTAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
21 14 0.26
22 13 0.25
23 14 0.26
24 8 0.15
25 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAATATGAATATTAAAAAAAT
Found at i:2313932 original size:46 final size:45
Alignment explanation
Indices: 2313876--2313999 Score: 110
Period size: 46 Copynumber: 2.7 Consensus size: 45
2313866 ATATGAATTT
* * ** *
2313876 AATAAAAATATATAATATAATTATTAATTTATTAAAATTTATTTA
1 AATATAAATATATAATATAATTATTAATTTAATAAAAAATATATA
*
2313921 AATATATAATATTTTAAATATAATTA-TAA-TTAATAAAAAATATATA
1 AATATA-AATA-TAT-AATATAATTATTAATTTAATAAAAAATATATA
*
2313967 AATATAATATAAATAA-ATAAATTATTAAATTTA
1 AATATAA-ATATATAATAT-AATTATT-AATTTA
2314000 CGTGGTCAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
43 2 0.03
44 7 0.11
45 8 0.13
46 28 0.44
47 8 0.13
48 10 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (45 bp):
AATATAAATATATAATATAATTATTAATTTAATAAAAAATATATA
Found at i:2313956 original size:27 final size:27
Alignment explanation
Indices: 2313885--2313996 Score: 63
Period size: 27 Copynumber: 4.1 Consensus size: 27
2313875 TAATAAAAAT
*
2313885 ATATAA-TATAATTATTAATTTATTAA
1 ATATAATTATAATTAATAATTTATTAA
* *
2313911 A-ATTTATT-TAAATATATAATATT-TTAA
1 ATA-TAATTATAATTA-ATAAT-TTATTAA
**
2313938 ATATAATTATAATTAATAAAAAATATATAA
1 ATATAATTATAATTAAT--AATTTAT-TAA
* *
2313968 ATATAA-TATAAATAAATAAATTATTAA
1 ATATAATTAT-AATTAATAATTTATTAA
2313995 AT
1 AT
2313997 TTACGTGGTC
Statistics
Matches: 66, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
25 1 0.02
26 8 0.12
27 21 0.32
28 15 0.23
29 6 0.09
30 15 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATAATTATAATTAATAATTTATTAA
Found at i:2314362 original size:14 final size:14
Alignment explanation
Indices: 2314345--2314392 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2314335 ATTTCAAAAT
*
2314345 ATTTTAAAAATAAA
1 ATTTTAAAAACAAA
*
2314359 ATTTTAAAAACATA
1 ATTTTAAAAACAAA
* *
2314373 ATTTTATATACAAA
1 ATTTTAAAAACAAA
2314387 TATTTT
1 -ATTTT
2314393 TCTAAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 23 0.82
15 5 0.18
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAAACAAA
Found at i:2314899 original size:11 final size:11
Alignment explanation
Indices: 2314885--2314909 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2314875 TGATAAATTT
2314885 ATTTAATTTTA
1 ATTTAATTTTA
2314896 ATTTAATTTTA
1 ATTTAATTTTA
2314907 ATT
1 ATT
2314910 ATTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:2315196 original size:8 final size:8
Alignment explanation
Indices: 2315183--2315216 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
2315173 ATCATAAAAT
2315183 AAATTTTA
1 AAATTTTA
2315191 AAATTTTA
1 AAATTTTA
2315199 AAA-TTTA
1 AAATTTTA
2315206 AAA-TTTA
1 AAATTTTA
2315213 AAAT
1 AAAT
2315217 AAATTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTTA
Found at i:2315205 original size:15 final size:14
Alignment explanation
Indices: 2315182--2315216 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2315172 GATCATAAAA
*
2315182 TAAATTTTAAAATTT
1 TAAAATTTAAAA-TT
2315197 TAAAATTTAAAATT
1 TAAAATTTAAAATT
2315211 TAAAAT
1 TAAAAT
2315217 AAATTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAAAATTTAAAATT
Found at i:2315231 original size:16 final size:15
Alignment explanation
Indices: 2315210--2315264 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
2315200 AATTTAAAAT
2315210 TTAAAATAAATTAAA
1 TTAAAATAAATTAAA
*
2315225 CTTAAAATAATTTAAA
1 -TTAAAATAAATTAAA
2315241 TTCAAAATAAATATAAA
1 TT-AAAATAAAT-TAAA
*
2315258 TTCAAAT
1 TTAAAAT
2315265 TAACTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.06
16 26 0.76
17 6 0.18
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAATAAATTAAA
Found at i:2315400 original size:38 final size:38
Alignment explanation
Indices: 2315349--2315425 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2315339 AAAATAACTT
2315349 TTGCAAACATAAGCAATAAATTATTGCAACATTGTTGA
1 TTGCAAACATAAGCAATAAATTATTGCAACATTGTTGA
2315387 TTGCAAACATAAGCAATAAATTATTGCAACATTGTTGA
1 TTGCAAACATAAGCAATAAATTATTGCAACATTGTTGA
2315425 T
1 T
2315426 GTAGGTGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (38 bp):
TTGCAAACATAAGCAATAAATTATTGCAACATTGTTGA
Found at i:2316471 original size:7 final size:7
Alignment explanation
Indices: 2316459--2316488 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2316449 TTGACCACCG
2316459 AAAGGCA
1 AAAGGCA
2316466 AAAGGCA
1 AAAGGCA
*
2316473 AAAGGCG
1 AAAGGCA
2316480 AAAGGCA
1 AAAGGCA
2316487 AA
1 AA
2316489 TTACATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.13, G:0.30, T:0.00
Consensus pattern (7 bp):
AAAGGCA
Found at i:2318747 original size:16 final size:17
Alignment explanation
Indices: 2318718--2318749 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2318708 GCCAAAACAT
2318718 TAAAAAAATGAATAAAA
1 TAAAAAAATGAATAAAA
2318735 TAAAAAAAT-AATAAA
1 TAAAAAAATGAATAAA
2318750 TTCAATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
TAAAAAAATGAATAAAA
Found at i:2318932 original size:29 final size:29
Alignment explanation
Indices: 2318891--2318952 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
2318881 TTTTTTTCTC
* * *
2318891 AAAT-AAATATGTATAATTGATTAATTGT
1 AAATGAAAAATGTATAACTGATTAACTGT
*
2318919 AAATGAAAAATGTATAACTGATTCACTGT
1 AAATGAAAAATGTATAACTGATTAACTGT
2318948 AAATG
1 AAATG
2318953 CGAATGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (29 bp):
AAATGAAAAATGTATAACTGATTAACTGT
Found at i:2320370 original size:16 final size:17
Alignment explanation
Indices: 2320344--2320385 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2320334 ATAATAAAAT
2320344 ATAATAATTT-AAATATAA
1 ATAA-AATTTAAAAT-TAA
2320362 A-AAAATTTAAAATTAA
1 ATAAAATTTAAAATTAA
2320378 ATAAAATT
1 ATAAAATT
2320386 ACATCAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.41
17 12 0.55
18 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAATTTAAAATTAA
Found at i:2320383 original size:17 final size:17
Alignment explanation
Indices: 2320344--2320385 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2320334 ATAATAAAAT
2320344 ATAATAATTTAAATATAA
1 ATAA-AATTTAAATATAA
2320362 A-AAAATTTAAA-ATTAA
1 ATAAAATTTAAATA-TAA
2320378 ATAAAATT
1 ATAAAATT
2320386 ACATCAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 12 0.55
17 8 0.36
18 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAATTTAAATATAA
Found at i:2321649 original size:9 final size:9
Alignment explanation
Indices: 2321637--2321668 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2321627 TATTTAATTT
2321637 ATTTTTTAA
1 ATTTTTTAA
*
2321646 ATTTTTTAT
1 ATTTTTTAA
2321655 ATTTTTTAA
1 ATTTTTTAA
2321664 ATTTT
1 ATTTT
2321669 ATCAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:2323222 original size:145 final size:148
Alignment explanation
Indices: 2322939--2323225 Score: 463
Period size: 145 Copynumber: 2.0 Consensus size: 148
2322929 TTGCCTTTCT
* * *
2322939 AATTTATGTTGATGGAAGATGAACATTAAATCACTAGGCAATTTGAATCTCGAAAAGAAGAAAAA
1 AATTTATCTTGATGGAAGATGAACATCAAATCACTAGGCAATTTGAATCTCCAAAAGAAGAAAAA
*
2323004 AGATGTTCTTTTTGAGTTTTACGCGGGATATCATGGGTTTGTTTTAAGCAGTGATAAAATTTTGG
66 AGATATTCTTTTTGAGTTTTACGCGGGATATCATGGGTTTGTTTTAAGCAGTGATAAAATTTTGG
2323069 AAAACATTATTAAGTTAA
131 AAAACATTATTAAGTTAA
* *
2323087 AATTTATCTTGATGG-A-A-GAACATCAAATTACTAGGCAATTTGAATCTCCAAAAGGAGAAAAA
1 AATTTATCTTGATGGAAGATGAACATCAAATCACTAGGCAATTTGAATCTCCAAAAGAAGAAAAA
* * * *
2323149 AGATATTCTTTTTGAGTTTTATGTGGGATTTCATGGGTTTGTTTTAAGCAGTGTTAAAATTTTGG
66 AGATATTCTTTTTGAGTTTTACGCGGGATATCATGGGTTTGTTTTAAGCAGTGATAAAATTTTGG
2323214 AAAACATTATTA
131 AAAACATTATTA
2323226 CGTTGTTTCA
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
145 113 0.88
146 1 0.01
147 1 0.01
148 14 0.11
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (148 bp):
AATTTATCTTGATGGAAGATGAACATCAAATCACTAGGCAATTTGAATCTCCAAAAGAAGAAAAA
AGATATTCTTTTTGAGTTTTACGCGGGATATCATGGGTTTGTTTTAAGCAGTGATAAAATTTTGG
AAAACATTATTAAGTTAA
Found at i:2330595 original size:28 final size:28
Alignment explanation
Indices: 2330558--2330615 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
2330548 ACAAACAAAA
* * * *
2330558 TAATTTAATATAAATATAATTTTTAAAT
1 TAATTAAATATAAATAAAATATATAAAT
*
2330586 TAATTAAATATTAATAAAATATATAAAT
1 TAATTAAATATAAATAAAATATATAAAT
2330614 TA
1 TA
2330616 TGTTAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TAATTAAATATAAATAAAATATATAAAT
Found at i:2331135 original size:3 final size:3
Alignment explanation
Indices: 2331127--2331160 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
2331117 TTTTAAACAC
2331127 AAT AAT AAT AAT AAT AAT AAAT AAT AATT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AA
2331161 AAAATATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2331151 original size:10 final size:9
Alignment explanation
Indices: 2331127--2331160 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
2331117 TTTTAAACAC
2331127 AATAATAAT
1 AATAATAAT
2331136 AATAATAAT
1 AATAATAAT
2331145 AAATAATAATT
1 -AATAATAA-T
2331156 AATAA
1 AATAA
2331161 AAAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 13 0.57
11 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATAAT
Found at i:2331507 original size:8 final size:9
Alignment explanation
Indices: 2331489--2331599 Score: 58
Period size: 8 Copynumber: 12.6 Consensus size: 9
2331479 ATATTTTCAC
2331489 ATTTAATAT
1 ATTTAATAT
2331498 ATTTAA-AT
1 ATTTAATAT
*
2331506 ATTTTATCAT
1 ATTTAAT-AT
*
2331516 ATTATATTTAT
1 ATT-TA-ATAT
*
2331527 ATTTAAAAT
1 ATTTAATAT
2331536 ATTT--TAT
1 ATTTAATAT
*
2331543 ATTTATATAA
1 ATTTA-ATAT
2331553 ACTTTAATA-
1 A-TTTAATAT
*
2331562 AATTAATA-
1 ATTTAATAT
2331570 ATTT-ATATT
1 ATTTAATA-T
*
2331579 ATATAA-AT
1 ATTTAATAT
2331587 ATTT-ATAT
1 ATTTAATAT
2331595 ATTTA
1 ATTTA
2331600 TACTATAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
7 10 0.13
8 26 0.33
9 17 0.22
10 14 0.18
11 10 0.13
12 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTAATAT
Found at i:2331528 original size:29 final size:28
Alignment explanation
Indices: 2331495--2331550 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
2331485 TCACATTTAA
2331495 TATATTT-AAATATTTTATCATATTATATT
1 TATATTTAAAATATTTTAT-AT-TTATATT
2331524 TATATTTAAAATATTTTATATTTATAT
1 TATATTTAAAATATTTTATATTTATAT
2331551 AAACTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
29 9 0.35
30 11 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TATATTTAAAATATTTTATATTTATATT
Found at i:2331587 original size:18 final size:17
Alignment explanation
Indices: 2331521--2331614 Score: 61
Period size: 16 Copynumber: 5.5 Consensus size: 17
2331511 ATCATATTAT
2331521 ATTTATATTTA-AAATA
1 ATTTATATTTATAAATA
*
2331537 TTTTATATTTATATAA-A
1 ATTTATATTTATA-AATA
* ** *
2331554 CTTTA-ATAAATTAATA
1 ATTTATATTTATAAATA
2331570 ATTTATATTATATAAATA
1 ATTTATATT-TATAAATA
* *
2331588 TTTATATATTTATACTATA
1 ATT-TATATTTATA-AATA
2331607 A-TTATATT
1 ATTTATATT
2331615 AAATTTTATT
Statistics
Matches: 59, Mismatches: 12, Indels: 13
0.70 0.14 0.15
Matches are distributed among these distances:
15 2 0.03
16 19 0.32
17 14 0.24
18 15 0.25
19 9 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTTATAAATA
Found at i:2331611 original size:19 final size:19
Alignment explanation
Indices: 2331566--2331613 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2331556 TTAATAAATT
2331566 AATAATT-TATATTATATA
1 AATAATTATATATTATATA
*
2331584 AATATTTATATATT-TATA
1 AATAATTATATATTATATA
*
2331602 CTATAATTATAT
1 -AATAATTATAT
2331614 TAAATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATAATTATATATTATATA
Found at i:2334524 original size:13 final size:13
Alignment explanation
Indices: 2334506--2334530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2334496 ACTTTACAAG
2334506 AATTTTTAATATA
1 AATTTTTAATATA
2334519 AATTTTTAATAT
1 AATTTTTAATAT
2334531 TTTAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTTAATATA
Found at i:2335600 original size:19 final size:19
Alignment explanation
Indices: 2335562--2335611 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2335552 AAATAGACGT
* *
2335562 AAATATATTTAATATTTTTAT
1 AAAT-TATTT-ATATATTTAA
*
2335583 AAATTTTTTATATATTTAA
1 AAATTATTTATATATTTAA
2335602 AAATTATTTA
1 AAATTATTTA
2335612 AAAAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 17 0.68
20 4 0.16
21 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTATTTATATATTTAA
Found at i:2335758 original size:94 final size:102
Alignment explanation
Indices: 2335562--2335767 Score: 254
Period size: 105 Copynumber: 2.1 Consensus size: 102
2335552 AAATAGACGT
* *
2335562 AAATATATTTAATATTTTTATAAATTTTTTATATATTTAAAAATTATTTAAAAAATTATATTTTT
1 AAATAAATTTAATATTTTTATAAATTTTTTATATATTTAAAAA-TATTTAAAAAAATATATTTTT
*
2335627 ATATTTTAATGAAAATATATTAGATATAATTACATATTTA
65 ATATTTTAA-GAAAATATATTA-ATATAATGACATATTTA
2335667 AAATAAATTTAATATTTTT-TAAATTTTTTAATATATTTAAAAA-ATTTATAAAAAAT-TATTTT
1 AAATAAATTTAATATTTTTATAAATTTTTT-ATATATTTAAAAATATTTA-AAAAAATATATTTT
*
2335729 T-TA-TTT-A-AAAATATATT-ATAT-GTGA-ATATTTA
64 TATATTTTAAGAAAATATATTAATATAATGACATATTTA
2335761 AAA-AAAT
1 AAATAAAT
2335768 AAAAAATCTA
Statistics
Matches: 95, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
93 4 0.04
94 10 0.11
95 2 0.02
96 4 0.04
98 10 0.11
100 1 0.01
101 3 0.03
102 2 0.02
103 12 0.13
104 16 0.17
105 31 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (102 bp):
AAATAAATTTAATATTTTTATAAATTTTTTATATATTTAAAAATATTTAAAAAAATATATTTTTA
TATTTTAAGAAAATATATTAATATAATGACATATTTA
Found at i:2336684 original size:50 final size:48
Alignment explanation
Indices: 2336626--2336739 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 48
2336616 AGATTAAGTT
* * * *
2336626 TAATCGTGTCGTATCGTA-TGAATGTTAACAGATCAATTTTAATTATGTCG
1 TAATCGTGTCATATCGTATTAAAT-TTAAAAGATCAATTTTAA--ATGTAG
* * * *
2336676 TAATCGTGTCTTATCATATTAAATTTAAAAGATCCATTTTAAATGTAT
1 TAATCGTGTCATATCGTATTAAATTTAAAAGATCAATTTTAAATGTAG
2336724 TAATCGTGTCATATCG
1 TAATCGTGTCATATCG
2336740 CATATAACAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 18 0.33
50 32 0.59
51 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (48 bp):
TAATCGTGTCATATCGTATTAAATTTAAAAGATCAATTTTAAATGTAG
Found at i:2342446 original size:13 final size:13
Alignment explanation
Indices: 2342428--2342466 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2342418 AAAATATATT
2342428 ATAATATTTTAAA
1 ATAATATTTTAAA
*
2342441 ATAATACTTTTATA
1 ATAATA-TTTTAAA
*
2342455 ATTATATTTTAA
1 ATAATATTTTAA
2342467 TAAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
ATAATATTTTAAA
Found at i:2342469 original size:14 final size:14
Alignment explanation
Indices: 2342428--2342469 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2342418 AAAATATATT
2342428 ATAATATTTTAA-A
1 ATAATATTTTAATA
2342441 ATAATACTTTT-ATA
1 ATAATA-TTTTAATA
*
2342455 ATTATATTTTAATA
1 ATAATATTTTAATA
2342469 A
1 A
2342470 ATAAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATATTTTAATA
Found at i:2346430 original size:13 final size:14
Alignment explanation
Indices: 2346401--2346438 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
2346391 ATTTAATTTA
*
2346401 TTTAAATAAATATT
1 TTTAAATAAATAAT
2346415 TTTAAA-AAATAAT
1 TTTAAATAAATAAT
2346428 TTTAAATAAAT
1 TTTAAATAAAT
2346439 TATATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATAAATAAT
Found at i:2347333 original size:16 final size:17
Alignment explanation
Indices: 2347304--2347336 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2347294 CAAATATAAA
2347304 TAAAAAATAAAAATATTT
1 TAAAAAAT-AAAATATTT
2347322 TAAAAAAT-AAATATT
1 TAAAAAATAAAATATT
2347337 CAAATGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATAAAATATTT
Found at i:2347508 original size:21 final size:21
Alignment explanation
Indices: 2347483--2347526 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2347473 TACATATTTT
2347483 AAAA-TAACTTTAAAATAATAA
1 AAAATTAACTTTAAAA-AATAA
*
2347504 AAAATTAATTTTAAAAAATAA
1 AAAATTAACTTTAAAAAATAA
2347525 AA
1 AA
2347527 CATATACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTAACTTTAAAAAATAA
Found at i:2350774 original size:11 final size:11
Alignment explanation
Indices: 2350758--2350790 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2350748 AGATTATTAA
2350758 TTTTAAATATT
1 TTTTAAATATT
2350769 TTTTAAAT-TT
1 TTTTAAATATT
*
2350779 TTTTTAATATT
1 TTTTAAATATT
2350790 T
1 T
2350791 AAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:2354263 original size:17 final size:19
Alignment explanation
Indices: 2354229--2354274 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
2354219 TATTAATAAT
*
2354229 TATAATTAA-ATTTAAATA
1 TATAAATAATATTTAAATA
*
2354247 -A-AAATAATATTTTAATA
1 TATAAATAATATTTAAATA
2354264 TATAAATAATA
1 TATAAATAATA
2354275 ATTCGGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 1 0.04
19 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TATAAATAATATTTAAATA
Found at i:2354272 original size:19 final size:18
Alignment explanation
Indices: 2354239--2354274 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2354229 TATAATTAAA
2354239 TTTAAATAAAAATAATAT
1 TTTAAATAAAAATAATAT
*
2354257 TTTAATATATAAATAATA
1 TTTAA-ATAAAAATAATA
2354275 ATTCGGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAAATAAAAATAATAT
Found at i:2354898 original size:33 final size:32
Alignment explanation
Indices: 2354860--2355048 Score: 106
Period size: 35 Copynumber: 5.7 Consensus size: 32
2354850 AATATAAATT
2354860 TAATATAAATATATGTATATTTTAAAAATTATA
1 TAATATAAATATAT-TATATTTTAAAAATTATA
* * *
2354893 TAATATAAAT-TATTAATATATTATAATTTATA
1 TAATATAAATATATT-ATATTTTAAAAATTATA
* *
2354925 TAAATATAAAATATATAAATATTTTAAATGAAAT-TA
1 T-AATAT-AAATATAT-TATATTTTAAA--AATTATA
* * *
2354961 TAATAACAAATATA-TA-ATATT-AATATATATA
1 TAAT-ATAAATATATTATATTTTAAAAAT-TATA
*
2354992 TAAATATAAA-ATA-TATATTTTAAAAAAATAATA
1 T-AATATAAATATATTATATTTT--AAAAATTATA
*
2355025 TGAATATGAAA-ATATTATAATTTA
1 T-AATAT-AAATATATTATATTTTA
2355049 TATAAATATA
Statistics
Matches: 120, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
29 1 0.01
30 6 0.05
31 14 0.12
32 25 0.21
33 26 0.22
34 14 0.12
35 28 0.23
36 4 0.03
37 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (32 bp):
TAATATAAATATATTATATTTTAAAAATTATA
Found at i:2354911 original size:40 final size:40
Alignment explanation
Indices: 2354840--2355064 Score: 103
Period size: 39 Copynumber: 5.5 Consensus size: 40
2354830 TTTGATATAA
*
2354840 TATAAAAATTAATATAA-ATTTAATATAAATATATGTAT-ATT
1 TATAAAAATT-ATATAATA-TAAATATAAATATAT-TATAATT
*
2354881 T-TAAAAATTATATAATATAAATTATTAATATATTATAATT
1 TATAAAAATTATATAATATAAA-TATAAATATATTATAATT
* * *
2354921 TATATAAA-TATAAAATATATAAATATTTTAAATGAAATTATAA-T
1 TATAAAAATTAT-ATA-ATATAAATA---TAAAT-ATATTATAATT
* * * * *
2354965 AACAAATATATAATATTAATATATATATAAATATAAAATATATATT
1 TATAAA-A-ATTATA-TAATATAAATATAAATAT--ATTATA-ATT
*
2355011 T-TAAAAA--A-ATAATATGAATATGAAA-ATATTATAATT
1 TATAAAAATTATATAATATAAATAT-AAATATATTATAATT
* *
2355047 TATATAAA-TATAAAATAT
1 TATAAAAATTATATAATAT
2355065 TTTAAATGAA
Statistics
Matches: 141, Mismatches: 21, Indels: 46
0.68 0.10 0.22
Matches are distributed among these distances:
36 4 0.03
37 10 0.07
38 1 0.01
39 30 0.21
40 30 0.21
41 11 0.08
42 8 0.06
43 6 0.04
44 14 0.10
45 13 0.09
46 11 0.08
47 3 0.02
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (40 bp):
TATAAAAATTATATAATATAAATATAAATATATTATAATT
Found at i:2354912 original size:20 final size:22
Alignment explanation
Indices: 2354839--2354939 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 22
2354829 ATTTGATATA
*
2354839 ATATAAAAAT-TAATATAAATTT
1 ATATAAATATATAATATAAA-TT
*
2354861 AATATAAATATAT-GTAT--ATT
1 -ATATAAATATATAATATAAATT
* *
2354881 TTAAAAATTATATAATATAAATT
1 ATATAAA-TATATAATATAAATT
*
2354904 AT-T-AATATAT--TATAATTT
1 ATATAAATATATAATATAAATT
*
2354922 ATATAAATATAAAATATA
1 ATATAAATATATAATATA
2354940 TAAATATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
18 9 0.15
19 6 0.10
20 18 0.30
21 6 0.10
22 4 0.07
23 16 0.27
24 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
ATATAAATATATAATATAAATT
Found at i:2354932 original size:15 final size:15
Alignment explanation
Indices: 2354921--2355008 Score: 63
Period size: 15 Copynumber: 5.4 Consensus size: 15
2354911 TATTATAATT
2354921 TATATAAATATAAAA
1 TATATAAATATAAAA
*
2354936 TATATAAATATTTTAAA
1 TATATAAATA--TAAAA
*
2354953 TGAAATTATAATA-ACAAA
1 T-ATA-TA-AATATA-AAA
2354971 TATAT-AATATTAATATA
1 TATATAAATA-TAA-A-A
2354988 TATATAAATATAAAA
1 TATATAAATATAAAA
2355003 TATATA
1 TATATA
2355009 TTTTAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
14 4 0.07
15 18 0.31
16 4 0.07
17 16 0.28
18 10 0.17
19 2 0.03
20 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:2354940 original size:67 final size:63
Alignment explanation
Indices: 2354861--2355065 Score: 201
Period size: 67 Copynumber: 3.2 Consensus size: 63
2354851 ATATAAATTT
2354861 AATATAAATATATGTATATTTTAAAAATTATATAATATAAATTATTAATATATTATAATTTATAT
1 AATATAAATATAT-TATATTTTAAAAA-TATATAATATAAA-TATTAATATATTATAATTTATAT
2354926 A
63 A
* * * *
2354927 AATATAAAATATATAAATATTTTAAATGAA-ATTATAATAACAAATATATAATAT-TAAT-ATAT
1 AATAT-AAATATAT-TATATTTTAAA--AATA-TATAAT-ATAAATAT-TAATATATTATAATTT
2354989 ATATA
59 ATATA
* * *
2354994 AATATAAA-ATA-TATATTTTAAAAA-A-ATAATATGAATATGAAAATATTATAATTTATATA
1 AATATAAATATATTATATTTTAAAAATATATAATATAAATATTAATATATTATAATTTATATA
2355053 AATATAAA-ATATT
1 AATATAAATATATT
2355066 TTAAATGAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 24
0.77 0.08 0.16
Matches are distributed among these distances:
57 4 0.03
58 9 0.08
59 24 0.20
60 1 0.01
61 3 0.03
63 10 0.08
65 3 0.03
66 8 0.07
67 32 0.27
68 12 0.10
69 12 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (63 bp):
AATATAAATATATTATATTTTAAAAATATATAATATAAATATTAATATATTATAATTTATATA
Found at i:2354986 original size:6 final size:7
Alignment explanation
Indices: 2354889--2355008 Score: 55
Period size: 7 Copynumber: 17.9 Consensus size: 7
2354879 TTTTAAAAAT
2354889 TATATAA
1 TATATAA
2354896 TATA-AA
1 TATATAA
2354902 T-TATTAA
1 TATA-TAA
*
2354909 TATATTA
1 TATATAA
*
2354916 TA-AT-T
1 TATATAA
2354921 TATATAAA
1 TATAT-AA
*
2354929 TATAAAA
1 TATATAA
2354936 TATATAAA
1 TATAT-AA
*
2354944 TATTTTAA
1 TA-TATAA
2354952 -ATGA-AA
1 TAT-ATAA
2354958 T-TATAA
1 TATATAA
*
2354964 TA-ACAAA
1 TATA-TAA
2354971 TATATAA
1 TATATAA
2354978 TAT-TAA
1 TATATAA
2354984 TATAT-A
1 TATATAA
2354990 TATA-AA
1 TATATAA
*
2354996 TATAAAA
1 TATATAA
2355003 TATATA
1 TATATA
2355009 TTTTAAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 34
0.66 0.08 0.26
Matches are distributed among these distances:
5 5 0.06
6 31 0.36
7 35 0.41
8 13 0.15
9 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:2354991 original size:59 final size:59
Alignment explanation
Indices: 2354907--2355094 Score: 181
Period size: 59 Copynumber: 3.2 Consensus size: 59
2354897 ATAAATTATT
* * *
2354907 AATATATTATAATTTATATAAATATAAAATATATAAATATTTTAAATGAAATTATAATAACA
1 AATATATAAT-ATTAATATATATAT-AAATATATAAATATTTTAAATGAAATTATAATAA-A
* **
2354969 AATATATAATATTAATATATATATAAATATAAAATATATATTTTAAA--AAA--ATAATATG
1 AATATATAATATTAATATATATATAAATAT---ATAAATATTTTAAATGAAATTATAATAAA
* *
2355027 AATATGAAAATATT-ATAATTTATATAAATATA-AAATATTTTAAATGAAATTATAATAAA
1 AATAT-ATAATATTAAT-ATATATATAAATATATAAATATTTTAAATGAAATTATAATAAA
*
2355086 AAAATATAA
1 AATATATAA
2355095 AAATAATTTT
Statistics
Matches: 104, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
55 11 0.11
56 1 0.01
57 3 0.03
58 10 0.10
59 36 0.35
60 6 0.06
61 15 0.14
62 9 0.09
63 13 0.12
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (59 bp):
AATATATAATATTAATATATATATAAATATATAAATATTTTAAATGAAATTATAATAAA
Found at i:2354992 original size:17 final size:17
Alignment explanation
Indices: 2354834--2355009 Score: 57
Period size: 17 Copynumber: 10.6 Consensus size: 17
2354824 TAAAAATTTG
*
2354834 ATATA-ATATAAAAATTA
1 ATATATATAT-AATATTA
* * *
2354851 ATATAAATTTAATATAA
1 ATATATATATAATATTA
* *
2354868 ATATATGTAT-ATTTTA
1 ATATATATATAATATTA
* *
2354884 A-AAATTATATAATATAA
1 ATATA-TATATAATATTA
*
2354901 AT-TATTAATATATTA-TA
1 ATATA-T-ATATAATATTA
*
2354918 ATTTATATA-AATA-TA
1 ATATATATATAATATTA
*
2354933 AAATATATA-AATATT-
1 ATATATATATAATATTA
* * * * *
2354948 TTAAATGAAATTATAATA
1 ATATAT-ATATAATATTA
* *
2354966 ACAAATATATAATATTA
1 ATATATATATAATATTA
2354983 ATATATATATAA-ATATA
1 ATATATATATAATAT-TA
*
2355000 AAATATATAT
1 ATATATATAT
2355010 TTTAAAAAAA
Statistics
Matches: 116, Mismatches: 32, Indels: 22
0.68 0.19 0.13
Matches are distributed among these distances:
15 21 0.18
16 17 0.15
17 62 0.53
18 16 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATATATATAATATTA
Found at i:2355109 original size:126 final size:130
Alignment explanation
Indices: 2354838--2355099 Score: 306
Period size: 126 Copynumber: 2.0 Consensus size: 130
2354828 AATTTGATAT
* *
2354838 AATATA-AAAATTAATATAAATTTAATATAAATATATGTATATTTTAAAAATTATATAATATAAA
1 AATATATAATATTAATATAAATTAAATATAAATATA-GTATATTTTAAAAA-TATATAATATAAA
* * ** * **
2354902 TTATTAATATATTATAATTTATATAAATATAAAATATATAAATATTTTAAATGAAATTATAATAA
64 TTATGAAAATATTATAATTTATATAAATATAAAATATATAAATAAATTAAATAAAAAAATAATAA
2354967 CA
129 CA
* *
2354969 AATATATAATATTAATATATATATAAATATAAA-ATA-TATATTTTAAAAA-A-ATAATATGAA-
1 AATATATAATATTAATATAAAT-TAAATATAAATATAGTATATTTTAAAAATATATAATATAAAT
*
2355029 TATGAAAATATTATAATTTATATAAATATAAAATATTTTAAATGAAATTATAATAAAAAAAT-AT
65 TATGAAAATATTATAATTTATATAAATATAAAATA-TATAAAT-AAATTA-AATAAAAAAATAAT
2355093 AA-A
127 AACA
2355096 AATA
1 AATA
2355100 ATTTTATTAA
Statistics
Matches: 114, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
126 33 0.29
127 20 0.18
128 9 0.08
129 8 0.07
130 13 0.11
131 6 0.05
132 16 0.14
133 9 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (130 bp):
AATATATAATATTAATATAAATTAAATATAAATATAGTATATTTTAAAAATATATAATATAAATT
ATGAAAATATTATAATTTATATAAATATAAAATATATAAATAAATTAAATAAAAAAATAATAACA
Found at i:2357070 original size:19 final size:19
Alignment explanation
Indices: 2357048--2357087 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2357038 AACATTTTAT
2357048 TATTTAAAAAATATTAAAA
1 TATTTAAAAAATATTAAAA
** *
2357067 TATTTTTAAAATATTATAA
1 TATTTAAAAAATATTAAAA
2357086 TA
1 TA
2357088 ATATCAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTAAAAAATATTAAAA
Found at i:2357388 original size:3 final size:3
Alignment explanation
Indices: 2357373--2357416 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2357363 AATTTTTCTT
* * *
2357373 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2357417 GCAGGTTGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2358048 original size:16 final size:17
Alignment explanation
Indices: 2358027--2358066 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2358017 GTCTAATTAG
*
2358027 TTAAATTTATA-TTAAA
1 TTAAATTTAAATTTAAA
2358043 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
2358060 -TAAATTT
1 TTAAATTT
2358067 TTTTGTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:2358186 original size:30 final size:30
Alignment explanation
Indices: 2358097--2358190 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
2358087 TTATTTGAAT
* * *
2358097 TATTA-TTTAAAAAATAAAA-ATATTTTTA
1 TATTATTTTAAATAATAAAATAAATTTTAA
* *
2358125 T-TTATAATTAATATAATAATAATAGATTTTAA
1 TATTAT-TTTAA-ATAATAA-AATAAATTTTAA
2358157 TATTATTTTAAATAATAAAATAAATTTTAA
1 TATTATTTTAAATAATAAAATAAATTTTAA
2358187 -ATTA
1 TATTA
2358191 ATCTAGACCC
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
27 3 0.06
28 1 0.02
29 8 0.15
30 17 0.31
31 9 0.17
32 12 0.22
33 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
TATTATTTTAAATAATAAAATAAATTTTAA
Found at i:2358323 original size:7 final size:7
Alignment explanation
Indices: 2358311--2358340 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2358301 GACTTTGATT
2358311 ATTTTAA
1 ATTTTAA
2358318 ATTTTAA
1 ATTTTAA
2358325 ATTTTAA
1 ATTTTAA
2358332 ATTTTAA
1 ATTTTAA
2358339 AT
1 AT
2358341 GTATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:2358393 original size:25 final size:25
Alignment explanation
Indices: 2358336--2358393 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2358326 TTTTAAATTT
*
2358336 TAAATGTATTTAAATTAATATAAAAA
1 TAAAT-TATTAAAATTAATATAAAAA
* *
2358362 TATATTATTAAAATT-ATTTAAAAA
1 TAAATTATTAAAATTAATATAAAAA
2358386 CTAAATTA
1 -TAAATTA
2358394 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAATTATTAAAATTAATATAAAAA
Found at i:2358857 original size:19 final size:18
Alignment explanation
Indices: 2358788--2358857 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
2358778 TTAACTTATT
2358788 TTATAAT-TAAATATATA
1 TTATAATATAAATATATA
* * *
2358805 TTATATATATTAATTTTTA
1 TTATA-ATATAAATATATA
* *
2358824 TTA-CATAAAATATATAATA
1 TTATAATATAA-ATAT-ATA
2358843 TTATAATATAAATAT
1 TTATAATATAAATAT
2358858 TAAAAAAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
17 9 0.24
18 5 0.13
19 19 0.50
20 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATAATATAAATATATA
Found at i:2359275 original size:12 final size:12
Alignment explanation
Indices: 2359227--2359277 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
2359217 ATATAAATAG
2359227 ATTTAAATA-AA
1 ATTTAAATATAA
*
2359238 ATTTAAAATTTATA
1 ATTT-AAATATA-A
*
2359252 TTTTAAAT-TAA
1 ATTTAAATATAA
2359263 ATTTAAATATAA
1 ATTTAAATATAA
2359275 ATT
1 ATT
2359278 ATATTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 12 0.36
12 12 0.36
13 5 0.15
14 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAAATATAA
Found at i:2359747 original size:17 final size:16
Alignment explanation
Indices: 2359725--2359758 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2359715 TTTTTAATAT
2359725 TATTTTAAATAATAAAA
1 TATTTTAAATAA-AAAA
2359742 TATTTTAAATAAAAAA
1 TATTTTAAATAAAAAA
2359758 T
1 T
2359759 TAAATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTTTAAATAAAAAA
Found at i:2360506 original size:22 final size:22
Alignment explanation
Indices: 2360468--2360536 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
2360458 CAATCCATCA
* * *
2360468 ATTTAATAATTTATATATTTTT
1 ATTTAATAATATATATAATTAT
2360490 ATTTAAT-ATATAGTATAATTAT
1 ATTTAATAATATA-TATAATTAT
*
2360512 ATTTAA-AGTATTATAATAATTAT
1 ATTTAATAATA-TAT-ATAATTAT
2360535 AT
1 AT
2360537 AAATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.10
22 23 0.59
23 12 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTTAATAATATATATAATTAT
Found at i:2360560 original size:16 final size:16
Alignment explanation
Indices: 2360530--2360574 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2360520 TATTATAATA
2360530 ATTATATAA-ATTTAT
1 ATTATATAATATTTAT
2360545 -TTGATATAATATTTAT
1 ATT-ATATAATATTTAT
2360561 ATTATATAATATTT
1 ATTATATAATATTT
2360575 TAATTAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.07
15 6 0.22
16 17 0.63
17 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTATATAATATTTAT
Found at i:2360580 original size:16 final size:15
Alignment explanation
Indices: 2360528--2360580 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
2360518 AGTATTATAA
2360528 TAATTATATAA-ATT
1 TAATTATATAATATT
*
2360542 TATTTGATATAATATT
1 TAATT-ATATAATATT
2360558 TATATTATATAATATTT
1 TA-ATTATATAATA-TT
2360575 TAATTA
1 TAATTA
2360581 ATGTGTGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 17 0.52
17 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TAATTATATAATATT
Found at i:2363993 original size:21 final size:21
Alignment explanation
Indices: 2363969--2364011 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2363959 ATTGATAAGT
2363969 AAAGAACAAATTT-CTTTTCTA
1 AAAGAA-AAATTTCCTTTTCTA
*
2363990 AAAGGAAAATTTCCTTTTCTA
1 AAAGAAAAATTTCCTTTTCTA
2364011 A
1 A
2364012 TAACTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (21 bp):
AAAGAAAAATTTCCTTTTCTA
Found at i:2364851 original size:22 final size:22
Alignment explanation
Indices: 2364773--2364855 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 22
2364763 ATTTAGATTC
* *
2364773 AAAAATAAATATTAAATATATTTA
1 AAAAATATAT-TTATATAT-TTTA
2364797 AGATAAATATATTTA-AT-TTTT-
1 A-A-AAATATATTTATATATTTTA
* *
2364818 -TAAATATTTTTATATATTTTA
1 AAAAATATATTTATATATTTTA
2364839 AAAAATATATTTATATA
1 AAAAATATATTTATATA
2364856 ATAATATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
18 10 0.21
19 2 0.04
20 4 0.08
22 17 0.35
23 1 0.02
24 3 0.06
25 4 0.08
26 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
AAAAATATATTTATATATTTTA
Found at i:2364861 original size:16 final size:14
Alignment explanation
Indices: 2364829--2364899 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
2364819 AAATATTTTT
2364829 ATATATTTTAAAAA
1 ATATATTTTAAAAA
* *
2364843 ATATA-TTTATATA
1 ATATATTTTAAAAA
2364856 ATA-ATATTTAAAAA
1 ATATAT-TTTAAAAA
2364870 ATATA--TTAAATATA
1 ATATATTTTAAA-A-A
2364884 A-ATATTTTAAAAA
1 ATATATTTTAAAAA
2364897 ATA
1 ATA
2364900 AAAATTACGA
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
12 6 0.13
13 15 0.33
14 18 0.40
15 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATTTTAAAAA
Found at i:2364887 original size:26 final size:28
Alignment explanation
Indices: 2364831--2364899 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
2364821 ATATTTTTAT
*
2364831 ATATTTTAAAAAATATATTTATATAATA
1 ATATTTTAAAAAATATATTAATATAATA
2364859 ATA-TTTAAAAAATATATTAA-AT-ATAA
1 ATATTTTAAAAAATATATTAATATAAT-A
2364885 ATATTTTAAAAAATA
1 ATATTTTAAAAAATA
2364900 AAAATTACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 2 0.05
26 6 0.16
27 27 0.71
28 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTTTAAAAAATATATTAATATAATA
Found at i:2366761 original size:18 final size:16
Alignment explanation
Indices: 2366720--2366771 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
2366710 TAAAATTCAG
*
2366720 TTAATTTGATCATTTT
1 TTAATTTGATAATTTT
2366736 TTATATTTGAGTAATTTAT
1 TTA-ATTTGA-TAATTT-T
*
2366755 TTAATTTTTATAATTTT
1 TTAA-TTTGATAATTTT
2366772 AAAATCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 12 0.40
19 8 0.27
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (16 bp):
TTAATTTGATAATTTT
Found at i:2370065 original size:21 final size:21
Alignment explanation
Indices: 2370041--2370097 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2370031 ACCTTCAATT
2370041 TCTGCAACTAAGCCTGTAACA
1 TCTGCAACTAAGCCTGTAACA
* *
2370062 TCTGCAACAAAGCCTGTAATA
1 TCTGCAACTAAGCCTGTAACA
*
2370083 TCTGCTACTAAGCCT
1 TCTGCAACTAAGCCT
2370098 ACAATAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TCTGCAACTAAGCCTGTAACA
Found at i:2370103 original size:21 final size:21
Alignment explanation
Indices: 2370024--2370103 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
2370014 ACATTACAGT
* * *
2370024 CAACTAAACCTTCAATTTCTG
1 CAACTAAGCCTGCAATATCTG
* *
2370045 CAACTAAGCCTGTAACATCTG
1 CAACTAAGCCTGCAATATCTG
* *
2370066 CAACAAAGCCTGTAATATCTG
1 CAACTAAGCCTGCAATATCTG
* *
2370087 CTACTAAGCCTACAATA
1 CAACTAAGCCTGCAATA
2370104 AAACCTGTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (21 bp):
CAACTAAGCCTGCAATATCTG
Found at i:2372218 original size:3 final size:3
Alignment explanation
Indices: 2372210--2372249 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2372200 TGCAGATCTG
2372210 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2372250 TTGCCTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2372780 original size:20 final size:20
Alignment explanation
Indices: 2372755--2372793 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2372745 AAATTATATT
*
2372755 TAAAATATT-ATATATTTAAA
1 TAAAAT-TTAATATAATTAAA
2372775 TAAAATTTAATATAATTAA
1 TAAAATTTAATATAATTAA
2372794 TAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAATTTAATATAATTAAA
Found at i:2372800 original size:17 final size:17
Alignment explanation
Indices: 2372774--2372825 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
2372764 ATATATTTAA
2372774 ATAAAATTTAATATAAT
1 ATAAAATTTAATATAAT
*
2372791 -TAATAATTT-ATATTAT
1 ATAA-AATTTAATATAAT
*
2372807 ATAAATTTTAATAT-AT
1 ATAAAATTTAATATAAT
2372823 ATA
1 ATA
2372826 TTTATTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAATTTAATATAAT
Found at i:2372816 original size:16 final size:15
Alignment explanation
Indices: 2372795--2372836 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2372785 TATAATTAAT
2372795 AATTTATATTATATA
1 AATTTATATTATATA
*
2372810 AATTT-TAATATATA
1 AATTTATATTATATA
*
2372824 TATTTAT-TTATAT
1 AATTTATATTATAT
2372837 CTTAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTATATTATATA
Found at i:2372833 original size:33 final size:33
Alignment explanation
Indices: 2372760--2372836 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
2372750 ATATTTAAAA
2372760 TATTATATATTTAAATAAAATTTAATATAATTAAT
1 TATT-TATA-TTAAATAAAATTTAATATAATTAAT
* * * *
2372795 AATTTATATTATATAAATTTTAATAT-ATATATT
1 TATTTATATTAAATAAAATTTAATATAAT-TAAT
2372828 TATTTATAT
1 TATTTATAT
2372837 CTTAATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 2 0.06
33 27 0.75
34 4 0.11
35 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TATTTATATTAAATAAAATTTAATATAATTAAT
Found at i:2373444 original size:78 final size:79
Alignment explanation
Indices: 2373315--2373468 Score: 213
Period size: 78 Copynumber: 2.0 Consensus size: 79
2373305 TTTTTACCTA
* * *
2373315 ATCAATTTGGTTTTTTACGGACAGAATCGATTTTGAACTGGTTCAATCAATTATCAGCTCT-ATA
1 ATCAATTTGGTTTTTTACGGACAGAACCAATTTTGAACTGGTTCAATCAATTAACAGCTCTAATA
2373379 TATGAATCGGATTG
66 TATGAATCGGATTG
* * * * *
2373393 ATCAATTTGGTTTTTTGCTGACTGAACCAATTTTGGA-TGGGTTCAATCAATTAACAGTTCTAAT
1 ATCAATTTGGTTTTTTACGGACAGAACCAATTTTGAACT-GGTTCAATCAATTAACAGCTCTAAT
2373457 ATATGAATCGGA
65 ATATGAATCGGA
2373469 CTGAACCACC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 1 0.02
78 51 0.77
79 14 0.21
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (79 bp):
ATCAATTTGGTTTTTTACGGACAGAACCAATTTTGAACTGGTTCAATCAATTAACAGCTCTAATA
TATGAATCGGATTG
Found at i:2377093 original size:27 final size:26
Alignment explanation
Indices: 2377057--2377124 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
2377047 AGTAATTTAC
2377057 ATATTTATATTATATTTAAAATATTA
1 ATATTTATATTATATTTAAAATATTA
* *
2377083 TATATTTATA-TAAATTTTAAATATTA
1 -ATATTTATATTATATTTAAAATATTA
*
2377109 ATAATTTATTTTATAT
1 AT-ATTTATATTATAT
2377125 AAATTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.06
26 20 0.57
27 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATTTATATTATATTTAAAATATTA
Found at i:2377097 original size:19 final size:21
Alignment explanation
Indices: 2377057--2377096 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2377047 AGTAATTTAC
*
2377057 ATATT-TATATTATATTTAAA
1 ATATTATATATTATATATAAA
2377077 ATATTATATATT-TATATAAA
1 ATATTATATATTATATATAAA
2377097 TTTTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTATATATTATATATAAA
Found at i:2385561 original size:2 final size:2
Alignment explanation
Indices: 2385554--2385606 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2385544 CAAATGAGTA
2385554 AG AG AG 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 AG AG AG
*
2385596 AG GG AG AG AG A
1 AG AG AG AG AG A
2385607 AGAAGAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2388438 original size:19 final size:18
Alignment explanation
Indices: 2388401--2388448 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
2388391 GATTTAAAGT
*
2388401 AAAA-TATAAATATTTTA
1 AAAATTATATATATTTTA
* *
2388418 AATATTTTATATATATTTA
1 AAAATTATATATAT-TTTA
2388437 AAAATTATATAT
1 AAAATTATATAT
2388449 TTTATTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 3 0.12
18 7 0.29
19 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAATTATATATATTTTA
Found at i:2388470 original size:25 final size:26
Alignment explanation
Indices: 2388419--2388471 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2388409 AATATTTTAA
*
2388419 ATATTTTATATATATTTAAAAATTAT
1 ATATTTTATATATATTTAAAAAATAT
*
2388445 ATATTTTATTTATA-TTAAAAAATAT
1 ATATTTTATATATATTTAAAAAATAT
2388470 AT
1 AT
2388472 TGAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATTTTATATATATTTAAAAAATAT
Found at i:2390426 original size:7 final size:7
Alignment explanation
Indices: 2390416--2390475 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
2390406 ATATTTAATT
2390416 ATTTTAA
1 ATTTTAA
2390423 ATTTTAA
1 ATTTTAA
2390430 ATTTTAA
1 ATTTTAA
**
2390437 AAGTTATA
1 ATTTTA-A
*
2390445 A-TTTAT
1 ATTTTAA
2390451 ATTTT-A
1 ATTTTAA
*
2390457 TTTTTAA
1 ATTTTAA
*
2390464 ATTATAA
1 ATTTTAA
2390471 ATTTT
1 ATTTT
2390476 TTTATTAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 5 0.12
7 34 0.83
8 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
ATTTTAA
Found at i:2395386 original size:6 final size:6
Alignment explanation
Indices: 2395371--2395404 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2395361 TCTATAACAT
*
2395371 AAAAAA AAAAAC AAAAAC AAAAAC AAAAATC AAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA-C AAA
2395405 CCAAACCCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:2396169 original size:16 final size:16
Alignment explanation
Indices: 2396144--2396195 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
2396134 ATATATTTTT
*
2396144 ATTTATAAAAATATAA
1 ATTTAAAAAAATATAA
2396160 ATTTAAAAAAA-ATAA
1 ATTTAAAAAAATATAA
2396175 ATTAATAAAAAAATATCAA
1 ATT--TAAAAAAATAT-AA
2396194 AT
1 AT
2396196 ATATGTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 8 0.26
18 2 0.06
19 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTTAAAAAAATATAA
Found at i:2396174 original size:15 final size:16
Alignment explanation
Indices: 2396144--2396189 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2396134 ATATATTTTT
*
2396144 ATTTATAAAAATATAA
1 ATTTATAAAAAAATAA
2396160 ATTTA-AAAAAAATAA
1 ATTTATAAAAAAATAA
*
2396175 ATTAATAAAAAAATA
1 ATTTATAAAAAAATA
2396190 TCAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTTATAAAAAAATAA
Found at i:2397024 original size:33 final size:33
Alignment explanation
Indices: 2396987--2397051 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2396977 ATTTTATATT
* *
2396987 TTTATATAAAATTTGATATGTTTA-ATAATTTAA
1 TTTATATAAAATTTAATATATTTATAT-ATTTAA
*
2397020 TTTATATAAATTTTAATATATTTATATATTTA
1 TTTATATAAAATTTAATATATTTATATATTTA
2397052 TATTATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (33 bp):
TTTATATAAAATTTAATATATTTATATATTTAA
Found at i:2398301 original size:2 final size:2
Alignment explanation
Indices: 2398294--2398323 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2398284 TGGAAAAGAA
2398294 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
2398324 GCGTACGTAT
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:2398632 original size:16 final size:17
Alignment explanation
Indices: 2398611--2398669 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
2398601 CTTATTAAAA
2398611 AAAATAATTTAAA-TTT
1 AAAATAATTTAAACTTT
*
2398627 AAAATAATTTAAACTTA
1 AAAATAATTTAAACTTT
* *
2398644 AAAATAATATAAATTTT
1 AAAATAATTTAAACTTT
*
2398661 AAATTAATT
1 AAAATAATT
2398670 GAATACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 13 0.36
17 23 0.64
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATTTAAACTTT
Found at i:2398647 original size:17 final size:16
Alignment explanation
Indices: 2398610--2398658 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
2398600 ACTTATTAAA
2398610 AAAAATAATTTAAATT
1 AAAAATAATTTAAATT
*
2398626 TAAAATAATTTAAACTT
1 AAAAATAATTTAAA-TT
*
2398643 AAAAATAATATAAATT
1 AAAAATAATTTAAATT
2398659 TTAAATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATAATTTAAATT
Found at i:2399482 original size:17 final size:18
Alignment explanation
Indices: 2399448--2399483 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2399438 TGAATATTTT
2399448 TCTCAATTATTAATAAAA
1 TCTCAATTATTAATAAAA
*
2399466 TCTCTATTATT-ATAAAA
1 TCTCAATTATTAATAAAA
2399483 T
1 T
2399484 TTTTAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
TCTCAATTATTAATAAAA
Found at i:2402316 original size:16 final size:16
Alignment explanation
Indices: 2402297--2402327 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2402287 ATATAAATTA
*
2402297 AAAATTTTATATAATG
1 AAAATTGTATATAATG
2402313 AAAATTGTATATAAT
1 AAAATTGTATATAAT
2402328 ATGTGAGTCC
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:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AAAATTGTATATAATG
Found at i:2407474 original size:25 final size:23
Alignment explanation
Indices: 2407440--2407490 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 23
2407430 ATTATTCAAA
2407440 TTTGATTAAAATTTGAGGTTTAAT
1 TTTGATTAAAATTTGAGG-TTAAT
2407464 TTTGAGTTAAAATTTGAGGTTAAT
1 TTTGA-TTAAAATTTGAGGTTAAT
2407488 TTT
1 TTT
2407491 AATTTGGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (23 bp):
TTTGATTAAAATTTGAGGTTAAT
Found at i:2407479 original size:12 final size:13
Alignment explanation
Indices: 2407437--2407486 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
2407427 TTAATTATTC
2407437 AAATTTGA--TTA
1 AAATTTGAGGTTA
*
2407448 AAATTTGAGGTTT
1 AAATTTGAGGTTA
*
2407461 AATTTTGA-GTTA
1 AAATTTGAGGTTA
2407473 AAATTTGAGGTTA
1 AAATTTGAGGTTA
2407486 A
1 A
2407487 TTTTAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 8 0.25
12 10 0.31
13 14 0.44
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (13 bp):
AAATTTGAGGTTA
Found at i:2407684 original size:18 final size:20
Alignment explanation
Indices: 2407645--2407682 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2407635 TTTTAAATTC
2407645 AATATAAATTAAAAATTTTT
1 AATATAAATTAAAAATTTTT
*
2407665 AATATTAATT-AAAATTTT
1 AATATAAATTAAAAATTTT
2407683 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATAAATTAAAAATTTTT
Found at i:2411611 original size:2 final size:2
Alignment explanation
Indices: 2411604--2411630 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2411594 ATTAAATTGT
2411604 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2411631 TTGTTTCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2411992 original size:12 final size:12
Alignment explanation
Indices: 2411977--2412001 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2411967 ATATTTTATT
2411977 TTTAAAAATATA
1 TTTAAAAATATA
2411989 TTTAAAAATATA
1 TTTAAAAATATA
2412001 T
1 T
2412002 ATATCTAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAAAATATA
Found at i:2412148 original size:28 final size:27
Alignment explanation
Indices: 2412107--2412161 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
2412097 TAATATTTAT
* * *
2412107 TTTTTTAAATAAAAATTTAAGTTTAAA
1 TTTTATAAATAAAAAATTAACTTTAAA
2412134 TTTTATAAATAAAAAAATTAACTTTAAA
1 TTTTATAAAT-AAAAAATTAACTTTAAA
2412162 AGAGCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TTTTATAAATAAAAAATTAACTTTAAA
Found at i:2412818 original size:16 final size:16
Alignment explanation
Indices: 2412756--2412820 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 16
2412746 TAATAATTTT
2412756 AAATAATATAA-AT-A
1 AAATAATATAATATAA
* *
2412770 AAATAA-AAAATAATTA
1 AAATAATATAAT-ATAA
2412786 AAATAATATATATTATAA
1 AAATAATATA-A-TATAA
2412804 AAATAATATAATATAA
1 AAATAATATAATATAA
2412820 A
1 A
2412821 CAAGTATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 3 0.07
14 6 0.14
15 2 0.05
16 13 0.31
17 3 0.07
18 14 0.33
19 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATATAATATAA
Found at i:2412888 original size:18 final size:18
Alignment explanation
Indices: 2412785--2412889 Score: 63
Period size: 18 Copynumber: 5.7 Consensus size: 18
2412775 AAAAATAATT
2412785 AAAATAATAT-ATATTATA
1 AAAATAATATAATATTA-A
2412803 AAAATAATATAATA-TAA
1 AAAATAATATAATATTAA
* * * *
2412820 ACAAGTATTTTAATGTTTATA
1 A-AAATAATATAAT-ATTA-A
* *
2412841 TAAAT-ATATAATATCTTA
1 AAAATAATATAATAT-TAA
**
2412859 AATGTAATTATAATATTAA
1 AAAATAA-TATAATATTAA
2412878 AAAATAATATAA
1 AAAATAATATAA
2412890 ATATAATATA
Statistics
Matches: 63, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
17 2 0.03
18 30 0.48
19 17 0.27
20 13 0.21
21 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATAATATAATATTAA
Found at i:2412897 original size:11 final size:11
Alignment explanation
Indices: 2412867--2412907 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2412857 TAAATGTAAT
2412867 TATAATATTAAAA
1 TATAATA-T-AAA
*
2412880 AATAATATAAA
1 TATAATATAAA
2412891 TATAATATAAA
1 TATAATATAAA
2412902 TATAAT
1 TATAAT
2412908 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 19 0.73
12 1 0.04
13 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAATATAAA
Found at i:2413073 original size:14 final size:15
Alignment explanation
Indices: 2413044--2413073 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2413034 TCATAACTAA
2413044 TTTTAAAATTATATT
1 TTTTAAAATTATATT
2413059 TTTTAAAATTA-ATT
1 TTTTAAAATTATATT
2413073 T
1 T
2413074 AATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAAAATTATATT
Found at i:2416057 original size:2 final size:2
Alignment explanation
Indices: 2416050--2416090 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
2416040 TCTTCAATGG
2416050 AT AT AT AT AT AT AT AT AT CAT AT AT AT AT AT CAT 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
2416091 GATTAATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2416074 original size:13 final size:13
Alignment explanation
Indices: 2416050--2416090 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
2416040 TCTTCAATGG
2416050 ATATAT-ATATAT
1 ATATATCATATAT
2416062 ATATATCATATAT
1 ATATATCATATAT
2416075 ATATATCATATAT
1 ATATATCATATAT
2416088 ATA
1 ATA
2416091 GATTAATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 6 0.21
13 22 0.79
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATCATATAT
Found at i:2416665 original size:3 final size:3
Alignment explanation
Indices: 2416637--2416678 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
2416627 GGCGTGTGGG
*
2416637 ATT ATT AATT ATT TTT AATT -TT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT -ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT AT
2416679 CTATCTATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.79
4 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2416851 original size:8 final size:9
Alignment explanation
Indices: 2416838--2416898 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
2416828 ATATAAAATA
2416838 TTATAT-TT
1 TTATATATT
2416846 TTATATATT
1 TTATATATT
* *
2416855 TTTTATATA
1 TTATATATT
*
2416864 TTA-ATAAT
1 TTATATATT
*
2416872 TTATTTATT
1 TTATATATT
2416881 TTATATATAT
1 TTATATAT-T
*
2416891 TTTTATAT
1 TTATATAT
2416899 GTATGTATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 12 0.29
9 21 0.51
10 8 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATATT
Found at i:2416859 original size:11 final size:11
Alignment explanation
Indices: 2416839--2416983 Score: 53
Period size: 11 Copynumber: 12.0 Consensus size: 11
2416829 TATAAAATAT
2416839 TATA-TTTTTA
1 TATATTTTTTA
2416849 TATATTTTTTA
1 TATATTTTTTA
2416860 TATATTAATAATTTA
1 TATATT--T--TTTA
* *
2416875 TTTATTTTATA
1 TATATTTTTTA
2416886 TATATTTTTATA
1 TATATTTTT-TA
*
2416898 TGTATGTATATTTA
1 TATAT-T-T-TTTA
* *
2416912 TAT-TATGTGTA
1 TATAT-TTTTTA
*
2416923 TATCATTTTTAA
1 TAT-ATTTTTTA
*
2416935 GTA-ATGTTTTA
1 -TATATTTTTTA
*
2416946 AATATTTTTTA
1 TATATTTTTTA
2416957 TAAATATTATATTTA
1 T--ATATT-T-TTTA
2416972 TATTATTTTTTA
1 TA-TATTTTTTA
2416984 CGTTTAAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
10 5 0.05
11 41 0.41
12 13 0.13
13 15 0.15
14 10 0.10
15 16 0.16
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (11 bp):
TATATTTTTTA
Found at i:2416886 original size:33 final size:31
Alignment explanation
Indices: 2416820--2416898 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 31
2416810 GTATTTGGAT
2416820 TATTTTTTATATAAAATATTATATTTTTATA
1 TATTTTTTATATAAAATATTATATTTTTATA
* *
2416851 TATTTTTTATATATTAATAATTTATTTATTTTATA
1 TATTTTTTATATA-AAAT-A-TTATAT-TTTTATA
2416886 TATATTTTTATAT
1 TAT-TTTTTATAT
2416899 GTATGTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 13 0.32
32 3 0.07
33 1 0.02
34 5 0.12
35 10 0.24
36 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTTTTTATATAAAATATTATATTTTTATA
Found at i:2417556 original size:11 final size:11
Alignment explanation
Indices: 2417542--2417600 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 11
2417532 TAAAATATTA
2417542 TTTTTATATAT
1 TTTTTATATAT
2417553 TTTTTATATAT
1 TTTTTATATAT
2417564 TAATAATTTAT-T-T
1 T--T--TTTATATAT
2417577 TATTTTATATAT
1 T-TTTTATATAT
2417589 ATTTTTATATAT
1 -TTTTTATATAT
2417601 ATGTGTGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
10 5 0.12
11 13 0.32
12 13 0.32
13 4 0.10
14 1 0.02
15 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTATATAT
Found at i:2417578 original size:31 final size:31
Alignment explanation
Indices: 2417519--2417598 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 31
2417509 ATGTTCATGT
*
2417519 TATTTTTTGTATTTAAAATATTATTTTTATA
1 TATTTTTTATATTTAAAATATTATTTTTATA
*
2417550 TATTTTTTATATATTAATAATTTATTTTATTTTATA
1 TATTTTTTATAT-TTAA-AA--TATTAT-TTTTATA
2417586 TATATTTTTATAT
1 TAT-TTTTTATAT
2417599 ATATGTGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 11 0.27
32 4 0.10
33 2 0.05
35 5 0.12
36 10 0.24
37 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (31 bp):
TATTTTTTATATTTAAAATATTATTTTTATA
Found at i:2417838 original size:17 final size:17
Alignment explanation
Indices: 2417803--2417836 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2417793 GCTTTAATTT
2417803 TTTATATAGATATTAAA
1 TTTATATAGATATTAAA
*
2417820 TTTATATTATATATTAA
1 TTTATA-TAGATATTAA
2417837 TTCATGCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATATAGATATTAAA
Found at i:2418481 original size:11 final size:10
Alignment explanation
Indices: 2418460--2418499 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
2418450 TTGTCAAGAG
2418460 AAAAAGAAAA
1 AAAAAGAAAA
2418470 AAAAAGATAAA
1 AAAAAGA-AAA
*
2418481 AAAAAGAGAA
1 AAAAAGAAAA
2418491 AAAAAGAAA
1 AAAAAGAAA
2418500 TAATTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:2419482 original size:11 final size:11
Alignment explanation
Indices: 2419466--2419510 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
2419456 TTGTCAAGAG
2419466 AAAAAGAAAAA
1 AAAAAGAAAAA
* *
2419477 AAAAAGATAGA
1 AAAAAGAAAAA
* *
2419488 AAAAAGGAGAA
1 AAAAAGAAAAA
2419499 AAAAAGAAAAA
1 AAAAAGAAAAA
2419510 A
1 A
2419511 TTATGTATTC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Done.