Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 101 of 226
Found at i:34739278 original size:39 final size:39
Alignment explanation
Indices: 34739224--34739302 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
34739214 AAGCTTGGCC
34739224 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
1 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
34739263 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
1 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
34739302 A
1 A
34739303 GGAAGAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (39 bp):
AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
Found at i:34743798 original size:20 final size:19
Alignment explanation
Indices: 34743749--34743839 Score: 53
Period size: 20 Copynumber: 4.6 Consensus size: 19
34743739 TAACAGATGA
*
34743749 ATCGAAGTGCTAACAGAGGC
1 ATCGAAGTGC-AACAGAAGC
*
34743769 AT-GATTGTGCAATCAGAAGC
1 ATCGA-AGTGCAA-CAGAAGC
*
34743789 ATCGAAGTGCAA-ACGTAGAC
1 ATCGAAGTGCAACA-GAAG-C
* * *
34743809 ACCGAAGTGTAACAGAGGC
1 ATCGAAGTGCAACAGAAGC
34743828 A-CTGAAGTGCAA
1 ATC-GAAGTGCAA
34743840 AAAGAGGCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.04
19 17 0.31
20 33 0.60
21 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.16
Consensus pattern (19 bp):
ATCGAAGTGCAACAGAAGC
Found at i:34745636 original size:42 final size:42
Alignment explanation
Indices: 34745518--34745636 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
34745508 TTGTGCTTGT
* * *
34745518 GCCACAAGGGCATGTGTCCAGGTCATGTGAGCCACTGACTTAA
1 GCCACAAGGGCGTGTGT-CAGGCCGTGTGAGCCACTGACTTAA
* * * * *
34745561 GCCACACGGGTGTGTGCCAGGCCGTGTAAGCCACTGACTTGA
1 GCCACAAGGGCGTGTGTCAGGCCGTGTGAGCCACTGACTTAA
* * *
34745603 TCCACAAGGGCGTGTGTGAGGCCGTGTGGGCCAC
1 GCCACAAGGGCGTGTGTCAGGCCGTGTGAGCCAC
34745637 ATGAGCCGGC
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
42 48 0.79
43 13 0.21
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (42 bp):
GCCACAAGGGCGTGTGTCAGGCCGTGTGAGCCACTGACTTAA
Found at i:34753365 original size:19 final size:20
Alignment explanation
Indices: 34753269--34753404 Score: 139
Period size: 20 Copynumber: 6.8 Consensus size: 20
34753259 GTAGATGCGT
* *
34753269 AACAGATGCACCAAAGTGCT
1 AACAGAGGCACCAAAGTGCA
* * * **
34753289 GATAGAGGCACGATTGTGCA
1 AACAGAGGCACCAAAGTGCA
*
34753309 ATCAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* * *
34753329 AACATAGACACCAAAGTG-T
1 AACAGAGGCACCAAAGTGCA
* *
34753348 AATAGAGGCACTAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
34753368 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
*
34753388 AACAGAGGCACCGAAGT
1 AACAGAGGCACCAAAGT
34753405 TCAATCCTGT
Statistics
Matches: 90, Mismatches: 25, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
19 14 0.16
20 76 0.84
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.12
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:34753374 original size:59 final size:60
Alignment explanation
Indices: 34753277--34753391 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 60
34753267 GTAACAGATG
* ** *
34753277 CACCAAAGTGCTGATAGAGGCACGATTGTGCAATCAGAGGCACCAAAGTGCAAACATAGA
1 CACCAAAGTGCTAATAGAGGCACGAAAGTGCAAACAGAGGCACCAAAGTGCAAACATAGA
*
34753337 CACCAAAGTG-TAATAGAGGCACTAAAGTGCAAACAGAGGCACCAAAGTGCAAACA
1 CACCAAAGTGCTAATAGAGGCACGAAAGTGCAAACAGAGGCACCAAAGTGCAAACA
34753392 GAGGCACCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 40 0.80
60 10 0.20
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (60 bp):
CACCAAAGTGCTAATAGAGGCACGAAAGTGCAAACAGAGGCACCAAAGTGCAAACATAGA
Found at i:34753568 original size:77 final size:77
Alignment explanation
Indices: 34753441--34753597 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 77
34753431 ACCCTATTGG
34753441 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
1 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
34753506 ATACACATTCTT
66 ATACACATTCTT
*
34753518 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTTGTTACTTT
1 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
34753583 ATACACATTCTT
66 ATACACATTCTT
34753595 CAT
1 CAT
34753598 CCGGAATTAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (77 bp):
CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
ATACACATTCTT
Found at i:34759872 original size:19 final size:19
Alignment explanation
Indices: 34759827--34759875 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
34759817 TCTAAAACTG
34759827 ATATTACA-GAACATAAAT
1 ATATTACATGAACATAAAT
* *
34759845 ATATAACATGAACA-CAAT
1 ATATTACATGAACATAAAT
34759863 ATGATTACATGAA
1 AT-ATTACATGAA
34759876 TTTTTCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (19 bp):
ATATTACATGAACATAAAT
Found at i:34765764 original size:6 final size:6
Alignment explanation
Indices: 34765753--34765777 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34765743 ATTATTTGTG
34765753 TCATGT TCATGT TCATGT TCATGT T
1 TCATGT TCATGT TCATGT TCATGT T
34765778 TTTCTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TCATGT
Found at i:34769508 original size:16 final size:15
Alignment explanation
Indices: 34769466--34769511 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
34769456 AAAATCAAGG
34769466 GAAGATAAAA-GATT
1 GAAGATAAAATGATT
34769480 G-AGATTAAAATGATT
1 GAAGA-TAAAATGATT
34769495 GAAGATAAAGATGATT
1 GAAGATAAA-ATGATT
34769511 G
1 G
34769512 GTTGATCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.11
14 6 0.21
15 9 0.32
16 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (15 bp):
GAAGATAAAATGATT
Found at i:34770415 original size:6 final size:6
Alignment explanation
Indices: 34770404--34770428 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34770394 TTTATTTGTG
34770404 TCATGT TCATGT TCATGT TCATGT T
1 TCATGT TCATGT TCATGT TCATGT T
34770429 TTTCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TCATGT
Found at i:34780804 original size:15 final size:15
Alignment explanation
Indices: 34780784--34780817 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34780774 GTTTACTTTC
*
34780784 AATAAATTGGTTATT
1 AATAAATTGGTGATT
34780799 AATAAATTGGTGATT
1 AATAAATTGGTGATT
34780814 AATA
1 AATA
34780818 TATAGGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (15 bp):
AATAAATTGGTGATT
Found at i:34781553 original size:103 final size:105
Alignment explanation
Indices: 34781439--34781638 Score: 264
Period size: 105 Copynumber: 1.9 Consensus size: 105
34781429 ATCATACTAG
*
34781439 GAAAATAAAATA-TTATTTTTTTAGAAAATGGTT-CGACCATT-TTTCATCCAGCTGTAAACTAA
1 GAAAATAAAATACTTATTTTTTTAGAAAATGGTTAC-ACCATTGTTT-ATCCAGCTATAAACTAA
* * * * *
34781501 TTTATACTTCTCTTTTATTGTT-TTTTTTCCATATTTTGGAC
64 TTCACACTTCCCTTTTATGGTTCTTTATTCCATATTTTGGAC
* * *
34781542 GAAAATAAAATATCTTTTTTTTTTAGAAAATGGTTACATCATTGTTTATCCAGCTATACACTAAT
1 GAAAATAAAATA-CTTATTTTTTTAGAAAATGGTTACACCATTGTTTATCCAGCTATAAACTAAT
34781607 TCACACTTCCCTTTTATGGTTCTTTATTCCAT
65 TCACACTTCCCTTTTATGGTTCTTTATTCCAT
34781639 GCTTTGAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
103 12 0.14
105 58 0.70
106 13 0.16
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (105 bp):
GAAAATAAAATACTTATTTTTTTAGAAAATGGTTACACCATTGTTTATCCAGCTATAAACTAATT
CACACTTCCCTTTTATGGTTCTTTATTCCATATTTTGGAC
Found at i:34786448 original size:22 final size:22
Alignment explanation
Indices: 34786423--34786498 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
34786413 AATATTTAGC
* * *
34786423 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
34786445 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
*
34786467 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAAA
34786489 CATGAGAGCT
1 CATGAGAGCT
34786499 CATTTCAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:34804079 original size:22 final size:21
Alignment explanation
Indices: 34804014--34804080 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
34804004 GTGAATATCT
*
34804014 ACACACCCATGTGAAAGAGGC
1 ACACGCCCATGTGAAAGAGGC
* * *
34804035 ACACGCCCCTTTGAAAGAAGC
1 ACACGCCCATGTGAAAGAGGC
34804056 ACACGCCCATGTGAAAAGAGGC
1 ACACGCCCATGTG-AAAGAGGC
34804078 ACA
1 ACA
34804081 TGGCCGTGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 28 0.74
22 10 0.26
ACGTcount: A:0.37, C:0.30, G:0.22, T:0.10
Consensus pattern (21 bp):
ACACGCCCATGTGAAAGAGGC
Found at i:34804912 original size:7 final size:7
Alignment explanation
Indices: 34804894--34804935 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
34804884 TTCCCAAGTA
34804894 AAATAA-
1 AAATAAT
34804900 AAATAAT
1 AAATAAT
34804907 AAATAAT
1 AAATAAT
34804914 AAATAGAT
1 AAATA-AT
*
34804922 AAAAATAT
1 AAATA-AT
34804930 AAATAA
1 AAATAA
34804936 GTATCTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 6 0.19
7 13 0.42
8 12 0.39
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:34804916 original size:16 final size:17
Alignment explanation
Indices: 34804895--34804935 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
34804885 TCCCAAGTAA
34804895 AATAAA-AATAATAAAT
1 AATAAATAATAATAAAT
34804911 AATAAATAGATAA-AAAT
1 AATAAATA-ATAATAAAT
34804928 -ATAAATAA
1 AATAAATAA
34804936 GTATCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.57
17 5 0.22
18 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AATAAATAATAATAAAT
Found at i:34809038 original size:4 final size:4
Alignment explanation
Indices: 34809024--34809083 Score: 59
Period size: 4 Copynumber: 14.5 Consensus size: 4
34809014 TTAAACTAAG
* * *
34809024 TAAA AAAA TAAA TAAA TAAA TAAA TATAA -AACTT TAAA AAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAA--A TAAA TAAA TAAA TAAA
34809074 TAAA TAAA TA
1 TAAA TAAA TA
34809084 TAAAACTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
3 1 0.02
4 41 0.89
5 2 0.04
6 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:34809062 original size:34 final size:34
Alignment explanation
Indices: 34809024--34809093 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
34809014 TTAAACTAAG
34809024 TAAAAAAATAAATAAATAAATAAATATAAAACTT
1 TAAAAAAATAAATAAATAAATAAATATAAAACTT
34809058 TAAAAAAATAAATAAATAAATAAATATAAAACTT
1 TAAAAAAATAAATAAATAAATAAATATAAAACTT
34809092 TA
1 TA
34809094 CAACTTGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (34 bp):
TAAAAAAATAAATAAATAAATAAATATAAAACTT
Found at i:34810601 original size:2 final size:2
Alignment explanation
Indices: 34810594--34810618 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34810584 CATGATTCAC
34810594 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
34810619 CTCAATTGAT
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:34817336 original size:52 final size:51
Alignment explanation
Indices: 34817249--34817406 Score: 182
Period size: 50 Copynumber: 3.1 Consensus size: 51
34817239 AATGCATGGC
*
34817249 TTAA-GATGCAAAC-TAAATGAACA-AATGAGTTACATAATGCATGACTTAAT
1 TTAATGATGCAAACTTAAAT-AACATGA-GAGTTACATAATGCATGACTTAAT
* *
34817299 TTAATGATGCAAACTTTAAATAACATGGGAGTTACATAATGCAT-ATCATAAT
1 TTAATGATGCAAAC-TTAAATAACATGAGAGTTACATAATGCATGA-CTTAAT
* * *
34817351 TT-ATGATGGAAACTTAACTAACATGAGAGTTACATAATGCATGACTTTAT
1 TTAATGATGCAAACTTAAATAACATGAGAGTTACATAATGCATGACTTAAT
*
34817401 TAAATG
1 TTAATG
34817407 CAGAACACAT
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
50 36 0.39
51 24 0.26
52 27 0.29
53 5 0.05
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (51 bp):
TTAATGATGCAAACTTAAATAACATGAGAGTTACATAATGCATGACTTAAT
Found at i:34821493 original size:6 final size:6
Alignment explanation
Indices: 34821482--34821506 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34821472 ACATGAAAAG
34821482 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
34821507 TTAAATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:34821893 original size:17 final size:17
Alignment explanation
Indices: 34821871--34821907 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
34821861 AATTATATAA
34821871 AAATAAATAATG-AAAAT
1 AAATAAATAA-GAAAAAT
34821888 AAATAAATAAGAAAAAT
1 AAATAAATAAGAAAAAT
34821905 AAA
1 AAA
34821908 AAAACGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAATAAATAAGAAAAAT
Found at i:34832362 original size:29 final size:29
Alignment explanation
Indices: 34832311--34832398 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 29
34832301 GGACGTTACA
* * * *
34832311 ACTGGTACACAGTACCTAGAACTGTAATC
1 ACTGGCACAAAGTACTTGGAACTGTAATC
* * *
34832340 A-TGGGCACAGAGTTCTTGGAACTATAA-C
1 ACT-GGCACAAAGTACTTGGAACTGTAATC
* *
34832368 ACTGGTACAAAGTACTTGAAACTGTAATC
1 ACTGGCACAAAGTACTTGGAACTGTAATC
34832397 AC
1 AC
34832399 CTGCAACTAG
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
28 22 0.49
29 23 0.51
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (29 bp):
ACTGGCACAAAGTACTTGGAACTGTAATC
Found at i:34836769 original size:24 final size:24
Alignment explanation
Indices: 34836742--34836788 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
34836732 CAAAGGCTTA
34836742 ACCTTTAATTCAGCTAAAATAAAC
1 ACCTTTAATTCAGCTAAAATAAAC
*
34836766 ACCTTTAATTTAGCTAAAATAAA
1 ACCTTTAATTCAGCTAAAATAAA
34836789 ACCGTCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (24 bp):
ACCTTTAATTCAGCTAAAATAAAC
Found at i:34839093 original size:25 final size:25
Alignment explanation
Indices: 34839055--34839123 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
34839045 TCCTATACAT
* *
34839055 GTATGCTCATACGAGCTGTAGATTG
1 GTATGCTCACACGAGCTGTAGATCG
* *
34839080 GTATGCTCACACGAGATATAGATCG
1 GTATGCTCACACGAGCTGTAGATCG
* *
34839105 GTATGCTCTCATGAGCTGT
1 GTATGCTCACACGAGCTGT
34839124 GGGTCGAAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAGATCG
Found at i:34854516 original size:26 final size:26
Alignment explanation
Indices: 34854487--34854540 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
34854477 GATACAAGTG
34854487 TTTTGTTTTATCCTCTTTTTACTAAA
1 TTTTGTTTTATCCTCTTTTTACTAAA
34854513 TTTTGTTTTATCCTCTTTTTACTAAA
1 TTTTGTTTTATCCTCTTTTTACTAAA
34854539 TT
1 TT
34854541 AACCAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTTGTTTTATCCTCTTTTTACTAAA
Found at i:34854947 original size:29 final size:29
Alignment explanation
Indices: 34854914--34854976 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
34854904 AGAAGAAACT
*
34854914 AAATTAATTAATTTTAATATCATGGTAAC
1 AAATTAATTAATTTTAATATCATAGTAAC
34854943 AAATTAATTAATTTTAATATCATAGTAAC
1 AAATTAATTAATTTTAATATCATAGTAAC
34854972 AAATT
1 AAATT
34854977 GAGTGACATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (29 bp):
AAATTAATTAATTTTAATATCATAGTAAC
Found at i:34877151 original size:10 final size:10
Alignment explanation
Indices: 34877108--34877152 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
34877098 AATATGAATA
*
34877108 TGATGAATTT
1 TGATTAATTT
*
34877118 TAATTAATTT
1 TGATTAATTT
34877128 TGTAGTTAATTT
1 TG-A-TTAATTT
34877140 TGATTAATTT
1 TGATTAATTT
34877150 TGA
1 TGA
34877153 CTATTTTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (10 bp):
TGATTAATTT
Found at i:34881214 original size:22 final size:22
Alignment explanation
Indices: 34881189--34881256 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
34881179 AGAAGTAGAA
34881189 GTTAAACATGAGAGCTTAGTAC
1 GTTAAACATGAGAGCTTAGTAC
34881211 GTTAAACATGAGAGCTTAGTAC
1 GTTAAACATGAGAGCTTAGTAC
*
34881233 GTGAAACATGAGAGCTTAGTAC
1 GTTAAACATGAGAGCTTAGTAC
34881255 GT
1 GT
34881257 ACTATCAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.26
Consensus pattern (22 bp):
GTTAAACATGAGAGCTTAGTAC
Found at i:34885341 original size:16 final size:15
Alignment explanation
Indices: 34885301--34885347 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
34885291 AAAAAAGATG
34885301 ATAATTAT-T-AATAT
1 ATAATTATATCAAT-T
*
34885315 ATAATTATATCCATT
1 ATAATTATATCAATT
34885330 ATAATATATATCAATT
1 ATAAT-TATATCAATT
34885346 AT
1 AT
34885348 TATCAGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATTATATCAATT
Found at i:34889526 original size:21 final size:21
Alignment explanation
Indices: 34889496--34889539 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34889486 ATTTAATCAA
34889496 TTTAGCTTGAATTTAATTT-GT
1 TTTAGCTTG-ATTTAATTTCGT
* *
34889517 TTTAGGTTGATTTCATTTCGT
1 TTTAGCTTGATTTAATTTCGT
34889538 TT
1 TT
34889540 GTTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.18, C:0.07, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTAGCTTGATTTAATTTCGT
Found at i:34890330 original size:15 final size:15
Alignment explanation
Indices: 34890310--34890347 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
34890300 AACTCAATAT
34890310 TTACTTGTCACTTTA
1 TTACTTGTCACTTTA
34890325 TTACTTGTCACTTTA
1 TTACTTGTCACTTTA
34890340 TTACTTGT
1 TTACTTGT
34890348 TGCGATTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (15 bp):
TTACTTGTCACTTTA
Found at i:34892710 original size:11 final size:11
Alignment explanation
Indices: 34892685--34892722 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
34892675 TAACATGTTG
34892685 AATTTTA-ATT
1 AATTTTATATT
*
34892695 AATTTTATAAT
1 AATTTTATATT
*
34892706 AATTTTTTATT
1 AATTTTATATT
34892717 AATTTT
1 AATTTT
34892723 GATTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:34896006 original size:41 final size:42
Alignment explanation
Indices: 34895941--34896236 Score: 436
Period size: 42 Copynumber: 7.1 Consensus size: 42
34895931 GTTTGCAGCG
*
34895941 TTTTTTCTTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGC-T
1 TTTTTTC-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
* * *
34895983 TTTTTTCTAAGCGCCTCTGAAGAACATGGTCTTTAGCGGCCT
1 TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
34896025 TTTTTT-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
1 TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
* * *
34896066 TTCTTTCTAAGCGCCACTAAAGAACATGTTCTTTAGCGGCGT
1 TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
*
34896108 TTTTTTCTAAGCGCCGCTAAAGAATATGGTCTTTAGCGGCG-
1 TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
* *
34896149 TTTTTTCTAAGCGCCTCTGAAGAACATGGTCTTTAGCGGCGT
1 TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
* * * *
34896191 TTCTTTCTAAGCGCTGCTAAAGAACATGGTCTTTAGTGGTGT
1 TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
34896233 TTTT
1 TTTT
34896237 ATACAAAAAC
Statistics
Matches: 228, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
41 105 0.46
42 123 0.54
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGT
Found at i:34896160 original size:125 final size:125
Alignment explanation
Indices: 34895938--34896236 Score: 467
Period size: 125 Copynumber: 2.4 Consensus size: 125
34895928 AACGTTTGCA
*
34895938 GCGTTT-TTTCTTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGC-TTTTTTTCTAAGCGCCTCT
1 GCGTTTCTTTC-TAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCT
* *
34896001 GAAGAACATGGTCTTTAGCGGCCTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
65 AAAGAACATGGTCTTTAGCGGCCTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
* * *
34896062 GCGTTTCTTTCTAAGCGCCACTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
1 GCGTTTCTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTA
* * * *
34896127 AAGAATATGGTCTTTAGCGGCGTTTTTTCTAAGCGCCTCTGAAGAACATGGTCTTTAGCG
66 AAGAACATGGTCTTTAGCGGCCTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
* *
34896187 GCGTTTCTTTCTAAGCGCTGCTAAAGAACATGGTCTTTAGTGGTGTTTTT
1 GCGTTTCTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTTT
34896237 ATACAAAAAC
Statistics
Matches: 158, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
124 36 0.23
125 122 0.77
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (125 bp):
GCGTTTCTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTA
AAGAACATGGTCTTTAGCGGCCTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
Found at i:34896235 original size:83 final size:82
Alignment explanation
Indices: 34895938--34896236 Score: 463
Period size: 83 Copynumber: 3.6 Consensus size: 82
34895928 AACGTTTGCA
* *
34895938 GCGTTTTTTCTTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCTTTTTTTCTAAGCGCCTCTGA
1 GCGTTTTTTC-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAGCGCCTCTGA
34896003 AGAACATGGTCTTTAGCG
65 AGAACATGGTCTTTAGCG
* * * *
34896021 GCCTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGCGCCACTAA
1 GCGTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT-TTTCTAAGCGCCTCTGA
*
34896086 AGAACATGTTCTTTAGCG
65 AGAACATGGTCTTTAGCG
*
34896104 GCGTTTTTTTCTAAGCGCCGCTAAAGAATATGGTCTTTAGCGGCGTTTTTTCTAAGCGCCTCTGA
1 GCG-TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAGCGCCTCTGA
34896169 AGAACATGGTCTTTAGCG
65 AGAACATGGTCTTTAGCG
* * *
34896187 GCGTTTCTTTCTAAGCGCTGCTAAAGAACATGGTCTTTAGTGGTGTTTTT
1 GCGTTT-TTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
34896237 ATACAAAAAC
Statistics
Matches: 196, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
82 38 0.19
83 116 0.59
84 42 0.21
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (82 bp):
GCGTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAGCGCCTCTGAA
GAACATGGTCTTTAGCG
Found at i:34896580 original size:21 final size:20
Alignment explanation
Indices: 34896554--34896624 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
34896544 TTTTGTTCTA
34896554 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTC-CTCGCTGCAGC
34896575 CTCTGCTTCCTTCGCTGCAGC
1 CTCTGCTTCC-TCGCTGCAGC
* ** *
34896596 CGCTGCTTCCCTTACTGCCGC
1 CTCTGCTT-CCTCGCTGCAGC
34896617 CTCTGCTT
1 CTCTGCTT
34896625 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.93
22 2 0.05
ACGTcount: A:0.04, C:0.44, G:0.18, T:0.34
Consensus pattern (20 bp):
CTCTGCTTCCTCGCTGCAGC
Found at i:34903081 original size:27 final size:26
Alignment explanation
Indices: 34903034--34903084 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
34903024 TCTTACATTT
* *
34903034 AAATAATTAATACCTATTTATTTAAC
1 AAATAAATAATACCTACTTATTTAAC
34903060 AAATAAATAATTACCTACTTATTTA
1 AAATAAATAA-TACCTACTTATTTA
34903085 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAAATAATACCTACTTATTTAAC
Found at i:34903943 original size:41 final size:41
Alignment explanation
Indices: 34903777--34903945 Score: 141
Period size: 41 Copynumber: 4.1 Consensus size: 41
34903767 TTTTGTTACT
* * * * * *
34903777 ATTAGCGGCACTTCGTCAAAAACGCCGCTAAAGCTAC-ATTC
1 ATTAGCGGCGCTTAGACAAAAACGCCACTAAAGGTCCGA-TC
* *
34903818 ATTAGCGGCGCTTAGACAAAAGCGCCACTAAA-GCCCG-TGC
1 ATTAGCGGCGCTTAGACAAAAACGCCACTAAAGGTCCGAT-C
* * * * *
34903858 AGTAGCAGCGCATAGACATAAACGCCACTAAAGG-CCTGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCACTAAAGGTCC-GATC
*
34903899 ATTAGCGGCGCTTA-ACTAAAAACGCCGCTAAAGGTCCGATC
1 ATTAGCGGCGCTTAGAC-AAAAACGCCACTAAAGGTCCGATC
34903940 ATTAGC
1 ATTAGC
34903946 TTCGCATCCG
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
39 1 0.01
40 33 0.33
41 65 0.64
42 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.18
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGACAAAAACGCCACTAAAGGTCCGATC
Found at i:34904092 original size:40 final size:40
Alignment explanation
Indices: 34904043--34904121 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
34904033 GATTCCTATT
* *
34904043 TTTAGCGGCGATTTTGGAAATACGCCGCTGATGCTCGATC
1 TTTAGCGGCGATTTTGGAAAAACGCCGCTAATGCTCGATC
* *
34904083 TTTAGCGGCGCTTTTGTAAAAACGCCGCTAATGCTCGAT
1 TTTAGCGGCGATTTTGGAAAAACGCCGCTAATGCTCGAT
34904122 TTTGAGTGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGATTTTGGAAAAACGCCGCTAATGCTCGATC
Found at i:34904137 original size:40 final size:40
Alignment explanation
Indices: 34904043--34904154 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 40
34904033 GATTCCTATT
** * * *
34904043 TTTAGCGGCGATTTTGGAAATACGCCGCTGATGCTCGATC
1 TTTAGCGGCCCTTTTGTAAAAACGCCGCTAATGCTCGATC
*
34904083 TTTAGCGGCGCTTTTGTAAAAACGCCGCTAATGCTCGAT-
1 TTTAGCGGCCCTTTTGTAAAAACGCCGCTAATGCTCGATC
* **
34904122 TTTGAGTGGCCCTTTTGTTCCAAACGCCGCTAA
1 TTT-AGCGGCCCTTTTG-TAAAAACGCCGCTAA
34904155 ATGTGCCGCT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.05
40 46 0.74
41 13 0.21
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (40 bp):
TTTAGCGGCCCTTTTGTAAAAACGCCGCTAATGCTCGATC
Found at i:34904763 original size:18 final size:18
Alignment explanation
Indices: 34904740--34904775 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34904730 AATTATAAGT
34904740 TTTTTATAA-TTTTTAAAA
1 TTTTTA-AATTTTTTAAAA
34904758 TTTTTAAATTTTTTAAAA
1 TTTTTAAATTTTTTAAAA
34904776 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAAATTTTTTAAAA
Found at i:34907021 original size:113 final size:112
Alignment explanation
Indices: 34906747--34907022 Score: 261
Period size: 113 Copynumber: 2.4 Consensus size: 112
34906737 TGGACGTCGG
* *
34906747 ATACATATATTTCAAAAAGAACAAAGGTTGTTCTAAGTGTTTCTATATATTTTAAAGGATCCTTA
1 ATACAAATATTTCAAAAA-ATCAAAGGTT-TTCTAAGT-TTTCTATATATTTTAAAGGATCCTTA
* * * ** * * **
34906812 GAAATAATATTCTTATATCTATGTTTGAATATGTCGGACATGAATATCTC
63 GAAATAATATTCCTATATCTATATTTGAATATATCAAACAAGAATAACAA
* ** *
34906862 ATACAAATATTTTAAAAGAAT-AAATATTTTTCT-AGTTTTTTCTATATA-TTTAGAGGATCCTT
1 ATACAAATATTTCAAAA-AATCAAA-GGTTTTCTAAG--TTTTCTATATATTTTAAAGGATCCTT
** * *
34906924 AGGGATTATATTCCTATATCTATATTTGAATATATCAAACAAGGATAACAA
62 AGAAATAATATTCCTATATCTATATTTGAATATATCAAACAAGAATAACAA
* *
34906975 ATACAGATATTTCAAAAAATCAAAGGTTTATCTAAGTTTACATATATA
1 ATACAAATATTTCAAAAAATCAAAGGTTT-TCTAAGTTTTC-TATATA
34907023 GATGATCCTT
Statistics
Matches: 129, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
112 10 0.08
113 80 0.62
114 19 0.15
115 19 0.15
116 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (112 bp):
ATACAAATATTTCAAAAAATCAAAGGTTTTCTAAGTTTTCTATATATTTTAAAGGATCCTTAGAA
ATAATATTCCTATATCTATATTTGAATATATCAAACAAGAATAACAA
Found at i:34912994 original size:45 final size:45
Alignment explanation
Indices: 34912943--34913033 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
34912933 ATACTTCTCG
34912943 ATGGAAAAGGTCCACTTATATCAATGAAAACAATCAAATAGCTTT
1 ATGGAAAAGGTCCACTTATATCAATGAAAACAATCAAATAGCTTT
34912988 ATGGAAAAGGTCCACTTATATCAATGAAAACAATCAAATAGCTTT
1 ATGGAAAAGGTCCACTTATATCAATGAAAACAATCAAATAGCTTT
34913033 A
1 A
34913034 CACACTTTTA
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:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (45 bp):
ATGGAAAAGGTCCACTTATATCAATGAAAACAATCAAATAGCTTT
Found at i:34924102 original size:50 final size:50
Alignment explanation
Indices: 34923978--34924269 Score: 259
Period size: 50 Copynumber: 5.7 Consensus size: 50
34923968 GATAATAACA
* * ** * *
34923978 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCTTATAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
34924027 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
34924077 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCCCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
34924127 TGCCAACT-TCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
34924177 TGCCAACT-CCATGTCTCAGACATGGTCTTGCATAGGACCTCTCATAATCTTAACGA
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A---T--CGG
* *
34924233 TGCCAATGCCATGTCTCAGTCATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
34924270 TCTCATTCCC
Statistics
Matches: 200, Mismatches: 33, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 123 0.62
51 1 0.00
54 1 0.00
55 1 0.00
56 34 0.17
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:34929119 original size:25 final size:25
Alignment explanation
Indices: 34929091--34929259 Score: 123
Period size: 25 Copynumber: 6.8 Consensus size: 25
34929081 CTGTTATTTA
*
34929091 GCTCTTATGAGCATCCCGATATATG
1 GCTCTTATGAGCTTCCCGATATATG
* *
34929116 GCTCTCT-TGAGCTTCCCGTTATTTG
1 GCTCT-TATGAGCTTCCCGATATATG
* * *
34929141 GCTCTCACGAGCTTCCCGATA-ACTA
1 GCTCTTATGAGCTTCCCGATATA-TG
** *
34929166 GCTCGCATGAGCTTCCCGAT-TACG
1 GCTCTTATGAGCTTCCCGATATATG
*
34929190 GCTCTTATGAGCTTCCC-ATTACATG
1 GCTCTTATGAGCTTCCCGA-TATATG
** *
34929215 GCTCACATGAGCTTCTC-ATTATATG
1 GCTCTTATGAGCTTCCCGA-TATATG
** *
34929240 GCTCGAAAGAGCTTCCCGAT
1 GCTCTTATGAGCTTCCCGAT
34929260 TACATGCTCG
Statistics
Matches: 113, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.01
24 16 0.14
25 94 0.83
26 2 0.02
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATATATG
Found at i:34929158 original size:50 final size:49
Alignment explanation
Indices: 34929074--34929276 Score: 153
Period size: 50 Copynumber: 4.1 Consensus size: 49
34929064 CATCTCGCAA
* * * * * *
34929074 GAGCGTCCTGTTATTTAGCTCTTATGAGCATCCCGATATATGGCTCTCTT
1 GAGCTTCCCGTTATTTGGCTCTTATGAGCTTCCCGATA-ATGGCTCACAT
* * * *
34929124 GAGCTTCCCGTTATTTGGCTCTCACGAGCTTCCCGATAACTAGCTCGCAT
1 GAGCTTCCCGTTATTTGGCTCTTATGAGCTTCCCGATAA-TGGCTCACAT
*
34929174 GAGCTTCCCG--ATTACGGCTCTTATGAGCTTCCC-ATTACATGGCTCACAT
1 GAGCTTCCCGTTATT-TGGCTCTTATGAGCTTCCCGA-TA-ATGGCTCACAT
* * * ** * *
34929223 GAGCTTCTCATTATATGGCTCGAAAGAGCTTCCCGATTACAT-GCTCGCAT
1 GAGCTTCCCGTTATTTGGCTCTTATGAGCTTCCCGA-TA-ATGGCTCACAT
34929273 GAGC
1 GAGC
34929277 ATACCTGTAT
Statistics
Matches: 124, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
48 4 0.03
49 35 0.28
50 76 0.61
51 9 0.07
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (49 bp):
GAGCTTCCCGTTATTTGGCTCTTATGAGCTTCCCGATAATGGCTCACAT
Found at i:34929244 original size:74 final size:74
Alignment explanation
Indices: 34929097--34929262 Score: 176
Period size: 74 Copynumber: 2.2 Consensus size: 74
34929087 TTTAGCTCTT
* * * ** *
34929097 ATGAGCATCCCGATATATGGCTCTCTTGAGCTTCCCGTTATTTGGCTCTCACGAGCTTCCCGATA
1 ATGAGCTTCCCGAT-TACGGCTCTCTTGAGCTTCCCATTACATGGCTCACACGAGCTTCCCGATA
*
34929162 ACTAGCTCGC
65 ACTAGCTCGA
* *
34929172 ATGAGCTTCCCGATTACGGCTCT-TATGAGCTTCCCATTACATGGCTCACATGAGCTTCTC-ATT
1 ATGAGCTTCCCGATTACGGCTCTCT-TGAGCTTCCCATTACATGGCTCACACGAGCTTCCCGA-T
*
34929235 ATA-TGGCTCGA
64 A-ACTAGCTCGA
*
34929246 AAGAGCTTCCCGATTAC
1 ATGAGCTTCCCGATTAC
34929263 ATGCTCGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
73 2 0.03
74 61 0.79
75 14 0.18
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (74 bp):
ATGAGCTTCCCGATTACGGCTCTCTTGAGCTTCCCATTACATGGCTCACACGAGCTTCCCGATAA
CTAGCTCGA
Found at i:34929269 original size:99 final size:99
Alignment explanation
Indices: 34929091--34929276 Score: 241
Period size: 99 Copynumber: 1.9 Consensus size: 99
34929081 CTGTTATTTA
* * * * * ** *
34929091 GCTCTTATGAGCATCCCGATATATGGCTCTCTTGAGCTTCCCGTTATTTGGCTCTCACGAGCTTC
1 GCTCTTATGAGCATCCCGATACATGGCTCACATGAGCTTCCCATTATATGGCTCGAAAGAGCTTC
34929156 CCGATAACTAGCTCGCATGAGCTTCCCGATTACG
66 CCGATAACTAGCTCGCATGAGCTTCCCGATTACG
* *
34929190 GCTCTTATGAGCTTCCC-ATTACATGGCTCACATGAGCTTCTCATTATATGGCTCGAAAGAGCTT
1 GCTCTTATGAGCATCCCGA-TACATGGCTCACATGAGCTTCCCATTATATGGCTCGAAAGAGCTT
*
34929254 CCCGATTAC-ATGCTCGCATGAGC
65 CCCGATAACTA-GCTCGCATGAGC
34929277 ATACCTGTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
98 2 0.03
99 72 0.97
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (99 bp):
GCTCTTATGAGCATCCCGATACATGGCTCACATGAGCTTCCCATTATATGGCTCGAAAGAGCTTC
CCGATAACTAGCTCGCATGAGCTTCCCGATTACG
Found at i:34931610 original size:179 final size:179
Alignment explanation
Indices: 34931310--34931664 Score: 638
Period size: 179 Copynumber: 2.0 Consensus size: 179
34931300 CACAATTTAC
* *
34931310 TTAATCTTATTTATCTACAAATCAAACAAATTGGATTCCATCATGAAATTCCACTATCCACTATT
1 TTAATCTTATTTATCTACAAATCAAACAAAGTGGATTCCATCATGAAATTCCACTATCCACTACT
* *
34931375 AATAATTGCTCTTTTGTTCTATTAGCTAATTAAAAATCTATAGCGATTAAACTTTTATCATTTTT
66 AACAATTGCTCTTTTGTTCTATTAGCTAATTAAAAATCTATAGCGATTAAACTTTTACCATTTTT
34931440 ACGATTTAATCCTTATACTTTAATTAACTATCAATTTAATAAAATTGCT
131 ACGATTTAATCCTTATACTTTAATTAACTATCAATTTAATAAAATTGCT
* *
34931489 TTAATCTTATTTATCTACTAATCAAACAACGTGGATTCCATCATGAAATTCCACTATCCACTACT
1 TTAATCTTATTTATCTACAAATCAAACAAAGTGGATTCCATCATGAAATTCCACTATCCACTACT
*
34931554 AACAATTGCTCTTTTGTTCTATTAGCTAATTAAAAATCTATATCGATTAAACTTTTACCATTTTT
66 AACAATTGCTCTTTTGTTCTATTAGCTAATTAAAAATCTATAGCGATTAAACTTTTACCATTTTT
*
34931619 ATGATTTAATCCTTATACTTTAATTAACTATCAATTTAATAAAATT
131 ACGATTTAATCCTTATACTTTAATTAACTATCAATTTAATAAAATT
34931665 ACTAGACCGA
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
179 168 1.00
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (179 bp):
TTAATCTTATTTATCTACAAATCAAACAAAGTGGATTCCATCATGAAATTCCACTATCCACTACT
AACAATTGCTCTTTTGTTCTATTAGCTAATTAAAAATCTATAGCGATTAAACTTTTACCATTTTT
ACGATTTAATCCTTATACTTTAATTAACTATCAATTTAATAAAATTGCT
Found at i:34932610 original size:42 final size:41
Alignment explanation
Indices: 34932532--34932611 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
34932522 AAAGTCCATC
* * * * *
34932532 TTCAATCTTTTCTCAACCATATCCATTTTTTGTAACTCTTT
1 TTCAATCTTTCCTCAAACATATCCAATTTCTCTAACTCTTT
*
34932573 TTCAATCTTTGCCTCAAACATATTCAATTTCTCTAACTC
1 TTCAATCTTT-CCTCAAACATATCCAATTTCTCTAACTC
34932612 CTTTAGATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 10 0.31
42 22 0.69
ACGTcount: A:0.25, C:0.26, G:0.03, T:0.46
Consensus pattern (41 bp):
TTCAATCTTTCCTCAAACATATCCAATTTCTCTAACTCTTT
Found at i:34947932 original size:21 final size:21
Alignment explanation
Indices: 34947908--34947955 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
34947898 ACGGTTTGCA
* *
34947908 CACACGGA-TGTGTGGAATAGT
1 CACACGAAGTGTGTGG-ATAGC
34947929 CACAC-AAGTGTGTGGATAGC
1 CACACGAAGTGTGTGGATAGC
34947949 CACACGA
1 CACACGA
34947956 CCGTGTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (21 bp):
CACACGAAGTGTGTGGATAGC
Found at i:34949199 original size:40 final size:42
Alignment explanation
Indices: 34949132--34949225 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 42
34949122 GCCTAGAATT
34949132 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAATAAAAATTAAAAAAAGTATTTTAAAAA
34949176 TATTTTAAAATT-AA-AAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAATAAAAATTAAAAAAAGTATTTTAAAAA
* *
34949216 AATTTAAAAA
1 TATTTTAAAA
34949226 AAATTTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
40 34 0.71
41 2 0.04
43 6 0.12
44 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (42 bp):
TATTTTAAAATTAAATAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:34949202 original size:11 final size:11
Alignment explanation
Indices: 34949188--34949254 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
34949178 TTTTAAAATT
34949188 AAAAAAA-TTA
1 AAAAAAATTTA
*
34949198 AAAAAAGTATTTT
1 AAAAAA--ATTTA
34949211 AAAAAAATTTA
1 AAAAAAATTTA
34949222 AAAAAAATTT-
1 AAAAAAATTTA
*
34949232 --TAAAA-TT-
1 AAAAAAATTTA
34949239 AAAAAAATTTA
1 AAAAAAATTTA
34949250 AAAAA
1 AAAAA
34949255 GTATTTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
9 4 0.09
10 8 0.17
11 19 0.41
12 1 0.02
13 8 0.17
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (11 bp):
AAAAAAATTTA
Found at i:34949215 original size:23 final size:22
Alignment explanation
Indices: 34949186--34949236 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
34949176 TATTTTAAAA
34949186 TTAAAAAAA-TTAAAAAAAGTATT
1 TTAAAAAAATTTAAAAAAA--ATT
34949209 TTAAAAAAATTTAAAAAAAATT
1 TTAAAAAAATTTAAAAAAAATT
34949231 TTAAAA
1 TTAAAA
34949237 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.33
23 9 0.33
24 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAAAAATTTAAAAAAAATT
Found at i:34949232 original size:51 final size:51
Alignment explanation
Indices: 34949166--34949263 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
34949156 TAAAAAAAGT
* *
34949166 ATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAA
1 ATTTAAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAA
*
34949217 ATTTAAAAAAAATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAA
1 ATTTAAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAA
34949264 TAGTATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (51 bp):
ATTTAAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAA
Found at i:34949254 original size:12 final size:12
Alignment explanation
Indices: 34949138--34949236 Score: 51
Period size: 12 Copynumber: 8.0 Consensus size: 12
34949128 AATTTATTTT
34949138 AAAAA-TTAAAA
1 AAAAATTTAAAA
34949149 TAAAAA-TTAAAA
1 -AAAAATTTAAAA
* *
34949161 AAAGTATTTTAAA
1 AAA-AATTTAAAA
* *
34949174 AATATTTTAAAATTA
1 AAAAATTT-AAA--A
*
34949189 AAAAAATTAAAA
1 AAAAATTTAAAA
* *
34949201 AAAGTATTT-TAA
1 AAA-AATTTAAAA
34949213 AAAAATTTAAAA
1 AAAAATTTAAAA
*
34949225 AAAATTTTAAAA
1 AAAAATTTAAAA
34949237 TTAAAAAAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
11 7 0.11
12 37 0.57
13 12 0.18
14 3 0.05
15 6 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AAAAATTTAAAA
Found at i:34949260 original size:12 final size:10
Alignment explanation
Indices: 34949182--34949254 Score: 64
Period size: 10 Copynumber: 7.3 Consensus size: 10
34949172 AAAATATTTT
34949182 AAAA-TTAAA
1 AAAATTTAAA
*
34949191 AAAATTAAAA
1 AAAATTTAAA
34949201 AAAGTATTTTAAA
1 AAA--A-TTTAAA
34949214 AAAATTTAAAA
1 AAAATTT-AAA
*
34949225 AAAATTT--T
1 AAAATTTAAA
34949233 AAAA-TTAAA
1 AAAATTTAAA
34949242 AAAATTTAAA
1 AAAATTTAAA
34949252 AAA
1 AAA
34949255 GTATTTTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 8 0.15
10 18 0.35
11 11 0.21
12 1 0.02
13 8 0.15
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:34949319 original size:5 final size:5
Alignment explanation
Indices: 34949309--34949340 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
34949299 ATTTATTATT
34949309 CGGGC CGGGC CGGGC CGGGC CGGGCC CGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGG-C CGGGC C
34949341 AAAAAAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.44, G:0.56, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:34949807 original size:9 final size:9
Alignment explanation
Indices: 34949793--34949820 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
34949783 TATAGTTTGA
34949793 TATTCGAAT
1 TATTCGAAT
34949802 TATTCGAAT
1 TATTCGAAT
34949811 TATTCGAAT
1 TATTCGAAT
34949820 T
1 T
34949821 CAAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:34956863 original size:16 final size:16
Alignment explanation
Indices: 34956817--34956864 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
34956807 TCATCCTAAT
34956817 TATA-AAAAAAT-TAA
1 TATATAAAAAATATAA
34956831 TATATAAAAATATATAA
1 TATATAAAAA-ATATAA
* *
34956848 TATTTTAAAAATATAA
1 TATATAAAAAATATAA
34956864 T
1 T
34956865 GATAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 4 0.14
15 5 0.17
16 9 0.31
17 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATAAAAAATATAA
Found at i:34958095 original size:15 final size:15
Alignment explanation
Indices: 34958071--34958104 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34958061 TATGTGTTTG
*
34958071 TATTTATTTATTATT
1 TATTTATTTATCATT
*
34958086 TATTTGTTTATCATT
1 TATTTATTTATCATT
34958101 TATT
1 TATT
34958105 AACATTGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTATTTATCATT
Found at i:34958136 original size:23 final size:23
Alignment explanation
Indices: 34958110--34958168 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
34958100 TTATTAACAT
**
34958110 TGTTCATGAACATATTCGTTTAA
1 TGTTCATGAACATATTCAATTAA
* *
34958133 TGTTCGTGAACATGTTCAATTAA
1 TGTTCATGAACATATTCAATTAA
34958156 -GTTACATGAACAT
1 TGTT-CATGAACAT
34958169 GTTTGTGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (23 bp):
TGTTCATGAACATATTCAATTAA
Found at i:34960103 original size:12 final size:11
Alignment explanation
Indices: 34960086--34960120 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
34960076 AACAAATCCT
34960086 CTCTCATATTTC
1 CTCTCA-ATTTC
34960098 CTCTCAA-TTC
1 CTCTCAATTTC
34960108 CTCTCAATTTC
1 CTCTCAATTTC
34960119 CT
1 CT
34960121 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:34960168 original size:51 final size:54
Alignment explanation
Indices: 34960101--34960224 Score: 193
Period size: 51 Copynumber: 2.4 Consensus size: 54
34960091 ATATTTCCTC
*
34960101 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATA-TTT-A-ATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTTAATATT
*
34960151 TCAATTTCCTCTCAATTTTCTTCAAAAATTCTCTCAAATCCATATTTTGAATATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTT-AATATT
34960206 TCAATTTCCTCTCAATTTC
1 TCAATTTCCTCTCAATTTC
34960225 TTTTTTTAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
50 4 0.06
51 37 0.56
52 3 0.05
54 1 0.02
55 21 0.32
ACGTcount: A:0.29, C:0.26, G:0.01, T:0.44
Consensus pattern (54 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTTAATATT
Found at i:34962565 original size:23 final size:23
Alignment explanation
Indices: 34962535--34962755 Score: 130
Period size: 29 Copynumber: 8.9 Consensus size: 23
34962525 TTTGATGTAA
34962535 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
34962558 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
34962581 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
34962610 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
* *
34962639 TAAAAATCCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
34962661 TAAAAACCCTAACCTAATTTACT
1 TAAAAACCCTAACCTAATTTAAT
34962684 TAAAAATCCTAAACCCTAACCTAATTTAAT
1 T---AA----AAACCCTAACCTAATTTAAT
* *
34962714 TTAAAACCCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
34962736 TAAAAACTCTAACCTAATTT
1 TAAAAACCCTAACCTAATTT
34962756 GATAATTTTA
Statistics
Matches: 162, Mismatches: 13, Indels: 45
0.74 0.06 0.20
Matches are distributed among these distances:
21 16 0.10
22 19 0.12
23 37 0.23
24 13 0.08
25 3 0.02
26 2 0.01
27 4 0.02
29 48 0.30
30 20 0.12
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:34962592 original size:18 final size:20
Alignment explanation
Indices: 34962546--34962588 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
34962536 AAAAACCCTA
34962546 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
34962567 TAGCCTAATTTAATTAAAAACC
1 -A-CCTAATTTAATTAAAAACC
34962589 CTAACCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:34962598 original size:52 final size:53
Alignment explanation
Indices: 34962538--34962725 Score: 214
Period size: 45 Copynumber: 3.6 Consensus size: 53
34962528 GATGTAATAA
* *
34962538 AAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCT
1 AAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAATCCT
34962591 -AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAATCCT
1 AAACCCTAACCTAATTTAATT--AAA----AACCCTAACCTAATTTAATTAAAAATCCT
* *
34962649 AAACCCT----T-A---ACTTAAAAACCCTAACCTAATTTACTTAAAAATCCT
1 AAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAATCCT
*
34962694 AAACCCTAACCTAATTTAATTTAAAACCCTAA
1 AAACCCTAACCTAATTTAATTAAAAACCCTAA
34962726 ACCCTTAACT
Statistics
Matches: 114, Mismatches: 6, Indels: 30
0.76 0.04 0.20
Matches are distributed among these distances:
45 35 0.31
49 4 0.04
50 1 0.01
51 3 0.03
52 20 0.18
53 13 0.11
54 4 0.04
55 1 0.01
58 27 0.24
59 6 0.05
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.29
Consensus pattern (53 bp):
AAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAATCCT
Found at i:34962602 original size:29 final size:29
Alignment explanation
Indices: 34962539--34962655 Score: 165
Period size: 29 Copynumber: 4.2 Consensus size: 29
34962529 ATGTAATAAA
34962539 AACCCTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
34962562 AACCCTAGCCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
34962591 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
34962620 AACCCTAACCTAATTTAATTAAAAATCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
34962649 AAACCCT
1 -AACCCT
34962656 TAACTTAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
23 19 0.23
25 3 0.04
29 56 0.67
30 6 0.07
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:34962664 original size:22 final size:22
Alignment explanation
Indices: 34962634--34962700 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
34962624 CTAACCTAAT
34962634 TTAA-TTAAAAATCCTAAACCC
1 TTAACTTAAAAATCCTAAACCC
* *
34962655 TTAACTTAAAAACCCT-AACCTAA
1 TTAACTTAAAAATCCTAAACC--C
*
34962678 TTTACTTAAAAATCCTAAACCC
1 TTAACTTAAAAATCCTAAACCC
34962700 T
1 T
34962701 AACCTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 8 0.22
22 11 0.30
23 14 0.38
24 4 0.11
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAACTTAAAAATCCTAAACCC
Found at i:34962698 original size:30 final size:30
Alignment explanation
Indices: 34962664--34962730 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
34962654 CTTAACTTAA
* *
34962664 AAACCCTAACCTAATTTACTTAAAAATCCT
1 AAACCCTAACCTAATTTAATTAAAAACCCT
*
34962694 AAACCCTAACCTAATTTAATTTAAAACCCT
1 AAACCCTAACCTAATTTAATTAAAAACCCT
34962724 AAACCCT
1 AAACCCT
34962731 TAACTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (30 bp):
AAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:34962729 original size:75 final size:74
Alignment explanation
Indices: 34962591--34962755 Score: 276
Period size: 75 Copynumber: 2.2 Consensus size: 74
34962581 TAAAAACCCT
*
34962591 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAATCCTAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
34962656 TAACTTAAA
66 TAACTTAAA
* * *
34962665 AACCCTAACCTAATTTACTTAAAAATCCTAAACCCTAACCTAATTTAATTTAAAACCCTAAACCC
1 AACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAAACCC
34962730 TTAACTTAAA
65 TTAACTTAAA
*
34962740 AACTCTAACCTAATTT
1 AACCCTAACCTAATTT
34962756 GATAATTTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 27 0.32
75 58 0.68
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (74 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
TAACTTAAA
Found at i:34963782 original size:236 final size:238
Alignment explanation
Indices: 34963340--34963793 Score: 822
Period size: 236 Copynumber: 1.9 Consensus size: 238
34963330 CGCCTTGGTT
* *
34963340 TTGTTAATTTCTTGAACTACCTTATTGCACCATACATGACCTTCCTACATCTGGCCTGCATAACT
1 TTGTTAATTTCTTGAACTACCTTACTGCACCATACATGACCTCCCTACATCTGGCCTGCATAACT
*
34963405 TGCTGCTCGCTTTGAAAATAGCGCCGTCAAACGAAAATATGTCTCTCGCACAACCGATGTTATCG
66 TGCTGCTCGCTTTGAAAATAGCACCGTCAAACGAAAATATGTCTCTCGCACAACCGATGTTATCG
34963470 GTAGATGGCGCGTTCCTTTAAGAACAGAATTTATGCATTCCGCCAGGCTCGACATTATATGACCA
131 GTAGATGGCGCGTTCCTTTAAGAACAGAATTTATGCATTCCGCCAGGCTCGACATTATATGACCA
*
34963535 TATCGTAGGCCATCGTCGTATGCATTCTGCCATCACCTTAGCC
196 TATCGTAGGCCACCGTCGTATGCATTCTGCCATCACCTTAGCC
*
34963578 TTGTTAATTTCTTGAACTACCTTACTGCACCATACATGACCTCCCTGCATCTGGCCTGCATAACT
1 TTGTTAATTTCTTGAACTACCTTACTGCACCATACATGACCTCCCTACATCTGGCCTGCATAACT
*
34963643 TGCTGCTCGCTTTGGAAATAGCACCGTCAAACG-AAA-ATGTCTCTCGCACAACCGATGTTATCG
66 TGCTGCTCGCTTTGAAAATAGCACCGTCAAACGAAAATATGTCTCTCGCACAACCGATGTTATCG
* *
34963706 GTAGATGGCGCGTTCCTTTAAGAACAGAATTTATGCATTCTGCCAGGCTCGACATTATATGGCCA
131 GTAGATGGCGCGTTCCTTTAAGAACAGAATTTATGCATTCCGCCAGGCTCGACATTATATGACCA
34963771 TATCGTAGGCCACCGTCGTATGC
196 TATCGTAGGCCACCGTCGTATGC
34963794 TTGTGCCCAC
Statistics
Matches: 208, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
236 112 0.54
237 3 0.01
238 93 0.45
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (238 bp):
TTGTTAATTTCTTGAACTACCTTACTGCACCATACATGACCTCCCTACATCTGGCCTGCATAACT
TGCTGCTCGCTTTGAAAATAGCACCGTCAAACGAAAATATGTCTCTCGCACAACCGATGTTATCG
GTAGATGGCGCGTTCCTTTAAGAACAGAATTTATGCATTCCGCCAGGCTCGACATTATATGACCA
TATCGTAGGCCACCGTCGTATGCATTCTGCCATCACCTTAGCC
Found at i:34965232 original size:12 final size:12
Alignment explanation
Indices: 34965215--34965240 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34965205 CTGTTGGAAT
34965215 AGGCTCCGGTTC
1 AGGCTCCGGTTC
34965227 AGGCTCCGGTTC
1 AGGCTCCGGTTC
34965239 AG
1 AG
34965241 AAAATAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.31, G:0.35, T:0.23
Consensus pattern (12 bp):
AGGCTCCGGTTC
Found at i:34966276 original size:121 final size:122
Alignment explanation
Indices: 34966097--34966415 Score: 403
Period size: 121 Copynumber: 2.6 Consensus size: 122
34966087 TCACGAGGGT
* * * *
34966097 GCGATTTCATAAATTCTTCTCAAATAGCATCTTGCTAGAAACGATTTTATATTATTTGCTCAGAA
1 GCGATTTC-GAAATTCTTCTCAAATAGCATCATGCTAGAAGCGATTTTATACTATTTGCTCAGAA
34966162 ACGTCAAAAA-AATTATTTCTTACATGACCTACTGTAGCAAAAACGCG-C-TGACTAGGCC
65 ACGTCAAAAATAATTATTTCTTACATGACCTACTGTAGCAAAAACGCGCCATGA--AGG-C
* * *
34966220 GCGATTTC-ACATTCTTCTCAAATAGCATCCTCCTAGAAGCGATTTTATACTATTTGCTCAGAAA
1 GCGATTTCGAAATTCTTCTCAAATAGCATCATGCTAGAAGCGATTTTATACTATTTGCTCAGAAA
* *
34966284 CGTCAAAAAAATAATTATTTCTTCCGTGACCTACTGTAGCAAAAACGCGTCCATGAAGGC
66 CGTC--AAAAATAATTATTTCTTACATGACCTACTGTAGCAAAAACGCG-CCATGAAGGC
* * * ** *
34966344 GCGATTTCGTAAATTCTTCTCAAATACCATCATGCTAGAAGTGATTTTATGCTATTTTATCAAAA
1 GCGATTTCG-AAATTCTTCTCAAATAGCATCATGCTAGAAGCGATTTTATACTATTTGCTCAGAA
34966409 ACGTCAA
65 ACGTCAA
34966416 CTCGAAATTA
Statistics
Matches: 172, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
121 55 0.32
123 13 0.08
124 46 0.27
125 3 0.02
126 52 0.30
127 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (122 bp):
GCGATTTCGAAATTCTTCTCAAATAGCATCATGCTAGAAGCGATTTTATACTATTTGCTCAGAAA
CGTCAAAAATAATTATTTCTTACATGACCTACTGTAGCAAAAACGCGCCATGAAGGC
Found at i:34972070 original size:6 final size:6
Alignment explanation
Indices: 34972059--34972089 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
34972049 TTTTGGGGTA
34972059 TTAGGG TTAGGG TTAGGG -TAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
34972090 TTGGTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
TTAGGG
Found at i:34972082 original size:11 final size:11
Alignment explanation
Indices: 34972059--34972088 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
34972049 TTTTGGGGTA
34972059 TTAGGGTTAGGG
1 TTAGGG-TAGGG
34972071 TTAGGGTAGGG
1 TTAGGGTAGGG
34972082 TTAGGGT
1 TTAGGGT
34972089 TTTGGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (11 bp):
TTAGGGTAGGG
Found at i:34972268 original size:89 final size:88
Alignment explanation
Indices: 34972163--34972430 Score: 245
Period size: 96 Copynumber: 2.9 Consensus size: 88
34972153 TTTTGCCAAT
* * * **
34972163 TAAATTAATTATAAATTTTTCAAAATTGGATTA-GGTTTCGTGTTTATTGTTTTTTAAGAAAAAA
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAAAG-TTTTTAAG-AAAAA
34972227 ATCAATAAAATTAGGGTTACTTGAG
64 ATCAATAAAATTAGGGTTACTTGAG
* * * * * * * *
34972252 TAATTTAATTAAAAATTATTTAAAAATCAGATAATGGTTTAGAG-TTAAGGGTTTTTAAGGAAAA
1 TAAATTAATTATAAATT-TTTAAAAATTAGATTAGGGTTTAGTGTTTAA-AGTTTTTAAGAAAAA
34972316 ATCAAATAAATTAGGGTTCAGGGTTACTTGAG
64 ATC-AATAAA--A---TT-AGGGTTACTTGAG
*
34972348 TAAATTAATTATAAATTTTTATAAAATTAGATTAGGGTTTAGTGTTTAGAGTTTTTAAGTAAAAA
1 TAAATTAATTATAAATTTTTA-AAAATTAGATTAGGGTTTAGTGTTTAAAGTTTTTAAG-AAAAA
* *
34972413 CTTAA-ATAAATTAGGGTT
64 ATCAATA-AAATTAGGGTT
34972431 TGAGGTTTGG
Statistics
Matches: 143, Mismatches: 22, Indels: 27
0.74 0.11 0.14
Matches are distributed among these distances:
89 22 0.15
90 35 0.24
91 10 0.07
92 1 0.01
94 1 0.01
95 7 0.05
96 59 0.41
97 8 0.06
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40
Consensus pattern (88 bp):
TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAAAGTTTTTAAGAAAAAAT
CAATAAAATTAGGGTTACTTGAG
Found at i:34972356 original size:96 final size:97
Alignment explanation
Indices: 34972239--34972430 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 97
34972229 CAATAAAATT
* * *
34972239 AGGGTTACTTGAGTAATTTAATTAAAAATTATTTA-AAAATCAGATAATGGTTTAGAGTTAAGGG
1 AGGGTTACTTGAGTAAATTAATTAAAAATT-TTTATAAAATCAGATAAGGGTTTAGAGTTAAGAG
34972303 TTTTTAAGGAAAAA-TCAAATAAATTAGGGTTC
65 TTTTTAAGGAAAAACTCAAATAAATTAGGGTTC
* * * * *
34972335 AGGGTTACTTGAGTAAATTAATTATAAATTTTTATAAAATTAGATTAGGGTTTAGTGTTTAGAGT
1 AGGGTTACTTGAGTAAATTAATTAAAAATTTTTATAAAATCAGATAAGGGTTTAGAGTTAAGAGT
* *
34972400 TTTTAAGTAAAAACTTAAATAAATTAGGGTT
66 TTTTAAGGAAAAACTCAAATAAATTAGGGTT
34972431 TGAGGTTTGG
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
95 4 0.05
96 64 0.76
97 16 0.19
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (97 bp):
AGGGTTACTTGAGTAAATTAATTAAAAATTTTTATAAAATCAGATAAGGGTTTAGAGTTAAGAGT
TTTTAAGGAAAAACTCAAATAAATTAGGGTTC
Found at i:34972703 original size:126 final size:125
Alignment explanation
Indices: 34972470--34972758 Score: 427
Period size: 126 Copynumber: 2.3 Consensus size: 125
34972460 TTGTTAATTT
* * * *
34972470 AAAGAAGCTCCCACGTGGACTCACTTTTACTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCT-CCACGTGGACGCGCTTTTGCTACAGTAACTCCTGAAAAAATAATTTCGAGTAGAC
* * * * *
34972535 GTTTCTGAGCAAATAGTGTCAAAAATGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTATTG
65 ATTTCTGAGCAAATAGTGTAAAAAACGCTTTAAACAAGATGCTTTGTCAGCAGAAGTACTG
* * *
34972596 AAAGAAGCTCCAATGTGGACGCGTTTTTGCTACAGTAACTCCTTAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCC-ACGTGGACGCGCTTTTGCTACAGTAACTCCTGAAAAAATAATTTCGAGTAGAC
34972661 ATTTCTGAGCAAATAGTGTAAAAAACGCTTTAAAC-AGAATGCTTTGTCAGCAGAAGTACTG
65 ATTTCTGAGCAAATAGTGTAAAAAACGCTTTAAACAAG-ATGCTTTGTCAGCAGAAGTACTG
34972722 AAAGAAGCTCTCACGTGGACGCGCTTTTGCTACAGTA
1 AAAGAAGCTC-CACGTGGACGCGCTTTTGCTACAGTA
34972759 GCGCATGTTT
Statistics
Matches: 146, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
125 4 0.03
126 141 0.97
127 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (125 bp):
AAAGAAGCTCCACGTGGACGCGCTTTTGCTACAGTAACTCCTGAAAAAATAATTTCGAGTAGACA
TTTCTGAGCAAATAGTGTAAAAAACGCTTTAAACAAGATGCTTTGTCAGCAGAAGTACTG
Found at i:34975887 original size:29 final size:29
Alignment explanation
Indices: 34975854--34975912 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
34975844 AATATTCAAC
*
34975854 ATATTACAATACGTAAAAG-AATTTCTATT
1 ATATTA-AAAACGTAAAAGAAATTTCTATT
*
34975883 ATATTAAAAATGTAAAAGTAAATTTCTATT
1 ATATTAAAAACGTAAAAG-AAATTTCTATT
34975913 TTAGTACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 6 0.23
30 10 0.38
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATTAAAAACGTAAAAGAAATTTCTATT
Found at i:34978193 original size:13 final size:13
Alignment explanation
Indices: 34978174--34978207 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
34978164 AATTTTTACG
34978174 ATTTAAAAA-AAA
1 ATTTAAAAATAAA
34978186 ATTTTAAAAATAAA
1 A-TTTAAAAATAAA
34978200 ATTTAAAA
1 ATTTAAAA
34978208 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 15 0.75
14 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTTAAAAATAAA
Found at i:34978265 original size:11 final size:11
Alignment explanation
Indices: 34978251--34978315 Score: 94
Period size: 11 Copynumber: 5.9 Consensus size: 11
34978241 TTTAAATAGA
34978251 AATTTGAGAGG
1 AATTTGAGAGG
34978262 AATTTGAGAGG
1 AATTTGAGAGG
*
34978273 AAATTGAGAGG
1 AATTTGAGAGG
* *
34978284 AATTTGAAAGA
1 AATTTGAGAGG
*
34978295 AAATTGAGAGG
1 AATTTGAGAGG
34978306 AATTTGAGAG
1 AATTTGAGAG
34978316 AATATTAGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:34978317 original size:22 final size:22
Alignment explanation
Indices: 34978248--34978340 Score: 116
Period size: 22 Copynumber: 4.2 Consensus size: 22
34978238 TCTTTTAAAT
*
34978248 AGAAATTTGAGAGGAATTTGAG
1 AGAAAATTGAGAGGAATTTGAG
* *
34978270 AGGAAATTGAGAGGAATTTGAA
1 AGAAAATTGAGAGGAATTTGAG
34978292 AGAAAATTGAGAGGAATTTGAG
1 AGAAAATTGAGAGGAATTTGAG
* * *
34978314 AGAATATT-AGAGACAAATTGAG
1 AGAAAATTGAGAG-GAATTTGAG
34978336 AGAAA
1 AGAAA
34978341 GGATTTAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 4 0.07
22 57 0.93
ACGTcount: A:0.47, C:0.01, G:0.29, T:0.23
Consensus pattern (22 bp):
AGAAAATTGAGAGGAATTTGAG
Found at i:34978862 original size:9 final size:9
Alignment explanation
Indices: 34978839--34978884 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
34978829 GAATTTTATG
*
34978839 ATTCGAATA
1 ATTCAAATA
*
34978848 ACTCAAATA
1 ATTCAAATA
34978857 ATTCAAATA
1 ATTCAAATA
*
34978866 ACTCAAATA
1 ATTCAAATA
*
34978875 ATTCGAATA
1 ATTCAAATA
34978884 A
1 A
34978885 CATATTAGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (9 bp):
ATTCAAATA
Found at i:34978865 original size:18 final size:18
Alignment explanation
Indices: 34978839--34978885 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
34978829 GAATTTTATG
34978839 ATTCGAATAACTCAAATA
1 ATTCGAATAACTCAAATA
*
34978857 ATTCAAATAACTCAAATA
1 ATTCGAATAACTCAAATA
34978875 ATTCGAATAAC
1 ATTCGAATAAC
34978886 ATATTAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (18 bp):
ATTCGAATAACTCAAATA
Found at i:34980569 original size:13 final size:13
Alignment explanation
Indices: 34980553--34980623 Score: 88
Period size: 13 Copynumber: 5.5 Consensus size: 13
34980543 TTTAAACTAA
34980553 ACTTTTCCACAGC
1 ACTTTTCCACAGC
* *
34980566 ACTTTTCAAAAGC
1 ACTTTTCCACAGC
*
34980579 ACTTTTCCACAAC
1 ACTTTTCCACAGC
* *
34980592 ACTTTTCAAAAGC
1 ACTTTTCCACAGC
*
34980605 ACTTTTCCACAAC
1 ACTTTTCCACAGC
34980618 ACTTTT
1 ACTTTT
34980624 TAAAAGCATT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (13 bp):
ACTTTTCCACAGC
Found at i:34980571 original size:26 final size:26
Alignment explanation
Indices: 34980553--34980631 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
34980543 TTTAAACTAA
*
34980553 ACTTTTCCACAGCACTTTTCAAAAGC
1 ACTTTTCCACAACACTTTTCAAAAGC
34980579 ACTTTTCCACAACACTTTTCAAAAGC
1 ACTTTTCCACAACACTTTTCAAAAGC
*
34980605 ACTTTTCCACAACACTTTTTAAAAGC
1 ACTTTTCCACAACACTTTTCAAAAGC
34980631 A
1 A
34980632 TTGCCATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (26 bp):
ACTTTTCCACAACACTTTTCAAAAGC
Found at i:34988469 original size:21 final size:22
Alignment explanation
Indices: 34988435--34988477 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
34988425 CAACGGGTAA
*
34988435 AGTTCTGATATGAAAC-AATATG
1 AGTTCTGAAATG-AACTAATATG
34988457 AGTTC-GAAATGAACTAATATG
1 AGTTCTGAAATGAACTAATATG
34988478 GGTATATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
AGTTCTGAAATGAACTAATATG
Found at i:34992889 original size:27 final size:27
Alignment explanation
Indices: 34992518--34992879 Score: 465
Period size: 27 Copynumber: 13.4 Consensus size: 27
34992508 CCCTAAAATA
* * *
34992518 GGTAAAATAACCAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
34992545 GGTAAGATGACCAAAATACCTCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
34992572 AGTAAAATGATCAAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* **
34992599 GGTAAAATGACCGGAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
34992626 GATAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
34992653 GGTAAAATGATCGAAATACTCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
34992680 GGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
34992707 GGTAGAATGATCGAAATATCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
34992734 GGTAAAATGACCGATATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
34992761 GGTAAAATGATCGAAATA-CCCTATTAG
1 GGTAAAATGACCGAAATACCCCCA-TAG
34992788 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
34992815 GGTAGAATGGCCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
34992842 GGTAAAATGATCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
34992869 GGTAAAATGAC
1 GGTAAAATGAC
34992880 TGTTATACCC
Statistics
Matches: 289, Mismatches: 44, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 4 0.01
27 281 0.97
28 4 0.01
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:34996163 original size:23 final size:21
Alignment explanation
Indices: 34996136--34996182 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
34996126 TTTTTTCAAA
34996136 TTTTATAT-TTTGCACAAACTTTT
1 TTTTATATATTTG-A-AAA-TTTT
34996159 TTTTATATATTTGAAAATTTT
1 TTTTATATATTTGAAAATTTT
34996180 TTT
1 TTT
34996183 AATCGAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
22 3 0.13
23 9 0.39
24 4 0.17
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTATATATTTGAAAATTTT
Found at i:34998490 original size:21 final size:22
Alignment explanation
Indices: 34998456--34998498 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
34998446 CAACGGGTAA
*
34998456 AGTTCTGATATGAAAC-AATATG
1 AGTTCTGAAATG-AACTAATATG
34998478 AGTTC-GAAATGAACTAATATG
1 AGTTCTGAAATGAACTAATATG
34998499 GGTATATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
AGTTCTGAAATGAACTAATATG
Found at i:35000742 original size:33 final size:33
Alignment explanation
Indices: 35000673--35000982 Score: 132
Period size: 33 Copynumber: 8.7 Consensus size: 33
35000663 ATATAAAGGG
*
35000673 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
35000700 GGTTGCTAAGTGCTGATTCCCTGGATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
35000733 GGTTGCTAAGTGCCGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
35000775 GGTTGCTAAGT-CTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
35000807 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAG-
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
*
35000848 GTGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 G-GTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * * **
35000882 GTTTGCTTAGTGCTGATTCCACTATATTTTTGAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGA-ATCATT---GGT
* *
35000919 GAAAGGGGTTGCTAAGTGCTGATTCCCAGAATCACTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
35000958 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
35000983 TAACGGATAA
Statistics
Matches: 214, Mismatches: 31, Indels: 69
0.68 0.10 0.22
Matches are distributed among these distances:
27 21 0.10
31 2 0.01
32 14 0.07
33 65 0.30
34 18 0.08
35 2 0.01
36 4 0.02
37 5 0.02
38 4 0.02
39 7 0.03
40 6 0.03
41 13 0.06
42 34 0.16
43 19 0.09
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:35000958 original size:76 final size:75
Alignment explanation
Indices: 35000696--35000981 Score: 412
Period size: 74 Copynumber: 3.8 Consensus size: 75
35000686 TGATTCCCCC
* * *
35000696 AAGGGGTTGCTAAGTGCTGATTCCCTGGATCATTGGTGGTTGCTAAGTGCCGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
35000761 TTAAATGTGA
66 TTAAATGTGA
*
35000771 AAGGGGTTGCTAAGT-CTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
35000835 TTAAATGTGA
66 TTAAATGTGA
* * * * **
35000845 AAGGTGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGTTTGCTTAGTGCTGATTCCACTATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-T
* * *
35000910 TTTGAAGGTGA
65 CTTAAATGTGA
* * *
35000921 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
35000982 ATAACGGATA
Statistics
Matches: 186, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
74 69 0.37
75 56 0.30
76 61 0.33
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:35006965 original size:20 final size:20
Alignment explanation
Indices: 35006940--35007016 Score: 102
Period size: 20 Copynumber: 3.7 Consensus size: 20
35006930 CTGTTCAAAT
35006940 CCTATAATCATAACTCGATA
1 CCTATAATCATAACTCGATA
*
35006960 CCTATAATCATAACT-GTTCAAA
1 CCTATAATCATAACTCG---ATA
35006982 TCCTATAATCATAACTCGATA
1 -CCTATAATCATAACTCGATA
35007003 CCTATAATCATAAC
1 CCTATAATCATAAC
35007017 CTGCCAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.02
20 29 0.58
21 2 0.04
22 2 0.04
23 15 0.30
24 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (20 bp):
CCTATAATCATAACTCGATA
Found at i:35006989 original size:43 final size:43
Alignment explanation
Indices: 35006928--35007016 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
35006918 AATTTAGGTC
35006928 AACTGTTCAAATCCTATAATCATAACTCGATACCTATAATCAT
1 AACTGTTCAAATCCTATAATCATAACTCGATACCTATAATCAT
35006971 AACTGTTCAAATCCTATAATCATAACTCGATACCTATAATCAT
1 AACTGTTCAAATCCTATAATCATAACTCGATACCTATAATCAT
35007014 AAC
1 AAC
35007017 CTGCCAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.31
Consensus pattern (43 bp):
AACTGTTCAAATCCTATAATCATAACTCGATACCTATAATCAT
Found at i:35006990 original size:23 final size:23
Alignment explanation
Indices: 35006928--35006997 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
35006918 AATTTAGGTC
35006928 AACTGTTCAAATCCTATAATCAT
1 AACTGTTCAAATCCTATAATCAT
*
35006951 AAC---TC-GATACCTATAATCAT
1 AACTGTTCAAAT-CCTATAATCAT
35006971 AACTGTTCAAATCCTATAATCAT
1 AACTGTTCAAATCCTATAATCAT
35006994 AACT
1 AACT
35006998 CGATACCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 16 0.40
23 20 0.50
24 2 0.05
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (23 bp):
AACTGTTCAAATCCTATAATCAT
Found at i:35007376 original size:12 final size:12
Alignment explanation
Indices: 35007359--35007384 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35007349 ACCCCAAAAC
35007359 CCGTGTGTTAGG
1 CCGTGTGTTAGG
35007371 CCGTGTGTTAGG
1 CCGTGTGTTAGG
35007383 CC
1 CC
35007385 ATGTAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (12 bp):
CCGTGTGTTAGG
Found at i:35008523 original size:37 final size:37
Alignment explanation
Indices: 35008408--35008527 Score: 125
Period size: 37 Copynumber: 3.2 Consensus size: 37
35008398 TCCATCTGAA
* *
35008408 AACACGCCAGAAGCTCATAAGAGCTAATCCACCCGAT
1 AACACGCCAGATGCTCATAAGAGCTAATCCACCCAAT
* ** ** * * *
35008445 AACATGCCA-ATTGCTCCGAAGAGCTTGTCCAACTAAA
1 AACACGCCAGA-TGCTCATAAGAGCTAATCCACCCAAT
*
35008482 AACACGCCAGATGCTCATTAGAGCTAATCCACCCAAT
1 AACACGCCAGATGCTCATAAGAGCTAATCCACCCAAT
35008519 AACACGCCA
1 AACACGCCA
35008528 AAACAAGGAG
Statistics
Matches: 62, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 1 0.02
37 60 0.97
38 1 0.02
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.17
Consensus pattern (37 bp):
AACACGCCAGATGCTCATAAGAGCTAATCCACCCAAT
Found at i:35011389 original size:19 final size:20
Alignment explanation
Indices: 35011351--35011395 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
35011341 TCACTCAGCT
* *
35011351 AAATTTAGCTCCTTATTTTC
1 AAATTTAGCCCCTTAATTTC
35011371 AAATTTA-CCCCTTAATTTC
1 AAATTTAGCCCCTTAATTTC
35011390 AAATTT
1 AAATTT
35011396 TTTACAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTTAGCCCCTTAATTTC
Found at i:35016349 original size:16 final size:16
Alignment explanation
Indices: 35016325--35016358 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35016315 TCGATAAGAT
* *
35016325 TTAATTCTATATTTCA
1 TTAACTCTATAATTCA
35016341 TTAACTCTATAATTCA
1 TTAACTCTATAATTCA
35016357 TT
1 TT
35016359 TTATACTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAACTCTATAATTCA
Found at i:35017180 original size:50 final size:50
Alignment explanation
Indices: 35017056--35017345 Score: 278
Period size: 50 Copynumber: 5.7 Consensus size: 50
35017046 GATAATAACA
* * ** * * *
35017056 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * ** *
35017105 TACCAATGCCATATCCCAGATATGGTCCTACATGGGAGTTCTCATATCGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
35017155 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
35017205 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
35017255 TGCCAACGCTATGTCCCAGGCATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
35017311 TGCCAATGCCATGTCCCAGGCATGGTCTTACATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
35017346 AATCTCATTC
Statistics
Matches: 201, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.00
49 36 0.18
50 128 0.64
53 2 0.01
56 34 0.17
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:35017724 original size:30 final size:30
Alignment explanation
Indices: 35017690--35017746 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
35017680 ATTGACTTTT
35017690 ACTTTGGCAAAATTACA-TTTTTACCCCTAA
1 ACTTTGGCAAAATTACACTTTTT-CCCCTAA
* * *
35017720 ACTTTTGCATATTTACACTTTTTCCCC
1 ACTTTGGCAAAATTACACTTTTTCCCC
35017747 AAAGCTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (30 bp):
ACTTTGGCAAAATTACACTTTTTCCCCTAA
Found at i:35020359 original size:54 final size:54
Alignment explanation
Indices: 35020274--35020387 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
35020264 GGACACACGA
* * *
35020274 CCGTGTCCTTGCCCGTGTAACTCACTGACTTGAGACACATGGTCGTGTC-TCAGC
1 CCGTGTCCTTGCCCGTGTAACTCACTAACTTGAGACACATGGCCATGTCGT-AGC
* * *
35020328 CCGTG-CCTTTGCTCGTGTAACTCACTAACTTGGGTCACATGGCCATGTCGTAGC
1 CCGTGTCC-TTGCCCGTGTAACTCACTAACTTGAGACACATGGCCATGTCGTAGC
35020382 CCGTGT
1 CCGTGT
35020388 GTCAGCTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
53 2 0.04
54 48 0.94
55 1 0.02
ACGTcount: A:0.16, C:0.31, G:0.25, T:0.29
Consensus pattern (54 bp):
CCGTGTCCTTGCCCGTGTAACTCACTAACTTGAGACACATGGCCATGTCGTAGC
Found at i:35020618 original size:19 final size:19
Alignment explanation
Indices: 35020594--35020685 Score: 91
Period size: 18 Copynumber: 4.9 Consensus size: 19
35020584 TTAAAAACAC
*
35020594 CATATTTCATTTCTCATCT
1 CATATTTCATTTCTCATTT
*
35020613 CATA-TTCATTTC-AAGTTT
1 CATATTTCATTTCTCA-TTT
* * *
35020631 TACATCTCATTTCATCATTT
1 CATATTTCATTTC-TCATTT
*
35020651 CATATTTCATTTCTCATAT
1 CATATTTCATTTCTCATTT
35020670 CATA-TTCATTTCTCAT
1 CATATTTCATTTCTCAT
35020686 ATTTTCTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
17 1 0.02
18 24 0.41
19 20 0.34
20 13 0.22
21 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.01, T:0.51
Consensus pattern (19 bp):
CATATTTCATTTCTCATTT
Found at i:35028725 original size:21 final size:21
Alignment explanation
Indices: 35028701--35028743 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35028691 CAAAATCCAT
*
35028701 TTCATCATCTCCTTCTTCTTC
1 TTCATCATCTCCTTCCTCTTC
* *
35028722 TTCATCCTTTCCTTCCTCTTC
1 TTCATCATCTCCTTCCTCTTC
35028743 T
1 T
35028744 CTTTCATGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCATCATCTCCTTCCTCTTC
Found at i:35036538 original size:18 final size:16
Alignment explanation
Indices: 35036501--35036540 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35036491 AAAGAACAAA
*
35036501 AAAAATAAAAAAATTG
1 AAAAATAAAAAAAATG
35036517 AAAAATAAAACAAAATG
1 AAAAATAAAA-AAAATG
35036534 TAAAAAT
1 -AAAAAT
35036541 TCTTTAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAAATAAAAAAAATG
Found at i:35041552 original size:12 final size:12
Alignment explanation
Indices: 35041535--35041559 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35041525 TTAGTTTGCT
35041535 GCCTAGCACACG
1 GCCTAGCACACG
35041547 GCCTAGCACACG
1 GCCTAGCACACG
35041559 G
1 G
35041560 GCGTGTAGGG
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:0.24, C:0.40, G:0.28, T:0.08
Consensus pattern (12 bp):
GCCTAGCACACG
Found at i:35043089 original size:75 final size:75
Alignment explanation
Indices: 35042963--35043109 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 75
35042953 GAAAACTAGG
* *
35042963 ATTATCCCTTTATTAATAGTGAAGGCAAATGAAATGTTAAAAAAATGAATTATATTCTTTCCAAA
1 ATTATCCCTTTATTAATAGAGAAGGCAAATGAAAAGTTAAAAAAATGAATTATATTCTTTCCAAA
35043028 AGAATATAGA
66 AGAATATAGA
* * * *
35043038 ATTATTCCTTTATTAATAGAGAAGGCAAATGAAAAGTTCAAAAAA-GAAATTATCTTCTTTCTAA
1 ATTATCCCTTTATTAATAGAGAAGGCAAATGAAAAGTTAAAAAAATG-AATTATATTCTTTCCAA
35043102 AAGAATAT
65 AAGAATAT
35043110 TAATTTACAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 1 0.02
75 64 0.98
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (75 bp):
ATTATCCCTTTATTAATAGAGAAGGCAAATGAAAAGTTAAAAAAATGAATTATATTCTTTCCAAA
AGAATATAGA
Found at i:35043192 original size:45 final size:42
Alignment explanation
Indices: 35043143--35043277 Score: 122
Period size: 45 Copynumber: 3.2 Consensus size: 42
35043133 GACCGAAATT
35043143 AATTAATATAACTATTTATATTAATAAATTTAGTAAAATATATAC
1 AATTAATATAA-T-TTTATATTAATAAA-TTAGTAAAATATATAC
* *
35043188 AATT-A-AT-ATTTTATATTAATAAA--A-TCATATACTA-AC
1 AATTAATATAATTTTATATTAATAAATTAGTAAAATA-TATAC
* *
35043224 AAGTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATAC
1 AATTAATATAA-T-TTTATATTAATAAATT-AGTAAAATATATAC
35043269 AATTAATAT
1 AATTAATAT
35043278 TTTGTATGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
36 10 0.14
37 4 0.06
38 2 0.03
39 1 0.01
40 15 0.21
41 15 0.21
42 1 0.01
43 2 0.03
44 3 0.04
45 19 0.26
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (42 bp):
AATTAATATAATTTTATATTAATAAATTAGTAAAATATATAC
Found at i:35043201 original size:40 final size:40
Alignment explanation
Indices: 35043157--35043296 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
35043147 AATATAACTA
*
35043157 TTTATATTAATAAATTTAGTAAAATATATACAATTAATAT
1 TTTATATTAATAAATTCAGTAAAATATATACAATTAATAT
* * * * *
35043197 TTTATATTAATAAAATCA-TATACTA-ACAAGTAATATAAT-T
1 TTTATATTAATAAATTCAGTAAAATATA-TA-CAAT-TAATAT
*
35043237 GTTTATATTAATAAATTCGGTAAAATATATACAATTAATAT
1 -TTTATATTAATAAATTCAGTAAAATATATACAATTAATAT
* *
35043278 TTTGTATGAATCAAATTCA
1 TTTATATTAAT-AAATTCA
35043297 TATACTAATT
Statistics
Matches: 77, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 33 0.43
41 30 0.39
42 6 0.08
43 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (40 bp):
TTTATATTAATAAATTCAGTAAAATATATACAATTAATAT
Found at i:35043243 original size:81 final size:82
Alignment explanation
Indices: 35043146--35043304 Score: 248
Period size: 81 Copynumber: 2.0 Consensus size: 82
35043136 CGAAATTAAT
* *
35043146 TAATATAACTATTTATATTAATAAATTTAGTAAAATATATACAATTAATATTTTATATTAAT-AA
1 TAATATAACTATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTATATGAATCAA
35043210 AATCATATACTAACAAG
66 AATCATATACTAACAAG
* * * *
35043227 TAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAA
1 TAATATAACTATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTATATGAATCAA
*
35043292 ATTCATATACTAA
66 AATCATATACTAA
35043305 TTATATCTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 56 0.80
82 14 0.20
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (82 bp):
TAATATAACTATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTATATGAATCAA
AATCATATACTAACAAG
Found at i:35046294 original size:24 final size:24
Alignment explanation
Indices: 35046225--35046295 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
35046215 TTCCGAGCAT
* * *
35046225 AAAGAAAAGAGCAAGGGAGTGAGG
1 AAAGAGAAGAGTAAGGGAATGAGG
* *
35046249 AAAGGGAAGA-T-AGTGAGGATGAGG
1 AAAGAGAAGAGTAAG-G-GAATGAGG
35046273 AAAGAGAAGAGTAAGGGAATGAG
1 AAAGAGAAGAGTAAGGGAATGAG
35046296 ATGGATTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 29 0.81
25 2 0.06
26 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.42, T:0.08
Consensus pattern (24 bp):
AAAGAGAAGAGTAAGGGAATGAGG
Found at i:35051082 original size:51 final size:50
Alignment explanation
Indices: 35050950--35051233 Score: 315
Period size: 51 Copynumber: 5.6 Consensus size: 50
35050940 TCGATACACG
* * *
35050950 TAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAA-TCTTTTCGGTTCACA
* *
35051000 TAGTGGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTAT-ACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AATCTTTTCGGT-TCACA
* * * *
35051051 TAGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAATC-TTT-TCGGTTCACA
* * *
35051102 TAGTAGCCTTCACACAGTACTACACACGTGACCAAATCTTCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AATCTTTTCGGTTCACA
* * * *
35051153 TTGTAGCCTTCACTTAGGACTACACATGTGACC-ATCATTTATCGGTTCACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAATC-TTT-TCGGTTCACA
*
35051204 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
35051234 TTCATTGATA
Statistics
Matches: 194, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
49 5 0.03
50 37 0.19
51 146 0.75
52 3 0.02
53 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAATCTTTTCGGTTCACA
Found at i:35051125 original size:102 final size:102
Alignment explanation
Indices: 35050944--35051233 Score: 429
Period size: 102 Copynumber: 2.9 Consensus size: 102
35050934 TATCATTCGA
* * * * *** *
35050944 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTGGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGGTTCACGTAGTAGCC
* *
35051008 TTCACATAGTACTACACACGTGACCAAAGCTTTTCGG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
* *
35051045 TATACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGGTTCACGTAGTAGCC
*
35051110 TTCACACAGTACTACACACGTGACCAAATCTTCTCGG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
* * *
35051147 TACACATTGTAGCCTTCACTTAGGACTACACATGTGACCATCATTTATCGGTTCACATAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGGTTCACGTAGTAGCC
35051212 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
35051234 TTCATTGATA
Statistics
Matches: 170, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
101 39 0.23
102 131 0.77
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGGTTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
Found at i:35051225 original size:153 final size:151
Alignment explanation
Indices: 35050940--35051229 Score: 379
Period size: 153 Copynumber: 1.9 Consensus size: 151
35050930 CTTTTATCAT
* * * * * *
35050940 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAATTTTACGGTACACATAGTA
* **
35051005 GCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTATACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGGACTACACACGTGACCAAA-CTTTTCGGTATACATAGTAGCCTTCACACAGTA
35051070 CTACACATGTGACCATCATTTA
130 CTACACATGTGACCATCATTTA
* *
35051092 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAATCTTCT-CGGTACACATTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAT-TT-TACGGTACACATAG
* * *
35051156 TAGCCTTCACTTAGGACTACACATGTGACC-ATCATTTATCGGT-TCACATAGTAGCCTTCACAC
64 TAGCCTTCACATAGGACTACACACGTGACCAAAC-TTT-TCGGTAT-ACATAGTAGCCTTCACAC
35051219 AGTACTACACA
126 AGTACTACACA
35051230 CGTGTTCATT
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
151 1 0.01
152 48 0.40
153 69 0.58
154 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (151 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAATTTTACGGTACACATAGTA
GCCTTCACATAGGACTACACACGTGACCAAACTTTTCGGTATACATAGTAGCCTTCACACAGTAC
TACACATGTGACCATCATTTA
Found at i:35070041 original size:92 final size:92
Alignment explanation
Indices: 35069884--35070061 Score: 338
Period size: 92 Copynumber: 1.9 Consensus size: 92
35069874 TATATCTGGT
*
35069884 ACTTTTAAAAATATAATCATCTCGTGTATATATTATTATTCAACATTTAAGTTTTAAATAATGAT
1 ACTTTTAAAAATATAATCATCCCGTGTATATATTATTATTCAACATTTAAGTTTTAAATAATGAT
35069949 AACTTACTAGTAAGACACAATGATATA
66 AACTTACTAGTAAGACACAATGATATA
*
35069976 ACTTTTAAAAATATAATCATCCCGTGTATATATTATTATTCAACATTTAAGTTTTATATAATGAT
1 ACTTTTAAAAATATAATCATCCCGTGTATATATTATTATTCAACATTTAAGTTTTAAATAATGAT
35070041 AACTTACTAGTAAGACACAAT
66 AACTTACTAGTAAGACACAAT
35070062 TAAGGTTATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 84 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (92 bp):
ACTTTTAAAAATATAATCATCCCGTGTATATATTATTATTCAACATTTAAGTTTTAAATAATGAT
AACTTACTAGTAAGACACAATGATATA
Found at i:35070637 original size:32 final size:32
Alignment explanation
Indices: 35070596--35070660 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
35070586 CTTATTAACA
35070596 TTCACAATCTAATCAAGGTGTTAAAAAAAATC
1 TTCACAATCTAATCAAGGTGTTAAAAAAAATC
35070628 TTCACAATCTAATCAAGGTGTTAAAAAAAATC
1 TTCACAATCTAATCAAGGTGTTAAAAAAAATC
35070660 T
1 T
35070661 AACCTTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (32 bp):
TTCACAATCTAATCAAGGTGTTAAAAAAAATC
Found at i:35072257 original size:66 final size:66
Alignment explanation
Indices: 35072129--35072257 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
35072119 GCTCTTATCA
* * * * *
35072129 GATAGCTGTCAACTGTGGCGACAATTCTGAATGCCATCTGGAATTAACTTATGCAGCGACATTGC
1 GATAGCTGTCAACTGTGGCGACAATTCAGAACGCAATCTGGAATTAACTCATGCAGCAACATTGC
35072194 G
66 G
* * * *
35072195 GATATCTGTCAACTGTGGCGACAATTCCAG-ACGCAATCTGTAATTAACTCATGTATCAACATT
1 GATAGCTGTCAACTGTGGCGACAATT-CAGAACGCAATCTGGAATTAACTCATGCAGCAACATT
35072258 AGTGCAGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (66 bp):
GATAGCTGTCAACTGTGGCGACAATTCAGAACGCAATCTGGAATTAACTCATGCAGCAACATTGC
G
Found at i:35073735 original size:18 final size:18
Alignment explanation
Indices: 35073714--35073758 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
35073704 TAGCAACTTT
*
35073714 TTCTTCTTTAGCAACAAC
1 TTCTTCTTTAACAACAAC
* *
35073732 TTCTGCTTCAACAACAAC
1 TTCTTCTTTAACAACAAC
35073750 TTCTTCTTT
1 TTCTTCTTT
35073759 TACAGTATCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.04, T:0.42
Consensus pattern (18 bp):
TTCTTCTTTAACAACAAC
Done.