Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 400 of 427
Found at i:115941627 original size:19 final size:22
Alignment explanation
Indices: 115941578--115941629 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
115941568 TTAACAATAT
115941578 AATAAAAAATAGTTATATTAAA
1 AATAAAAAATAGTTATATTAAA
**
115941600 AATTTAAAATA-TT-T-TTAAA
1 AATAAAAAATAGTTATATTAAA
115941619 AATAAAAAATA
1 AATAAAAAATA
115941630 AAAATATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.54
20 1 0.04
21 2 0.08
22 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AATAAAAAATAGTTATATTAAA
Found at i:115943165 original size:14 final size:14
Alignment explanation
Indices: 115943143--115943172 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
115943133 AAATATTAAG
115943143 TAAAGTTTTTATTT
1 TAAAGTTTTTATTT
*
115943157 TAAATTTTTTATTT
1 TAAAGTTTTTATTT
115943171 TA
1 TA
115943173 TTTTGTCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TAAAGTTTTTATTT
Found at i:115944071 original size:23 final size:23
Alignment explanation
Indices: 115944041--115944108 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
115944031 CACTAATGTT
* * *
115944041 AAGGATTTCACGATTTGGTTCTA
1 AAGGATTTCACAATTTCGTTCCA
115944064 AAGGATTTCACAATTTCGTTCCA
1 AAGGATTTCACAATTTCGTTCCA
115944087 AAGGATTTCACAATTTCGTTCC
1 AAGGATTTCACAATTTCGTTCC
115944109 TAATAGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (23 bp):
AAGGATTTCACAATTTCGTTCCA
Found at i:115944477 original size:16 final size:16
Alignment explanation
Indices: 115944456--115944491 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
115944446 GAATGCTAAC
*
115944456 GATTTAGGTATTTCAA
1 GATTTAGGGATTTCAA
*
115944472 GATTTAGGGATTTGAA
1 GATTTAGGGATTTCAA
115944488 GATT
1 GATT
115944492 GTTAGGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.42
Consensus pattern (16 bp):
GATTTAGGGATTTCAA
Found at i:115945130 original size:30 final size:30
Alignment explanation
Indices: 115945094--115945150 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
115945084 TTGTTTTATG
*
115945094 GTTTTTTAAT-ATTATTTAATAAAAAATTAA
1 GTTTTTTAATAAATATTT-ATAAAAAATTAA
*
115945124 GTTTTTTCATAAATATTTATAAAAAAT
1 GTTTTTTAATAAATATTTATAAAAAAT
115945151 AATAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (30 bp):
GTTTTTTAATAAATATTTATAAAAAATTAA
Found at i:115948980 original size:56 final size:56
Alignment explanation
Indices: 115948918--115949029 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
115948908 TTTAGCTTTG
115948918 AAGGTAATGTCTTCAACATCTATCTTGTAATTTTCGTGAATTTTCTTTATCATTGT
1 AAGGTAATGTCTTCAACATCTATCTTGTAATTTTCGTGAATTTTCTTTATCATTGT
115948974 AAGGTAATGTCTTCAACATCTATCTTGTAATTTTCGTGAATTTTCTTTATCATTGT
1 AAGGTAATGTCTTCAACATCTATCTTGTAATTTTCGTGAATTTTCTTTATCATTGT
115949030 TTGGTTGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (56 bp):
AAGGTAATGTCTTCAACATCTATCTTGTAATTTTCGTGAATTTTCTTTATCATTGT
Found at i:115952169 original size:3 final size:3
Alignment explanation
Indices: 115952161--115952185 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
115952151 GCACAATCAC
115952161 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
115952186 ATTTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:115963619 original size:25 final size:24
Alignment explanation
Indices: 115963566--115963613 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
115963556 ATTAGCATTT
* *
115963566 AATTATTTTTTAAAAATTTACAAA
1 AATTATTTTTAAAAAAATTACAAA
115963590 AATTATTTTTAAAAAAATTA-AAA
1 AATTATTTTTAAAAAAATTACAAA
115963613 A
1 A
115963614 TCATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTATTTTTAAAAAAATTACAAA
Found at i:115965216 original size:20 final size:21
Alignment explanation
Indices: 115965193--115965245 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
115965183 AGAAAAATTA
*
115965193 AATATAATTTTGA-TTGAAAT
1 AATATAATTTTAAGTTGAAAT
*
115965213 AATAAAATTTTAAGTTGAAAT
1 AATATAATTTTAAGTTGAAAT
*
115965234 ATTAT-ATTTTAA
1 AATATAATTTTAA
115965246 AATTTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (21 bp):
AATATAATTTTAAGTTGAAAT
Found at i:115967673 original size:15 final size:15
Alignment explanation
Indices: 115967653--115967686 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
115967643 TTTTTCCTAT
115967653 TTTAAATACAAAATA
1 TTTAAATACAAAATA
**
115967668 TTTAAATATGAAATA
1 TTTAAATACAAAATA
115967683 TTTA
1 TTTA
115967687 TTTTATATCA
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:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTAAATACAAAATA
Found at i:115968160 original size:2 final size:2
Alignment explanation
Indices: 115968153--115968179 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115968143 ATTATGATTC
115968153 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
115968180 ATTTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115971336 original size:25 final size:26
Alignment explanation
Indices: 115971253--115971351 Score: 119
Period size: 28 Copynumber: 3.7 Consensus size: 26
115971243 GTTCTTGGGG
* *
115971253 ACTCTTATCTGAAAGATAGTCCATGCGG
1 ACTCTTATTTGAAAGATA-T-CATGCGA
*
115971281 ACTCTTACTTGAAAGATAGTTCATGCGA
1 ACTCTTATTTGAAAGATA--TCATGCGA
*
115971309 ACTTTTATTTGAAAGATA-CATGCGA
1 ACTCTTATTTGAAAGATATCATGCGA
115971334 ACTCTTATTTGAAAGATA
1 ACTCTTATTTGAAAGATA
115971352 ATCTCGCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
25 24 0.38
28 38 0.60
29 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (26 bp):
ACTCTTATTTGAAAGATATCATGCGA
Found at i:115974444 original size:25 final size:24
Alignment explanation
Indices: 115974416--115974474 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
115974406 TGGATCCGGG
* *
115974416 TTTTGTG-TTCGAAAATTTATTATTA
1 TTTTGTGTTTAGAAAA--TATTAATA
*
115974441 TTTTATGTTTAGAAAATATTAATA
1 TTTTGTGTTTAGAAAATATTAATA
115974465 TTTTGT-TTTA
1 TTTTGTGTTTA
115974475 ATTTCTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.14
24 12 0.41
25 6 0.21
26 7 0.24
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (24 bp):
TTTTGTGTTTAGAAAATATTAATA
Found at i:115974654 original size:7 final size:7
Alignment explanation
Indices: 115974644--115974677 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
115974634 TTAATTAATA
115974644 ATTTTTT
1 ATTTTTT
115974651 ATTTTTT
1 ATTTTTT
*
115974658 ATTTTTA
1 ATTTTTT
115974665 ACTTTTTT
1 A-TTTTTT
115974673 ATTTT
1 ATTTT
115974678 AATTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:115974686 original size:22 final size:22
Alignment explanation
Indices: 115974645--115974686 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
115974635 TAATTAATAA
*
115974645 TTTTTTATTTTTTATTTTTAAC
1 TTTTTTATTTTTAATTTTTAAC
115974667 TTTTTTA-TTTTAATTATTTA
1 TTTTTTATTTTTAATT-TTTA
115974687 TAGCAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTTATTTTTAATTTTTAAC
Found at i:115975684 original size:65 final size:65
Alignment explanation
Indices: 115975562--115975684 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 65
115975552 ATCCGTATTT
* * * * *
115975562 TTAAAAATTTTTCACACATATATTTATTATTTAATTTTTAGTTTCTCAGTAAATTATAGATATAC
1 TTAAAAATTTCTCACAAATATATTTATAATATAATTTTTAGTTTCTCAATAAATTATAGATATAC
* * * *
115975627 TTAAATATTTCTCACAAATATATTTCTAATATAATTTTTAGTTTCTTAATAATTTATA
1 TTAAAAATTTCTCACAAATATATTTATAATATAATTTTTAGTTTCTCAATAAATTATA
115975685 TATTATTTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 49 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.50
Consensus pattern (65 bp):
TTAAAAATTTCTCACAAATATATTTATAATATAATTTTTAGTTTCTCAATAAATTATAGATATAC
Found at i:115979922 original size:21 final size:20
Alignment explanation
Indices: 115979888--115979931 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
115979878 TTTTCCATTC
* *
115979888 TTTTCTGCTTCTCCCTCTAT
1 TTTTCTCCTTCTCCATCTAT
*
115979908 TTTTCTCCTTTCTCCATCTCT
1 TTTTCTCC-TTCTCCATCTAT
115979929 TTT
1 TTT
115979932 AATGTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.05, C:0.34, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTCTCCTTCTCCATCTAT
Found at i:115979931 original size:20 final size:19
Alignment explanation
Indices: 115979881--115979931 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
115979871 TTCTTTATTT
*
115979881 TCCAT-TCTTTTCTGCTTC
1 TCCATCTCTTTTCTCCTTC
* *
115979899 TCCCTCTATTTTTCTCCTTTC
1 TCCATCT-CTTTTCTCC-TTC
115979920 TCCATCTCTTTT
1 TCCATCTCTTTT
115979932 AATGTAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 4 0.16
19 1 0.04
20 11 0.44
21 9 0.36
ACGTcount: A:0.06, C:0.35, G:0.02, T:0.57
Consensus pattern (19 bp):
TCCATCTCTTTTCTCCTTC
Found at i:115982014 original size:39 final size:39
Alignment explanation
Indices: 115981922--115982016 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 39
115981912 ATGGTGCGGT
* *
115981922 GAGTTAAAAGCTCCCAATTGTCCTCCGAACAGTTAACGA
1 GAGTTAAAAGCTCTCAATTGTCCTCCAAACAGTTAACGA
* *
115981961 GAGTTAAAAACTCTCAATTGTCCTCCAAACAGTTAGCGA
1 GAGTTAAAAGCTCTCAATTGTCCTCCAAACAGTTAACGA
115982000 GAGTTAAAAGCTCTCAA
1 GAGTTAAAAGCTCTCAA
115982017 CTATCGTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (39 bp):
GAGTTAAAAGCTCTCAATTGTCCTCCAAACAGTTAACGA
Found at i:115982959 original size:16 final size:16
Alignment explanation
Indices: 115982938--115982985 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
115982928 AAAAATCTAC
115982938 TTAATTATAAAATATA
1 TTAATTATAAAATATA
*
115982954 TTAATTAT-CAA-AT-
1 TTAATTATAAAATATA
*
115982967 TTAATTATAAATTATA
1 TTAATTATAAAATATA
115982983 TTA
1 TTA
115982986 TAGTTTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
15 4 0.15
16 11 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAATTATAAAATATA
Found at i:115984698 original size:13 final size:13
Alignment explanation
Indices: 115984682--115984706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
115984672 TATATGACAT
115984682 TTTGATATTGATA
1 TTTGATATTGATA
115984695 TTTGATATTGAT
1 TTTGATATTGAT
115984707 TGTTATTGAA
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTGATATTGATA
Found at i:115985421 original size:2 final size:2
Alignment explanation
Indices: 115985414--115985444 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
115985404 ATTGGTTGGT
115985414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
115985445 GTAGCACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115986577 original size:26 final size:26
Alignment explanation
Indices: 115986548--115986600 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
115986538 TCAAACATGC
115986548 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
115986574 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
115986600 A
1 A
115986601 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:115988116 original size:26 final size:26
Alignment explanation
Indices: 115988080--115988189 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
115988070 CATGAAATTC
115988080 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
115988106 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
115988132 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
115988158 TTGTCATGAAACACTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
115988184 TTATCA
1 TTATCA
115988190 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:115991239 original size:29 final size:28
Alignment explanation
Indices: 115991201--115991282 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
115991191 CAGAAATTAA
*
115991201 TTAATTATTTTAAAATTTAGAAATATTTT
1 TTAATGATTTTAAAATTTA-AAATATTTT
* *
115991230 TTAATGATTTT-TATTATTAAAATATTTT
1 TTAATGATTTTAAAAT-TTAAAATATTTT
*
115991258 TTTA-GATTTTTAAAATTTTAAAATA
1 TTAATGA-TTTTAAAA-TTTAAAATA
115991283 ATTAATTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.05
28 18 0.42
29 22 0.51
30 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TTAATGATTTTAAAATTTAAAATATTTT
Found at i:115992911 original size:6 final size:7
Alignment explanation
Indices: 115992894--115992918 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
115992884 TTCAATAGTT
115992894 AAAAAAC
1 AAAAAAC
115992901 AAAAAAC
1 AAAAAAC
115992908 AAAAAAC
1 AAAAAAC
115992915 AAAA
1 AAAA
115992919 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:115993809 original size:12 final size:12
Alignment explanation
Indices: 115993792--115993826 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
115993782 GCGGAAATGG
115993792 AAAAATAAGAAA
1 AAAAATAAGAAA
115993804 AAAAATAAGAAA
1 AAAAATAAGAAA
*
115993816 AATAA-AAGAAA
1 AAAAATAAGAAA
115993827 GAACCACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAATAAGAAA
Found at i:115997897 original size:5 final size:6
Alignment explanation
Indices: 115997879--115997917 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
115997869 TCACTGTCTC
**
115997879 TTGTTT TTGTTT TTGTTT TTGCTTT TACTTT TTGTTT TT
1 TTGTTT TTGTTT TTGTTT TTG-TTT TTGTTT TTGTTT TT
115997918 CCTGTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.03, C:0.05, G:0.13, T:0.79
Consensus pattern (6 bp):
TTGTTT
Found at i:115997930 original size:19 final size:19
Alignment explanation
Indices: 115997888--115997930 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
115997878 CTTGTTTTTG
*
115997888 TTTTTGTTTTTGCTTTTAC
1 TTTTTGTTTTTCCTTTTAC
*
115997907 TTTTTGTTTTTCCTGTTTTC
1 TTTTTGTTTTTCCT-TTTAC
115997927 TTTT
1 TTTT
115997931 ATTATTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (19 bp):
TTTTTGTTTTTCCTTTTAC
Found at i:115998280 original size:205 final size:205
Alignment explanation
Indices: 115997928--115998344 Score: 834
Period size: 205 Copynumber: 2.0 Consensus size: 205
115997918 CCTGTTTTCT
115997928 TTTATTATTTCCTACCCTTTGCAATTTTACTTATTTGTAAAGCCTTTTTCTGGTTTAGATGAACT
1 TTTATTATTTCCTACCCTTTGCAATTTTACTTATTTGTAAAGCCTTTTTCTGGTTTAGATGAACT
115997993 TGCTTTGTCAATTAATTTTGTAAGGCATCATTAAACACTCCTCTTAATATGCGTGTAAATAAATG
66 TGCTTTGTCAATTAATTTTGTAAGGCATCATTAAACACTCCTCTTAATATGCGTGTAAATAAATG
115998058 AAAACTTCTGTGTCTCAGAACATTGAGGTTGAAGAAGAGCGTGTTGATGATCGTTCAGTTGATGA
131 AAAACTTCTGTGTCTCAGAACATTGAGGTTGAAGAAGAGCGTGTTGATGATCGTTCAGTTGATGA
115998123 CCTCTTGTCA
196 CCTCTTGTCA
115998133 TTTATTATTTCCTACCCTTTGCAATTTTACTTATTTGTAAAGCCTTTTTCTGGTTTAGATGAACT
1 TTTATTATTTCCTACCCTTTGCAATTTTACTTATTTGTAAAGCCTTTTTCTGGTTTAGATGAACT
115998198 TGCTTTGTCAATTAATTTTGTAAGGCATCATTAAACACTCCTCTTAATATGCGTGTAAATAAATG
66 TGCTTTGTCAATTAATTTTGTAAGGCATCATTAAACACTCCTCTTAATATGCGTGTAAATAAATG
115998263 AAAACTTCTGTGTCTCAGAACATTGAGGTTGAAGAAGAGCGTGTTGATGATCGTTCAGTTGATGA
131 AAAACTTCTGTGTCTCAGAACATTGAGGTTGAAGAAGAGCGTGTTGATGATCGTTCAGTTGATGA
115998328 CCTCTTGTCA
196 CCTCTTGTCA
115998338 TTTATTA
1 TTTATTA
115998345 ATGGAGACAA
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 212 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (205 bp):
TTTATTATTTCCTACCCTTTGCAATTTTACTTATTTGTAAAGCCTTTTTCTGGTTTAGATGAACT
TGCTTTGTCAATTAATTTTGTAAGGCATCATTAAACACTCCTCTTAATATGCGTGTAAATAAATG
AAAACTTCTGTGTCTCAGAACATTGAGGTTGAAGAAGAGCGTGTTGATGATCGTTCAGTTGATGA
CCTCTTGTCA
Found at i:116004424 original size:19 final size:19
Alignment explanation
Indices: 116004400--116004436 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
116004390 TTAGTCCCGG
116004400 AATTTGGCACCTGAACTTC
1 AATTTGGCACCTGAACTTC
*
116004419 AATTTGGCACTTGAACTT
1 AATTTGGCACCTGAACTT
116004437 GGATTGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (19 bp):
AATTTGGCACCTGAACTTC
Found at i:116034633 original size:2 final size:2
Alignment explanation
Indices: 116034626--116034674 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
116034616 ATCTTTTACT
116034626 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
116034668 TC TC TC T
1 TC TC TC T
116034675 AACACACGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:116038845 original size:26 final size:25
Alignment explanation
Indices: 116038807--116038860 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
116038797 CTTATAATTT
116038807 TTATACTTCTTAAAAATTTTAAAAA
1 TTATACTTCTTAAAAATTTTAAAAA
* *
116038832 TTATAACTTTTTAAAATTTTTAAAAA
1 TTAT-ACTTCTTAAAAATTTTAAAAA
116038858 TTA
1 TTA
116038861 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATACTTCTTAAAAATTTTAAAAA
Found at i:116039292 original size:16 final size:16
Alignment explanation
Indices: 116039271--116039308 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
116039261 TTATAATTTT
116039271 TTTTTAATTTTAAATA
1 TTTTTAATTTTAAATA
116039287 TTTTT-ATTTTAAATA
1 TTTTTAATTTTAAATA
116039302 TTTTTAA
1 TTTTTAA
116039309 AATTATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTAATTTTAAATA
Found at i:116045357 original size:12 final size:13
Alignment explanation
Indices: 116045335--116045362 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
116045325 ATGGCAGTAC
116045335 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
116045348 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
116045361 AA
1 AA
116045363 CTTGCCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:116070023 original size:23 final size:23
Alignment explanation
Indices: 116069993--116070038 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
116069983 AGAAGGATAT
116069993 TAGGGCATGGGTGGCCATTTGGA
1 TAGGGCATGGGTGGCCATTTGGA
116070016 TAGGGCATGGGTGGCCATTTGGA
1 TAGGGCATGGGTGGCCATTTGGA
116070039 GGCTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.43, T:0.26
Consensus pattern (23 bp):
TAGGGCATGGGTGGCCATTTGGA
Found at i:116070299 original size:38 final size:39
Alignment explanation
Indices: 116070228--116070305 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
116070218 GTACCAGTAC
*
116070228 TCACTGCAAATGATGAGGTTATTATAAGCTGTAAACGTT
1 TCACTGCAAATGATGAGATTATTATAAGCTGTAAACGTT
* * * *
116070267 TCACTGCAAATGGT-AGATTATTGTAAGTTGTAAATGTT
1 TCACTGCAAATGATGAGATTATTATAAGCTGTAAACGTT
116070305 T
1 T
116070306 GGCCATCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 21 0.62
39 13 0.38
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (39 bp):
TCACTGCAAATGATGAGATTATTATAAGCTGTAAACGTT
Found at i:116079547 original size:10 final size:10
Alignment explanation
Indices: 116079524--116079564 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
116079514 TGTAATTTAA
116079524 AATAATT-TT
1 AATAATTCTT
116079533 AATAATCTCTT
1 AATAAT-TCTT
116079544 -ATAATTCTT
1 AATAATTCTT
*
116079553 AATAATTTTT
1 AATAATTCTT
116079563 AA
1 AA
116079565 ATATTTATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 10 0.36
10 16 0.57
11 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (10 bp):
AATAATTCTT
Found at i:116083830 original size:49 final size:49
Alignment explanation
Indices: 116083769--116083872 Score: 201
Period size: 49 Copynumber: 2.1 Consensus size: 49
116083759 TAATTAAGAA
116083769 AAATAATTTTAAAAAATAAATAAATAATAAATACACAATATACAAGTAG
1 AAATAATTTTAAAAAATAAATAAATAATAAATACACAATATACAAGTAG
116083818 AAATAATTTTAAAAAATAAATAAATAATAAATACACAATATACAAGTAG
1 AAATAATTTTAAAAAATAAATAAATAATAAATACACAATATACAAGTAG
116083867 -AATAAT
1 AAATAAT
116083873 ATGGAATCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 6 0.11
49 49 0.89
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (49 bp):
AAATAATTTTAAAAAATAAATAAATAATAAATACACAATATACAAGTAG
Found at i:116084169 original size:15 final size:15
Alignment explanation
Indices: 116084144--116084182 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
116084134 ACGGTAAAGT
*
116084144 ATAAT-AAAATAGTA
1 ATAATAAAAATAATA
116084158 ATAATAAAAATAATA
1 ATAATAAAAATAATA
*
116084173 ATACTAAAAA
1 ATAATAAAAA
116084183 CAATTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:116085124 original size:17 final size:15
Alignment explanation
Indices: 116085091--116085126 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
116085081 GAGGTTTAGG
116085091 TGGGTTTTGGGGTAT
1 TGGGTTTTGGGGTAT
116085106 TGGGTTATTGGGTGTAT
1 TGGGTT-TTGGG-GTAT
116085123 TGGG
1 TGGG
116085127 CTTAGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.44
Consensus pattern (15 bp):
TGGGTTTTGGGGTAT
Found at i:116087026 original size:49 final size:49
Alignment explanation
Indices: 116086853--116087097 Score: 247
Period size: 49 Copynumber: 4.9 Consensus size: 49
116086843 TCTATTTTGA
* * * * ** *
116086853 GGTCGCATGTGTAGTACTAAGTGCAGGTTACTATGTTTACTTGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* * * * **
116086904 GATCACATGTATAGCACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
116086953 AGGTCACGTCTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
116087003 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * * * *
116087052 GGTCGCATGTGTAATACTATGTGCATGTTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
116087098 GCTATGGCTA
Statistics
Matches: 161, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
49 86 0.53
50 41 0.25
51 34 0.21
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:116087047 original size:99 final size:101
Alignment explanation
Indices: 116086862--116087047 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 101
116086852 AGGTCGCATG
* * * **
116086862 TGTAGTACTAAGTGCAGGTTACTATGTTTACTTGAAAACTGTGATCACATGTATAGCACTAAGTG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGAAAACTGTGATCACATGTATAGCACTAAGTG
*
116086927 CAGGCTACTACGTGTATCAGATGGTTAGGTCACGTC
66 CAGGCTACTACGTGTACCAGATGGTTAGGTCACGTC
* * * * *
116086963 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACGTGTGTAGTACTAAGTG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGAAAACTGTGATCACATGTATAGCACTAAGTG
116087026 CAGGCTACTACGTGTACCAGAT
66 CAGGCTACTACGTGTACCAGAT
116087048 AATTGGTCGC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 41 0.55
100 1 0.01
101 32 0.43
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGAAAACTGTGATCACATGTATAGCACTAAGTG
CAGGCTACTACGTGTACCAGATGGTTAGGTCACGTC
Found at i:116089662 original size:21 final size:22
Alignment explanation
Indices: 116089609--116089662 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
116089599 AAATTCGGCT
116089609 CTATTTAATTTTTAATATTCAA
1 CTATTTAATTTTTAATATTCAA
* * *
116089631 -AATTTATATTTTT-ATTTTTAA
1 CTATTTA-ATTTTTAATATTCAA
116089652 CTATTTAATTT
1 CTATTTAATTT
116089663 CATCTAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (22 bp):
CTATTTAATTTTTAATATTCAA
Found at i:116089742 original size:24 final size:24
Alignment explanation
Indices: 116089697--116089745 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
116089687 TTATAATTTT
* *
116089697 TTTTTATAATTGGGGTGGAAAATA
1 TTTTTATAATTGGAGTGAAAAATA
*
116089721 TTTTTATAATTGAGAGTAAAAAATA
1 TTTTTATAATTG-GAGTGAAAAATA
116089746 AATTGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (24 bp):
TTTTTATAATTGGAGTGAAAAATA
Found at i:116090626 original size:26 final size:26
Alignment explanation
Indices: 116090588--116090637 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
116090578 TTGGGTTTGT
* * *
116090588 GATTTAAGATTTAGGGTTTGAGTTTA
1 GATTCAAGATTTAAGATTTGAGTTTA
*
116090614 GATTCAAGGTTTAAGATTTGAGTT
1 GATTCAAGATTTAAGATTTGAGTT
116090638 CAGAATTGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.44
Consensus pattern (26 bp):
GATTCAAGATTTAAGATTTGAGTTTA
Found at i:116099364 original size:26 final size:26
Alignment explanation
Indices: 116099335--116099442 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
116099325 TGGTACAAAT
116099335 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
116099361 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
116099387 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
116099413 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
116099439 TGAT
1 TGAT
116099443 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:116100942 original size:26 final size:25
Alignment explanation
Indices: 116100878--116100952 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
116100868 AAAAGTAGCT
* * *
116100878 AAATTACTATAATACCCCTATGTATGA
1 AAATTACTGTTATACCCCTA-G-GTGA
*
116100905 AAATTACAGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGGTG-A
116100931 AAATTACTGTTATACCCCTAGG
1 AAATTACTGTTATACCCCTAGG
116100953 GTTAATTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.05
26 23 0.55
27 17 0.40
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (25 bp):
AAATTACTGTTATACCCCTAGGTGA
Found at i:116101096 original size:27 final size:27
Alignment explanation
Indices: 116101056--116101169 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
116101046 AGGAAGCGTC
116101056 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* *
116101083 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
*
116101110 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* * * *
116101137 TTGGTGGCTCTGCCATAA-TATTTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
116101164 CTGGTG
1 CTGGTG
116101170 ACTTCGTCAC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.09
27 65 0.88
28 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:116101142 original size:54 final size:54
Alignment explanation
Indices: 116101056--116101169 Score: 176
Period size: 54 Copynumber: 2.1 Consensus size: 54
116101046 AGGAAGCGTC
116101056 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACA-ATATCTGTAT
* * * *
116101110 CTGGTGGCTATGCCACGATTATCTGATTTGGTGGCTCTGCCATAATATTTGTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACAATATCTGTAT
116101164 CTGGTG
1 CTGGTG
116101170 ACTTCGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 7 0.13
54 48 0.87
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACAATATCTGTAT
Found at i:116106757 original size:2 final size:2
Alignment explanation
Indices: 116106750--116106783 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
116106740 TGAGTCTTTT
116106750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116106784 GTAGATCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:116112230 original size:20 final size:20
Alignment explanation
Indices: 116112205--116112247 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
116112195 AATTTTGGGC
116112205 TTCCATAAGAGGAAAGAACA
1 TTCCATAAGAGGAAAGAACA
116112225 TTCCATAAGAGGAAAGAACA
1 TTCCATAAGAGGAAAGAACA
116112245 TTC
1 TTC
116112248 GCTAGGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (20 bp):
TTCCATAAGAGGAAAGAACA
Found at i:116116414 original size:25 final size:26
Alignment explanation
Indices: 116116385--116116451 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
116116375 TAAGGTTATT
*
116116385 TATATAATTATTTTAAAATT-AAAAA
1 TATATAATTAATTTAAAATTAAAAAA
** *
116116410 TATATAAAAAATTAAAAATTAAAAAA
1 TATATAATTAATTTAAAATTAAAAAA
116116436 TATATAAATTAATTTA
1 TATAT-AATTAATTTA
116116452 TATATAATGC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
25 16 0.48
26 10 0.30
27 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TATATAATTAATTTAAAATTAAAAAA
Found at i:116116444 original size:16 final size:15
Alignment explanation
Indices: 116116399--116116447 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
116116389 TAATTATTTT
116116399 AAAATTAAAAATATATAA
1 AAAATT-AAAA-AT-TAA
116116417 AAAATTAAAAATTAA
1 AAAATTAAAAATTAA
*
116116432 AAAATATATAAATTAA
1 AAAAT-TAAAAATTAA
116116448 TTTATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.28
16 11 0.38
17 4 0.14
18 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTAAAAATTAA
Found at i:116117980 original size:12 final size:12
Alignment explanation
Indices: 116117963--116118020 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
116117953 ATAACAAGAC
*
116117963 ATAAAAATATAT
1 ATAAAAATATAA
116117975 AT-AAAAT-TAA
1 ATAAAAATATAA
*
116117985 ATGAAATATATAA
1 AT-AAAAATATAA
*
116117998 ATAAAAATATAT
1 ATAAAAATATAA
*
116118010 ACAAAAATATA
1 ATAAAAATATA
116118021 CTAATTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.11
11 5 0.13
12 24 0.63
13 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
ATAAAAATATAA
Found at i:116118983 original size:11 final size:10
Alignment explanation
Indices: 116118958--116118988 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
116118948 ATAGAATAAA
116118958 TTTAAAAAAT
1 TTTAAAAAAT
116118968 TTTAAAAAAT
1 TTTAAAAAAT
116118978 TGTTAAAAAAT
1 T-TTAAAAAAT
116118989 GAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TTTAAAAAAT
Found at i:116125688 original size:27 final size:27
Alignment explanation
Indices: 116125624--116125689 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 27
116125614 AATGAATTTA
* *
116125624 ATATTAAATTTAATTTAATATTTATCTAG
1 ATATT-AATTT-ATTTAATATTAATATAG
*
116125653 ATAGT-ATTTA-TTAATATTAATATGAG
1 ATATTAATTTATTTAATATTAATAT-AG
116125679 ATATTAATTTA
1 ATATTAATTTA
116125690 ATATTAATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 11 0.35
26 7 0.23
27 9 0.29
29 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (27 bp):
ATATTAATTTATTTAATATTAATATAG
Found at i:116129019 original size:25 final size:25
Alignment explanation
Indices: 116128991--116129052 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
116128981 TTTCTAACTA
* *
116128991 ATCACTAAATTGATAAAATTTTCCT
1 ATCAATAAATTCATAAAATTTTCCT
** *
116129016 ATCAATATTTTCATACAATTTTCCT
1 ATCAATAAATTCATAAAATTTTCCT
116129041 ATCATATAAATT
1 ATCA-ATAAATT
116129053 TTCAAGCAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.44
Consensus pattern (25 bp):
ATCAATAAATTCATAAAATTTTCCT
Found at i:116130862 original size:34 final size:34
Alignment explanation
Indices: 116130824--116130891 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
116130814 CAAAGGCATC
116130824 ACATATCTGATTCTTTCCATTTAGTTGGCTAACA
1 ACATATCTGATTCTTTCCATTTAGTTGGCTAACA
116130858 ACATATCTGATTCTTTCCATTTAGTTGGCTAACA
1 ACATATCTGATTCTTTCCATTTAGTTGGCTAACA
116130892 CTGAATGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (34 bp):
ACATATCTGATTCTTTCCATTTAGTTGGCTAACA
Found at i:116134381 original size:33 final size:33
Alignment explanation
Indices: 116134344--116134407 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
116134334 CAACCATCAG
116134344 ATAATCAAGAGTTGCAAAAACCTTAAATGAAAA
1 ATAATCAAGAGTTGCAAAAACCTTAAATGAAAA
116134377 ATAATCAAGAGTTGCAAAAACCTTAAATGAA
1 ATAATCAAGAGTTGCAAAAACCTTAAATGAA
116134408 CATTGCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (33 bp):
ATAATCAAGAGTTGCAAAAACCTTAAATGAAAA
Found at i:116137261 original size:20 final size:19
Alignment explanation
Indices: 116137236--116137289 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
116137226 TAAAAAAATT
* *
116137236 ATTTTTAAATTTTTTTATAA
1 ATTTTTAAATATTATTA-AA
116137256 ATTTTTAAATATTATTAAA
1 ATTTTTAAATATTATTAAA
*
116137275 ATTTATAAAATATTA
1 ATTT-TTAAATATTA
116137290 AATAAAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTAAATATTATTAAA
Found at i:116137792 original size:17 final size:18
Alignment explanation
Indices: 116137772--116137805 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
116137762 TTAAAGAAAA
*
116137772 TTAAATTTTA-ATATTTT
1 TTAAACTTTATATATTTT
116137789 TTAAACTTTATATATTT
1 TTAAACTTTATATATTT
116137806 AAAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAACTTTATATATTTT
Found at i:116142680 original size:13 final size:14
Alignment explanation
Indices: 116142656--116142692 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
116142646 CTTATGTTTT
116142656 ATATATATAATATA
1 ATATATATAATATA
116142670 ATATA-ATAATATA
1 ATATATATAATATA
116142683 ATATACTATA
1 ATATA-TATA
116142693 TATTAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.62
14 5 0.24
15 3 0.14
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATAATATA
Found at i:116145484 original size:49 final size:49
Alignment explanation
Indices: 116145428--116145522 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
116145418 ATTTAAATTA
* *
116145428 ACATGTTTACTAGTAAATAGATTAAATTTTTAATTTTCATATAAAGTTC
1 ACATGTTTACTAATAAATAGATTAAATTTTTAATTTTCATAAAAAGTTC
* *
116145477 ACATGTTTATTAATAAATAGATTAATTTTTTAATTTTCATAAAAAG
1 ACATGTTTACTAATAAATAGATTAAATTTTTAATTTTCATAAAAAG
116145523 CAAAAGATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (49 bp):
ACATGTTTACTAATAAATAGATTAAATTTTTAATTTTCATAAAAAGTTC
Found at i:116145894 original size:42 final size:42
Alignment explanation
Indices: 116145835--116145914 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
116145825 TTTTACTCTA
*
116145835 AACCCAAAACTTAAAACCC-CAAACTTAGAACCTTGAACTTGT
1 AACCCAAAACTTAAAACCCTCAAACTT-GAACATTGAACTTGT
* * *
116145877 AACCCATAACTTCAAACCCTTAAACTTGAACATTGAAC
1 AACCCAAAACTTAAAACCCTCAAACTTGAACATTGAAC
116145915 CTTAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 27 0.82
43 6 0.18
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (42 bp):
AACCCAAAACTTAAAACCCTCAAACTTGAACATTGAACTTGT
Found at i:116147524 original size:19 final size:19
Alignment explanation
Indices: 116147500--116147538 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
116147490 ATAAAAGTTA
116147500 ACTTTAAGTTTAATTACAT
1 ACTTTAAGTTTAATTACAT
*
116147519 ACTTTAATTTTAATTACAT
1 ACTTTAAGTTTAATTACAT
116147538 A
1 A
116147539 TATTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (19 bp):
ACTTTAAGTTTAATTACAT
Found at i:116153090 original size:18 final size:18
Alignment explanation
Indices: 116153047--116153123 Score: 55
Period size: 20 Copynumber: 4.0 Consensus size: 18
116153037 ATTTATTTCA
* *
116153047 TATATATTTTTATCATTT
1 TATATATTTATATAATTT
116153065 TAATTATATTTATATAATTT
1 T-A-TATATTTATATAATTT
* * *
116153085 TCTATAATTCTATAATATT
1 TATATATTTATATAAT-TT
*
116153104 TAAATATTTAAATATAATTT
1 TATATATTT--ATATAATTT
116153124 GTTGAAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
18 13 0.29
19 9 0.20
20 17 0.38
21 6 0.13
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATTTATATAATTT
Found at i:116154985 original size:18 final size:19
Alignment explanation
Indices: 116154964--116155006 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
116154954 TGTTATAAAA
*
116154964 ATATT-ATATTAATTATAT
1 ATATTAATAATAATTATAT
116154982 ATATTAAATAATAATTATAT
1 ATATT-AATAATAATTATAT
116155002 ATATT
1 ATATT
116155007 TTATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
20 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTAATAATAATTATAT
Found at i:116158365 original size:3 final size:3
Alignment explanation
Indices: 116158357--116158381 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
116158347 TCAGAGCTTA
116158357 GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG G
116158382 AGTGCCCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:116159906 original size:17 final size:17
Alignment explanation
Indices: 116159886--116159919 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
116159876 AATACATTCA
116159886 AAAATAAATTAAAATTT
1 AAAATAAATTAAAATTT
116159903 AAAATAAATTAAAATTT
1 AAAATAAATTAAAATTT
116159920 TATCGAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAAATTAAAATTT
Found at i:116160170 original size:16 final size:15
Alignment explanation
Indices: 116160149--116160193 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
116160139 GATTAACTAT
*
116160149 TTTTTTATAATTTTTA
1 TTTTTTA-AATTTATA
116160165 TTTTTTAAAATTTATA
1 TTTTTT-AAATTTATA
116160181 TATTTTTAAATTT
1 T-TTTTTAAATTT
116160194 CTAAAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATTTATA
Found at i:116160198 original size:25 final size:23
Alignment explanation
Indices: 116160152--116160208 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
116160142 TAACTATTTT
* *
116160152 TTTATAATTTTTATTTTTTAAAA
1 TTTATAATTTTTAATTTCTAAAA
116160175 TTTATATATTTTTAAATTTCTAAAA
1 TTTATA-ATTTTT-AATTTCTAAAA
116160200 TGTT-TAATT
1 T-TTATAATT
116160209 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 6 0.21
24 9 0.31
25 12 0.41
26 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTATAATTTTTAATTTCTAAAA
Found at i:116160274 original size:66 final size:64
Alignment explanation
Indices: 116160158--116160279 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 64
116160148 TTTTTTTATA
* *
116160158 ATTTTTATTTTTTAAAATTTATATATTTTTAAATTTCTAAAATGTTTAATTATTTTTTATTTTT
1 ATTTTTATTTTTTAAAATATATATATTTTAAAATTTCTAAAATGTTTAATTATTTTTTATTTTT
116160222 ATTTTTATTTTTTTATAAA-ATATATAATTTATAAAATTT-TAAAATGTTTAATTATTTT
1 ATTTTTA-TTTTTTA-AAATATATAT-ATTT-TAAAATTTCTAAAATGTTTAATTATTTT
116160280 AACGATTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
64 7 0.13
65 12 0.23
66 26 0.50
67 7 0.13
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (64 bp):
ATTTTTATTTTTTAAAATATATATATTTTAAAATTTCTAAAATGTTTAATTATTTTTTATTTTT
Found at i:116160428 original size:17 final size:18
Alignment explanation
Indices: 116160408--116160453 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
116160398 TTTTTAAAAA
116160408 ATATTTTTAAATTTATT-
1 ATATTTTTAAATTTATTG
* *
116160425 ATATATTTTTAATTTCTTG
1 ATAT-TTTTAAATTTATTG
116160444 AT-TTTTTAAA
1 ATATTTTTAAA
116160454 AAATATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 10 0.42
18 12 0.50
19 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
ATATTTTTAAATTTATTG
Found at i:116160478 original size:12 final size:12
Alignment explanation
Indices: 116160463--116160488 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
116160453 AAAATATATG
116160463 TATTTATATTTT
1 TATTTATATTTT
116160475 TATTTATATTTT
1 TATTTATATTTT
116160487 TA
1 TA
116160489 AAATTTTTCA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:116161565 original size:137 final size:135
Alignment explanation
Indices: 116161314--116161580 Score: 392
Period size: 137 Copynumber: 2.0 Consensus size: 135
116161304 TGGAGTCTCA
* * * *
116161314 ATTATTAATTTTAGGCCTATGAGGAGAAGATTGAGATAGGATATTATCTAATAGTCAAATTTGGT
1 ATTATTAATTTTAGGCCTATGAAGAGAAAATTGAGATAGGATATTATCTAACAGTCAAACTTGGT
*
116161379 TTTCATATAACCACTGGACAAGAAGGGACTATGCATAATGATCCCAATTTTTATGAACCTAAAAT
66 TTTCA-ATAACCACTGGACAAGAAGGGACTATGCATAATCATCCCAA-TTTTATGAACCTAAAAT
116161444 TTCAGCT
129 TTCAGCT
116161451 ATTATTAATTTTAGGCCTATGAAGAGAAAATTGAGATAGGATATTATCTAACAGTCAAACTTGGT
1 ATTATTAATTTTAGGCCTATGAAGAGAAAATTGAGATAGGATATTATCTAACAGTCAAACTTGGT
* * ** * *
116161516 TTTGC-ATAATCACTGGACGAGAAGGGACTATGCATCCTCATCCCAAATTTTGTGAACCTACAAT
66 TTT-CAATAACCACTGGACAAGAAGGGACTATGCATAATCATCCC-AATTTTATGAACCTAAAAT
116161580 T
129 T
116161581 ACAACTCTCA
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
136 50 0.43
137 66 0.56
138 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (135 bp):
ATTATTAATTTTAGGCCTATGAAGAGAAAATTGAGATAGGATATTATCTAACAGTCAAACTTGGT
TTTCAATAACCACTGGACAAGAAGGGACTATGCATAATCATCCCAATTTTATGAACCTAAAATTT
CAGCT
Found at i:116173196 original size:12 final size:12
Alignment explanation
Indices: 116173181--116173211 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
116173171 TTCTCTTTTA
116173181 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
116173193 TTTTTCTTTCTC
1 TTTTTCTTTCCC
116173205 TTTTTCT
1 TTTTTCT
116173212 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:116173608 original size:15 final size:14
Alignment explanation
Indices: 116173590--116173620 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
116173580 TTAATTTATT
116173590 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
116173605 TAATAATAATCTAA
1 TAATAATAATCTAA
116173619 TA
1 TA
116173621 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:116173631 original size:21 final size:20
Alignment explanation
Indices: 116173607--116173675 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
116173597 AATGCTAATA
116173607 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
116173628 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
116173647 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
116173668 ATAATAAT
1 ATAATAAT
116173676 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:116177829 original size:2 final size:2
Alignment explanation
Indices: 116177822--116177846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116177812 AAGTAAATTA
116177822 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
116177847 ACACTAATGC
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:116178002 original size:31 final size:32
Alignment explanation
Indices: 116177942--116178002 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
116177932 TATAATAGTG
* * *
116177942 AAATAGTAACAAAATATTGAAAAAAAACAAGA
1 AAATAGCAACAAAACAATGAAAAAAAACAAGA
*
116177974 AAATAGCAACAAAACAAT-AAAAACAACAA
1 AAATAGCAACAAAACAATGAAAAAAAACAA
116178003 CAAAGCGACG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (32 bp):
AAATAGCAACAAAACAATGAAAAAAAACAAGA
Found at i:116181797 original size:28 final size:28
Alignment explanation
Indices: 116181731--116181786 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
116181721 TGGACTTATT
116181731 AAATTGATTAAAGCATATACACCTTTCA
1 AAATTGATTAAAGCATATACACCTTTCA
116181759 AAATTGATTAAAGCATATACACCTTTCA
1 AAATTGATTAAAGCATATACACCTTTCA
116181787 CTTTGCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (28 bp):
AAATTGATTAAAGCATATACACCTTTCA
Found at i:116187455 original size:3 final size:3
Alignment explanation
Indices: 116187447--116187484 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
116187437 TTGCTGATGC
* *
116187447 TGT TGT TGT TGC TGG TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
116187485 AAAGTGCTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.37, T:0.61
Consensus pattern (3 bp):
TGT
Found at i:116187458 original size:18 final size:18
Alignment explanation
Indices: 116187435--116187475 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
116187425 GAGCCACAGC
116187435 TGTTGCTGATGCTGTTGT
1 TGTTGCTGATGCTGTTGT
* *
116187453 TGTTGCTGGTGTTGTTGT
1 TGTTGCTGATGCTGTTGT
116187471 TGTTG
1 TGTTG
116187476 TTGTTGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.07, G:0.37, T:0.54
Consensus pattern (18 bp):
TGTTGCTGATGCTGTTGT
Found at i:116187459 original size:12 final size:12
Alignment explanation
Indices: 116187433--116187481 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
116187423 CTGAGCCACA
* *
116187433 GCTGTTGCTGAT
1 GCTGTTGTTGTT
116187445 GCTGTTGTTGTT
1 GCTGTTGTTGTT
*
116187457 GCTGGTGTTGTT
1 GCTGTTGTTGTT
*
116187469 GTTGTTGTTGTT
1 GCTGTTGTTGTT
116187481 G
1 G
116187482 TTGAAAGTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.02, C:0.08, G:0.37, T:0.53
Consensus pattern (12 bp):
GCTGTTGTTGTT
Found at i:116188739 original size:20 final size:19
Alignment explanation
Indices: 116188714--116188771 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
116188704 AATTAAGTTT
116188714 ATTTAAAATAAAAATACTAA
1 ATTTAAAATAAAAA-ACTAA
*
116188734 ATTTAAAATAAAAAATTAA
1 ATTTAAAATAAAAAACTAA
116188753 ATATTAAATATTAAAAAAC
1 AT-TTAAA-A-TAAAAAAC
116188772 ACTTTTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.18
20 19 0.58
21 1 0.03
22 7 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTTAAAATAAAAAACTAA
Found at i:116188970 original size:23 final size:23
Alignment explanation
Indices: 116188944--116189004 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
116188934 AAAAATCATG
**
116188944 TATAATATTTAAAAATATTTTTT
1 TATAATATTTAAAAATATAATTT
*
116188967 TATAAAATTCTAAAATATATAATTT
1 TATAATATT-TAAAA-ATATAATTT
116188992 TA-AAT-TTTAAAAA
1 TATAATATTTAAAAA
116189005 GTCAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 1 0.03
22 5 0.16
23 10 0.31
24 7 0.22
25 9 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAATATTTAAAAATATAATTT
Found at i:116189012 original size:30 final size:31
Alignment explanation
Indices: 116188964--116189034 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
116188954 AAAAATATTT
*
116188964 TTTTATAAAATTCTAAAATATATAAT-TT-TAAA
1 TTTTA-AAAAGTCTAAAATA-A-AATATTATAAA
116188996 TTTTAAAAAGTC-AAAATAAAATATTATAAA
1 TTTTAAAAAGTCTAAAATAAAATATTATAAA
*
116189026 ATTTAAAAA
1 TTTTAAAAA
116189035 ATTTAGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 3 0.09
30 18 0.51
31 6 0.17
32 5 0.14
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (31 bp):
TTTTAAAAAGTCTAAAATAAAATATTATAAA
Found at i:116191604 original size:30 final size:30
Alignment explanation
Indices: 116191570--116191635 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
116191560 GGCAGATTTT
* *
116191570 TTAAAAGTTAG-AGAAAAAATTTTAGGTCCC
1 TTAAAAGTTAGTAAAAAAAATTTT-GGGCCC
*
116191600 TTAAAAGTTGGTAAAAAAAATTTTGGGCCC
1 TTAAAAGTTAGTAAAAAAAATTTTGGGCCC
116191630 TTAAAA
1 TTAAAA
116191636 ACTAGAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (30 bp):
TTAAAAGTTAGTAAAAAAAATTTTGGGCCC
Found at i:116192411 original size:27 final size:26
Alignment explanation
Indices: 116192376--116192429 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
116192366 AAGGTATTAA
116192376 AAATAATA-TAACAAGTTTGTTAATATT
1 AAATAATATTAA-AA-TTTGTTAATATT
* *
116192403 AAATGATATTTAAATTTGTTAATATT
1 AAATAATATTAAAATTTGTTAATATT
116192429 A
1 A
116192430 TGAGAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.54
27 9 0.38
28 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (26 bp):
AAATAATATTAAAATTTGTTAATATT
Found at i:116198724 original size:19 final size:19
Alignment explanation
Indices: 116198697--116198735 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
116198687 ATTGTGTGAC
*
116198697 TCGATTTGGTATTTTTTAA
1 TCGAGTTGGTATTTTTTAA
*
116198716 TCGAGTTGGTGTTTTTTAA
1 TCGAGTTGGTATTTTTTAA
116198735 T
1 T
116198736 GTCATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (19 bp):
TCGAGTTGGTATTTTTTAA
Found at i:116209348 original size:28 final size:28
Alignment explanation
Indices: 116209315--116209373 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
116209305 TACACAAGAG
116209315 AAAGGACATTACATATCTAAAAGAACAT
1 AAAGGACATTACATATCTAAAAGAACAT
116209343 AAAGGACATTACATATCTAAAAGAACAT
1 AAAGGACATTACATATCTAAAAGAACAT
116209371 AAA
1 AAA
116209374 AGGCTTTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (28 bp):
AAAGGACATTACATATCTAAAAGAACAT
Found at i:116211996 original size:11 final size:11
Alignment explanation
Indices: 116211967--116211997 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
116211957 ACCTGGAGCA
*
116211967 ATATTCAAATG
1 ATATTCAGATG
116211978 ATATTCAGATG
1 ATATTCAGATG
116211989 ATATTCAGA
1 ATATTCAGA
116211998 ACTTAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (11 bp):
ATATTCAGATG
Found at i:116213303 original size:20 final size:20
Alignment explanation
Indices: 116213275--116213318 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
116213265 ACTACAAAGG
116213275 AAATGAATTCAGATTAAAAA-
1 AAATGAATT-AGATTAAAAAT
* *
116213295 AAATTAATTATATTAAAAAT
1 AAATGAATTAGATTAAAAAT
116213315 AAAT
1 AAAT
116213319 CAAGTAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATGAATTAGATTAAAAAT
Found at i:116232089 original size:10 final size:10
Alignment explanation
Indices: 116232074--116232223 Score: 75
Period size: 10 Copynumber: 15.6 Consensus size: 10
116232064 AATTAGAAAC
116232074 AAAAATTTAT
1 AAAAATTTAT
116232084 AAAAA-TTATT
1 AAAAATTTA-T
* *
116232094 AAAAAATTGT
1 AAAAATTTAT
*
116232104 AAAATTTTAT
1 AAAAATTTAT
*
116232114 -AAAATTCAT
1 AAAAATTTAT
*
116232123 GAAAATTTAT
1 AAAAATTTAT
*
116232133 -AAAATATAT
1 AAAAATTTAT
* *
116232142 AGAAATATA-
1 AAAAATTTAT
116232151 AAAAATTTAT
1 AAAAATTTAT
* **
116232161 --AAAGTCGT
1 AAAAATTTAT
*
116232169 AAGAATATTAT
1 AAAAAT-TTAT
*
116232180 AAAAA-ATAT
1 AAAAATTTAT
*
116232189 AAAGAA-ATAT
1 AAA-AATTTAT
116232199 -AAAATTTAT
1 AAAAATTTAT
*
116232208 AAAAATATAT
1 AAAAATTTAT
116232218 AAAAAT
1 AAAAAT
116232224 CATCATATCA
Statistics
Matches: 107, Mismatches: 22, Indels: 22
0.71 0.15 0.15
Matches are distributed among these distances:
8 7 0.07
9 36 0.34
10 56 0.52
11 8 0.07
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:116232173 original size:28 final size:30
Alignment explanation
Indices: 116232124--116232221 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 30
116232114 AAAATTCATG
116232124 AAAATTTATAAAATATATAGAA-A-TATAA
1 AAAATTTATAAAATATATAGAATATTATAA
* *
116232152 AAAATTTATAAAGTCGTA-AGAATATTATAA
1 AAAATTTATAAAAT-ATATAGAATATTATAA
* *
116232182 AAAA--TATAAAGAAATATAAAAT-TTAT-A
1 AAAATTTATAAA-ATATATAGAATATTATAA
*
116232209 AAAATATATAAAA
1 AAAATTTATAAAA
116232222 ATCATCATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 5 0.09
28 30 0.53
29 13 0.23
30 9 0.16
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAATTTATAAAATATATAGAATATTATAA
Found at i:116232199 original size:19 final size:19
Alignment explanation
Indices: 116232133--116232222 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 19
116232123 GAAAATTTAT
*
116232133 AAAATATAT-AGAAATATA
1 AAAATATATAAAAAATATA
* * * *
116232151 AAAA-ATTTATAAAGTCGTA
1 AAAATATATAAAAAAT-ATA
*
116232170 AGAATATTATAAAAAATATA
1 AAAATA-TATAAAAAATATA
**
116232190 AAGAA-ATATAAAATTTATA
1 AA-AATATATAAAAAATATA
116232209 AAAATATATAAAAA
1 AAAATATATAAAAA
116232223 TCATCATATC
Statistics
Matches: 52, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
17 3 0.06
18 9 0.17
19 26 0.50
20 5 0.10
21 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (19 bp):
AAAATATATAAAAAATATA
Found at i:116232447 original size:19 final size:19
Alignment explanation
Indices: 116232425--116232466 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
116232415 TTTTTTAATC
*
116232425 TTTAAT-AAATTTTAATTTT
1 TTTAATGAAA-TTTAATATT
*
116232444 TTTATTGAAATTTAATATT
1 TTTAATGAAATTTAATATT
116232463 TTTA
1 TTTA
116232467 TTTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTAATGAAATTTAATATT
Found at i:116234281 original size:17 final size:17
Alignment explanation
Indices: 116234261--116234293 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
116234251 TGGGTTTTAT
116234261 TTAAAAAAATTAAATTG
1 TTAAAAAAATTAAATTG
*
116234278 TTAAAAATATTAAATT
1 TTAAAAAAATTAAATT
116234294 TTAGTTGACT
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TTAAAAAAATTAAATTG
Found at i:116234555 original size:23 final size:23
Alignment explanation
Indices: 116234529--116234574 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
116234519 TGAGATAAAC
**
116234529 AAATAAACCTTAAAAGCAAAGCA
1 AAATAAAAATTAAAAGCAAAGCA
*
116234552 AAATAAAAATTAAAAGGAAAGCA
1 AAATAAAAATTAAAAGCAAAGCA
116234575 TTGCATTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.13
Consensus pattern (23 bp):
AAATAAAAATTAAAAGCAAAGCA
Found at i:116234942 original size:24 final size:25
Alignment explanation
Indices: 116234915--116234974 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
116234905 TTTTTAATGT
* *
116234915 TTATTTTTTTCG-TCAACTTAATTA
1 TTATTTTTTTAGTTAAACTTAATTA
* *
116234939 TTATTATTTTAGTTAAATTTAATTA
1 TTATTTTTTTAGTTAAACTTAATTA
*
116234964 TTAATTTTTTA
1 TTATTTTTTTA
116234975 AAAAGAGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (25 bp):
TTATTTTTTTAGTTAAACTTAATTA
Found at i:116246173 original size:13 final size:13
Alignment explanation
Indices: 116246139--116246176 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
116246129 TTTATTTAGG
*
116246139 TTATATATAAATA
1 TTATATATAATTA
116246152 -T-TATATAATTA
1 TTATATATAATTA
116246163 TTATATATAATTA
1 TTATATATAATTA
116246176 T
1 T
116246177 AAACCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATATAATTA
Found at i:116246500 original size:18 final size:18
Alignment explanation
Indices: 116246456--116246500 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
116246446 ATAATATGTT
* **
116246456 AAAAAATAATAAAGCATA
1 AAAAAAAAATAAAAAATA
*
116246474 AAAGAAAAATAAAAAATA
1 AAAAAAAAATAAAAAATA
116246492 AAAAAAAAA
1 AAAAAAAAA
116246501 CAAACAGAGA
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:0.82, C:0.02, G:0.04, T:0.11
Consensus pattern (18 bp):
AAAAAAAAATAAAAAATA
Found at i:116248065 original size:23 final size:23
Alignment explanation
Indices: 116248036--116248111 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 23
116248026 AGACACTTTA
116248036 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
* * *
116248059 TGTGTCGTA--TCAGACAACTCG
1 TGTGTCGTATTTTAGGCACCTCG
* **
116248080 TGTGTCG--TTTTAGGCACTTTA
1 TGTGTCGTATTTTAGGCACCTCG
116248101 TGTGTCGTATT
1 TGTGTCGTATT
116248112 CTGATCAGGA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 29 0.73
23 11 0.28
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (23 bp):
TGTGTCGTATTTTAGGCACCTCG
Found at i:116252223 original size:41 final size:41
Alignment explanation
Indices: 116252178--116252258 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
116252168 GAAGATCCAT
116252178 GATCAATCAAAGCATAAGCAGGCTCAGAATACAGTAAAAAG
1 GATCAATCAAAGCATAAGCAGGCTCAGAATACAGTAAAAAG
116252219 GATCAATCAAAGCATAAGCAGGCTCAGAATACAGTAAAAA
1 GATCAATCAAAGCATAAGCAGGCTCAGAATACAGTAAAAA
116252259 TATACCTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (41 bp):
GATCAATCAAAGCATAAGCAGGCTCAGAATACAGTAAAAAG
Found at i:116253272 original size:2 final size:2
Alignment explanation
Indices: 116253265--116253289 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116253255 CCATGTATCA
116253265 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
116253290 CCATAATTGA
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:116258878 original size:46 final size:46
Alignment explanation
Indices: 116258828--116259003 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
116258818 TGGTTGAGCA
116258828 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
116258874 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
116258919 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
116258967 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
116259004 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:116258984 original size:93 final size:93
Alignment explanation
Indices: 116258825--116258996 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
116258815 GGATGGTTGA
* *
116258825 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
116258890 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
116258918 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
116258983 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
116258997 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:116266456 original size:46 final size:46
Alignment explanation
Indices: 116266406--116266581 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
116266396 TGGTTGAGCA
116266406 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
116266452 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
116266497 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
116266545 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
116266582 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:116266562 original size:93 final size:93
Alignment explanation
Indices: 116266403--116266574 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
116266393 GGATGGTTGA
* *
116266403 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
116266468 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
116266496 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
116266561 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
116266575 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:116275743 original size:12 final size:12
Alignment explanation
Indices: 116275726--116275750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
116275716 AGTTTACTTT
116275726 ATATTAGTGGTG
1 ATATTAGTGGTG
116275738 ATATTAGTGGTG
1 ATATTAGTGGTG
116275750 A
1 A
116275751 GCGTTTGATT
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:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (12 bp):
ATATTAGTGGTG
Found at i:116276076 original size:9 final size:9
Alignment explanation
Indices: 116276056--116276135 Score: 56
Period size: 9 Copynumber: 8.4 Consensus size: 9
116276046 TTTTAGAAAA
116276056 TTTTTAAA-
1 TTTTTAAAT
116276064 TTTTTAAAT
1 TTTTTAAAT
116276073 TTTTTATATAT
1 TTTTTA-A-AT
116276084 TTTTTAAAT
1 TTTTTAAAT
*
116276093 AAATTTTAAAT
1 --TTTTTAAAT
*
116276104 TTTTGAAAAT
1 TTTT-TAAAT
*
116276114 TATTTT-ATT
1 T-TTTTAAAT
*
116276123 TTTTTTAAT
1 TTTTTAAAT
116276132 TTTT
1 TTTT
116276136 GTTGTGAAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 12 0.21
9 20 0.34
10 7 0.12
11 19 0.33
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:116276118 original size:20 final size:18
Alignment explanation
Indices: 116276046--116276120 Score: 53
Period size: 20 Copynumber: 3.8 Consensus size: 18
116276036 AAAATTATTA
*
116276046 TTTTAGAAAATTTTTAAAT
1 TTTTA-AAATTTTTTAAAT
116276065 TTTT-AAATTTTTTATATATT
1 TTTTAAAATTTTTTA-A-A-T
**
116276085 TTTTAAATAAATTTTAAAT
1 TTTTAAA-ATTTTTTAAAT
116276104 TTTTGAAAATTATTTTA
1 TTTT-AAAATT-TTTTA
116276121 TTTTTTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
17 9 0.20
18 1 0.02
19 11 0.25
20 14 0.32
21 3 0.07
22 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTAAAATTTTTTAAAT
Found at i:116282139 original size:22 final size:22
Alignment explanation
Indices: 116282091--116282158 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
116282081 ATACCTAAAT
*
116282091 AATAAT-AAAATAATAATAGCAA
1 AATAATGAAAA-AATAATAACAA
* * *
116282113 TATAATTG-CAAAATGATAACAA
1 AATAA-TGAAAAAATAATAACAA
116282135 AATAATGAAAAAATAATAACAA
1 AATAATGAAAAAATAATAACAA
116282157 AA
1 AA
116282159 CAACAATAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 2 0.06
22 31 0.86
23 3 0.08
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (22 bp):
AATAATGAAAAAATAATAACAA
Found at i:116286606 original size:24 final size:21
Alignment explanation
Indices: 116286559--116286598 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
116286549 ATTTCTACCG
116286559 CTATAATATCTAATCTCACCA
1 CTATAATATCTAATCTCACCA
116286580 CTATAATAAT-TAATCTCAC
1 CTATAAT-ATCTAATCTCAC
116286599 AACAACTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTATAATATCTAATCTCACCA
Found at i:116290922 original size:22 final size:23
Alignment explanation
Indices: 116290882--116290943 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
116290872 ATGGTTTCTT
*
116290882 AAATAATTATAAAATTTATAAAA
1 AAATAATTATAAAAATTATAAAA
* *
116290905 AAATAATT-TAAAAATTATTAAG
1 AAATAATTATAAAAATTATAAAA
*
116290927 AAAT-A-TAAAAAAATTAT
1 AAATAATTATAAAAATTAT
116290944 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 15 0.44
23 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATAATTATAAAAATTATAAAA
Found at i:116292468 original size:112 final size:112
Alignment explanation
Indices: 116292269--116292484 Score: 362
Period size: 112 Copynumber: 1.9 Consensus size: 112
116292259 GTGATGCTCA
*
116292269 TTTTTATTTAATGCCAAGATAGCTTAGCCCATTATTTACTTTTGTTTTGAATAATTAATGAAGAA
1 TTTTTATTTAATGCCAAGATAGCTTAGCCCATTATTTACTTTTATTTTGAATAATTAATGAAGAA
* * *
116292334 ACTCTCATTAATCCAATGATAAAAGATATTCATATTAATAAATCGTG
66 ACTCTCATTAATCCAATAATAAAAAATATTCATAATAATAAATCGTG
* *
116292381 TTTTTATTTAATGCCAAGTTAGCTTAGCTCATTATTTACTTTTATTTTGAATAATTAATGAAGAA
1 TTTTTATTTAATGCCAAGATAGCTTAGCCCATTATTTACTTTTATTTTGAATAATTAATGAAGAA
116292446 ACT-TCTATTAATCCAATAATAAAAAATATTCATAATAAT
66 ACTCTC-ATTAATCCAATAATAAAAAATATTCATAATAAT
116292485 GAATTGTATG
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 2 0.02
112 95 0.98
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (112 bp):
TTTTTATTTAATGCCAAGATAGCTTAGCCCATTATTTACTTTTATTTTGAATAATTAATGAAGAA
ACTCTCATTAATCCAATAATAAAAAATATTCATAATAATAAATCGTG
Found at i:116303013 original size:71 final size:71
Alignment explanation
Indices: 116302880--116303014 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 71
116302870 AGTAGATTGC
* *
116302880 TTCCTCGTTGATTCAATCCATAGCCCTCATTAAGGCTCAATTCAAGTCATAACATGGAAAGGAAA
1 TTCCTCATTGATTCAATCCATAGCCCTCATTAAGGCTCAATTCAAGTCATAACATAGAAAGGAAA
116302945 AGATCA
66 AGATCA
* * ** * *
116302951 TTCCTCATTGATTCAATCCATTGCTCTTGTTCAGGCTCAATTCAAGTCATATGCATAG-AAGGAA
1 TTCCTCATTGATTCAATCCATAGCCCTCATTAAGGCTCAATTCAAGTCATA-ACATAGAAAGGAA
116303015 CAATATAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 51 0.93
72 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (71 bp):
TTCCTCATTGATTCAATCCATAGCCCTCATTAAGGCTCAATTCAAGTCATAACATAGAAAGGAAA
AGATCA
Found at i:116305679 original size:3 final size:3
Alignment explanation
Indices: 116305671--116305695 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
116305661 TTCCTTTTTA
116305671 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
116305696 GTGGGTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:116306532 original size:18 final size:20
Alignment explanation
Indices: 116306511--116306547 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
116306501 ATTTAATTTT
116306511 ATTAATATA-ATA-TTTTAC
1 ATTAATATAGATAGTTTTAC
*
116306529 ATTATTATAGATAGTTTTA
1 ATTAATATAGATAGTTTTA
116306548 GATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTAATATAGATAGTTTTAC
Done.