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 407 of 427
Found at i:118179752 original size:9 final size:9
Alignment explanation
Indices: 118179738--118179771 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
118179728 ATCGAAGAGA
118179738 AAAAAAATT
1 AAAAAAATT
118179747 AAAAAAATT
1 AAAAAAATT
*
118179756 AAAAAATTT
1 AAAAAAATT
118179765 AAAAAAA
1 AAAAAAA
118179772 AAATTAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAAAATT
Found at i:118189901 original size:23 final size:23
Alignment explanation
Indices: 118189871--118189915 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
118189861 AAACTCATCA
*
118189871 ATAATAAAATTTAAACTTTTAAC
1 ATAATAAAATTTAAACATTTAAC
*
118189894 ATAATAAATTTTAAACATTTAA
1 ATAATAAAATTTAAACATTTAA
118189916 TTTTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATAAAATTTAAACATTTAAC
Found at i:118192125 original size:13 final size:13
Alignment explanation
Indices: 118192104--118192149 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
118192094 TTTTATTATT
*
118192104 TTTATATAAAATA
1 TTTAAATAAAATA
118192117 TTTAAATAAAATAA
1 TTTAAATAAAAT-A
*
118192131 TTAAAATAAAATA
1 TTTAAATAAAATA
*
118192144 TCTAAA
1 TTTAAA
118192150 CACATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TTTAAATAAAATA
Found at i:118192149 original size:14 final size:13
Alignment explanation
Indices: 118192109--118192149 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
118192099 TTATTTTTAT
*
118192109 ATAAAATATTTAA
1 ATAAAATATTAAA
118192122 ATAAAATAATTAAA
1 ATAAAAT-ATTAAA
118192136 ATAAAATATCTAAA
1 ATAAAATAT-TAAA
118192150 CACATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAATATTAAA
Found at i:118192267 original size:22 final size:22
Alignment explanation
Indices: 118192240--118192285 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
118192230 TATGTATCAC
118192240 AATTCATCAAATATTAAACCTA
1 AATTCATCAAATATTAAACCTA
118192262 AATTCATCAAATATTAAACCTA
1 AATTCATCAAATATTAAACCTA
118192284 AA
1 AA
118192286 ATAAATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTCATCAAATATTAAACCTA
Found at i:118193816 original size:2 final size:2
Alignment explanation
Indices: 118193809--118193837 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
118193799 TACTCAATCA
118193809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
118193838 ACATTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118194581 original size:33 final size:32
Alignment explanation
Indices: 118194524--118194604 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
118194514 AAGCTCACCC
* *
118194524 ATATTATTTTTTAATTT-CTTTTTAAAAATATTT
1 ATATTA-TTTTTAATTTAATATTTAAAAAT-TTT
*
118194557 ATATTATTTTTAATTTAATATTTAATAATTTT
1 ATATTATTTTTAATTTAATATTTAAAAATTTT
* *
118194589 A-AATATTTTTATTTTA
1 ATATTATTTTTAATTTA
118194605 TAAACAGGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 13 0.31
32 14 0.33
33 15 0.36
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (32 bp):
ATATTATTTTTAATTTAATATTTAAAAATTTT
Found at i:118195206 original size:17 final size:17
Alignment explanation
Indices: 118195186--118195220 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
118195176 ATTAAACTTG
* *
118195186 AAAAATGAGTTTTTAAA
1 AAAAATGACTATTTAAA
118195203 AAAAATGACTATTTAAA
1 AAAAATGACTATTTAAA
118195220 A
1 A
118195221 TATTAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (17 bp):
AAAAATGACTATTTAAA
Found at i:118199403 original size:32 final size:32
Alignment explanation
Indices: 118199357--118199423 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
118199347 AAAAAGTTCT
118199357 TATTCGATCTCAGGTTAACTTTAAAGCATTCC
1 TATTCGATCTCAGGTTAACTTTAAAGCATTCC
*
118199389 TATTTGATCTCAGGTTAACTTTAAAGCATTCC
1 TATTCGATCTCAGGTTAACTTTAAAGCATTCC
118199421 TAT
1 TAT
118199424 GCCCATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (32 bp):
TATTCGATCTCAGGTTAACTTTAAAGCATTCC
Found at i:118209348 original size:20 final size:20
Alignment explanation
Indices: 118209325--118209362 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
118209315 TTTTATATAT
*
118209325 TTTTTAGAATTTTTTAAAGA
1 TTTTTAGAATATTTTAAAGA
*
118209345 TTTTTATAATATTTTAAA
1 TTTTTAGAATATTTTAAA
118209363 TATATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTAGAATATTTTAAAGA
Found at i:118209364 original size:9 final size:9
Alignment explanation
Indices: 118209326--118209415 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 9
118209316 TTTATATATT
*
118209326 TTTTAGAATT
1 TTTTA-AATA
*
118209336 TTTTAAAGA
1 TTTTAAATA
118209345 TTTTTATAATA
1 -TTTTA-AATA
118209356 TTTTAAATA
1 TTTTAAATA
* *
118209365 TATATAAAAA
1 T-TTTAAATA
**
118209375 TTTGGAAT-
1 TTTTAAATA
118209383 TTTATAAATA
1 TTT-TAAATA
118209393 TTTT-AAT-
1 TTTTAAATA
*
118209400 TTTTAATTA
1 TTTTAAATA
118209409 TTTTAAA
1 TTTTAAA
118209416 AAATTTAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 15
0.68 0.15 0.17
Matches are distributed among these distances:
7 4 0.07
8 8 0.13
9 20 0.33
10 25 0.42
11 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (9 bp):
TTTTAAATA
Found at i:118209410 original size:16 final size:17
Alignment explanation
Indices: 118209346--118209414 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
118209336 TTTTAAAGAT
118209346 TTTTAT-AATATTTTAAA
1 TTTTATAAATATTTT-AA
* * *
118209363 TATATATAAAAATTTGGAA
1 T-TTTATAAATATTT-TAA
118209382 TTTTATAAATATTTTAA
1 TTTTATAAATATTTTAA
*
118209399 TTTT-TAATTATTTTAA
1 TTTTATAAATATTTTAA
118209415 AAAATTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
16 11 0.26
17 7 0.17
18 15 0.36
19 9 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTATAAATATTTTAA
Found at i:118212521 original size:21 final size:22
Alignment explanation
Indices: 118212472--118212531 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
118212462 CCATTTAAAA
118212472 AAAAAACTTTACAATTTTAATGAT
1 AAAAAA-TTTA-AATTTTAATGAT
*
118212496 --TAAATTTAAATTTTAA-GAT
1 AAAAAATTTAAATTTTAATGAT
118212515 AAAAAATTT-AATTTTAA
1 AAAAAATTTAAATTTTAA
118212532 ATTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 3 0.09
20 16 0.50
21 10 0.31
22 3 0.09
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (22 bp):
AAAAAATTTAAATTTTAATGAT
Found at i:118212549 original size:28 final size:29
Alignment explanation
Indices: 118212495--118212567 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
118212485 ATTTTAATGA
118212495 TTAAATTTAAA--TTTTAAGATAAAAAAT
1 TTAAATTTAAATTTTTTAAGATAAAAAAT
* *
118212522 TTAATTTTAAATTTTTTAA-ATACAAAAT
1 TTAAATTTAAATTTTTTAAGATAAAAAAT
* *
118212550 TTAAATTTCACTTTTTTA
1 TTAAATTTAAATTTTTTA
118212568 TCAAAAATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.26
28 23 0.59
29 6 0.15
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (29 bp):
TTAAATTTAAATTTTTTAAGATAAAAAAT
Found at i:118215451 original size:22 final size:22
Alignment explanation
Indices: 118215409--118215454 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
118215399 TGTAATAAAA
**
118215409 TTTTAATTTAATATATTTAATT
1 TTTTAATTTAATATAAATAATT
118215431 TTTTAATTTAAT-TCAAATAATT
1 TTTTAATTTAATAT-AAATAATT
118215453 TT
1 TT
118215455 ACTCAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTAATTTAATATAAATAATT
Found at i:118219345 original size:150 final size:150
Alignment explanation
Indices: 118219070--118219405 Score: 390
Period size: 150 Copynumber: 2.2 Consensus size: 150
118219060 ATATAGCAAA
* * * * * *
118219070 ACACTATTATGATTCAAGCAAGATGAAATCCGAATTGACGGGAAAGATTTTGGCAGTGGCAAGCA
1 ACACTATTATGATTCAAGTAAGGTGAAATCCGAATCGACGGGAAAGATTCTGACACTGGCAAGCA
* * *
118219135 AATCTTCCTTCAAACATCCCATTGATGACCATAAGAGTTCCAATTCCATTGCTTCATTGGAATAC
66 AATCTTCCTTCAAACATCCCATCGATGACCATAAGACTTCCAATTCCATCGCTTCATTGGAATAC
* * *
118219200 GAGCAAA-CTGTGTCTGGTGT
131 GA-AAAACCTGTGCCTGGTGC
* * ** *
118219220 ACACTATTATGATTCTAGTAAGGTAAAATCCGAATCGGTGGGAAAGATTCTGACAACT-GCAATC
1 ACACTATTATGATTCAAGTAAGGTGAAATCCGAATCGACGGGAAAGATTCTGAC-ACTGGCAAGC
* * ** *
118219284 AAGTCTTCC-TCAAAGCATCCCATCGATGATCATAAGACTTCTGATTCCATCGCTTCGTTGGAAT
65 AAATCTTCCTTCAAA-CATCCCATCGATGACCATAAGACTTCCAATTCCATCGCTTCATTGGAAT
*
118219348 ATGAAAAACCTGTGCCTGGTGC
129 ACGAAAAACCTGTGCCTGGTGC
* * *
118219370 ACACTATTATGACTCGAGTAAGGTGAAATCTGAATC
1 ACACTATTATGATTCAAGTAAGGTGAAATCCGAATC
118219406 AGTGAGAAGC
Statistics
Matches: 156, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
149 8 0.05
150 146 0.94
151 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (150 bp):
ACACTATTATGATTCAAGTAAGGTGAAATCCGAATCGACGGGAAAGATTCTGACACTGGCAAGCA
AATCTTCCTTCAAACATCCCATCGATGACCATAAGACTTCCAATTCCATCGCTTCATTGGAATAC
GAAAAACCTGTGCCTGGTGC
Found at i:118219525 original size:132 final size:132
Alignment explanation
Indices: 118219287--118219537 Score: 353
Period size: 132 Copynumber: 1.9 Consensus size: 132
118219277 TGCAATCAAG
* * * *
118219287 TCTTCCTCAAAGCATCCCATCGATGATCATAAGACTTCTGATTCCATCGCTTCGTTGGAATATGA
1 TCTTCCTCAAAGCATCCCATCGATGATCATAAGACTTCTAACTCCATCGCTTCATTGCAATATGA
* * *
118219352 AAAACCTGTGCCTGGTGCACACTATTATGACTCGAGTAAGGTGAAATCTGAATCAGTGAGAAGCA
66 AAAAACTGTGCCTGGTGCACACTATTATGACTCGAGCAAGGTGAAATCCGAATCAGTGAGAAGCA
118219417 AA
131 AA
* * * *
118219419 TCTTCCTTCAAA-CATCCCATTGATGATCATAAGAGTTCTAACTCCTTTCG-TTCATTGCAATCT
1 TCTTCC-TCAAAGCATCCCATCGATGATCATAAGACTTCTAACTCC-ATCGCTTCATTGCAATAT
* *
118219482 GAAAAAACTGTGCCTGGTGTACACTATTATGATTCGAGCAAGGTGAAATCCGAATC
64 GAAAAAACTGTGCCTGGTGCACACTATTATGACTCGAGCAAGGTGAAATCCGAATC
118219538 GGTGGGAAAG
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
132 96 0.92
133 8 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (132 bp):
TCTTCCTCAAAGCATCCCATCGATGATCATAAGACTTCTAACTCCATCGCTTCATTGCAATATGA
AAAAACTGTGCCTGGTGCACACTATTATGACTCGAGCAAGGTGAAATCCGAATCAGTGAGAAGCA
AA
Found at i:118232310 original size:20 final size:21
Alignment explanation
Indices: 118232280--118232318 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
118232270 AAAAGAAAGT
118232280 AAATAATATATATAAATATAA
1 AAATAATATATATAAATATAA
*
118232301 AAAT-ATATATTTAAATAT
1 AAATAATATATATAAATAT
118232319 GATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATATATATAAATATAA
Found at i:118232576 original size:15 final size:14
Alignment explanation
Indices: 118232524--118232575 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
118232514 TTACAAAAAT
*
118232524 TGTAGATTTAATTTA
1 TGTA-ATTTTATTTA
*
118232539 TGTACTTTTATTTA
1 TGTAATTTTATTTA
*
118232553 TTTAATTTTAGTTTA
1 TGTAATTTTA-TTTA
118232568 TGT-ATTTT
1 TGTAATTTT
118232576 TTGAATTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (14 bp):
TGTAATTTTATTTA
Found at i:118233188 original size:6 final size:6
Alignment explanation
Indices: 118233177--118233205 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
118233167 CAATCAACAC
118233177 ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
118233206 ATTATACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:118242023 original size:22 final size:23
Alignment explanation
Indices: 118241976--118242023 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
118241966 GGCTGCCATT
*
118241976 TGAGAGCTTAAGTTCATTATCTC
1 TGAGAGCTTAAGTTCAATATCTC
*
118241999 TGAGA-CTTCAGTTCCAATATC-C
1 TGAGAGCTTAAGTT-CAATATCTC
118242021 TGA
1 TGA
118242024 ACCATACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (23 bp):
TGAGAGCTTAAGTTCAATATCTC
Found at i:118249007 original size:27 final size:26
Alignment explanation
Indices: 118248976--118249044 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
118248966 TTATACTACA
118248976 AAATATTTATTATTAAAACATTAAATT
1 AAATATTTATTATTAAAACATT-AATT
* * *
118249003 AAATATTT-TT-TGAAGAATATTATTT
1 AAATATTTATTATTAA-AACATTAATT
118249028 AAA-ATTTATTATTAAAA
1 AAATATTTATTATTAAAA
118249045 TAAAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
24 4 0.11
25 13 0.37
26 10 0.29
27 8 0.23
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (26 bp):
AAATATTTATTATTAAAACATTAATT
Found at i:118249709 original size:15 final size:15
Alignment explanation
Indices: 118249689--118249717 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
118249679 GTGCTCTTGA
118249689 TTTTTTTCTTTTTCT
1 TTTTTTTCTTTTTCT
118249704 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
118249718 AGTTTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:118249723 original size:15 final size:15
Alignment explanation
Indices: 118249690--118249723 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
118249680 TGCTCTTGAT
**
118249690 TTTTTTCTTTTTCTT
1 TTTTTTCTTTTTCAG
118249705 TTTTTTCTTTTTCAG
1 TTTTTTCTTTTTCAG
118249720 TTTT
1 TTTT
118249724 CTTGCTTTGG
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:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTCAG
Found at i:118250258 original size:25 final size:25
Alignment explanation
Indices: 118250205--118250254 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
118250195 ATTTTTACTA
*
118250205 TAATAAACATATAATTTTATCATTT
1 TAATAAACATATAATTTTATAATTT
* *
118250230 TAAT-AACTTATATTTTTATAATTT
1 TAATAAACATATAATTTTATAATTT
118250254 T
1 T
118250255 TAATGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATAAACATATAATTTTATAATTT
Found at i:118250988 original size:11 final size:11
Alignment explanation
Indices: 118250931--118250988 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
118250921 ATATCTAAAT
*
118250931 AATAACAACAA
1 AATAATAACAA
118250942 AATAATAACAA
1 AATAATAACAA
*
118250953 TATATAATAGCAA
1 -A-ATAATAACAA
* *
118250966 AATAGTAGCAA
1 AATAATAACAA
*
118250977 AACAATAACAA
1 AATAATAACAA
118250988 A
1 A
118250989 TCAACATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 28 0.72
12 2 0.05
13 9 0.23
ACGTcount: A:0.66, C:0.12, G:0.05, T:0.17
Consensus pattern (11 bp):
AATAATAACAA
Found at i:118253587 original size:30 final size:29
Alignment explanation
Indices: 118253523--118253589 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
118253513 AACTATATAT
118253523 ATTTATTATTATAAATCGAGAAAAAATAA
1 ATTTATTATTATAAATCGAGAAAAAATAA
118253552 ATTTATTATTATAAATCGAGAAAAAATAA
1 ATTTATTATTATAAATCGAGAAAAAATAA
118253581 ATTTTATTA
1 A-TTTATTA
118253590 ATAATATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (29 bp):
ATTTATTATTATAAATCGAGAAAAAATAA
Found at i:118256866 original size:46 final size:45
Alignment explanation
Indices: 118256806--118256971 Score: 211
Period size: 46 Copynumber: 3.8 Consensus size: 45
118256796 TTTGACATGA
* * * * *
118256806 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCT-TCAGGT
*
118256852 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCT-TCAGGT
118256898 TGCCATGGTATCTTTCAACCATGGTCTT--ACA----C-TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTTCAGGT
118256936 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
118256972 CATATCAGAG
Statistics
Matches: 107, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
38 34 0.32
40 3 0.03
44 3 0.03
46 67 0.63
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTTCAGGT
Found at i:118256943 original size:38 final size:38
Alignment explanation
Indices: 118256892--118256967 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
118256882 ACATTTTATA
118256892 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
118256930 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
118256968 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:118259132 original size:11 final size:11
Alignment explanation
Indices: 118259116--118259167 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
118259106 TATACTAAAT
118259116 AAATAATAATA
1 AAATAATAATA
*
118259127 AAATAAT-ATT
1 AAATAATAATA
* *
118259137 AAATATCTCATA
1 AAATA-ATAATA
*
118259149 AAATATTAATA
1 AAATAATAATA
118259160 AAATAATA
1 AAATAATA
118259168 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:118262109 original size:45 final size:45
Alignment explanation
Indices: 118262001--118262173 Score: 216
Period size: 45 Copynumber: 4.0 Consensus size: 45
118261991 TTTGACATGA
* * * * * * *
118262001 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTATATCAGGT
118262047 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGT
118262092 TGCCATGGTATCTTTCAACCATGGTCTTACAC-------TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGT
118262130 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT-ATATCAG
118262174 AGAGCACACT
Statistics
Matches: 112, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
38 38 0.34
45 41 0.37
46 33 0.29
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGT
Found at i:118262137 original size:38 final size:38
Alignment explanation
Indices: 118262086--118262161 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
118262076 CACATTTATA
118262086 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
118262124 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
118262162 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:118264326 original size:11 final size:11
Alignment explanation
Indices: 118264310--118264361 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
118264300 TATACTAAAT
118264310 AAATAATAATA
1 AAATAATAATA
*
118264321 AAATAAT-ATT
1 AAATAATAATA
* *
118264331 AAATATCTCATA
1 AAATA-ATAATA
*
118264343 AAATATTAATA
1 AAATAATAATA
118264354 AAATAATA
1 AAATAATA
118264362 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:118265545 original size:46 final size:46
Alignment explanation
Indices: 118265495--118265670 Score: 219
Period size: 46 Copynumber: 3.8 Consensus size: 46
118265485 TGGTTGAGCA
*
118265495 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *** * * ** *
118265541 TCCGAACTCGTTGAGTTGAGTCGGAGTTCGAGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
118265588 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
118265634 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
118265671 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 71 0.67
47 35 0.33
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:118265651 original size:93 final size:93
Alignment explanation
Indices: 118265492--118265662 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
118265482 GGATGGTTGA
* *
118265492 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
118265557 TGAGTCGGAGTTCGAGAAATGTAACTAG
66 TGAGTCCGAGTTCGAGAAATGTAACTAG
*
118265585 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
118265650 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
118265663 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAAATGTAACTAG
Found at i:118268642 original size:15 final size:15
Alignment explanation
Indices: 118268594--118268672 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
118268584 ATATCTTGGG
*
118268594 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
118268609 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
118268624 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
118268639 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
118268654 TTT-TTTATTC-GGT
1 TTTCTTTATTCTGGA
118268667 TTTCTT
1 TTTCTT
118268673 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 5 0.09
14 7 0.13
15 41 0.77
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:118268680 original size:30 final size:30
Alignment explanation
Indices: 118268585--118268671 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
118268575 CATAGTATCA
* * * * *
118268585 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGGTTTCTC
118268615 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGGTTTCTC
*
118268645 TATCTTGGATTT-TTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGGTTTCT
118268672 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.14
29 8 0.16
30 33 0.67
31 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGGTTTCTC
Found at i:118277521 original size:15 final size:15
Alignment explanation
Indices: 118277501--118277529 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
118277491 ATTTTAAAAG
118277501 AAAAAGAAAAGAAGA
1 AAAAAGAAAAGAAGA
118277516 AAAAAGAAAAGAAG
1 AAAAAGAAAAGAAG
118277530 CCTTCTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAGA
Found at i:118288992 original size:17 final size:18
Alignment explanation
Indices: 118288965--118288999 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
118288955 AGTAGTGGAG
118288965 TTAAGATTTTATGTGTTA
1 TTAAGATTTTATGTGTTA
*
118288983 TTAA-ATTTTATTTGTTA
1 TTAAGATTTTATGTGTTA
118289000 AAAATTACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
TTAAGATTTTATGTGTTA
Found at i:118289267 original size:26 final size:24
Alignment explanation
Indices: 118289237--118289301 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 24
118289227 ATAATTTTAA
118289237 AAAATTTAAAAAAATATATAAATACAT
1 AAAATTTAAAAAAA-ATAT-AATA-AT
118289264 AAATATTTTAAAAAAAATATAATAAT
1 AAA-A-TTTAAAAAAAATATAATAAT
*
118289290 AAATTTTAAAAA
1 AAAATTTAAAAA
118289302 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
24 8 0.23
26 5 0.14
27 7 0.20
28 5 0.14
29 10 0.29
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAATTTAAAAAAAATATAATAAT
Found at i:118289281 original size:22 final size:24
Alignment explanation
Indices: 118289241--118289301 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 24
118289231 TTTTAAAAAA
118289241 TTTAAAAAAATATATAAATACATAAATAT
1 TTTAAAAAAA-ATAT-AATA-AT-AA-AT
118289270 TTTAAAAAAAATATAATAATAAAT
1 TTTAAAAAAAATATAATAATAAAT
118289294 TTTAAAAA
1 TTTAAAAA
118289302 TAAAAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.31
25 2 0.06
26 2 0.06
27 4 0.12
28 4 0.12
29 10 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TTTAAAAAAAATATAATAATAAAT
Found at i:118289306 original size:26 final size:28
Alignment explanation
Indices: 118289240--118289306 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
118289230 ATTTTAAAAA
*
118289240 ATTTAAAAAAATATATAAATACATAAAT
1 ATTTAAAAAAAAATATAAATACATAAAT
*
118289268 ATTTTAAAAAAAATAT-AATA-ATAAAT
1 ATTTAAAAAAAAATATAAATACATAAAT
118289294 -TTTAAAAATAAAA
1 ATTTAAAAA-AAAA
118289307 AATATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.20
26 10 0.29
27 4 0.11
28 14 0.40
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (28 bp):
ATTTAAAAAAAAATATAAATACATAAAT
Found at i:118289330 original size:19 final size:19
Alignment explanation
Indices: 118289276--118289331 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
118289266 ATATTTTAAA
*
118289276 AAAAATATAATAATAAATTTT
1 AAAAATATAAT--TATATTTT
**
118289297 AAAAATA-AAAAATATTTT
1 AAAAATATAATTATATTTT
118289315 AAAAATATAATTATATT
1 AAAAATATAATTATATT
118289332 AAATAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 13 0.45
19 7 0.24
20 2 0.07
21 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATATAATTATATTTT
Found at i:118289812 original size:18 final size:18
Alignment explanation
Indices: 118289774--118289826 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
118289764 TATTTAATAG
118289774 TAATATAATTTTATT-AATT
1 TAATAT-ATTTT-TTAAATT
118289793 TAATAT-TTATTTTAAATT
1 TAATATATT-TTTTAAATT
*
118289811 TATTATATTTTTTAAA
1 TAATATATTTTTTAAA
118289827 ATATTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.13
18 18 0.60
19 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATATATTTTTTAAATT
Found at i:118289933 original size:20 final size:22
Alignment explanation
Indices: 118289890--118289945 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
118289880 ATAATTTTTC
* **
118289890 ATTT-TATATATTTTTAAATTT
1 ATTTATATATTTTTTTAAAAAT
118289911 A-TTATA-ATTTTTTTAAAAAT
1 ATTTATATATTTTTTTAAAAAT
118289931 ATTTATATATTTTTT
1 ATTTATATATTTTTT
118289946 GAATTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 14 0.48
21 8 0.28
22 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTATATATTTTTTTAAAAAT
Found at i:118289955 original size:20 final size:20
Alignment explanation
Indices: 118289891--118289955 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
118289881 TAATTTTTCA
118289891 TTTTATATA-TTTTTAAATT
1 TTTTATATATTTTTTAAATT
* *
118289910 TATTATA-ATTTTTTTAAAAAT
1 TTTTATATA-TTTTTT-AAATT
* *
118289931 ATTTATATATTTTTTGAATT
1 TTTTATATATTTTTTAAATT
118289951 TTTTA
1 TTTTA
118289956 GAATTAGGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
18 1 0.03
19 6 0.17
20 12 0.34
21 15 0.43
22 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATATATTTTTTAAATT
Found at i:118290257 original size:2 final size:2
Alignment explanation
Indices: 118290250--118290281 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
118290240 GTGTTAAGAT
118290250 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
118290282 AATACATAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:118298034 original size:14 final size:14
Alignment explanation
Indices: 118298015--118298047 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
118298005 AATATATACA
118298015 AATATAATTACAAT
1 AATATAATTACAAT
118298029 AATATAATTACAAT
1 AATATAATTACAAT
118298043 AATAT
1 AATAT
118298048 CATTCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAATTACAAT
Found at i:118316081 original size:16 final size:16
Alignment explanation
Indices: 118316062--118316092 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
118316052 AATTGTTTCA
118316062 AATTTAGGTTATTTTG
1 AATTTAGGTTATTTTG
*
118316078 AATTTATGTTATTTT
1 AATTTAGGTTATTTT
118316093 ATATTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (16 bp):
AATTTAGGTTATTTTG
Found at i:118319393 original size:106 final size:105
Alignment explanation
Indices: 118319248--118319461 Score: 410
Period size: 106 Copynumber: 2.0 Consensus size: 105
118319238 TTCCTCCTTT
118319248 TTTTCTTTTCGTTTTTTCATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAA
1 TTTTCTTTTCGTTTTTTCATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAA
118319313 AAATCATGACATCATTTCCTCCATAGATAACGTTAATTCA
66 AAATCATGACATCATTTCCTCCATAGATAACGTTAATTCA
*
118319353 TTTTCTTTTCGTTTTTTTCATTTTAGGAGGAAAAGTAGGAATATAGGGCTCCTGCTCATTGATTA
1 TTTTCTTTTCG-TTTTTTCATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTA
118319418 AAAATCATGACATCATTTCCTCCATAGATAACGTTAATTCA
65 AAAATCATGACATCATTTCCTCCATAGATAACGTTAATTCA
118319459 TTT
1 TTT
118319462 ACTAAAAAGA
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 11 0.10
106 96 0.90
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (105 bp):
TTTTCTTTTCGTTTTTTCATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAA
AAATCATGACATCATTTCCTCCATAGATAACGTTAATTCA
Found at i:118319482 original size:106 final size:106
Alignment explanation
Indices: 118319266--118319484 Score: 314
Period size: 106 Copynumber: 2.1 Consensus size: 106
118319256 TCGTTTTTTC
118319266 ATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAAAAATCATGACATCATTTC
1 ATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAAAAATCATGACATCATTTC
* **** *** ***
118319331 CTCCATAGATAACGTTAATTCATTTTCTTTTCGTTTTTTTC
66 CTCCATAGATAACGTTAATTCATTTACTAAAAGTAGATGAA
*
118319372 ATTTTAGGAGGAAAAGTAGGAATATAGGGCTCCTGCTCATTGATTAAAAATCATGACATCATTTC
1 ATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAAAAATCATGACATCATTTC
118319437 CTCCATAGATAACGTTAATTCATTTACTAAAAAG-AGATGAA
66 CTCCATAGATAACGTTAATTCATTTACT-AAAAGTAGATGAA
118319478 ATTTTAG
1 ATTTTAG
118319485 TTCAAGGGTG
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
106 99 0.99
107 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (106 bp):
ATTTTAGGAGGAAAAGAAGGAATATAGGGCTCCTGCTCATTGATTAAAAATCATGACATCATTTC
CTCCATAGATAACGTTAATTCATTTACTAAAAGTAGATGAA
Found at i:118322490 original size:9 final size:10
Alignment explanation
Indices: 118322466--118322491 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
118322456 TTTATTTATA
118322466 TAAAAATAAT
1 TAAAAATAAT
118322476 TAAAAATAAT
1 TAAAAATAAT
118322486 TAAAAA
1 TAAAAA
118322492 CACTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:118322950 original size:14 final size:14
Alignment explanation
Indices: 118322931--118322995 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
118322921 CTACTATTTC
118322931 ACTATTATATTGTT
1 ACTATTATATTGTT
*
118322945 ACTATTTTATTGTT
1 ACTATTATATTGTT
*
118322959 ATTATATAATTATT-TT
1 ACTAT-T-A-TATTGTT
* *
118322975 ATTATTAAATTTGTT
1 ACTATTATA-TTGTT
118322990 ACTATT
1 ACTATT
118322996 TTAGAGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 1 0.02
14 20 0.49
15 9 0.22
16 7 0.17
17 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (14 bp):
ACTATTATATTGTT
Found at i:118333201 original size:13 final size:13
Alignment explanation
Indices: 118333185--118333212 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
118333175 TTAATCAAGT
118333185 TAACTGAAATTTA
1 TAACTGAAATTTA
118333198 TAACTGAAATTTA
1 TAACTGAAATTTA
118333211 TA
1 TA
118333213 TATGTTTTTT
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:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
TAACTGAAATTTA
Found at i:118333470 original size:25 final size:24
Alignment explanation
Indices: 118333436--118333491 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
118333426 CAATTTGGTC
*
118333436 ATATATTGGGCTTATATATAATATA
1 ATATATTGGGCTTATAAAT-ATATA
*
118333461 ATATGTTGGGCTTATAAATATATAA
1 ATATATTGGGCTTATAAATATAT-A
118333486 ATATAT
1 ATATAT
118333492 ATTATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (24 bp):
ATATATTGGGCTTATAAATATATA
Found at i:118334656 original size:28 final size:30
Alignment explanation
Indices: 118334608--118334668 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
118334598 AACTCCTCAG
** *
118334608 GTTGCAGAAAAGGAAATAAAGT-AGAG-AA
1 GTTGCAGAAAAAAAAAAAAAGTGAGAGCAA
118334636 GTTGCAGAAAAAAAAAAAAAGTGAGAGCAA
1 GTTGCAGAAAAAAAAAAAAAGTGAGAGCAA
118334666 GTT
1 GTT
118334669 AACAAGTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
29 4 0.14
30 5 0.18
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (30 bp):
GTTGCAGAAAAAAAAAAAAAGTGAGAGCAA
Found at i:118336095 original size:21 final size:21
Alignment explanation
Indices: 118336071--118336113 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
118336061 TTCTGATTCA
*
118336071 ATTATAATTC-AAATTTATGTT
1 ATTATAA-TCAAAATTCATGTT
118336092 ATTATAATCAAAATTCATGTT
1 ATTATAATCAAAATTCATGTT
118336113 A
1 A
118336114 AAATAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTATAATCAAAATTCATGTT
Found at i:118336718 original size:2 final size:2
Alignment explanation
Indices: 118336713--118336745 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
118336703 ACACACACAC
118336713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
118336746 AATACCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118337707 original size:24 final size:24
Alignment explanation
Indices: 118337669--118337714 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
118337659 AATAATTTTT
* *
118337669 TTTAAATATAATAAATCAAATACA
1 TTTAAAAATAATAAAACAAATACA
*
118337693 TTTAAAAATATTAAAACAAATA
1 TTTAAAAATAATAAAACAAATA
118337715 AAAAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTAAAAATAATAAAACAAATACA
Found at i:118337730 original size:11 final size:12
Alignment explanation
Indices: 118337716--118337748 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
118337706 AAACAAATAA
118337716 AAAATAATAC-T
1 AAAATAATACTT
*
118337727 AAAATAATTCTT
1 AAAATAATACTT
118337739 AAAATAATAC
1 AAAATAATAC
118337749 ACAAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATAATACTT
Found at i:118342403 original size:99 final size:99
Alignment explanation
Indices: 118342232--118342423 Score: 348
Period size: 99 Copynumber: 1.9 Consensus size: 99
118342222 AGATGATAGG
*
118342232 TTGATTGTAAGTAATAGAAGTATATGATATGCAGCAATTTTGGTGAAGACATTATTACTGCAAAA
1 TTGATTGTAAGTAATAGAAGTATATGATATGCAGCAATTATGGTGAAGACATTATTACTGCAAAA
118342297 TTGTCAAATGTGGCAGTGACTATCTGTTTCAAAT
66 TTGTCAAATGTGGCAGTGACTATCTGTTTCAAAT
* *
118342331 TTGATTGTAAGTTATAGAAGTATATGATATGCAGCAATTATGGTGATGACATTATTACTGCAAAA
1 TTGATTGTAAGTAATAGAAGTATATGATATGCAGCAATTATGGTGAAGACATTATTACTGCAAAA
*
118342396 TTGTCAAATGTGGCAGTGACTATTTGTT
66 TTGTCAAATGTGGCAGTGACTATCTGTT
118342424 AATATTTACA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (99 bp):
TTGATTGTAAGTAATAGAAGTATATGATATGCAGCAATTATGGTGAAGACATTATTACTGCAAAA
TTGTCAAATGTGGCAGTGACTATCTGTTTCAAAT
Found at i:118349334 original size:17 final size:19
Alignment explanation
Indices: 118349312--118349350 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
118349302 ATCAGACAAA
*
118349312 AAAAACCCA-TGAAT-AAC
1 AAAAACACATTGAATCAAC
118349329 AAAAACACATTGAATCAAC
1 AAAAACACATTGAATCAAC
118349348 AAA
1 AAA
118349351 CAAAGCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 5 0.26
19 6 0.32
ACGTcount: A:0.62, C:0.21, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAAACACATTGAATCAAC
Found at i:118349964 original size:19 final size:20
Alignment explanation
Indices: 118349928--118349966 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
118349918 GATTAGGGGC
118349928 TTAATTTGTAATTGTATATA
1 TTAATTTGTAATTGTATATA
*
118349948 TTAATTT-TAATTTTATATA
1 TTAATTTGTAATTGTATATA
118349967 ATTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTAATTTGTAATTGTATATA
Found at i:118349978 original size:16 final size:17
Alignment explanation
Indices: 118349928--118349977 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
118349918 GATTAGGGGC
118349928 TTAATTTGTAATTGTATATA
1 TTAATTT-TAATT-T-TATA
118349948 TTAATTTTAATTTTATA
1 TTAATTTTAATTTTATA
118349965 -TAATTTTATATTT
1 TTAATTTTA-ATTT
118349978 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.28
17 8 0.28
18 1 0.03
19 5 0.17
20 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTAATTTTAATTTTATA
Found at i:118349989 original size:13 final size:13
Alignment explanation
Indices: 118349958--118349995 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
118349948 TTAATTTTAA
*
118349958 TTTTATATAA-TT
1 TTTTATTTAATTT
*
118349970 TTATATTTAATTT
1 TTTTATTTAATTT
118349983 TTTTATTTAATTT
1 TTTTATTTAATTT
118349996 AATTGTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTTAATTT
Found at i:118350201 original size:30 final size:29
Alignment explanation
Indices: 118350160--118350216 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
118350150 ATTTGAACTA
*
118350160 AAATTAGAGTTTTACGTATATAATTACATT
1 AAATTAAAG-TTTACGTATATAATTACATT
*
118350190 AAATTAAAGTTTATGTATATAATTACA
1 AAATTAAAGTTTACGTATATAATTACA
118350217 CATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (29 bp):
AAATTAAAGTTTACGTATATAATTACATT
Found at i:118350210 original size:29 final size:30
Alignment explanation
Indices: 118350160--118350238 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
118350150 ATTTGAACTA
* *
118350160 AAATTAGAGTTTTACGTATATAATT-ACATT
1 AAATTAAAG-TTTATGTATATAATTAACATT
118350190 AAATTAAAGTTTATGTATATAATTACACATT
1 AAATTAAAGTTTATGTATATAATTA-ACATT
* *
118350221 AAA-AAAATTTTATGTATA
1 AAATTAAAGTTTATGTATA
118350239 ATTTTAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.33
30 21 0.49
31 8 0.19
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (30 bp):
AAATTAAAGTTTATGTATATAATTAACATT
Found at i:118350235 original size:30 final size:29
Alignment explanation
Indices: 118350169--118350238 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
118350159 AAAATTAGAG
* *
118350169 TTTTACGTATATAATTACATTAAATTAAA
1 TTTTATGTATATAATTACATTAAATAAAA
*
118350198 GTTTATGTATATAATTACACATTAAA-AAAA
1 TTTTATGTATATAATT--ACATTAAATAAAA
118350228 TTTTATGTATA
1 TTTTATGTATA
118350239 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.40
30 13 0.37
31 8 0.23
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTTATGTATATAATTACATTAAATAAAA
Found at i:118350375 original size:16 final size:17
Alignment explanation
Indices: 118350356--118350393 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
118350346 TTTTTTTTAA
118350356 ATAA-AGATTTTCTTAC
1 ATAAGAGATTTTCTTAC
*
118350372 ATAAAGAGATTTTCTTCC
1 AT-AAGAGATTTTCTTAC
118350390 ATAA
1 ATAA
118350394 TAAATTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 2 0.11
17 4 0.21
18 13 0.68
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (17 bp):
ATAAGAGATTTTCTTAC
Found at i:118353447 original size:19 final size:19
Alignment explanation
Indices: 118353402--118353441 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
118353392 CAATAAAAAT
118353402 AAATAAATAAATTATGAAG
1 AAATAAATAAATTATGAAG
118353421 AGAATAAATAGATATTATGAA
1 A-AATAAATA-A-ATTATGAA
118353442 AATAAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 8 0.44
21 1 0.06
22 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (19 bp):
AAATAAATAAATTATGAAG
Found at i:118359254 original size:23 final size:23
Alignment explanation
Indices: 118359224--118359306 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 23
118359214 GCTTTACTGA
* *
118359224 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
118359247 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
* *
118359268 TCAGACACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
118359290 T-AGGCACTTTATGTGTC
1 TCAGGCACCTCATGTGTC
118359307 ATATACTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 31 0.62
22 1 0.02
23 18 0.36
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:118359271 original size:21 final size:21
Alignment explanation
Indices: 118359236--118359296 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
118359226 AGGCACTTTA
118359236 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
*
118359259 TGTGTCGTATCAGACACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
118359280 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
118359297 TTTATGTGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 25 0.74
23 9 0.26
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:118365608 original size:27 final size:30
Alignment explanation
Indices: 118365569--118365623 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
118365559 ACAAATGAAT
*
118365569 AAAAGAAACAGAGTAAAGA-AA-AGAAACA
1 AAAAGAAACAGAGAAAAGAGAACAGAAACA
*
118365597 AAAAG-AATAGAGAAAAGAGAACAGAAA
1 AAAAGAAACAGAGAAAAGAGAACAGAAA
118365624 GCATTCGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 7 0.30
29 5 0.22
ACGTcount: A:0.71, C:0.05, G:0.20, T:0.04
Consensus pattern (30 bp):
AAAAGAAACAGAGAAAAGAGAACAGAAACA
Found at i:118366143 original size:21 final size:23
Alignment explanation
Indices: 118366084--118366149 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
118366074 GCTTTACTGA
118366084 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
118366107 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
118366129 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
118366150 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 4 0.11
23 17 0.47
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:118368593 original size:18 final size:20
Alignment explanation
Indices: 118368552--118368596 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
118368542 TAATCTAAGC
* *
118368552 TCAATATCAGTCGATATTTT
1 TCAATATCAATCGATATTTA
118368572 TCAATATCAATC-A-ATTTA
1 TCAATATCAATCGATATTTA
118368590 TCAATAT
1 TCAATAT
118368597 TACTCAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (20 bp):
TCAATATCAATCGATATTTA
Found at i:118368628 original size:18 final size:18
Alignment explanation
Indices: 118368604--118368677 Score: 87
Period size: 18 Copynumber: 4.1 Consensus size: 18
118368594 TATTACTCAA
118368604 TAACAATCAATTATTTAG
1 TAACAATCAATTATTTAG
*
118368622 TAGCAATCAATTATTCT-G
1 TAACAATCAATTATT-TAG
*
118368640 TAACAATTAATTATTTAG
1 TAACAATCAATTATTTAG
* * *
118368658 TAACAGTCAGTTATTCAG
1 TAACAATCAATTATTTAG
118368676 TA
1 TA
118368678 CTTTTATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
17 1 0.02
18 45 0.96
19 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (18 bp):
TAACAATCAATTATTTAG
Found at i:118368652 original size:36 final size:36
Alignment explanation
Indices: 118368604--118368673 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
118368594 TATTACTCAA
*
118368604 TAACAATCAATTATTTAGTAGCAATCAATTATTCTG
1 TAACAATCAATTATTTAGTAACAATCAATTATTCTG
* * *
118368640 TAACAATTAATTATTTAGTAACAGTCAGTTATTC
1 TAACAATCAATTATTTAGTAACAATCAATTATTC
118368674 AGTACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (36 bp):
TAACAATCAATTATTTAGTAACAATCAATTATTCTG
Found at i:118368997 original size:16 final size:15
Alignment explanation
Indices: 118368976--118369007 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
118368966 AATTTTCAAT
118368976 TTTCAATTAATACACA
1 TTTCAATTAAT-CACA
118368992 TTTCAATTAATCACA
1 TTTCAATTAATCACA
118369007 T
1 T
118369008 AAATTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTCAATTAATCACA
Found at i:118374871 original size:16 final size:16
Alignment explanation
Indices: 118374830--118374863 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
118374820 TACTTTACTT
*
118374830 TATATATATTATAATAA
1 TATA-ATATAATAATAA
118374847 TATAATATAATAATAA
1 TATAATATAATAATAA
118374863 T
1 T
118374864 TTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATATAATAATAA
Found at i:118376167 original size:20 final size:21
Alignment explanation
Indices: 118376142--118376180 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
118376132 TGATCTAATT
*
118376142 TTATTTTG-AATTTTTATTAC
1 TTATTTAGAAATTTTTATTAC
118376162 TTATTTAGAAATTTTTATT
1 TTATTTAGAAATTTTTATT
118376181 GTACTAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (21 bp):
TTATTTAGAAATTTTTATTAC
Found at i:118378165 original size:6 final size:6
Alignment explanation
Indices: 118378154--118378180 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
118378144 AAAAAGAAAG
118378154 AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAA
118378181 TAGAACCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:118380349 original size:16 final size:15
Alignment explanation
Indices: 118380324--118380362 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
118380314 TATAAGGGCC
118380324 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
118380339 AAAAGAAAAAAAAAAG
1 AAAA-AAAAAAAAAAG
118380355 AACAAAAA
1 AA-AAAAA
118380363 CAAGAATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.90, C:0.03, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:118380361 original size:19 final size:19
Alignment explanation
Indices: 118380325--118380361 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
118380315 ATAAGGGCCA
*
118380325 AAAAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAAACAAAAG
*
118380344 AAAAAAAAAAGAACAAAA
1 AAAAAAAAAAAAACAAAA
118380362 ACAAGAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAACAAAAG
Found at i:118383163 original size:11 final size:11
Alignment explanation
Indices: 118383147--118383177 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
118383137 AAATAATTGA
118383147 ATAAATTTTTT
1 ATAAATTTTTT
118383158 ATAAATTTTTT
1 ATAAATTTTTT
*
118383169 ATAACTTTT
1 ATAAATTTT
118383178 ATTTGTGAGA
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:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
ATAAATTTTTT
Found at i:118387810 original size:35 final size:37
Alignment explanation
Indices: 118387748--118387830 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 37
118387738 TATTAAAATA
118387748 TTTTTATTTTTATATATTTGAAATTT-AA-TTTTTAT
1 TTTTTATTTTTATATATTTGAAATTTAAATTTTTTAT
* * *
118387783 TTTTTATTTTTTTAT-TTTAGGATTTTAAATTTTTTAT
1 TTTTTATTTTTATATATTT-GAAATTTAAATTTTTTAT
118387820 TCTTTGTATTT
1 T-TTT-TATTT
118387831 AAAAATCCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 3 0.08
35 19 0.47
36 2 0.05
37 8 0.20
38 3 0.08
39 5 0.12
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.71
Consensus pattern (37 bp):
TTTTTATTTTTATATATTTGAAATTTAAATTTTTTAT
Found at i:118389728 original size:13 final size:13
Alignment explanation
Indices: 118389710--118389739 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
118389700 ATTGAAAACT
118389710 TCTTATTATACAC
1 TCTTATTATACAC
118389723 TCTTATTATACAC
1 TCTTATTATACAC
118389736 TCTT
1 TCTT
118389740 TGTGAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (13 bp):
TCTTATTATACAC
Found at i:118391743 original size:81 final size:81
Alignment explanation
Indices: 118391644--118391851 Score: 346
Period size: 81 Copynumber: 2.6 Consensus size: 81
118391634 CTTCATATAT
118391644 TCCCAATATCACATAGCATGGTTCATTCTATATTCATATCACATATC-TCGCATCAACTACATCA
1 TCCCAATATCACATAGCATGGTTCATTCTATATTCATATCACATATCAT-GCATCAACTACATCA
118391708 TACTATTTTCTACTTCA
65 TACTATTTTCTACTTCA
* * *
118391725 TCCCAATAACACAAAGCATGGTTCATTCTATATTCATATCACATATCATGCATCAACTATATCAT
1 TCCCAATATCACATAGCATGGTTCATTCTATATTCATATCACATATCATGCATCAACTACATCAT
*
118391790 GCTATTTTCTACTTCA
66 ACTATTTTCTACTTCA
* *
118391806 TCCCAATATCACATAGCATGGTTCATACTATATTCATGTCACATAT
1 TCCCAATATCACATAGCATGGTTCATTCTATATTCATATCACATAT
118391852 ACAAACTGAT
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
81 117 0.99
82 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (81 bp):
TCCCAATATCACATAGCATGGTTCATTCTATATTCATATCACATATCATGCATCAACTACATCAT
ACTATTTTCTACTTCA
Found at i:118394022 original size:50 final size:50
Alignment explanation
Indices: 118393918--118394079 Score: 243
Period size: 50 Copynumber: 3.2 Consensus size: 50
118393908 ACTTCTGATC
* * * * *
118393918 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATTAGTGATA
1 AGTGACAAATGATAAGTGGTAG-CTTAGCTACTCTTATCTGATCAGTGACA
118393969 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
* *
118394019 AGTGATAAGTGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
*
118394069 AGTGATAAATG
1 AGTGACAAATG
118394080 TGATCAGTGT
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 82 0.80
51 21 0.20
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (50 bp):
AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
Found at i:118395610 original size:21 final size:21
Alignment explanation
Indices: 118395586--118395650 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
118395576 AAGTCTAGCT
118395586 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
** *
118395607 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
118395625 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
118395646 GAAGC
1 GAAGC
118395651 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:118395627 original size:39 final size:39
Alignment explanation
Indices: 118395572--118395668 Score: 176
Period size: 39 Copynumber: 2.5 Consensus size: 39
118395562 TAATCTGAAA
* *
118395572 CCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACGGAAG
1 CCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGGAAG
118395611 CCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGGAAG
1 CCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGGAAG
118395650 CCCGAAGGCTAACTGAAGC
1 CCCGAAGGCTAACTGAAGC
118395669 TCATCAGAGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.36, C:0.25, G:0.26, T:0.13
Consensus pattern (39 bp):
CCCGAAGGCTAACTGAAGCACATAAGTGCTAAACGGAAG
Found at i:118398763 original size:21 final size:21
Alignment explanation
Indices: 118398739--118398780 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
118398729 TCTCTTTTTT
118398739 TTAGTGTTGTTTAAGAATCAA
1 TTAGTGTTGTTTAAGAATCAA
118398760 TTAGTGTTGTTTAAGAATCAA
1 TTAGTGTTGTTTAAGAATCAA
118398781 CTTTCACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (21 bp):
TTAGTGTTGTTTAAGAATCAA
Found at i:118408137 original size:14 final size:14
Alignment explanation
Indices: 118408120--118408187 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
118408110 TTGGTTCAAA
118408120 GTTTAGGGTTTAAT
1 GTTTAGGGTTTAAT
* *
118408134 GTTTAAGATTTAGAAT
1 GTTTAGGGTTT--AAT
*
118408150 -TTT-GAGTTTAAT
1 GTTTAGGGTTTAAT
* *
118408162 GTTTAGGATTTAAG
1 GTTTAGGGTTTAAT
*
118408176 GTTCAGGGTTTA
1 GTTTAGGGTTTA
118408188 GGATTTGAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 28 0.70
15 3 0.08
16 3 0.08
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTAAT
Found at i:118408186 original size:28 final size:28
Alignment explanation
Indices: 118408124--118408187 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
118408114 TTCAAAGTTT
*
118408124 AGGGTTTAATGTTTAAGATTTAGAATTT
1 AGGGTTTAATGTTTAAGATTTAGAATTC
* * * *
118408152 TGAGTTTAATGTTTAGGATTTA-AGGTTC
1 AGGGTTTAATGTTTAAGATTTAGA-ATTC
118408180 AGGGTTTA
1 AGGGTTTA
118408188 GGATTTGAGG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.45
Consensus pattern (28 bp):
AGGGTTTAATGTTTAAGATTTAGAATTC
Found at i:118419175 original size:29 final size:31
Alignment explanation
Indices: 118419126--118419197 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
118419116 TTTAAATTAG
*
118419126 TAAA-TAT-AAAATTACACTTT-ATCCCTTTA
1 TAAATTATAAAAATTACAATTTAAT-CCTTTA
118419155 -AAATTATAAAAATT-CAATTTAATCCTTTA
1 TAAATTATAAAAATTACAATTTAATCCTTTA
*
118419184 TAAATTATAGAAAT
1 TAAATTATAAAAAT
118419198 ATAAATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 3 0.08
29 14 0.38
30 20 0.54
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAATTATAAAAATTACAATTTAATCCTTTA
Found at i:118419217 original size:15 final size:15
Alignment explanation
Indices: 118419182--118419211 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
118419172 TTTAATCCTT
*
118419182 TATAAATTATAGAAA
1 TATAAATTATAAAAA
118419197 TATAAATTATAAAAA
1 TATAAATTATAAAAA
118419212 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TATAAATTATAAAAA
Found at i:118419735 original size:88 final size:87
Alignment explanation
Indices: 118419526--118420100 Score: 380
Period size: 88 Copynumber: 6.5 Consensus size: 87
118419516 TTCAATTAAT
* *
118419526 CCGAAAAATGAAATAAAATACATAGTAATTATTATAATTATTTCGGACAATAATAAAAATATTGT
1 CCGAAAAA-GAAATAAAATAAATAGTAATTATTATAATTA-TTC-TA-AA-AA-AAAAATATTGT
* * * * * **
118419591 TACAACA-TCATACTTAAGCTCAAGT-AT
60 TGCAACACT-ATACTCAAACTTAAATGCC
* * * *
118419618 CTGAAAACGAAATAAAATGAATGAGTAATTATTATAAATATTCTAAAAAGAAAAATATTGTTGCA
1 CCGAAAAAGAAATAAAATAAAT-AGTAATTATTATAATTATTCTAAAAA-AAAAATATTGTTGCA
* * *
118419683 ACATTAGACTCAAACTTAAGTGCC
64 ACACTATACTCAAACTTAAATGCC
* * * * *
118419707 CCGAAAAAGAAATAAAATAAATAATAATTGTTATAA-AATTACGAAAAAATAAAATAAAAATGTT
1 CCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATT-CTAAAAAA-AAAAT---ATTGTT
* * * * * * * * *
118419771 GTAGCACTAAACTTAAGCCTCAGTACC
61 GCAACACTATACTCAAACTTAAATGCC
* * ** *
118419798 CTGAAAAATAAATAAAATAAATAAAAATTATTATAATTATTCTAAAAAATTAAAAATATATATT-
1 CCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCT-AAAAA--AAAAATAT-TGTTG
*** * * *
118419862 -ATTGC-ATGCTC-AACTCCAAATGTC
62 CAACACTATACTCAAACT-TAAATGCC
* * *
118419886 TCGAAAAAGAAATAAAATAAATAGTAATTATAATAATTATTCTAAAAAAAATAATATTGTTGTAA
1 CCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCTAAAAAAAA-AATATTGTTGCAA
* *
118419951 CACCATACTCAAACTTAAATGTC
65 CACTATACTCAAACTTAAATGCC
* * * * * * * *
118419974 TCGAAAAAGAAATAAAATAAATAGCAATTATTATAATTAGTCT---GAAAAATTTTTTTTGCAGC
1 CCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCTAAAAAAAAAATATTGTTGCAAC
*
118420036 ACTATACTTAAACTTAAATGCC
66 ACTATACTCAAACTTAAATGCC
*
118420058 CAGAAAACA-AAATAAAATAAATAGTAATTATTATAATTATTCT
1 CCGAAAA-AGAAATAAAATAAATAGTAATTATTATAATTATTCT
118420101 GGAAAATAAA
Statistics
Matches: 383, Mismatches: 80, Indels: 48
0.75 0.16 0.09
Matches are distributed among these distances:
84 65 0.17
85 11 0.03
86 5 0.01
87 13 0.03
88 149 0.39
89 28 0.07
90 2 0.01
91 74 0.19
92 30 0.08
93 5 0.01
94 1 0.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.30
Consensus pattern (87 bp):
CCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCTAAAAAAAAAATATTGTTGCAAC
ACTATACTCAAACTTAAATGCC
Found at i:118420071 original size:84 final size:85
Alignment explanation
Indices: 118419879--118420108 Score: 277
Period size: 84 Copynumber: 2.7 Consensus size: 85
118419869 GCTCAACTCC
* * *
118419879 AAATGTCTCGAAAAAGAAATAAAATAAATAGTAATTATAATAATTATTCTAAAAAAAATAATATT
1 AAATGTCCCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCT--GAAAAAT-ATATT
*
118419944 GTTGTAACACCATACTCAAACTT
63 GTTGCAACACCATACTCAAACTT
* * * * *
118419967 AAATGTCTCGAAAAAGAAATAAAATAAATAGCAATTATTATAATTAGTCTGAAAAAT-TTTTTTT
1 AAATGTCCCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCTGAAAAATATATTGTT
* * *
118420031 GCAGCACTATACTTAAACTT
66 GCAACACCATACTCAAACTT
*
118420051 AAATG-CCCAGAAAACA-AAATAAAATAAATAGTAATTATTATAATTATTCTGGAAAATA
1 AAATGTCCC-GAAAA-AGAAATAAAATAAATAGTAATTATTATAATTATTCTGAAAAATA
118420109 AAAAAAATAG
Statistics
Matches: 125, Mismatches: 14, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
83 2 0.02
84 69 0.55
85 1 0.01
86 6 0.05
88 47 0.38
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (85 bp):
AAATGTCCCGAAAAAGAAATAAAATAAATAGTAATTATTATAATTATTCTGAAAAATATATTGTT
GCAACACCATACTCAAACTT
Found at i:118420518 original size:31 final size:32
Alignment explanation
Indices: 118420454--118420544 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 32
118420444 TTTAGTTATT
**
118420454 ATTTATATATTATTTATATTT-AGTATATTTAGA
1 ATTTAT-TATTATTTA-ATTTAAGTATAAATAGA
118420487 ATTTATTATTATTTAATTTAAGT-TAAATAGA
1 ATTTATTATTATTTAATTTAAGTATAAATAGA
** *
118420518 A-AAATTAATAATTTAATTTAAGTATAA
1 ATTTATT-ATTATTTAATTTAAGTATAA
118420545 TTAAAATAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
30 3 0.06
31 26 0.52
32 15 0.30
33 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (32 bp):
ATTTATTATTATTTAATTTAAGTATAAATAGA
Found at i:118420561 original size:36 final size:34
Alignment explanation
Indices: 118420486--118420562 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 34
118420476 GTATATTTAG
* *
118420486 AATTTATT-ATTATTTAATTTAAGTTAAATAGAA
1 AATTTATTAATAATTTAATTTAAGTTAAATAAAA
*
118420519 AA---ATTAATAATTTAATTTAAGTATAATTAAAA
1 AATTTATTAATAATTTAATTTAAGT-TAAATAAAA
118420551 TAATTTATTAAT
1 -AATTTATTAAT
118420563 TTAATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
30 3 0.09
31 15 0.43
32 7 0.20
33 4 0.11
36 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (34 bp):
AATTTATTAATAATTTAATTTAAGTTAAATAAAA
Found at i:118420977 original size:25 final size:25
Alignment explanation
Indices: 118420930--118420977 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
118420920 TATCTTCGTA
* *
118420930 ATAATTAAATAATATTTATTTTACT
1 ATAATTAAATAATATTAAATTTACT
118420955 ATAA-TAAATAAGTATTAAATTTA
1 ATAATTAAATAA-TATTAAATTTA
118420978 ATTCGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
ATAATTAAATAATATTAAATTTACT
Found at i:118421399 original size:12 final size:12
Alignment explanation
Indices: 118421382--118421415 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
118421372 CAGCCCATCG
118421382 ATATTAATTTTT
1 ATATTAATTTTT
*
118421394 ATATTATTTTTT
1 ATATTAATTTTT
118421406 ATA-TAATTTT
1 ATATTAATTTT
118421416 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:118421573 original size:30 final size:30
Alignment explanation
Indices: 118421537--118421596 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
118421527 ACTTAACAAG
118421537 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
*
118421567 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
118421597 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.30
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAAAAAAATTAA
Found at i:118422795 original size:12 final size:12
Alignment explanation
Indices: 118422780--118422804 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
118422770 CAGGGTTTAG
118422780 GTTTGGGTTCAA
1 GTTTGGGTTCAA
118422792 GTTTGGGTTCAA
1 GTTTGGGTTCAA
118422804 G
1 G
118422805 GTTTAATGGT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTGGGTTCAA
Found at i:118427215 original size:20 final size:20
Alignment explanation
Indices: 118427190--118427228 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
118427180 CTAAAAATAG
118427190 TAGGGTCAAGTCATGAACAT
1 TAGGGTCAAGTCATGAACAT
* *
118427210 TAGGGTCATGTCGTGAACA
1 TAGGGTCAAGTCATGAACA
118427229 GTAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (20 bp):
TAGGGTCAAGTCATGAACAT
Found at i:118427305 original size:30 final size:30
Alignment explanation
Indices: 118427264--118427330 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
118427254 TATTCCCATT
*
118427264 ATTAATAAGATACGAGATTAAATTACTCTC
1 ATTAATAAGATACGAGATAAAATTACTCTC
*
118427294 ATTATTAAGATACGAGATAAAATTACTCATC
1 ATTAATAAGATACGAGATAAAATTACTC-TC
*
118427325 TTTAAT
1 ATTAAT
118427331 CTACTTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (30 bp):
ATTAATAAGATACGAGATAAAATTACTCTC
Found at i:118428030 original size:16 final size:18
Alignment explanation
Indices: 118428009--118428048 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
118427999 AAGCTTGAAC
118428009 AAATAATTTT-TT-TAAA
1 AAATAATTTTATTATAAA
*
118428025 AAATAATTTTATTATATA
1 AAATAATTTTATTATAAA
118428043 AAATAA
1 AAATAA
118428049 ATTAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 2 0.10
18 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAATTTTATTATAAA
Found at i:118428716 original size:2 final size:2
Alignment explanation
Indices: 118428711--118428740 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
118428701 AAAAAAAACA
118428711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
118428741 TCATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118431181 original size:30 final size:30
Alignment explanation
Indices: 118431140--118431207 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
118431130 TTAAAATTTT
118431140 AATAAT-AAAATTACATTTTAA-CTTTCAAA
1 AATAATAAAAATT-CATTTTAATCTTTCAAA
* * *
118431169 AATGATAAAAATTTATTTTAATCTTTTAAA
1 AATAATAAAAATTCATTTTAATCTTTCAAA
118431199 AATAATAAA
1 AATAATAAA
118431208 TATATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (30 bp):
AATAATAAAAATTCATTTTAATCTTTCAAA
Found at i:118432854 original size:31 final size:31
Alignment explanation
Indices: 118432789--118432854 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 31
118432779 CAAAAAAAAT
*
118432789 TAAACATAAAATATATAATAAAATTTATATA
1 TAAACATAAAATATATAATAAAATTCATATA
118432820 TAAACA-AAAATA-A-AATAATAATTCCATATAA
1 TAAACATAAAATATATAATAA-AATT-CATAT-A
118432851 TAAA
1 TAAA
118432855 ACGAGATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 5 0.16
29 5 0.16
30 10 0.32
31 11 0.35
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (31 bp):
TAAACATAAAATATATAATAAAATTCATATA
Found at i:118438354 original size:114 final size:115
Alignment explanation
Indices: 118438207--118438435 Score: 336
Period size: 114 Copynumber: 2.0 Consensus size: 115
118438197 TCCTTTTAAA
* * * * *
118438207 GCACTTACAAAGCTTTTCAAAATTTTATTATTTACAAATGTGTCTTTAAAAATTCAAATCTAAAA
1 GCACTTACAAAACTCTTCAAAATTTTATCATTTACAAATATATCTTTAAAAATTCAAATCTAAAA
** * *
118438272 TCCAAAGTATAACATAT-GAAAAAATGCATAAA-CGTTGTTTATTTAAATT
66 TCCAAAACATAACATATAAAAAAAAT-CATAAATAGTTGTTTATTTAAATT
118438321 GCACTTACAAAACTCTTCAAAATTTTATCATTTACAAATATATCTTTAAAAATTCAAATCTAAAA
1 GCACTTACAAAACTCTTCAAAATTTTATCATTTACAAATATATCTTTAAAAATTCAAATCTAAAA
**
118438386 TTTAAAACATAACATATAAAAAAAATCATAAATAGTTGTTTATTTAAATT
66 TCCAAAACATAACATATAAAAAAAATCATAAATAGTTGTTTATTTAAATT
118438436 AAAAAAAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
114 79 0.77
115 23 0.23
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (115 bp):
GCACTTACAAAACTCTTCAAAATTTTATCATTTACAAATATATCTTTAAAAATTCAAATCTAAAA
TCCAAAACATAACATATAAAAAAAATCATAAATAGTTGTTTATTTAAATT
Found at i:118444187 original size:23 final size:24
Alignment explanation
Indices: 118444161--118444218 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
118444151 TTCAAAGATA
118444161 ATTTTAAAATCTAGGATTTT-AAT
1 ATTTTAAAATCTAGGATTTTGAAT
* *
118444184 ATTTTAGAATTTAGGATTTTGAAT
1 ATTTTAAAATCTAGGATTTTGAAT
*
118444208 TTTTATAAAAT
1 ATTT-TAAAAT
118444219 TATAACATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 18 0.62
24 6 0.21
25 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTTAAAATCTAGGATTTTGAAT
Found at i:118447791 original size:43 final size:43
Alignment explanation
Indices: 118447743--118447829 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
118447733 ACTAATGTAC
118447743 TATACACAAATTAAAATTAAAAATATCTATATTATATATAAAA
1 TATACACAAATTAAAATTAAAAATATCTATATTATATATAAAA
*
118447786 TATACACAAATTAAAATTACAAATATCTATATTATATATAAAA
1 TATACACAAATTAAAATTAAAAATATCTATATTATATATAAAA
118447829 T
1 T
118447830 TTAAAAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (43 bp):
TATACACAAATTAAAATTAAAAATATCTATATTATATATAAAA
Found at i:118451115 original size:68 final size:65
Alignment explanation
Indices: 118450902--118451122 Score: 214
Period size: 64 Copynumber: 3.4 Consensus size: 65
118450892 AAAATTTTGT
** * *
118450902 CTCTCTTGTACACATGGTGTACACATAGTATCACCCATGTGACCTAGCCA-CTTTA-TCTCGTAG
1 CTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTCGTAG
** * * * * * * * *
118450965 CTCTCTTGTTTACATGGTGTCCTTCACCTGGAACCACACATGCAACCTAGCTACATCTA-TCTTG
1 CTCTCTTGTACACATGGTG---TACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTCG
118451029 TAG
63 TAG
* *
118451032 CTCTCTTGTATACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCATAATGTCTCA
1 CTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTC-T-AT-TCTCG
118451097 TAG
63 TAG
*
118451100 CTCTCTTGTACACATGGTATACA
1 CTCTCTTGTACACATGGTGTACA
118451123 TCCCGTATTA
Statistics
Matches: 124, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
63 17 0.14
64 28 0.23
65 1 0.01
66 23 0.19
67 28 0.23
68 27 0.22
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (65 bp):
CTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTCGTAG
Found at i:118451614 original size:30 final size:29
Alignment explanation
Indices: 118451580--118451639 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
118451570 TCCTTAACTC
118451580 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGC-AAATTACAATTTTGCCCCT
* * *
118451610 AAACTTTTGCATATTACACTTTTGCCCCT
1 AAACTTTGGCAAATTACAATTTTGCCCCT
118451639 A
1 A
118451640 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (29 bp):
AAACTTTGGCAAATTACAATTTTGCCCCT
Found at i:118455952 original size:50 final size:50
Alignment explanation
Indices: 118455886--118456068 Score: 224
Period size: 56 Copynumber: 3.5 Consensus size: 50
118455876 CCATGGCAAC
118455886 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCATGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCATGGACAAATGA
* * *
118455936 AAGTGATAAGTAATAGCTTCGGCTACGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGC-T----T-CGGCTACACTTATCTGATCATGGACAAATGA
*
118455992 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAT-GACAAATAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC-ATGGACAAATGA
* * *
118456042 CAAGTGAAAAGTGGTAGCTTCTGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
118456069 CTGATCAGTG
Statistics
Matches: 115, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
50 42 0.37
51 26 0.23
55 2 0.02
56 45 0.39
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCATGGACAAATGA
Found at i:118456082 original size:31 final size:31
Alignment explanation
Indices: 118456044--118456161 Score: 182
Period size: 31 Copynumber: 3.8 Consensus size: 31
118456034 ACAAATAACA
*
118456044 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
118456075 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
118456106 AGTGAAAAATGGTAGCTTTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
118456137 AGTGAATAGTGATAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
118456162 AAGTGACAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:118456336 original size:49 final size:47
Alignment explanation
Indices: 118456183--118456401 Score: 211
Period size: 47 Copynumber: 4.7 Consensus size: 47
118456173 GATTTCCGTA
* * ** * * * *
118456183 TAAGACCATATCTGGGATATGGCATC-GGTGTGATATATGCTACTGTA
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTC-GTG
* * * *
118456230 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
*
118456276 TAAGATCATAGCTGGGCTATGGCATCAATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
*
118456325 TAAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTCGTG
118456367 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
118456402 AGATGTGTAA
Statistics
Matches: 153, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
41 1 0.01
42 35 0.23
44 1 0.01
45 1 0.01
46 26 0.17
47 39 0.25
48 14 0.09
49 36 0.24
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:118456368 original size:42 final size:43
Alignment explanation
Indices: 118456273--118456436 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 43
118456263 TATGTGATTC
* * *
118456273 GTGTAAGATCATAGCTGGGCTATGGCATCAATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATC--GAT-T-ATATGAAGA-T
*
118456320 ACGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
118456364 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
118456406 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
118456437 GAAAACGAAG
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 64 0.62
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 28 0.27
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:118456660 original size:23 final size:23
Alignment explanation
Indices: 118456629--118456679 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
118456619 ATGATATTTC
118456629 AAATACTTTGGTGAATAAAGCTT
1 AAATACTTTGGTGAATAAAGCTT
*
118456652 AAATCCTTTGGTGAATAAAGCTT
1 AAATACTTTGGTGAATAAAGCTT
118456675 AAATA
1 AAATA
118456680 TGAAATAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (23 bp):
AAATACTTTGGTGAATAAAGCTT
Found at i:118459736 original size:44 final size:45
Alignment explanation
Indices: 118459641--118459774 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
118459631 ACAGGACAGA
* **
118459641 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGTTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
118459687 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
118459731 ACAGGAATAATTCATGTAAGTCCATGTCAAAGATATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
118459775 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 35 0.47
45 1 0.01
46 38 0.51
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Done.