Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 13 of 208
Found at i:3978970 original size:22 final size:22
Alignment explanation
Indices: 3978945--3978987 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3978935 TAATTCCAAG
3978945 TTTAAATT-TGTACTAACTATTC
1 TTTAAATTATGT-CTAACTATTC
**
3978967 TTTATTTTATGTCTAACTATT
1 TTTAAATTATGTCTAACTATT
3978988 GTAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAAATTATGTCTAACTATTC
Found at i:3982434 original size:24 final size:21
Alignment explanation
Indices: 3982378--3982435 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 21
3982368 AATTCAGGGT
3982378 TTTAATATTTATTTATAATTA
1 TTTAATATTTATTTATAATTA
*
3982399 TTTAAT-TATATTTA-AATTAAA
1 TTTAATATTTATTTATAATT--A
3982420 TTGTTAATATTTATTT
1 -T-TTAATATTTATTT
3982436 TTAAGTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 4 0.13
20 7 0.23
21 7 0.23
22 1 0.03
23 5 0.17
24 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAATATTTATTTATAATTA
Found at i:3983783 original size:16 final size:16
Alignment explanation
Indices: 3983764--3983797 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3983754 CATTTCAAGT
3983764 TTAGGGTAACTTTGGG
1 TTAGGGTAACTTTGGG
* *
3983780 TTAGGGTCATTTTGGG
1 TTAGGGTAACTTTGGG
3983796 TT
1 TT
3983798 GTACATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (16 bp):
TTAGGGTAACTTTGGG
Found at i:3989383 original size:5 final size:5
Alignment explanation
Indices: 3989373--3989398 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3989363 TGAGCATTCG
3989373 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
3989399 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:3990439 original size:9 final size:9
Alignment explanation
Indices: 3990425--3990461 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3990415 TATAGTTTGA
3990425 TATTCGAAT
1 TATTCGAAT
3990434 TATTCGAAT
1 TATTCGAAT
*
3990443 TATTCGAGT
1 TATTCGAAT
3990452 TATTCGAAT
1 TATTCGAAT
3990461 T
1 T
3990462 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3991539 original size:23 final size:25
Alignment explanation
Indices: 3991491--3991548 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
3991481 AATTTAGTTC
**
3991491 ATTTACTTTTCAAAATT-TTTTAAA-
1 ATTTA-TTTTCAAAATTGTTGAAAAT
3991515 ATTTATTTTC-AAATTGTTGAGAAAT
1 ATTTATTTTCAAAATTGTTGA-AAAT
3991540 ATTTATTTT
1 ATTTATTTT
3991549 AATATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 7 0.24
24 8 0.28
25 9 0.31
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (25 bp):
ATTTATTTTCAAAATTGTTGAAAAT
Found at i:3993030 original size:28 final size:28
Alignment explanation
Indices: 3992977--3993031 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3992967 TATATTAATG
* * *
3992977 ATAAAAAAAAGTAAACTTTTCTTTATCA
1 ATAAAAAAAAGTAAAATTGTCATTATCA
3993005 ATAAAATAAAA-TAAAATTGTCATTATC
1 ATAAAA-AAAAGTAAAATTGTCATTATC
3993032 CCATGAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (28 bp):
ATAAAAAAAAGTAAAATTGTCATTATCA
Found at i:3993228 original size:26 final size:27
Alignment explanation
Indices: 3993190--3993242 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
3993180 TTTTCCATAA
3993190 TATGGAAATCAAAATCAATGAAGACTT
1 TATGGAAATCAAAATCAATGAAGACTT
* *
3993217 TATGTAAA-CAAATTCAATGAAGACTT
1 TATGGAAATCAAAATCAATGAAGACTT
3993243 GCAAATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.28
Consensus pattern (27 bp):
TATGGAAATCAAAATCAATGAAGACTT
Found at i:3993641 original size:16 final size:17
Alignment explanation
Indices: 3993622--3993654 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3993612 GATTGAGCAA
3993622 ATCAAAT-CAAGATTCG
1 ATCAAATACAAGATTCG
*
3993638 ATCAAATACAGGATTCG
1 ATCAAATACAAGATTCG
3993655 TCGATGACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (17 bp):
ATCAAATACAAGATTCG
Found at i:3994296 original size:50 final size:50
Alignment explanation
Indices: 3994237--3994332 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
3994227 TTAATTATTA
*
3994237 AATGCGTTTGGAAGTAGCGCCATACTTATTACATTCCGTAAACCTCTCCC
1 AATGCGTTTGGAAGCAGCGCCATACTTATTACATTCCGTAAACCTCTCCC
* * * * *
3994287 AATGCGTTTGGGAGCAGGGCTATACTTATTACCTTCCGTAAGCCTC
1 AATGCGTTTGGAAGCAGCGCCATACTTATTACATTCCGTAAACCTC
3994333 CTCATGCATC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (50 bp):
AATGCGTTTGGAAGCAGCGCCATACTTATTACATTCCGTAAACCTCTCCC
Found at i:3994532 original size:20 final size:20
Alignment explanation
Indices: 3994507--3994550 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3994497 CTAGCCCAAA
3994507 TTTTTTA-TTTTTAAAATATT
1 TTTTTTATTTTTTAAAA-ATT
3994527 TTTTTTATTTTTTAAAAATT
1 TTTTTTATTTTTTAAAAATT
3994547 TTTT
1 TTTT
3994551 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTATTTTTTAAAAATT
Found at i:3994562 original size:22 final size:20
Alignment explanation
Indices: 3994514--3994566 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3994504 AAATTTTTTA
*
3994514 TTTTTAAAATATTTTTTTTAT
1 TTTTTAAAA-ATTTTTTGTAT
*
3994535 TTTTTAAAAATTTTTTGGTGT
1 TTTTTAAAAATTTTTT-GTAT
3994556 TTATTTAAAAA
1 TT-TTTAAAAA
3994567 ATGGGACGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 7 0.25
21 13 0.46
22 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTTAAAAATTTTTTGTAT
Found at i:4005248 original size:17 final size:17
Alignment explanation
Indices: 4005226--4005260 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4005216 AAATGCCAAA
* *
4005226 ACTACAATTACAAGTAT
1 ACTACAAGTACAAATAT
4005243 ACTACAAGTACAAATAT
1 ACTACAAGTACAAATAT
4005260 A
1 A
4005261 TGCCTAACCG
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:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (17 bp):
ACTACAAGTACAAATAT
Found at i:4008409 original size:11 final size:11
Alignment explanation
Indices: 4008393--4008417 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4008383 GGGTTCTATG
4008393 TAATAATATTA
1 TAATAATATTA
4008404 TAATAATATTA
1 TAATAATATTA
4008415 TAA
1 TAA
4008418 AAATTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATAATATTA
Found at i:4010776 original size:21 final size:21
Alignment explanation
Indices: 4010747--4010789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4010737 TTTTTAATTT
*
4010747 TTAATTTTTTAAATATTTTTA
1 TTAACTTTTTAAATATTTTTA
* *
4010768 TTAACTTTTTAATTTTTTTTA
1 TTAACTTTTTAAATATTTTTA
4010789 T
1 T
4010790 GAAGTACAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTAACTTTTTAAATATTTTTA
Found at i:4013958 original size:40 final size:39
Alignment explanation
Indices: 4013914--4013998 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 39
4013904 GACCCAGCCC
4013914 AAATATTTAATAAATATA-TATTTTTA-ATTTTTTAATTTTA
1 AAATATTT-ATAAA-ATACT-TTTTTATATTTTTTAATTTTA
* *
4013954 AAATATTTTTAAAATACTTTTTTATTATTTTTTATTTTTA
1 AAATATTTATAAAATACTTTTTTA-TATTTTTTAATTTTA
4013994 AAATA
1 AAATA
4013999 AATTTTTGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
38 9 0.22
39 5 0.12
40 26 0.65
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (39 bp):
AAATATTTATAAAATACTTTTTTATATTTTTTAATTTTA
Found at i:4026405 original size:3 final size:3
Alignment explanation
Indices: 4026397--4026422 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4026387 GTTTTTGCCT
4026397 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
4026423 TCTTTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4027791 original size:3 final size:3
Alignment explanation
Indices: 4027783--4027847 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
4027773 ATGAAAAACC
* *
4027783 ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATT
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
4027829 GTA ATA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
4027848 GTCCGTTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4033070 original size:3 final size:3
Alignment explanation
Indices: 4033062--4033096 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4033052 TTGGTCATAC
4033062 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4033097 ATGTTTTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4033458 original size:19 final size:19
Alignment explanation
Indices: 4033397--4033460 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
4033387 ATAGCAGAGG
* *
4033397 ATTTTCCTCAACCGAAAAT
1 ATTTTCCGCAACTGAAAAT
* * * *
4033416 ATTCTCTGCAACAGTCAGAAT
1 ATTTTCCGCAAC--TGAAAAT
4033437 ATTTTCCGCAACTGAAAAT
1 ATTTTCCGCAACTGAAAAT
4033456 ATTTT
1 ATTTT
4033461 AAAAATATCT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (19 bp):
ATTTTCCGCAACTGAAAAT
Found at i:4037284 original size:2 final size:2
Alignment explanation
Indices: 4037277--4037304 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4037267 ATATCTGCTT
4037277 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
4037305 CAATATCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4039760 original size:27 final size:29
Alignment explanation
Indices: 4039727--4039788 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
4039717 TTTGAGATTT
4039727 TAAATTCAAAAAAAT-AAAAT-AAAGGAC
1 TAAATTCAAAAAAATAAAAATAAAAGGAC
***
4039754 TAAATTCTTTAAAATAAAAATAAAAGGAC
1 TAAATTCAAAAAAATAAAAATAAAAGGAC
4039783 TAAATT
1 TAAATT
4039789 ATGAATATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 12 0.40
28 5 0.17
29 13 0.43
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (29 bp):
TAAATTCAAAAAAATAAAAATAAAAGGAC
Found at i:4044548 original size:17 final size:16
Alignment explanation
Indices: 4044526--4044580 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
4044516 TGAATATATA
4044526 AAAAAATTTCAAAAATT
1 AAAAAATTT-AAAAATT
*
4044543 AAAAAATGTATAAAATT
1 AAAAAATTTA-AAAATT
**
4044560 ATTAAATATTAAAAATT
1 AAAAAAT-TTAAAAATT
4044577 AAAA
1 AAAA
4044581 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 1 0.03
17 27 0.90
18 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAAAATTTAAAAATT
Found at i:4046034 original size:18 final size:17
Alignment explanation
Indices: 4045981--4046034 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 17
4045971 CGACTTAGCC
*
4045981 TTTTTT-TAGTTTGTAA
1 TTTTTTATATTTTGTAA
* * *
4045997 TGTTTTATATTATGTTA
1 TTTTTTATATTTTGTAA
4046014 TTTTTATATATTTTGTAA
1 TTTTT-TATATTTTGTAA
4046032 TTT
1 TTT
4046035 ATAACACATG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 5 0.17
17 11 0.38
18 13 0.45
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTGTAA
Found at i:4047869 original size:9 final size:9
Alignment explanation
Indices: 4047857--4047924 Score: 100
Period size: 9 Copynumber: 7.6 Consensus size: 9
4047847 TCAATTTGGT
4047857 TAATTCGGG
1 TAATTCGGG
*
4047866 TAATTCGGT
1 TAATTCGGG
*
4047875 TAATTCAGG
1 TAATTCGGG
4047884 TAATTCGGG
1 TAATTCGGG
*
4047893 TAATTCGGT
1 TAATTCGGG
4047902 TAATTCGGG
1 TAATTCGGG
*
4047911 TAATTCGGT
1 TAATTCGGG
4047920 TAATT
1 TAATT
4047925 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (9 bp):
TAATTCGGG
Found at i:4047887 original size:27 final size:27
Alignment explanation
Indices: 4047857--4047924 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
4047847 TCAATTTGGT
4047857 TAATTCGGGTAATTCGGTTAATTCAGG
1 TAATTCGGGTAATTCGGTTAATTCAGG
*
4047884 TAATTCGGGTAATTCGGTTAATTCGGG
1 TAATTCGGGTAATTCGGTTAATTCAGG
*
4047911 TAATTCGGTTAATT
1 TAATTCGGGTAATT
4047925 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (27 bp):
TAATTCGGGTAATTCGGTTAATTCAGG
Found at i:4057033 original size:21 final size:20
Alignment explanation
Indices: 4057009--4057059 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
4056999 GTAGTGGCAT
*
4057009 TGAGATTAATTATTATAGCGA
1 TGAGATTAA-TATTATAGCAA
*
4057030 TGAGATTAGATATTCTAGCAA
1 TGAGATTA-ATATTATAGCAA
4057051 TGAGATTAA
1 TGAGATTAA
4057060 AAACAGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (20 bp):
TGAGATTAATATTATAGCAA
Found at i:4057767 original size:27 final size:26
Alignment explanation
Indices: 4057723--4057776 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
4057713 ATAATAATGT
4057723 TATTTTAAAAATAAAAATAAAAATTA
1 TATTTTAAAAATAAAAATAAAAATTA
*
4057749 TATTTTAAAAATAAAAAATAAAGATTA
1 TATTTTAAAAAT-AAAAATAAAAATTA
4057776 T
1 T
4057777 TTAATAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
TATTTTAAAAATAAAAATAAAAATTA
Found at i:4060777 original size:19 final size:21
Alignment explanation
Indices: 4060739--4060777 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4060729 AATAGGGTAT
4060739 TTAAATCACATATATTCTCAA
1 TTAAATCACATATATTCTCAA
4060760 TTAAATCACA-AT-TTCTCA
1 TTAAATCACATATATTCTCA
4060778 CATTTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATCACATATATTCTCAA
Found at i:4060979 original size:6 final size:6
Alignment explanation
Indices: 4060968--4061012 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
4060958 ATTCCCACTC
* * * *
4060968 ATAATA ATAATA ATACTA ATAATA ATATTA ATACTA ATATTA ATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATA
4061013 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAATA
Found at i:4060991 original size:18 final size:18
Alignment explanation
Indices: 4060968--4061012 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4060958 ATTCCCACTC
4060968 ATAATAATAATAATACTA
1 ATAATAATAATAATACTA
*
4060986 ATAATAATATTAATACTA
1 ATAATAATAATAATACTA
*
4061004 ATATTAATA
1 ATAATAATA
4061013 CTTACCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAATAATAATACTA
Found at i:4061014 original size:12 final size:12
Alignment explanation
Indices: 4060972--4061012 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
4060962 CCACTCATAA
*
4060972 TAATAATAATAC
1 TAATAATAATAT
4060984 TAATAATAATAT
1 TAATAATAATAT
*
4060996 TAATACTAATAT
1 TAATAATAATAT
4061008 TAATA
1 TAATA
4061013 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:4061905 original size:2 final size:2
Alignment explanation
Indices: 4061898--4061924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4061888 TTTATTAAGA
4061898 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
4061925 CACATATTTT
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:4067301 original size:23 final size:24
Alignment explanation
Indices: 4067256--4067305 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
4067246 TTTTTCTTTC
*
4067256 TTTCTTTCCTTCCTTCCTTCTCTG
1 TTTCTTTCCTTCCTCCCTTCTCTG
*
4067280 TTTCTTT-CTTTCTCCCTTCTCTG
1 TTTCTTTCCTTCCTCCCTTCTCTG
4067303 TTT
1 TTT
4067306 TGTTTTGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.00, C:0.34, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTCTTTCCTTCCTCCCTTCTCTG
Found at i:4067309 original size:28 final size:27
Alignment explanation
Indices: 4067245--4067310 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
4067235 TTCTCTTTTT
* *
4067245 CTTTTTCTTTCTTTCTTTCCTTCCTTC
1 CTTTTTGTTTCTTTCTTTCCTCCCTTC
*
4067272 CTTCTCTGTTTCTTTCTTT-CTCCCTTC
1 CTT-TTTGTTTCTTTCTTTCCTCCCTTC
4067299 TCTGTTTTGTTT
1 -CT-TTTTGTTT
4067311 TGCTCTCTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 10 0.31
28 21 0.66
29 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65
Consensus pattern (27 bp):
CTTTTTGTTTCTTTCTTTCCTCCCTTC
Found at i:4067362 original size:8 final size:8
Alignment explanation
Indices: 4067349--4067430 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
4067339 TGTCATATAT
4067349 ATATAATA
1 ATATAATA
4067357 ATATAAT-
1 ATATAATA
4067364 A-AT-ATA
1 ATATAATA
4067370 ATATAAT-
1 ATATAATA
4067377 ATATTAATA
1 ATA-TAATA
4067386 ATA-ATATA
1 ATATA-ATA
*
4067394 ATATAAAA
1 ATATAATA
* *
4067402 ACATAATC
1 ATATAATA
4067410 AT-TACTATA
1 ATATA--ATA
4067419 ATATAATA
1 ATATAATA
4067427 ATAT
1 ATAT
4067431 TTTTTAACAC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
7 9 0.16
8 34 0.59
9 8 0.14
10 2 0.03
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:4067364 original size:5 final size:5
Alignment explanation
Indices: 4067343--4067426 Score: 61
Period size: 5 Copynumber: 16.6 Consensus size: 5
4067333 TTTCTTTGTC
4067343 ATATA TATATA ATA-A TATAATA ATATA ATATA ATAT- AT-TA ATAATA
1 ATATA -ATATA ATATA -AT-ATA ATATA ATATA ATATA ATATA AT-ATA
* *
4067389 ATATA ATATA A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA ATATA ATATA AT-A-TA ATATA ATATA ATA
4067427 ATATTTTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
3 3 0.05
4 7 0.11
5 37 0.57
6 14 0.22
7 4 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:4067408 original size:24 final size:24
Alignment explanation
Indices: 4067345--4067427 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
4067335 TCTTTGTCAT
4067345 ATATATATAATAAT-ATAATAATATA
1 ATATA-ATAA-AATAATAATAATATA
* *
4067370 ATATAATATATTAATAATAATATA
1 ATATAATAAAATAATAATAATATA
* *
4067394 ATATAA-AAACATAATCATTACTATA
1 ATATAATAAA-ATAAT-AATAATATA
4067419 ATATAATAA
1 ATATAATAA
4067428 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 4 0.08
24 24 0.50
25 18 0.38
26 2 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAATAAAATAATAATAATATA
Found at i:4072874 original size:50 final size:50
Alignment explanation
Indices: 4072763--4073009 Score: 248
Period size: 50 Copynumber: 4.8 Consensus size: 50
4072753 ATTTGGATAA
*
4072763 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
4072819 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * * *
4072869 AGAGGTCCCCCGTAAGACCATGTCTGGGATATGGAATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
4072919 AGA-ACTCCCATGTAAGGCCATATCTGGGACATGGCATTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
4072968 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4073010 TGTTATTATC
Statistics
Matches: 164, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 80 0.49
53 3 0.02
55 1 0.01
56 40 0.24
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:4077171 original size:99 final size:103
Alignment explanation
Indices: 4076997--4077232 Score: 259
Period size: 99 Copynumber: 2.3 Consensus size: 103
4076987 TGATAATAAC
* ** ** * * * *
4076997 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--TGCCAATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-CGGTGCCAACGCCATG
* **
4077060 TCCCAGATATGGTCTTACATGGGAGTTCTCAT-A-TC-G
65 TCCCAGACATGGTCTTACATGGGACCTCTCATGACTCAG
* *
4077096 GTGCC-ATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGT
*
4077160 CCCAGGCATGGTCTTACATGGGACCTCTCATGATCTCAATG
66 CCCAGACATGGTCTTACATGGGACCTCTCATGA-CTC-A-G
4077201 ATGCCAATGCCATGTCCCAGACATGGTCTTAC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTAC
4077233 ATGGGATCTC
Statistics
Matches: 111, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
97 1 0.01
98 33 0.30
99 44 0.40
100 1 0.01
102 2 0.02
105 5 0.05
106 25 0.23
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (103 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGT
CCCAGACATGGTCTTACATGGGACCTCTCATGACTCAG
Found at i:4077175 original size:50 final size:50
Alignment explanation
Indices: 4076998--4077243 Score: 255
Period size: 49 Copynumber: 4.8 Consensus size: 50
4076988 GATAATAACA
* ** * * *
4076998 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* ** *
4077047 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
4077097 TGCC-ATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
4077146 TGCCAACGCCATGTCCCAGGCATGGTCTTACATGGGACCTCTCATGATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
*
4077202 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4077244 TTATCCAAAT
Statistics
Matches: 165, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 82 0.50
50 37 0.22
53 5 0.03
56 40 0.24
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:4080759 original size:20 final size:20
Alignment explanation
Indices: 4080734--4080774 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4080724 TGTGTCTCCA
4080734 AAATAAAATTGGTGGCAATT
1 AAATAAAATTGGTGGCAATT
*
4080754 AAATAAAATTTGTGGCAATT
1 AAATAAAATTGGTGGCAATT
4080774 A
1 A
4080775 TCATGCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (20 bp):
AAATAAAATTGGTGGCAATT
Found at i:4085534 original size:2 final size:2
Alignment explanation
Indices: 4085527--4085577 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4085517 ATAGTAAGTG
4085527 TA TA TA TA 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 TA TA TA TA
4085569 TA TA TA TA T
1 TA TA TA TA T
4085578 GTTAAGTATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4088076 original size:24 final size:23
Alignment explanation
Indices: 4088045--4088089 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4088035 CATACATACC
* *
4088045 TTATTATATATCTTTATATCTTA
1 TTATTATATATATCTATATCTTA
4088068 TTATGTATATATATCTATATCT
1 TTAT-TATATATATCTATATCT
4088090 CTTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTATATATATCTATATCTTA
Found at i:4088619 original size:29 final size:29
Alignment explanation
Indices: 4088542--4088623 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
4088532 TTATTTGGTG
*
4088542 TTAATTTATTTATTTATTTATTTACGTGCTCA
1 TTAATTT-TTTATTT-TTTATTTAAGTGCT-A
*
4088574 TT-ATTATTTT-TATTTTATTTAAGTGCT-
1 TTAATT-TTTTATTTTTTATTTAAGTGCTA
4088601 TTAATTTTTTATTTGTTTATTTA
1 TTAATTTTTTATTT-TTTATTTA
4088624 CTTTTATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 6 0.14
28 5 0.12
29 21 0.49
30 2 0.05
31 6 0.14
32 3 0.07
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.66
Consensus pattern (29 bp):
TTAATTTTTTATTTTTTATTTAAGTGCTA
Found at i:4088630 original size:18 final size:17
Alignment explanation
Indices: 4088607--4088645 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
4088597 TGCTTTAATT
*
4088607 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
4088625 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
4088642 TTTT
1 TTTT
4088646 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:4089239 original size:109 final size:111
Alignment explanation
Indices: 4089019--4089270 Score: 384
Period size: 109 Copynumber: 2.3 Consensus size: 111
4089009 NNNNNNNNNN
* * * *
4089019 AAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCTCGTTCAACCAAATGACTAAATAATATCCT
1 AAAACGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCATTCAACCAAATGACT-AATAATATCCT
* *
4089084 TTTAAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
65 TGTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
*
4089131 AAAACGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCATTCAACCAAATGGCT-A-AATATCCTT
1 AAAACGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCATTCAACCAAATGACTAATAATATCCTT
4089194 GTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
66 GTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
* * *
4089240 -GAGCGTGCCCTAATGTGCTGGGTTTCGATTT
1 AAAACGTGCCCTAATGTGCTGGGTGTCGATTT
4089271 CTCGATTGAC
Statistics
Matches: 130, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
108 28 0.22
109 53 0.41
110 1 0.01
112 48 0.37
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (111 bp):
AAAACGTGCCCTAATGTGCTGGGTGTCGATTTTTCTCATTCAACCAAATGACTAATAATATCCTT
GTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
Found at i:4092246 original size:19 final size:19
Alignment explanation
Indices: 4092178--4092252 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 19
4092168 AATTAATACA
4092178 CAATTCACATATTCACATAT
1 CAATTCACA-ATTCACATAT
* *
4092198 C--TTCA-AATCTCATATCT
1 CAATTCACAAT-TCACATAT
* **
4092215 CGATTTTCAATTCACATAT
1 CAATTCACAATTCACATAT
4092234 CAATTCACAATTCACATAT
1 CAATTCACAATTCACATAT
4092253 TCACACAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
16 2 0.05
17 8 0.19
18 4 0.10
19 24 0.57
20 4 0.10
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.37
Consensus pattern (19 bp):
CAATTCACAATTCACATAT
Found at i:4093186 original size:13 final size:14
Alignment explanation
Indices: 4093163--4093195 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4093153 CTCAATTTTC
*
4093163 CCTTTTCTTTCTTT
1 CCTTCTCTTTCTTT
4093177 -CTTCTCTTTCTTT
1 CCTTCTCTTTCTTT
4093190 CCTTCT
1 CCTTCT
4093196 TTCCTTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
CCTTCTCTTTCTTT
Found at i:4101785 original size:18 final size:18
Alignment explanation
Indices: 4101754--4101788 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4101744 ATTTCAATAA
**
4101754 ATAAAATATTATAAAATT
1 ATAAAATAAAATAAAATT
4101772 ATAAAATAAAATAAAAT
1 ATAAAATAAAATAAAAT
4101789 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAATAAAATAAAATT
Found at i:4111135 original size:22 final size:21
Alignment explanation
Indices: 4111107--4111159 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
4111097 TATTTCTTAT
4111107 TTTTTTAATATTAATATAATTA
1 TTTTTTAATATTAATAT-ATTA
*
4111129 TTTTTTAATATTAATATATTT
1 TTTTTTAATATTAATATATTA
4111150 TTTATTTAAT
1 TTT-TTTAAT
4111160 TAGATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTAATATTAATATATTA
Found at i:4111138 original size:16 final size:18
Alignment explanation
Indices: 4111117--4111153 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4111107 TTTTTTAATA
4111117 TTAATA-TAAT-TATTTT
1 TTAATATTAATATATTTT
4111133 TTAATATTAATATATTTT
1 TTAATATTAATATATTTT
4111151 TTA
1 TTA
4111154 TTTAATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 4 0.21
18 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATATTAATATATTTT
Found at i:4111158 original size:16 final size:17
Alignment explanation
Indices: 4111117--4111161 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
4111107 TTTTTTAATA
4111117 TTAATA-TAATTATTTT
1 TTAATATTAATTATTTT
4111133 TTAATATTAATATATTTT
1 TTAATATTAAT-TATTTT
4111151 TT-AT-TTAATTA
1 TTAATATTAATTA
4111162 GATTTTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 6 0.22
18 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATATTAATTATTTT
Found at i:4111654 original size:20 final size:20
Alignment explanation
Indices: 4111631--4111669 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4111621 TTTTTTAAAA
4111631 TTTTAAAATATTAAAAATAT
1 TTTTAAAATATTAAAAATAT
* * *
4111651 TTTTATATTTTTAAAAATA
1 TTTTAAAATATTAAAAATA
4111670 ATTAAATACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATATTAAAAATAT
Found at i:4114064 original size:12 final size:12
Alignment explanation
Indices: 4114044--4114074 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4114034 GGAAAACAGG
4114044 AAAGAAGATGAA
1 AAAGAAGATGAA
*
4114056 AAAGGAGATGAA
1 AAAGAAGATGAA
4114068 AAAGAAG
1 AAAGAAG
4114075 CGACAAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (12 bp):
AAAGAAGATGAA
Found at i:4119804 original size:16 final size:16
Alignment explanation
Indices: 4119783--4119824 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
4119773 AATAAGTGGT
4119783 TGAATTGGTTAACTTG
1 TGAATTGGTTAACTTG
4119799 TGAATTGGTTAACTTG
1 TGAATTGGTTAACTTG
*
4119815 TGAATCGGTT
1 TGAATTGGTT
4119825 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (16 bp):
TGAATTGGTTAACTTG
Found at i:4123475 original size:13 final size:13
Alignment explanation
Indices: 4123442--4123482 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
4123432 ATATTTTTTA
4123442 TTTTTAAAA-A-T
1 TTTTTAAAATACT
*
4123453 ATTTTAAAATACT
1 TTTTTAAAATACT
*
4123466 TTTTTTAAATACT
1 TTTTTAAAATACT
4123479 TTTT
1 TTTT
4123483 AATTTTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 8 0.32
12 1 0.04
13 16 0.64
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAAATACT
Found at i:4128892 original size:21 final size:21
Alignment explanation
Indices: 4128866--4128919 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
4128856 CAGCAGTGGT
*
4128866 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
4128887 GGTGAGATTAGATATTGTAGC
1 GGTGAGATTAGATACTGTAGC
* *
4128908 AGTAAGATTAGA
1 GGTGAGATTAGA
4128920 AACATGATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:4134530 original size:21 final size:22
Alignment explanation
Indices: 4134505--4134559 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
4134495 AACAGCGGTG
*
4134505 GCGGTGAGATTAGT-TATTGTA
1 GCGGTGAGATTAGTATACTGTA
4134526 GCGGTGAGATT-GTATACTGTA
1 GCGGTGAGATTAGTATACTGTA
4134547 GCGGTGAGATTAG
1 GCGGTGAGATTAG
4134560 AAACAATGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.36, T:0.33
Consensus pattern (22 bp):
GCGGTGAGATTAGTATACTGTA
Found at i:4145908 original size:24 final size:25
Alignment explanation
Indices: 4145863--4145909 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
4145853 TTCACCTAAA
**
4145863 GACTAAATTTAATTTTTTTTATTGG
1 GACTAAATTTAATTTTAATTATTGG
4145888 GACTAAATTT-ATTTTAATTATT
1 GACTAAATTTAATTTTAATTATT
4145910 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (25 bp):
GACTAAATTTAATTTTAATTATTGG
Found at i:4152865 original size:4 final size:4
Alignment explanation
Indices: 4152856--4152897 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
4152846 GTACATTTGT
* *
4152856 TTTA TTTA TTTA CTTA TTTA TTTA TTTA TTTA CTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4152898 TTTTCTTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:4152888 original size:69 final size:69
Alignment explanation
Indices: 4152761--4152890 Score: 163
Period size: 69 Copynumber: 1.9 Consensus size: 69
4152751 TTTTAGACAT
** * *
4152761 TTAAATTTAATATTACCTATGTTTGTTTTATCGATTTATTTATTTATCATTCTTTTTACTTCTAA
1 TTAAATTTAATATTACCTACATTTGTTTTATCGATTTACTTATTTATCATTCTATTTACTTCTAA
4152826 ATAC
66 ATAC
** ** *
4152830 TTAAATTTAATATTATGTACATTTGTTTTATTTATTTACTTATTTATTTATT-TATTTACTT
1 TTAAATTTAATATTACCTACATTTGTTTTATCGATTTACTTATTTA-TCATTCTATTTACTT
4152891 ATTATTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
69 47 0.92
70 4 0.08
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (69 bp):
TTAAATTTAATATTACCTACATTTGTTTTATCGATTTACTTATTTATCATTCTATTTACTTCTAA
ATAC
Found at i:4156698 original size:25 final size:25
Alignment explanation
Indices: 4156670--4156747 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
4156660 AAAATTCATA
4156670 AAAATTTAGTCAATATTTTTTATTG
1 AAAATTTAGTCAATATTTTTTATTG
*** *
4156695 AAAAAACA-TCAATTCAACTTTTT-TT-
1 AAAATTTAGTCAA-T--ATTTTTTATTG
4156720 -AAATTTAGTCAATATTTTTTATTG
1 AAAATTTAGTCAATATTTTTTATTG
4156744 AAAA
1 AAAA
4156748 AACATCAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 6 0.16
23 2 0.05
24 9 0.24
25 13 0.34
26 2 0.05
27 6 0.16
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (25 bp):
AAAATTTAGTCAATATTTTTTATTG
Found at i:4156707 original size:24 final size:24
Alignment explanation
Indices: 4156679--4156756 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
4156669 AAAAATTTAG
4156679 TCAATATTTTTTATTGAAAAAACA
1 TCAATATTTTTTATTGAAAAAACA
* ** *
4156703 TCAATTCAACTTTTT-TT-AAATTTA-G
1 TCAA-T--ATTTTTTATTGAAA-AAACA
4156728 TCAATATTTTTTATTGAAAAAACA
1 TCAATATTTTTTATTGAAAAAACA
4156752 TCAAT
1 TCAAT
4156757 TCAACTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 6 0.15
23 3 0.08
24 13 0.33
25 8 0.21
26 3 0.08
27 6 0.15
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (24 bp):
TCAATATTTTTTATTGAAAAAACA
Found at i:4156724 original size:49 final size:49
Alignment explanation
Indices: 4156671--4156768 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
4156661 AAATTCATAA
4156671 AAATTTAGTCAATATTTTTTATTGAAAAAACATCAATTCAACTTTTTTT
1 AAATTTAGTCAATATTTTTTATTGAAAAAACATCAATTCAACTTTTTTT
4156720 AAATTTAGTCAATATTTTTTATTGAAAAAACATCAATTCAACTTTTTTT
1 AAATTTAGTCAATATTTTTTATTGAAAAAACATCAATTCAACTTTTTTT
4156769 TAAAGGTTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (49 bp):
AAATTTAGTCAATATTTTTTATTGAAAAAACATCAATTCAACTTTTTTT
Found at i:4158598 original size:59 final size:61
Alignment explanation
Indices: 4158535--4158675 Score: 198
Period size: 59 Copynumber: 2.3 Consensus size: 61
4158525 TATTTTTTTA
4158535 TATATTTATTTATTTATTATTCTTCACTTTTTAAATACC-T-TAATATTATTTATA-ATATT
1 TATATTTATTTATTTATTATTCTTCACTTTTTAAATACCATCTAATATTATTTATATATA-T
* *
4158594 TATATTTATTTATTTATTATTCTTTACTTTTTAAATACCTAAATCTAATATTATTTATATCTAT
1 TATATTTATTTATTTATTATTCTTCACTTTTTAAATACC---ATCTAATATTATTTATATATAT
*
4158658 TGTATTTATTTATTTATT
1 TATATTTATTTATTTATT
4158676 TATTTGTTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
59 38 0.52
63 1 0.01
64 32 0.44
65 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (61 bp):
TATATTTATTTATTTATTATTCTTCACTTTTTAAATACCATCTAATATTATTTATATATAT
Found at i:4158803 original size:69 final size:69
Alignment explanation
Indices: 4158666--4158824 Score: 176
Period size: 69 Copynumber: 2.3 Consensus size: 69
4158656 ATTGTATTTA
* * * * * * * *
4158666 TTTATTTATTTATTTGTTCATTATTC-TTTTACCTTTTAGACATTTAAATTTAATATTACCTATG
1 TTTATTTATTTATTTATTTATCATTCTTTTTA-CTTTTAAATACTTAAATTTAATATTATCTATA
4158730 TTTGT
65 TTTGT
** * * *
4158735 TTTATCGATTTATTTATTTATCATTCTTTTTACTTCTAAATACTTAAATTTAATATTATGTACAT
1 TTTATTTATTTATTTATTTATCATTCTTTTTACTTTTAAATACTTAAATTTAATATTATCTATAT
4158800 TTGT
66 TTGT
*
4158804 TTTATTTATTTACTTATTTAT
1 TTTATTTATTTATTTATTTAT
4158825 TTATTCATTC
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
69 68 0.93
70 5 0.07
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.60
Consensus pattern (69 bp):
TTTATTTATTTATTTATTTATCATTCTTTTTACTTTTAAATACTTAAATTTAATATTATCTATAT
TTGT
Found at i:4158813 original size:4 final size:4
Alignment explanation
Indices: 4158804--4158850 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
4158794 GTACATTTGT
* * * *
4158804 TTTA TTTA TTTA CTTA TTTA TTTA TTCA TTCA TTTA TTTG TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4158851 TTTTTCTTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:4164541 original size:27 final size:28
Alignment explanation
Indices: 4164474--4164543 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
4164464 CAAGTGTTTC
*
4164474 AATTTCATACAATGTCATCAATCTCAATCT
1 AATTT-ATAC-ATATCATCAATCTCAATCT
*
4164504 AATTTATACATATCATCAATCT-ATTACT
1 AATTTATACATATCATCAATCTCAAT-CT
4164532 -ATTTATACATAT
1 AATTTATACATAT
4164544 ATCTCCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 14 0.38
28 14 0.38
29 4 0.11
30 5 0.14
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (28 bp):
AATTTATACATATCATCAATCTCAATCT
Found at i:4164884 original size:20 final size:20
Alignment explanation
Indices: 4164859--4164898 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4164849 AATATTTTCT
*
4164859 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
4164879 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
4164899 TCATCTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:4164901 original size:34 final size:35
Alignment explanation
Indices: 4164847--4164913 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
4164837 CAAACACCAG
* * *
4164847 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATCTTACAGAAAAGT
*
4164882 AAAACATTTTCCAG-AAATCATCTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATCTTACAGAAAA
4164914 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATCTTACAGAAAAGT
Found at i:4165054 original size:26 final size:22
Alignment explanation
Indices: 4165001--4165061 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 22
4164991 ATCATCAATT
4165001 AATATACATATATATAAATATTC
1 AATAT-CATATATATAAATATTC
*
4165024 AATATCATATAGTATAATTCATATC
1 AATATCATATA-TATAAAT-AT-TC
4165049 ACATATCATATAT
1 A-ATATCATATAT
4165062 TAATAATGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.18
23 11 0.33
24 2 0.06
25 4 0.12
26 10 0.30
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
AATATCATATATATAAATATTC
Found at i:4169177 original size:41 final size:42
Alignment explanation
Indices: 4169099--4169182 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 42
4169089 TAAAAAATAT
* * *
4169099 TTATATTAAAAAATACTACCATAAATTTAATAAATGTT-TTG
1 TTATATTAAAAAACACTACAATAAATATAATAAATGTTATTG
4169140 TTATATTAAAAAACAC-A-AATAAATATAATAAATATGTTATTG
1 TTATATTAAAAAACACTACAATAAATATAAT-AA-ATGTTATTG
4169182 T
1 T
4169183 ATTAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 10 0.27
40 3 0.08
41 20 0.54
42 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (42 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATGTTATTG
Found at i:4169334 original size:31 final size:31
Alignment explanation
Indices: 4169297--4169365 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
4169287 ATTTAATATA
4169297 AATATAA-AATATATATAATTATTATT-TAACAT
1 AATATAATAATATA-AT-ATTATT-TTATAACAT
4169329 -ATATAATTAATATAATATTATTTTATAACAT
1 AATATAA-TAATATAATATTATTTTATAACAT
4169360 AATATA
1 AATATA
4169366 TTTGGGCTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
30 2 0.06
31 18 0.55
32 7 0.21
33 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
AATATAATAATATAATATTATTTTATAACAT
Found at i:4169643 original size:2 final size:2
Alignment explanation
Indices: 4169636--4169686 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4169626 AATTTTTGTG
4169636 TA TA TA TA 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 TA TA TA TA
4169678 TA TA TA TA T
1 TA TA TA TA T
4169687 TCTAAAAATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4172971 original size:18 final size:18
Alignment explanation
Indices: 4172948--4172982 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4172938 GTAAAGGATC
*
4172948 AGGATCAGCGTCAGCCAA
1 AGGATCAGCATCAGCCAA
4172966 AGGATCAGCATCAGCCA
1 AGGATCAGCATCAGCCA
4172983 CACCTAAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.26, T:0.11
Consensus pattern (18 bp):
AGGATCAGCATCAGCCAA
Found at i:4174468 original size:20 final size:20
Alignment explanation
Indices: 4174425--4174585 Score: 88
Period size: 20 Copynumber: 8.2 Consensus size: 20
4174415 AATTACAAAG
* ** *
4174425 AAAAATTCAAAATAACATTC
1 AAAAATTTAAAATAATTTTA
4174445 AAAAATTTAAAATAATTTT-
1 AAAAATTTAAAATAATTTTA
*
4174464 TAAAATTTAAAAT-A-TTTA
1 AAAAATTTAAAATAATTTTA
*
4174482 TAAAATTTTCAAAATTTATATTTTA
1 -AAAAATTT-AAAA--TA-ATTTTA
*
4174507 AAAAATTATAAAA-AATTATA
1 AAAAATT-TAAAATAATTTTA
*
4174527 AAAAATTT-AAA-AATTGTA
1 AAAAATTTAAAATAATTTTA
* **
4174545 AAAAATATAAAA-AAGGTT-
1 AAAAATTTAAAATAATTTTA
*
4174563 AAAATTTTAAAA-AATTTCTA
1 AAAAATTTAAAATAATTT-TA
4174583 AAA
1 AAA
4174586 TAATAATTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.03
18 30 0.27
19 26 0.23
20 35 0.31
21 1 0.01
22 1 0.01
24 11 0.10
25 5 0.04
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTTA
Found at i:4174480 original size:9 final size:9
Alignment explanation
Indices: 4174445--4174579 Score: 98
Period size: 9 Copynumber: 14.9 Consensus size: 9
4174435 AATAACATTC
4174445 AAAAATTTA
1 AAAAATTTA
*
4174454 AAATAATTTT
1 AAA-AATTTA
*
4174464 TAAAATTTA
1 AAAAATTTA
*
4174473 AAATATTTA
1 AAAAATTTA
* *
4174482 TAAAATTTT
1 AAAAATTTA
*
4174491 CAAAATTT-
1 AAAAATTTA
* *
4174499 -ATATTTTA
1 AAAAATTTA
4174507 AAAAATTATA
1 AAAAATT-TA
4174517 AAAAATTATA
1 AAAAATT-TA
4174527 AAAAATTT-
1 AAAAATTTA
4174535 AAAAATTGTA
1 AAAAATT-TA
*
4174545 AAAAATATA
1 AAAAATTTA
*
4174554 AAAAAGGTT-
1 AAAAA-TTTA
*
4174563 AAAATTTTA
1 AAAAATTTA
4174572 AAAAATTT
1 AAAAATTT
4174580 CTAAAATAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
7 5 0.05
8 9 0.09
9 52 0.53
10 33 0.33
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (9 bp):
AAAAATTTA
Found at i:4174520 original size:10 final size:10
Alignment explanation
Indices: 4174505--4174558 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
4174495 ATTTATATTT
4174505 TAAAAAATTA
1 TAAAAAATTA
4174515 TAAAAAATTA
1 TAAAAAATTA
4174525 TAAAAAATT-
1 TAAAAAATTA
*
4174534 T-AAAAATTG
1 TAAAAAATTA
4174543 TAAAAAA-TA
1 TAAAAAATTA
4174552 TAAAAAA
1 TAAAAAA
4174559 GGTTAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 7 0.17
9 10 0.24
10 24 0.59
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:4174576 original size:10 final size:10
Alignment explanation
Indices: 4174445--4174585 Score: 75
Period size: 10 Copynumber: 14.3 Consensus size: 10
4174435 AATAACATTC
4174445 AAAAA-TTTA
1 AAAAATTTTA
4174454 AAATAATTTT-
1 AAA-AATTTTA
*
4174464 TAAAA-TTTA
1 AAAAATTTTA
*
4174473 AAATA-TTTA
1 AAAAATTTTA
*
4174482 TAAAATTTTCA
1 AAAAATTTT-A
4174493 AAATTTATATTTTA
1 AAA---A-ATTTTA
*
4174507 AAAAATTATA
1 AAAAATTTTA
*
4174517 AAAAATTATA
1 AAAAATTTTA
4174527 AAAAA-TTT-
1 AAAAATTTTA
*
4174535 AAAAATTGTA
1 AAAAATTTTA
*
4174545 AAAAA-TATA
1 AAAAATTTTA
**
4174554 AAAAAGGTT-
1 AAAAATTTTA
4174563 -AAAATTTTA
1 AAAAATTTTA
4174572 AAAAATTTCTA
1 AAAAATTT-TA
4174583 AAA
1 AAA
4174586 TAATAATTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
8 14 0.14
9 27 0.26
10 40 0.39
11 12 0.12
14 5 0.05
15 5 0.05
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:4175104 original size:15 final size:17
Alignment explanation
Indices: 4175075--4175107 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4175065 TTTTTAATTC
4175075 TATGTTTATTAATTTTA
1 TATGTTTATTAATTTTA
4175092 TATGTTT-TT-ATTTTA
1 TATGTTTATTAATTTTA
4175107 T
1 T
4175108 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
TATGTTTATTAATTTTA
Found at i:4181806 original size:31 final size:32
Alignment explanation
Indices: 4181757--4181816 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
4181747 GGGGCCTGAA
4181757 AACTTAAATAAAAAACTTTCGAATAGTTCTGT
1 AACTTAAATAAAAAACTTTCGAATAGTTCTGT
* *
4181789 AACTTAAAT-GAAAACTTTTGAATAGTTC
1 AACTTAAATAAAAAACTTTCGAATAGTTC
4181817 AATGATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (32 bp):
AACTTAAATAAAAAACTTTCGAATAGTTCTGT
Found at i:4182686 original size:31 final size:31
Alignment explanation
Indices: 4182650--4182725 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
4182640 TTAACGGCTT
*
4182650 AGTGACTAAAATGTTATAACACGTTAACGTA
1 AGTGACTAAAATGTTACAACACGTTAACGTA
*
4182681 AGTGACTAAAATGTTACAACACGTTAATGTA
1 AGTGACTAAAATGTTACAACACGTTAACGTA
4182712 AGTGACTAAAATGT
1 AGTGACTAAAATGT
4182726 AACATTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (31 bp):
AGTGACTAAAATGTTACAACACGTTAACGTA
Found at i:4183671 original size:36 final size:36
Alignment explanation
Indices: 4183631--4183703 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
4183621 AGAAGTTTAA
* *
4183631 AGAAGCTGTCACGAG-TATAATTGATCGAGTTTGGGC
1 AGAAGCTGTCACGGGAT-TAATTGATCGAGCTTGGGC
*
4183667 AGAAGCTGTCATGGGATTAATTGATCGAGCTTGGGC
1 AGAAGCTGTCACGGGATTAATTGATCGAGCTTGGGC
4183703 A
1 A
4183704 TGCACTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (36 bp):
AGAAGCTGTCACGGGATTAATTGATCGAGCTTGGGC
Found at i:4185569 original size:31 final size:31
Alignment explanation
Indices: 4185534--4185597 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4185524 GCCCCACCTT
*
4185534 TATTAT-TT-TTTTAATTTTTTAAAAATATTTA
1 TATTATATTATTTTAA-TATTTAAAAAT-TTTA
*
4185565 TATTATATTATTTTAATATTTAATAATTTTA
1 TATTATATTATTTTAATATTTAAAAATTTTA
4185596 TA
1 TA
4185598 CATTCTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 12 0.41
32 11 0.38
33 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTATATTATTTTAATATTTAAAAATTTTA
Found at i:4199006 original size:11 final size:11
Alignment explanation
Indices: 4198990--4199027 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
4198980 TTATAAAATG
4198990 ACAATATCTCA
1 ACAATATCTCA
4199001 ACAATATCTCA
1 ACAATATCTCA
4199012 ACAATATCTCA
1 ACAATATCTCA
4199023 ACAAT
1 ACAAT
4199028 TGATAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAATATCTCA
Found at i:4202270 original size:92 final size:91
Alignment explanation
Indices: 4202113--4202321 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
4202103 TTGATTTTAG
* * * *
4202113 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
4202178 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
4202205 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
4202269 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
4202297 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
4202322 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:4202284 original size:24 final size:25
Alignment explanation
Indices: 4202249--4202296 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
4202239 TTATGAAATT
4202249 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
4202273 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
4202297 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:4202450 original size:66 final size:64
Alignment explanation
Indices: 4202375--4202585 Score: 194
Period size: 66 Copynumber: 3.4 Consensus size: 64
4202365 AAATATATTT
*
4202375 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTAAAGTATCATATATTATGATTTGAGTAAATTCATATAA
4202440 G
64 G
* * * **
4202441 AATATTAATTATTAAGAATTTTA-TTAAATTA-CATAT-TT-T-AATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
4202495 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTAAAGTATCATATATTATGATTTGAGTAAATTCATATA
4202559 AG
63 AG
*
4202561 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
4202586 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 7 0.06
57 7 0.06
58 3 0.03
59 2 0.02
60 6 0.05
61 2 0.02
62 3 0.03
63 7 0.06
64 7 0.06
65 9 0.08
66 32 0.28
67 5 0.04
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTATTTAAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:4202477 original size:120 final size:120
Alignment explanation
Indices: 4202337--4202629 Score: 484
Period size: 120 Copynumber: 2.4 Consensus size: 120
4202327 AATTATTTTA
* * * *
4202337 AATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
4202399 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
4202457 AATTTTATTAAATTACATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
4202522 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
4202577 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
4202630 TAAATATGAT
Statistics
Matches: 163, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
119 6 0.04
120 155 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:4202497 original size:15 final size:15
Alignment explanation
Indices: 4202473--4202513 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4202463 ATTAAATTAC
4202473 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
4202487 ATATATTTAATAATA
1 ATATATTTAATTATA
4202502 AT-TATGTTAATT
1 ATATAT-TTAATT
4202514 TATATTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:4202612 original size:16 final size:16
Alignment explanation
Indices: 4202591--4202632 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
4202581 TTATTAAATT
*
4202591 ATATATTTTAATTATA
1 ATATATTTTAATAATA
4202607 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
4202622 AT-TATGTTTAA
1 ATATAT-TTTAA
4202633 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:4202617 original size:15 final size:15
Alignment explanation
Indices: 4202582--4202623 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4202572 TTAAGAATTT
*
4202582 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4202596 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4202610 TATTTAATAATAAT
1 TATTTAATTATAAT
4202624 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4202743 original size:153 final size:153
Alignment explanation
Indices: 4202566--4202852 Score: 502
Period size: 153 Copynumber: 1.9 Consensus size: 153
4202556 ATAAGAATAT
* * *
4202566 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
* * * *
4202631 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATACCAA
66 AAAAATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
4202696 TAATTACCAAAAAAAATTTCTGC
131 TAATTACCAAAAAAAATTTCTGC
*
4202719 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
4202784 AAAAATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAAAATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
4202849 TAAT
131 TAAT
4202853 CATTTACCAA
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
153 126 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (153 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
AAAAATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATTACCAAAAAAAATTTCTGC
Found at i:4206456 original size:2 final size:2
Alignment explanation
Indices: 4206451--4206477 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4206441 TATATATATA
4206451 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4206478 ATATGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4207703 original size:2 final size:2
Alignment explanation
Indices: 4207696--4207720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4207686 AAAATTGGAC
4207696 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4207721 GTAAAAGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4208042 original size:2 final size:2
Alignment explanation
Indices: 4208037--4208070 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4208027 GCAACTTAAC
4208037 AT AT 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 AT AT
4208071 TATTTTTCAT
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):
AT
Found at i:4208504 original size:20 final size:19
Alignment explanation
Indices: 4208475--4208525 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
4208465 TATATAAATA
*
4208475 TTTTTA-ATAAATGTTTAT
1 TTTTTAGATAAATATTTAT
*
4208493 TGTTTTAGATAATTATTTAT
1 T-TTTTAGATAAATATTTAT
4208513 TTGTTTAGATAAA
1 TT-TTTAGATAAA
4208526 AGAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 6 0.22
20 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTTTAGATAAATATTTAT
Found at i:4222575 original size:22 final size:21
Alignment explanation
Indices: 4222549--4222589 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4222539 AATTTAAATG
4222549 ATTATACTTTAATTTTATATTA
1 ATTAT-CTTTAATTTTATATTA
* *
4222571 ATTATTTTTTATTTTATAT
1 ATTATCTTTAATTTTATAT
4222590 CTAACTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTATCTTTAATTTTATATTA
Found at i:4227602 original size:72 final size:72
Alignment explanation
Indices: 4227517--4227792 Score: 394
Period size: 72 Copynumber: 3.8 Consensus size: 72
4227507 TTTAGAAGAA
* * * *
4227517 TTCGACGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATG-CAATATGAGTCAAC
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAACTGCTT-GGACAATATGAGTCAAC
**
4227581 TTAGA-TTT
65 TT-GACAGT
** *
4227589 TTTAATGCATCTTATAACAATTTGAGTGGCTCAATTCCAAACTGCTTGGACAATATGAGTCAACT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAACTGCTTGGACAATATGAGTCAACT
4227654 TGACAGT
66 TGACAGT
* *
4227661 TTCGATGTATCTTATAACAATTTGAGTGGCTCAATTCCAAACTGCTTGGACAATATGAGTCAACT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAACTGCTTGGACAATATGAGTCAACT
4227726 TGACAGT
66 TGACAGT
* * *
4227733 TTCGATGTATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTGGGCAATATGAGT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAACTGCTTGGACAATATGAGT
4227793 GCTCTCTATT
Statistics
Matches: 187, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
71 3 0.02
72 184 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (72 bp):
TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAACTGCTTGGACAATATGAGTCAACT
TGACAGT
Found at i:4230906 original size:110 final size:110
Alignment explanation
Indices: 4230665--4231071 Score: 640
Period size: 110 Copynumber: 3.7 Consensus size: 110
4230655 GATAAACGAG
* * *
4230665 AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * * *
4230729 TTGAAATTTTT--GAAGGGGTATTTAGCTATTTGGTTGAATGAGAA
66 TTGAAATTTTTAAGAA-GGATATTAAGCCATTTGGTTGAACGAGAA
* * *
4230773 AAATCGACACCCAGCACCTTAGGGCATATTTTCTCAAATTTCTAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
4230838 TTGAAATTTTTAAGAAGGATATTAAGCCATTTGGTTGAACGAGAA
66 TTGAAATTTTTAAGAAGGATATTAAGCCATTTGGTTGAACGAGAA
*
4230883 AAATCGACACACAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
4230948 TTGAAATTTTTAAGAAGGATATTAAGCCATTTGGTTGAACGAGAA
66 TTGAAATTTTTAAGAAGGATATTAAGCCATTTGGTTGAACGAGAA
* * *
4230993 AAATCGACACCCAACACCTTAGGGCACGTTTTCTCGAATTTCTCAAACGCAAAACATTGCTTTAT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTC-CAAACGCAAAACATTGCCTTAT
*
4231058 TTTAAAATTTTTAA
65 TTTGAAATTTTTAA
4231072 TTTTGAAGTA
Statistics
Matches: 276, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
108 25 0.09
109 44 0.16
110 170 0.62
111 37 0.13
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (110 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTGAAATTTTTAAGAAGGATATTAAGCCATTTGGTTGAACGAGAA
Found at i:4237524 original size:22 final size:23
Alignment explanation
Indices: 4237499--4237548 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
4237489 ACTGCTCTGC
*
4237499 AATTTAAAATCCACCTGAAA-TT
1 AATTTAAAATCCACCCGAAAGTT
**
4237521 AATTTCCAATCCACCCGAAAGTT
1 AATTTAAAATCCACCCGAAAGTT
4237544 -ATTTA
1 AATTTA
4237549 TACTTTGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (23 bp):
AATTTAAAATCCACCCGAAAGTT
Found at i:4245321 original size:23 final size:23
Alignment explanation
Indices: 4245286--4245329 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
4245276 GAGTGAAAAA
4245286 AAAATACT-AAAAATCATATTTGT
1 AAAATACTAAAAAAT-ATATTTGT
* *
4245309 AAAATATTTAAAAATATATTT
1 AAAATACTAAAAAATATATTT
4245330 ATCTTTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATACTAAAAAATATATTTGT
Found at i:4247271 original size:7 final size:7
Alignment explanation
Indices: 4247263--4247307 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
4247253 TTTTACACCT
*
4247263 TAAACCT
1 TAAACCC
4247270 TAAACCC
1 TAAACCC
4247277 TAAACCC
1 TAAACCC
4247284 TAAACCC
1 TAAACCC
*
4247291 TAGACCC
1 TAAACCC
*
4247298 TAAATCC
1 TAAACCC
4247305 TAA
1 TAA
4247308 CAGCACCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.42, C:0.36, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:4248267 original size:21 final size:19
Alignment explanation
Indices: 4248231--4248272 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
4248221 TATGATGAAT
4248231 AAATACTATAAATTATGTA
1 AAATACTATAAATTATGTA
*
4248250 AAATATCTATACAATTATTTA
1 AAATA-CTATA-AATTATGTA
4248271 AA
1 AA
4248273 CCCCTGGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATACTATAAATTATGTA
Found at i:4250626 original size:2 final size:2
Alignment explanation
Indices: 4250614--4250661 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4250604 TGAAATTACA
*
4250614 AT AT TT AT AT AT 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 AT AT AT AT AT AT
4250656 AT AT AT
1 AT AT AT
4250662 TGAAGTAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4251939 original size:154 final size:152
Alignment explanation
Indices: 4251593--4251942 Score: 483
Period size: 154 Copynumber: 2.3 Consensus size: 152
4251583 ACCAATTATT
* * *
4251593 CGTATTTTGGCCATTTGTTTGTATTTTTTT-CCCGGATTTTATTACTTTTAAAAAAATACTATTT
1 CGTATTTCGGCCCTTTGTTTGTATTTTTTTCCCCAGATTTTATTACTTTTAAAAAAATACTATTT
* * *
4251657 TCTAATTTTTTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTACTT
66 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTACTT
**
4251722 TTTAAATAAATTTAGAAAAACT
131 TTTAAATAAATTTAGAAAAAAA
* * * * * *
4251744 CTTATTTCAGCCCTTTGTTCGTATTTTTTTCCCGA-ATTTTATTACTTTCAATAAAAATATATTA
1 CGTATTTCGGCCCTTTGTTTGTATTTTTTTCCCCAGATTTTATTACTTT---TAAAAAAATACTA
4251808 TTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGT
63 TTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGT
**
4251872 GTTTTTTAAATAAATTTA-AAAAAAA
127 ACTTTTTAAATAAATTTAGAAAAAAA
*
4251897 CGTATTTCGGCCCTTTGTTTGTATTTTTTTCCCCAGAGTTTATTAC
1 CGTATTTCGGCCCTTTGTTTGTATTTTTTTCCCCAGATTTTATTAC
4251943 NNNNNNNNNN
Statistics
Matches: 172, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
151 38 0.22
152 2 0.01
153 36 0.21
154 95 0.55
155 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.52
Consensus pattern (152 bp):
CGTATTTCGGCCCTTTGTTTGTATTTTTTTCCCCAGATTTTATTACTTTTAAAAAAATACTATTT
TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTACTT
TTTAAATAAATTTAGAAAAAAA
Found at i:4256653 original size:17 final size:18
Alignment explanation
Indices: 4256631--4256666 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4256621 GTTTTTGAAT
*
4256631 GGAGGAGATTAAT-AAAA
1 GGAGGAAATTAATCAAAA
4256648 GGAGGAAATTAATCAAAA
1 GGAGGAAATTAATCAAAA
4256666 G
1 G
4256667 CAGTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.17
Consensus pattern (18 bp):
GGAGGAAATTAATCAAAA
Found at i:4259585 original size:35 final size:35
Alignment explanation
Indices: 4259539--4259609 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
4259529 TTATAGGTAA
* *
4259539 ACTACACTTAATGTTTTTAAATTATTGGTAAGTTT
1 ACTACACTTAATGTTTCTAAATTATTAGTAAGTTT
*
4259574 ACTACATTTAATGTTTCTAAATTATTAGTAAGTTT
1 ACTACACTTAATGTTTCTAAATTATTAGTAAGTTT
4259609 A
1 A
4259610 TTTTTTGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (35 bp):
ACTACACTTAATGTTTCTAAATTATTAGTAAGTTT
Found at i:4261097 original size:30 final size:32
Alignment explanation
Indices: 4261040--4261102 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
4261030 AAATAATTTA
* * *
4261040 AAAATGTAAAAAAAAAATTATAAAAAGTTCAT
1 AAAATGTAAAAAAAAAATAACAAAAAGTACAT
*
4261072 AAAAT-TAAAAAAAAAA-AACATAAAGTACAT
1 AAAATGTAAAAAAAAAATAACAAAAAGTACAT
4261102 A
1 A
4261103 TGGATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 11 0.41
31 11 0.41
32 5 0.19
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (32 bp):
AAAATGTAAAAAAAAAATAACAAAAAGTACAT
Found at i:4264330 original size:160 final size:159
Alignment explanation
Indices: 4264034--4264370 Score: 593
Period size: 160 Copynumber: 2.1 Consensus size: 159
4264024 GTTAATTGAT
* * *
4264034 TTTAAGTTGGATGCTTAACATCGTATTTAACGTCCAAGTTGTGTTCTGTTGTTATTGTCTATTTT
1 TTTAAGTTGGATGCTTAACATCATATTTAACGCCCAAGTTGTGTTCTATTGTTATTGTCTATTTT
4264099 CTGACCAATAACCCTTTCGAGTTTGTTACATTATAACCTCTTTTGTCTTCATGAGTATTAATTCG
66 CTGACCAATAACCCTTTCGAGTTTGTTACATTATAACCTCTTTTGTCTTCATGAGTATTAATTCG
* *
4264164 ATTTTGTATTATTTGTGATGCCAATTAAC
131 ATTTTGTATTATCTGCGATGCCAATTAAC
*
4264193 TTTAAGTTGGATGCTTAACATCATATTTAACGCCCAAGTTTTGTTCTATTGTTATTGTCTATTTT
1 TTTAAGTTGGATGCTTAACATCATATTTAACGCCCAAGTTGTGTTCTATTGTTATTGTCTATTTT
*
4264258 CTGACCCAATAACCCTTTCGAGTTTGTTACATTATAACCTCTTTTGTCTTCGTGAGTATTAATTC
66 CTGA-CCAATAACCCTTTCGAGTTTGTTACATTATAACCTCTTTTGTCTTCATGAGTATTAATTC
4264323 GATTTTGTATTATCTGCGATGCCAATTAAC
130 GATTTTGTATTATCTGCGATGCCAATTAAC
*
4264353 TTTAAGTTGGGTGCTTAA
1 TTTAAGTTGGATGCTTAA
4264371 AAATCCCATA
Statistics
Matches: 169, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
159 65 0.38
160 104 0.62
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.45
Consensus pattern (159 bp):
TTTAAGTTGGATGCTTAACATCATATTTAACGCCCAAGTTGTGTTCTATTGTTATTGTCTATTTT
CTGACCAATAACCCTTTCGAGTTTGTTACATTATAACCTCTTTTGTCTTCATGAGTATTAATTCG
ATTTTGTATTATCTGCGATGCCAATTAAC
Found at i:4272780 original size:40 final size:41
Alignment explanation
Indices: 4272735--4272814 Score: 135
Period size: 42 Copynumber: 2.0 Consensus size: 41
4272725 TACATTACAC
*
4272735 TCTTAAAAGAGAT-AAATTCGAGCTTTTAAGATGACATTAT
1 TCTTAAAAGAGATAAAATTCGAGCTTTAAAGATGACATTAT
4272775 TCTTAAAAGAGATACAAATTCGAGCTTTAAAGATGACATT
1 TCTTAAAAGAGATA-AAATTCGAGCTTTAAAGATGACATT
4272815 GTTTAAAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 13 0.35
42 24 0.65
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (41 bp):
TCTTAAAAGAGATAAAATTCGAGCTTTAAAGATGACATTAT
Found at i:4272821 original size:40 final size:40
Alignment explanation
Indices: 4272735--4272823 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 40
4272725 TACATTACAC
* *
4272735 TCTTAAAAGAGATAAATTCGAGCTTTTAAGATGACATTAT
1 TCTTAAAAGAGATAAATTCGAGCTTTAAAGATGACATTAG
4272775 TCTTAAAAGAGATACAAATTCGAGCTTTAAAGATGACATT-G
1 TCTTAAAAGAGAT--AAATTCGAGCTTTAAAGATGACATTAG
4272816 T-TTAAAAG
1 TCTTAAAAG
4272824 TATATTTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 20 0.44
41 1 0.02
42 24 0.53
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (40 bp):
TCTTAAAAGAGATAAATTCGAGCTTTAAAGATGACATTAG
Found at i:4273113 original size:20 final size:20
Alignment explanation
Indices: 4273067--4273114 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
4273057 CGAACTCAAG
* * *
4273067 TTTAAGATT-GGGTTTAGGG
1 TTTAAGGTTCGGGTTTAAGA
4273086 TTTAAGGTTCGGGTTTAAGA
1 TTTAAGGTTCGGGTTTAAGA
*
4273106 TTTGAGGTT
1 TTTAAGGTT
4273115 TCCAGATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (20 bp):
TTTAAGGTTCGGGTTTAAGA
Found at i:4274754 original size:2 final size:2
Alignment explanation
Indices: 4274747--4274778 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4274737 TTTATATTAG
4274747 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
4274779 ATTTGTTATT
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:4277253 original size:2 final size:2
Alignment explanation
Indices: 4277246--4277270 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4277236 CTAAAATCGA
4277246 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
4277271 CTCACGCCTT
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:4287882 original size:25 final size:25
Alignment explanation
Indices: 4287848--4287898 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
4287838 ATTAAGCTTT
*
4287848 TAAGCCCCCTCAAATCTGTAACCTC
1 TAAGCCCCCTCAAATCTGCAACCTC
* *
4287873 TAAGCTCCCTCGAATCTGCAACCTC
1 TAAGCCCCCTCAAATCTGCAACCTC
4287898 T
1 T
4287899 TAGAATGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.39, G:0.10, T:0.25
Consensus pattern (25 bp):
TAAGCCCCCTCAAATCTGCAACCTC
Found at i:4291042 original size:7 final size:7
Alignment explanation
Indices: 4291030--4291065 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
4291020 AGGGAAGGTA
4291030 GTATTTG
1 GTATTTG
4291037 GTATTTG
1 GTATTTG
4291044 GTATTTG
1 GTATTTG
4291051 GTATTTG
1 GTATTTG
4291058 GTATTTG
1 GTATTTG
4291065 G
1 G
4291066 GGGACGTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.56
Consensus pattern (7 bp):
GTATTTG
Found at i:4294778 original size:26 final size:26
Alignment explanation
Indices: 4294726--4294781 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
4294716 TTGAGTATAT
** *
4294726 TTTAAGTATCAAATTGAGACAAAAAA
1 TTTAAGTATCAAAAGGAGAAAAAAAA
4294752 TTTAAGTATCAAAAGGA-AAAAACAAA
1 TTTAAGTATCAAAAGGAGAAAAA-AAA
4294778 TTTA
1 TTTA
4294782 CTTTCAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (26 bp):
TTTAAGTATCAAAAGGAGAAAAAAAA
Found at i:4295149 original size:29 final size:29
Alignment explanation
Indices: 4295089--4295149 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
4295079 TGGGGAAAAT
* *
4295089 GGCCCATTCCGGTAAATAATAAAATACCG
1 GGCCCATTCCGGTAAATAATAAAAAACAG
* ** *
4295118 GGCCCATTTCGGTAAATTTTAAAAAATAG
1 GGCCCATTCCGGTAAATAATAAAAAACAG
4295147 GGC
1 GGC
4295150 TTTTATGTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATAAAAAACAG
Done.