Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 161 of 208
Found at i:52271027 original size:13 final size:13
Alignment explanation
Indices: 52271009--52271040 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
52270999 TTATTGTGTG
52271009 GAATTGAATAACA
1 GAATTGAATAACA
52271022 GAATTGAATAACA
1 GAATTGAATAACA
52271035 G-ATTGA
1 GAATTGA
52271041 TTGTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (13 bp):
GAATTGAATAACA
Found at i:52273178 original size:16 final size:16
Alignment explanation
Indices: 52273157--52273224 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
52273147 TTTGGTTCGC
52273157 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
52273173 TGTATTGGATTAGAGC
1 TGTATTGGATTAGAGG
52273189 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52273205 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52273221 TGTA
1 TGTA
52273225 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.25, C:0.01, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52273487 original size:18 final size:17
Alignment explanation
Indices: 52273460--52273494 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52273450 TTATTTTTAA
*
52273460 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52273478 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52273495 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52273560 original size:157 final size:157
Alignment explanation
Indices: 52273347--52273663 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
52273337 TAGAATACCC
*
52273347 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* * *
52273412 TTATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTTTTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
52273477 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
52273504 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* *
52273569 ATATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
52273634 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
52273661 TTA
1 TTA
52273664 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:52273634 original size:16 final size:16
Alignment explanation
Indices: 52273597--52273638 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52273587 TTAATCATAT
*
52273597 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52273613 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52273628 TTAAAATATAT
1 TTAAAATATAT
52273639 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52273645 original size:14 final size:15
Alignment explanation
Indices: 52273606--52273647 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52273596 TTTAAACATA
*
52273606 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52273621 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52273635 A-TATAATTTAATA
1 ATTATAATTAAATA
52273648 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52277386 original size:35 final size:35
Alignment explanation
Indices: 52277342--52277426 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
52277332 ACCTACTTTT
*
52277342 AAAGAGTTGGGATAGAC-CACTCTATGCCAACCTTAA
1 AAAG-GTTGGGATAGACTCA-TCTAAGCCAACCTTAA
* *
52277378 AAAGGTTGGGATTA-ACTCATCTAAGGCAACTTTAA
1 AAAGGTTGGGA-TAGACTCATCTAAGCCAACCTTAA
*
52277413 ACAGGTTGGGATAG
1 AAAGGTTGGGATAG
52277427 GCCTTACATG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
34 2 0.05
35 32 0.76
36 8 0.19
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (35 bp):
AAAGGTTGGGATAGACTCATCTAAGCCAACCTTAA
Found at i:52278993 original size:25 final size:25
Alignment explanation
Indices: 52278957--52279013 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
52278947 ACCATTTTAG
52278957 ATTATTTGTTTTAAAATCTATTATGT
1 ATTA-TTGTTTTAAAATCTATTATGT
* *
52278983 ATTATTGTTTTGAAATTTATTATGT
1 ATTATTGTTTTAAAATCTATTATGT
52279008 ATTATT
1 ATTATT
52279014 CACTGTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (25 bp):
ATTATTGTTTTAAAATCTATTATGT
Found at i:52281568 original size:22 final size:24
Alignment explanation
Indices: 52281527--52281572 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
52281517 GAGATGAAAA
52281527 AAAATAATATAATTTTAATTTATT
1 AAAATAATATAATTTTAATTTATT
52281551 AAAATAATAT-A-TTTAATTTATT
1 AAAATAATATAATTTTAATTTATT
52281573 CAAGTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATAATATAATTTTAATTTATT
Found at i:52282332 original size:16 final size:16
Alignment explanation
Indices: 52282311--52282346 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
52282301 TTTGGTTCGC
52282311 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52282327 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52282343 TGTA
1 TGTA
52282347 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52282590 original size:25 final size:25
Alignment explanation
Indices: 52282558--52282612 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
52282548 TAATTTAATC
*
52282558 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
52282582 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
52282607 ATATAT
1 ATATAT
52282613 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:52282794 original size:47 final size:46
Alignment explanation
Indices: 52282743--52282903 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
52282733 GATTTAATAA
52282743 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
52282790 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
52282831 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
52282878 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
52282904 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:52295799 original size:19 final size:20
Alignment explanation
Indices: 52295757--52295799 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
52295747 TCATGCTTTC
*
52295757 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
52295777 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
52295795 TATTC
1 TATTC
52295800 TACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:52296174 original size:45 final size:44
Alignment explanation
Indices: 52295986--52296177 Score: 233
Period size: 45 Copynumber: 4.3 Consensus size: 44
52295976 GGTAGTAGTG
* *
52295986 ACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTA
1 ACAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATC-GTA
* * * *
52296031 ACAATAAC-GTTAACAGTATTCGCCACATAAAGTGCCGAATCGATA
1 ACAGTAACAG-TAACAGTATTCGACACACAAAGTGTCGAATCG-TA
**
52296076 ACAGTAATGGTAACAGTATTCGACACACAAAGTGTCGAATCGGTA
1 ACAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATC-GTA
* * *
52296121 ATAGTAACAGTAACAGTATTTGAGACACAAAGTGTCGAATCAGTA
1 ACAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATC-GTA
52296166 ACAGTAACAGTA
1 ACAGTAACAGTA
52296178 GTCGGTATAT
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
44 2 0.02
45 121 0.97
46 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (44 bp):
ACAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCGTA
Found at i:52297904 original size:68 final size:67
Alignment explanation
Indices: 52297832--52298049 Score: 160
Period size: 64 Copynumber: 3.2 Consensus size: 67
52297822 AATTAATAGC
52297832 ATAAATTATATAAATATATGATGATGTTCGAATGTATAATACAAATTCTTTGAGTTGAATTTAAT
1 ATAAATTATATAAATATATGATGA-GTTCGAATGTATAATACAAATTCTTTGAGTTGAATTTAAT
*
52297897 GAT
65 GTT
* ** * ** * * * *
52297900 ATAAATTGTATGTATGTATG-TG-GTTCGAATAAATGATGC-AATGT-TTTGAATTGAATGTAAT
1 ATAAATTATATAAATATATGATGAGTTCGAATGTATAATACAAAT-TCTTTGAGTTGAATTTAAT
52297961 GTT
65 GTT
* * * *
52297964 ATGAAATATATATATATATATATAAAAGAGGTTAGAATGTA-AGATACAAGTTTCTTTGAGTTGA
1 AT-AAAT-TATATA-A-ATATAT-GATGA-GTTCGAATGTATA-ATACAA-ATTCTTTGAGTTGA
52298028 ATTTAATGTT
58 ATTTAATGTT
52298038 A-ATAATTATATA
1 ATA-AATTATATA
52298050 TAATTATACA
Statistics
Matches: 111, Mismatches: 25, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
64 22 0.20
65 18 0.16
66 4 0.04
67 2 0.02
68 21 0.19
70 1 0.01
72 18 0.16
73 5 0.05
74 20 0.18
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (67 bp):
ATAAATTATATAAATATATGATGAGTTCGAATGTATAATACAAATTCTTTGAGTTGAATTTAATG
TT
Found at i:52298308 original size:41 final size:41
Alignment explanation
Indices: 52298263--52298354 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
52298253 GGCTATGTGC
* *
52298263 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * *
52298304 CTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
52298345 CTAGCAGGCT
1 CTAGCAGGCT
52298355 AGGAGCCGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:52299075 original size:12 final size:12
Alignment explanation
Indices: 52299051--52299085 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
52299041 CAGGAAATTC
*
52299051 TATA-ATTTTTA
1 TATATATTTATA
52299062 TATATATTTATA
1 TATATATTTATA
52299074 TATATATTTATA
1 TATATATTTATA
52299086 GTTTTGCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATTTATA
Found at i:52300617 original size:20 final size:24
Alignment explanation
Indices: 52300573--52300618 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
52300563 CTCTTATTCC
52300573 CTTTCTCTATAATATTTCCTATCA
1 CTTTCTCTATAATATTTCCTATCA
52300597 CTTTCTCT-T-AT-TTTCCT-TCA
1 CTTTCTCTATAATATTTCCTATCA
52300617 CT
1 CT
52300619 AATATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 2 0.09
23 1 0.05
24 8 0.36
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.54
Consensus pattern (24 bp):
CTTTCTCTATAATATTTCCTATCA
Found at i:52303266 original size:25 final size:25
Alignment explanation
Indices: 52303236--52303320 Score: 138
Period size: 25 Copynumber: 3.5 Consensus size: 25
52303226 TGCTCTCATC
52303236 TCCTCTACTGGTGCTGGTTCTTTGT
1 TCCTCTACTGGTGCTGGTTCTTTGT
*
52303261 TCCTCTGCTGGTGCT--TTCTTTGT
1 TCCTCTACTGGTGCTGGTTCTTTGT
*
52303284 TCCTCTGCTGGTGCTGGTTCTTTGT
1 TCCTCTACTGGTGCTGGTTCTTTGT
52303309 TCCTCTACTGGT
1 TCCTCTACTGGT
52303321 TCTTTGTTCC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
23 23 0.41
25 33 0.59
ACGTcount: A:0.02, C:0.26, G:0.24, T:0.48
Consensus pattern (25 bp):
TCCTCTACTGGTGCTGGTTCTTTGT
Found at i:52303271 original size:19 final size:19
Alignment explanation
Indices: 52303247--52303333 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
52303237 CCTCTACTGG
52303247 TGCTGGTTCTTTGTTCCTC
1 TGCTGGTTCTTTGTTCCTC
52303266 TGCTGGTGCTTTCTTTGTTCCTCTGC
1 TGCT-G-G--TTCTTTGTT-C-CT-C
52303292 TGGTGCTGGTTCTTTGTTCCTC
1 ---TGCTGGTTCTTTGTTCCTC
*
52303314 TACTGGTTCTTTGTTCCTC
1 TGCTGGTTCTTTGTTCCTC
52303333 T
1 T
52303334 TCTCCACCAG
Statistics
Matches: 57, Mismatches: 1, Indels: 20
0.73 0.01 0.26
Matches are distributed among these distances:
19 23 0.40
20 1 0.02
21 1 0.02
22 1 0.02
23 11 0.19
24 2 0.04
25 11 0.19
26 1 0.02
27 1 0.02
28 1 0.02
29 4 0.07
ACGTcount: A:0.01, C:0.25, G:0.22, T:0.52
Consensus pattern (19 bp):
TGCTGGTTCTTTGTTCCTC
Found at i:52305321 original size:117 final size:116
Alignment explanation
Indices: 52305114--52305342 Score: 363
Period size: 117 Copynumber: 2.0 Consensus size: 116
52305104 TACGCATATT
*
52305114 AATATCCTTTTAAAAAAATTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAAAAAACGTAC
1 AATATCCTTTTAAAAAAATTCAAAAAAAGGCAATGTTTTGCGTTTGGAAATTCGAAAAAACGTAC
52305179 CCCAATGTGCTAGGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATAGCCA
66 CCCAATGTGCTAGGTTTCGA-TTTT-TCGTTCGACCAAATAGCCAAATAGCCA
* * *
52305232 AATATCCTTTT-AAAAATTTCAAAAAAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGC
1 AATATCCTTTTAAAAAAATTCAAAAAAAGGCAATGTTTTGCGTTTGGAAATTCGAAAAAACGTAC
* *
52305296 CCTAATGTGCT-GTGTTTCGATTTTTCGTTTGACCAAATAGCCAAATA
66 CCCAATGTGCTAG-GTTTCGATTTTTCGTTCGACCAAATAGCCAAATA
52305343 TCCTCTTAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
115 22 0.21
116 5 0.05
117 66 0.63
118 11 0.11
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (116 bp):
AATATCCTTTTAAAAAAATTCAAAAAAAGGCAATGTTTTGCGTTTGGAAATTCGAAAAAACGTAC
CCCAATGTGCTAGGTTTCGATTTTTCGTTCGACCAAATAGCCAAATAGCCA
Found at i:52309680 original size:15 final size:15
Alignment explanation
Indices: 52309660--52309692 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52309650 AATCATTGGG
52309660 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
52309675 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
52309690 TTG
1 TTG
52309693 TCAACAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:52312541 original size:9 final size:9
Alignment explanation
Indices: 52312529--52312614 Score: 75
Period size: 9 Copynumber: 9.4 Consensus size: 9
52312519 TTTTGTTAAA
*
52312529 AATTACCCT
1 AATTACCCG
*
52312538 AATTACCCA
1 AATTACCCG
*
52312547 AATTACTCG
1 AATTACCCG
52312556 AATTACCCG
1 AATTACCCG
52312565 AATTGA-CCG
1 AATT-ACCCG
*
52312574 AATTAACCG
1 AATTACCCG
**
52312583 AATTACCAAA
1 AATTACC-CG
*
52312593 AAATACCCG
1 AATTACCCG
*
52312602 AATTACCCA
1 AATTACCCG
52312611 AATT
1 AATT
52312615 TTTTTTATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
8 1 0.02
9 54 0.87
10 7 0.11
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:52319878 original size:110 final size:110
Alignment explanation
Indices: 52319683--52319903 Score: 406
Period size: 110 Copynumber: 2.0 Consensus size: 110
52319673 TATCGATTAT
*
52319683 TTTACCCCAAGTATTGATACTCGTGCTATGGTATCAATATCAAATTATGATACTGACTTCCTGCA
1 TTTACCCCAAGTATTGATACTCGTGCTATGGTATCAATATCAAATTACGATACTGACTTCCTGCA
52319748 CTTTCAAAAATCATGAAGGTATCATTTTTAAAACCTGAATATCAA
66 CTTTCAAAAATCATGAAGGTATCATTTTTAAAACCTGAATATCAA
* *
52319793 TTTACCCCAAGTATTGATGCTCGTGCTATGGTATCAATATCAAATTACGTTACTGACTTCCTGCA
1 TTTACCCCAAGTATTGATACTCGTGCTATGGTATCAATATCAAATTACGATACTGACTTCCTGCA
*
52319858 CTTTCAAAAATCATGGAGGTATCATTTTTAAAACCTGAATATCAA
66 CTTTCAAAAATCATGAAGGTATCATTTTTAAAACCTGAATATCAA
52319903 T
1 T
52319904 ATATCTGCGC
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (110 bp):
TTTACCCCAAGTATTGATACTCGTGCTATGGTATCAATATCAAATTACGATACTGACTTCCTGCA
CTTTCAAAAATCATGAAGGTATCATTTTTAAAACCTGAATATCAA
Found at i:52327271 original size:32 final size:32
Alignment explanation
Indices: 52327232--52327294 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
52327222 TATCTAATCT
*
52327232 CACCGCCACCGT-TGTTTTTACACTAACCACAC
1 CACCGCCACC-TCTATTTTTACACTAACCACAC
52327264 CACCGCCACCTCTATTTTTACACTAACCACA
1 CACCGCCACCTCTATTTTTACACTAACCACA
52327295 GCTAAACGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.27, C:0.41, G:0.06, T:0.25
Consensus pattern (32 bp):
CACCGCCACCTCTATTTTTACACTAACCACAC
Found at i:52336320 original size:56 final size:56
Alignment explanation
Indices: 52336234--52336346 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
52336224 TTCAACACAC
*
52336234 TTTGTCAACCAAAACTCATCGGCCCAGGGGGTTTGATACTCTAATCACAAACTCAG
1 TTTGTCAACCAAAACACATCGGCCCAGGGGGTTTGATACTCTAATCACAAACTCAG
52336290 TTTGTCAACCAAAACACATCGGCCCAGGGGGTTTGATACTCTAATCACAAACTCAG
1 TTTGTCAACCAAAACACATCGGCCCAGGGGGTTTGATACTCTAATCACAAACTCAG
52336346 T
1 T
52336347 AGACTTAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (56 bp):
TTTGTCAACCAAAACACATCGGCCCAGGGGGTTTGATACTCTAATCACAAACTCAG
Found at i:52339431 original size:8 final size:8
Alignment explanation
Indices: 52339418--52339444 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
52339408 TGAACCTCTC
52339418 ATATACAT
1 ATATACAT
52339426 ATATACAT
1 ATATACAT
52339434 ATATACAT
1 ATATACAT
52339442 ATA
1 ATA
52339445 CATACATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATACAT
Found at i:52342660 original size:18 final size:19
Alignment explanation
Indices: 52342639--52342674 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52342629 ACTTAGACGT
52342639 TTTAATTA-CTTTAGTTTA
1 TTTAATTATCTTTAGTTTA
*
52342657 TTTAATTATGTTTAGTTT
1 TTTAATTATCTTTAGTTT
52342675 CTTACAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTAATTATCTTTAGTTTA
Found at i:52347170 original size:14 final size:14
Alignment explanation
Indices: 52347151--52347184 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
52347141 TTTGTGGTTC
52347151 ATGTTTTTAAGTAT
1 ATGTTTTTAAGTAT
52347165 ATG-TTTTAAGTAT
1 ATGTTTTTAAGTAT
*
52347178 CTGTTTT
1 ATGTTTT
52347185 ACCTTCTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (14 bp):
ATGTTTTTAAGTAT
Found at i:52347173 original size:13 final size:13
Alignment explanation
Indices: 52347155--52347185 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52347145 TGGTTCATGT
52347155 TTTTAAGTATATG
1 TTTTAAGTATATG
*
52347168 TTTTAAGTATCTG
1 TTTTAAGTATATG
52347181 TTTTA
1 TTTTA
52347186 CCTTCTGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (13 bp):
TTTTAAGTATATG
Found at i:52347823 original size:24 final size:22
Alignment explanation
Indices: 52347783--52347835 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
52347773 ACAATACGAA
* *
52347783 AAAATTATTTTTTACCAACTTT
1 AAAATTTTTTTTTACCAAATTT
52347805 AAAATTTTTTTATTAACCAAATTT
1 AAAATTTTTTT-TT-ACCAAATTT
52347829 AAAATTT
1 AAAATTT
52347836 AAATATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 10 0.37
23 2 0.07
24 15 0.56
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATTTTTTTTTACCAAATTT
Found at i:52347842 original size:24 final size:24
Alignment explanation
Indices: 52347796--52347844 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52347786 ATTATTTTTT
* ***
52347796 ACCAACTTTAAAATTTTTTTATTA
1 ACCAAATTTAAAATTTAAATATTA
52347820 ACCAAATTTAAAATTTAAATATTA
1 ACCAAATTTAAAATTTAAATATTA
52347844 A
1 A
52347845 AATTTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (24 bp):
ACCAAATTTAAAATTTAAATATTA
Found at i:52347846 original size:14 final size:13
Alignment explanation
Indices: 52347823--52347857 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
52347813 TTTATTAACC
52347823 AAATTTAAAATTT
1 AAATTTAAAATTT
52347836 AAATATTAAAATTT
1 AAAT-TTAAAATTT
*
52347850 AATTTTAA
1 AAATTTAA
52347858 GTAAGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:52348208 original size:26 final size:26
Alignment explanation
Indices: 52348178--52348231 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
52348168 CTCAAACTAG
52348178 AATCTAGATATCAAATTGGTCTCTAT
1 AATCTAGATATCAAATTGGTCTCTAT
* *
52348204 AATCTAGATTTTAAATTGGTCTCTAT
1 AATCTAGATATCAAATTGGTCTCTAT
52348230 AA
1 AA
52348232 ATTTTGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (26 bp):
AATCTAGATATCAAATTGGTCTCTAT
Found at i:52349967 original size:35 final size:36
Alignment explanation
Indices: 52349919--52349987 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
52349909 ATTTGTTAGA
52349919 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
52349955 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
52349988 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:52350743 original size:75 final size:75
Alignment explanation
Indices: 52350620--52350770 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
52350610 ATGTATCTTC
52350620 ATCTGGCACATCCAAACGTAAAAGAAAAAGTGGTCAAGAAAGTCTCGTTGATGAACAAATTAAAT
1 ATCTGGCACATCCAAACGTAAAAGAAAAAGTGGTCAAGAAAGTCTCGTTGATGAACAAATTAAAT
52350685 TTGTGGGTGA
66 TTGTGGGTGA
52350695 ATCTGGCACATCCAAACGTAAAAGAAAAAGTGGTCAAGAAAGTCTCGTTGATGAACAAATTAAAT
1 ATCTGGCACATCCAAACGTAAAAGAAAAAGTGGTCAAGAAAGTCTCGTTGATGAACAAATTAAAT
52350760 TTGTGGGTGA
66 TTGTGGGTGA
52350770 A
1 A
52350771 CAACTTGGCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (75 bp):
ATCTGGCACATCCAAACGTAAAAGAAAAAGTGGTCAAGAAAGTCTCGTTGATGAACAAATTAAAT
TTGTGGGTGA
Found at i:52351122 original size:72 final size:72
Alignment explanation
Indices: 52351005--52351148 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
52350995 TTGATACATT
*
52351005 TATGTGGTGTAATATTATGTACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
52351070 TTGGATA
66 TTGGATA
*
52351077 TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
52351142 TTGGATA
66 TTGGATA
52351149 ATATTATTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:52351386 original size:12 final size:12
Alignment explanation
Indices: 52351315--52351386 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
52351305 AAATCATTGC
52351315 AATATATGTAAA
1 AATATATGTAAA
* * **
52351327 AACA-ATTTATT
1 AATATATGTAAA
52351338 AATATAT-TAATA
1 AATATATGTAA-A
* **
52351350 AATATATATATT
1 AATATATGTAAA
52351362 AATATATGT-AA
1 AATATATGTAAA
52351373 AATATATGTAAA
1 AATATATGTAAA
52351385 AA
1 AA
52351387 CAACTTTTCC
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
11 18 0.41
12 24 0.55
13 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (12 bp):
AATATATGTAAA
Found at i:52351439 original size:32 final size:33
Alignment explanation
Indices: 52351398--52351482 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
52351388 AACTTTTCCG
* *
52351398 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACAGCA
* *
52351430 GAAAATATTTTACA-CAGATTTACCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACAGCA
* *
52351462 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
52351483 ATTTTACAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACAGCA
Found at i:52351521 original size:34 final size:35
Alignment explanation
Indices: 52351463--52351529 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
52351453 CAAACAGCAG
52351463 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
52351498 AAAATATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
52351530 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:52354881 original size:39 final size:39
Alignment explanation
Indices: 52354789--52355037 Score: 254
Period size: 39 Copynumber: 6.4 Consensus size: 39
52354779 GGATCTTCGT
* * * **
52354789 TGATACACAAGTTATCCATAAGCTCACAGAGGAGCTTCCC
1 TGATACACAACTTATCC-TTAGCTCACGGAGGAGCTTTGC
* * * *
52354829 TGATA-ACACCTTATCCTTCGCTCACGCATGAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
* * * *
52354867 TGATACACAGCTTATTCATAAGCTCACAGG-GGAGATTTGC
1 TGATACACAACTTA-TCCTTAGCTCAC-GGAGGAGCTTTGC
*
52354907 TGATACACAACTTGTCCTTAGCTCACGGA-GAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
* * * *
52354945 TGATACACAACTTATCCATAAGCTTAAGG-GTAGCTTTGC
1 TGATACACAACTTATCC-TTAGCTCACGGAGGAGCTTTGC
* *
52354984 TGATACACAACTTCTCCTTAGCTCATGGAGGAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
52355023 TGATACACAACTTAT
1 TGATACACAACTTAT
52355038 AAAGCCGTTC
Statistics
Matches: 170, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
38 54 0.32
39 81 0.48
40 34 0.20
41 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (39 bp):
TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
Found at i:52354887 original size:78 final size:77
Alignment explanation
Indices: 52354735--52355037 Score: 324
Period size: 78 Copynumber: 3.8 Consensus size: 77
52354725 AAGCTTGCAT
* * * * * *
52354735 AGGGAGCTTTGCTGGTACACAAGTTCATCACTTAAGCTCATATGG-GATCTTCGTTGATACACAA
1 AGGGAGCTTTGCTGATACACAACTT-ATC-CTT-AGCTC--ACGGAGAGCTTTGCTGATACACAA
*
52354799 GTTATCCATAAGCTCAC
61 CTTATCCATAAGCTCAC
** * * * *
52354816 AGAGGAGCTTCCCTGATA-ACACCTTATCCTTCGCTCACGCATGAGCTTTGCTGATACACAGCTT
1 AG-GGAGCTTTGCTGATACACAACTTATCCTTAGCTCACGGA-GAGCTTTGCTGATACACAACTT
*
52354880 ATTCATAAGCTCAC
64 ATCCATAAGCTCAC
* *
52354894 AGGGGAGATTTGCTGATACACAACTTGTCCTTAGCTCACGGAGAGCTTTGCTGATACACAACTTA
1 A-GGGAGCTTTGCTGATACACAACTTATCCTTAGCTCACGGAGAGCTTTGCTGATACACAACTTA
*
52354959 TCCATAAGCTTA-
65 TCCATAAGCTCAC
* *
52354971 AGGGTAGCTTTGCTGATACACAACTTCTCCTTAGCTCATGGAGGAGCTTTGCTGATACACAACTT
1 AGGG-AGCTTTGCTGATACACAACTTATCCTTAGCTCACGGA-GAGCTTTGCTGATACACAACTT
52355036 AT
64 AT
52355038 AAAGCCGTTC
Statistics
Matches: 188, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
76 5 0.03
77 35 0.19
78 103 0.55
79 23 0.12
80 3 0.02
81 7 0.04
82 12 0.06
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (77 bp):
AGGGAGCTTTGCTGATACACAACTTATCCTTAGCTCACGGAGAGCTTTGCTGATACACAACTTAT
CCATAAGCTCAC
Found at i:52362987 original size:42 final size:42
Alignment explanation
Indices: 52362905--52362992 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
52362895 CACCATATTG
*
52362905 TGGACAAGCCACCAGTAATTGCAGATAAACTGCCAAAAATATA
1 TGGACAAGCCACCAG-AATTGCAGATAAACTGCCAAAAATACA
* * * *
52362948 TGGACAAGCCACTAG-ATCTGTAGATAAACTGCTAGAAATACA
1 TGGACAAGCCACCAGAAT-TGCAGATAAACTGCCAAAAATACA
52362990 TGG
1 TGG
52362993 TTAAACTACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.05
42 23 0.59
43 14 0.36
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (42 bp):
TGGACAAGCCACCAGAATTGCAGATAAACTGCCAAAAATACA
Found at i:52378817 original size:35 final size:35
Alignment explanation
Indices: 52378773--52378857 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
52378763 ACCTACTTTT
*
52378773 AAAGAGTTGGGATAGAC-CACTCTATGCCAACCTTAA
1 AAAG-GTTGGGATAGACTCA-TCTAAGCCAACCTTAA
* * *
52378809 AAAGGTTGGGATTGACTCATCTAAGGCAACTTTAA
1 AAAGGTTGGGATAGACTCATCTAAGCCAACCTTAA
*
52378844 ACAGGTTGGGATAG
1 AAAGGTTGGGATAG
52378858 GCCTTACCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 36 0.86
36 6 0.14
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (35 bp):
AAAGGTTGGGATAGACTCATCTAAGCCAACCTTAA
Found at i:52383696 original size:82 final size:82
Alignment explanation
Indices: 52383585--52384084 Score: 786
Period size: 82 Copynumber: 6.1 Consensus size: 82
52383575 CATGGGGATG
* * ** * *
52383585 AGATTTGTGTTTTTAGTCTGCTCCACTACTATTTAGGGAGATAAGACTGGATGTGATCTGCTCCA
1 AGATCTGTGGTTTT-GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCA
*
52383650 CTACTACTTAGGGAGATA
65 CTACTGCTTAGGGAGATA
*
52383668 AGATCTGTGGTTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
1 AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
52383733 TACTGCTTAGGGAGATA
66 TACTGCTTAGGGAGATA
* * *
52383750 AGATCTGTGGTTTCGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
1 AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
*
52383815 TATTGCTTAGGGAGATA
66 TACTGCTTAGGGAGATA
52383832 AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
1 AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
* * *
52383897 TATTACTTAGAGAGATA
66 TACTGCTTAGGGAGATA
* * * *
52383914 AGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCAC
1 AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
*
52383979 TACTGCTTAGAGAGATA
66 TACTGCTTAGGGAGATA
* *
52383996 AGATCTGTGGTTTTGTCTGCTCCACTACTACTTAGGGAGATAAGACTGGATGCGATCTGCTCCAC
1 AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
52384061 TACTGCTTAGGGAGATA
66 TACTGCTTAGGGAGATA
52384078 AGA-CTGT
1 AGATCTGT
52384085 AATCTTCGAT
Statistics
Matches: 388, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
81 4 0.01
82 372 0.96
83 12 0.03
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (82 bp):
AGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCAC
TACTGCTTAGGGAGATA
Found at i:52384321 original size:134 final size:133
Alignment explanation
Indices: 52384129--52384768 Score: 885
Period size: 134 Copynumber: 4.8 Consensus size: 133
52384119 TAAGATTACT
* * *
52384129 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATATTCGATCTGCTTCTCTG
1 GGCTTCAATGTACTCCACTGT-A-GTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTG
* * *
52384194 CCAAATATAGGAAGGCAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGA
64 CCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC-AATACAGGGAGATAGA
52384259 GTTATC
128 GTTATC
* * * *
52384265 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTCTTTACC
1 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
* *
52384330 AAATACAGGAAGGCAAGATCTGCAATCTTTAATCTATTCCACTGCCAA-CCAGGGAGATAGAGTT
66 AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAATACAGGGAGATAGAGTT
52384394 ATC
131 ATC
* * * *
52384397 GGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACT-
1 GGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTG
* *** * * ** * ** *
52384461 ACTGCT-TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CTGT-CTAGGGAGACAGA
64 CCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAATAC-AGGGAGATAGA
52384523 GTTATC
128 GTTATC
52384529 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
1 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
*
52384594 AAATACAGGAAGGCAAGATCTGCAATCTTCAATTTATTCCACTGCCAAATACAGGGAGATAGAGT
66 AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC-AATACAGGGAGATAGAGT
52384659 TATC
130 TATC
* *
52384663 GGCTTCAATGTACTCCACTATAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCC
1 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
*
52384728 AAATACAGGAAGGTAAGATCTGCAATCTTCAATCTACTTCC
66 AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA-TTCC
52384769 TACCAATATA
Statistics
Matches: 441, Mismatches: 53, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
130 34 0.08
131 4 0.01
132 148 0.34
133 5 0.01
134 223 0.51
135 6 0.01
136 21 0.05
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (133 bp):
GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAATACAGGGAGATAGAGTT
ATC
Found at i:52384472 original size:44 final size:44
Alignment explanation
Indices: 52384424--52384518 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
52384414 CTGTAGTCAC
* * *
52384424 AGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTG-CTT
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTACTGTC-T
* * *
52384468 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGTCT
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTACTGTCT
52384512 AGGGAGA
1 AGGGAGA
52384519 CAGAGTTATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
44 43 0.98
45 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTACTGTCT
Found at i:52384585 original size:264 final size:269
Alignment explanation
Indices: 52384129--52384768 Score: 873
Period size: 264 Copynumber: 2.4 Consensus size: 269
52384119 TAAGATTACT
* * * * * *
52384129 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATATTCGATCTGCTTCTCTG
1 GGCTTCAATGTACTCCACTGTAGTC-CAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTG
* * *
52384194 CCAAATATAGGAAGGCAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGA
65 ACAAATATAGGAAGACAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGACAGA
52384259 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTC
130 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTC
* * *
52384324 TTTACCAAATACAGGAAGGCAAGATCTGCAATCTTTAATCTATTCCACTGCC-AA-CCAGGGAGA
195 TCTACCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGA
52384387 TAGAGTTATC
260 TAGAGTTATC
*
52384397 GGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACT-
1 GGCTTCAATGTACTCCACTGTAGTC-CAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTG
*** * * * **
52384461 ACTGCT-TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-C-TGT-CTAGGGAGACAG
65 ACAAATATAGGAAGACAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATAC-AGGGAGACAG
* *
52384522 AGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
129 AGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTT
* *
52384587 CTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATTTATTCCACTGCCAAATACAGGGAG
194 CTCTACCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAG
52384652 ATAGAGTTATC
259 ATAGAGTTATC
* * * * *
52384663 GGCTTCAATGTACTCCACTATAGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGC
1 GGCTTCAATGTACTCCACTGTAGTCCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTGA
* ** * *
52384727 CAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTACTTCC
66 CAAATATAGGAAGACAAAATCTGTAATCTTCAATCTA-TTCC
52384769 TACCAATATA
Statistics
Matches: 327, Mismatches: 39, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
263 1 0.00
264 156 0.48
265 5 0.02
266 103 0.31
267 6 0.02
268 56 0.17
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (269 bp):
GGCTTCAATGTACTCCACTGTAGTCCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTGA
CAAATATAGGAAGACAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGACAGAG
TTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTCT
CTACCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGAT
AGAGTTATC
Found at i:52384800 original size:44 final size:45
Alignment explanation
Indices: 52384701--52385151 Score: 346
Period size: 44 Copynumber: 10.2 Consensus size: 45
52384691 GAGGTAAAAT
* * * * * ** *
52384701 CTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGAT
1 CTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGACAAGAC
* * *
52384747 CTGCAATCTTCAATCTACTTC-CTACCAATATAGGAAGACAGGAC
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * *
52384791 CTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * * * *
52384835 TTACTTTCTTCGATCCAC-TCCCTACCAATATAGGGAGACAGGAC
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * *
52384879 CTGTTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * *
52384923 CTGC-ATCTTGGATCCACTTC-CTATCAATATAGGAAGACATGAC
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * * * *
52384966 CAGCCATCTTCGATCTACTTCAC-GCCAATACATGAAGATAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * * * *
52385010 CTTCTTTCTTTGATCTACTTCGCTACCAGTATGGGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* *
52385055 CTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGAC
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * *
52385098 CTGCTATTTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
*
52385142 CTGCTTTCTT
1 CTGCTATCTT
52385152 TTATGACTTC
Statistics
Matches: 309, Mismatches: 87, Indels: 20
0.74 0.21 0.05
Matches are distributed among these distances:
42 1 0.00
43 58 0.19
44 204 0.66
45 28 0.09
46 18 0.06
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (45 bp):
CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
Found at i:52384821 original size:88 final size:88
Alignment explanation
Indices: 52384701--52385118 Score: 446
Period size: 88 Copynumber: 4.7 Consensus size: 88
52384691 GAGGTAAAAT
* * * ** * * *
52384701 CTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTACT
1 CTGCCATCTTCGATCTACTTCAC-GCC-AATACATGAAGACAAGATCTGCTATCTTCGATCCACT
52384766 TCCTACCAATATAGGAAGACAGGAC
64 TCCTACCAATATAGGAAGACAGGAC
* * * * *
52384791 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTACTTTCTTCGATCCACTCC
1 CTGCCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCCACTTC
*
52384856 CTACCAATATAGGGAGACAGGAC
66 CTACCAATATAGGAAGACAGGAC
** *
52384879 CTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-ATCTTGGATCCACTTC
1 CTGCCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCCACTTC
* *
52384943 CTATCAATATAGGAAGACATGAC
66 CTACCAATATAGGAAGACAGGAC
* * * * * *
52384966 CAGCCATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTTCTTTCTTTGATCTACTTC
1 CTGCCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCCACTTC
* * * *
52385031 GCTACCAGTATGGGAAGACAAGAT
66 -CTACCAATATAGGAAGACAGGAC
* * * * * * * *
52385055 CTG-CATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATTTTCGATCTACTT
1 CTGCCATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTCGATCCACTT
52385118 C
65 C
52385119 ACGCCAATAC
Statistics
Matches: 277, Mismatches: 48, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
87 77 0.28
88 157 0.57
89 23 0.08
90 20 0.07
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (88 bp):
CTGCCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCCACTTC
CTACCAATATAGGAAGACAGGAC
Found at i:52385065 original size:175 final size:178
Alignment explanation
Indices: 52384699--52385093 Score: 491
Period size: 175 Copynumber: 2.2 Consensus size: 178
52384689 GGGAGGTAAA
* * ** *
52384699 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTA
1 ATCTGCCATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCCA
* *
52384764 CTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
66 CTTCCTACCAATATAGGAAGACAGGACCAGCCATCTTCGATCTACTTCACGCCAATACATGAAGA
*
52384829 CAAGATTTACTTTCTTCGATCCACTCCCTACCAATATAGGGAGACAGG
131 CAAGATTTACTTTCTTCGATCCACTCCCTACCAATATAGGGAGACAAG
* ** * **
52384877 ACCTGTTATCTTCGATCTACTTCAC-GCC-AATACATGAAGACAAGATCTGC-ATCTTGGATCCA
1 ATCTGCCATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCCA
* *
52384939 CTTCCTATCAATATAGGAAGACATGACCAGCCATCTTCGATCTACTTCACGCCAATACATGAAGA
66 CTTCCTACCAATATAGGAAGACAGGACCAGCCATCTTCGATCTACTTCACGCCAATACATGAAGA
* * * * *
52385004 TAAGATCTT-CTTTCTTTGATCTACTTCGCTACCAGTAT-GGGAAGACAAG
131 CAAGAT-TTACTTTCTTCGATCCAC-TCCCTACCAATATAGGG-AGACAAG
* * *
52385053 ATCTG-CATCTTCGATCCACTTC-CTACC-AATATAGGAAGACA
1 ATCTGCCATCTTCGATCTACTTCACTGCCAAATACAGGAAGACA
52385094 GGACCTGCTA
Statistics
Matches: 186, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
174 1 0.01
175 120 0.65
176 42 0.23
177 3 0.02
178 20 0.11
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (178 bp):
ATCTGCCATCTTCGATCTACTTCACTGCCAAATACAGGAAGACAAGATCTGCAATCTTCAATCCA
CTTCCTACCAATATAGGAAGACAGGACCAGCCATCTTCGATCTACTTCACGCCAATACATGAAGA
CAAGATTTACTTTCTTCGATCCACTCCCTACCAATATAGGGAGACAAG
Found at i:52385083 original size:132 final size:132
Alignment explanation
Indices: 52384912--52385152 Score: 410
Period size: 132 Copynumber: 1.8 Consensus size: 132
52384902 GCCAATACAT
* * *
52384912 GAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGACATGACCAGCCATCTTC
1 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCAGCCATCTTC
* *
52384977 GATCTACTTCACGCCAATACATGAAGATAAGATCTTCTTTCTTTGATCTACTTCGCTACCAGTAT
66 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCTACCAGTAT
52385042 GG
131 GG
* * *
52385044 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATTTTC
1 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCAGCCATCTTC
52385109 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTT
66 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTT
52385153 TATGACTTCA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 101 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (132 bp):
GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCAGCCATCTTC
GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCTACCAGTAT
GG
Found at i:52388078 original size:62 final size:62
Alignment explanation
Indices: 52387989--52388157 Score: 258
Period size: 62 Copynumber: 2.8 Consensus size: 62
52387979 ACTTTTGGAT
**
52387989 TTTAGGAAATTTATTATATAAAATGAAATGTAATGTTGATGCATGAATGCGTATTTTTGAAG
1 TTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATGCGTATTTTTGAAG
* *
52388051 TTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATGCGTATTTTTGGAT
1 TTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATGCGTATTTTTGAAG
*
52388113 TTTAGGAAA--T-TTAT-TGC-ATGCAATGTAATGTTGATGCATGAATGC
1 TTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATGC
52388158 AAAAAAGAGA
Statistics
Matches: 102, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
57 27 0.26
58 3 0.03
59 4 0.04
60 1 0.01
62 67 0.66
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (62 bp):
TTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATGCGTATTTTTGAAG
Found at i:52395405 original size:15 final size:15
Alignment explanation
Indices: 52395385--52395417 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52395375 AATCATTGGG
52395385 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
52395400 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
52395415 TTG
1 TTG
52395418 TCAACAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:52401041 original size:19 final size:19
Alignment explanation
Indices: 52401013--52401054 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
52401003 CATGTATAAA
52401013 TTTTAGTTTTTTATTTCAT
1 TTTTAGTTTTTTATTTCAT
* *
52401032 TTTTATTTTTTTATTTTAT
1 TTTTAGTTTTTTATTTCAT
52401051 TTTT
1 TTTT
52401055 CTTATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTAGTTTTTTATTTCAT
Found at i:52401414 original size:7 final size:7
Alignment explanation
Indices: 52401402--52401499 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
52401392 CTGACCCTTG
52401402 AAACCCT
1 AAACCCT
52401409 AAACCCT
1 AAACCCT
52401416 AAATCCCT
1 AAA-CCCT
*
52401424 AACCCCT
1 AAACCCT
*
52401431 AACCCCT
1 AAACCCT
52401438 AAATCCCCCT
1 AAA---CCCT
52401448 -AACCCTT
1 AAACCC-T
* *
52401455 AAAGCAT
1 AAACCCT
*
52401462 AACCCCT
1 AAACCCT
*
52401469 AACCCCT
1 AAACCCT
* *
52401476 AAATCTT
1 AAACCCT
*
52401483 AAATCCT
1 AAACCCT
52401490 AAACCCT
1 AAACCCT
52401497 AAA
1 AAA
52401500 TCCATACCCC
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
6 3 0.04
7 55 0.75
8 9 0.12
9 2 0.03
10 4 0.05
ACGTcount: A:0.39, C:0.41, G:0.01, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:52401427 original size:21 final size:21
Alignment explanation
Indices: 52401403--52401499 Score: 72
Period size: 21 Copynumber: 4.4 Consensus size: 21
52401393 TGACCCTTGA
52401403 AACCCTAAACCCTAAATCCCT
1 AACCCTAAACCCTAAATCCCT
*
52401424 AACCCCTAACCCCTAAATCCCCCT
1 AA-CCCTAAACCCTAAAT--CCCT
* * *
52401448 AACCCTTAAAGCAT-AACCCCT
1 AACCC-TAAACCCTAAATCCCT
* *
52401469 AACCCCTAAATCTTAAAT-CCT
1 AA-CCCTAAACCCTAAATCCCT
52401490 AAACCCTAAA
1 -AACCCTAAA
52401500 TCCATACCCC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
21 24 0.39
22 21 0.34
23 5 0.08
24 11 0.18
ACGTcount: A:0.38, C:0.41, G:0.01, T:0.20
Consensus pattern (21 bp):
AACCCTAAACCCTAAATCCCT
Found at i:52402066 original size:41 final size:41
Alignment explanation
Indices: 52402021--52402174 Score: 195
Period size: 41 Copynumber: 3.8 Consensus size: 41
52402011 TTTTATTATT
* *
52402021 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* ** *
52402062 ATTAGCGACGCTACTTC-AAAACGCCGCTAAAGCCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
52402102 ATTAGCGGCACTTTTTCAAAAACACCGCTAAA-GCCCTGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC-GAGC
* *
52402143 AGTAGCAGCGCTTTTTCAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
52402175 AGCCTATTTT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 36 0.38
41 59 0.62
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:52402161 original size:81 final size:82
Alignment explanation
Indices: 52402021--52402174 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 82
52402011 TTTTATTATT
* ** * *
52402021 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCTCGAGCATTAGCGACGCTACTTC-AAAACG
1 ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCCTCGAGCAGTAGCGACGCTACTTCAAAAACG
52402085 CCGCTAAAGCCCCGAGC
66 CCGCTAAAGCCCCGAGC
**
52402102 ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCC-CTGAGCAGTAGC-AGCGCTTTTTCAAAAA
1 ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCCTC-GAGCAGTAGCGA-CGCTACTTCAAAAA
52402165 CGCCGCTAAA
64 CGCCGCTAAA
52402175 AGCCTATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
80 2 0.03
81 47 0.75
82 14 0.22
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (82 bp):
ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCCTCGAGCAGTAGCGACGCTACTTCAAAAACG
CCGCTAAAGCCCCGAGC
Found at i:52403434 original size:37 final size:37
Alignment explanation
Indices: 52403384--52403468 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
52403374 TTGAAGCCTA
52403384 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
1 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
52403421 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
1 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
*
52403458 TGAAGATGAGG
1 TGGAGA-GAGG
52403469 CTTGGAGCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 42 0.91
38 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.34, T:0.24
Consensus pattern (37 bp):
TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
Found at i:52404777 original size:3 final size:3
Alignment explanation
Indices: 52404769--52404806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
52404759 AATACACCAC
52404769 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
52404807 AGTAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:52425594 original size:50 final size:50
Alignment explanation
Indices: 52425517--52425657 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 50
52425507 TTGACGCTAA
* * * **
52425517 TAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCATTGTAGTGGAG
1 TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCATTGTAGCAGAG
**
52425567 TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGTGTTGTAGCAGAG
1 TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCATTGTAGCAGAG
*
52425617 TAGATTGAAGCCACGACGGTGAATCTTA-TCTCCCTAGCATT
1 TAGATTGAAGCCACAACGGTGAATCTTACT-TCCCTAGCATT
52425658 AAGGCTTGGA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 79 0.99
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (50 bp):
TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCATTGTAGCAGAG
Found at i:52425783 original size:50 final size:50
Alignment explanation
Indices: 52425729--52426008 Score: 165
Period size: 50 Copynumber: 5.6 Consensus size: 50
52425719 GGTATTACAA
*
52425729 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCTCTGACGGTGTAG
1 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
* ** * * *** **
52425779 TGGAACAGATTGAAGTTACGACGGTGAATCTGT--TTCCCTGATATTACAG
1 TGGAATAGATTGAAGCCACAACAGTGAATCT-TACTTCCCTGACGGTGTAG
**
52425828 TGGAATAGATTGAAGCCACAAC-GACAAATCTTACTTCCCT-AGCGGTGTAG
1 TGGAATAGATTGAAGCCACAACAG-TGAATCTTACTTCCCTGA-CGGTGTAG
* * * *** * ** * *
52425878 TGGAATAGATTGAAGCTACGATAGTGAATCTGGTTTCCCCGACATTGCAA
1 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
** * ** * * * *
52425928 TTAAAAAGATTGAAGCCACAATGGTGAATCTTACCTCCCTGGCGATGCA-
1 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
* * * *
52425977 TGGAATAGATTAAAGTCACAACGGCGAATCTT
1 TGGAATAGATTGAAGCCACAACAGTGAATCTT
52426009 GTTTCCCCTA
Statistics
Matches: 167, Mismatches: 56, Indels: 15
0.70 0.24 0.06
Matches are distributed among these distances:
48 2 0.01
49 59 0.35
50 103 0.62
51 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (50 bp):
TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
Found at i:52426022 original size:99 final size:100
Alignment explanation
Indices: 52425735--52426041 Score: 318
Period size: 99 Copynumber: 3.1 Consensus size: 100
52425725 ACAATGGAAT
* * * * *
52425735 AGATTGAAGCCACAACAGTGAATCTTACTTCTCTGACGGTGTAGTGGAACAGATTGAAGTTACGA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
* * ** *
52425800 CGGTGAATC-TGTTT-CCCTGATATTACAGTGGAAT
66 CGGTGAATCTTGTTTCCCCT-ACATTGCAGTTAAAA
*** *
52425834 AGATTGAAGCCACAACGACAAATCTTACTTCCCTAGCGGTGTAGTGGAATAGATTGAAG-CTACG
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTC-ACG
** * * *
52425898 ATAGTGAATCTGGTTTCCCCGACATTGCAATTAAAA
65 ACGGTGAATCTTGTTTCCCCTACATTGCAGTTAAAA
* * * * * *
52425934 AGATTGAAGCCACAATGGTGAATCTTACCTCCCTGGCGATGCA-TGGAATAGATTAAAGTCACAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
*
52425998 CGGCGAATCTTGTTTCCCCTACATTGCAGTTAAACA
66 CGGTGAATCTTGTTTCCCCTACATTGCAGTTAAA-A
52426034 A-ATTGAAG
1 AGATTGAAG
52426042 AAAACAATCC
Statistics
Matches: 168, Mismatches: 35, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
99 114 0.68
100 51 0.30
101 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
CGGTGAATCTTGTTTCCCCTACATTGCAGTTAAAA
Found at i:52426106 original size:42 final size:42
Alignment explanation
Indices: 52426052--52426353 Score: 194
Period size: 44 Copynumber: 7.1 Consensus size: 42
52426042 AAAACAATCC
*
52426052 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCT
** * *** ***
52426094 TATCTCTTTGAAGTTGTAGAATAGCAGA-TCGCATCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-CAGATCT
*
52426135 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAAT-A-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT----AAAATCAGATCT
* *
52426179 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCT
* ** ** *
52426221 TATCTCTCTGAAGTTGC-GAAGAGCAGA-CCACATACAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-CAGATCT
* *
52426261 TATCTTCCTGAAGTTGCAGTGGAATAGACAGA--AGAAATCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGG---AG-CAGATTA-AAATCAGATCT
* **
52426305 TATCTCCCTGAAGTTTCAGTGGAGTGGATTAAAAAAT-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT--AAAATCAGATCT
52426348 TATCTC
1 TATCTC
52426354 TATAAATTAT
Statistics
Matches: 197, Mismatches: 41, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
40 28 0.14
41 43 0.22
42 45 0.23
43 13 0.07
44 59 0.30
45 7 0.04
46 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCT
Found at i:52426319 original size:126 final size:127
Alignment explanation
Indices: 52426038--52426354 Score: 451
Period size: 126 Copynumber: 2.5 Consensus size: 127
52426028 TAAACAAATT
* *
52426038 GAAGAAAACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTTT
1 GAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
* * * * * **
52426103 GAAGTTGTAGAATAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
66 GAAGTTGTAGAAGAGCAGACCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACA
*
52426165 GAAGAAAAT-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCAGATCTTATCTCTC
1 GAAG-AAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTC
* * *
52426229 TGAAGTTG-CGAAGAGCAGACCACATACAGTCTTATCTTCCTGAAGTTGCAGTGGAATAGACA
65 TGAAGTTGTAGAAGAGCAGACCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACA
* *
52426291 GAAGAAATCAATCCTATCTCCCTGAAGTTTCAGTGGAGTGGATTAAAAAAT-AGATCTTATCTCT
1 GAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT--AAAATCAGATCTTATCTCT
52426355 ATAAATTATA
Statistics
Matches: 170, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
125 4 0.02
126 81 0.48
127 78 0.46
128 7 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (127 bp):
GAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
GAAGTTGTAGAAGAGCAGACCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACA
Found at i:52427951 original size:25 final size:24
Alignment explanation
Indices: 52427905--52427951 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
52427895 AGTTACAATT
*
52427905 ATTATTATTGTATTATATATCACC
1 ATTATTATTGTATTATAGATCACC
* *
52427929 ATTATTTTTAGTATTATCGATCA
1 ATTATTATT-GTATTATAGATCA
52427952 TTGTTATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTATTATTGTATTATAGATCACC
Found at i:52433808 original size:17 final size:18
Alignment explanation
Indices: 52433786--52433820 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52433776 GGTTCATGGC
*
52433786 AACGATA-CATCAAGTTT
1 AACGATACCATAAAGTTT
52433803 AACGATACCATAAAGTTT
1 AACGATACCATAAAGTTT
52433821 TTTGGCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
AACGATACCATAAAGTTT
Found at i:52435734 original size:21 final size:20
Alignment explanation
Indices: 52435682--52435724 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
52435672 ACGGGTTAGT
52435682 TTGACTATAATAGTTAATAAA
1 TTGA-TATAATAGTTAATAAA
*
52435703 TTGATCATAATAGTTCATAAA
1 TTGAT-ATAATAGTTAATAAA
52435724 T
1 T
52435725 AATATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (20 bp):
TTGATATAATAGTTAATAAA
Found at i:52441519 original size:3 final size:3
Alignment explanation
Indices: 52441511--52441536 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52441501 AGTGGCCGGT
52441511 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
52441537 TCCTTCTGGT
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:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:52444784 original size:36 final size:37
Alignment explanation
Indices: 52444744--52444816 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
52444734 ACTTTACTGC
* *
52444744 TTTCGATTAGAA-TGAGGGAAAATTCTGGCTTACTAT
1 TTTCGATTAGAATTCAGGGAAAATTCTGGATTACTAT
52444780 TTTCGATTAGAATTTTCAGGGAAAATTCTGGATTACT
1 TTTCGATTAGAA--TTCAGGGAAAATTCTGGATTACT
52444817 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 12 0.38
39 20 0.62
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (37 bp):
TTTCGATTAGAATTCAGGGAAAATTCTGGATTACTAT
Found at i:52452918 original size:7 final size:7
Alignment explanation
Indices: 52452908--52452932 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52452898 GTTTTAGTAA
52452908 TTAGATT
1 TTAGATT
52452915 TTAGATT
1 TTAGATT
52452922 TTAGATT
1 TTAGATT
52452929 TTAG
1 TTAG
52452933 TTAGATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
TTAGATT
Found at i:52454540 original size:49 final size:48
Alignment explanation
Indices: 52454442--52454538 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 48
52454432 TATAAAATAT
*
52454442 ATAAATATAAATATAAAAAAATTCAGAAACATATATATAATCTAGAAA
1 ATAAATATAAATATAAAAAAATTCAGAAACATATATATAATCTAAAAA
* *
52454490 ATAACATATAAATTATAAAAAAATTTATAAA-A-ATATGATAAT-TAAAAA
1 ATAA-ATATAAA-TATAAAAAAATTCAGAAACATATAT-ATAATCTAAAAA
52454538 A
1 A
52454539 ATTAGTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
48 14 0.33
49 13 0.30
50 16 0.37
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (48 bp):
ATAAATATAAATATAAAAAAATTCAGAAACATATATATAATCTAAAAA
Found at i:52455059 original size:20 final size:21
Alignment explanation
Indices: 52455036--52455077 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52455026 TATCATTAGA
52455036 AATTT-TAAAAAATCAAAAAT
1 AATTTATAAAAAATCAAAAAT
* *
52455056 AATTTATAAAAATTGAAAAAT
1 AATTTATAAAAAATCAAAAAT
52455077 A
1 A
52455078 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTTATAAAAAATCAAAAAT
Found at i:52458005 original size:18 final size:18
Alignment explanation
Indices: 52457979--52458023 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
52457969 ATGTGAGAAT
*
52457979 TGATGTTCACATTTTAAA
1 TGATGTTCACATTTCAAA
*
52457997 TGATATTCACATTTCAAA
1 TGATGTTCACATTTCAAA
52458015 TGATGTTCA
1 TGATGTTCA
52458024 AATTGATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TGATGTTCACATTTCAAA
Found at i:52458552 original size:72 final size:72
Alignment explanation
Indices: 52458447--52458618 Score: 233
Period size: 72 Copynumber: 2.4 Consensus size: 72
52458437 AACAACAATG
* * * * *
52458447 CTAAA-CTAGTTTTATCAATAGTTATTTACGTTTGGTTTTTGGATATTGAATTTATGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTG
52458511 ATTTAT-
66 ATTTATA
* * *
52458517 GTGTAATCTAGTTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACT
1 CT-AAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACT
52458582 GATTTATA
65 GATTTATA
*
52458590 CTAAAT-TAATTTTATCAATAGTTGTTTAT
1 CTAAATCTAGTTTTATCAATAGTTGTTTAT
52458619 ATATGATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 23 0.26
72 62 0.71
73 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.53
Consensus pattern (72 bp):
CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTG
ATTTATA
Found at i:52458641 original size:71 final size:72
Alignment explanation
Indices: 52458456--52458642 Score: 191
Period size: 72 Copynumber: 2.6 Consensus size: 72
52458446 GCTAAACTAG
* ** * * * * * * *
52458456 TTTTATCAATAGTTATTTACGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTATCTGA
*
52458521 AATCTAG
66 AATCTAA
* * * *
52458528 TTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTGATTTATACT-
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTAT-CTG
52458592 AAAT-TAA
65 AAATCTAA
*
52458599 TTTTATCAATAGTTGTTTATATATGAT-TTTGGATGTTCAAATTT
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATT-AAATTT
52458643 TTTCATAGGT
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
70 9 0.09
71 31 0.31
72 58 0.59
73 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTATCTGA
AATCTAA
Found at i:52460008 original size:15 final size:15
Alignment explanation
Indices: 52459988--52460019 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52459978 AGAAGGTGAT
52459988 GATGATGACGACGAC
1 GATGATGACGACGAC
*
52460003 GATGATGATGACGAC
1 GATGATGACGACGAC
52460018 GA
1 GA
52460020 CGATAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (15 bp):
GATGATGACGACGAC
Found at i:52460008 original size:18 final size:18
Alignment explanation
Indices: 52459985--52460030 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
52459975 TCGAGAAGGT
52459985 GATGATGATGACGACGAC
1 GATGATGATGACGACGAC
52460003 GATGATGATGACGACGAC
1 GATGATGATGACGACGAC
*
52460021 GATAATGATG
1 GATGATGATG
52460031 GTGATGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (18 bp):
GATGATGATGACGACGAC
Found at i:52460010 original size:21 final size:21
Alignment explanation
Indices: 52459984--52460042 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
52459974 GTCGAGAAGG
*
52459984 TGATGATGATGACGACGACGA
1 TGATGATGATGACGACGACAA
* *
52460005 TGATGATGACGACGACGATAA
1 TGATGATGATGACGACGACAA
* *
52460026 TGATGGTGATGATGACG
1 TGATGATGATGACGACG
52460043 GTGAATCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (21 bp):
TGATGATGATGACGACGACAA
Found at i:52464955 original size:40 final size:40
Alignment explanation
Indices: 52464918--52465103 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
52464908 GCTACTCGTT
* *
52464918 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
52464958 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
52464998 CAAATGCCTTCGGGACTTAACCCGGATTCAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
52465038 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
52465079 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
52465104 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 113 0.86
41 15 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:52465022 original size:80 final size:81
Alignment explanation
Indices: 52464885--52465103 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 81
52464875 AAATCACGTA
* * ** *
52464885 CCTTCGGAAT-TTAA-CCGGATATAG-CTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTA
1 CCTTCGG-ATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATT-
*
52464946 TAGTAACTCGCACAAATG
64 CAGTAACTCGCACAAATG
* * *
52464964 CCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCACAAATGCCTTCGGGACTTAACCCGGATTC
1 CCTTC-GGATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATTC
52465027 AGTAACTCGCACAAATG
65 AGTAACTCGCACAAATG
** * *
52465044 CCTTCGGATCTTAGTCCGGATATGGTCACCTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGA
52465104 CATCATTCAA
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
79 13 0.11
80 94 0.79
81 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (81 bp):
CCTTCGGATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATTCA
GTAACTCGCACAAATG
Found at i:52472929 original size:40 final size:40
Alignment explanation
Indices: 52472885--52473070 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
52472875 GCTACCCGTT
* * *
52472885 CAAATGGCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
52472925 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
**
52472965 CAAATGCCTTCAAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * **
52473005 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAACA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
52473046 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
52473071 CATCATTCAA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 2 0.02
40 112 0.88
41 14 0.11
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:52475037 original size:42 final size:40
Alignment explanation
Indices: 52474986--52475081 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
52474976 CTAAATCATG
*
52474986 TCCACATCAGCGCGATGTCAAG-GGACGTGTCAGCAAATCGCA
1 TCCACATCAGCGCGAT-T--AGCGGACGTGGCAGCAAATCGCA
* *
52475028 TCCACATCAGCGCGATTTGCTGACGTGGCAGCAAATCGCA
1 TCCACATCAGCGCGATTAGCGGACGTGGCAGCAAATCGCA
* *
52475068 TCCACGTAAGCGCG
1 TCCACATCAGCGCG
52475082 CTTTGTGGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.02
40 30 0.62
41 1 0.02
42 16 0.33
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (40 bp):
TCCACATCAGCGCGATTAGCGGACGTGGCAGCAAATCGCA
Found at i:52475064 original size:40 final size:40
Alignment explanation
Indices: 52475009--52475086 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
52474999 GATGTCAAGG
* *
52475009 GACGTGTCAGCAAATCGCATCCACATCAGCGCGATTTGCT
1 GACGTGGCAGCAAATCGCATCCACATAAGCGCGATTTGCT
* *
52475049 GACGTGGCAGCAAATCGCATCCACGTAAGCGCGCTTTG
1 GACGTGGCAGCAAATCGCATCCACATAAGCGCGATTTG
52475087 TGGTCATGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (40 bp):
GACGTGGCAGCAAATCGCATCCACATAAGCGCGATTTGCT
Found at i:52475100 original size:40 final size:40
Alignment explanation
Indices: 52475013--52475102 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
52475003 TCAAGGGACG
* *
52475013 TGTCAGCAAATCGCATCCACATCAGCGCGATTTGCTGACG
1 TGTCAGCAAATCGCATCCACATAAGCGCGATTTGCTGACA
* * * *
52475053 TGGCAGCAAATCGCATCCACGTAAGCGCGCTTTG-TGGTCA
1 TGTCAGCAAATCGCATCCACATAAGCGCGATTTGCT-GACA
52475093 TGTCAGCAAA
1 TGTCAGCAAA
52475103 GCGCGCTGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
TGTCAGCAAATCGCATCCACATAAGCGCGATTTGCTGACA
Found at i:52475599 original size:127 final size:124
Alignment explanation
Indices: 52475318--52475883 Score: 672
Period size: 124 Copynumber: 4.5 Consensus size: 124
52475308 GATAAAATCA
* * * * * * * * * *
52475318 AAGCAGGATGATTTATCA-AAGGATTTTTGAAGTCACTCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
* * *
52475382 AGATCCTGGAAAAATAATTTTGAGTTAACGTTTCTAAGCAAATAGTTTAAAAAAA-GCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAG--TAAAAAAACGCTTC
*
52475442 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGAGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
* * *
52475507 TGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTAACGTTTCTGAGCAAATAG--TAAAAAAACGCTTC
* *
52475569 AAGCAGGATGCTTTATGAGAAGAAATTGTGAAATCGCGCTCAT-GTGGACACGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGC-CCTCGTGGACACGCTTTTGCTACAG
* * * *
52475633 TAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTTTGAGCAAATAGTATAAAAACGCTGC
65 TAGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAAAAAAACGCTTC
* *
52475693 AAGTAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAG
* * * * * * *
52475757 TAAGTTCTGGAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAAAAAAACGCTTC
* * * * * * * **
52475817 TAGTAGGATTCTTTATGAGAAGAATTTGTGAAATCGCACCCACATGGACGCATTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
52475882 AG
66 AG
52475884 CATGTTTGGG
Statistics
Matches: 387, Mismatches: 48, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
123 4 0.01
124 189 0.49
125 47 0.12
126 73 0.19
127 72 0.19
128 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAAAAAAACGCTTC
Found at i:52479021 original size:20 final size:21
Alignment explanation
Indices: 52478973--52479027 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
52478963 TTGGTTTTTT
*
52478973 ATTTAAGGGTTACGATTTTAA
1 ATTTAAGGGTTACGATCTTAA
* * *
52478994 AGTTAAGGGTTATGGTCTT-A
1 ATTTAAGGGTTACGATCTTAA
52479014 ATTTAAGGGTTACG
1 ATTTAAGGGTTACG
52479028 GTTTTTAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.40
Consensus pattern (21 bp):
ATTTAAGGGTTACGATCTTAA
Found at i:52479044 original size:20 final size:21
Alignment explanation
Indices: 52478965--52479057 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
52478955 AGTTAGTGTT
* *
52478965 GGTTTTTTATTTAAGGGTTAC
1 GGTTTTTAAGTTAAGGGTTAC
* * *
52478986 GATTTTAAAGTTAAGGGTTAT
1 GGTTTTTAAGTTAAGGGTTAC
* *
52479007 GG-TCTTAATTTAAGGGTTAC
1 GGTTTTTAAGTTAAGGGTTAC
*
52479027 GGTTTTTAAGTTAA-GGTTAG
1 GGTTTTTAAGTTAAGGGTTAC
52479047 GGTTTTTAAGT
1 GGTTTTTAAGT
52479058 GGGTTGGGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.46
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGGTTAC
Found at i:52481528 original size:90 final size:90
Alignment explanation
Indices: 52481373--52481596 Score: 378
Period size: 90 Copynumber: 2.5 Consensus size: 90
52481363 GCAAAGTGTG
52481373 AAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTT
1 AAAAGTAGGTATGGTGTTTC-GTGAAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTT
52481438 CCGTGAAGAAAACCATACTGAGTTGTT
65 CCGTGAAGAAAACCATACTGAGTTG-T
*
52481465 AAAAGTAGGTATGGTGTTTCGTAAAG-AAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTC
1 AAAAGTAGGTATGGTGTTTCGTGAAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTC
*
52481529 GGTGAAGAAAACCATACTGAGTTGT
66 CGTGAAGAAAACCATACTGAGTTGT
* *
52481554 GAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTT
1 AAAAGTAGGTATGGTGTTT-CGTGAAGAAAACCATACTGAGTT
52481597 ATAGCAATGT
Statistics
Matches: 125, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
89 18 0.14
90 67 0.54
91 20 0.16
92 20 0.16
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (90 bp):
AAAAGTAGGTATGGTGTTTCGTGAAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTC
CGTGAAGAAAACCATACTGAGTTGT
Found at i:52481560 original size:45 final size:46
Alignment explanation
Indices: 52481369--52481596 Score: 381
Period size: 46 Copynumber: 5.0 Consensus size: 46
52481359 TATGGCAAAG
* *
52481369 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
52481415 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
* * *
52481461 TGTTAAAAGTAGGTATGGTGTTT-CGTAAAG-AAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
*
52481505 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
52481551 TGTG-AAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
52481596 T
1 T
52481597 ATAGCAATGT
Statistics
Matches: 170, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
44 35 0.21
45 52 0.31
46 83 0.49
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
Found at i:52481967 original size:22 final size:22
Alignment explanation
Indices: 52481939--52482332 Score: 338
Period size: 22 Copynumber: 18.5 Consensus size: 22
52481929 GGGGTGTTAA
*
52481939 GGTTAGGGTCTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
52481961 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
*
52481983 GGTTAAGG-TTTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52482003 GGTTAGGATTTTTAGGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52482025 GTTTATGGTTTTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
52482046 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
*
52482068 GTTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* ** *
52482090 GATTAAAGTTTTTAAGTTAAAG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52482112 GTTTAGGGTTTTTAAGTTAAAG
1 GGTTAGGGTTTTTAAGTTAAGG
*
52482134 GTTTAGGG--TTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
52482154 GG-TAGGG---TTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52482171 GGTTCAGAGTTTTTAATTTAAGG
1 GGTT-AGGGTTTTTAAGTTAAGG
* *
52482194 GTTTAAAGG-TTTTAAGTTAAGG
1 GGTT-AGGGTTTTTAAGTTAAGG
* *
52482216 AGTTAGGG--TTTAGGTTAAGAG
1 GGTTAGGGTTTTTAAGTTAAG-G
** * *
52482237 TTTTATGATTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
52482259 GTTTAAGG-TTTTAATTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
*
52482279 AGTTAGGAG-TTTTAAGGTT-A-G
1 GGTTAGG-GTTTTTAA-GTTAAGG
*
52482300 GGTTAGGGTTTTTAGGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52482322 GTTTAAGGTTT
1 GGTTAGGGTTT
52482333 GTCAATTAAA
Statistics
Matches: 306, Mismatches: 49, Indels: 34
0.79 0.13 0.09
Matches are distributed among these distances:
17 3 0.01
18 10 0.03
19 8 0.03
20 38 0.12
21 79 0.26
22 152 0.50
23 16 0.05
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.42
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAGTTAAGG
Found at i:52481996 original size:43 final size:42
Alignment explanation
Indices: 52481949--52482332 Score: 365
Period size: 43 Copynumber: 9.0 Consensus size: 42
52481939 GGTTAGGGTC
*
52481949 TTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGGTTAAGGT
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
* * *
52481992 TTTAAGTTAAGGGTTAGGATTTTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGG-T
*
52482035 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGG-T
** * *
52482078 TTTAAGTTAAGGGATTAAAGTTTTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAAGG-T
* *
52482122 TTTAAGTTAAAGGTTTAGGG--TTTAAGTTAAGGG-GT-AGG-
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
* * *
52482160 GTTAAGTTAAGGGTTCAGAGTTTTTAATTTAAGGGTTTAAAGGT
1 TTTAAGTTAAGGGTT-AGGGTTTTTAAGTTAAGGGTTT-AAGGT
* * * *
52482204 TTTAAGTTAAGGAGTTAGGG--TTTAGGTTAAGAGTTTTATGATT
1 TTTAAGTTAAGG-GTTAGGGTTTTTAAGTTAAG-GGTTTAAG-GT
* * * *
52482247 TTTAAGTTAAGGGTTTAAGG-TTTTAATTTAAGAG-TTAGGAGT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAAG-GT
*
52482289 TTTAAGGTT-AGGGTTAGGGTTTTTAGGTTAAGGGTTTAAGGT
1 TTTAA-GTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
52482331 TT
1 TT
52482333 GTCAATTAAA
Statistics
Matches: 283, Mismatches: 40, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
37 6 0.02
38 10 0.04
40 14 0.05
41 7 0.02
42 81 0.29
43 96 0.34
44 62 0.22
45 7 0.02
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
Found at i:52495257 original size:21 final size:21
Alignment explanation
Indices: 52495231--52495391 Score: 198
Period size: 21 Copynumber: 7.6 Consensus size: 21
52495221 TCAAATTATA
52495231 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
52495252 TTTAAGTTAAGTGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * * *
52495273 TTTTATTTAAGGGTTACGATT
1 TTTAAGTTAAGGGTTAGGGTT
* *
52495294 TTAAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
52495316 CTTAATTTAAGGGTTACGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
52495337 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
52495359 TTTAAGTTAAGGGTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
52495379 TTTAAGTTAAGGG
1 TTTAAGTTAAGGG
52495392 GTTATGTAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.12
21 69 0.58
22 35 0.30
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:52495386 original size:85 final size:85
Alignment explanation
Indices: 52495232--52495397 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
52495222 CAAATTATAT
* * * * *
52495232 TTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTATTTAAGGGTTACGATTTTA
1 TTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTACGATTTTA
*
52495297 AAGTTAAGGGTTTATGGTTC
66 AAGTTAAGGGGTTATGGTTC
* * *
52495317 TTAATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTT
1 TTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTACGATTTT
52495382 -AAGTTAAGGGGTTATG
65 AAAGTTAAGGGGTTATG
52495398 TAATAGCCTG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 44 0.62
86 27 0.38
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (85 bp):
TTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTACGATTTTA
AAGTTAAGGGGTTATGGTTC
Found at i:52495394 original size:43 final size:43
Alignment explanation
Indices: 52495231--52495391 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 43
52495221 TCAAATTATA
* * *
52495231 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* * * *
52495273 TTTTATTTAAGGGTTACGATTTTAAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* *
52495316 CTTAATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
*
52495359 TTTAAGTTAAGGGTTAGGGTTTT-AAGTTAAGGG
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGG
52495392 GTTATGTAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 38 0.37
43 66 0.63
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
Found at i:52497921 original size:46 final size:46
Alignment explanation
Indices: 52497846--52498076 Score: 399
Period size: 46 Copynumber: 5.0 Consensus size: 46
52497836 TATGGCAAAG
* *
52497846 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
52497892 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
* * * *
52497938 TGTTAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
*
52497984 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
52498030 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
52498076 T
1 T
52498077 ATAGCAATGT
Statistics
Matches: 175, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 175 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
Found at i:52498454 original size:22 final size:22
Alignment explanation
Indices: 52498429--52498827 Score: 415
Period size: 22 Copynumber: 18.5 Consensus size: 22
52498419 GGGTGTTACA
*
52498429 GGTTAGGGTCTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
52498451 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
52498473 GGTTAGGGTTTTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52498494 GGTTAGGATTTTTAGGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52498516 GTTTATGGTTTTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
52498537 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
*
52498559 GTTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* ** *
52498581 GATTAAAGTTTTTAAGTTAAAG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52498603 GTTTAGGGTTTTTAAGTTAAAG
1 GGTTAGGGTTTTTAAGTTAAGG
*
52498625 GTTTAGGG--TTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
52498645 GG-TAGGG--TTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52498663 GGTTCAGAGTTTTTAATTTAAGG
1 GGTT-AGGGTTTTTAAGTTAAGG
* *
52498686 GTTTAAGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
52498708 AGTTAGGGTTTTTAGGTTAAGA
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
52498730 GTTTATGATTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
52498752 GTTTAAGGTTTTTAATTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52498773 AGTTAGGAG-TTTTAAGGTTTA-G
1 GGTTAGG-GTTTTTAA-GTTAAGG
*
52498795 GGTTAGGGTTTTTAGGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
52498817 GTTTAAGGTTT
1 GGTTAGGGTTT
52498828 GTCAATTAAA
Statistics
Matches: 317, Mismatches: 49, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
18 3 0.01
19 16 0.05
20 15 0.05
21 54 0.17
22 225 0.71
23 4 0.01
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.43
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAGTTAAGG
Found at i:52498513 original size:43 final size:43
Alignment explanation
Indices: 52498431--52498827 Score: 466
Period size: 44 Copynumber: 9.2 Consensus size: 43
52498421 GTGTTACAGG
* *
52498431 TTAGGGTCTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGG
1 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGT
* *
52498475 TTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
*
52498518 TTATGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
** *
52498561 TTAGGGTTTTTAAGTTAAGGGATTAAAGTTTTTAAGTTAAAGGT
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT
*
52498605 TTAGGGTTTTTAAGTTAAAGGTTTAGGG--TTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGT
* * *
52498646 GTAGGG--TTTAAGTTAAGGGTTCAGAGTTTTTAATTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTT-AGGGTTTTTAAGTTAAGGGT
* * *
52498688 TTAAGGTTTTTAAGTTAAGGAGTTAGGGTTTTTAGGTTAAGAGT
1 TTAGGGTTTTTAAGTTAAGG-GTTAGGGTTTTTAAGTTAAGGGT
* * * * *
52498732 TTATGATTTTTAAGTTAAGGGTTTAAGGTTTTTAATTTAAGAG-
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT
* *
52498775 TTAGGAG-TTTTAAGGTTTAGGGTTAGGGTTTTTAGGTTAAGGGT
1 TTAGG-GTTTTTAA-GTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
*
52498819 TTAAGGTTT
1 TTAGGGTTT
52498828 GTCAATTAAA
Statistics
Matches: 301, Mismatches: 38, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
38 6 0.02
39 11 0.04
41 17 0.06
42 16 0.05
43 111 0.37
44 133 0.44
45 7 0.02
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.44
Consensus pattern (43 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
Found at i:52499372 original size:18 final size:18
Alignment explanation
Indices: 52499345--52499379 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52499335 GGAAAAGGAA
* *
52499345 ACATATAAGGGTTAAGAT
1 ACATAAAAGGGCTAAGAT
52499363 ACATAAAAGGGCTAAGA
1 ACATAAAAGGGCTAAGA
52499380 AACGCACCTG
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:0.49, C:0.09, G:0.23, T:0.20
Consensus pattern (18 bp):
ACATAAAAGGGCTAAGAT
Found at i:52500040 original size:7 final size:7
Alignment explanation
Indices: 52500030--52500055 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52500020 TTATATACAT
52500030 AATACTA
1 AATACTA
52500037 AATACTA
1 AATACTA
52500044 AATACTA
1 AATACTA
52500051 AATAC
1 AATAC
52500056 CAATAGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:52500261 original size:20 final size:20
Alignment explanation
Indices: 52500224--52500261 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52500214 TTTATTTTTA
*
52500224 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
52500244 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
52500262 TACCTCCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:52501254 original size:51 final size:51
Alignment explanation
Indices: 52501199--52501298 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
52501189 AATTATTTAA
52501199 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAGATT
* * * *
52501250 AAATATGGATTTCAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
52501299 GGAAATTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:52501296 original size:11 final size:11
Alignment explanation
Indices: 52501276--52501333 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
52501266 GAAATTTGGA
*
52501276 AGGAATTTGAG
1 AGGAAATTGAG
*
52501287 AGCAAATTGAG
1 AGGAAATTGAG
*
52501298 AGGAAATTTAG
1 AGGAAATTGAG
52501309 AGGAAATTGAG
1 AGGAAATTGAG
52501320 AGGAAATTTGAG
1 AGGAAA-TTGAG
52501332 AG
1 AG
52501334 AGGATTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 34 0.83
12 7 0.17
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:52501301 original size:22 final size:23
Alignment explanation
Indices: 52501279--52501333 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
52501269 ATTTGGAAGG
52501279 AATTTGAGAGCAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGGA
*
52501302 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGGA
52501324 AATTTGAGAG
1 AATTTGAGAG
52501334 AGGATTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGGA
Found at i:52501575 original size:40 final size:42
Alignment explanation
Indices: 52501520--52501621 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 42
52501510 CACAAAGCAT
* * *
52501520 GCTGACATGGACGCGATTTACTGCCACGTCAGCT-A-ACCGC
1 GCTGACGTGGACGCGATTTACTGACACGTCACCTGACACCGC
* * *
52501560 GCTGACGTGGACGCGATTTGCTGACACGTCCCCTGACATCGC
1 GCTGACGTGGACGCGATTTACTGACACGTCACCTGACACCGC
* *
52501602 GCTGACGTGAACGCAATTTA
1 GCTGACGTGGACGCGATTTA
52501622 AAGGAAAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 29 0.57
41 1 0.02
42 21 0.41
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (42 bp):
GCTGACGTGGACGCGATTTACTGACACGTCACCTGACACCGC
Found at i:52506940 original size:21 final size:21
Alignment explanation
Indices: 52506914--52506954 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52506904 AAACAATGAT
52506914 AAAAAGTATCAATACATTTTC
1 AAAAAGTATCAATACATTTTC
* *
52506935 AAAAAGTATCTATACCTTTT
1 AAAAAGTATCAATACATTTT
52506955 ACCAAGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAAAGTATCAATACATTTTC
Found at i:52507718 original size:27 final size:27
Alignment explanation
Indices: 52507668--52507719 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
52507658 ACTAACATAT
*
52507668 ATATAATTATTATTTAATATATAATTA
1 ATATAATTATTATTTAATAAATAATTA
*
52507695 ATATAATTATT-TTTTATAAAATAAT
1 ATATAATTATTATTTAAT-AAATAAT
52507720 ATTTTTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATATAATTATTATTTAATAAATAATTA
Found at i:52512172 original size:18 final size:18
Alignment explanation
Indices: 52512141--52512188 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
52512131 ATATAATTTT
*
52512141 AAATAATTTTTAAAATTCA
1 AAAT-ATTTATAAAATTCA
*
52512160 AAATATTTATAAAAATTCT
1 AAATATTTAT-AAAATTCA
52512179 AAA-ATTTATA
1 AAATATTTATA
52512189 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTTATAAAATTCA
Found at i:52512232 original size:12 final size:10
Alignment explanation
Indices: 52512195--52512234 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
52512185 TATATTTTTT
52512195 AAAAATTATA
1 AAAAATTATA
*
52512205 AAAAATTCTA
1 AAAAATTATA
52512215 AAAAATATATA
1 AAAAAT-TATA
52512226 AAGAAATTA
1 AA-AAATTA
52512235 AAACATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 15 0.58
11 7 0.27
12 4 0.15
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:52512237 original size:19 final size:18
Alignment explanation
Indices: 52512192--52512246 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
52512182 ATTTATATTT
52512192 TTTAAAAATTATAAAAAA
1 TTTAAAAATTATAAAAAA
52512210 TTCTAAAAAATATATAAAGAAA
1 TT-T-AAAAAT-TATAAA-AAA
52512232 -TTAAAACATTA-AAAA
1 TTTAAAA-ATTATAAAA
52512247 TTTTCTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 1 0.03
18 5 0.16
19 7 0.22
20 9 0.28
21 7 0.22
22 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
TTTAAAAATTATAAAAAA
Found at i:52521854 original size:29 final size:29
Alignment explanation
Indices: 52521821--52521879 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52521811 CATCTCTTGG
52521821 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
52521850 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
52521879 T
1 T
52521880 TTCTGGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAGCATTTAATTTCACTACCTCTTTTAC
Found at i:52522048 original size:66 final size:65
Alignment explanation
Indices: 52521960--52522095 Score: 254
Period size: 66 Copynumber: 2.1 Consensus size: 65
52521950 GCTTAAAGTT
*
52521960 TATATGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGGAATTATACACCTTTCA
1 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATC-GGAATTATACACCTTTCA
52522025 C
65 C
52522026 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
1 TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
52522091 TATAC
1 TATAC
52522096 TTAAATCTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 24 0.35
66 45 0.65
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (65 bp):
TATACGTTGTGGGTGTTACATAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCAC
Found at i:52522696 original size:161 final size:163
Alignment explanation
Indices: 52522496--52523610 Score: 944
Period size: 164 Copynumber: 6.9 Consensus size: 163
52522486 ATTTCATGGA
* *
52522496 TGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* *
52522561 CTATTTTAT-T-ATGCTTATTTTGTTTTTGTTTCAATAAGT-AAATAGGTTTTCAAATTAGATAT
66 CTATTTTATATAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAAT-GGTTTTCAAATTATATAT
**
52522623 CTTTTAACGATACTTAAAGTTTATATTTTA-CGAG
130 CTTTTAACGATACTTAAAGTTTATATTCCATC-AG
* * * * *
52522657 TGTTATATAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * * * * *
52522722 TTATTTTATTATAAATGCTTATTTTGTTTCTATTTTAATAAGTAAGACGGTTTTCGAATTATATA
66 CTATTTTA-TAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATA
* *
52522787 TCTTTTAACGATACTAATTAAAGTTTATATTTCAT-TG
129 TCTTTTAACGATAC---TTAAAGTTTATATTCCATCAG
*
52522824 TG-TACTATAAATG-TTAATTTTGCTTTCGTTATCGGAATCATCCACCTTTCACTATACCTAAAC
1 TGTTA-TATAAATGCTT-ATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAAC
* * *
52522887 CTCTATTTTATCATAGATGCTTACTTTTGTTTTTATTTTAATAAGTATAATGATTTTTGAATTAT
64 CTCTATTTTAT-ATA-ATGCTTA-TTTTGTTTTTGTTTTAATAAGTA-AA--A----TG-GTTTT
* * *
52522952 AATGAATTATATATCTTTTAACGATATTTAAAGTTTATATTTCATC-G
118 CA--AATTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * **
52522999 TACG-T-TATAAATGCTTATTTTAC-TTC-TT-T---TA-CA-ATACC--T-A--A-ACTTGTA-
1 T--GTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAAC
* ** * *
52523047 -T-T-TTATTATA-AATGATTATTTTGTTCCTGTTTTAATAGGCAAAATGG-TTTCAAATTATAT
64 CTCTATT-TTATATAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATAT
* * *
52523107 ATCTTTTAACGATGCCTAAAGTTTATATTCCAT-TG
128 ATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * ** *
52523142 TGTTCTATAAATACTTATTTTGCTTTCGTTATCGGAATCGTACACTTTTTTCTATACCTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* *
52523207 ATATTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAATTTATATA
66 CTATTTTA-TAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATA
52523272 TCTTTTAACGATACTTAAAGTTTATATTCCATC-G
129 TCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * * * * *
52523306 TGTTTTATAAATTCTTATTTCGCTTTCGTTATCGGAATCATACATCTTTTATTATACTTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * * *
52523371 GTATTTTATTATAAATGCTTATTTTG-TTTT-TATTATTAAGTAAGATGGTTTTCAAATTATATA
66 CTATTTTA-TAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATA
* *
52523434 TCTTTTAACGATGAC-TAAA-TCTATACTCCATC-G
129 TCTTTTAACGAT-ACTTAAAGTTTATATTCCATCAG
* * * * *
52523467 TGTCT-TATAAATGCTTATTTT-CTTTGGTTATTGAAATCATATACCTTTTACTATACCTAAACC
1 TGT-TATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACC
* * * * * * * *
52523530 -CGTATTTTATTATAAATACTTATTTTGTATTTATTTTAATATGCAGATTGGTTTTCAAATTATG
65 TC-TATTTTA-TAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATA
*
52523594 TATCTTTT-ACAATACTT
127 TATCTTTTAACGATACTT
52523611 GTAATTTATG
Statistics
Matches: 787, Mismatches: 106, Indels: 122
0.78 0.10 0.12
Matches are distributed among these distances:
141 1 0.00
142 1 0.00
143 55 0.07
144 3 0.00
145 5 0.01
146 1 0.00
147 2 0.00
149 1 0.00
150 1 0.00
151 4 0.01
153 3 0.00
154 18 0.02
155 6 0.01
156 2 0.00
157 7 0.01
158 5 0.01
159 2 0.00
160 64 0.08
161 112 0.14
162 79 0.10
163 39 0.05
164 126 0.16
165 56 0.07
166 8 0.01
167 73 0.09
168 40 0.05
169 2 0.00
171 1 0.00
172 1 0.00
173 2 0.00
174 3 0.00
175 35 0.04
176 5 0.01
177 2 0.00
178 22 0.03
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (163 bp):
TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
CTATTTTATATAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATATC
TTTTAACGATACTTAAAGTTTATATTCCATCAG
Found at i:52528273 original size:17 final size:17
Alignment explanation
Indices: 52528250--52528317 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
52528240 AGCTCTAGTA
52528250 CTGGCGAACTCCTATGT
1 CTGGCGAACTCCTATGT
* * *
52528267 TTGGCGAACTCTTATGC
1 CTGGCGAACTCCTATGT
* * *
52528284 CCGGCAAACCCCTATGT
1 CTGGCGAACTCCTATGT
**
52528301 CTAACGAACTCCTATGT
1 CTGGCGAACTCCTATGT
52528318 TTGACAAACA
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (17 bp):
CTGGCGAACTCCTATGT
Found at i:52528431 original size:13 final size:13
Alignment explanation
Indices: 52528409--52528461 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
52528399 GGCAAACTCA
*
52528409 CCTATGGTGAACC
1 CCTATCGTGAACC
52528422 CCTATCGTGAACTC
1 CCTATCGTGAAC-C
* * *
52528436 ACCTATGGCGAACG
1 -CCTATCGTGAACC
52528450 CCTATCGTGAAC
1 CCTATCGTGAAC
52528462 TGCCTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 21 0.66
14 1 0.03
15 10 0.31
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (13 bp):
CCTATCGTGAACC
Found at i:52528434 original size:28 final size:28
Alignment explanation
Indices: 52528403--52528462 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
52528393 CCTTATGGCA
*
52528403 AACTCACCTATGGTGAACCCCTATCGTG
1 AACTCACCTATGGCGAACCCCTATCGTG
*
52528431 AACTCACCTATGGCGAACGCCTATCGTG
1 AACTCACCTATGGCGAACCCCTATCGTG
52528459 AACT
1 AACT
52528463 GCCTTAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (28 bp):
AACTCACCTATGGCGAACCCCTATCGTG
Found at i:52528448 original size:15 final size:15
Alignment explanation
Indices: 52528396--52528448 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
52528386 GAGTAACCCT
*
52528396 TATGGCAAACTCACC
1 TATGGCGAACTCACC
*
52528411 TATGGTGAAC-C-CC
1 TATGGCGAACTCACC
* *
52528424 TATCGTGAACTCACC
1 TATGGCGAACTCACC
52528439 TATGGCGAAC
1 TATGGCGAAC
52528449 GCCTATCGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 11 0.35
14 2 0.06
15 18 0.58
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (15 bp):
TATGGCGAACTCACC
Found at i:52537754 original size:13 final size:13
Alignment explanation
Indices: 52537731--52537783 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
52537721 AATTAAGGCA
*
52537731 GTTCACGATAGGG
1 GTTCACCATAGGG
*
52537744 GTTCGCCATAGGTG
1 GTTCACCATAGG-G
*
52537758 AGTTCACGATAGGG
1 -GTTCACCATAGGG
52537772 GTTCACCATAGG
1 GTTCACCATAGG
52537784 TGAGTTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (13 bp):
GTTCACCATAGGG
Found at i:52537770 original size:28 final size:28
Alignment explanation
Indices: 52537730--52537789 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
52537720 GAATTAAGGC
*
52537730 AGTTCACGATAGGGGTTCGCCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
52537758 AGTTCACGATAGGGGTTCACCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
52537786 AGTT
1 AGTT
52537790 TGCCATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
AGTTCACGATAGGGGTTCACCATAGGTG
Done.