Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 19 of 378
Found at i:5127062 original size:87 final size:87
Alignment explanation
Indices: 5126936--5127212 Score: 249
Period size: 87 Copynumber: 3.2 Consensus size: 87
5126926 TTTCAGCTTT
* *
5126936 TTACCCTACTGCTTA-GGG-TCAAGGCTCATCGTCTTTGATCTG-CTCCACTACTGCTTAGGGAG
1 TTACCCTACTGCTTAGGGGTTCAAGGCTCATCGCCTTTGATCTGTCTCC-CTACCGCTTAGGGAG
* *
5126998 A-GAAGATCTGAAAATTTAGCCTA
65 ATG-AGATCTGAAAATTCAACCTA
* * * * * *
5127021 TTACCCTACTGCTCAGGGGTTTAAGGTTTATCGCCTTTGATCTGTTTCCCTACCGCTTAGGGTGA
1 TTACCCTACTGCTTAGGGGTTCAAGGCTCATCGCCTTTGATCTGTCTCCCTACCGCTTAGGGAGA
* *
5127086 TGAGATCTGTAAATTCAACCTG
66 TGAGATCTGAAAATTCAACCTA
* * * * * * * *
5127108 TTACCCTACTGCTTAGGGGTTCAAGGCCCTTCGTCTTCGACCTGTTTCCCTACTGCGTAAGGG-G
1 TTACCCTACTGCTTAGGGGTTCAAGGCTCATCGCCTTTGATCTGTCTCCCTACCGC-TTAGGGAG
* * * * * *
5127172 TTAAGATCTGTAAATCCAGCCTG
65 ATGAGATCTGAAAATTCAACCTA
*
5127195 TTACCCTACTACTTAGGG
1 TTACCCTACTGCTTAGGG
5127213 AGATAAGGCT
Statistics
Matches: 159, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
85 14 0.09
86 3 0.02
87 133 0.84
88 9 0.06
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (87 bp):
TTACCCTACTGCTTAGGGGTTCAAGGCTCATCGCCTTTGATCTGTCTCCCTACCGCTTAGGGAGA
TGAGATCTGAAAATTCAACCTA
Found at i:5127283 original size:86 final size:85
Alignment explanation
Indices: 5127062--5127491 Score: 366
Period size: 86 Copynumber: 5.0 Consensus size: 85
5127052 CGCCTTTGAT
* * * *
5127062 CTGTTTCCCTACCGCTTAGGGTGATGAGATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGG-
1 CTGTTTCCCTACTGCTTAGGG-GTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGA
* * * ** *
5127126 GTTCAAGGCCCTTCGTCTTCGAC
65 GAT-AAAG-CCTTTGAATTCAAC
* * *
5127149 CTGTTTCCCTACTGCGTAAGGGGTTAAGATCTGTAAATCCAGCCTGTTACCCTACTACTTAGGGA
1 CTGTTTCCCTACTGC-TTAGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGA
*
5127214 GAT-AAGGCTTGTGAATTCAAC
65 GATAAAGCCTT-TGAATTCAAC
* * * * *
5127235 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGG-TTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGA
* ** * *
5127300 GTTAAAGCCCTTTGTCTTCGAT
65 GATAAAG-CCTTTGAATTCAAC
* * * ** * *
5127322 CTGTTTCCCTACTGCTTAGGAAGATAAGATCTG-CAATTTGGTCTGTTACCCTAATGCTTAGGG-
1 CTGTTTCCCTACTGCTTAGG-GGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGA
* * ** * *
5127385 GTTTAAAACCTTTCGTCTTCGAT
65 G-ATAAAGCCTTT-GAATTCAAC
*
5127408 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCATAGGGA
1 CTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGA
*
5127473 GAT-AAGGCTTGTGAATTCA
65 GATAAAGCCTT-TGAATTCA
5127492 CCGATTCTAC
Statistics
Matches: 278, Mismatches: 52, Indels: 27
0.78 0.15 0.08
Matches are distributed among these distances:
85 15 0.05
86 136 0.49
87 115 0.41
88 12 0.04
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (85 bp):
CTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
ATAAAGCCTTTGAATTCAAC
Found at i:5127352 original size:173 final size:174
Alignment explanation
Indices: 5127062--5127471 Score: 454
Period size: 173 Copynumber: 2.4 Consensus size: 174
5127052 CGCCTTTGAT
* * * * * *
5127062 CTGTTTCCCTACCGCTTAGGGTGATGAGATCTGTAAATTCAACCTGTTACCCTACTGCTTA-GGG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
* * *
5127126 GTTCAAGGCCCTTCGTCTTCGACCTGTTTCCCTACTGCGTAAGGGGTTAAGATCTGTAAATCCAG
66 GTTCAAAGCCCTTCGTCTTCGACCTGTTTCCCTACTGCGTAAGGAGATAAGATCTG-AAATCCAG
* **
5127191 CCTGTTACCCTACTACTTAGGGAG-AT-AAGGCTTGT-GAATTCAAC
130 CCTGTTACCCTAATACTTAGGG-GTATAAAACCTT-TCGAATTCAAC
* * * *
5127235 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
* * * * ***
5127300 GTT-AAAGCCCTTTGTCTTCGATCTGTTTCCCTACTGC-TTAGGAAGATAAGATCTGCAATTTGG
66 GTTCAAAGCCCTTCGTCTTCGACCTGTTTCCCTACTGCGTAAGG-AGATAAGATCTGAAATCCAG
* * * ** * *
5127363 TCTGTTACCCTAATGCTTAGGGGTTTAAAACCTTTCGTCTTCGAT
130 CCTGTTACCCTAATACTTAGGGGTATAAAACCTTTCGAATTCAAC
* *
5127408 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCATAGGG
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
5127472 AGATAAGGCT
Statistics
Matches: 196, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
171 1 0.01
172 29 0.15
173 160 0.82
174 6 0.03
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (174 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
GTTCAAAGCCCTTCGTCTTCGACCTGTTTCCCTACTGCGTAAGGAGATAAGATCTGAAATCCAGC
CTGTTACCCTAATACTTAGGGGTATAAAACCTTTCGAATTCAAC
Found at i:5127462 original size:43 final size:43
Alignment explanation
Indices: 5127062--5127471 Score: 233
Period size: 43 Copynumber: 9.5 Consensus size: 43
5127052 CGCCTTTGAT
* * * * * *
5127062 CTGTTTCCCTACCGCTTAGGGTGATGAGATCTGTAAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
** *
5127105 CTGTTACCCTACTGCTTA-GGGGTTCAAGGCCCTTCGT--CTTC-GAC
1 CTGTTACCCTACTGCTTAGGGGGTT-AA-GATC-T-GTAAATTCAG-C
* * * *
5127149 CTGTTTCCCTACTGCGTAAGGGGTTAAGATCTGTAAATCCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* * * * * *
5127192 CTGTTACCCTACTACTTAGGGAGATAAG-GCTTGTGAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAATTCAGC
* * *
5127235 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATTCGGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* ** * *** *
5127278 TTGTTACCCTACTGCTTAGGGGGTTAAAGCCCTTTGTCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGATCTGTAAATTCAG-C
* ** * * ** *
5127322 CTGTTTCCCTACTGCTTAGGAAGATAAGATCTG-CAATTTGGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* * * * * *** *
5127364 CTGTTACCCTAATGCTTAGGGGTTTAAAACCTTTCGTCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAG-C
*
5127408 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
*
5127451 CTGTTACCCTACTGCATAGGG
1 CTGTTACCCTACTGCTTAGGG
5127472 AGATAAGGCT
Statistics
Matches: 270, Mismatches: 79, Indels: 36
0.70 0.21 0.09
Matches are distributed among these distances:
41 2 0.01
42 33 0.12
43 139 0.51
44 87 0.32
45 7 0.03
46 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
Found at i:5127714 original size:67 final size:66
Alignment explanation
Indices: 5127556--5127751 Score: 261
Period size: 67 Copynumber: 3.0 Consensus size: 66
5127546 CATCTATGTT
* * * * * *
5127556 TATGCCAAATAATTAGGACGCTATGATTGAAATGAATCAAATGCTCCTAACTA-A-ATGTAATGC
1 TATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGA
*
5127619 T
66 A
* *
5127620 TATGTCAAATAATTAGGATGCCATGATCAAAATGAATCAAATGCTCCTAACTAGATGTTGTTATG
1 TATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATG-TGTTATG
5127685 AA
65 AA
* * *
5127687 TGTGTCAAATAATTAAGATGCTATGATCGAAATGAATCAAATGCTCCTAATTAGATGTGTTATGA
1 TATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGA
5127752 CTGACATATG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
64 48 0.42
65 1 0.01
66 8 0.07
67 58 0.50
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (66 bp):
TATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGA
A
Found at i:5134376 original size:3 final size:3
Alignment explanation
Indices: 5134368--5134462 Score: 79
Period size: 3 Copynumber: 32.0 Consensus size: 3
5134358 GGGTAAAAAT
* ** *
5134368 ATA ATA ATA ATA ATA ATA AT- ATA ATA GTA GCA ATA ATG ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
5134415 A-A GTA ATAA ATC ATA ATG ATA ATA ATG ATA ATA AT- ATA AGTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
5134460 ATA
1 ATA
5134463 TAAGTAAATA
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
2 5 0.07
3 62 0.85
4 6 0.08
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5134409 original size:23 final size:23
Alignment explanation
Indices: 5134376--5134419 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5134366 ATATAATAAT
5134376 AATAATAATAAT-ATAATAGTAGC
1 AATAATAATAATAATAA-AGTAGC
*
5134399 AATAATGATAATAATAAAGTA
1 AATAATAATAATAATAAAGTA
5134420 ATAAATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAATAAAGTAGC
Found at i:5134630 original size:3 final size:3
Alignment explanation
Indices: 5134624--5134690 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
5134614 AATAACGATA
* * *
5134624 AAT AAT AAT AGT GAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5134672 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
5134691 GTAGTAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5134630 original size:24 final size:24
Alignment explanation
Indices: 5134576--5134630 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
5134566 AAACAGTAAT
5134576 AATAATATATTAATAAGAACAAAA
1 AATAATATATTAATAAGAACAAAA
* * * * *
5134600 AACAATATATTTATAATAACGATA
1 AATAATATATTAATAAGAACAAAA
5134624 AATAATA
1 AATAATA
5134631 ATAGTGATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (24 bp):
AATAATATATTAATAAGAACAAAA
Found at i:5134743 original size:23 final size:23
Alignment explanation
Indices: 5134717--5134792 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 23
5134707 TAATAGCATA
5134717 ATAGTATTAGAAATATATAATAT
1 ATAGTATTAGAAATATATAATAT
*
5134740 ATAGTATTAGAGATAAATACATAATAT
1 ATAGTATT--AG--AAATATATAATAT
*
5134767 ATACATATTAGAAATAATCATAATAT
1 ATA-GTATTAGAAAT-AT-ATAATAT
5134793 TAAAAAAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
23 8 0.19
24 4 0.09
25 3 0.07
26 9 0.21
27 15 0.35
28 4 0.09
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.36
Consensus pattern (23 bp):
ATAGTATTAGAAATATATAATAT
Found at i:5134757 original size:27 final size:28
Alignment explanation
Indices: 5134727--5134792 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
5134717 ATAGTATTAG
* * *
5134727 AAATATATAATATATA-GTATTAGAGAT
1 AAATACATAATATATACATATTAGAAAT
5134754 AAATACATAATATATACATATTAGAAAT
1 AAATACATAATATATACATATTAGAAAT
5134782 -AAT-CATAATAT
1 AAATACATAATAT
5134793 TAAAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.23
27 18 0.51
28 9 0.26
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (28 bp):
AAATACATAATATATACATATTAGAAAT
Found at i:5165450 original size:15 final size:15
Alignment explanation
Indices: 5165430--5165464 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5165420 ATATCAATAT
* *
5165430 TTTTAAGTATTATTA
1 TTTTAAATAATATTA
5165445 TTTTAAATAATATTA
1 TTTTAAATAATATTA
5165460 TTTTA
1 TTTTA
5165465 CATTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTTAAATAATATTA
Found at i:5173635 original size:16 final size:16
Alignment explanation
Indices: 5173613--5173651 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5173603 GTTTGGTTCA
* *
5173613 CTGTAATGGAATAGAG
1 CTGTAATGAAATAAAG
*
5173629 TTGTAATGAAATAAAG
1 CTGTAATGAAATAAAG
5173645 CTGTAAT
1 CTGTAAT
5173652 TAGTAATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (16 bp):
CTGTAATGAAATAAAG
Found at i:5174874 original size:29 final size:24
Alignment explanation
Indices: 5174830--5174886 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 24
5174820 GAAATATACG
5174830 ATATATAATATTGAAAGTAAATACATA
1 ATATATAATATTGAAA-T-AAT-CATA
5174857 ATATATACATATTAGAAATAATCATA
1 ATATATA-ATATT-GAAATAATCATA
5174883 ATAT
1 ATAT
5174887 TAGAAACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 8 0.29
27 10 0.36
28 6 0.21
29 4 0.14
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (24 bp):
ATATATAATATTGAAATAATCATA
Found at i:5175056 original size:2 final size:2
Alignment explanation
Indices: 5175049--5175073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5175039 CAATATTAAA
5175049 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5175074 AAATGTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5175749 original size:39 final size:38
Alignment explanation
Indices: 5175620--5175809 Score: 272
Period size: 38 Copynumber: 4.9 Consensus size: 38
5175610 ATTCCATTCC
* * *
5175620 CCCCATGCTACTTTGTTTTATTATTAATCAAAACCACT
1 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCACT
5175658 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCACT
1 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCACT
* *
5175696 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTT
1 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCA-CT
* *
5175735 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTT
1 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCAC-T
* * *
5175774 CCTCATACTATTTTGTTTTATTATTAATTAAAACCA
1 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCA
5175810 TACTTTATTT
Statistics
Matches: 140, Mismatches: 10, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
38 70 0.50
39 70 0.50
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (38 bp):
CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCACT
Found at i:5175765 original size:77 final size:77
Alignment explanation
Indices: 5175620--5175809 Score: 283
Period size: 77 Copynumber: 2.5 Consensus size: 77
5175610 ATTCCATTCC
* * *
5175620 CCCCATGCTACTTTGTTTTATTATTAATCAAAACCACTCCCCATGCTATTTTGTTTTATTGTTAA
1 CCCCATGCTATTTTGTTTTATTATTAATTAAAACCACTCCCCATACTATTTTGTTTTATTGTTAA
5175685 TTAAAACCAC-T
66 TTAAAACCACTT
* * *
5175696 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTTCCCCATACTATTTTGTTTTATTGTTA
1 CCCCATGCTATTTTGTTTTATTATTAATTAAAACCA-CTCCCCATACTATTTTGTTTTATTGTTA
*
5175761 ATTAAAACTACTT
65 ATTAAAACCACTT
* *
5175774 CCTCATACTATTTTGTTTTATTATTAATTAAAACCA
1 CCCCATGCTATTTTGTTTTATTATTAATTAAAACCA
5175810 TACTTTATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
76 32 0.32
77 36 0.36
78 33 0.33
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (77 bp):
CCCCATGCTATTTTGTTTTATTATTAATTAAAACCACTCCCCATACTATTTTGTTTTATTGTTAA
TTAAAACCACTT
Found at i:5176864 original size:45 final size:45
Alignment explanation
Indices: 5176814--5176899 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
5176804 CGATATCTGC
* * *
5176814 TATCTTTGATCTGCCCCCCGTCTACTACAGAGACGTCAAATCTAT
1 TATCTTCGATCTGCCCCCCGTCTAATACAGAGACGCCAAATCTAT
* * *
5176859 TATCTTCGATCTGCTCCCCTTCTAATACAGCGACGCCAAAT
1 TATCTTCGATCTGCCCCCCGTCTAATACAGAGACGCCAAAT
5176900 TTGCTTCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (45 bp):
TATCTTCGATCTGCCCCCCGTCTAATACAGAGACGCCAAATCTAT
Found at i:5177633 original size:205 final size:205
Alignment explanation
Indices: 5176997--5177712 Score: 917
Period size: 205 Copynumber: 3.5 Consensus size: 205
5176987 CTGCTTCTTC
* * * * * * * *
5176997 GATTTGTTCCCTGACAATACAGATATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCACATGA
1 GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
* * *
5177062 AAGCCAAATGAACTATGA--TTCGATTTGCTCCTTGTAAGCATAAGGGTGCTAAACCATCTTGGA
66 AAGCCAAATCAACTAT-ATCTTCGATTTGCTCCTTGTAAACATAAGGATGCTAAACCATCTTGGA
* *
5177125 TCCGCTTCAGCATAAACATCCG-AAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAG
130 TCCGCTTCAGCATAAACATCTGAAAGTC-AGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAG
5177189 ATGCCAAACTTT
194 ATGCCAAACTTT
* *
5177201 GATTCGTTCTCTGACAATACAGAGACGAAAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
1 GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
** * * * *** *
5177266 AAGCCAAATCAGTTATATCTTCGATCTACTCCCTGCCGA-ATACAGAGA-GATAAGATCTGTCAT
66 AAGCCAAATCAACTATATCTTCGATTTGCTCCTTGTAAACATA-AG-GATGCTAA-A-C---CAT
** * * *
5177329 CTTGGATCTACTTCAGCGTAAACATCTGAAGGTAAGATCTGCTATGTGTCTGC-CTTCCATCAAA
124 CTTGGATCCGCTTCAGCATAAACATCTGAAAGTCAGATCTGCTATGTGTCTGCTC-TCCATCAAA
* *
5177393 GTGGAA-ATGCCAGACTTC
188 GT-GAAGATGCCAAACTTT
* * *
5177411 GATTTGTTCTTTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACGTAAACACGTGA
1 GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
* * *
5177476 AAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACATAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAACTATATCTTCGATTTGCTCCTTGTAAACATAAGGATGCTAAACCATCTTGGAT
*
5177541 CCGCTTCAGCATAAACATCTGAAATTCAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAGAT
131 CCGCTTCAGCATAAACATCTGAAAGTCAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAGAT
5177606 GCCAAACTTT
196 GCCAAACTTT
*
5177616 GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
1 GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
5177681 AAGCCAAATCAACTATATCTTCG-TTATGCTCC
66 AAGCCAAATCAACTATATCTTCGATT-TGCTCC
5177713 CCGCCGAATA
Statistics
Matches: 433, Mismatches: 62, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
203 1 0.00
204 76 0.18
205 178 0.41
206 3 0.01
207 1 0.00
208 1 0.00
209 4 0.01
210 161 0.37
211 8 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (205 bp):
GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
AAGCCAAATCAACTATATCTTCGATTTGCTCCTTGTAAACATAAGGATGCTAAACCATCTTGGAT
CCGCTTCAGCATAAACATCTGAAAGTCAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAGAT
GCCAAACTTT
Found at i:5185340 original size:47 final size:47
Alignment explanation
Indices: 5185231--5185341 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
5185221 CCGGGATAAG
* *
5185231 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
5185278 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTTG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
5185325 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
5185342 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:5186114 original size:4 final size:4
Alignment explanation
Indices: 5186105--5186133 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5186095 CCCTTTTCTA
5186105 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
5186134 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:5192863 original size:39 final size:38
Alignment explanation
Indices: 5192732--5192882 Score: 212
Period size: 38 Copynumber: 3.9 Consensus size: 38
5192722 ATTCCATTCC
* * * * *
5192732 CCCCATGCTACTTTGTTTTATTATTAATCAAATCCACT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACCACT
5192770 CCCCATACTATTTTGTTTTATTGTTAATTAAAACCACT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACCACT
* * *
5192808 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACCA-CT
*
5192847 TCCCATACTATTTTGTTTTATTGTTAATTAAAACCA
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACCA
5192883 TACTATTTTG
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 67 0.66
39 34 0.34
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTGTTAATTAAAACCACT
Found at i:5192873 original size:77 final size:76
Alignment explanation
Indices: 5192732--5192882 Score: 230
Period size: 77 Copynumber: 2.0 Consensus size: 76
5192722 ATTCCATTCC
*
5192732 CCCCATGCTACTTTGTTTTATTATTAATCAAATCCACTCCCCATACTATTTTGTTTTATTGTTAA
1 CCCCATGCTACTTTGTTTTATTATTAATCAAAACCACTCCCCATACTATTTTGTTTTATTGTTAA
5192797 TTAAAACCACT
66 TTAAAACCACT
* * * * * *
5192808 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTTTCCCATACTATTTTGTTTTATTGTTA
1 CCCCATGCTACTTTGTTTTATTATTAATCAAAACCA-CTCCCCATACTATTTTGTTTTATTGTTA
5192873 ATTAAAACCA
65 ATTAAAACCA
5192883 TACTATTTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
76 31 0.46
77 36 0.54
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (76 bp):
CCCCATGCTACTTTGTTTTATTATTAATCAAAACCACTCCCCATACTATTTTGTTTTATTGTTAA
TTAAAACCACT
Found at i:5192911 original size:31 final size:31
Alignment explanation
Indices: 5192849--5192923 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 31
5192839 AACTATTTTC
* *
5192849 CCATACTATTTTGTTTTATTGTTAATTAAAA
1 CCATACTATTTTGTTTTATTATTAATAAAAA
*
5192880 CCATACTATTTTGTTTT-TTA-TCATAAAAA
1 CCATACTATTTTGTTTTATTATTAATAAAAA
*
5192909 --A-ACTATTTTTTTTTA
1 CCATACTATTTTGTTTTA
5192924 AAAAAAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 12 0.31
27 1 0.03
29 7 0.18
30 2 0.05
31 17 0.44
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (31 bp):
CCATACTATTTTGTTTTATTATTAATAAAAA
Found at i:5204661 original size:21 final size:22
Alignment explanation
Indices: 5204632--5204672 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5204622 GATAAATTAC
5204632 TATACATTTA-AATATTTTTCA
1 TATACATTTATAATATTTTTCA
* *
5204653 TATATATTTATAATCTTTTT
1 TATACATTTATAATATTTTT
5204673 TTTTTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (22 bp):
TATACATTTATAATATTTTTCA
Found at i:5206337 original size:2 final size:2
Alignment explanation
Indices: 5206330--5206354 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5206320 TGTGATAAGT
5206330 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5206355 TACCTGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5214490 original size:29 final size:29
Alignment explanation
Indices: 5214448--5214504 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5214438 AAAATTAGTG
*
5214448 CTGTAAACATGATTAGAAGGCTTTCTTTT
1 CTGTAAACATGATTAGAACGCTTTCTTTT
5214477 CTGTAAACATGATTAGAACGCTTTCTTT
1 CTGTAAACATGATTAGAACGCTTTCTTT
5214505 CACTTGAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (29 bp):
CTGTAAACATGATTAGAACGCTTTCTTTT
Found at i:5222936 original size:13 final size:13
Alignment explanation
Indices: 5222918--5222944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5222908 ATATATTGTT
5222918 AAATTATCACAGA
1 AAATTATCACAGA
5222931 AAATTATCACAGA
1 AAATTATCACAGA
5222944 A
1 A
5222945 TATATACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
AAATTATCACAGA
Found at i:5237065 original size:1 final size:1
Alignment explanation
Indices: 5237021--5237045 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5237011 CTTAACTCTC
5237021 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
5237046 GGGAATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5237590 original size:13 final size:14
Alignment explanation
Indices: 5237548--5237591 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
5237538 TTTTATCCTG
*
5237548 AATCTCGAATCTTA
1 AATCTCGAACCTTA
*
5237562 AATCTCGAACCCTA
1 AATCTCGAACCTTA
*
5237576 AA-CTTGAACCTTA
1 AATCTCGAACCTTA
5237589 AAT
1 AAT
5237592 TTAAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (14 bp):
AATCTCGAACCTTA
Found at i:5237682 original size:26 final size:28
Alignment explanation
Indices: 5237629--5237688 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
5237619 CCTAAACAAC
* *
5237629 TTAGG-TTCAATGTTCAGAGTTT-GGGG
1 TTAGGATTCAATGTTCAGAGTTTAAGGT
*
5237655 TTAGGATTCAATGTT-TGAGTTTAAGGT
1 TTAGGATTCAATGTTCAGAGTTTAAGGT
5237682 TTAGGAT
1 TTAGGAT
5237689 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.42
Consensus pattern (28 bp):
TTAGGATTCAATGTTCAGAGTTTAAGGT
Found at i:5239578 original size:12 final size:13
Alignment explanation
Indices: 5239554--5239612 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
5239544 TAATAGTATC
5239554 ATTTCGATATTTA
1 ATTTCGATATTTA
5239567 ATTTCGTATTTAAGTTTA
1 ATTTCG-A--T-A-TTTA
5239585 ATTTCGATATTTA
1 ATTTCGATATTTA
*
5239598 ATTT-GATATCTA
1 ATTTCGATATTTA
5239610 ATT
1 ATT
5239613 AAATGACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 10 0.25
13 14 0.35
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 10 0.25
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTTCGATATTTA
Found at i:5239586 original size:18 final size:19
Alignment explanation
Indices: 5239563--5239598 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5239553 CATTTCGATA
5239563 TTTAATTTCG-TATTTAAG
1 TTTAATTTCGATATTTAAG
5239581 TTTAATTTCGATATTTAA
1 TTTAATTTCGATATTTAA
5239599 TTTGATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTAATTTCGATATTTAAG
Found at i:5240977 original size:11 final size:11
Alignment explanation
Indices: 5240963--5241014 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
5240953 TCTTTCAATA
5240963 TTCTCTCAAAT
1 TTCTCTCAAAT
5240974 TTCTCTCAAA-
1 TTCTCTCAAAT
5240984 -TCTCTCAAAT
1 TTCTCTCAAAT
* *
5240994 TTCTATTAAAT
1 TTCTCTCAAAT
*
5241005 TCCTCTCAAA
1 TTCTCTCAAA
5241015 ACTCTCATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.26
11 25 0.74
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:5240986 original size:31 final size:31
Alignment explanation
Indices: 5240963--5241021 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5240953 TCTTTCAATA
* *
5240963 TTCTCTCAAATTTCTCTCAAATCTCTCAAAT
1 TTCTATCAAATTCCTCTCAAATCTCTCAAAT
* *
5240994 TTCTATTAAATTCCTCTCAAAACTCTCA
1 TTCTATCAAATTCCTCTCAAATCTCTCA
5241022 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.41
Consensus pattern (31 bp):
TTCTATCAAATTCCTCTCAAATCTCTCAAAT
Found at i:5241004 original size:20 final size:21
Alignment explanation
Indices: 5240957--5241014 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
5240947 CTTCAATCTT
*
5240957 TCAATATTCTCTCAAATTTCTC
1 TCAA-ATTCTCTCAAATTTCTA
5240979 TCAAA-TCTCTCAAATTTCTA
1 TCAAATTCTCTCAAATTTCTA
*
5240999 TTAAATTCCTCTCAAA
1 TCAAATT-CTCTCAAA
5241015 ACTCTCATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 12 0.38
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (21 bp):
TCAAATTCTCTCAAATTTCTA
Found at i:5241070 original size:16 final size:15
Alignment explanation
Indices: 5241041--5241071 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5241031 TCAAAAAAGC
*
5241041 TCTAATTTTATTTTT
1 TCTAAATTTATTTTT
5241056 TCTAAATTTATTTTT
1 TCTAAATTTATTTTT
5241071 T
1 T
5241072 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTAAATTTATTTTT
Found at i:5242182 original size:7 final size:7
Alignment explanation
Indices: 5242170--5242196 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5242160 TAGTGGATTC
5242170 GTATTTA
1 GTATTTA
5242177 GTATTTA
1 GTATTTA
5242184 GTATTTA
1 GTATTTA
5242191 GTATTT
1 GTATTT
5242197 TTTATTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
GTATTTA
Found at i:5243583 original size:116 final size:116
Alignment explanation
Indices: 5243221--5243949 Score: 1300
Period size: 116 Copynumber: 6.3 Consensus size: 116
5243211 TATTTGTACA
5243221 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
*
5243286 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAATGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
*
5243337 AACATTTTGAATATTTTTATATTATTTCATTTAATTAGATAAAAGGTTGTTTTAAATAAAGT-AT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
*
5243401 TATAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
5243452 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
5243517 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
*
5243568 AATATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAA-GTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
*
5243632 TGTAATTTACTTTTATATTTTTAATAAAATAGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
5243683 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* *
5243748 TGTAATTTACTTTTATATTTTTAATAAAATAGAAATTATTTTAGATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
* * *
5243799 AACATTTTGAATATTTTTATATTATTTCATGTGATAATATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* * **
5243864 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAAC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
* *
5243915 AATATTTTAAATATTTTTATATTATTTCATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
5243950 AAAATATAAA
Statistics
Matches: 590, Mismatches: 21, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
115 225 0.38
116 365 0.62
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (116 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
Found at i:5243640 original size:231 final size:232
Alignment explanation
Indices: 5243221--5243949 Score: 1309
Period size: 231 Copynumber: 3.2 Consensus size: 232
5243211 TATTTGTACA
5243221 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
*
5243286 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAATGCAACATTTTGAATAT
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATAT
*
5243351 TTTTATATTATTTCATTTAATTAGATAAAAGGTTGTTTTAAATAAAGT-ATTATAATTTACTTTT
131 TTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTATAATTTACTTTT
5243415 ATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
196 ATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
5243452 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
*
5243517 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAATATTTTGAATAT
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATAT
*
5243582 TTTTATATTATTTCATGTAATTAGATAAAA-GTTGTTTTAAATAAAGTAATTGTAATTTACTTTT
131 TTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTATAATTTACTTTT
*
5243646 ATATTTTTAATAAAATAGAAATTATTTTAAATAAGGC
196 ATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
5243683 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* *
5243748 TGTAATTTACTTTTATATTTTTAATAAAATAGAAATTATTTTAGATAAGGCAACATTTTGAATAT
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATAT
* * *
5243813 TTTTATATTATTTCATGTGATAATATAAAAGGTTGTTTTAAATAAAGTAATTATAATTTACTTTT
131 TTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTATAATTTACTTTT
* **
5243878 ATATTTTTAATAAAATGAAAATTATTTTAAATAAAAC
196 ATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
* *
5243915 AATATTTTAAATATTTTTATATTATTTCATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
5243950 AAAATATAAA
Statistics
Matches: 478, Mismatches: 18, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
230 17 0.04
231 362 0.76
232 99 0.21
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (232 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATAT
TTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTATAATTTACTTTT
ATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
Found at i:5247188 original size:126 final size:126
Alignment explanation
Indices: 5246958--5247495 Score: 814
Period size: 126 Copynumber: 4.3 Consensus size: 126
5246948 GCCCAAGTTA
* * *
5246958 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAG
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
**
5247023 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * * *
5247084 TTTCAGAGACCACTATAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
5247149 TGCATCCTGCTTGAAGCGTTTTT-ACCACTATTTGCGCAGACATGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* *
5247210 TTTCAGAGACTACTGTAGTCAAAA-AGTGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCT-AAC
1 TTTCAGAGACTACTGTAG-CAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAA-
* *
5247273 AATGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
64 AATGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * * *
5247336 TTTCAGATACTAATATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTACTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
5247401 TGCATCTTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTC-AAATTTTTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
*
5247461 TTTCAGAGACTACTGTAGCAAAAGAACGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
5247496 AGAAGCTTTT
Statistics
Matches: 373, Mismatches: 33, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
125 47 0.13
126 319 0.86
127 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:5247722 original size:98 final size:99
Alignment explanation
Indices: 5247613--5247791 Score: 272
Period size: 98 Copynumber: 1.8 Consensus size: 99
5247603 CCTAAAATTC
* * ** * *
5247613 TAATCTAATTTTTTTTAAATTTA-TAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTG
1 TAATCTAA-TTTTTTTAAAATTAGTAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTA
5247677 A-TTTTTTTCCTTAAAAACCATAAACATTAAACCA
65 ATTTTTTTTCCTTAAAAACCATAAACATTAAACCA
*
5247711 TAATCTAATTTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCCTAATTTATTTAA
1 TAATCTAATTTTTTTAAAATTAGTAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTAA
5247776 TTTTTTTTCCTTAAAA
66 TTTTTTTTCCTTAAAA
5247792 CCTTAAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
97 13 0.18
98 44 0.61
99 15 0.21
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.45
Consensus pattern (99 bp):
TAATCTAATTTTTTTAAAATTAGTAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTAA
TTTTTTTTCCTTAAAAACCATAAACATTAAACCA
Found at i:5255110 original size:28 final size:26
Alignment explanation
Indices: 5255039--5255132 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 26
5255029 ATTAGAAAAA
5255039 TATTATT-GTATATATCTTTGAAAATTTT
1 TATTATTAGTATAT-T-TTTG-AAATTTT
* *
5255067 TATTATTTACTGTATTATTTGAAATTTT
1 TATTA-TTAGTATATT-TTTGAAATTTT
* * *
5255095 TATTATTAGATATATTTATAAAATTAT
1 TATTATTAG-TATATTTTTGAAATTTT
5255122 TATTATTAGTA
1 TATTATTAGTA
5255133 ATTAAATAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 20 0.36
28 22 0.40
29 7 0.13
30 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (26 bp):
TATTATTAGTATATTTTTGAAATTTT
Found at i:5257510 original size:60 final size:60
Alignment explanation
Indices: 5257433--5257569 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 60
5257423 AATTGTGTTA
* *
5257433 ATATGGGC-AAGACCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * * * *
5257493 ATATGGGGT-AGGCCCAATATACTCTGATACTGTAAGGGGTTATGGCCCAGATTAATATTG
1 ATATGGGCTAAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
5257553 ATATGGGCTAAGGCCCA
1 ATATGGGCTAAGGCCCA
5257570 GTTAACACTG
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
59 1 0.02
60 48 0.75
61 15 0.23
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (60 bp):
ATATGGGCTAAGGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:5259234 original size:43 final size:43
Alignment explanation
Indices: 5259133--5259322 Score: 346
Period size: 43 Copynumber: 4.4 Consensus size: 43
5259123 ACGCCACAAA
5259133 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTT-CCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
5259175 AAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
5259218 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
5259261 AAACGCCGCTATAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
5259304 AAACGCCGCTAAAAGTCAT
1 AAACGCCGCTAAAGGTCAT
5259323 AAAATTTAAA
Statistics
Matches: 142, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 37 0.26
43 105 0.74
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
Found at i:5259501 original size:19 final size:18
Alignment explanation
Indices: 5259457--5259502 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
5259447 ATCAAATTAA
*
5259457 AATAAAAATAAAATATAG
1 AATAAAAATAAAATAAAG
* *
5259475 AATCAAAACTAAAATAAAT
1 AAT-AAAAATAAAATAAAG
5259494 AATAAAAAT
1 AATAAAAAT
5259503 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAAAAATAAAATAAAG
Found at i:5263913 original size:3 final size:3
Alignment explanation
Indices: 5263907--5263950 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
5263897 TTTTTCTCTT
*
5263907 TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5263951 TACTAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5264695 original size:7 final size:7
Alignment explanation
Indices: 5264683--5264739 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
5264673 CCCATGGCCA
5264683 TTAAACC
1 TTAAACC
5264690 TTAAACC
1 TTAAACC
*
5264697 ATAAAACC
1 -TTAAACC
*
5264705 CTAAACC
1 TTAAACC
* *
5264712 ATAGACC
1 TTAAACC
**
5264719 TTAAATA
1 TTAAACC
5264726 TTAAACC
1 TTAAACC
5264733 TTAAACC
1 TTAAACC
5264740 CCAAAATAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (7 bp):
TTAAACC
Found at i:5264703 original size:15 final size:15
Alignment explanation
Indices: 5264680--5264739 Score: 70
Period size: 14 Copynumber: 4.1 Consensus size: 15
5264670 ACACCCATGG
5264680 CCATTAAACCTTAAA
1 CCATTAAACCTTAAA
* *
5264695 CCATAAAACCCTAAA
1 CCATTAAACCTTAAA
*
5264710 CCA-TAGACCTTAAA
1 CCATTAAACCTTAAA
*
5264724 -TATTAAACCTTAAA
1 CCATTAAACCTTAAA
5264738 CC
1 CC
5264740 CCAAAATAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 1 0.03
14 18 0.51
15 16 0.46
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (15 bp):
CCATTAAACCTTAAA
Found at i:5265058 original size:40 final size:41
Alignment explanation
Indices: 5264964--5265157 Score: 223
Period size: 40 Copynumber: 4.7 Consensus size: 41
5264954 TTATATGACC
* * * *
5264964 TTTAACGGCGTTTTGAGCATAAACGCCACTATTGCTCTGGTT
1 TTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCTGGTT
* *
5265006 TTTAACGGCGTTTTACCAAAAATGCCGCTATTGCTCT-GTT
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGTT
****
5265046 TTTAGTC-GCGTTTTTGGGAAAACGCCGCTATTGCTCTGGTT
1 TTTAG-CGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGTT
*
5265087 TTTAGCGGCGTTTTTACCAAAAACGCCGCTATTGCTCT-ATT
1 TTTAGCGGCG-TTTTACCAAAAACGCCGCTATTGCTCTGGTT
* *
5265128 TTTAGCGGCATTTTAGCAAAAACGCCGCTA
1 TTTAGCGGCGTTTTACCAAAAACGCCGCTA
5265158 ATGTACAATT
Statistics
Matches: 131, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
40 52 0.40
41 42 0.32
42 37 0.28
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGTT
Found at i:5265150 original size:82 final size:81
Alignment explanation
Indices: 5264964--5265157 Score: 264
Period size: 82 Copynumber: 2.4 Consensus size: 81
5264954 TTATATGACC
* * * *
5264964 TTTAACGGCGTTTTGAGCATAAACGCCACTATTGCTCTGGTTTTTAACGGCGTTTTACCAAAAAT
1 TTTAGCGGCGTTTT-AGCAAAAACGCCGCTATTGCTCTGGTTTTTAACGGCGTTTTACCAAAAAC
*
5265029 GCCGCTATTGCTCTGTT
65 GCCGCTATTGCTCTATT
* ** *
5265046 TTTAGTC-GCGTTTTTGGGAAAACGCCGCTATTGCTCTGGTTTTTAGCGGCGTTTTTACCAAAAA
1 TTTAG-CGGCGTTTTAGCAAAAACGCCGCTATTGCTCTGGTTTTTAACGGCG-TTTTACCAAAAA
5265110 CGCCGCTATTGCTCTATT
64 CGCCGCTATTGCTCTATT
*
5265128 TTTAGCGGCATTTTAGCAAAAACGCCGCTA
1 TTTAGCGGCGTTTTAGCAAAAACGCCGCTA
5265158 ATGTACAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
81 32 0.33
82 63 0.66
83 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (81 bp):
TTTAGCGGCGTTTTAGCAAAAACGCCGCTATTGCTCTGGTTTTTAACGGCGTTTTACCAAAAACG
CCGCTATTGCTCTATT
Found at i:5265169 original size:40 final size:41
Alignment explanation
Indices: 5264964--5265198 Score: 169
Period size: 40 Copynumber: 5.8 Consensus size: 41
5264954 TTATATGACC
* * * * * **
5264964 TTTAACGGCGTTTTGAGCATAAACGCCACTATTGCTCTGGTT
1 TTTAGCGGCGTTTTTAGCAAAAACGCCGCTAATGCTC-AATT
* * * * **
5265006 TTTAACGGCG-TTTTACCAAAAATGCCGCTATTGCTCTGTT
1 TTTAGCGGCGTTTTTAGCAAAAACGCCGCTAATGCTCAATT
** * **
5265046 TTTAGTC-GCGTTTTT-GGGAAAACGCCGCTATTGCTCTGGTT
1 TTTAG-CGGCGTTTTTAGCAAAAACGCCGCTAATGCTC-AATT
* * *
5265087 TTTAGCGGCGTTTTTACCAAAAACGCCGCTATTGCTCTATT
1 TTTAGCGGCGTTTTTAGCAAAAACGCCGCTAATGCTCAATT
*
5265128 TTTAGCGGC-ATTTTAGCAAAAACGCCGCTAATG-TACAATT
1 TTTAGCGGCGTTTTTAGCAAAAACGCCGCTAATGCT-CAATT
*
5265168 TTT-GCGGCGTTTTTTG-ATAAAACGCCGCTAA
1 TTTAGCGGCGTTTTTAGCA-AAAACGCCGCTAA
5265199 AAACGCCGCT
Statistics
Matches: 162, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
39 7 0.04
40 74 0.46
41 53 0.33
42 28 0.17
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAGCAAAAACGCCGCTAATGCTCAATT
Found at i:5265201 original size:12 final size:12
Alignment explanation
Indices: 5265186--5265211 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5265176 GTTTTTTGAT
5265186 AAAACGCCGCTA
1 AAAACGCCGCTA
5265198 AAAACGCCGCTA
1 AAAACGCCGCTA
5265210 AA
1 AA
5265212 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:5268023 original size:17 final size:17
Alignment explanation
Indices: 5268001--5268037 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5267991 ATTTTTAATG
5268001 TTTGCAATATTTCAATT
1 TTTGCAATATTTCAATT
5268018 TTTGCAATATTTCAATT
1 TTTGCAATATTTCAATT
5268035 TTT
1 TTT
5268038 TTTTTTTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTGCAATATTTCAATT
Found at i:5270831 original size:20 final size:22
Alignment explanation
Indices: 5270802--5270851 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
5270792 TTATTATATA
*
5270802 TACAACATATTTATCTATTTAG
1 TACAATATATTTATCTATTTAG
5270824 TACAATATATATTTATCTATTTAG
1 TAC-A-ATATATTTATCTATTTAG
5270848 TACA
1 TACA
5270852 GTATTTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 3 0.12
23 2 0.08
24 20 0.80
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (22 bp):
TACAATATATTTATCTATTTAG
Found at i:5275793 original size:3 final size:3
Alignment explanation
Indices: 5275787--5275860 Score: 52
Period size: 3 Copynumber: 26.0 Consensus size: 3
5275777 AATAGTGATG
* * *
5275787 ATA ATA ATA ATA GTA GTA A-A ATA A-A GATA AT- ATA GTAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA AT-A ATA ATA
*
5275830 ATA ATA ATA ATA ATA GTA ATA A-A A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5275861 GTAGTGATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
2 11 0.19
3 44 0.76
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:5275816 original size:23 final size:23
Alignment explanation
Indices: 5275787--5275860 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
5275777 AATAGTGATG
*
5275787 ATAATAATAATAGTAGTAAAATA
1 ATAATAATAATAGTAATAAAATA
5275810 A-AGATAAT-ATAGTAAATAAAATA
1 ATA-ATAATAATAGT-AATAAAATA
5275833 ATAATAATAATAGTAATAAAA-A
1 ATAATAATAATAGTAATAAAATA
5275855 ATAATA
1 ATAATA
5275861 GTAGTGATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
22 13 0.28
23 27 0.59
24 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (23 bp):
ATAATAATAATAGTAATAAAATA
Found at i:5275835 original size:17 final size:19
Alignment explanation
Indices: 5275787--5275865 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 19
5275777 AATAGTGATG
5275787 ATAATAATAATAGTAGTAAA
1 ATAA-AATAATAGTAGTAAA
*
5275807 ATAAAGATAATATAGTAAATAAA
1 ATAAA-AT-A-ATAGT-AGTAAA
*
5275830 ATAATAATAATAATAGTAATA
1 ATAA-AATAATAGTAGTAA-A
5275851 A-AAAATAATAGTAGT
1 ATAAAATAATAGTAGT
5275866 GATATTAGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 12 0.24
20 12 0.24
21 7 0.14
22 6 0.12
23 11 0.22
24 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (19 bp):
ATAAAATAATAGTAGTAAA
Found at i:5275989 original size:2 final size:2
Alignment explanation
Indices: 5275973--5276008 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5275963 GTAAATAATA
*
5275973 AT AT AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5276009 AAATATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5276079 original size:18 final size:18
Alignment explanation
Indices: 5276049--5276092 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5276039 GGTCTAATAC
*
5276049 TAAG-ATAATAATGATGG
1 TAAGAATAAAAATGATGG
*
5276066 TAAGAATAAAAATGTTGG
1 TAAGAATAAAAATGATGG
*
5276084 TAATAATAA
1 TAAGAATAA
5276093 TAATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (18 bp):
TAAGAATAAAAATGATGG
Found at i:5276190 original size:21 final size:21
Alignment explanation
Indices: 5276166--5276210 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5276156 ATGATGATGT
*
5276166 TAATATATTAAATAAAAATAA
1 TAATATAGTAAATAAAAATAA
* * *
5276187 TAATGTAGTAAGTAATAATAA
1 TAATATAGTAAATAAAAATAA
5276208 TAA
1 TAA
5276211 GGTATAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
TAATATAGTAAATAAAAATAA
Found at i:5276287 original size:3 final size:3
Alignment explanation
Indices: 5276279--5276316 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5276269 GGATATATGT
5276279 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5276317 GATGATGATG
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5276377 original size:18 final size:18
Alignment explanation
Indices: 5276335--5276393 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
5276325 TGATGATGGG
*
5276335 AATAATAATAGTGAATAT
1 AATAATAATAGTGAAAAT
* *
5276353 AAATAATAGTCGTGAAAAT
1 -AATAATAATAGTGAAAAT
*
5276372 AATAATAATAGTGACAAT
1 AATAATAATAGTGAAAAT
5276390 AATA
1 AATA
5276394 GAGATAACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (18 bp):
AATAATAATAGTGAAAAT
Found at i:5276675 original size:28 final size:29
Alignment explanation
Indices: 5276639--5276706 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
5276629 ATAAAAATAC
*
5276639 AATAATAATATATTA-AATAACAA-ATGAT
1 AATAATAATATATGATAATAACAAGA-GAT
*
5276667 AATAATAATA-ATGATAATAATAAGAGAT
1 AATAATAATATATGATAATAACAAGAGAT
*
5276695 AACAATAATATA
1 AATAATAATATA
5276707 CTACCTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 29 0.85
29 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (29 bp):
AATAATAATATATGATAATAACAAGAGAT
Found at i:5276681 original size:15 final size:15
Alignment explanation
Indices: 5276639--5276689 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
5276629 ATAAAAATAC
*
5276639 AATAATAAT-ATATT
1 AATAATAATGATAAT
*
5276653 AAATAACAAATGATAAT
1 -AATAA-TAATGATAAT
5276670 AATAATAATGATAAT
1 AATAATAATGATAAT
5276685 AATAA
1 AATAA
5276690 GAGATAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 19 0.61
16 8 0.26
17 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
AATAATAATGATAAT
Found at i:5278052 original size:17 final size:17
Alignment explanation
Indices: 5278030--5278063 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5278020 TCTAAACATT
5278030 GCATAACTTGCATTACA
1 GCATAACTTGCATTACA
5278047 GCATAACTTGCATTACA
1 GCATAACTTGCATTACA
5278064 TAATATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
GCATAACTTGCATTACA
Found at i:5288382 original size:7 final size:7
Alignment explanation
Indices: 5288370--5288416 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
5288360 AATTCAGAAA
5288370 GCAGCAG
1 GCAGCAG
5288377 GCAGCAG
1 GCAGCAG
5288384 GCAGCAG
1 GCAGCAG
5288391 GCAGCAG
1 GCAGCAG
5288398 GCAGCAG
1 GCAGCAG
5288405 GCAGCAG
1 GCAGCAG
5288412 GCAGC
1 GCAGC
5288417 TAGCTTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.28, C:0.30, G:0.43, T:0.00
Consensus pattern (7 bp):
GCAGCAG
Found at i:5289791 original size:19 final size:19
Alignment explanation
Indices: 5289767--5289808 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
5289757 TTTGTTTGTT
5289767 TTAAAGCAAAATTTAAAAG
1 TTAAAGCAAAATTTAAAAG
5289786 TTAAAGCAAAATTTAAAAG
1 TTAAAGCAAAATTTAAAAG
5289805 TTAA
1 TTAA
5289809 TTCTTGCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (19 bp):
TTAAAGCAAAATTTAAAAG
Found at i:5297757 original size:2 final size:2
Alignment explanation
Indices: 5297750--5297786 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5297740 AATCAATTTC
5297750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5297787 TTTAAATGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5303262 original size:35 final size:35
Alignment explanation
Indices: 5303223--5303353 Score: 111
Period size: 35 Copynumber: 3.6 Consensus size: 35
5303213 CATGGCAAAG
*
5303223 TGTGATATGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACCGAGT
* * *
5303258 TGTGAAATGTAGTTATAGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTAT-G--GTATC--ATCCATACCGAGT
** ** *
5303298 TAAGAAATGTAGGTATGACAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACCGAGT
*
5303333 TGTAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
5303354 TTCAATGAGG
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
34 1 0.01
35 40 0.54
36 1 0.01
37 2 0.03
38 4 0.05
39 1 0.01
40 25 0.34
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACCGAGT
Found at i:5308830 original size:128 final size:128
Alignment explanation
Indices: 5308669--5308967 Score: 365
Period size: 129 Copynumber: 2.3 Consensus size: 128
5308659 GATAAATCGA
* * * **
5308669 AACCCAGCACG-TAGGGCACAATTTCTCGAAATTTCCAAACACGAAATATTGCCTTGTTTTTTAA
1 AACCCAGCACGATAGGGCACGATTCCTCG-AATTTCCAAACACG-AACATTGCCTT-CATTTTAA
*
5308733 A-ATTTAGAAAACATGAGTGAAATTCTAAAGAAATATTCGATTA-TTTGAACAAAC-AGGAAATT
63 AGATTTAGAAAACATGAGTGAAATTCTAAAGAAATATTCGATCATTTTGAACAAACGA-GAAATT
5308795 GT-
127 -TC
* * * *
5308797 AACCCAACACGATAGGGCACGATTCCCCGAATTTCCAAACTTCGAACGTTGCCTTCATTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAAC-ACGAACATTGCCTTCATTTTAAA-
** *
5308862 GATTTTTAAAACATGAGTGAAATTCTAAAGGAATATTCGATCATTTTGAACAAACGAGAAATTTC
64 GATTTAGAAAACATGAGTGAAATTCTAAAGAAATATTCGATCATTTTGAACAAACGAGAAATTTC
* *
5308927 AACCTAGCACGATAGGGCACGATTCCTCGAATTTCTAAACA
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACA
5308968 TCAAACATCG
Statistics
Matches: 146, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
127 7 0.05
128 30 0.21
129 55 0.38
130 53 0.36
131 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (128 bp):
AACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACACGAACATTGCCTTCATTTTAAAGA
TTTAGAAAACATGAGTGAAATTCTAAAGAAATATTCGATCATTTTGAACAAACGAGAAATTTC
Found at i:5308989 original size:130 final size:129
Alignment explanation
Indices: 5308740--5308978 Score: 347
Period size: 130 Copynumber: 1.8 Consensus size: 129
5308730 TAAAATTTAG
*
5308740 AAAACATGAGTGAAATTCTAAAGAAATATTCGATTATTTGAACAAACAGGAAATTGTAACCCAAC
1 AAAACATGAGTGAAATTCTAAAGAAATATTCGATCATTTGAACAAACAGGAAATTGTAACCCAAC
* * * *
5308805 ACGATAGGGCACGATTCCCCGAATTTCCAAACTTCGAACGTTGCCTTCATTTTAAAGGATTTTT
66 ACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATCGCCTTCATTTTAAAGGATTTTT
* *
5308869 AAAACATGAGTGAAATTCTAAAGGAATATTCGATCATTTTGAACAAAC-GAGAAATT-TCAACCT
1 AAAACATGAGTGAAATTCTAAAGAAATATTCGATCA-TTTGAACAAACAG-GAAATTGT-AACCC
* * *
5308932 AGCACGATAGGGCACGATTCCTCGAATTTCTAAACATCAAACATCGC
63 AACACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATCGC
5308979 TTTAGTTTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
129 36 0.37
130 61 0.63
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (129 bp):
AAAACATGAGTGAAATTCTAAAGAAATATTCGATCATTTGAACAAACAGGAAATTGTAACCCAAC
ACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATCGCCTTCATTTTAAAGGATTTTT
Found at i:5310065 original size:3 final size:3
Alignment explanation
Indices: 5310053--5310293 Score: 97
Period size: 3 Copynumber: 81.0 Consensus size: 3
5310043 GCAATAGTAC
* * *
5310053 TAA T-A TAA TAA TAA -AG TAGA AAA TAA TAA TAA TAA TACA TTAA TAG
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A -TAA TAA
* * * * * * *
5310099 GAA TAA TAA TAG T-A TAT TAA TAA TAA CAA TAA CAGA AAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* * * * *
5310144 TGA -AA TAA TAA TAA TAA TAA -AC TAA GGAA TAA TAA TAA GAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * * * * *
5310188 CAA TAA T-A TAAA TAA TAA TAA GAGA -AA TAG CAA CAA TAA TAG TAA
1 TAA TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * * *
5310233 TAA -AA GAA TAA AAA TGA TAA TAA TAA TAA TAG CAA TAA TAA TAGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
5310278 -AT TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
5310294 AGTAAATCAA
Statistics
Matches: 173, Mismatches: 47, Indels: 36
0.68 0.18 0.14
Matches are distributed among these distances:
2 13 0.08
3 147 0.85
4 11 0.06
5 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:5310107 original size:23 final size:23
Alignment explanation
Indices: 5310077--5310120 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5310067 AGTAGAAAAT
5310077 AATAATAATAATACATTAATAGG
1 AATAATAATAATACATTAATAGG
* *
5310100 AATAATAATAGTATATTAATA
1 AATAATAATAATACATTAATA
5310121 ATAACAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (23 bp):
AATAATAATAATACATTAATAGG
Found at i:5310123 original size:20 final size:20
Alignment explanation
Indices: 5310057--5310129 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 20
5310047 TAGTACTAAT
* *
5310057 ATAATAATAA-AGTAGA-AA
1 ATAATAATAATAGTACATTA
*
5310075 ATAATAATAATAATACATTA
1 ATAATAATAATAGTACATTA
*
5310095 ATAGGAATAATAATAGTATATTA
1 AT---AATAATAATAGTACATTA
*
5310118 ATAATAACAATA
1 ATAATAATAATA
5310130 ACAGAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.23
19 4 0.09
20 12 0.27
23 18 0.41
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAATAATAGTACATTA
Found at i:5310129 original size:23 final size:23
Alignment explanation
Indices: 5310074--5310130 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
5310064 TAAAGTAGAA
5310074 AATAATAATAATAATACATTAAT
1 AATAATAATAATAATACATTAAT
** * *
5310097 AGGAATAATAATAGTATATTAAT
1 AATAATAATAATAATACATTAAT
*
5310120 AATAACAATAA
1 AATAATAATAA
5310131 CAGAAAATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (23 bp):
AATAATAATAATAATACATTAAT
Found at i:5311138 original size:12 final size:11
Alignment explanation
Indices: 5311121--5311160 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
5311111 TTATTATCTA
5311121 TTTGCTATTGCT
1 TTTGCT-TTGCT
5311133 TTTGCTTTGCT
1 TTTGCTTTGCT
*
5311144 TGTTGCTTTGGT
1 T-TTGCTTTGCT
5311156 TTTGC
1 TTTGC
5311161 AGGTGCTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.03, C:0.15, G:0.23, T:0.60
Consensus pattern (11 bp):
TTTGCTTTGCT
Found at i:5312917 original size:47 final size:47
Alignment explanation
Indices: 5312864--5313036 Score: 194
Period size: 47 Copynumber: 3.7 Consensus size: 47
5312854 CGGATATTTG
*
5312864 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
5312911 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC--
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTA
*
5312960 -G--TCTGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
5313004 GGCATCCGAGCTCGTTGAGTTAAGTCAGAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
5313037 ACTTATGGAT
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 27 0.26
47 56 0.54
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:5312977 original size:93 final size:92
Alignment explanation
Indices: 5312869--5313082 Score: 365
Period size: 93 Copynumber: 2.3 Consensus size: 92
5312859 ATTTGGGCAT
* *
5312869 CCGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTAA
* *
5312934 GTCCGAGTTCACTTATGGATGCGAACGT
66 GTCAGAGTTCACTTATGGATGCG-ACGC
*
5312962 CTGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTAA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTAA
5313027 GTCAGAGTTCACTTATGGATGCGACGC
66 GTCAGAGTTCACTTATGGATGCGACGC
*
5313054 CCGAGCTCGTTGAGTTGAGTCCGAGTTCG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCG
5313083 CTTATGGGCG
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 30 0.26
93 84 0.74
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (92 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTAA
GTCAGAGTTCACTTATGGATGCGACGC
Found at i:5313080 original size:45 final size:45
Alignment explanation
Indices: 5312916--5313089 Score: 183
Period size: 45 Copynumber: 3.8 Consensus size: 45
5312906 AACTAGGCAT
*
5312916 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-ACGC
* * * * * *
5312962 CTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGACGC
* *
5313007 ATCCGAGCTCGTTGAGTTAAGTCAGAGTTCACTTATGGATGCGACGC
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGACGC
*
5313054 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5313090 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
43 4 0.04
45 37 0.36
46 27 0.26
47 28 0.27
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGACGC
Found at i:5321174 original size:22 final size:21
Alignment explanation
Indices: 5321093--5321176 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 21
5321083 GCACATACAT
5321093 AATATATATATACTATATAAAA
1 AATATATATATA-TATATAAAA
* *
5321115 AATATGTGCGAAATATAT-TAAAA
1 AATATAT---ATATATATATAAAA
* *
5321138 ATATAGACATGATATATATAAACA
1 A-ATATATAT-ATATATATAAA-A
5321162 AATATATATATATAT
1 AATATATATATATAT
5321177 GTATGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
21 1 0.02
22 18 0.38
23 16 0.34
24 8 0.17
25 4 0.09
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (21 bp):
AATATATATATATATATAAAA
Found at i:5321989 original size:27 final size:27
Alignment explanation
Indices: 5321951--5322005 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5321941 GAACAGGCCA
5321951 GTCGCTGTCGTGTCGTCCGCCGTGCCG
1 GTCGCTGTCGTGTCGTCCGCCGTGCCG
* *
5321978 GTCGCTGTCGTGTCTTCCGTCGTGCCG
1 GTCGCTGTCGTGTCGTCCGCCGTGCCG
5322005 G
1 G
5322006 CCACCGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.36, T:0.29
Consensus pattern (27 bp):
GTCGCTGTCGTGTCGTCCGCCGTGCCG
Found at i:5325932 original size:29 final size:30
Alignment explanation
Indices: 5325866--5325932 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
5325856 GATAAAATTT
* ** *
5325866 TAATTTTATAATTTTTAAAGGATTAAATTA
1 TAATTTTATAACTTAGAAAGGATTAAAATA
5325896 -AATTTTTATAACTTAGAAA-GATTAAAATA
1 TAA-TTTTATAACTTAGAAAGGATTAAAATA
5325925 TAATTTTA
1 TAATTTTA
5325933 CTTTTACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (30 bp):
TAATTTTATAACTTAGAAAGGATTAAAATA
Found at i:5326650 original size:2 final size:2
Alignment explanation
Indices: 5326632--5326680 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
5326622 TTCGTCTTCA
* * *
5326632 AT AT AT AC AT AT CT AT AT AT AT AT AT AT AT AT AT AG AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5326673 AT AT AT AT
1 AT AT AT AT
5326681 TTTCGCATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5327627 original size:36 final size:37
Alignment explanation
Indices: 5327570--5327659 Score: 146
Period size: 36 Copynumber: 2.4 Consensus size: 37
5327560 TTTTATGTGT
*
5327570 TATTTAAGTTATCATTAGACATATATTTTAACATTTATA
1 TATTTAATTTA-CA-TAGACATATATTTTAACATTTATA
5327609 T-TTTAATTTACATAGACATATATTTTAACATTTATA
1 TATTTAATTTACATAGACATATATTTTAACATTTATA
5327645 TATTTAATTTACATA
1 TATTTAATTTACATA
5327660 TATTACATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 25 0.51
37 15 0.31
38 8 0.16
39 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (37 bp):
TATTTAATTTACATAGACATATATTTTAACATTTATA
Found at i:5331167 original size:16 final size:17
Alignment explanation
Indices: 5331146--5331184 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
5331136 ATGTGGGTAA
5331146 AAAATAAAA-TTAATAT
1 AAAATAAAATTTAATAT
5331162 AAAATAAAATTTTAATAT
1 AAAATAAAA-TTTAATAT
5331180 AAAAT
1 AAAAT
5331185 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
18 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAAATTTAATAT
Found at i:5331205 original size:16 final size:17
Alignment explanation
Indices: 5331155--5331205 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 17
5331145 AAAAATAAAA
**
5331155 TTAATATAAAATAAAATT
1 TTAATATAAAAT-ATTTT
*
5331173 TTAATATAAAATTTTTT
1 TTAATATAAAATATTTT
*
5331190 TTAAT-TAATATATTTT
1 TTAATATAAAATATTTT
5331206 CAATAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 9 0.32
17 7 0.25
18 12 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATAAAATATTTT
Found at i:5331272 original size:7 final size:7
Alignment explanation
Indices: 5331260--5331305 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
5331250 TTGTTGATAA
5331260 GATACAT
1 GATACAT
5331267 GATACAT
1 GATACAT
5331274 GATACAT
1 GATACAT
5331281 GATAC--
1 GATACAT
5331286 GATACAT
1 GATACAT
5331293 GATACAT
1 GATACAT
5331300 GATACA
1 GATACA
5331306 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
7 32 0.86
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (7 bp):
GATACAT
Found at i:5331289 original size:19 final size:19
Alignment explanation
Indices: 5331267--5331304 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5331257 TAAGATACAT
5331267 GATACATGATACATGATAC
1 GATACATGATACATGATAC
5331286 GATACATGATACATGATAC
1 GATACATGATACATGATAC
5331305 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
GATACATGATACATGATAC
Found at i:5331290 original size:26 final size:26
Alignment explanation
Indices: 5331254--5331305 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5331244 ATATAATTGT
5331254 TGATAAGATACATGATACATGATACA
1 TGATAAGATACATGATACATGATACA
*
5331280 TGATACGATACATGATACATGATACA
1 TGATAAGATACATGATACATGATACA
5331306 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (26 bp):
TGATAAGATACATGATACATGATACA
Found at i:5331313 original size:2 final size:2
Alignment explanation
Indices: 5331306--5331336 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5331296 ACATGATACA
5331306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5331337 ACAATATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5331410 original size:20 final size:20
Alignment explanation
Indices: 5331372--5331408 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5331362 TGCCGCTATT
5331372 AAGAGAAAATTAATAAAATC
1 AAGAGAAAATTAATAAAATC
*
5331392 AAGAGTAAATT-ATAAAA
1 AAGAGAAAATTAATAAAA
5331409 ATAATCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (20 bp):
AAGAGAAAATTAATAAAATC
Found at i:5332901 original size:15 final size:14
Alignment explanation
Indices: 5332862--5332891 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5332852 AAATATTAGA
5332862 TTTAAAAAATAAAT
1 TTTAAAAAATAAAT
5332876 TTTAAAAAATAAAT
1 TTTAAAAAATAAAT
5332890 TT
1 TT
5332892 ATTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTAAAAAATAAAT
Found at i:5346824 original size:79 final size:79
Alignment explanation
Indices: 5346693--5346843 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 79
5346683 CTGTAGTAAG
* * * * *
5346693 AAATGGCACTTCAAGTTAAGCTGCAAAGAGTGAAATGATTACCTAGTCACTAAGGGAAAATGTAT
1 AAATGACACTTCAAGTCAAGCTGCAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
*
5346758 GGAACTCCTATAAA
66 GAAACTCCTATAAA
** *
5346772 AAATGACACTTCAAGTCAATTTGTAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
1 AAATGACACTTCAAGTCAAGCTGCAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
5346837 GAAACTC
66 GAAACTC
5346844 TTTAATATGA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (79 bp):
AAATGACACTTCAAGTCAAGCTGCAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
GAAACTCCTATAAA
Found at i:5352012 original size:19 final size:19
Alignment explanation
Indices: 5351988--5352027 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5351978 TAAAATAAAG
5351988 AATGATTAGTCTGAATTTA
1 AATGATTAGTCTGAATTTA
5352007 AATGATTAGTCTGAATTTA
1 AATGATTAGTCTGAATTTA
5352026 AA
1 AA
5352028 CTTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (19 bp):
AATGATTAGTCTGAATTTA
Found at i:5355062 original size:60 final size:60
Alignment explanation
Indices: 5354969--5355089 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
5354959 ACTGACTATG
5354969 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAAG-TATATAT
1 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATG-AGTTATATAT
5355029 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
1 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
5355089 G
1 G
5355090 CATGGCCAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 2 0.03
60 58 0.97
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (60 bp):
GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
Found at i:5355745 original size:38 final size:36
Alignment explanation
Indices: 5355676--5355746 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
5355666 TATTTACAAT
*
5355676 TTTTTATAATTTTAATGATTTTAATTTTAAAAATAG
1 TTTTTATAATTTTAATGATTTTAAATTTAAAAATAG
**
5355712 TTTTTATAATTTTTTTGAATTTTTAAATTTAAAAA
1 TTTTTATAATTTTAATG-A-TTTTAAATTTAAAAA
5355747 ATCAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 15 0.50
37 1 0.03
38 14 0.47
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (36 bp):
TTTTTATAATTTTAATGATTTTAAATTTAAAAATAG
Found at i:5360451 original size:128 final size:127
Alignment explanation
Indices: 5360216--5360534 Score: 406
Period size: 128 Copynumber: 2.5 Consensus size: 127
5360206 GAAAATTCCT
* * * *
5360216 TAAAACGAAGGCAATATTTGATGCTTGAAAATTCGGGGAATCGTGCCCTATCGTGCTAGGTTTCG
1 TAAAAC-AAGGCAATGTTTGATGTTTGAAAATTCGGGGAATCGTGCCCTATTGTGCTGGGTTTCG
* *
5360281 ATTTCCCGTTTATTCAAAATAATCGAATATTCCTTTAGAATTTCACTT-GTGTTTTTCTAAATTC
65 ATTTCCCGTTTATTCAAAATAATCGAATATTCCTTTAGAATTTCA-TTCGTATTCTT-TAAATTC
* * * *
5360345 TGAAACAAGGCAATGTTTGATATTTGAAAATTCGGGGAATCGTGCCCTATTGTACTGGGTTTCTA
1 TAAAACAAGGCAATGTTTGATGTTTGAAAATTCGGGGAATCGTGCCCTATTGTGCTGGGTTTCGA
** *
5360410 TTTCTTGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCATTCGTATTCTTTAAATTC
66 TTTCCCGTTTATTCAAAATAATCGAATATTCCTTTAGAATTTCATTCGTATTCTTTAAATTC
* ** * * * * * *
5360472 TAAAACAAAGCAATGTTCAATGTTTGGAAGTTTGAGGAATCGTGCCCTACTGTGTTGGGTTTC
1 TAAAACAAGGCAATGTTTGATGTTTGAAAATTCGGGGAATCGTGCCCTATTGTGCTGGGTTTC
5360535 AGTTTTTCGT
Statistics
Matches: 164, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
127 60 0.37
128 99 0.60
129 5 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (127 bp):
TAAAACAAGGCAATGTTTGATGTTTGAAAATTCGGGGAATCGTGCCCTATTGTGCTGGGTTTCGA
TTTCCCGTTTATTCAAAATAATCGAATATTCCTTTAGAATTTCATTCGTATTCTTTAAATTC
Found at i:5378259 original size:132 final size:132
Alignment explanation
Indices: 5378051--5378353 Score: 344
Period size: 132 Copynumber: 2.3 Consensus size: 132
5378041 AGAAAATCGA
*** * * ** * **
5378051 AACCCAGCAC-AGTAGGGCACGATTCTTTGAATTTCTAAACATCGAGTATTGCCTTGTTTTTTAG
1 AACCCAGCACGA-TAGGGCACGATTCCACGAATTGCCAAACATCGAACATTACCTTGTTTTAAAG
* * ** *
5378115 AATTTTTAAG-AAACATGAGGGAAATTCTAAAGGGGATGTTCGATTATTTTGAACCAAC-AGGAA
65 AATTTTTAAGAAAACATGAAGGAAATTCCAAA-GGGACATTCGATTATTTTGAACAAACGA-GAA
*
5378178 ATTGC
128 ATTAC
* *
5378183 AACCCAGCACGATAGGGCACAATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCACGAATTGCCAAACATCGAACATTACCTT-GTTTTAAAG
* * *
5378248 AGTTTTT-AGAAAACATGAATGAAATTCCAAAGGGACATTCGATTGTTTTGAACAAACGAGAAAT
65 AATTTTTAAGAAAACATGAAGGAAATTCCAAAGGGACATTCGATTATTTTGAACAAACGAGAAAT
5378312 TAC
130 TAC
*
5378315 AACCCAGCACGTTAGGGCACGATTCCACGAATTGCCAAA
1 AACCCAGCACGATAGGGCACGATTCCACGAATTGCCAAA
5378354 TATCAAATCT
Statistics
Matches: 144, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
132 111 0.77
133 33 0.23
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (132 bp):
AACCCAGCACGATAGGGCACGATTCCACGAATTGCCAAACATCGAACATTACCTTGTTTTAAAGA
ATTTTTAAGAAAACATGAAGGAAATTCCAAAGGGACATTCGATTATTTTGAACAAACGAGAAATT
AC
Found at i:5378370 original size:132 final size:134
Alignment explanation
Indices: 5378113--5378387 Score: 337
Period size: 132 Copynumber: 2.1 Consensus size: 134
5378103 CTTGTTTTTT
* * ** *
5378113 AGAATTTTTAAGAAACATGAGGGAAATTCTAAAGGGGATGTTCGATTATTTTGAACCAACAGGAA
1 AGAATTTTTAAGAAACATGAAGGAAATTCCAAAGGGGACATTCGATTATTTTGAACAAACAGGAA
* *
5378178 ATTGCAACCCAGCACGATAGGGCACAATTCCCCGAATTGCCAAACATCGAACATTACCTTC-GTT
66 ATTACAACCCAGCACGATAGGGCACAATTCCACGAATTGCCAAACATCGAACATTACCTTCAGTT
5378242 TTAA
131 TTAA
* * *
5378246 AGAGTTTTT-AGAAAACATGAATGAAATTCCAAA-GGGACATTCGATTGTTTTGAACAAAC-GAG
1 AGAATTTTTAAG-AAACATGAAGGAAATTCCAAAGGGGACATTCGATTATTTTGAACAAACAG-G
* * * *
5378308 AAATTACAACCCAGCACGTTAGGGCACGATTCCACGAATTGCCAAATATC-AA-ATCTCGCCTTC
64 AAATTACAACCCAGCACGATAGGGCACAATTCCACGAATTGCCAAACATCGAACAT-T-ACCTTC
*
5378371 ATTTTTAA
127 AGTTTTAA
5378379 AGAATTTTT
1 AGAATTTTT
5378388 GAACGAATAA
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
130 2 0.02
131 4 0.03
132 75 0.62
133 40 0.33
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (134 bp):
AGAATTTTTAAGAAACATGAAGGAAATTCCAAAGGGGACATTCGATTATTTTGAACAAACAGGAA
ATTACAACCCAGCACGATAGGGCACAATTCCACGAATTGCCAAACATCGAACATTACCTTCAGTT
TTAA
Found at i:5391086 original size:40 final size:40
Alignment explanation
Indices: 5391029--5391105 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
5391019 TAAAGTTATT
* *
5391029 CATAACATGCCCCGAGCTTTGCCAACTTCCTTTCATGAAC
1 CATAACATGCCCAGAGCTATGCCAACTTCCTTTCATGAAC
* *
5391069 CATAACATGCCTAGAGCTATGTCAACTTCCTTTCATG
1 CATAACATGCCCAGAGCTATGCCAACTTCCTTTCATG
5391106 TTTAGAGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (40 bp):
CATAACATGCCCAGAGCTATGCCAACTTCCTTTCATGAAC
Found at i:5413970 original size:6 final size:6
Alignment explanation
Indices: 5413959--5414025 Score: 77
Period size: 6 Copynumber: 11.2 Consensus size: 6
5413949 CAACCCAATC
*
5413959 TTTATT TTTATT TTTATT TTTA-- TTTATT TTTTTT TTTATT ATTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT
5414006 ATTT-TCT TTTATT TTTATT T
1 -TTTAT-T TTTATT TTTATT T
5414026 CATTTTAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 4 0.07
6 38 0.70
7 12 0.22
ACGTcount: A:0.16, C:0.01, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:5413987 original size:22 final size:21
Alignment explanation
Indices: 5413959--5414031 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 21
5413949 CAACCCAATC
5413959 TTTATTTTTATTTTTATTTTTA
1 TTTATTTTT-TTTTTATTTTTA
5413981 TTTATTTTTTTTTTTATTATTTA
1 TTTA-TTTTTTTTTTATT-TTTA
*
5414004 -TTA-TTTTCTTTTATTTTTA
1 TTTATTTTTTTTTTATTTTTA
5414023 TTTCATTTT
1 TTT-ATTTT
5414032 AGTTAAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.09
20 13 0.29
21 1 0.02
22 18 0.40
23 9 0.20
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTATTTTTTTTTTATTTTTA
Found at i:5414032 original size:16 final size:15
Alignment explanation
Indices: 5413963--5414025 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 15
5413953 CCAATCTTTA
5413963 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
5413978 TTATTTATTTTT-TTT
1 TT-TTTATTTTTATTT
5413993 TTTATTATTTATTATTT
1 TTT-TTATTT-TTATTT
5414010 TCTTTTATTTTTATTT
1 T-TTTTATTTTTATTT
5414026 CATTTTAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.02
15 13 0.30
16 17 0.40
17 10 0.23
18 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTTATTT
Found at i:5415208 original size:118 final size:117
Alignment explanation
Indices: 5414985--5415214 Score: 379
Period size: 118 Copynumber: 2.0 Consensus size: 117
5414975 TGTTTTCCAT
* *
5414985 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGTTGTCATTC
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGTTGTCATTC
5415050 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
5415102 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTT-GGTTGTCATT
****
5415167 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
65 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
5415215 ACCGGAAATA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 50 0.48
118 54 0.52
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (117 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGTTGTCATTC
TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:5418029 original size:20 final size:19
Alignment explanation
Indices: 5418004--5418065 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 19
5417994 TAACATGTGC
5418004 ATAATACGATATTAAAAAAT
1 ATAATA-GATATTAAAAAAT
5418024 ATAATATAGTATATTAAAAAAT
1 AT-A-ATAG-ATATTAAAAAAT
*
5418046 ATAATATAGTATTAAAAAAT
1 ATAATAGA-TATTAAAAAAT
5418066 GTATACATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 16 0.43
21 3 0.08
22 17 0.46
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAATAGATATTAAAAAAT
Found at i:5418039 original size:22 final size:22
Alignment explanation
Indices: 5418012--5418080 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
5418002 GCATAATACG
5418012 ATATTAAAAAATATAATATAGT
1 ATATTAAAAAATATAATATAGT
5418034 ATATTAAAAAATATAATATAG-
1 ATATTAAAAAATATAATATAGT
* *
5418055 -TATTAAAAAATGTATACATAGT
1 ATATTAAAAAATATA-ATATAGT
5418077 ATAT
1 ATAT
5418081 ATACTAGGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 13 0.31
21 5 0.12
22 21 0.50
23 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATTAAAAAATATAATATAGT
Found at i:5418373 original size:26 final size:24
Alignment explanation
Indices: 5418333--5418392 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
5418323 TTATTTTATT
* * *
5418333 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
5418357 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
5418383 AAATAAATAT
1 AAATAAATAT
5418393 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:5418404 original size:22 final size:22
Alignment explanation
Indices: 5418363--5418421 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
5418353 ATAATAAATC
* *
5418363 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
5418383 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
5418405 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
5418422 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:5418743 original size:24 final size:25
Alignment explanation
Indices: 5418695--5418746 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
5418685 ATAGTAATAG
* *
5418695 TATATACATAATATAGTTATTAAAAA
1 TATATACATAACATAG-TATGAAAAA
5418721 TATATACATAACATA-TATGAAAAA
1 TATATACATAACATAGTATGAAAAA
5418745 TA
1 TA
5418747 CAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
TATATACATAACATAGTATGAAAAA
Found at i:5419013 original size:25 final size:24
Alignment explanation
Indices: 5418973--5419020 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
5418963 GTATTGATTA
5418973 AAAATAATACTAATAATAGTAATAGT
1 AAAATAATACTAATAA-A-TAATAGT
5418999 AAAAT-ATACTAATAAATAATAG
1 AAAATAATACTAATAAATAATAG
5419021 ATATAGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 10 0.45
26 5 0.23
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (24 bp):
AAAATAATACTAATAAATAATAGT
Found at i:5419326 original size:24 final size:24
Alignment explanation
Indices: 5419266--5419386 Score: 70
Period size: 24 Copynumber: 4.9 Consensus size: 24
5419256 ATATGATAAC
5419266 ATAAAAATATATA-ACTAATAATA-T
1 ATAAAAATATATACA-TAAT-ATAGT
* * *
5419290 TTAAGAATGTATACATAATATAGT
1 ATAAAAATATATACATAATATAGT
* *
5419314 ATAAAAATATATATATACGTAATATAGA
1 AT--AAA-A-ATATATACATAATATAGT
** * *
5419342 ATTTAAA-ATATACCTAATATATT
1 ATAAAAATATATACATAATATAGT
5419365 A-AAAGAATATATACATAATATA
1 ATAAA-AATATATACATAATATA
5419387 AAGTTAAGAA
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 19 0.26
24 30 0.41
25 2 0.03
26 3 0.04
27 1 0.01
28 17 0.23
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (24 bp):
ATAAAAATATATACATAATATAGT
Found at i:5419500 original size:22 final size:22
Alignment explanation
Indices: 5419481--5419537 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
5419471 ATACTAATGC
5419481 TAATAAATAAT-AAATATAATAA
1 TAAT-AATAATAAAATATAATAA
* *
5419503 TAATAGTAATAAAATATAATAG
1 TAATAATAATAAAATATAATAA
5419525 TATATATATAATA
1 TA-ATA-ATAATA
5419538 TTAAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 16 0.55
23 3 0.10
24 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
TAATAATAATAAAATATAATAA
Found at i:5419537 original size:19 final size:18
Alignment explanation
Indices: 5419481--5419538 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 18
5419471 ATACTAATGC
*
5419481 TAATA-AATAATAA-ATA
1 TAATATAATAGTAATATA
5419497 TAATAATAATAGTAATA-A
1 TAAT-ATAATAGTAATATA
5419515 -AATATAATAGTATATATA
1 TAATATAATAGTA-ATATA
5419533 TAATAT
1 TAATAT
5419539 TAAAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 13 0.37
17 7 0.20
18 9 0.26
19 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAATATAATAGTAATATA
Found at i:5421130 original size:16 final size:16
Alignment explanation
Indices: 5421109--5421165 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
5421099 TATTTCTTCC
5421109 AAAAATTCTAAATTCT
1 AAAAATTCTAAATTCT
5421125 AAAAATTC-AAA---T
1 AAAAATTCTAAATTCT
*
5421137 AAGAAAATCTAAATTTCT
1 AA-AAATTCTAAA-TTCT
5421155 AAAAATT-TAAA
1 AAAAATTCTAAA
5421166 ACTTTATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 3 0.09
15 3 0.09
16 12 0.36
17 4 0.12
18 3 0.09
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAAATTCTAAATTCT
Found at i:5421342 original size:17 final size:18
Alignment explanation
Indices: 5421317--5421355 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5421307 TCAAAAGTTA
*
5421317 TATACTTTTTT-AATTCT
1 TATAATTTTTTCAATTCT
*
5421334 TATAATTTTTTCAATTTT
1 TATAATTTTTTCAATTCT
5421352 TATA
1 TATA
5421356 TAATATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (18 bp):
TATAATTTTTTCAATTCT
Found at i:5421359 original size:20 final size:19
Alignment explanation
Indices: 5421314--5421372 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
5421304 TTTTCAAAAG
*
5421314 TTATATACTTTTTTAA-TT
1 TTATATAATTTTTTAATTT
*
5421332 CT-TATAATTTTTTCAATTT
1 TTATATAATTTTTT-AATTT
*
5421351 TTATATAATATTTTGAATTT
1 TTATATAAT-TTTTTAATTT
5421371 TT
1 TT
5421373 TAATTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 10 0.30
18 3 0.09
19 3 0.09
20 13 0.39
21 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATATAATTTTTTAATTT
Found at i:5421392 original size:29 final size:30
Alignment explanation
Indices: 5421333--5421401 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
5421323 TTTTTAATTC
*
5421333 TTAT-AATTTTTTCAATTTTTATATAATAT
1 TTATCAATTTTTTCAATTTATATATAATAT
*
5421362 TT-TGAATTTTTT-AATTTATAT-TATATAAT
1 TTATCAATTTTTTCAATTTATATATA-AT-AT
5421391 TTATCAATTTT
1 TTATCAATTTT
5421402 CAAAACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
27 2 0.06
28 11 0.32
29 14 0.41
30 7 0.21
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
TTATCAATTTTTTCAATTTATATATAATAT
Found at i:5424963 original size:12 final size:12
Alignment explanation
Indices: 5424945--5424987 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5424935 TAACTACATA
5424945 AAAAATATATTT
1 AAAAATATATTT
* *
5424957 TAAAATATATAT
1 AAAAATATATTT
*
5424969 GAAAA-ATATTT
1 AAAAATATATTT
5424980 AAAAATAT
1 AAAAATAT
5424988 CCATCAATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AAAAATATATTT
Found at i:5425143 original size:23 final size:23
Alignment explanation
Indices: 5425116--5425160 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5425106 TATTTGGAAT
*
5425116 TTTTTTTA-TTTTCACATTTTAA
1 TTTTTTTATTTTTCAAATTTTAA
5425138 TTTTTTTATTTTTCAAATTTTAA
1 TTTTTTTATTTTTCAAATTTTAA
5425161 AATTCAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTTTATTTTTCAAATTTTAA
Done.