Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 180 of 182
Found at i:54831102 original size:19 final size:19
Alignment explanation
Indices: 54831078--54831114 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
54831068 TTGAAAACTG
54831078 ATTTTCAACCTCAACGATA
1 ATTTTCAACCTCAACGATA
54831097 ATTTTCAACCTCAACGAT
1 ATTTTCAACCTCAACGAT
54831115 GAACACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTTTCAACCTCAACGATA
Found at i:54834082 original size:31 final size:31
Alignment explanation
Indices: 54834012--54834083 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
54834002 AGATTAAATC
* *
54834012 CGAGTTCAATGACCAAAATAAACTTAATTGT
1 CGAGTTCAAAGACCAAAATAAACTTAATTAT
* * * *
54834043 -GAAATTCAAAGACCAAAGTGAATTTAATTAT
1 CG-AGTTCAAAGACCAAAATAAACTTAATTAT
54834074 CGAGTTCAAA
1 CGAGTTCAAA
54834084 AACTAAAAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
30 1 0.03
31 30 0.94
32 1 0.03
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (31 bp):
CGAGTTCAAAGACCAAAATAAACTTAATTAT
Found at i:54841355 original size:2 final size:2
Alignment explanation
Indices: 54841348--54841372 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54841338 AGATTTAGGT
54841348 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
54841373 TTCTTGGACT
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:54842919 original size:6 final size:6
Alignment explanation
Indices: 54842908--54842934 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
54842898 AAGTGATGCT
54842908 ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATA
54842935 AAATTGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:54852401 original size:60 final size:60
Alignment explanation
Indices: 54852337--54852474 Score: 179
Period size: 62 Copynumber: 2.3 Consensus size: 60
54852327 GATAAAATTG
* *
54852337 AATAGTTGAGTGACTATTTTGTAACTTTTCATAGTTGGGTGACTC-AAAAAGAAATTCACT
1 AATAGTTGAGTGACTATTTTGTAACTTTTCATAGTTGGATAAC-CAAAAAAGAAATTCACT
* * *
54852397 AATAGTCGAGTGATCATTTTTTGTAACTTTTCATAGTTGGATAACCAAAAAAGAAATTTACT
1 AATAGTTGAGTGA-C-TATTTTGTAACTTTTCATAGTTGGATAACCAAAAAAGAAATTCACT
* *
54852459 AACAGTTGGGTGACTA
1 AATAGTTGAGTGACTA
54852475 CTACTGCAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
60 13 0.20
61 3 0.05
62 50 0.76
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (60 bp):
AATAGTTGAGTGACTATTTTGTAACTTTTCATAGTTGGATAACCAAAAAAGAAATTCACT
Found at i:54866327 original size:70 final size:70
Alignment explanation
Indices: 54866253--54866393 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
54866243 TTTGAGCTAA
54866253 ATCTCACAAATTATTAATATATCATCATTTTATGTTTATATATTGCATACAAAAATAATTATATT
1 ATCTCACAAATTATTAATATATCATCATTTTATGTTTATATATTGCATACAAAAATAATTATATT
54866318 TATCT
66 TATCT
54866323 ATCTCACAAATTATTAATATATCATCATTTTATGTTTATATATTGCATACAAAAATAATTATATT
1 ATCTCACAAATTATTAATATATCATCATTTTATGTTTATATATTGCATACAAAAATAATTATATT
54866388 TATCT
66 TATCT
54866393 A
1 A
54866394 ATATACAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (70 bp):
ATCTCACAAATTATTAATATATCATCATTTTATGTTTATATATTGCATACAAAAATAATTATATT
TATCT
Found at i:54868857 original size:23 final size:22
Alignment explanation
Indices: 54868809--54868857 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
54868799 TTAAATTTTT
* **
54868809 AAATTTAAAAATTAAAGAGACC
1 AAATTTAAAAATTAAAAAGAAA
*
54868831 AAATTCTAAAAATTAAAAATAAA
1 AAATT-TAAAAATTAAAAAGAAA
54868854 AAAT
1 AAAT
54868858 AAAAAATCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.24
Consensus pattern (22 bp):
AAATTTAAAAATTAAAAAGAAA
Found at i:54883775 original size:31 final size:31
Alignment explanation
Indices: 54883737--54883801 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
54883727 TACCTGTCAG
54883737 GTCCTTTTATTATAGGGAATGATTCAAATTA
1 GTCCTTTTATTATAGGGAATGATTCAAATTA
54883768 GTCCTTTTATTATAGGGAATGATTCAAATTA
1 GTCCTTTTATTATAGGGAATGATTCAAATTA
54883799 GTC
1 GTC
54883802 ATTAGTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (31 bp):
GTCCTTTTATTATAGGGAATGATTCAAATTA
Found at i:54889976 original size:25 final size:26
Alignment explanation
Indices: 54889940--54889990 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
54889930 GTGGCACTTA
54889940 TAAATTG-AAAAAAAAATAATTAAAC
1 TAAATTGAAAAAAAAAATAATTAAAC
*
54889965 TAAATTATAAAAAAAAAATAATTAAA
1 TAAATT-GAAAAAAAAAATAATTAAA
54889991 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
27 17 0.74
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (26 bp):
TAAATTGAAAAAAAAAATAATTAAAC
Found at i:54890563 original size:30 final size:30
Alignment explanation
Indices: 54890521--54890578 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
54890511 AAAATTTGGA
*
54890521 TAACATAATATAATTTAAGTATCACTTAGG
1 TAACATAATATAATTTAAGCATCACTTAGG
*
54890551 TAACA-AAGTATAATTTAGGCATCACTTA
1 TAACATAA-TATAATTTAAGCATCACTTA
54890579 TGACAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (30 bp):
TAACATAATATAATTTAAGCATCACTTAGG
Found at i:54903328 original size:22 final size:22
Alignment explanation
Indices: 54903289--54903333 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54903279 AATTAAGCTT
*
54903289 AGGGCTAATAATATATTTTATA
1 AGGGCTAATAATATATTTGATA
*
54903311 AGGGC-AATAATGTAATTTGATA
1 AGGGCTAATAATAT-ATTTGATA
54903333 A
1 A
54903334 TATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGGCTAATAATATATTTGATA
Found at i:54908448 original size:19 final size:18
Alignment explanation
Indices: 54908424--54908474 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
54908414 TGTAATTTAC
54908424 TTTATATTTACAAATATTG
1 TTTATATTTA-AAATATTG
*
54908443 TTTATAATATAAAATATTG
1 TTTAT-ATTTAAAATATTG
54908462 TTTA-ATATTAAAA
1 TTTATAT-TTAAAA
54908475 ACAATGGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
19 17 0.61
20 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (18 bp):
TTTATATTTAAAATATTG
Found at i:54909349 original size:14 final size:15
Alignment explanation
Indices: 54909330--54909368 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54909320 CACCATAACC
54909330 ATAAATATTAGA-AA
1 ATAAATATTAGACAA
* *
54909344 ATAAATATTTGACAT
1 ATAAATATTAGACAA
54909359 ATAAATATTA
1 ATAAATATTA
54909369 TATATAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (15 bp):
ATAAATATTAGACAA
Found at i:54911239 original size:13 final size:13
Alignment explanation
Indices: 54911221--54911249 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
54911211 TTTTAAAAAT
54911221 AAAAAAATT-ATA
1 AAAAAAATTCATA
54911233 AAAAAAATTCATA
1 AAAAAAATTCATA
54911246 AAAA
1 AAAA
54911250 TTAATAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAATTCATA
Found at i:54913074 original size:15 final size:15
Alignment explanation
Indices: 54913054--54913105 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
54913044 TCTGTACATA
54913054 CGAACCCCCCGTATG
1 CGAACCCCCCGTATG
**** *
54913069 CGAACCTTGTGTATA
1 CGAACCCCCCGTATG
54913084 CGAACCCCCCGTATG
1 CGAACCCCCCGTATG
*
54913099 CAAACCC
1 CGAACCC
54913106 TATGTATGCG
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.25, C:0.40, G:0.17, T:0.17
Consensus pattern (15 bp):
CGAACCCCCCGTATG
Found at i:54913112 original size:30 final size:30
Alignment explanation
Indices: 54913051--54913117 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
54913041 TAATCTGTAC
* * *
54913051 ATACGAACCCCCCGTATGCGAACCTTGTGT
1 ATACGAACCCCCCGTATGCAAACCCTATGT
54913081 ATACGAACCCCCCGTATGCAAACCCTATGT
1 ATACGAACCCCCCGTATGCAAACCCTATGT
*
54913111 ATGCGAA
1 ATACGAA
54913118 ACCTTATAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (30 bp):
ATACGAACCCCCCGTATGCAAACCCTATGT
Found at i:54913133 original size:29 final size:29
Alignment explanation
Indices: 54913100--54913185 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
54913090 CCCCGTATGC
*
54913100 AAACCCTATGTATGCGAA-ACCTTATAGGA
1 AAACCCCATGTATGCGAACACC-TATAGGA
* *
54913129 AAACCCCCTGTATGCGAACACCTATAGGC
1 AAACCCCATGTATGCGAACACCTATAGGA
* * *
54913158 GAGCCCCATGTATGTGAATC-CCTATAGG
1 AAACCCCATGTATGCGAA-CACCTATAGG
54913186 TGACCTCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (29 bp):
AAACCCCATGTATGCGAACACCTATAGGA
Found at i:54913202 original size:30 final size:29
Alignment explanation
Indices: 54913149--54913205 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
54913139 TATGCGAACA
* *
54913149 CCTATAGGCGAGCCCCATGTATGTGAATC
1 CCTATAGGCGACCCCCATATATGTGAATC
*
54913178 CCTATAGGTGACCTCCCATATATGTGAA
1 CCTATAGGCGACC-CCCATATATGTGAA
54913206 CACATATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (29 bp):
CCTATAGGCGACCCCCATATATGTGAATC
Found at i:54913352 original size:45 final size:45
Alignment explanation
Indices: 54913303--54913410 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
54913293 CTGTTATGCC
* * **
54913303 ATGCGAACTCTATCTG-TATAACATGCAAACCCTACATGCACTAAT
1 ATGCGAACCCTATATGTTAT-ACATGCAAACCCTACATGCAAGAAT
** *
54913348 ATGCGAACCCTATATGTTATTTATGCAAACTCTACATGCAAGAAT
1 ATGCGAACCCTATATGTTATACATGCAAACCCTACATGCAAGAAT
*
54913393 ATGCGAACCCTATTTGTT
1 ATGCGAACCCTATATGTT
54913411 TATTTTGTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 51 0.94
46 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (45 bp):
ATGCGAACCCTATATGTTATACATGCAAACCCTACATGCAAGAAT
Found at i:54913356 original size:23 final size:23
Alignment explanation
Indices: 54913320--54913404 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
54913310 CTCTATCTGT
*
54913320 ATAACATGCAAACCCTACATGCA
1 ATAATATGCAAACCCTACATGCA
* * * **
54913343 CTAATATGCGAACCCTATATGTT
1 ATAATATGCAAACCCTACATGCA
* *
54913366 AT-TTATGCAAACTCTACATGCA
1 ATAATATGCAAACCCTACATGCA
* *
54913388 AGAATATGCGAACCCTA
1 ATAATATGCAAACCCTA
54913405 TTTGTTTATT
Statistics
Matches: 44, Mismatches: 17, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
22 15 0.34
23 29 0.66
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (23 bp):
ATAATATGCAAACCCTACATGCA
Found at i:54913424 original size:45 final size:45
Alignment explanation
Indices: 54913325--54913433 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
54913315 TCTGTATAAC
* **
54913325 ATGCAAACCCTACATGCACTAATATGCGAACCCTATATGTTATTT
1 ATGCAAACTCTACATGCAAGAATATGCGAACCCTATATGTTATTT
*
54913370 ATGCAAACTCTACATGCAAGAATATGCGAACCCTATTTGTTTATTT
1 ATGCAAACTCTACATGCAAGAATATGCGAACCCTATATG-TTATTT
** *
54913416 -TGTGAACTCTATATGCAA
1 ATGCAAACTCTACATGCAA
54913434 ACCTTGATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 50 0.89
46 6 0.11
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (45 bp):
ATGCAAACTCTACATGCAAGAATATGCGAACCCTATATGTTATTT
Found at i:54914161 original size:3 final size:3
Alignment explanation
Indices: 54914153--54914192 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
54914143 CGTGTTCCAC
54914153 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54914193 GCATTATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54916914 original size:29 final size:29
Alignment explanation
Indices: 54916872--54916959 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
54916862 CCCCCTGTAT
* *
54916872 GCGAGCCCCATGTATGCGAATCCTTATAG
1 GCGAGCCCCATGTATGTGAATCCCTATAG
* *
54916901 GCGAACCCCCTGTATGTGAA-CACCTATAG
1 GCGAGCCCCATGTATGTGAATC-CCTATAG
*
54916930 GCGAGCCTCATGTATGTGAATCCCTATAG
1 GCGAGCCCCATGTATGTGAATCCCTATAG
54916959 G
1 G
54916960 TGACCTCCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 48 0.96
30 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (29 bp):
GCGAGCCCCATGTATGTGAATCCCTATAG
Found at i:54917138 original size:23 final size:23
Alignment explanation
Indices: 54917100--54917156 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
54917090 CTGTATAACT
* *
54917100 TGCGAATCCTATATGCACTAATA
1 TGCGAACCCTACATGCACTAATA
*
54917123 TGTGAACCCTACATGCACTAATA
1 TGCGAACCCTACATGCACTAATA
54917146 TGCGAACCCTA
1 TGCGAACCCTA
54917157 TATGTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (23 bp):
TGCGAACCCTACATGCACTAATA
Found at i:54917802 original size:29 final size:30
Alignment explanation
Indices: 54917768--54917829 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
54917758 ACTTATTTTA
54917768 TTGTTAATTTT-TTATTACTTTA-AAGACAT
1 TTGTTAATTTTGTTATTACTTTAGAAG-CAT
*
54917797 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTTAATTTTGTTATTACTTTAGAAGCAT
54917827 TTG
1 TTG
54917830 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.37
30 16 0.53
31 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTACTTTAGAAGCAT
Found at i:54921349 original size:30 final size:30
Alignment explanation
Indices: 54921315--54921376 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
54921305 AATACCGGAG
* *
54921315 ACCAAGTAAAATACTTAAGTAATGTTAAAT
1 ACCAAGTAAAATACCTAAGTAATGTAAAAT
54921345 ACCAAGTAAAATACCTAAGTAATGTAAAAT
1 ACCAAGTAAAATACCTAAGTAATGTAAAAT
54921375 AC
1 AC
54921377 TTAAGGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (30 bp):
ACCAAGTAAAATACCTAAGTAATGTAAAAT
Found at i:54934808 original size:18 final size:18
Alignment explanation
Indices: 54934756--54934809 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54934746 CAGGGTGGGC
*
54934756 AATTT-TTATTTTATTT-
1 AATTTATTATTATATTTA
* *
54934772 AATATTAATA-TAAATTTA
1 AAT-TTATTATTATATTTA
54934790 AATTTATTATTATATTTA
1 AATTTATTATTATATTTA
54934808 AA
1 AA
54934810 ATAATTATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
18 14 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTATTATTATATTTA
Found at i:54948866 original size:38 final size:35
Alignment explanation
Indices: 54948824--54948895 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
54948814 ATTATTTAAA
54948824 ATAATAAAAATATAAA-AAAATTATATTTATATATTTTT
1 ATAAT-AAAATATAAATAAAATTA-ATTT-TAT-TTTTT
* *
54948862 ATAATTAAATTTAAATAAAATTAATTTTATTTTT
1 ATAATAAAATATAAATAAAATTAATTTTATTTTT
54948896 CAAAGAGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 4 0.13
36 3 0.10
37 12 0.39
38 12 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATAATAAAATATAAATAAAATTAATTTTATTTTTT
Found at i:54948979 original size:42 final size:43
Alignment explanation
Indices: 54948917--54948998 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
54948907 ACTTTAGATA
* *
54948917 GATATTAATTTGTTTAAATTT-AAATTTCATTAAATATATTGG
1 GATATTAATTTGTTCAAATTTAAAAATTCATTAAATATATTGG
*
54948959 GATATTAATTTGTTCGAATTTAAAAATTCATTAAATATAT
1 GATATTAATTTGTTCAAATTTAAAAATTCATTAAATATAT
54948999 AAAATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 19 0.53
43 17 0.47
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.48
Consensus pattern (43 bp):
GATATTAATTTGTTCAAATTTAAAAATTCATTAAATATATTGG
Found at i:54949240 original size:29 final size:30
Alignment explanation
Indices: 54949182--54949240 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 30
54949172 ATCGCAAAAT
* *
54949182 TATATATGAATTTTGAATTAATTTGTAATTG
1 TATATATGAATTTTGAATT-ATGTGCAATTG
54949213 TATATATGAATTTT-AATT-TGGTGCAATT
1 TATATATGAATTTTGAATTAT-GTGCAATT
54949241 ATACATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.04
29 6 0.24
30 4 0.16
31 14 0.56
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.51
Consensus pattern (30 bp):
TATATATGAATTTTGAATTATGTGCAATTG
Found at i:54949484 original size:29 final size:30
Alignment explanation
Indices: 54949438--54949496 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
54949428 AAATTGAATC
*
54949438 AAATCAAGATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
54949468 AAATCAAAATTT-ATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
54949497 TTAAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:54958097 original size:2 final size:2
Alignment explanation
Indices: 54958090--54958238 Score: 298
Period size: 2 Copynumber: 74.5 Consensus size: 2
54958080 ACCAATTCAT
54958090 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
54958132 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
54958174 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
54958216 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
54958239 TATATCGTGC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 147 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54958493 original size:39 final size:39
Alignment explanation
Indices: 54958450--54958580 Score: 172
Period size: 39 Copynumber: 3.3 Consensus size: 39
54958440 GGTTTTTAAC
* *
54958450 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCATGT
* * * *
54958489 CCGGATATATTTCTAGCACATAGCCTACGGATCTCATGT
1 CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCATGT
* *
54958528 CCGGATATTTTTCCAGCATATAGCCTGCGGACTTCATGT
1 CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCATGT
*
54958567 CTGGATATATTTTC
1 CCGGATAT-TTTTC
54958581 AATCTCATAC
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 73 0.94
40 5 0.06
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCATGT
Found at i:54966995 original size:23 final size:23
Alignment explanation
Indices: 54966969--54967066 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
54966959 ATAAGTGCCA
54966969 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54966992 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54967015 CACTG-GATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54967037 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54967060 CACTGAT
1 CACTGAT
54967067 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54967034 original size:45 final size:45
Alignment explanation
Indices: 54966976--54967064 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
54966966 CCACACTGAT
*
54966976 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
54967021 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
54967065 ATCAATAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (45 bp):
ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:54973571 original size:23 final size:23
Alignment explanation
Indices: 54973545--54973597 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
54973535 ATAAGTGCCA
54973545 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54973568 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54973591 CACTGAT
1 CACTGAT
54973598 CAATAACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54974617 original size:50 final size:50
Alignment explanation
Indices: 54974542--54974641 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
54974532 AAGAAGATGG
54974542 ACACTTATTTTCTCTTTATTTTGTCTTTTACCCAATTTGGACAAAAATGC
1 ACACTTATTTTCTCTTTATTTTGTCTTTTACCCAATTTGGACAAAAATGC
*
54974592 ACACTTATTTTCTCTTTATTTTGTCTTTTACCCATTTTGGACAAAAATGC
1 ACACTTATTTTCTCTTTATTTTGTCTTTTACCCAATTTGGACAAAAATGC
54974642 CCTTGACCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (50 bp):
ACACTTATTTTCTCTTTATTTTGTCTTTTACCCAATTTGGACAAAAATGC
Found at i:54986513 original size:19 final size:19
Alignment explanation
Indices: 54986489--54986536 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
54986479 GTGTCCCTTA
54986489 TTTTTCAAAATTTT-CATCT
1 TTTTTCAAAATTTTCCAT-T
* *
54986508 TTTTTCTAACTTTTCCATT
1 TTTTTCAAAATTTTCCATT
54986527 TTGTTTCAAA
1 TT-TTTCAAA
54986537 TTGACCTCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTCAAAATTTTCCATT
Found at i:54994761 original size:43 final size:43
Alignment explanation
Indices: 54994692--54994783 Score: 98
Period size: 43 Copynumber: 2.1 Consensus size: 43
54994682 GTGACATGGT
* * *
54994692 CGTGTGACCCAATATCAAATGCACACATGGGCAGG-CGCACGGC
1 CGTGTGACCCAATATCAAATACACACACGGGC-GGACACACGGC
* * *
54994735 CGTGTGACCTTAAT-TCAAATATACACACGGGCGGACACACGGT
1 CGTGTGACC-CAATATCAAATACACACACGGGCGGACACACGGC
54994778 CGTGTG
1 CGTGTG
54994784 TCTCGACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 2 0.05
43 36 0.88
44 3 0.07
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (43 bp):
CGTGTGACCCAATATCAAATACACACACGGGCGGACACACGGC
Found at i:54994976 original size:11 final size:11
Alignment explanation
Indices: 54994960--54994984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54994950 GTGTATGTTT
54994960 ATTGTGAATTG
1 ATTGTGAATTG
54994971 ATTGTGAATTG
1 ATTGTGAATTG
54994982 ATT
1 ATT
54994985 AATTGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (11 bp):
ATTGTGAATTG
Found at i:55004470 original size:17 final size:17
Alignment explanation
Indices: 55004448--55004481 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55004438 TATTCTTTGC
*
55004448 TTTGTGGATTAGCTAAT
1 TTTGTGGATTAGATAAT
55004465 TTTGTGGATTAGATAAT
1 TTTGTGGATTAGATAAT
55004482 GAATATTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTGTGGATTAGATAAT
Found at i:55007204 original size:19 final size:19
Alignment explanation
Indices: 55007180--55007227 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
55007170 GTGTCCCTTA
55007180 TTTTTCAAAATTTT-CATCT
1 TTTTTCAAAATTTTCCAT-T
* *
55007199 TTTTTCTAACTTTTCCATT
1 TTTTTCAAAATTTTCCATT
55007218 TTGTTTCAAA
1 TT-TTTCAAA
55007228 TTGACCTCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTCAAAATTTTCCATT
Found at i:55016662 original size:136 final size:125
Alignment explanation
Indices: 55016467--55016906 Score: 508
Period size: 125 Copynumber: 3.4 Consensus size: 125
55016457 AATAAGAGAG
* * * * * * *
55016467 TAAAATCAAAATAACAACGAAAATAAAAAATCGAGCACACTCCTTAGCATCGCACCTTAAATGCA
1 TAAAAACAAAAGAAGAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
* * * *
55016532 AGATCATACCTTAACGTAGACAACATAGAAACTCCGAAACATTATAGCAAGAATACTCCG
66 AGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGAATACTCCA
* *
55016592 TAAAAACAACCAAGCTCAATAATAGAGTAAA-AACAAAATAACAA-CGAGCACTCCTTAGCATCA
1 TAAAAACAA--AAG---AAGAACA-A--AAATAA-AAAAT--CAAGC-A-CACTCCTTAGCATCA
* *
55016655 CACCTTAAATGTAAGATCATCCCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAAA
53 CACCTTAAATGTAAGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGA
55016720 ATACTCCA
118 ATACTCCA
* * *
55016728 TGAAAACAAAAGAAGAACAAAAATTAGAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
1 TAAAAACAAAAGAAGAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
* * *
55016793 AGATCATACCTTAACATAGACAACCTAAAAACTCCAAAAAATTGTAGCAAGAATACTCCA
66 AGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGAATACTCCA
* * * *
55016853 TAAAAACAAAAGAACG-ACGAAAATTAAAAATCGAGCACACTCGTTAGCATCACA
1 TAAAAACAAAAGAA-GAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACA
55016907 AAACATCAGA
Statistics
Matches: 270, Mismatches: 29, Indels: 32
0.82 0.09 0.10
Matches are distributed among these distances:
125 138 0.51
126 5 0.02
127 3 0.01
128 7 0.03
129 1 0.00
130 5 0.02
131 6 0.02
132 2 0.01
133 8 0.03
134 4 0.01
135 3 0.01
136 88 0.33
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (125 bp):
TAAAAACAAAAGAAGAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
AGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGAATACTCCA
Found at i:55025439 original size:31 final size:31
Alignment explanation
Indices: 55025404--55025462 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
55025394 AATGCCATGT
*
55025404 TATCAAGTTTAGGGACTAA-ATTGAAAAAGGA
1 TATCAAATTTAGGGACTAATA-TGAAAAAGGA
55025435 TATCAAATTTAGGGACTAATATGAAAAA
1 TATCAAATTTAGGGACTAATATGAAAAA
55025463 ATAGGACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (31 bp):
TATCAAATTTAGGGACTAATATGAAAAAGGA
Found at i:55025702 original size:2 final size:2
Alignment explanation
Indices: 55025695--55025746 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
55025685 GCCATGGTTA
* * *
55025695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AC AT AC AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
55025736 AT AT CT AT AT A
1 AT AT AT AT AT A
55025747 CTCTATTTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55029541 original size:14 final size:14
Alignment explanation
Indices: 55029522--55029549 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55029512 TGTTGGTATG
55029522 AAATAAATTTAACA
1 AAATAAATTTAACA
55029536 AAATAAATTTAACA
1 AAATAAATTTAACA
55029550 GTATTAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAATTTAACA
Found at i:55047218 original size:3 final size:3
Alignment explanation
Indices: 55047210--55047235 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55047200 ATTGATCAAT
55047210 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
55047236 TTTTGTTTTT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55054727 original size:21 final size:20
Alignment explanation
Indices: 55054694--55054732 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55054684 TGACCTCACA
55054694 TTTTAATATTAGAATTTTTC
1 TTTTAATATTAGAATTTTTC
*
55054714 TTTTAGATTTTAG-ATTTTT
1 TTTTA-ATATTAGAATTTTT
55054733 TGAACCGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTAATATTAGAATTTTTC
Found at i:55056868 original size:4 final size:4
Alignment explanation
Indices: 55056861--55056891 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
55056851 GTGCGTGTAT
55056861 GTGA GTGA GTGA GTGA GTGA GTGA GTGA GTG
1 GTGA GTGA GTGA GTGA GTGA GTGA GTGA GTG
55056892 TGAGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.52, T:0.26
Consensus pattern (4 bp):
GTGA
Found at i:55067431 original size:31 final size:30
Alignment explanation
Indices: 55067395--55067468 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
55067385 CACTATCAAC
* *
55067395 TTAATTTAATTACATTATATAACATTTTAAT
1 TTAATTTAATTACATTACATAACA-ATTAAT
* * *
55067426 TTAATTTAATCACATTACGTAATAATTAAT
1 TTAATTTAATTACATTACATAACAATTAAT
55067456 TTAATTTAATTAC
1 TTAATTTAATTAC
55067469 CATATTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (30 bp):
TTAATTTAATTACATTACATAACAATTAAT
Found at i:55067646 original size:5 final size:5
Alignment explanation
Indices: 55067636--55067710 Score: 141
Period size: 5 Copynumber: 15.0 Consensus size: 5
55067626 CATCCGTACA
*
55067636 CATAT CATAT CATAT CATAT CATAT TATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
55067686 CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT
55067711 ATGTAATAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 68 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
CATAT
Found at i:55068772 original size:9 final size:9
Alignment explanation
Indices: 55068747--55068785 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
55068737 TTAGGAATGA
*
55068747 AAAAAGAAC
1 AAAAAGAAG
55068756 AGAAAAGAAG
1 A-AAAAGAAG
55068766 AAAAAGAAG
1 AAAAAGAAG
*
55068775 AAGAAGAAG
1 AAAAAGAAG
55068784 AA
1 AA
55068786 GCAAAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:55073080 original size:27 final size:27
Alignment explanation
Indices: 55073029--55073079 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
55073019 TTTTTCAATG
*
55073029 AATTAAAAAATTGAAGTATAAAAAAGA
1 AATTAAAAAATGGAAGTATAAAAAAGA
55073056 AATTAAAAAA-GGAAGTATAAAAAA
1 AATTAAAAAATGGAAGTATAAAAAA
55073080 AATCAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.20
Consensus pattern (27 bp):
AATTAAAAAATGGAAGTATAAAAAAGA
Found at i:55093282 original size:31 final size:31
Alignment explanation
Indices: 55093247--55093305 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
55093237 TAAAACTTAT
*
55093247 GCCCCAATACGAGAAAAATTACCTAATTTAA
1 GCCCCAATACGAGAAAAATTACCAAATTTAA
* *
55093278 GCCCCAATATGAGAATAATTACCAAATT
1 GCCCCAATACGAGAAAAATTACCAAATT
55093306 CAGAGACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (31 bp):
GCCCCAATACGAGAAAAATTACCAAATTTAA
Found at i:55094726 original size:22 final size:22
Alignment explanation
Indices: 55094690--55094755 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 22
55094680 ATATTAAAAC
* * **
55094690 CCTAAACTCTTAACCCTACTAT
1 CCTAAACACTAAACCCTAAGAT
55094712 CCTAAACACTAAA-CCTAAGAT
1 CCTAAACACTAAACCCTAAGAT
* *
55094733 CATAAACACTAACCCCTAA-AT
1 CCTAAACACTAAACCCTAAGAT
55094754 CC
1 CC
55094756 GAGAGTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.41, C:0.35, G:0.02, T:0.23
Consensus pattern (22 bp):
CCTAAACACTAAACCCTAAGAT
Found at i:55096114 original size:30 final size:31
Alignment explanation
Indices: 55096044--55096114 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
55096034 GGTAAGTTTG
* *
55096044 AGGACCAAATTGATAGAATTTGTAAATGTGA
1 AGGACTAAATTGATAGAATATGTAAATGTGA
*
55096075 AGGATTAAATTGATAGAATATGTAATAT-T-A
1 AGGACTAAATTGATAGAATATGTAA-ATGTGA
55096105 AGGACTAAAT
1 AGGACTAAAT
55096115 GTGTTATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 23 0.66
32 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (31 bp):
AGGACTAAATTGATAGAATATGTAAATGTGA
Found at i:55105821 original size:12 final size:12
Alignment explanation
Indices: 55105804--55105830 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55105794 AAGAGAAGGA
55105804 TGATGATGATGG
1 TGATGATGATGG
55105816 TGATGATGATGG
1 TGATGATGATGG
55105828 TGA
1 TGA
55105831 GGACCTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (12 bp):
TGATGATGATGG
Found at i:55118200 original size:3 final size:3
Alignment explanation
Indices: 55118186--55118232 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
55118176 TCTTCCTCCG
* *
55118186 CCA CCG CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCT CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
55118233 TCCGTTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.28, C:0.68, G:0.02, T:0.02
Consensus pattern (3 bp):
CCA
Found at i:55118393 original size:9 final size:9
Alignment explanation
Indices: 55118354--55118396 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
55118344 AACTTCTCCA
55118354 CTACTACTC
1 CTACTACTC
* *
55118363 CTACTCCTA
1 CTACTACTC
*
55118372 CTCCTACTC
1 CTACTACTC
*
55118381 CTACTACTT
1 CTACTACTC
55118390 CTACTAC
1 CTACTAC
55118397 CAACAACAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (9 bp):
CTACTACTC
Found at i:55118394 original size:6 final size:6
Alignment explanation
Indices: 55118357--55118385 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
55118347 TTCTCCACTA
55118357 CTACTC CTACTC CTACTC CTACTC CTACT
1 CTACTC CTACTC CTACTC CTACTC CTACT
55118386 ACTTCTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
CTACTC
Found at i:55118396 original size:12 final size:12
Alignment explanation
Indices: 55118349--55118396 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
55118339 TCAAAAACTT
55118349 CTCC-ACTACTA
1 CTCCTACTACTA
*
55118360 CTCCTACTCCTA
1 CTCCTACTACTA
*
55118372 CTCCTACTCCTA
1 CTCCTACTACTA
* *
55118384 CTACTTCTACTA
1 CTCCTACTACTA
55118396 C
1 C
55118397 CAACAACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.33
Consensus pattern (12 bp):
CTCCTACTACTA
Found at i:55129354 original size:3 final size:3
Alignment explanation
Indices: 55129346--55129393 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
55129336 GGTTTTATAG
55129346 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55129394 GGGGTTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55131783 original size:3 final size:3
Alignment explanation
Indices: 55131775--55131807 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
55131765 AATGAGTAGG
55131775 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55131808 GGGTAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55138136 original size:31 final size:32
Alignment explanation
Indices: 55138101--55138160 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
55138091 ACACATCAGC
55138101 AAAAATAAAAGAAA-ATTCAATTTTTTTTGTA
1 AAAAATAAAAGAAATATTCAATTTTTTTTGTA
*
55138132 AAAAATAAAAGAAATATTTAATTTTTTTT
1 AAAAATAAAAGAAATATTCAATTTTTTTT
55138161 ACTAGAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (32 bp):
AAAAATAAAAGAAATATTCAATTTTTTTTGTA
Found at i:55138848 original size:6 final size:6
Alignment explanation
Indices: 55138837--55138891 Score: 76
Period size: 6 Copynumber: 9.2 Consensus size: 6
55138827 AGAGAACAAC
* *
55138837 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ACTT-AC ATTAAG
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA A-TTAAA ATTAAA
55138885 ATTAAA A
1 ATTAAA A
55138892 GAAACCAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
5 2 0.05
6 40 0.91
7 2 0.05
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:55143171 original size:45 final size:45
Alignment explanation
Indices: 55143120--55143206 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
55143110 CTTTTTTTTT
55143120 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTATCTA
1 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTATCTA
55143165 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTAT
1 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTAT
55143207 AAAACTCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.43
Consensus pattern (45 bp):
ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTATCTA
Found at i:55143895 original size:25 final size:25
Alignment explanation
Indices: 55143866--55143917 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
55143856 TATATAATTT
55143866 AAGTTTA-AGAAAATAATTTTTATAC
1 AAGTTTATA-AAAATAATTTTTATAC
* *
55143891 AAGTTTATAAAAGTTATTTTTATAC
1 AAGTTTATAAAAATAATTTTTATAC
55143916 AA
1 AA
55143918 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
AAGTTTATAAAAATAATTTTTATAC
Found at i:55145921 original size:22 final size:22
Alignment explanation
Indices: 55145850--55145922 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 22
55145840 AAAAATGGAG
*
55145850 AAAATTATGTTTAACCCCTT-A
1 AAAATTATGTTTAATCCCTTAA
* ** ***
55145871 AAAATGATGAATAATAAATTAA
1 AAAATTATGTTTAATCCCTTAA
* *
55145893 TACATTATGTTTAATCCCTTAA
1 AAAATTATGTTTAATCCCTTAA
55145915 AAAATTAT
1 AAAATTAT
55145923 TATTCAATTC
Statistics
Matches: 34, Mismatches: 17, Indels: 1
0.65 0.33 0.02
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAATTATGTTTAATCCCTTAA
Found at i:55148416 original size:13 final size:13
Alignment explanation
Indices: 55148398--55148422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55148388 AACTGCAGAT
55148398 CGTTACAATATCA
1 CGTTACAATATCA
55148411 CGTTACAATATC
1 CGTTACAATATC
55148423 TATTTAGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
CGTTACAATATCA
Found at i:55151114 original size:16 final size:17
Alignment explanation
Indices: 55151093--55151132 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
55151083 TTAATTTAAT
55151093 TTAAATTATTTT-TCAA
1 TTAAATTATTTTCTCAA
*
55151109 TTAAATAATTTTCTCAA
1 TTAAATTATTTTCTCAA
*
55151126 TTCAATT
1 TTAAATT
55151133 CTAATCACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATTTTCTCAA
Found at i:55152407 original size:46 final size:46
Alignment explanation
Indices: 55152356--55152450 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
55152346 ATTAAAATTA
* *
55152356 AAACTTAGAAACCAAA-CATTAA-ATATATAGTTTGGAGAACAACATT
1 AAACTT-GAAACCAAAGC-CTAACATATATAGTTAGGAGAACAACATT
* * *
55152402 AAACTTTAAATCAAAGCCTAACCTATATAGTTAGGAGAACAACATT
1 AAACTTGAAACCAAAGCCTAACATATATAGTTAGGAGAACAACATT
55152448 AAA
1 AAA
55152451 ATTAAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 10 0.24
46 32 0.76
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (46 bp):
AAACTTGAAACCAAAGCCTAACATATATAGTTAGGAGAACAACATT
Found at i:55162219 original size:3 final size:3
Alignment explanation
Indices: 55162213--55162260 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
55162203 ATCATCATCG
* * * *
55162213 GAA GAA GAA GAA GAG GAG GAA GAA GAA GAA GAG GAA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
55162261 CCTGGAGTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55162233 original size:18 final size:18
Alignment explanation
Indices: 55162212--55162260 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
55162202 AATCATCATC
55162212 GGAAGAAGAAGAAGAGGA
1 GGAAGAAGAAGAAGAGGA
55162230 GGAAGAAGAAGAAGAGGA
1 GGAAGAAGAAGAAGAGGA
* *
55162248 AGAAGAAGGAGAA
1 GGAAGAAGAAGAA
55162261 CCTGGAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (18 bp):
GGAAGAAGAAGAAGAGGA
Found at i:55162234 original size:15 final size:15
Alignment explanation
Indices: 55162216--55162255 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
55162206 ATCATCGGAA
*
55162216 GAAGAAGAAGAGGAG
1 GAAGAAGAAGAAGAG
55162231 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
55162246 GAAGAAGAAG
1 GAAGAAGAAG
55162256 GAGAACCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:55162545 original size:21 final size:19
Alignment explanation
Indices: 55162521--55162570 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
55162511 AAAAAAAGCA
*
55162521 ATTATATTATAATTTTATTAC
1 ATTATATTA-AATTATATT-C
55162542 ATTATAATTAAATTATATTC
1 ATTAT-ATTAAATTATATTC
55162562 ATT-TATTAA
1 ATTATATTAA
55162571 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 4 0.15
21 13 0.48
22 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTATATTAAATTATATTC
Found at i:55162804 original size:15 final size:15
Alignment explanation
Indices: 55162762--55162805 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55162752 TATTTAACAT
* *
55162762 AAATTTATATAAACT
1 AAATTTATATATACC
*
55162777 AATATTAATATATACC
1 AA-ATTTATATATACC
55162793 AAATTTATATATA
1 AAATTTATATATA
55162806 TATTAATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTATATATACC
Found at i:55175245 original size:10 final size:10
Alignment explanation
Indices: 55175166--55175248 Score: 112
Period size: 10 Copynumber: 8.3 Consensus size: 10
55175156 TGGGCTATGT
*
55175166 CATCAGTGAT
1 CATCAGTGAA
55175176 CATCAGTGAA
1 CATCAGTGAA
* *
55175186 CATCAATGAT
1 CATCAGTGAA
*
55175196 CATCAGTGAT
1 CATCAGTGAA
55175206 CATCAGTGAA
1 CATCAGTGAA
*
55175216 TATCAGTGAA
1 CATCAGTGAA
*
55175226 CTTCAGTGAA
1 CATCAGTGAA
55175236 CATCAGTGAA
1 CATCAGTGAA
55175246 CAT
1 CAT
55175249 AAGACCATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 64 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (10 bp):
CATCAGTGAA
Found at i:55177034 original size:20 final size:20
Alignment explanation
Indices: 55177009--55177058 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
55176999 TTGATTAAGG
55177009 TATCGATACCTTGGATGTGA
1 TATCGATACCTTGGATGTGA
*
55177029 TATCGATACCTTGGATGTGG
1 TATCGATACCTTGGATGTGA
55177049 TATCGATACC
1 TATCGATACC
55177059 AAAATTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACCTTGGATGTGA
Found at i:55186554 original size:22 final size:23
Alignment explanation
Indices: 55186529--55186575 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
55186519 ATGTATTTAT
*
55186529 TTTATATATTTTTA-TAATTAAA
1 TTTAAATATTTTTATTAATTAAA
* *
55186551 TTTAAATTTTTTTATTATTTAAA
1 TTTAAATATTTTTATTAATTAAA
55186574 TT
1 TT
55186576 GAATTCAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAATATTTTTATTAATTAAA
Found at i:55188589 original size:25 final size:24
Alignment explanation
Indices: 55188555--55188602 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
55188545 GATTGAAGAT
55188555 CAATTTTTATTAT-AAGATCATTTTC
1 CAATTTTTATT-TCAAGATC-TTTTC
55188580 CAATTTTTATTTCAAGATCTTTT
1 CAATTTTTATTTCAAGATCTTTT
55188603 AGCATCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (24 bp):
CAATTTTTATTTCAAGATCTTTTC
Found at i:55195566 original size:19 final size:20
Alignment explanation
Indices: 55195528--55195573 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
55195518 AACCCCAAAT
55195528 CCTTGAACCCTCAACATGAA
1 CCTTGAACCCTCAACATGAA
*
55195548 CCTTGAACCC-CAACTTGAA
1 CCTTGAACCCTCAACATGAA
*
55195567 CCATGAA
1 CCTTGAA
55195574 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.35, C:0.35, G:0.11, T:0.20
Consensus pattern (20 bp):
CCTTGAACCCTCAACATGAA
Found at i:55196464 original size:32 final size:31
Alignment explanation
Indices: 55196419--55196514 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
55196409 CTTAGATAAT
55196419 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
55196450 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
55196482 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
55196513 TT
1 TT
55196515 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:55197893 original size:3 final size:3
Alignment explanation
Indices: 55197885--55197920 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55197875 AACCGTAGGT
55197885 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
55197921 GCAGAGCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:55199471 original size:16 final size:16
Alignment explanation
Indices: 55199427--55199474 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
55199417 AACTGCAATT
55199427 TATTAAATAAAA-ATTA
1 TATT-AATAAAATATTA
55199443 TATTAATTAAAATATTA
1 TATTAA-TAAAATATTA
*
55199460 TTTTAATAAAATATT
1 TATTAATAAAATATT
55199475 TAATTTCACG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.62
17 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATAAAATATTA
Found at i:55201079 original size:26 final size:25
Alignment explanation
Indices: 55201050--55201108 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
55201040 CCCTTAACCT
*
55201050 TTTTTAAAAAAATTTAGATT-TTTAC
1 TTTTTAAAAAAAGTTAGATTGTTT-C
*
55201075 ATTTTTCAAAAACAGTTAGATTGTTTC
1 -TTTTT-AAAAAAAGTTAGATTGTTTC
55201102 TTTTTAA
1 TTTTTAA
55201109 TAGAAATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 2 0.07
26 10 0.34
27 14 0.48
28 3 0.10
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (25 bp):
TTTTTAAAAAAAGTTAGATTGTTTC
Found at i:55201316 original size:29 final size:27
Alignment explanation
Indices: 55201284--55201341 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
55201274 GCCGCTTTTT
*
55201284 AAAAA-AAATTAAAGATCAAATTTAACTA
1 AAAAATAAAATAAAGATCAAA-TTAA-TA
* *
55201312 AAAAATTAAATAAATATCAAATTAATA
1 AAAAATAAAATAAAGATCAAATTAATA
55201339 AAA
1 AAA
55201342 GATGTAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 9 0.35
29 12 0.46
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (27 bp):
AAAAATAAAATAAAGATCAAATTAATA
Found at i:55201350 original size:28 final size:29
Alignment explanation
Indices: 55201293--55201350 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
55201283 TAAAAAAAAT
55201293 TAAAGATCAAATTTAACTAAAAAATTAAA
1 TAAAGATCAAATTTAACTAAAAAATTAAA
* *
55201322 TAAATATCAAA-TTAA-TAAAAGATGTAAA
1 TAAAGATCAAATTTAACTAAAAAAT-TAAA
55201350 T
1 T
55201351 GTTAGAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 9 0.35
29 10 0.38
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (29 bp):
TAAAGATCAAATTTAACTAAAAAATTAAA
Found at i:55204739 original size:54 final size:54
Alignment explanation
Indices: 55204671--55204777 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
55204661 ATTATAAGTA
*
55204671 CTAATCTTTTCTAGGGTAGGTATAAAATTGTTAGCCACTATCATTTATATTATT
1 CTAATATTTTCTAGGGTAGGTATAAAATTGTTAGCCACTATCATTTATATTATT
55204725 CTAATATTTTCTAGGGTAGGTATAAAATTGTTAGCCACTATCATTTATATTAT
1 CTAATATTTTCTAGGGTAGGTATAAAATTGTTAGCCACTATCATTTATATTAT
55204778 GCATGAATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (54 bp):
CTAATATTTTCTAGGGTAGGTATAAAATTGTTAGCCACTATCATTTATATTATT
Found at i:55218154 original size:16 final size:16
Alignment explanation
Indices: 55218116--55218157 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
55218106 TAATTTATCA
55218116 AATAAAA-A-TATATT
1 AATAAAATATTATATT
55218130 AATTAAAATATTATATT
1 AA-TAAAATATTATATT
55218147 AATAAAATATT
1 AATAAAATATT
55218158 TAATTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 5 0.20
16 10 0.40
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAAATATTATATT
Found at i:55220724 original size:2 final size:2
Alignment explanation
Indices: 55220717--55220749 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55220707 ACAATTGTTA
55220717 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55220750 ATAACTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55221037 original size:20 final size:20
Alignment explanation
Indices: 55220988--55221039 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
55220978 CTGAACCCTA
*
55220988 AACCCCAAACCTAAACCCAT
1 AACCCCAAATCTAAACCCAT
* * * *
55221008 AATCCTAAATCTAAACTCGT
1 AACCCCAAATCTAAACCCAT
55221028 AACCCCAAATCT
1 AACCCCAAATCT
55221040 TTGAACCCTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.19
Consensus pattern (20 bp):
AACCCCAAATCTAAACCCAT
Found at i:55222649 original size:3 final size:3
Alignment explanation
Indices: 55222641--55222670 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55222631 AACCGTAGGT
55222641 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
55222671 GCAGAGCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:55224722 original size:23 final size:24
Alignment explanation
Indices: 55224662--55224721 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 24
55224652 GACTTTTTTT
*
55224662 AAAAATTAAGGATCAAAATTAACTAA
1 AAAAATTAA-AATC-AAATTAACTAA
55224688 AAAAATTAAAATCAAATTAAC-AA
1 AAAAATTAAAATCAAATTAACTAA
55224711 AAAAATATAAA
1 AAAAAT-TAAA
55224722 TGTTAAAGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 8 0.25
24 12 0.38
25 3 0.09
26 9 0.28
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.22
Consensus pattern (24 bp):
AAAAATTAAAATCAAATTAACTAA
Found at i:55225157 original size:21 final size:23
Alignment explanation
Indices: 55225115--55225157 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
55225105 ACTACTTCTA
55225115 TTCTCTAATATAAACTATTAAAT
1 TTCTCTAATATAAACTATTAAAT
55225138 TTCT-TAA-ATAAA-TATATAAA
1 TTCTCTAATATAAACTAT-TAAA
55225158 CTCAATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 3 0.16
23 4 0.21
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TTCTCTAATATAAACTATTAAAT
Found at i:55225337 original size:20 final size:20
Alignment explanation
Indices: 55225312--55225361 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
55225302 TGGCTTAAAA
55225312 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
55225332 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
55225349 GTGGTAGTGGATT
1 TTGGTAGTGGATT
55225362 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:55229976 original size:20 final size:20
Alignment explanation
Indices: 55229951--55230000 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
55229941 TGGCTTAAAA
55229951 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
55229971 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
55229988 GTGGTAGTGGATT
1 TTGGTAGTGGATT
55230001 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:55232255 original size:17 final size:16
Alignment explanation
Indices: 55232226--55232265 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
55232216 TACTTTATCA
55232226 AATAAAA-ATTATATT
1 AATAAAATATTATATT
55232241 AATTAAAATATTATATT
1 AA-TAAAATATTATATT
55232258 AATAAAAT
1 AATAAAAT
55232266 GTTTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 11 0.48
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAAATATTATATT
Found at i:55232394 original size:18 final size:18
Alignment explanation
Indices: 55232334--55232395 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
55232324 TAATAAATAA
*
55232334 AATTAAATATATTAATTT
1 AATTAAATATATAAATTT
*
55232352 AATAAAATAT-TAAATTTTCT
1 AATTAAATATATAAA--TT-T
*
55232372 AATTAAATATATCAATTT
1 AATTAAATATATAAATTT
55232390 AATTAA
1 AATTAA
55232396 CTATTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.08
18 16 0.44
19 4 0.11
20 10 0.28
21 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAAATATATAAATTT
Found at i:55232653 original size:12 final size:13
Alignment explanation
Indices: 55232625--55232657 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55232615 AATTTCATCT
*
55232625 TTAATTAATTAAA
1 TTAATAAATTAAA
55232638 TTAATAAATT-AA
1 TTAATAAATTAAA
55232650 TTAATAAA
1 TTAATAAA
55232658 ATTGATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAATAAATTAAA
Found at i:55232741 original size:15 final size:16
Alignment explanation
Indices: 55232718--55232750 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
55232708 TAAGAGATAA
55232718 TATAAACAAT-TATTT
1 TATAAACAATCTATTT
*
55232733 TATATACAATCTATTT
1 TATAAACAATCTATTT
55232749 TA
1 TA
55232751 ACTTTTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAACAATCTATTT
Found at i:55238680 original size:16 final size:16
Alignment explanation
Indices: 55238638--55238684 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
55238628 AACTATAATT
*
55238638 TATTAAATAAAA-ATTA
1 TATT-AATAAAATATCA
55238654 TATTAATTAAAATATCA
1 TATTAA-TAAAATATCA
*
55238671 TTTTAATAAAATAT
1 TATTAATAAAATAT
55238685 TTAATTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 17 0.63
17 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAATAAAATATCA
Found at i:55240238 original size:101 final size:101
Alignment explanation
Indices: 55240038--55240230 Score: 377
Period size: 101 Copynumber: 1.9 Consensus size: 101
55240028 CCACGGATTT
*
55240038 GTTCCCTTTTTTAATTTGATCCTCAATTAGTTGGGCCCCTGAGGAAGGGACGCGTGGCCTGAAAA
1 GTTCCCTTTTTTAATTTGATCCTCAATTAGTTGGGCCCCTAAGGAAGGGACGCGTGGCCTGAAAA
55240103 TCGGGTTTATTACCCATTTGGTCCTTCGCCCTTTCA
66 TCGGGTTTATTACCCATTTGGTCCTTCGCCCTTTCA
55240139 GTTCCCTTTTTTAATTTGATCCTCAATTAGTTGGGCCCCTAAGGAAGGGACGCGTGGCCTGAAAA
1 GTTCCCTTTTTTAATTTGATCCTCAATTAGTTGGGCCCCTAAGGAAGGGACGCGTGGCCTGAAAA
55240204 TCGGGTTTATTACCCATTTGGTCCTTC
66 TCGGGTTTATTACCCATTTGGTCCTTC
55240231 TTCCTTTCGC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 91 1.00
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (101 bp):
GTTCCCTTTTTTAATTTGATCCTCAATTAGTTGGGCCCCTAAGGAAGGGACGCGTGGCCTGAAAA
TCGGGTTTATTACCCATTTGGTCCTTCGCCCTTTCA
Found at i:55240529 original size:18 final size:18
Alignment explanation
Indices: 55240508--55240556 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
55240498 CTATTATAAC
55240508 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
55240526 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
55240544 TA-TTATATATATC
1 TATTTATATATATC
55240557 TATATATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 10 0.37
19 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:55240733 original size:30 final size:29
Alignment explanation
Indices: 55240697--55240753 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
55240687 ATACATATAT
55240697 ATATACATACTTACACTATTTTATTTTACG
1 ATATACATACTTACA-TATTTTATTTTACG
* *
55240727 ATATACATACTTATATCTTTTATTTTA
1 ATATACATACTTACATATTTTATTTTA
55240754 TGTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATACATACTTACATATTTTATTTTACG
Found at i:55244793 original size:5 final size:5
Alignment explanation
Indices: 55244783--55244812 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
55244773 ATCTTTATTT
55244783 AAATA AAATA AAATA AAATA AAAGTA AAAT
1 AAATA AAATA AAATA AAATA AAA-TA AAAT
55244813 CCATATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:55245746 original size:13 final size:14
Alignment explanation
Indices: 55245709--55245748 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
55245699 CTAAATCATT
*
55245709 AAACCTTGAACCTC
1 AAACCTTGAACCCC
55245723 AAATCCTTGAACCCC
1 AAA-CCTTGAACCCC
55245738 AAA-CTTGAACC
1 AAACCTTGAACC
55245749 ATGAATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 3 0.12
15 13 0.54
ACGTcount: A:0.38, C:0.35, G:0.07, T:0.20
Consensus pattern (14 bp):
AAACCTTGAACCCC
Found at i:55247169 original size:41 final size:41
Alignment explanation
Indices: 55247108--55247387 Score: 479
Period size: 41 Copynumber: 6.8 Consensus size: 41
55247098 AACACCAACC
55247108 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
* * * *
55247149 CACTGGCACTTAGCTTGCTAGGGGTAAAGCCTGATTCAATA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
55247190 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
*
55247231 CACTGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
*
55247272 CACGGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
* * *
55247313 CACCGGCCCTTAGCCTGCTAGGCATAAAGCCTGATTCTGTA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
55247354 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGA
1 CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGA
55247388 AAATCTCAAT
Statistics
Matches: 223, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 223 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (41 bp):
CACCGGCACTTAGCCTGCTAGGCGTAAAGCCTGATTCAGTA
Found at i:55251834 original size:15 final size:17
Alignment explanation
Indices: 55251809--55251841 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55251799 TTGAATGGAA
55251809 TTATATTTGAAT-TATT
1 TTATATTTGAATATATT
55251825 TTAT-TTTGAATATATT
1 TTATATTTGAATATATT
55251841 T
1 T
55251842 AGATCAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TTATATTTGAATATATT
Found at i:55254529 original size:42 final size:43
Alignment explanation
Indices: 55254483--55254577 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 43
55254473 AGACAAAGAC
** *
55254483 CTTTAGCGGGGCTTTAGT-GGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCACTTTAGTGGGAAACGCCGCTAAAGATCAGGGT
* * * * **
55254525 CTTTATCGGCATTTTTGTGGGAAATGCCGCTAAAGATTGGGGT
1 CTTTAGCGGCACTTTAGTGGGAAACGCCGCTAAAGATCAGGGT
55254568 CTTTAGCGGC
1 CTTTAGCGGC
55254578 GCTCTTACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 13 0.31
43 29 0.69
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCACTTTAGTGGGAAACGCCGCTAAAGATCAGGGT
Found at i:55254636 original size:43 final size:43
Alignment explanation
Indices: 55254571--55254754 Score: 219
Period size: 43 Copynumber: 4.3 Consensus size: 43
55254561 TTGGGGTCTT
* * * *
55254571 TAGCGGCGCTCTTACTACAAACGCCACAATAGACCCTGAGCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
*
55254614 TAGCGGCGCTTTTTCTAAAAACGCCGCAATAGACACC-GATCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGAC-CCTGATCTA
* * *** * *
55254657 TAGCGGCGCTTCTCCCGCAAACGCCTCAATAGACCCCGATCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
* *
55254700 TAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTGATCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
55254743 TAGCGGCG-TTTT
1 TAGCGGCGCTTTT
55254755 CAGGAAAAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
42 6 0.05
43 112 0.93
44 2 0.02
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (43 bp):
TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
Found at i:55254701 original size:86 final size:86
Alignment explanation
Indices: 55254588--55254750 Score: 256
Period size: 86 Copynumber: 1.9 Consensus size: 86
55254578 GCTCTTACTA
* * *
55254588 CAAACGCCACAATAGACCCTGAGCTATAGCGGCGCTTTTTCTAAAAACGCCGCAATAGACACC-G
1 CAAACGCCACAATAGACCCCGAGCTATAGCGGCGCTTTTACAAAAAACGCCGCAATAGAC-CCTG
55254652 ATCTATAGCGGCGCTTCTCCCG
65 ATCTATAGCGGCGCTTCTCCCG
* * *
55254674 CAAACGCCTCAATAGACCCCGATCTATAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTGA
1 CAAACGCCACAATAGACCCCGAGCTATAGCGGCGCTTTTACAAAAAACGCCGCAATAGACCCTGA
55254739 TCTATAGCGGCG
66 TCTATAGCGGCG
55254751 TTTTCAGGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
85 2 0.03
86 68 0.97
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (86 bp):
CAAACGCCACAATAGACCCCGAGCTATAGCGGCGCTTTTACAAAAAACGCCGCAATAGACCCTGA
TCTATAGCGGCGCTTCTCCCG
Found at i:55254793 original size:31 final size:29
Alignment explanation
Indices: 55254738--55254797 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
55254728 GTAGACCCTG
*
55254738 ATCTATAGCGGCGTTTTCAGGAAAAGCGCC
1 ATCTATAGCGGCGTTTTCACGAAAA-CGCC
* *
55254768 ATCTTTAGCGGCGCTTTTCCCGAAAACGCC
1 ATCTATAGCGGCG-TTTTCACGAAAACGCC
55254798 GCTAAAGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (29 bp):
ATCTATAGCGGCGTTTTCACGAAAACGCC
Found at i:55254890 original size:43 final size:44
Alignment explanation
Indices: 55254768--55254890 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 44
55254758 GAAAAGCGCC
* * *
55254768 ATCTTTAGCGGCGCTTTTCCCGAAAACGCCGCTAAA-GACCATG
1 ATCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAATAACCATG
* * * * *
55254811 ATCTTTAGTGGCGCTTTTTCCACAAACGCCGGTAAATAACC-TT
1 ATCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAATAACCATG
* * *
55254854 CTCTTTAGCGGCGCTTTTACAAAAAACGCCACTAAAT
1 ATCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAT
55254891 TTGGCAGATT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
43 62 0.95
44 3 0.05
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (44 bp):
ATCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAATAACCATG
Found at i:55255250 original size:21 final size:21
Alignment explanation
Indices: 55255196--55255307 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
55255186 TTTGACGCTG
*
55255196 CTCTGCTTCCCTGGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
55255217 TTTTACTTGCCTCGCTACAGC
1 CTCTGCTTCCCTCGCTGCAGC
55255238 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
55255259 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
55255280 CTTTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
55255301 ATCTGCT
1 CTCTGCT
55255308 CTAAGCTGTT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.06, C:0.40, G:0.19, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:55255266 original size:42 final size:42
Alignment explanation
Indices: 55255196--55255297 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
55255186 TTTGACGCTG
* * *
55255196 CTCTGCTTCCCTGGCTGCAGCTTTTACTTGC-CTCGCTACAGC
1 CTCTGCTTCCCTCGCTGCAGCCTGTACTT-CTCTCGCTACAGC
* *
55255238 CTCTGCTTCCCTCGCTGCAGCCTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGCCTGTACTTCTCTCGCTACAGC
* * *
55255280 CTTTGCTTCTCTTGCTGC
1 CTCTGCTTCCCTCGCTGC
55255298 CGCATCTGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 1 0.02
42 50 0.98
ACGTcount: A:0.06, C:0.40, G:0.19, T:0.35
Consensus pattern (42 bp):
CTCTGCTTCCCTCGCTGCAGCCTGTACTTCTCTCGCTACAGC
Found at i:55255367 original size:64 final size:65
Alignment explanation
Indices: 55255284--55255421 Score: 208
Period size: 64 Copynumber: 2.1 Consensus size: 65
55255274 TGCCGCCTTT
* *
55255284 GCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTTGAACCT
1 GCTTCTC-TGCTGCCGCATCTACTCTAAGCTGCTGCTGGAGTTCTTCATATCTTT-GTTGAACCT
55255348 CA
64 CA
* *
55255350 GCTTCTC-GCTGCTGCATCTACTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTTTTGAACCTCA
1 GCTTCTCTGCTGCCGCATCTACTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTGAACCTCA
55255414 GCTTCTCT
1 GCTTCTCT
55255422 CGATGTTGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
64 55 0.83
65 4 0.06
66 7 0.11
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (65 bp):
GCTTCTCTGCTGCCGCATCTACTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTGAACCTCA
Found at i:55260896 original size:18 final size:18
Alignment explanation
Indices: 55260873--55260908 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55260863 ATAGTTACGC
55260873 TATGTAAGTTATGTATTA
1 TATGTAAGTTATGTATTA
*
55260891 TATGTAAGTTATTTATTA
1 TATGTAAGTTATGTATTA
55260909 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
TATGTAAGTTATGTATTA
Found at i:55261074 original size:16 final size:16
Alignment explanation
Indices: 55261053--55261097 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
55261043 ATTAAAAAAA
55261053 TGTAAGTTATGT-AGAT
1 TGTAAGTTATGTAAG-T
55261069 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
55261085 TGTAAGTTATGTA
1 TGTAAGTTATGTA
55261098 TAATATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 26 0.93
17 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:55261081 original size:9 final size:9
Alignment explanation
Indices: 55261052--55261097 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
55261042 AATTAAAAAA
55261052 ATGTAAGTT
1 ATGTAAGTT
*
55261061 ATGT-AGAT
1 ATGTAAGTT
55261069 -TGTAAGTT
1 ATGTAAGTT
55261077 ATGTAAG-T
1 ATGTAAGTT
55261085 -TGTAAGTT
1 ATGTAAGTT
55261093 ATGTA
1 ATGTA
55261098 TAATATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
7 9 0.29
8 8 0.26
9 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:55261133 original size:34 final size:34
Alignment explanation
Indices: 55261085--55261416 Score: 375
Period size: 34 Copynumber: 10.1 Consensus size: 34
55261075 TTATGTAAGT
* * *
55261085 TGTAAGTTATGTATAATATTAATTAACTAACTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* *
55261119 TGTAATTTAAGTATAATATTAA-T--GTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* * *
55261150 TGTAATTAACGTATAATATTAATTAATTAAGTCA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
55261184 TGTAATTTATGTATAATATTAATGT-A--AA-TTA
1 TGTAATTTATGTATAATATTAAT-TAATTAAGTTA
* *
55261215 TGTAATTAATGTATAATATTAATTAATTAAGTCA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* *
55261249 TATAATTTATGTATAATATTAA-T--GTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* * *
55261280 TGTAATTAATGTATAATATTAATCAATTAAGTCA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* **
55261314 TATAATTTATGTATAATATTAA-T--GCAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
*
55261345 TGTAATATATGTATAATATTAATTAATTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* *
55261379 TGTAATTTATGTATAATATTAAATAATCAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
55261413 TGTA
1 TGTA
55261417 TAATATTAAT
Statistics
Matches: 249, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.00
31 102 0.41
32 4 0.02
33 4 0.02
34 137 0.55
35 1 0.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (34 bp):
TGTAATTTATGTATAATATTAATTAATTAAGTTA
Done.