Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold345
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: 201931
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 2 of 2
Found at i:167974 original size:9 final size:10
Alignment explanation
Indices: 167944--167988 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
167934 GAACAAATTT
167944 AATTAATAAAA
1 AATTAAT-AAA
*
167955 AATTAACAAA
1 AATTAATAAA
167965 AATT-ATAAA
1 AATTAATAAA
167974 AATTAATAAA
1 AATTAATAAA
167984 AATTA
1 AATTA
167989 TTTTTTATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 8 0.26
10 17 0.55
11 6 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AATTAATAAA
Found at i:167976 original size:19 final size:19
Alignment explanation
Indices: 167952--167989 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
167942 TTAATTAATA
167952 AAAAATTAACAAAAATTAT
1 AAAAATTAACAAAAATTAT
*
167971 AAAAATTAATAAAAATTAT
1 AAAAATTAACAAAAATTAT
167990 TTTTTATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTAACAAAAATTAT
Found at i:168407 original size:21 final size:21
Alignment explanation
Indices: 168383--168428 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
168373 AGGTAAAAGA
*
168383 ATATTTAGT-TTTTATATTGTT
1 ATATTTAATATTTTA-ATTGTT
*
168404 ATATTTAATATTTTAATTTTT
1 ATATTTAATATTTTAATTGTT
168425 ATAT
1 ATAT
168429 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
ATATTTAATATTTTAATTGTT
Found at i:168462 original size:18 final size:17
Alignment explanation
Indices: 168434--168473 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
168424 TATATATTTT
168434 AAATT-ATAATAAATAAA
1 AAATTAATAAT-AATAAA
*
168451 AAATTAATAATATTAAA
1 AAATTAATAATAATAAA
168468 AAATTA
1 AAATTA
168474 TTTAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTAATAATAATAAA
Found at i:168481 original size:19 final size:18
Alignment explanation
Indices: 168447--168495 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
168437 TTATAATAAA
*
168447 TAAAAAATTA-ATAATAT
1 TAAAAAATTATTTAATAT
168464 TAAAAAATTATTTAAATAT
1 TAAAAAATTATTT-AATAT
*
168483 TAATAAAAATATT
1 TAA-AAAATTATT
168496 ATATAATGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 8 0.30
20 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAAATTATTTAATAT
Found at i:168578 original size:18 final size:19
Alignment explanation
Indices: 168555--168590 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
168545 GTTATGGATC
*
168555 AAATTT-AATTTTTATATA
1 AAATTTAAAATTTTATATA
168573 AAATTTAAAATTTTATAT
1 AAATTTAAAATTTTATAT
168591 CACATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTTAAAATTTTATATA
Found at i:168641 original size:21 final size:22
Alignment explanation
Indices: 168603--168643 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
168593 CATTATATAT
*
168603 TAATATTTTATTAATATTAAAA
1 TAATATTTTAATAATATTAAAA
*
168625 TAAT-TTTTAATATTATTAA
1 TAATATTTTAATAATATTAA
168644 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTTTAATAATATTAAAA
Found at i:168670 original size:14 final size:14
Alignment explanation
Indices: 168653--168698 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
168643 ATTATTTTTT
*
168653 ATTTATTATATAAA
1 ATTTATAATATAAA
* *
168667 ATTTAAAATATTAA
1 ATTTATAATATAAA
168681 ATTTAATAATATAAA
1 ATTT-ATAATATAAA
168696 ATT
1 ATT
168699 AAAATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTATAATATAAA
Found at i:168684 original size:28 final size:26
Alignment explanation
Indices: 168651--168723 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 26
168641 TAATTATTTT
168651 TTATTTATTATATAAAATTTAAAATA
1 TTATTTATTATATAAAATTTAAAATA
*
168677 TTAAATTTAATAATATAAAA-TTAAAATA
1 TT--ATTT-ATTATATAAAATTTAAAATA
* *
168705 TTTTTTATTATATACAATT
1 TTATTTATTATATAAAATT
168724 ATTATCAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 9 0.23
26 6 0.15
28 14 0.36
29 10 0.26
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATTTATTATATAAAATTTAAAATA
Found at i:168691 original size:15 final size:14
Alignment explanation
Indices: 168660--168706 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
168650 TTTATTTATT
*
168660 ATATAAAATTTAAA
1 ATATTAAATTTAAA
168674 ATATTAAATTTAATA
1 ATATTAAATTTAA-A
*
168689 ATA-TAAAATTAAA
1 ATATTAAATTTAAA
168702 ATATT
1 ATATT
168707 TTTTATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTAAATTTAAA
Found at i:168785 original size:16 final size:15
Alignment explanation
Indices: 168749--168785 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
168739 TTATTTTTTA
168749 AAAATATTTTTAATC
1 AAAATATTTTTAATC
*
168764 AAAATATTTTTCATC
1 AAAATATTTTTAATC
168779 AATAATA
1 AA-AATA
168786 CTTAAACTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATATTTTTAATC
Found at i:170005 original size:16 final size:16
Alignment explanation
Indices: 169984--170073 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
169974 GTTTCTTCAC
*
169984 AAAATATTTTTTATTA
1 AAAATATTTTATATTA
*
170000 AAAATATCTTAT-TTA
1 AAAATATTTTATATTA
* * * *
170015 AAGATAATTAATATTT
1 AAAATATTTTATATTA
170031 AAAATGA-TTTATATTA
1 AAAAT-ATTTTATATTA
* *
170047 AAAATAATTTATATTT
1 AAAATATTTTATATTA
170063 AAAATAATTTT
1 AAAAT-ATTTT
170074 TGTTATCATC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
15 12 0.21
16 41 0.71
17 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (16 bp):
AAAATATTTTATATTA
Found at i:170031 original size:17 final size:16
Alignment explanation
Indices: 170009--170072 Score: 92
Period size: 16 Copynumber: 3.9 Consensus size: 16
169999 AAAAATATCT
*
170009 TATTTAAAGATAATTAA
1 TATTTAAA-ATAATTTA
*
170026 TATTTAAAATGATTTA
1 TATTTAAAATAATTTA
*
170042 TATTAAAAATAATTTA
1 TATTTAAAATAATTTA
170058 TATTTAAAATAATTT
1 TATTTAAAATAATTT
170073 TTGTTATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 34 0.81
17 8 0.19
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTTAAAATAATTTA
Found at i:170067 original size:32 final size:30
Alignment explanation
Indices: 169984--170068 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 30
169974 GTTTCTTCAC
* * *
169984 AAAATATTTTTTATTAAAAATATCTTATTTA
1 AAAATAATTTATATTTAAAATAT-TTATTTA
* *
170015 AAGATAATTAATATTTAAAATGATTTATATTA
1 AAAATAATTTATATTTAAAAT-ATTTAT-TTA
170047 AAAATAATTTATATTTAAAATA
1 AAAATAATTTATATTTAAAATA
170069 ATTTTTGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (30 bp):
AAAATAATTTATATTTAAAATATTTATTTA
Found at i:170297 original size:24 final size:23
Alignment explanation
Indices: 170270--170328 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 23
170260 TATGATTATA
170270 TTTAAATAATTTTTTTAATTTTTT
1 TTTAAATAATTTTTTT-ATTTTTT
170294 TTTAAATATGTATTTTTTTATTTTTT
1 TTTAAATA---ATTTTTTTATTTTTT
*
170320 TTAAAATAA
1 TTTAAATAA
170329 ATAATAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.03
24 8 0.26
26 14 0.45
27 8 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTAAATAATTTTTTTATTTTTT
Found at i:171319 original size:19 final size:20
Alignment explanation
Indices: 171297--171352 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
171287 TATATAATTT
171297 TTTAAAATATT-AATAAAT-A
1 TTTAAAAT-TTAAATAAATAA
171316 TTT-AAATTTAAATAAATAA
1 TTTAAAATTTAAATAAATAA
*
171335 TTT-AATTTATAAATAAAT
1 TTTAAAATT-TAAATAAAT
171353 TTACGTGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 2 0.06
18 11 0.33
19 11 0.33
20 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAATTTAAATAAATAA
Found at i:171329 original size:18 final size:20
Alignment explanation
Indices: 171297--171352 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
171287 TATATAATTT
* *
171297 TTTAAAATATTAATAAAT-A
1 TTTAAATTATAAATAAATAA
171316 TTTAAATT-TAAATAAATAA
1 TTTAAATTATAAATAAATAA
*
171335 TTTAATTTATAAATAAAT
1 TTTAAATTATAAATAAAT
171353 TTACGTGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.25
19 15 0.47
20 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATTATAAATAAATAA
Found at i:173962 original size:60 final size:60
Alignment explanation
Indices: 173898--174023 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
173888 ATATGATATA
* * * * * *
173898 ATATAAATATATTAAAAT-ATTAAAATTTATATATAATATAAATTATTAATAT-ATAAAATT
1 ATATAAATATA-AAAAATAAATAAAATTAAAATATAATA-AAATTATAAATATGATAAAAAT
* *
173958 ATATAAATATAAAAAATAAATATAATTAAAATATAATAAATTTATAAATATGATAAAAAT
1 ATATAAATATAAAAAATAAATAAAATTAAAATATAATAAAATTATAAATATGATAAAAAT
174018 ATATAA
1 ATATAA
174024 TTTTTTCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 16 0.29
60 40 0.71
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (60 bp):
ATATAAATATAAAAAATAAATAAAATTAAAATATAATAAAATTATAAATATGATAAAAAT
Found at i:173995 original size:16 final size:16
Alignment explanation
Indices: 173879--173999 Score: 74
Period size: 16 Copynumber: 7.4 Consensus size: 16
173869 CAATTAAAAA
*
173879 ATAATTAAAATATGAT
1 ATAATTAAAATATAAT
*
173895 ATAATATAAATATATTAAA
1 ATAAT-TAAA-ATA-TAAT
*
173914 AT-ATTAAAATTTATAT
1 ATAATTAAAATATA-AT
*
173930 ATAATATAAATTATTAAT
1 ATAAT-TAAAATA-TAAT
173948 AT-A-TAAAAT-T-AT
1 ATAATTAAAATATAAT
*
173960 ATAAATATAAAAAATAAAT
1 AT-AAT-TAAAATAT-AAT
173979 ATAATTAAAATATAAT
1 ATAATTAAAATATAAT
173995 A-AATT
1 ATAATT
174000 TATAAATATG
Statistics
Matches: 82, Mismatches: 9, Indels: 29
0.68 0.08 0.24
Matches are distributed among these distances:
12 4 0.05
13 1 0.01
14 1 0.01
15 11 0.13
16 19 0.23
17 19 0.23
18 17 0.21
19 10 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAATTAAAATATAAT
Found at i:174036 original size:28 final size:28
Alignment explanation
Indices: 173899--174020 Score: 86
Period size: 24 Copynumber: 4.8 Consensus size: 28
173889 TATGATATAA
* *
173899 TATAAATAT-ATTAAAATATTA-AAATT
1 TATAAATATAATAAAAATATAATAAATT
* * *
173925 TAT--ATATAATATAAAT-T-ATTAATA
1 TATAAATATAATAAAAATATAATAAATT
* *
173949 TATAAA-ATTATATAAATATAA-AAA--
1 TATAAATATAATAAAAATATAATAAATT
*
173973 -ATAAATATAATTAAAATATAATAAATT
1 TATAAATATAATAAAAATATAATAAATT
*
174000 TATAAATATGATAAAAATATA
1 TATAAATATAATAAAAATATA
174021 TAATTTTTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
23 6 0.08
24 23 0.31
25 19 0.26
26 7 0.09
27 1 0.01
28 18 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
TATAAATATAATAAAAATATAATAAATT
Found at i:175622 original size:15 final size:15
Alignment explanation
Indices: 175598--175633 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
175588 TTTTAAAAAA
*
175598 TATAAT-TATAATCT
1 TATAATATATAATAT
175612 TATAATATATAATAT
1 TATAATATATAATAT
175627 TATAATA
1 TATAATA
175634 AATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATATATAATAT
Found at i:175758 original size:25 final size:27
Alignment explanation
Indices: 175730--175802 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
175720 CGTATTACTT
* *
175730 ATAAATTAGATAAAT-ATTA-TTAAAA
1 ATAAAATAGATAAATAATAATTTAAAA
**
175755 ATAAAATATTTAAATAATAATTTAAAA
1 ATAAAATAGATAAATAATAATTTAAAA
* *
175782 ATAAAATAAAT-AATGATAATT
1 ATAAAATAGATAAATAATAATT
175803 ATTTATCAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 12 0.31
26 12 0.31
27 15 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
ATAAAATAGATAAATAATAATTTAAAA
Found at i:175764 original size:14 final size:14
Alignment explanation
Indices: 175747--175789 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
175737 AGATAAATAT
175747 TATTAAAAATAAAA
1 TATTAAAAATAAAA
*
175761 TATT-TAAATAATAA
1 TATTAAAAATAA-AA
175775 T-TTAAAAATAAAA
1 TATTAAAAATAAAA
175788 TA
1 TA
175790 AATAATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATTAAAAATAAAA
Found at i:175800 original size:26 final size:27
Alignment explanation
Indices: 175749--175802 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
175739 ATAAATATTA
**
175749 TTAAAAATAAAATATTTAAATAATAAT
1 TTAAAAATAAAATAAATAAATAATAAT
*
175776 TTAAAAATAAAATAAAT-AATGATAAT
1 TTAAAAATAAAATAAATAAATAATAAT
175802 T
1 T
175803 ATTTATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
TTAAAAATAAAATAAATAAATAATAAT
Found at i:176228 original size:16 final size:17
Alignment explanation
Indices: 176207--176254 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
176197 ATGTAAAAAT
176207 ATTTAAAATTATTTT-A
1 ATTTAAAATTATTTTAA
176223 ATTTAAAATT-TTTATAA
1 ATTTAAAATTATTT-TAA
*
176240 ATTTAAATTTATTTT
1 ATTTAAAATTATTTT
176255 TAAGTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 11 0.39
18 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAAATTATTTTAA
Found at i:176588 original size:2 final size:2
Alignment explanation
Indices: 176581--176611 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
176571 ATCGGATGTT
*
176581 TA TA TA TA TA AA 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 T
176612 TTTGCTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:177502 original size:2 final size:2
Alignment explanation
Indices: 177497--177529 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
177487 TCTCCTTTAA
177497 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
177530 TTTTCATTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:179259 original size:20 final size:19
Alignment explanation
Indices: 179234--179316 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
179224 TATATATTTT
179234 ATATTTAAATTTAAATAAAA
1 ATATTTAAA-TTAAATAAAA
** *
179254 ATATTTTTATTATAA-AATA
1 ATATTTAAATTA-AATAAAA
*
179273 ATAATTTAAATTAAATTAAA
1 AT-ATTTAAATTAAATAAAA
* *
179293 TTATTTTAAATT-TATAAAA
1 ATA-TTTAAATTAAATAAAA
179312 ATATT
1 ATATT
179317 ATTTAAAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 2 0.04
19 18 0.38
20 28 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTTAAATTAAATAAAA
Found at i:180184 original size:64 final size:62
Alignment explanation
Indices: 180066--180250 Score: 185
Period size: 64 Copynumber: 2.9 Consensus size: 62
180056 TCACGTTTTT
* * * * * *
180066 GCCAAATTAACGCTACAGTGTCCAACTTTGGCAACTAAATGCAGCAATTCAATTGCCATTTTCG
1 GCCAAATCAATGCTACAATATCCAA-GTTGGCAACTAAATGCAGCAATTCAATTGCCA-TTTCA
* * * * *
180130 GCCAAA-CTAATGCTATAATCTCTTAAGTTGGCAACTAAAT-CTAGTAATTTAATTGCCATTTCA
1 GCCAAATC-AATGCTACAATATC-CAAGTTGGCAACTAAATGC-AGCAATTCAATTGCCATTTCA
* * *
180193 GCCAAATCAATGCTACAATATCCAAGTTGGCAACTAATTTCAGCAGTTCAATTGCCAT
1 GCCAAATCAATGCTACAATATCCAAGTTGGCAACTAAATGCAGCAATTCAATTGCCAT
180251 AAGAGTCTCT
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
62 29 0.29
63 24 0.24
64 44 0.44
65 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (62 bp):
GCCAAATCAATGCTACAATATCCAAGTTGGCAACTAAATGCAGCAATTCAATTGCCATTTCA
Found at i:180662 original size:23 final size:23
Alignment explanation
Indices: 180605--180652 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
180595 AAATATATTT
180605 TATGT-TAAATTTAATTACAAAA
1 TATGTATAAATTTAATTACAAAA
180627 TATGTATAAATTTATATTA-AAAA
1 TATGTATAAATTTA-ATTACAAAA
180650 TAT
1 TAT
180653 TTTTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
TATGTATAAATTTAATTACAAAA
Found at i:182378 original size:23 final size:22
Alignment explanation
Indices: 182316--182386 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
182306 TTTAATTTTA
*
182316 ATTAT-AAAAT-ATATAAATATT
1 ATTATAAAAATAATATTAA-ATT
* *
182337 AATATAAAAATAATTTTAACATT
1 ATTATAAAAATAATATTAA-ATT
182360 ATTATAAATAATAA-ATTAAATT
1 ATTATAAA-AATAATATTAAATT
*
182382 TTTAT
1 ATTAT
182387 CCACATCAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.10
22 12 0.30
23 19 0.47
24 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTATAAAAATAATATTAAATT
Found at i:183341 original size:34 final size:33
Alignment explanation
Indices: 183293--183513 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 33
183283 TGGTAAAAAC
* *
183293 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAAGCTACCAAAT
* * * *
183326 CTACTATTTAGTCAACAATAGTAAGTTACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
* *
183360 CACCCATTTAATCAATAATGGTAAGCTATCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
**
183394 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * * *
183428 CTCCCATTTAGTCAATAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
183462 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
183496 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
183514 TCTCCCACTT
Statistics
Matches: 155, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
33 19 0.12
34 135 0.87
35 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:183409 original size:68 final size:68
Alignment explanation
Indices: 183295--183509 Score: 272
Period size: 68 Copynumber: 3.2 Consensus size: 68
183285 GTAAAAACCA
* * * * *
183295 CCATTTAATCAACAATGGCAACCTACCAAATCTACT-ATTTAGTCAACAATAGTAAGTTACCAAA
1 CCATTTAATCAATAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCAAA
183359 TCAC
65 TCAC
* * * *
183363 CCATTTAATCAATAATGGTAAGCTATCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
*
183428 CTC
66 CAC
* * * * *
183431 CCATTTAGTCAATAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
183496 CA-
66 CAC
183498 CCATTTAATCAA
1 CCATTTAATCAA
183510 CAATTCTCCC
Statistics
Matches: 126, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 14 0.11
68 112 0.89
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (68 bp):
CCATTTAATCAATAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:183438 original size:102 final size:101
Alignment explanation
Indices: 183293--183513 Score: 298
Period size: 102 Copynumber: 2.2 Consensus size: 101
183283 TGGTAAAAAC
* * ***
183293 CACCATTTAATCAACAATGGCAACCTACCAAATCTACTATTTAGTCAACAATAGTAAGTTACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
* * *
183358 ATCACCCATTTAATCAATAATGGTAAGCTATCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * * *
183394 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAATAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCA
183459 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
183496 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
183514 TCTCCCACTT
Statistics
Matches: 102, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 16 0.16
102 86 0.84
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:187813 original size:34 final size:34
Alignment explanation
Indices: 187766--187983 Score: 178
Period size: 34 Copynumber: 6.4 Consensus size: 34
187756 GGTAAAAACC
* *
187766 ACCATTTAATCAACAATGGCAACCTACTAAATCT
1 ACCATTTAATCAACAATGGTAACCTACCAAATCT
* * *
187800 ACCATTTAGTCAACAATGATAAGCC-ATCAAATC-
1 ACCATTTAATCAACAATGGTAA-CCTACCAAATCT
* * *
187833 ACCCATTTAATCAATAATAGTAAGCTACCAAAT-T
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
* **
187867 TCTCATTTAATCAACAATGGTAAGTTACCAAATCT
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
* * *
187902 CCCATTTAATCAACAATGGCAA-ATCACCAAATC-
1 ACCATTTAATCAACAATGGTAACCT-ACCAAATCT
* * * *
187935 ACTAATTTAATCAGCAATGATAAACTACCAAATC-
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
*
187969 ACCGTTTAATCAACA
1 ACCATTTAATCAACA
187984 CTTTACCACC
Statistics
Matches: 148, Mismatches: 27, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
33 15 0.10
34 128 0.86
35 5 0.03
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATCT
Found at i:187881 original size:68 final size:67
Alignment explanation
Indices: 187767--187983 Score: 231
Period size: 68 Copynumber: 3.2 Consensus size: 67
187757 GTAAAAACCA
* * * *
187767 CCATTTAATCAACAATGGCAACCTACTAAATCTAC-CATTTAGTCAACAATGATAAGCCATCAAA
1 CCATTTAATCAACAATGGCAA-CTACCAAAT-TACTCATTTAATCAACAATGATAAGCTACCAAA
187831 TCAC
64 TCAC
* * * * * *
187835 CCATTTAATCAATAATAGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGTTACCAAAT
1 CCATTTAATCAACAATGGCAA-CTACCAAATTACTCATTTAATCAACAATGATAAGCTACCAAAT
*
187900 CTC
65 CAC
* * * * *
187903 CCATTTAATCAACAATGGCAAATCACCAAATCACTAATTTAATCAGCAATGATAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACT-ACCAAATTACTCATTTAATCAACAATGATAAGCTACCAAAT
187968 CA-
65 CAC
*
187970 CCGTTTAATCAACA
1 CCATTTAATCAACA
187984 CTTTACCACC
Statistics
Matches: 122, Mismatches: 25, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
67 16 0.13
68 106 0.87
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAACTACCAAATTACTCATTTAATCAACAATGATAAGCTACCAAATC
AC
Found at i:187963 original size:102 final size:102
Alignment explanation
Indices: 187768--187967 Score: 240
Period size: 102 Copynumber: 2.0 Consensus size: 102
187758 TAAAAACCAC
* * * * *
187768 CATTTAATCAACAATGGCAACCTACTAAATCTACCATTTAGTCAACAATGATAAGCCATCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGACAAACCACCAAATC
* * *
187833 ACCCATTTAATCAATAATAGTAAGCTACCAAATTTCT
66 ACCAATTTAATCAACAATAGTAAACTACCAAATTTCT
* ** * * *
187870 CATTTAATCAACAATGGTAAGTTACCAAATCTCCCATTTAATCAACAATGGCAAATCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGACAAACCACCAAATC
* *
187935 ACTAATTTAATCAGCAAT-GATAAACTACCAAAT
66 ACCAATTTAATCAACAATAG-TAAACTACCAAAT
187968 CACCGTTTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 1 0.01
102 80 0.99
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (102 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGACAAACCACCAAATC
ACCAATTTAATCAACAATAGTAAACTACCAAATTTCT
Found at i:188829 original size:29 final size:28
Alignment explanation
Indices: 188775--188833 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
188765 TATGGCCCTC
*
188775 TTAAACACCCAAAATCCTAAGAAAATTT
1 TTAAACACCCAAAATCCTAACAAAATTT
*
188803 TTAAA-ACCCGAAATCCTAAAACAAAATTT
1 TTAAACACCCAAAATCCT--AACAAAATTT
188832 TT
1 TT
188834 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 11 0.41
28 5 0.19
29 11 0.41
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.27
Consensus pattern (28 bp):
TTAAACACCCAAAATCCTAACAAAATTT
Found at i:189463 original size:51 final size:53
Alignment explanation
Indices: 189402--189506 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 53
189392 AAAGTGAGAT
189402 TTTTTATTTTTATAAGTA-AAATTAAAAAAAT-TATT-ATATTTAATTTAA-TTA
1 TTTTTATTTTT-TAA-TATAAATTAAAAAAATATATTAATATTTAATTTAACTTA
** * *
189453 TTTTTATTTTTTAATATACTTTAAAAATATATATTAATTTTTAATTTAACTTA
1 TTTTTATTTTTTAATATAAATTAAAAAAATATATTAATATTTAATTTAACTTA
189506 T
1 T
189507 AAAATTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 2 0.04
50 13 0.28
51 15 0.33
52 12 0.26
53 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (53 bp):
TTTTTATTTTTTAATATAAATTAAAAAAATATATTAATATTTAATTTAACTTA
Found at i:189770 original size:15 final size:16
Alignment explanation
Indices: 189745--189774 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
189735 AAAAAATTTT
189745 ATATAAAATTTAATTC
1 ATATAAAATTTAATTC
189761 ATAT-AAATTTAATT
1 ATATAAAATTTAATT
189775 TATTAAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAAAATTTAATTC
Found at i:189882 original size:20 final size:19
Alignment explanation
Indices: 189828--189878 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 19
189818 CTTTTATTTT
189828 TTATTAAATATTAATTTAA
1 TTATTAAATATTAATTTAA
189847 --A-TAAAT-TT--TTTAA
1 TTATTAAATATTAATTTAA
189860 TTATTAAATATTAATTTAA
1 TTATTAAATATTAATTTAA
189879 ATTAAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
13 5 0.19
15 3 0.12
16 10 0.38
17 3 0.12
19 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTAAATATTAATTTAA
Found at i:189898 original size:32 final size:31
Alignment explanation
Indices: 189829--189898 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
189819 TTTTATTTTT
**
189829 TATTAAATATTAATTTAAATAAATTTTTTAA
1 TATTAAATATTAATTTAAATAAATAATTTAA
189860 TTATTAAATATTAATTTAAATTAAACTAATTTAA
1 -TATTAAATATTAATTTAAA-TAAA-TAATTTAA
189894 -ATTAA
1 TATTAA
189899 TAAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 24 0.71
33 4 0.12
34 6 0.18
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TATTAAATATTAATTTAAATAAATAATTTAA
Found at i:190121 original size:49 final size:50
Alignment explanation
Indices: 190030--190130 Score: 168
Period size: 49 Copynumber: 2.0 Consensus size: 50
190020 GTTGGCCCTC
190030 ACCTTTTTCCTTTGTTATTTTTTTTTTCTATGGTTATAAATTTTATTGCCG
1 ACCTTTTTCCTTTGTTA-TTTTTTTTTCTATGGTTATAAATTTTATTGCCG
* *
190081 ACCTTTTTTCTTTGTTA-TTTTTTTTCTGTGGTTATAAATTTTATTGCCG
1 ACCTTTTTCCTTTGTTATTTTTTTTTCTATGGTTATAAATTTTATTGCCG
190130 A
1 A
190131 TAGCATACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 32 0.67
51 16 0.33
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (50 bp):
ACCTTTTTCCTTTGTTATTTTTTTTTCTATGGTTATAAATTTTATTGCCG
Found at i:190945 original size:15 final size:16
Alignment explanation
Indices: 190925--190955 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
190915 ATACATATGT
190925 AAATATAAAT-TTTAA
1 AAATATAAATATTTAA
190940 AAATATAAATATTTAA
1 AAATATAAATATTTAA
190956 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAAATATTTAA
Found at i:190978 original size:15 final size:16
Alignment explanation
Indices: 190926--190976 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
190916 TACATATGTA
190926 AATATAAATTTTAAA-
1 AATATAAATTTTAAAT
190941 AATATAAATATTT-AAT
1 AATATAAAT-TTTAAAT
*
190957 -ATTTAAAATTTTAAAT
1 AATAT-AAATTTTAAAT
190973 AATA
1 AATA
190977 AATAAATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 17 0.59
16 10 0.34
17 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAAATTTTAAAT
Found at i:191885 original size:18 final size:18
Alignment explanation
Indices: 191862--191896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
191852 ATTTATATAT
* *
191862 TTTTAATTTTAGTTTAAC
1 TTTTAAATTGAGTTTAAC
191880 TTTTAAATTGAGTTTAA
1 TTTTAAATTGAGTTTAA
191897 GTTAAAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTTAAATTGAGTTTAAC
Found at i:192111 original size:17 final size:17
Alignment explanation
Indices: 192091--192125 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
192081 ATTTAAATCA
192091 AATTAAATTTT-ATTTTT
1 AATT-AATTTTAATTTTT
192108 AATTAATTTTAATTTTT
1 AATTAATTTTAATTTTT
192125 A
1 A
192126 TAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTAATTTTAATTTTT
Found at i:193886 original size:19 final size:19
Alignment explanation
Indices: 193862--193898 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
193852 TTAATTTTTA
193862 ATTA-TTTATTAATAAAATT
1 ATTATTTTA-TAATAAAATT
193881 ATTATTTTATAATAAAAT
1 ATTATTTTATAATAAAAT
193899 AATTTTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATTTTATAATAAAATT
Found at i:194362 original size:17 final size:16
Alignment explanation
Indices: 194340--194387 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 16
194330 ATATAGGTAA
194340 TTAAATTTAAATATAAT
1 TTAAATTTAAATAT-AT
194357 TTAAATTATTAAATATAT
1 TTAAA-T-TTAAATATAT
* *
194375 TAAAATATAAATA
1 TTAAATTTAAATA
194388 AAAATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.22
17 6 0.22
18 7 0.26
19 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAATATAT
Found at i:194377 original size:9 final size:9
Alignment explanation
Indices: 194346--194414 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 9
194336 GTAATTAAAT
194346 TTAAATATAA
1 TTAAATAT-A
194356 TTTAAAT-TA
1 -TTAAATATA
194365 TTAAATATA
1 TTAAATATA
194374 TTAAA-ATA
1 TTAAATATA
194382 -TAAATA-A
1 TTAAATATA
194389 --AAATATA
1 TTAAATATA
* *
194396 ATACATATA
1 TTAAATATA
194405 TTAAATATA
1 TTAAATATA
194414 T
1 T
194415 CATATTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.10
7 6 0.12
8 10 0.20
9 22 0.44
10 1 0.02
11 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAAATATA
Found at i:194907 original size:2 final size:2
Alignment explanation
Indices: 194900--194925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
194890 TCGTCCACAA
194900 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
194926 TACGTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197028 original size:34 final size:34
Alignment explanation
Indices: 196990--197090 Score: 121
Period size: 37 Copynumber: 2.9 Consensus size: 34
196980 TTTTAATAAG
* *
196990 TGTTAGGTAAATATATTAGGTGTGTTAGGTTGTA
1 TGTTAGGTAAATATATTAGGTGTGTTAAGTCGTA
* * *
197024 TGTTAAGTGAATAATATATTAAGTGTGTTAAGTCGTG
1 TGTT-AG-GTA-AATATATTAGGTGTGTTAAGTCGTA
*
197061 TGTTAGGTAAACATATTAGGTGTGTTAAGT
1 TGTTAGGTAAATATATTAGGTGTGTTAAGT
197091 AAACATATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 23 0.41
35 4 0.07
36 4 0.07
37 25 0.45
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.42
Consensus pattern (34 bp):
TGTTAGGTAAATATATTAGGTGTGTTAAGTCGTA
Found at i:197086 original size:22 final size:22
Alignment explanation
Indices: 197058--197112 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
197048 GTGTTAAGTC
*
197058 GTGTGTTAGGTAAACATATTAG
1 GTGTGTTAAGTAAACATATTAG
197080 GTGTGTTAAGTAAACATATTAG
1 GTGTGTTAAGTAAACATATTAG
* *
197102 ATGCGTTAAGT
1 GTGTGTTAAGT
197113 GAATTTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGTTAAGTAAACATATTAG
Found at i:201723 original size:21 final size:22
Alignment explanation
Indices: 201680--201725 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
201670 TCTTTATTAA
*
201680 GTGTGTTAGGTAAATATATTAG
1 GTGTGTTAGGTAAATATACTAG
* *
201702 GTGTGTTAGGT-GATATGCTAG
1 GTGTGTTAGGTAAATATACTAG
201723 GTG
1 GTG
201726 AGTAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.39
Consensus pattern (22 bp):
GTGTGTTAGGTAAATATACTAG
Found at i:201724 original size:34 final size:34
Alignment explanation
Indices: 201686--201783 Score: 106
Period size: 37 Copynumber: 2.8 Consensus size: 34
201676 TTAAGTGTGT
*
201686 TAGGTAAATATATTAGGTGTGTTAGGTGATATGC
1 TAGGTAAATATATTAAGTGTGTTAGGTGATATGC
* * * *
201720 TAGGTGAGTAATATATTAAGTGTATTAGGTGGTGTGT
1 TAGGT-A--AATATATTAAGTGTGTTAGGTGATATGC
* *
201757 TAAGTAAATATATTATGTGTGTTAGGT
1 TAGGTAAATATATTAAGTGTGTTAGGT
201784 AAACATATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
34 24 0.45
35 1 0.02
36 1 0.02
37 27 0.51
ACGTcount: A:0.30, C:0.01, G:0.29, T:0.41
Consensus pattern (34 bp):
TAGGTAAATATATTAAGTGTGTTAGGTGATATGC
Found at i:201778 original size:22 final size:22
Alignment explanation
Indices: 201751--201793 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
201741 GTATTAGGTG
*
201751 GTGTGTTAAGTAAATATATTAT
1 GTGTGTTAAGTAAACATATTAT
*
201773 GTGTGTTAGGTAAACATATTA
1 GTGTGTTAAGTAAACATATTA
201794 GGTATATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (22 bp):
GTGTGTTAAGTAAACATATTAT
Found at i:201803 original size:22 final size:22
Alignment explanation
Indices: 201760--201805 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
201750 GGTGTGTTAA
* * * *
201760 GTAAATATATTATGTGTGTTAG
1 GTAAACATATTAGGTATATTAG
201782 GTAAACATATTAGGTATATTAG
1 GTAAACATATTAGGTATATTAG
201804 GT
1 GT
201806 GAACTTATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (22 bp):
GTAAACATATTAGGTATATTAG
Done.