Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold500
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: 2046043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1966184 original size:34 final size:36
Alignment explanation
Indices: 1966139--1966206 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 36
1966129 TTTTAATATA
1966139 AAAATGATTAAT-TCTAATTATTTTAAAAT-ATTAAC
1 AAAATGATTAATATCT-ATTATTTTAAAATCATTAAC
* *
1966174 AAAAT-ATTAATATCTTTTATTTTATAATCATTA
1 AAAATGATTAATATCTATTATTTTAAAATCATTA
1966207 TGAGTATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (36 bp):
AAAATGATTAATATCTATTATTTTAAAATCATTAAC
Found at i:1966350 original size:3 final size:3
Alignment explanation
Indices: 1966342--1966366 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1966332 CTTTTAAAAT
1966342 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1966367 ATCTTTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1968915 original size:16 final size:16
Alignment explanation
Indices: 1968881--1968925 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1968871 TGATAAAATT
*
1968881 AAAAGTTTAAATTAAA
1 AAAAGTCTAAATTAAA
*
1968897 AAAAGTCTAAATTTCAA
1 AAAAGTCTAAA-TTAAA
1968914 AAAA-TCTAAATT
1 AAAAGTCTAAATT
1968926 GAACTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.08
16 16 0.62
17 8 0.31
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (16 bp):
AAAAGTCTAAATTAAA
Found at i:1969004 original size:20 final size:19
Alignment explanation
Indices: 1968960--1969004 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1968950 AGAGTAATTA
*
1968960 AATTATAATTAAAAACTTT
1 AATTATAAATAAAAACTTT
**
1968979 TCTTATAAAATAAAAACTTT
1 AATTAT-AAATAAAAACTTT
1968999 AATTAT
1 AATTAT
1969005 CTATTTTACT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATAAATAAAAACTTT
Found at i:1973642 original size:2 final size:2
Alignment explanation
Indices: 1973635--1973680 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1973625 TAGTGTTAGA
1973635 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1973677 CT CT
1 CT CT
1973681 TGTTTTTGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1980992 original size:2 final size:2
Alignment explanation
Indices: 1980987--1981026 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1980977 AGAGAGAATA
1980987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1981027 CAGCATGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1982149 original size:15 final size:16
Alignment explanation
Indices: 1982123--1982152 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1982113 GAGGAGTAGG
1982123 GGAAGAAGTCATCGTC
1 GGAAGAAGTCATCGTC
1982139 GGAAG-AGTCATCGT
1 GGAAGAAGTCATCGT
1982153 TGTTGTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.20
Consensus pattern (16 bp):
GGAAGAAGTCATCGTC
Found at i:1983152 original size:56 final size:56
Alignment explanation
Indices: 1983066--1983177 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
1983056 TCATATAGCA
*
1983066 AAGCAACTCTAACAACCATCTTATAAAATTTTTTCTGTGCACTTTTTATTTTTACT
1 AAGCAACTCTAACAACCATCTTACAAAATTTTTTCTGTGCACTTTTTATTTTTACT
1983122 AAGCAACTCTAACAACCATCTTACAAAATTTTTTCTGTGCACTTTTTATTTTTACT
1 AAGCAACTCTAACAACCATCTTACAAAATTTTTTCTGTGCACTTTTTATTTTTACT
1983178 TTTTTTTTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (56 bp):
AAGCAACTCTAACAACCATCTTACAAAATTTTTTCTGTGCACTTTTTATTTTTACT
Found at i:1984516 original size:10 final size:9
Alignment explanation
Indices: 1984495--1984526 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1984485 TTTGTCTTTG
*
1984495 AAAAGAAGA
1 AAAAAAAGA
1984504 AAAAAAAGA
1 AAAAAAAGA
1984513 AAAAAAAGA
1 AAAAAAAGA
1984522 AAAAA
1 AAAAA
1984527 CTAAATTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:1987145 original size:20 final size:21
Alignment explanation
Indices: 1987088--1987145 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1987078 TTTCAATTTA
1987088 ATATTA-AAAATAAAAATAATT
1 ATATTATAAAAT-AAAATAATT
*
1987109 ATATTAT--AATTAAATAATT
1 ATATTATAAAATAAAATAATT
*
1987128 -TTTTATAAAATAAAATAA
1 ATATTATAAAATAAAATAA
1987146 AATAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 12 0.39
21 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATTATAAAATAAAATAATT
Found at i:1989082 original size:16 final size:16
Alignment explanation
Indices: 1989061--1989159 Score: 101
Period size: 16 Copynumber: 6.2 Consensus size: 16
1989051 ATTGAATTAT
1989061 TTTTAAGTTTGAGTTA
1 TTTTAAGTTTGAGTTA
*
1989077 TTTTAAGTTTGAGTTG
1 TTTTAAGTTTGAGTTA
*
1989093 TTTT-AGTTTCAGATTA
1 TTTTAAGTTTGAG-TTA
* *
1989109 TTTTAAATTTGAATTA
1 TTTTAAGTTTGAGTTA
* * *
1989125 TTTTGAGTTCGAATTA
1 TTTTAAGTTTGAGTTA
* *
1989141 TTTCAAATTTGAGTTA
1 TTTTAAGTTTGAGTTA
1989157 TTT
1 TTT
1989160 CAAATTCGGA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
15 7 0.10
16 55 0.82
17 5 0.07
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (16 bp):
TTTTAAGTTTGAGTTA
Found at i:1990095 original size:16 final size:16
Alignment explanation
Indices: 1990076--1990146 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
1990066 ATAGTTCGAG
1990076 TCATTTCGAGTTCAGA
1 TCATTTCGAGTTCAGA
* *
1990092 TCATTTCGAGTTTAGG
1 TCATTTCGAGTTCAGA
* * *
1990108 TAATTTCGAATTCAAA
1 TCATTTCGAGTTCAGA
* *
1990124 TCATTTCAAGTTCAGG
1 TCATTTCGAGTTCAGA
1990140 TCATTTC
1 TCATTTC
1990147 AGGGTCAAGT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (16 bp):
TCATTTCGAGTTCAGA
Found at i:1990127 original size:32 final size:32
Alignment explanation
Indices: 1990078--1990146 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1990068 AGTTCGAGTC
* * * *
1990078 ATTTCGAGTTCAGATCATTTCGAGTTTAGGTA
1 ATTTCGAATTCAAATCATTTCAAGTTCAGGTA
*
1990110 ATTTCGAATTCAAATCATTTCAAGTTCAGGTC
1 ATTTCGAATTCAAATCATTTCAAGTTCAGGTA
1990142 ATTTC
1 ATTTC
1990147 AGGGTCAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
ATTTCGAATTCAAATCATTTCAAGTTCAGGTA
Found at i:1990147 original size:16 final size:16
Alignment explanation
Indices: 1990075--1990177 Score: 75
Period size: 16 Copynumber: 6.4 Consensus size: 16
1990065 GATAGTTCGA
*
1990075 GTCATTTCGAGTTCAG
1 GTCATTTCAAGTTCAG
* * *
1990091 ATCATTTCGAGTTTAG
1 GTCATTTCAAGTTCAG
* *
1990107 GTAATTTCGAA-TTCAA
1 GTCATTTC-AAGTTCAG
*
1990123 ATCATTTCAAGTTCAG
1 GTCATTTCAAGTTCAG
* * *
1990139 GTCATTTCAGGGTCAA
1 GTCATTTCAAGTTCAG
*
1990155 GTCATTTCAGGTTC-G
1 GTCATTTCAAGTTCAG
1990170 GATCATTT
1 G-TCATTT
1990178 TGGATTCGAG
Statistics
Matches: 68, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
15 3 0.04
16 64 0.94
17 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (16 bp):
GTCATTTCAAGTTCAG
Found at i:1990994 original size:7 final size:7
Alignment explanation
Indices: 1990984--1991009 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1990974 TGATTTTGAA
1990984 AATTTAT
1 AATTTAT
1990991 AATTTAT
1 AATTTAT
1990998 AATTTAT
1 AATTTAT
1991005 AATTT
1 AATTT
1991010 TTGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTAT
Found at i:1991656 original size:146 final size:146
Alignment explanation
Indices: 1991384--1991661 Score: 394
Period size: 146 Copynumber: 1.9 Consensus size: 146
1991374 CAAAATTTTA
* * * *
1991384 AAATTTTAGACTTGAAATTCATGATTTTAAAACTCATGAATTTAAAATTTTTTGTTTGAATAATT
1 AAATTTTAGACTTAAAATTCATGATGTTAAAACTCATAAATTTAAAATTTTTTATTTGAATAATT
* * * * * * *
1991449 GAGTTTTGGCTTTGATTTTAAATGAAAATTAATTTTCACTTTATAGTAGTAATGAAAAAGTGATT
66 AAATTTTAGATTTGATTTTAAATGAAAATTAATTCTCACTTTACAATAGTAATGAAAAAGTGATT
1991514 TTGTGAATTTTTACTT
131 TTGTGAATTTTTACTT
* * * *
1991530 AAATTTTAGATTTAAAATTTATGATGTTCAAGCTCATAAATTTAAAATTTTTTATTTGAATAATT
1 AAATTTTAGACTTAAAATTCATGATGTTAAAACTCATAAATTTAAAATTTTTTATTTGAATAATT
* * *
1991595 AAATTTTAGATTTGGTTTTAAATGAAAATTAATTCTCACTTTACAATAGTAATTAAGAAGTGATT
66 AAATTTTAGATTTGATTTTAAATGAAAATTAATTCTCACTTTACAATAGTAATGAAAAAGTGATT
1991660 TT
131 TT
1991662 ATAAATTCTT
Statistics
Matches: 114, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
146 114 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (146 bp):
AAATTTTAGACTTAAAATTCATGATGTTAAAACTCATAAATTTAAAATTTTTTATTTGAATAATT
AAATTTTAGATTTGATTTTAAATGAAAATTAATTCTCACTTTACAATAGTAATGAAAAAGTGATT
TTGTGAATTTTTACTT
Found at i:1991689 original size:14 final size:15
Alignment explanation
Indices: 1991663--1991691 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1991653 AGTGATTTTA
1991663 TAAATTCTTGAATTT
1 TAAATTCTTGAATTT
1991678 TAAATT-TTGAATTT
1 TAAATTCTTGAATTT
1991692 AAAACTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
TAAATTCTTGAATTT
Found at i:1997881 original size:24 final size:24
Alignment explanation
Indices: 1997849--1997896 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1997839 TTGCAGACAA
1997849 AGAATGACGATCCTTTATAATCAT
1 AGAATGACGATCCTTTATAATCAT
1997873 AGAATGACGATCCTTTATAATCAT
1 AGAATGACGATCCTTTATAATCAT
1997897 TGCCCACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (24 bp):
AGAATGACGATCCTTTATAATCAT
Found at i:1999203 original size:2 final size:2
Alignment explanation
Indices: 1999196--1999265 Score: 104
Period size: 2 Copynumber: 35.0 Consensus size: 2
1999186 CGAAAAGCAA
* * * *
1999196 AT AT AT AT AT AT AT AT AT AT TT GT AT CT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1999238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1999266 TATGATGATA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1999539 original size:19 final size:20
Alignment explanation
Indices: 1999516--1999562 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1999506 TAAATTACAC
1999516 TTAAATTATTATTTATTT-AA
1 TTAAATTATT-TTTATTTAAA
*
1999536 -TAAAATA-TTTTATTTAAA
1 TTAAATTATTTTTATTTAAA
1999554 TTAAATTAT
1 TTAAATTAT
1999563 AAAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTATTTTTATTTAAA
Found at i:2000051 original size:156 final size:156
Alignment explanation
Indices: 1999767--2000079 Score: 617
Period size: 156 Copynumber: 2.0 Consensus size: 156
1999757 TAGAAGATCC
1999767 ACCATGATTCCACATCGCATGAATTGCATGTGCCCTTCCCATCTAAATGTGTACATCAGCCCTCG
1 ACCATGATTCCACATCGCATGAATTGCATGTGCCCTTCCCATCTAAATGTGTACATCAGCCCTCG
*
1999832 ACCGCATTCACCCACCGGTCAGTACTATATATTCTTATTTCTACTGACATCTAATTGTAATTCTA
66 ACCGCATTCACCCACCGGTCAGTACAATATATTCTTATTTCTACTGACATCTAATTGTAATTCTA
1999897 AATCTAAAATATGTATGCATGCATGT
131 AATCTAAAATATGTATGCATGCATGT
1999923 ACCATGATTCCACATCGCATGAATTGCATGTGCCCTTCCCATCTAAATGTGTACATCAGCCCTCG
1 ACCATGATTCCACATCGCATGAATTGCATGTGCCCTTCCCATCTAAATGTGTACATCAGCCCTCG
1999988 ACCGCATTCACCCACCGGTCAGTACAATATATTCTTATTTCTACTGACATCTAATTGTAATTCTA
66 ACCGCATTCACCCACCGGTCAGTACAATATATTCTTATTTCTACTGACATCTAATTGTAATTCTA
2000053 AATCTAAAATATGTATGCATGCATGT
131 AATCTAAAATATGTATGCATGCATGT
2000079 A
1 A
2000080 TATGTATATA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (156 bp):
ACCATGATTCCACATCGCATGAATTGCATGTGCCCTTCCCATCTAAATGTGTACATCAGCCCTCG
ACCGCATTCACCCACCGGTCAGTACAATATATTCTTATTTCTACTGACATCTAATTGTAATTCTA
AATCTAAAATATGTATGCATGCATGT
Found at i:2000640 original size:13 final size:13
Alignment explanation
Indices: 2000622--2000651 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2000612 ATAAGAAAGA
2000622 GAAAAAAATTTAT
1 GAAAAAAATTTAT
2000635 GAAAAAAATTTAT
1 GAAAAAAATTTAT
2000648 -AAAA
1 GAAAA
2000652 TTTTAAGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (13 bp):
GAAAAAAATTTAT
Found at i:2000728 original size:5 final size:5
Alignment explanation
Indices: 2000718--2000793 Score: 50
Period size: 5 Copynumber: 15.0 Consensus size: 5
2000708 GATCTAAATA
* * *
2000718 AATTT AATTT AATATA AATTAT TATTT -ATTT AATTA AATAATT -ATTT
1 AATTT AATTT AAT-TT AATT-T AATTT AATTT AATTT AAT--TT AATTT
* *
2000765 TATTT AATTT TATTT AATTT AA-TT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
2000794 CTTTTAATAC
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 10 0.18
5 36 0.64
6 9 0.16
7 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:2000749 original size:21 final size:20
Alignment explanation
Indices: 2000719--2000773 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
2000709 ATCTAAATAA
*
2000719 ATTTAATTTAATATAAATTATT
1 ATTT-ATTTAAT-TAAATAATT
2000741 ATTTATTTAATTAAATAATT
1 ATTTATTTAATTAAATAATT
2000761 ATTTTATTTAATT
1 A-TTTATTTAATT
2000774 TTATTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 9 0.29
21 18 0.58
22 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATTTAATTAAATAATT
Found at i:2000779 original size:15 final size:15
Alignment explanation
Indices: 2000718--2000788 Score: 61
Period size: 16 Copynumber: 4.6 Consensus size: 15
2000708 GATCTAAATA
* *
2000718 AATTTAATTTAATAT
1 AATTTAATTTTATTT
* *
2000733 AAATTATTATTTATTT
1 AATTTAAT-TTTATTT
* *
2000749 AATTAAATAATTATTT
1 AATTTAAT-TTTATTT
*
2000765 TATTTAATTTTATTT
1 AATTTAATTTTATTT
2000780 AATTTAATT
1 AATTTAATT
2000789 AATTTCTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 20 0.47
16 23 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTAATTTTATTT
Found at i:2000801 original size:19 final size:19
Alignment explanation
Indices: 2000719--2000793 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
2000709 ATCTAAATAA
2000719 ATTTAATTTAATATAAATTATT
1 ATTTAATTTAAT-T-AATT-TT
*
2000741 ATTT-ATTTAATTAA--AT
1 ATTTAATTTAATTAATTTT
* * *
2000757 AATTATTTTATTTAATTTT
1 ATTTAATTTAATTAATTTT
2000776 ATTTAATTTAATTAATTT
1 ATTTAATTTAATTAATTT
2000794 CTTTTAATAC
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
16 4 0.10
17 8 0.19
19 18 0.43
20 1 0.02
21 7 0.17
22 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAATTTAATTAATTTT
Found at i:2000992 original size:2 final size:2
Alignment explanation
Indices: 2000985--2001017 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2000975 AGAGTAGGCT
2000985 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
2001018 AGCAATTGAA
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:2006338 original size:89 final size:88
Alignment explanation
Indices: 2006184--2006443 Score: 335
Period size: 89 Copynumber: 2.9 Consensus size: 88
2006174 TTTTAACATG
* * * * *
2006184 AAATTATGCATTCTATATATTTTGGTCAATAAGAAAAAAGTTAAAACTAAAATGAAGAGAGAATA
1 AAATTATGCATTTTATAGATTTTGGTAAATAAGAAAAAAATTAAAACTAAAATGAAGAGAAAATA
*
2006249 AAAATGAAACAAATTAGAA-TTG
66 AAAATGAAACAAATTAGAAGTTA
* * * * *
2006271 ACATTATGCCTTTTATAGATTTTGATGAATAAGGAAAAAAAATTAAAACTAAAATGAAAAGAAAA
1 AAATTATGCATTTTATAGATTTTGGTAAATAA-G-AAAAAAATTAAAACTAAAATGAAGAGAAAA
2006336 TAAAAATGAAACAAATTA-AAGTTA
64 TAAAAATGAAACAAATTAGAAGTTA
* * **
2006360 AAATTATGCATTTTAAAGATATTGGTAAATAAAGAAAAAGTTTAAAACTAAAATGAAGAGAAAAT
1 AAATTATGCATTTTATAGATTTTGGTAAAT-AAGAAAAAAATTAAAACTAAAATGAAGAGAAAAT
*
2006425 AAAAATGAAACAAAATAGA
65 AAAAATGAAACAAATTAGA
2006444 GCAATTGATT
Statistics
Matches: 148, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
87 26 0.18
88 47 0.32
89 73 0.49
90 2 0.01
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (88 bp):
AAATTATGCATTTTATAGATTTTGGTAAATAAGAAAAAAATTAAAACTAAAATGAAGAGAAAATA
AAAATGAAACAAATTAGAAGTTA
Found at i:2006439 original size:16 final size:17
Alignment explanation
Indices: 2006409--2006441 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2006399 GTTTAAAACT
*
2006409 AAAATGAAGAGAAAATA
1 AAAATGAAGACAAAATA
2006426 AAAATGAA-ACAAAATA
1 AAAATGAAGACAAAATA
2006442 GAGCAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAATGAAGACAAAATA
Found at i:2010992 original size:21 final size:22
Alignment explanation
Indices: 2010966--2011017 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
2010956 ACATTAGTCC
*
2010966 CAACCTATAGT-GTCACAATCA
1 CAACCTATACTAGTCACAATCA
*
2010987 CAACCTA-ACTAGTCTCAATCA
1 CAACCTATACTAGTCACAATCA
2011008 CAACCTATAC
1 CAACCTATAC
2011018 AGCCACCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.38, C:0.33, G:0.06, T:0.23
Consensus pattern (22 bp):
CAACCTATACTAGTCACAATCA
Found at i:2013349 original size:45 final size:45
Alignment explanation
Indices: 2013277--2013363 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
2013267 GTATTGGGGT
* ** * *
2013277 TTTAAGGTTTTAAAGTTTTAAGATTTTGGGGTGTAAGGTTTAAAG
1 TTTAAGATTTTAAAGGCTTAAGATTTTGAGGTGTAAAGTTTAAAG
* * *
2013322 TTTAAGATTTTAAAGGCTTAGGGTTTTGAGGTTTAAAGTTTA
1 TTTAAGATTTTAAAGGCTTAAGATTTTGAGGTGTAAAGTTTA
2013364 GAGGTCAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (45 bp):
TTTAAGATTTTAAAGGCTTAAGATTTTGAGGTGTAAAGTTTAAAG
Found at i:2015048 original size:21 final size:21
Alignment explanation
Indices: 2015024--2015064 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2015014 AAACCAAAAA
* *
2015024 GAAGAGAGAAGAAAAGAGGAG
1 GAAGAGAAAAGAAAAAAGGAG
2015045 GAAGAGAAAAGAAAAAAGGA
1 GAAGAGAAAAGAAAAAAGGA
2015065 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (21 bp):
GAAGAGAAAAGAAAAAAGGAG
Found at i:2015075 original size:21 final size:21
Alignment explanation
Indices: 2015032--2015092 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
2015022 AAGAAGAGAG
* * * *
2015032 AAGAAAAGAGGAGGAAGAGAA
1 AAGAAAAAAGGAAGAAAAAAA
2015053 AAGAAAAAAGGAAGAAAAAAA
1 AAGAAAAAAGGAAGAAAAAAA
*
2015074 AA-AGAAAAGGAA-AAAAAAA
1 AAGAAAAAAGGAAGAAAAAAA
2015093 GTGACCTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 19 0.54
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAGGAAGAAAAAAA
Found at i:2015668 original size:16 final size:15
Alignment explanation
Indices: 2015644--2015686 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2015634 TTTTTTATAT
*
2015644 ATAATAAAAATAAAAT
1 ATAA-AAAAATAAAAG
*
2015660 ATTAAAAAAATATAAG
1 A-TAAAAAAATAAAAG
2015676 ATAAAAAAATA
1 ATAAAAAAATA
2015687 TATTTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.42
16 11 0.46
17 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
ATAAAAAAATAAAAG
Found at i:2016159 original size:111 final size:110
Alignment explanation
Indices: 2015922--2016178 Score: 275
Period size: 111 Copynumber: 2.3 Consensus size: 110
2015912 ATTGACCTCG
* * * * * *
2015922 AAATAGATTATTATCTAGAGCCGTAAAGTGGCGTACAAAGGCTCTTTATATATAATAATTTATTT
1 AAATAGATTATTATCTAGAGTCATAAAGTGGCATACAAAGGCTCTTTATATAAAACAATTCATTT
* * *
2015987 TTCACGTAAATTACATAGTATTTAGACACCAAAGGATTGGCCCCA
66 TTCACATAAATTACATAGTATTGAGACACCAAAGGATTGGCCACA
** * ** *
2016032 AAATAGATTACAATCTAGAGTCATAAAGTAGCATACAAATGTTTTTTTATATAAAACAATTCATT
1 AAATAGATTATTATCTAGAGTCATAAAGTGGCATACAAA-GGCTCTTTATATAAAACAATTCATT
* * * *
2016097 TTTTACATAAATTATATAGTATTCGAG-CACCAAGGGATTTGCCACA
65 TTTCACATAAATTACATAGTATT-GAGACACCAAAGGATTGGCCACA
* * *
2016143 AAATTGATCATTATCTAGAAAT-ATAAAGTGGCATAC
1 AAATAGATTATTATCTAG-AGTCATAAAGTGGCATAC
2016179 GAACGCCTTT
Statistics
Matches: 119, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
110 33 0.28
111 82 0.69
112 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (110 bp):
AAATAGATTATTATCTAGAGTCATAAAGTGGCATACAAAGGCTCTTTATATAAAACAATTCATTT
TTCACATAAATTACATAGTATTGAGACACCAAAGGATTGGCCACA
Found at i:2018044 original size:14 final size:14
Alignment explanation
Indices: 2018007--2018054 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2017997 CCGAGGTTAG
* *
2018007 AGTTTAAAGTTTAG
1 AGTTTATAGTTTAA
*
2018021 GGTTTATAGTTTAA
1 AGTTTATAGTTTAA
* *
2018035 AGTTTGTAGTTTGA
1 AGTTTATAGTTTAA
2018049 AGTTTA
1 AGTTTA
2018055 CGGTTAGGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
AGTTTATAGTTTAA
Found at i:2018046 original size:21 final size:21
Alignment explanation
Indices: 2018007--2018054 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2017997 CCGAGGTTAG
*
2018007 AGTTTAAAGTTTAGGGTTT-A
1 AGTTTAAAGTTTAGAGTTTGA
2018027 TAGTTTAAAGTTT-GTAGTTTGA
1 -AGTTTAAAGTTTAG-AGTTTGA
2018049 AGTTTA
1 AGTTTA
2018055 CGGTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (21 bp):
AGTTTAAAGTTTAGAGTTTGA
Found at i:2018249 original size:45 final size:45
Alignment explanation
Indices: 2018177--2018270 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 45
2018167 GTATTGGGGT
* ** * *
2018177 TTTAAGGTTTTAAAGTTTTAAGATTTTGGGGTGTAAGGTTTAAAG
1 TTTAAGATTTTAAAGGCTTAAGATTTTGAGGTGTAAAGTTTAAAG
* * * *
2018222 TTTAAGATTTTAAAGGCTTAGGGTTTTGAGGTTTAAAGTTTAGAG
1 TTTAAGATTTTAAAGGCTTAAGATTTTGAGGTGTAAAGTTTAAAG
2018267 TTTA
1 TTTA
2018271 GAGGTCAAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.45
Consensus pattern (45 bp):
TTTAAGATTTTAAAGGCTTAAGATTTTGAGGTGTAAAGTTTAAAG
Found at i:2019954 original size:21 final size:21
Alignment explanation
Indices: 2019930--2019986 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2019920 AAACCAAAAA
* *
2019930 GAAGAGAGAAGAAAAGAGGAG
1 GAAGAGAAAAGAAAAAAGGAG
*
2019951 GAAGAGAAAAGAAAAAAGGAA
1 GAAGAGAAAAGAAAAAAGGAG
* *
2019972 GAAAAAAAAAGAAAA
1 GAAGAGAAAAGAAAA
2019987 GGAAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
GAAGAGAAAAGAAAAAAGGAG
Found at i:2020573 original size:16 final size:15
Alignment explanation
Indices: 2020549--2020591 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2020539 TTTTTTATAT
*
2020549 ATAATAAAAATAAAAT
1 ATAA-AAAAATAAAAG
*
2020565 ATTAAAAAAATATAAG
1 A-TAAAAAAATAAAAG
2020581 ATAAAAAAATA
1 ATAAAAAAATA
2020592 TATTTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.42
16 11 0.46
17 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
ATAAAAAAATAAAAG
Found at i:2021033 original size:111 final size:111
Alignment explanation
Indices: 2020871--2021083 Score: 268
Period size: 111 Copynumber: 1.9 Consensus size: 111
2020861 ACGAAGGCTC
* * * * * *
2020871 TTTATATATAATAATTTATTTTTCACGTAAATTACATAGTATTTAGACACCAAAGGATTGGCCCC
1 TTTATATAAAACAATTCATTTTTCACATAAATTACATAGTATTGAGACACCAAAGGATTGGCCAC
*
2020936 AAAATAGATTACAATCTAGAG-TCATAAAGTAGCATACAAATGTTTT
66 AAAATAGATCACAATCTAGAGAT-ATAAAGTAGCATACAAATGTTTT
* * * *
2020982 TTTATATAAAACAATTCATTTTTTACATAAATTATATAGTATTCGAG-CACCAAGGGATTTGCCA
1 TTTATATAAAACAATTCATTTTTCACATAAATTACATAGTATT-GAGACACCAAAGGATTGGCCA
** *
2021046 CAAAATAGATCATTATCTAGAGATATAAAGTGGCATAC
65 CAAAATAGATCACAATCTAGAGATATAAAGTAGCATAC
2021084 GAACGCCTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
111 83 0.97
112 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (111 bp):
TTTATATAAAACAATTCATTTTTCACATAAATTACATAGTATTGAGACACCAAAGGATTGGCCAC
AAAATAGATCACAATCTAGAGATATAAAGTAGCATACAAATGTTTT
Found at i:2021690 original size:3 final size:3
Alignment explanation
Indices: 2021684--2021744 Score: 106
Period size: 3 Copynumber: 20.3 Consensus size: 3
2021674 CTTTTTTTAA
2021684 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
2021730 AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
2021745 CTTTTTTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2032567 original size:30 final size:30
Alignment explanation
Indices: 2032533--2032632 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
2032523 AAAGCAAAGC
2032533 AAAAACAAAAAAGCAAAAAAAAGATTAAAA
1 AAAAACAAAAAAGCAAAAAAAAGATTAAAA
* ** *
2032563 AAAAAGAGCAAAGCAAAAAAAATATTAAAATA
1 AAAAACAAAAAAGCAAAAAAAAGATT-AAA-A
* **
2032595 AAAAAGCAAAGCAAACCAAAAAAAAGAGCAAAA
1 AAAAA-CAAA--AAAGCAAAAAAAAGATTAAAA
2032628 AAAAA
1 AAAAA
2032633 ACTTAGATGA
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
30 22 0.41
31 3 0.06
32 6 0.11
33 7 0.13
34 3 0.06
35 13 0.24
ACGTcount: A:0.76, C:0.09, G:0.09, T:0.06
Consensus pattern (30 bp):
AAAAACAAAAAAGCAAAAAAAAGATTAAAA
Found at i:2032608 original size:35 final size:30
Alignment explanation
Indices: 2032542--2032609 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
2032532 CAAAAACAAA
2032542 AAAGCAAAAAAAAGATTAAAAAAAAAGAGC
1 AAAGCAAAAAAAAGATTAAAAAAAAAGAGC
*
2032572 AAAGCAAAAAAAATATTAAAATAAAAA-AGC
1 AAAGCAAAAAAAAGATTAAAA-AAAAAGAGC
2032602 AAAGCAAA
1 AAAGCAAA
2032610 CCAAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.09
Consensus pattern (30 bp):
AAAGCAAAAAAAAGATTAAAAAAAAAGAGC
Found at i:2032615 original size:35 final size:30
Alignment explanation
Indices: 2032546--2032632 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 30
2032536 AACAAAAAAG
*
2032546 CAAAAAAAAGATTAAAAAAAAAGAGCAAAG
1 CAAAAAAAAGATTAAAAAAAAAGAGCAAAC
*
2032576 CAAAAAAAATATTAAAATAAAAAAGCAAAGCAAAC
1 CAAAAAAAAGATT-AAA-AAAAAAG---AGCAAAC
**
2032611 CAAAAAAAAGAGCAAAAAAAAA
1 CAAAAAAAAGATTAAAAAAAAA
2032633 ACTTAGATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 12 0.26
31 3 0.06
32 7 0.15
33 6 0.13
34 3 0.06
35 16 0.34
ACGTcount: A:0.75, C:0.09, G:0.09, T:0.07
Consensus pattern (30 bp):
CAAAAAAAAGATTAAAAAAAAAGAGCAAAC
Found at i:2032948 original size:14 final size:14
Alignment explanation
Indices: 2032929--2032956 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2032919 AATGTGTATA
2032929 AAGTCAAAACTGAT
1 AAGTCAAAACTGAT
2032943 AAGTCAAAACTGAT
1 AAGTCAAAACTGAT
2032957 TTGTATAAAG
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:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
AAGTCAAAACTGAT
Found at i:2037646 original size:28 final size:29
Alignment explanation
Indices: 2037605--2037660 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
2037595 ATAAAGAACA
*
2037605 TTTTTCCTCTAGTTCAGTTTGATCAATTC
1 TTTTTCCTCTAGTTCAATTTGATCAATTC
*
2037634 TTTTT-CTCTAGTTCAATTTTATCAATT
1 TTTTTCCTCTAGTTCAATTTGATCAATT
2037661 GCTTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTTTCCTCTAGTTCAATTTGATCAATTC
Found at i:2041097 original size:18 final size:18
Alignment explanation
Indices: 2041074--2041118 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2041064 TTGTTGGGTA
2041074 GGTGGAATAGGTGCATTG
1 GGTGGAATAGGTGCATTG
2041092 GGTGGAATAGGTGCATTG
1 GGTGGAATAGGTGCATTG
2041110 GGTGGAATA
1 GGTGGAATA
2041119 TGGAAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.04, G:0.44, T:0.27
Consensus pattern (18 bp):
GGTGGAATAGGTGCATTG
Found at i:2041339 original size:24 final size:25
Alignment explanation
Indices: 2041298--2041348 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
2041288 AAAGTTAATG
* *
2041298 ATTTAAAAAGGTTAAATCATTTTGA
1 ATTTAAAAAAGTTAAATCATTTAGA
2041323 ATTTAAAAAAGTT-AATCATTTAGA
1 ATTTAAAAAAGTTAAATCATTTAGA
2041347 AT
1 AT
2041349 CCTTAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTTAAAAAAGTTAAATCATTTAGA
Found at i:2045028 original size:7 final size:7
Alignment explanation
Indices: 2045018--2045212 Score: 61
Period size: 7 Copynumber: 27.9 Consensus size: 7
2045008 CAGATTTAAG
2045018 GTTTAGA
1 GTTTAGA
2045025 GTTT-GA
1 GTTTAGA
* *
2045031 GATTTGGG
1 G-TTTAGA
2045039 GTTTA-A
1 GTTTAGA
2045045 GATTTAGA
1 G-TTTAGA
*
2045053 CTTT-GA
1 GTTTAGA
*
2045059 GGTTTAGG
1 -GTTTAGA
*
2045067 GTTTAGG
1 GTTTAGA
2045074 GTTT-GA
1 GTTTAGA
2045080 TGTTTAGA
1 -GTTTAGA
2045088 GTTTAG-
1 GTTTAGA
*
2045094 GATTTAGG
1 G-TTTAGA
2045102 GTTT-GA
1 GTTTAGA
2045108 GATTTA-A
1 G-TTTAGA
2045115 GGTTT-GA
1 -GTTTAGA
*
2045122 GATTTAAA
1 G-TTTAGA
*
2045130 CTTT-GA
1 GTTTAGA
*
2045136 GGTTTAGG
1 -GTTTAGA
2045144 GTTTA-A
1 GTTTAGA
*
2045150 GGTTTAGG
1 -GTTTAGA
2045158 GTTT-GA
1 GTTTAGA
*
2045164 TGCTTAGA
1 -GTTTAGA
* *
2045172 GTTTGGG
1 GTTTAGA
*
2045179 GTTTAGG
1 GTTTAGA
*
2045186 GTTTAAA
1 GTTTAGA
*
2045193 GTTTAGG
1 GTTTAGA
*
2045200 GTTTAGG
1 GTTTAGA
2045207 GTTTAG
1 GTTTAG
2045213 GGATTTGGGT
Statistics
Matches: 141, Mismatches: 25, Indels: 44
0.67 0.12 0.21
Matches are distributed among these distances:
6 13 0.09
7 116 0.82
8 12 0.09
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.44
Consensus pattern (7 bp):
GTTTAGA
Found at i:2045052 original size:28 final size:28
Alignment explanation
Indices: 2045012--2045156 Score: 106
Period size: 28 Copynumber: 5.4 Consensus size: 28
2045002 AAAGTTCAGA
* * *
2045012 TTTAAGGTTTAGAGTTTGAGATTTGGGG
1 TTTAAGATTTAGACTTTGAGATTTAGGG
*
2045040 TTTAAGATTTAGACTTTGAGGTTTAGGG
1 TTTAAGATTTAGACTTTGAGATTTAGGG
* * *
2045068 TTTAGGGTTT-GA---T--G-TTTAGAG
1 TTTAAGATTTAGACTTTGAGATTTAGGG
* ** *
2045089 TTTAGGATTTAGGGTTTGAGATTTAAGG
1 TTTAAGATTTAGACTTTGAGATTTAGGG
* * *
2045117 TTTGAGATTTAAACTTTGAGGTTTAGGG
1 TTTAAGATTTAGACTTTGAGATTTAGGG
*
2045145 TTTAAGGTTTAG
1 TTTAAGATTTAG
2045157 GGTTTGATGC
Statistics
Matches: 89, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
21 15 0.17
22 2 0.02
24 1 0.01
25 1 0.01
27 3 0.03
28 67 0.75
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.44
Consensus pattern (28 bp):
TTTAAGATTTAGACTTTGAGATTTAGGG
Found at i:2045105 original size:21 final size:21
Alignment explanation
Indices: 2045010--2045212 Score: 95
Period size: 21 Copynumber: 9.7 Consensus size: 21
2045000 TCAAAGTTCA
*
2045010 GATTTAAGGTTTAGAGTTT-G
1 GATTTAGGGTTTAGAGTTTAG
*
2045030 AGATTTGGGGTTTA-AGATTTA-
1 -GATTTAGGGTTTAGAG-TTTAG
*
2045051 GACTTT-GAGGTTTAGGGTTTAG
1 GA-TTTAG-GGTTTAGAGTTTAG
* *
2045073 GGTTT-GATGTTTAGAGTTTAG
1 GATTTAG-GGTTTAGAGTTTAG
2045094 GATTTAGGGTTT-GAGATTTAAG
1 GATTTAGGGTTTAGAG-TTT-AG
* * *
2045116 G-TTT-GAGATTTAAACTTTGAG
1 GATTTAG-GGTTTAGAGTTT-AG
2045137 G-TTTAGGGTTTA-AGGTTTAG
1 GATTTAGGGTTTAGA-GTTTAG
* * * *
2045157 GGTTT-GATGCTTAGAGTTTGG
1 GATTTAG-GGTTTAGAGTTTAG
* *
2045178 GGTTTAGGGTTTAAAGTTTAG
1 GATTTAGGGTTTAGAGTTTAG
*
2045199 GGTTTAGGGTTTAG
1 GATTTAGGGTTTAG
2045213 GGATTTGGGT
Statistics
Matches: 143, Mismatches: 22, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
20 14 0.10
21 119 0.83
22 10 0.07
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.43
Consensus pattern (21 bp):
GATTTAGGGTTTAGAGTTTAG
Found at i:2045213 original size:7 final size:7
Alignment explanation
Indices: 2045059--2046037 Score: 695
Period size: 7 Copynumber: 140.6 Consensus size: 7
2045049 TAGACTTTGA
2045059 GGTTTAG
1 GGTTTAG
2045066 GGTTTAG
1 GGTTTAG
2045073 GGTTT-G
1 GGTTTAG
*
2045079 ATGTTTAG
1 -GGTTTAG
*
2045087 AGTTTAG
1 GGTTTAG
*
2045094 GATTTAG
1 GGTTTAG
2045101 GGTTT-G
1 GGTTTAG
* *
2045107 AGATTTAA
1 -GGTTTAG
2045115 GGTTT-G
1 GGTTTAG
* *
2045121 AGATTTAA
1 -GGTTTAG
**
2045129 ACTTT-G
1 GGTTTAG
2045135 AGGTTTAG
1 -GGTTTAG
*
2045143 GGTTTAA
1 GGTTTAG
2045150 GGTTTAG
1 GGTTTAG
2045157 GGTTT-G
1 GGTTTAG
* *
2045163 ATGCTTAG
1 -GGTTTAG
* *
2045171 AGTTTGG
1 GGTTTAG
2045178 GGTTTAG
1 GGTTTAG
*
2045185 GGTTTAA
1 GGTTTAG
*
2045192 AGTTTAG
1 GGTTTAG
2045199 GGTTTAG
1 GGTTTAG
2045206 GGTTTAG
1 GGTTTAG
2045213 GGATTT-G
1 GG-TTTAG
2045220 GG-TT-G
1 GGTTTAG
* *
2045225 GGGTTGG
1 GGTTTAG
*
2045232 GGTTTAA
1 GGTTTAG
2045239 GGTTTAG
1 GGTTTAG
* *
2045246 GGGTTGG
1 GGTTTAG
* *
2045253 GGTTCAA
1 GGTTTAG
2045260 GGTTTAAG
1 GGTTT-AG
*
2045268 GTTTTAGG
1 GGTTTA-G
*
2045276 GGTTTAA
1 GGTTTAG
2045283 GGTTT-G
1 GGTTTAG
* *
2045289 GAGTTCAC
1 G-GTTTAG
2045297 GGTTT-G
1 GGTTTAG
*
2045303 AGATTTAG
1 -GGTTTAG
*
2045311 GAGTTTCAC
1 G-GTTT-AG
2045320 GG-TTAG
1 GGTTTAG
*
2045326 GGTTTGGG
1 GGTTT-AG
* *
2045334 GGTCTGG
1 GGTTTAG
2045341 GGTTT-G
1 GGTTTAG
* *
2045347 GGTCTGG
1 GGTTTAG
* *
2045354 GGTCTGG
1 GGTTTAG
*
2045361 GGCTTT-T
1 GG-TTTAG
* *
2045368 GGATTGG
1 GGTTTAG
* *
2045375 GGCTTGG
1 GGTTTAG
* *
2045382 GGCTTGG
1 GGTTTAG
*
2045389 GGCTTAG
1 GGTTTAG
2045396 GGTTT-G
1 GGTTTAG
*
2045402 GGTTTCG
1 GGTTTAG
* *
2045409 AGTTTCG
1 GGTTTAG
* *
2045416 AGTTTGG
1 GGTTTAG
*
2045423 GGTTTTG
1 GGTTTAG
*
2045430 GGTTTCGG
1 GGTTT-AG
*
2045438 GGGTT-G
1 GGTTTAG
* *
2045444 GGGTTGG
1 GGTTTAG
2045451 GGTTT-G
1 GGTTTAG
*
2045457 GGTTTCG
1 GGTTTAG
*
2045464 AGTTATAG
1 GGTT-TAG
*
2045472 GGTTTGG
1 GGTTTAG
*
2045479 GGTTTGG
1 GGTTTAG
*
2045486 GGATT--
1 GGTTTAG
2045491 GGTTT-G
1 GGTTTAG
*
2045497 GGTTTGG
1 GGTTTAG
*
2045504 GGTTTGGG
1 GGTTT-AG
*
2045512 GGTTTGG
1 GGTTTAG
*
2045519 GGTTTGG
1 GGTTTAG
*
2045526 GGTTTGG
1 GGTTTAG
*
2045533 GGTTGAG
1 GGTTTAG
*
2045540 GGTGTGTGG
1 GGT-T-TAG
*
2045549 GGTTTGG
1 GGTTTAG
*
2045556 GGTGTTGG
1 GGT-TTAG
* *
2045564 GGAGTTGG
1 GG-TTTAG
2045572 GGTTT--
1 GGTTTAG
*
2045577 GGTAT-G
1 GGTTTAG
2045583 GGTTTGACG
1 GGTTT-A-G
2045592 GGTTT-G
1 GGTTTAG
*
2045598 GGGTT-G
1 GGTTTAG
2045604 GG-TTAGG
1 GGTTTA-G
2045611 GGTTTAG
1 GGTTTAG
2045618 GGTTTAAG
1 GGTTT-AG
2045626 GGTTTAG
1 GGTTTAG
2045633 GGTTTAAG
1 GGTTT-AG
2045641 GGTTTA-
1 GGTTTAG
2045647 GGTTTAG
1 GGTTTAG
2045654 GGTTTAG
1 GGTTTAG
2045661 GGTTTAG
1 GGTTTAG
2045668 GGTTTAAG
1 GGTTT-AG
*
2045676 GGTTGAG
1 GGTTTAG
2045683 GGTTTAG
1 GGTTTAG
2045690 GGTTTAGG
1 GGTTTA-G
2045698 GGTTTAG
1 GGTTTAG
2045705 GG-TTAG
1 GGTTTAG
2045711 GGTTTAG
1 GGTTTAG
2045718 GGTTTAG
1 GGTTTAG
*
2045725 GGTTGAG
1 GGTTTAG
2045732 GGTTTAG
1 GGTTTAG
*
2045739 GGATTA-
1 GGTTTAG
2045745 GGTTTAG
1 GGTTTAG
2045752 GG-TTAG
1 GGTTTAG
2045758 GGTTTAG
1 GGTTTAG
2045765 GGTTTAAG
1 GGTTT-AG
2045773 GGTTTAG
1 GGTTTAG
2045780 GGTTTAG
1 GGTTTAG
2045787 GGTTTTAG
1 GG-TTTAG
2045795 GG-TTAG
1 GGTTTAG
2045801 GG-TTAG
1 GGTTTAG
2045807 GGTTTAG
1 GGTTTAG
2045814 GGTTTAG
1 GGTTTAG
2045821 GGTTTAG
1 GGTTTAG
2045828 GGTTTTAG
1 GG-TTTAG
2045836 GGTTTAG
1 GGTTTAG
2045843 GGTTTTAG
1 GG-TTTAG
2045851 GGTTTAG
1 GGTTTAG
2045858 GGTTTAG
1 GGTTTAG
2045865 GGTTTAG
1 GGTTTAG
2045872 GGTTTAG
1 GGTTTAG
2045879 GGTTTAG
1 GGTTTAG
2045886 GGTTTAG
1 GGTTTAG
2045893 GGTTTAG
1 GGTTTAG
*
2045900 GGTTTCG
1 GGTTTAG
2045907 GGTTTAG
1 GGTTTAG
2045914 GGTTTAG
1 GGTTTAG
2045921 GGTTTAG
1 GGTTTAG
2045928 GGTTTAG
1 GGTTTAG
2045935 GG-TTAG
1 GGTTTAG
2045941 GG-TTAG
1 GGTTTAG
2045947 GGTTTAG
1 GGTTTAG
2045954 GG-TTAG
1 GGTTTAG
2045960 GG-TTAG
1 GGTTTAG
2045966 GGTTTAG
1 GGTTTAG
2045973 GG-TTA-
1 GGTTTAG
2045978 GGTTTAG
1 GGTTTAG
2045985 GGTTTAG
1 GGTTTAG
2045992 GGTTTAAG
1 GGTTT-AG
2046000 GGTTTTAG
1 GG-TTTAG
2046008 GGTTTAG
1 GGTTTAG
2046015 GGTTT-G
1 GGTTTAG
2046021 GG-TTAG
1 GGTTTAG
2046027 GGTTTAG
1 GGTTTAG
2046034 GGTT
1 GGTT
2046038 GCGGGT
Statistics
Matches: 812, Mismatches: 94, Indels: 132
0.78 0.09 0.13
Matches are distributed among these distances:
5 19 0.02
6 122 0.15
7 529 0.65
8 127 0.16
9 15 0.02
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:2045495 original size:40 final size:39
Alignment explanation
Indices: 2045429--2045529 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 39
2045419 TTGGGGTTTT
*
2045429 GGGTTTCGGGGGTTGGGGTTGGGGTTTGGGTTTCGAGTTAT-A
1 GGGTTT-GGGGTTTGGGGTT--GGTTTGGGTTTCGAGTT-TGA
* * *
2045471 GGGTTTGGGGTTTGGGGATTGGTTTGGGTTTGGGGTTTGG
1 GGGTTTGGGGTTTGGGG-TTGGTTTGGGTTTCGAGTTTGA
2045511 GGGTTTGGGGTTTGGGGTT
1 GGGTTTGGGGTTTGGGGTT
2045530 TGGGGTTGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
39 3 0.06
40 32 0.60
41 10 0.19
42 8 0.15
ACGTcount: A:0.04, C:0.02, G:0.53, T:0.41
Consensus pattern (39 bp):
GGGTTTGGGGTTTGGGGTTGGTTTGGGTTTCGAGTTTGA
Found at i:2045501 original size:18 final size:19
Alignment explanation
Indices: 2045472--2045532 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 19
2045462 CGAGTTATAG
2045472 GGTTTGGGGTTTGGGGATT
1 GGTTTGGGGTTTGGGGATT
*
2045491 GGTTT-GGGTTTGGGGTTT
1 GGTTTGGGGTTTGGGGATT
*
2045509 GGGGGTTTGGGGTTTGGGGTTT
1 ---GGTTTGGGGTTTGGGGATT
2045531 GG
1 GG
2045533 GGTTGAGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 12 0.32
19 7 0.19
21 5 0.14
22 13 0.35
ACGTcount: A:0.02, C:0.00, G:0.56, T:0.43
Consensus pattern (19 bp):
GGTTTGGGGTTTGGGGATT
Found at i:2045551 original size:16 final size:15
Alignment explanation
Indices: 2045419--2045578 Score: 98
Period size: 15 Copynumber: 11.3 Consensus size: 15
2045409 AGTTTCGAGT
*
2045419 TTGGGGTTTTGGGT-
1 TTGGGGTTTGGGGTG
*
2045433 TTCGGGGGTT-GGG-G
1 TT-GGGGTTTGGGGTG
2045447 TTGGGGTTT-GGGT-
1 TTGGGGTTTGGGGTG
* * *
2045460 TTCGAGTTATAGGGT-
1 TTGGGGTT-TGGGGTG
*
2045475 TTGGGGTTTGGGG-A
1 TTGGGGTTTGGGGTG
2045489 TT--GGTTT-GGGT-
1 TTGGGGTTTGGGGTG
2045500 TTGGGGTTTGGGG-G
1 TTGGGGTTTGGGGTG
2045514 TTTGGGGTTTGGGGT-
1 -TTGGGGTTTGGGGTG
2045529 TTGGGG-TTGAGGGTG
1 TTGGGGTTTG-GGGTG
2045544 TGTGGGGTTTGGGGTG
1 T-TGGGGTTTGGGGTG
*
2045560 TTGGGGAGTTGGGGT-
1 TTGGGG-TTTGGGGTG
2045575 TTGG
1 TTGG
2045579 TATGGGTTTG
Statistics
Matches: 120, Mismatches: 8, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
11 5 0.04
12 5 0.04
13 23 0.19
14 27 0.22
15 39 0.32
16 18 0.15
17 3 0.03
ACGTcount: A:0.04, C:0.01, G:0.55, T:0.40
Consensus pattern (15 bp):
TTGGGGTTTGGGGTG
Found at i:2045572 original size:23 final size:21
Alignment explanation
Indices: 2045475--2045578 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 21
2045465 GTTATAGGGT
*
2045475 TTGGGGTTTGGGGATTGGTTTGGG
1 TTGGGGTTTGGGGGTTGG---GGG
*
2045499 TTTGGGGTTTGGGGGTTTGGGGT
1 -TTGGGGTTTGGGGG-TTGGGGG
2045522 TTGGGGTTT-GGGGTTGAGGGTG
1 TTGGGGTTTGGGGGTTG-GGG-G
2045544 TGTGGGGTTTGGGGTGTTGGGGAG
1 T-TGGGGTTTGGGG-GTTGGGG-G
2045568 TTGGGGTTTGG
1 TTGGGGTTTGG
2045579 TATGGGTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
20 3 0.04
21 7 0.10
22 10 0.14
23 20 0.29
24 8 0.12
25 17 0.25
26 4 0.06
ACGTcount: A:0.03, C:0.00, G:0.58, T:0.39
Consensus pattern (21 bp):
TTGGGGTTTGGGGGTTGGGGG
Done.