Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1225
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: 73747
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Found at i:67 original size:18 final size:18
Alignment explanation
Indices: 27--68 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17 AATTTACGTG
*
27 TTTATTTTTTATATTTTT
1 TTTATTTATTATATTTTT
*
45 GTTATTTATTAT-TTATTT
1 TTTATTTATTATATT-TTT
63 TTTATT
1 TTTATT
69 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTATTTATTATATTTTT
Found at i:154 original size:23 final size:24
Alignment explanation
Indices: 108--166 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
98 ATATAAATTT
*
108 TTTATGTTTTTATATTCATGTTTTA
1 TTTAT-TTTTTATATTCATATTTTA
*
133 TTTATTTTTTATATT-TTATTTTA
1 TTTATTTTTTATATTCATATTTTA
* *
156 ATTAATTTTTA
1 TTTATTTTTTA
167 ATATAAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 15 0.50
24 10 0.33
25 5 0.17
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTATTTTTTATATTCATATTTTA
Found at i:163 original size:24 final size:25
Alignment explanation
Indices: 114--170 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
104 ATTTTTTATG
* *
114 TTTTTATA-TTCATGTTTTATTTAT
1 TTTTTATATTTCATGTTTAATTAAT
*
138 TTTTTATATTTTAT-TTTAATTAAT
1 TTTTTATATTTCATGTTTAATTAAT
*
162 TTTTAATAT
1 TTTTTATAT
171 AAGTGTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTTATATTTCATGTTTAATTAAT
Found at i:1055 original size:17 final size:18
Alignment explanation
Indices: 1029--1064 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1019 TTAAATTTAG
*
1029 TTATATAAAAT-TTTAAA
1 TTATAAAAAATATTTAAA
1046 TTATAAAAAATATTTAAA
1 TTATAAAAAATATTTAAA
1064 T
1 T
1065 AAATAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATAAAAAATATTTAAA
Found at i:1070 original size:19 final size:19
Alignment explanation
Indices: 1035--1086 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1025 TTAGTTATAT
*
1035 AAAAT-TTTAAAT-TATAA
1 AAAATATTTAAATAAATAA
1052 AAAATATTTAAATAAATAA
1 AAAATATTTAAATAAATAA
* *
1071 TAACTATTTAATATAA
1 AAAATATTTAA-ATAA
1087 TTTATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 13 0.45
20 4 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATTTAAATAAATAA
Found at i:3624 original size:11 final size:10
Alignment explanation
Indices: 3600--3635 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3590 GAATTAAATT
3600 TAAAATAATA
1 TAAAATAATA
3610 TAAAATAATTA
1 TAAAATAA-TA
*
3621 TAAAATTATA
1 TAAAATAATA
3631 TAAAA
1 TAAAA
3636 ATTAAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAATAATA
Found at i:3624 original size:21 final size:20
Alignment explanation
Indices: 3596--3635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3586 AATTGAATTA
3596 AATTTAAAATAATATAAAAT
1 AATTTAAAATAATATAAAAT
*
3616 AATTATAAAATTATATAAAA
1 AATT-TAAAATAATATAAAA
3636 ATTAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTTAAAATAATATAAAAT
Found at i:4352 original size:2 final size:2
Alignment explanation
Indices: 4345--4381 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4335 TTTCTTTCTT
4345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4382 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5900 original size:8 final size:8
Alignment explanation
Indices: 5862--5900 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
5852 AGCCATGGAA
*
5862 ATATATAT
1 ATATATTT
*
5870 ATATATAT
1 ATATATTT
5878 ATATATTT
1 ATATATTT
*
5886 ATTTATTT
1 ATATATTT
5894 ATATATT
1 ATATATT
5901 ACCAGCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATATATTT
Found at i:8164 original size:24 final size:23
Alignment explanation
Indices: 8124--8172 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
8114 AAAGTTTTTT
8124 AATTTTATTATTATATTTAAATAA
1 AATTTTATTATTATA-TTAAATAA
* *
8148 AATTTTA-TATTTTTATTATATAA
1 AATTTTATTA-TTATATTAAATAA
8171 AA
1 AA
8173 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTTATTATTATATTAAATAA
Found at i:9155 original size:27 final size:27
Alignment explanation
Indices: 9116--9190 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
9106 AATAAAAATT
* * *
9116 AATCATCAATTTTGACAAACATGAAAG
1 AATCACCATTTTTAACAAACATGAAAG
9143 AATCACCATTTTTAACAAACATGAAAG
1 AATCACCATTTTTAACAAACATGAAAG
9170 AATCACCATTTTTAACAAACA
1 AATCACCATTTTTAACAAACA
9191 CAAATAGTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.27
Consensus pattern (27 bp):
AATCACCATTTTTAACAAACATGAAAG
Found at i:13618 original size:23 final size:23
Alignment explanation
Indices: 13588--13635 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
13578 AATAAAAATT
13588 AACCATCA-ATTTGACAAACAACA
1 AACCATCATATTTGACAAAC-ACA
* *
13611 AACCATCATTTTTGATAAACACA
1 AACCATCATATTTGACAAACACA
13634 AA
1 AA
13636 GAAACCACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.50, C:0.23, G:0.04, T:0.23
Consensus pattern (23 bp):
AACCATCATATTTGACAAACACA
Found at i:14016 original size:6 final size:6
Alignment explanation
Indices: 14002--14040 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
13992 AGGACGATGA
* *
14002 ATGACC ATGATC ATGAGC ATGAGC ATGAGC ATGAGC ATG
1 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATG
14041 CTTGACAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (6 bp):
ATGAGC
Found at i:16012 original size:24 final size:24
Alignment explanation
Indices: 15985--16055 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
15975 ATTAAGTTTG
15985 TTGCCTGAATTGGATAAGAATGAC
1 TTGCCTGAATTGGATAAGAATGAC
16009 TTGCCAT-AATTGGATAAGAATGAC
1 TTGCC-TGAATTGGATAAGAATGAC
*
16033 TTGCCAGAATTGGATAAGAATGA
1 TTGCCTGAATTGGATAAGAATGA
16056 ACCACCTCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (24 bp):
TTGCCTGAATTGGATAAGAATGAC
Found at i:16432 original size:28 final size:29
Alignment explanation
Indices: 16401--16472 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
16391 TTTTTAAGTT
* *
16401 TAAGATTTATATTTTTATTT-TACTTAAA
1 TAAGATTTATATTTTAATTTGTAATTAAA
*
16429 TAAGTTTTA-ATTTTAATTTGTAATTAAA
1 TAAGATTTATATTTTAATTTGTAATTAAA
*
16457 TAA-ATTTTTATTTTAA
1 TAAGATTTATATTTTAA
16473 ATAAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 12 0.32
28 25 0.68
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (29 bp):
TAAGATTTATATTTTAATTTGTAATTAAA
Found at i:16469 original size:22 final size:20
Alignment explanation
Indices: 16437--16482 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
16427 AATAAGTTTT
*
16437 AATTTTAATTTGTAATTAAATA
1 AATTTTAATTT-TAAATAAA-A
*
16459 AATTTTTATTTTAAATAAAA
1 AATTTTAATTTTAAATAAAA
16479 AATT
1 AATT
16483 ATCTTTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTTTAATTTTAAATAAAA
Found at i:16561 original size:7 final size:7
Alignment explanation
Indices: 16545--16578 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
16535 TTATTTGATT
16545 AAAA-TA
1 AAAATTA
16551 AAAATTA
1 AAAATTA
16558 AAAATTA
1 AAAATTA
16565 AAAATTA
1 AAAATTA
16572 AAAATTA
1 AAAATTA
16579 TTTAAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:18818 original size:24 final size:24
Alignment explanation
Indices: 18777--18845 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 24
18767 TAAAAGTTAC
*
18777 CCTTTGTGTTTGTAAAAAATGGTT
1 CCTTTTTGTTTGTAAAAAATGGTT
* *
18801 CTTTTTTTTTTTGTAAAAAATGGTT
1 C-CTTTTTGTTTGTAAAAAATGGTT
18826 CCTTTTTGTTTGTAAAAAAT
1 CCTTTTTGTTTGTAAAAAAT
18846 AGTGACTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 18 0.46
25 21 0.54
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (24 bp):
CCTTTTTGTTTGTAAAAAATGGTT
Found at i:18858 original size:24 final size:24
Alignment explanation
Indices: 18810--18867 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
18800 TCTTTTTTTT
* ** *
18810 TTTGTAAAAAATGGTTCCTTTTTG
1 TTTGTAAAAAATAGTGACTTATTG
18834 TTTGTAAAAAATAGTGACTTATTG
1 TTTGTAAAAAATAGTGACTTATTG
*
18858 TTTGTCAAAA
1 TTTGTAAAAA
18868 TTTGTAGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (24 bp):
TTTGTAAAAAATAGTGACTTATTG
Found at i:23827 original size:19 final size:21
Alignment explanation
Indices: 23803--23853 Score: 79
Period size: 19 Copynumber: 2.5 Consensus size: 21
23793 CAACATTCAA
*
23803 TTTAATTTTATTATTA-CA-T
1 TTTAATTTTATTATTATAATT
23822 TTTAATTTTATTATTATAATT
1 TTTAATTTTATTATTATAATT
23843 TTTAATTTTAT
1 TTTAATTTTAT
23854 CGTTACAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 16 0.55
20 1 0.03
21 12 0.41
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTAATTTTATTATTATAATT
Found at i:24718 original size:22 final size:22
Alignment explanation
Indices: 24675--24721 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
24665 TTAAAAAATT
* ** *
24675 ATAAAATAAAATATTTTTAAAA
1 ATAAAATAAAAAATAATAAAAA
24697 ATAAAATAAAAAATAATAAAAA
1 ATAAAATAAAAAATAATAAAAA
24719 ATA
1 ATA
24722 TGTTTATCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAAATAAAAAATAATAAAAA
Found at i:24781 original size:13 final size:13
Alignment explanation
Indices: 24765--24798 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
24755 TTTTTAAAGT
24765 TTTTTAAAAATAA
1 TTTTTAAAAATAA
*
24778 TTTTAAAAAATAA
1 TTTTTAAAAATAA
*
24791 TTATTAAA
1 TTTTTAAA
24799 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTTAAAAATAA
Found at i:24787 original size:14 final size:14
Alignment explanation
Indices: 24770--24798 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24760 AAAGTTTTTT
24770 AAAAATAATT-TTA
1 AAAAATAATTATTA
24783 AAAAATAATTATTA
1 AAAAATAATTATTA
24797 AA
1 AA
24799 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAAATAATTATTA
Found at i:24847 original size:31 final size:31
Alignment explanation
Indices: 24775--24843 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
24765 TTTTTAAAAA
* * *
24775 TAATTTTAAAAAATAATTATTAAATTTTTTT
1 TAATTTTTAAAAATAATTATTAAATTATTAT
24806 TAATTTTTAAAAATAATTATT-AATTATTAT
1 TAATTTTTAAAAATAATTATTAAATTATTAT
24836 TAATTTTT
1 TAATTTTT
24844 TAAATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TAATTTTTAAAAATAATTATTAAATTATTAT
Found at i:29913 original size:18 final size:17
Alignment explanation
Indices: 29885--29926 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
29875 TCGAATCTCG
29885 TTATTTAAAATTACTAT
1 TTATTTAAAATTACTAT
29902 TTATTCTAAAATTACTAT
1 TTATT-TAAAATTACTAT
*
29920 TTTTTTA
1 TTATTTA
29927 TGAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTTAAAATTACTAT
Found at i:30473 original size:21 final size:23
Alignment explanation
Indices: 30447--30504 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
30437 AATTTTTTAT
*
30447 TTTGATTTATTT-T-TTATTTGA
1 TTTGATTCATTTATATTATTTGA
30468 TTTGATTCATTTATATTATTT-A
1 TTTGATTCATTTATATTATTTGA
*
30490 TATTTATT-ATTTATA
1 T-TTGATTCATTTATA
30505 AATAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 11 0.34
22 10 0.31
23 11 0.34
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTGATTCATTTATATTATTTGA
Found at i:30555 original size:21 final size:21
Alignment explanation
Indices: 30491--30555 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
30481 TATTATTTAT
30491 ATTTAT-TA-TTTATAAATAAA
1 ATTTATATATTTTAT-AATAAA
* *
30511 ATTT-TAT-TTTTATATTAAT
1 ATTTATATATTTTATAATAAA
30530 ATTTATATATTTTATAATAAA
1 ATTTATATATTTTATAATAAA
30551 ATTTA
1 ATTTA
30556 AATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 9 0.24
20 13 0.35
21 15 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATATATTTTATAATAAA
Found at i:33192 original size:34 final size:34
Alignment explanation
Indices: 33149--33220 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
33139 CAATCTCACC
33149 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
1 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
* * *
33183 TAAACTAATCTTCACGTCTATCCAAATGAAACTT
1 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
33217 TAAA
1 TAAA
33221 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.31
Consensus pattern (34 bp):
TAAACTAATCTTAACGTCTACCCAAATCAAACTT
Found at i:34119 original size:20 final size:21
Alignment explanation
Indices: 34091--34129 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
34081 ATAACTAAAT
*
34091 TAATTAAAT-TATTATTTATA
1 TAATAAAATATATTATTTATA
*
34111 TAATAAAATATTTTATTTA
1 TAATAAAATATATTATTTA
34130 AATTTAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATAAAATATATTATTTATA
Found at i:34513 original size:13 final size:14
Alignment explanation
Indices: 34491--34538 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
34481 TCTCTGAAAT
34491 TTTTTAAAAATAAA
1 TTTTTAAAAATAAA
34505 TTTTTAAAAAT-AA
1 TTTTTAAAAATAAA
* * *
34518 CTATTAAAAATAAT
1 TTTTTAAAAATAAA
34532 TTTTTAA
1 TTTTTAA
34539 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTTTAAAAATAAA
Found at i:34564 original size:21 final size:21
Alignment explanation
Indices: 34521--34563 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
34511 AAAATAACTA
*
34521 TTAAAAATAATTTTTTAATTT
1 TTAAAAATAATTTATTAATTT
34542 TTAAAAATAA-TTATTAATTT
1 TTAAAAATAATTTATTAATTT
34562 TT
1 TT
34564 TTATTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAAATAATTTATTAATTT
Found at i:40194 original size:16 final size:17
Alignment explanation
Indices: 40163--40195 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40153 AAAATTTTAA
*
40163 ATTTTTTATTTTGATTT
1 ATTTTTTATTTCGATTT
40180 ATTTTTTA-TTCGATTT
1 ATTTTTTATTTCGATTT
40196 GATCCATTCA
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:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTCGATTT
Found at i:40280 original size:21 final size:21
Alignment explanation
Indices: 40216--40280 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
40206 TATTATTTAT
40216 ATTTAT-TA-TTTATAAATAAA
1 ATTTATATATTTTAT-AATAAA
* *
40236 ATTT-TAT-TTTTATATTAAT
1 ATTTATATATTTTATAATAAA
40255 ATTTATATATTTTATAATAAA
1 ATTTATATATTTTATAATAAA
40276 ATTTA
1 ATTTA
40281 AATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 9 0.24
20 13 0.35
21 15 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATATATTTTATAATAAA
Found at i:42917 original size:34 final size:34
Alignment explanation
Indices: 42874--42945 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
42864 CAATCTCACC
42874 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
1 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
* * *
42908 TAAACTAATCTTCACGTCTATCCAAATGAAACTT
1 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
42942 TAAA
1 TAAA
42946 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.31
Consensus pattern (34 bp):
TAAACTAATCTTAACGTCTACCCAAATCAAACTT
Found at i:43845 original size:20 final size:21
Alignment explanation
Indices: 43817--43855 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
43807 ATAACTAAAT
*
43817 TAATTAAAT-TATTATTTATA
1 TAATAAAATATATTATTTATA
*
43837 TAATAAAATATTTTATTTA
1 TAATAAAATATATTATTTA
43856 AATTTAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATAAAATATATTATTTATA
Found at i:44235 original size:14 final size:14
Alignment explanation
Indices: 44218--44266 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
44208 TCTCTGAAAT
44218 TTTTTAAAAATAAA
1 TTTTTAAAAATAAA
44232 TTTTTAAAAA-ATAA
1 TTTTTAAAAATA-AA
* * *
44246 CTATTAAAAATAAT
1 TTTTTAAAAATAAA
44260 TTTTTAA
1 TTTTTAA
44267 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTTAAAAATAAA
Found at i:44292 original size:21 final size:21
Alignment explanation
Indices: 44249--44291 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
44239 AAAATAACTA
*
44249 TTAAAAATAATTTTTTAATTT
1 TTAAAAATAATTTATTAATTT
44270 TTAAAAATAA-TTATTAATTT
1 TTAAAAATAATTTATTAATTT
44290 TT
1 TT
44292 TTATTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAAATAATTTATTAATTT
Found at i:49923 original size:16 final size:17
Alignment explanation
Indices: 49892--49924 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49882 AAAATTTTAA
*
49892 ATTTTTTATTTTGATTT
1 ATTTTTTATTTCGATTT
49909 ATTTTTTA-TTCGATTT
1 ATTTTTTATTTCGATTT
49925 GATCCATTCA
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:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTCGATTT
Found at i:50009 original size:21 final size:21
Alignment explanation
Indices: 49945--50009 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
49935 TATTATTTAT
49945 ATTTAT-TA-TTTATAAATAAA
1 ATTTATATATTTTAT-AATAAA
* *
49965 ATTT-TAT-TTTTATATTAAT
1 ATTTATATATTTTATAATAAA
49984 ATTTATATATTTTATAATAAA
1 ATTTATATATTTTATAATAAA
50005 ATTTA
1 ATTTA
50010 AATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 9 0.24
20 13 0.35
21 15 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATATATTTTATAATAAA
Found at i:51500 original size:28 final size:27
Alignment explanation
Indices: 51442--51506 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
51432 TATTTGTTTG
* *
51442 TCAAAAATGGTAGTTATTTTGTGTTTG
1 TCAAAAATGGTAGTTATTTTGTATTTA
*
51469 TCAAAAATGGTGGTT-TCCTTTGTATTTA
1 TCAAAAATGGTAGTTAT--TTTGTATTTA
*
51497 TCAAATATGG
1 TCAAAAATGG
51507 AGGCTTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 14 0.44
28 17 0.53
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.45
Consensus pattern (27 bp):
TCAAAAATGGTAGTTATTTTGTATTTA
Found at i:57592 original size:28 final size:27
Alignment explanation
Indices: 57537--57607 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
57527 GCCACCCATT
57537 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
57564 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
57592 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
57608 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:59129 original size:34 final size:34
Alignment explanation
Indices: 59086--59157 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
59076 CAATCTCACC
59086 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
1 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
* *
59120 TAAACTAATCTTAACGTCTATCCAAATGAAACTT
1 TAAACTAATCTTAACGTCTACCCAAATCAAACTT
59154 TAAA
1 TAAA
59158 TTTAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (34 bp):
TAAACTAATCTTAACGTCTACCCAAATCAAACTT
Found at i:60057 original size:20 final size:21
Alignment explanation
Indices: 60029--60067 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
60019 ATAACTAAAT
*
60029 TAATTAAAT-TATTATTTATA
1 TAATAAAATATATTATTTATA
*
60049 TAATAAAATATTTTATTTA
1 TAATAAAATATATTATTTA
60068 AATTTAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATAAAATATATTATTTATA
Found at i:60451 original size:15 final size:14
Alignment explanation
Indices: 60425--60470 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
60415 TACCCTCTGA
60425 AATTTTTTAAAAAT
1 AATTTTTTAAAAAT
60439 AATTTTTTAAAAAAT
1 AATTTTTT-AAAAAT
* *
60454 AA-CTATTAAAAAT
1 AATTTTTTAAAAAT
60467 AATT
1 AATT
60471 ATTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 8 0.30
14 11 0.41
15 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTTTTAAAAAT
Found at i:60473 original size:13 final size:13
Alignment explanation
Indices: 60431--60475 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
60421 CTGAAATTTT
*
60431 TTAAAAATAATTTT
1 TTAAAAATAA-TTA
*
60445 TTAAAAAATAACTA
1 TT-AAAAATAATTA
60459 TTAAAAATAATTA
1 TTAAAAATAATTA
60472 TTAA
1 TTAA
60476 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 14 0.52
14 5 0.19
15 8 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAAAATAATTA
Found at i:60699 original size:15 final size:15
Alignment explanation
Indices: 60679--60709 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
60669 TCTGCCATCG
60679 CGAAATCTTTCCTTT
1 CGAAATCTTTCCTTT
60694 CGAAATCTTTCCTTT
1 CGAAATCTTTCCTTT
60709 C
1 C
60710 TTTCTTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (15 bp):
CGAAATCTTTCCTTT
Found at i:69887 original size:1 final size:1
Alignment explanation
Indices: 69877--69963 Score: 66
Period size: 1 Copynumber: 87.0 Consensus size: 1
69867 TGGCAATTGG
* * * ** * * * **
69877 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAGGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
69942 AGAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
69964 GTGAAGATTT
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:69910 original size:16 final size:16
Alignment explanation
Indices: 69891--69951 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
69881 AGAAAAAAAC
69891 AAAACAAAAAAAAGGA
1 AAAACAAAAAAAAGGA
* *
69907 AAAAGAAAAAAAA-AA
1 AAAACAAAAAAAAGGA
69922 CAAAACAAAAAAAAGGA
1 -AAAACAAAAAAAAGGA
*
69939 AAAAGAAAAAAAA
1 AAAACAAAAAAAA
69952 AACAAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
15 1 0.03
16 36 0.95
17 1 0.03
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAAAGGA
Found at i:69924 original size:32 final size:32
Alignment explanation
Indices: 69883--69963 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
69873 TTGGAAAAAG
69883 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
1 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
69915 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
1 AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
69947 AAAAAAACAAAA-AAAAA
1 AAAAAAACAAAACAAAAA
69964 GTGAAGATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 5 0.10
32 44 0.90
ACGTcount: A:0.86, C:0.06, G:0.07, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAACAAAAAAAAGGAAAAAGAAA
Done.