Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1983
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: 72718
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:3920 original size:5 final size:5
Alignment explanation
Indices: 3910--3941 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3900 CTACACTTAC
3910 TCTGA TCTGA TCTGA TCTGA TCTGA TCTGA TC
1 TCTGA TCTGA TCTGA TCTGA TCTGA TCTGA TC
3942 AATCCAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (5 bp):
TCTGA
Found at i:8732 original size:7 final size:7
Alignment explanation
Indices: 8714--8743 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
8704 TAAAACTATA
8714 TTTTAA-
1 TTTTAAT
8720 TTTTAAT
1 TTTTAAT
8727 TTTTAAT
1 TTTTAAT
8734 TTTTAAT
1 TTTTAAT
8741 TTT
1 TTT
8744 ATTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:13611 original size:4 final size:4
Alignment explanation
Indices: 13604--13674 Score: 54
Period size: 4 Copynumber: 17.2 Consensus size: 4
13594 TATTTATTTA
** * ** *
13604 TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC TGTT- AGTC TTTC TATC
1 TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC T-TTC TTTC TTTC TTTC
13654 TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC T
13675 CACGTTTGCT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
3 1 0.02
4 45 0.88
5 4 0.08
6 1 0.02
ACGTcount: A:0.04, C:0.25, G:0.06, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:13706 original size:50 final size:50
Alignment explanation
Indices: 13604--13706 Score: 172
Period size: 50 Copynumber: 2.1 Consensus size: 50
13594 TATTTATTTA
* *
13604 TTTCTTTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTTAGTCTTTCTATC
1 TTTCTTTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTCTTTCTATC
13654 TTTCTTTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACT-TTTCTATTC
1 TTTCTTTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTCTTTCTA-TC
13704 TTT
1 TTT
13707 ACTCATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 6 0.12
50 44 0.88
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.61
Consensus pattern (50 bp):
TTTCTTTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTCTTTCTATC
Found at i:13718 original size:14 final size:14
Alignment explanation
Indices: 13699--13729 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13689 GTAACTTTTC
13699 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
13713 TATTCTTTATTCAT
1 TATTCTTTACTCAT
13727 TAT
1 TAT
13730 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:14779 original size:15 final size:15
Alignment explanation
Indices: 14759--14791 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
14749 ATAATATCAT
14759 GAACAAAATGATACC
1 GAACAAAATGATACC
14774 GAACAAAATGATACC
1 GAACAAAATGATACC
14789 GAA
1 GAA
14792 TATCAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (15 bp):
GAACAAAATGATACC
Found at i:18625 original size:5 final size:5
Alignment explanation
Indices: 18615--18652 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
18605 ATTTGTGAAA
*
18615 AAAAT AAAAT AAAAT AAAAT AAAGAA AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AA
18653 CACACAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:26957 original size:12 final size:11
Alignment explanation
Indices: 26920--26956 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
26910 AAATAATAAG
*
26920 AAAAATT-AAG
1 AAAAATTGAAA
26930 AAAAATTGAAA
1 AAAAATTGAAA
26941 AAAAATTGAAA
1 AAAAATTGAAA
26952 AAAAA
1 AAAAA
26957 AACTGGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAATTGAAA
Found at i:28848 original size:18 final size:18
Alignment explanation
Indices: 28825--28872 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
28815 TGGTAGTTCC
28825 TTTTAAATAAAATATTAT
1 TTTTAAATAAAATATTAT
* *
28843 TTTT-AATAGAGATATTCT
1 TTTTAAATA-AAATATTAT
28861 TTTTAAA-AAAAT
1 TTTTAAATAAAAT
28873 GGATAAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.28
18 16 0.64
19 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (18 bp):
TTTTAAATAAAATATTAT
Found at i:34930 original size:7 final size:6
Alignment explanation
Indices: 34889--34929 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
34879 ATAATTTAAT
*
34889 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
34930 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:34930 original size:20 final size:20
Alignment explanation
Indices: 34892--34931 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34882 ATTTAATAAA
**
34892 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
34912 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
34932 ATATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:38956 original size:19 final size:20
Alignment explanation
Indices: 38934--38976 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
38924 AAATCAAATA
*
38934 ATTTATTA-TAAATATTATT
1 ATTTATTAGTAAATATAATT
38953 ATTT-TTAGTAAATATAATT
1 ATTTATTAGTAAATATAATT
38972 -TTTAT
1 ATTTAT
38977 ATGTGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTATTAGTAAATATAATT
Found at i:39185 original size:18 final size:18
Alignment explanation
Indices: 39141--39175 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39131 TTACATATAA
39141 AAATAATTATTTTATTTG
1 AAATAATTATTTTATTTG
39159 AAATAATTATTTTATTT
1 AAATAATTATTTTATTT
39176 TTTAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAATAATTATTTTATTTG
Found at i:39451 original size:21 final size:21
Alignment explanation
Indices: 39397--39453 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
39387 ATAAAAAGAG
*
39397 TTATTAATTAAAAAGATGAAT
1 TTATTAATTAAAAAAATGAAT
* **
39418 TAAAAAATT-AAAAAAT-ATAT
1 TTATTAATTAAAAAAATGA-AT
39438 TTATTAATTAAAAAAA
1 TTATTAATTAAAAAAA
39454 GCTTTGAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.52
21 12 0.44
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
TTATTAATTAAAAAAATGAAT
Found at i:41957 original size:20 final size:22
Alignment explanation
Indices: 41932--41971 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41922 TTAAAATTAA
41932 CTAAA-TT-AAAAATATAAAGT
1 CTAAATTTGAAAAATATAAAGT
41952 CTAAATTTGAAAAATATAAA
1 CTAAATTTGAAAAATATAAA
41972 AAATTAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (22 bp):
CTAAATTTGAAAAATATAAAGT
Found at i:49630 original size:6 final size:6
Alignment explanation
Indices: 49615--49647 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
49605 GCAAATCCTC
*
49615 AGGTTA AGGTTG AGGTTG AGGTTG AGGTTG AGG
1 AGGTTG AGGTTG AGGTTG AGGTTG AGGTTG AGG
49648 ACTAGTGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.30
Consensus pattern (6 bp):
AGGTTG
Found at i:51143 original size:9 final size:9
Alignment explanation
Indices: 51119--51153 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
51109 AAAAACAAAA
*
51119 ATATAATAA
1 ATATAATAT
51128 ATAATAATAT
1 AT-ATAATAT
51138 ATATAATAT
1 ATATAATAT
51147 ATATAAT
1 ATATAAT
51154 GTGAAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATAATAT
Found at i:51344 original size:30 final size:30
Alignment explanation
Indices: 51308--51368 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
51298 TCGTCAATAC
51308 TTAGTTTATTTAGTTGGTATCGAGTTAACT
1 TTAGTTTATTTAGTTGGTATCGAGTTAACT
51338 TTAGTTTATTTAGTTGGTATCGAGTTAACT
1 TTAGTTTATTTAGTTGGTATCGAGTTAACT
51368 T
1 T
51369 GTGATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.51
Consensus pattern (30 bp):
TTAGTTTATTTAGTTGGTATCGAGTTAACT
Found at i:52404 original size:22 final size:22
Alignment explanation
Indices: 52379--52426 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
52369 TTTGATAGGA
*
52379 AATT-AAAATATAAAAATAATTG
1 AATTAAAAATATAAAAA-AATAG
*
52401 AATTAAAAATATCAAAAAATAG
1 AATTAAAAATATAAAAAAATAG
52423 AATT
1 AATT
52427 TTTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
AATTAAAAATATAAAAAAATAG
Found at i:54346 original size:12 final size:12
Alignment explanation
Indices: 54323--54358 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
54313 ATTATGGAAT
*
54323 TGATTGTGATGA
1 TGATTATGATGA
*
54335 TGGTTATGATGA
1 TGATTATGATGA
54347 TGATTATGATGA
1 TGATTATGATGA
54359 CTACGACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.42
Consensus pattern (12 bp):
TGATTATGATGA
Found at i:60301 original size:6 final size:6
Alignment explanation
Indices: 60290--60315 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
60280 ACATTCAGTC
60290 AAAACA AAAACA AAAACA AAAACA AA
1 AAAACA AAAACA AAAACA AAAACA AA
60316 TATACAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Done.