Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2687
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: 13897
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Found at i:905 original size:3 final size:3
Alignment explanation
Indices: 897--931 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
887 TGGTTAAGTT
897 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
932 GTTTGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1666 original size:3 final size:3
Alignment explanation
Indices: 1658--1703 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1648 TTGATGGATT
1658 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1704 CATCCTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2366 original size:26 final size:26
Alignment explanation
Indices: 2318--2371 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2308 TCGAATTATT
** *
2318 ATTTAATTAAAAAATATTTTATTTAA
1 ATTTAATTAAAAAATATAATATTAAA
2344 ATTTAATTATAAAAATA-AATATTAAA
1 ATTTAATTA-AAAAATATAATATTAAA
2370 AT
1 AT
2372 ATATAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAATTAAAAAATATAATATTAAA
Found at i:3163 original size:14 final size:13
Alignment explanation
Indices: 3130--3170 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3120 TTACAAATTT
3130 AATATATATAA-A
1 AATATATATAATA
3142 AATA-ATATAATA
1 AATATATATAATA
*
3154 AATATGATATGATA
1 AATAT-ATATAATA
3168 AAT
1 AAT
3171 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
14 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (13 bp):
AATATATATAATA
Found at i:3163 original size:29 final size:29
Alignment explanation
Indices: 3092--3163 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
3082 ATCAAAATTG
*
3092 AACATAATATGA-ATATATAATAAAATTAT
1 AACA-AATATGATATATATAATAAAAATAT
* * *
3121 TACAAATTTAATATATATAA-AAATAATAT
1 AACAAATATGATATATATAATAAA-AATAT
*
3150 AATAAATATGATAT
1 AACAAATATGATAT
3164 GATAAATTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (29 bp):
AACAAATATGATATATATAATAAAAATAT
Found at i:3710 original size:11 final size:11
Alignment explanation
Indices: 3579--3712 Score: 70
Period size: 11 Copynumber: 12.5 Consensus size: 11
3569 AACGATATAA
*
3579 AAATATAATAC
1 AAATATAATAT
*
3590 AAAAATAATAT
1 AAATATAATAT
* *
3601 AAATATGATAC
1 AAATATAATAT
*
3612 AAATA-AATAA
1 AAATATAATAT
*
3622 AAATATCAAAAT
1 AAATAT-AATAT
**
3634 TTATATAATAT
1 AAATATAATAT
3645 AAAT-T-AT-T
1 AAATATAATAT
*
3653 -AACATAATACCTT
1 AAATATAATA---T
*
3666 AAATATCATCAT
1 AAATATAAT-AT
3678 -AATAT-ATA-
1 AAATATAATAT
3686 AAA-ATAATAT
1 AAATATAATAT
3696 AAATATAATAT
1 AAATATAATAT
3707 AAATAT
1 AAATAT
3713 TTAAATACTT
Statistics
Matches: 92, Mismatches: 17, Indels: 28
0.67 0.12 0.20
Matches are distributed among these distances:
7 2 0.02
8 4 0.04
9 10 0.11
10 14 0.15
11 46 0.50
12 8 0.09
13 1 0.01
14 6 0.07
15 1 0.01
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3712 original size:30 final size:30
Alignment explanation
Indices: 3590--3717 Score: 91
Period size: 30 Copynumber: 4.1 Consensus size: 30
3580 AATATAATAC
* * *
3590 AAAAATAATATAAATATGATACAAATAAAT
1 AAAAATAATATAAATATAATATAAATATAT
*
3620 AAAAAT-ATCAAAATTTATATAATATAAAT-TAT
1 AAAAATAAT-ATAA---ATATAATATAAATATAT
* * *
3652 TAACATAATACCTTAAATATCATCAT-AATATAT
1 AAAAATAATA---TAAATATAAT-ATAAATATAT
*
3685 AAAAATAATATAAATATAATATAAATATTT
1 AAAAATAATATAAATATAATATAAATATAT
3715 AAA
1 AAA
3718 TACTTCTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
29 4 0.05
30 27 0.36
32 16 0.21
33 26 0.35
35 2 0.03
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAAATAATATAAATATAATATAAATATAT
Found at i:4003 original size:23 final size:23
Alignment explanation
Indices: 3977--4025 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3967 AAAGGTTAAA
* *
3977 TTATTTAT-TTAATTTAATTAATT
1 TTATTTATATTAAGTTAA-AAATT
4000 TTATTTATATTAAGTTAAAAATT
1 TTATTTATATTAAGTTAAAAATT
4023 TTA
1 TTA
4026 AATTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTTATATTAAGTTAAAAATT
Found at i:4012 original size:19 final size:20
Alignment explanation
Indices: 3980--4017 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3970 GGTTAAATTA
3980 TTTATTTAATTTAA-TTAAT
1 TTTATTTAATTTAAGTTAAT
3999 TTTATTT-ATATTAAGTTAA
1 TTTATTTAAT-TTAAGTTAA
4018 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 11 0.65
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTATTTAATTTAAGTTAAT
Found at i:4030 original size:25 final size:24
Alignment explanation
Indices: 4002--4068 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
3992 AATTAATTTT
4002 ATTTATATTAAGTTAAAAA-TTTTAA
1 ATTTATATTAA--TAAAAATTTTTAA
*
4027 ATTTTTATTAATAAAAATGTTTTTAA
1 ATTTATATTAATAAAAA--TTTTTAA
4053 ATTTA-ATT-ATAAAAAT
1 ATTTATATTAATAAAAAT
4069 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 1 0.03
23 6 0.16
24 7 0.19
25 13 0.35
26 10 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
ATTTATATTAATAAAAATTTTTAA
Found at i:4057 original size:24 final size:25
Alignment explanation
Indices: 4021--4068 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
4011 AAGTTAAAAA
*
4021 TTTTAAATTTTTATTAATAAAAATGT
1 TTTTAAATTTTAATT-ATAAAAATGT
4047 TTTTAAA-TTTAATTATAAAAAT
1 TTTTAAATTTTAATTATAAAAAT
4069 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 6 0.29
26 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTAAATTTTAATTATAAAAATGT
Found at i:4785 original size:25 final size:23
Alignment explanation
Indices: 4757--4803 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4747 TAAAAAATTT
*
4757 ATATTATTAAATATATTTTAAAATA
1 ATATT-TTAAAT-TAATTTAAAATA
*
4782 ATATTTTTAATTAATTTAAAAT
1 ATATTTTAAATTAATTTAAAAT
4804 TTATGAGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATTAATTTAAAATA
Found at i:6206 original size:25 final size:27
Alignment explanation
Indices: 6168--6231 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
6158 TTAGATTAAA
* * **
6168 TATATATTTGATATAAATTTTTAAT-T
1 TATATTTTTTATATAAATTTAAAATAT
*
6194 T-TATTTTTTATATATATTTAAAATAT
1 TATATTTTTTATATAAATTTAAAATAT
6220 TATATTTTTTAT
1 TATATTTTTTAT
6232 TTTTATTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 18 0.58
26 3 0.10
27 10 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TATATTTTTTATATAAATTTAAAATAT
Found at i:6238 original size:27 final size:25
Alignment explanation
Indices: 6195--6250 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
6185 TTTTTAATTT
6195 TATTTTTTATATATATTTAAAATATTA
1 TATTTTTTATATATA-TTAAAATA-TA
* * *
6222 TATTTTTTATTTTTATTCAAATATA
1 TATTTTTTATATATATTAAAATATA
6247 TATT
1 TATT
6251 AAATATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 7 0.27
27 13 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTTTTATATATATTAAAATATA
Found at i:8135 original size:22 final size:21
Alignment explanation
Indices: 8075--8138 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
8065 ATCATATATT
8075 ATAA-TTAAATTAATTAAA-A
1 ATAATTTAAATTAATTAAATA
*
8094 ATATTATTTTAATTAA-TAAATA
1 ATA--ATTTAAATTAATTAAATA
8116 ATAATTTAAATTAATTTAAATA
1 ATAATTTAAATTAA-TTAAATA
8138 A
1 A
8139 AAAATAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.08
20 10 0.27
21 5 0.14
22 19 0.51
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTTAAATTAATTAAATA
Found at i:8325 original size:5 final size:5
Alignment explanation
Indices: 8315--8409 Score: 83
Period size: 5 Copynumber: 19.0 Consensus size: 5
8305 ATTTTTTAAA
8315 AATAT AATAT AATAT AATAT AATAT ATATAAT AATAT AA-A- AA-AT AATAT
1 AATAT AATAT AATAT AATAT AATAT A-AT-AT AATAT AATAT AATAT AATAT
* * *
8364 AATA- ATTAT GATAT ATATTT AAATAT AAT-T AATAT AAATAT AATAT
1 AATAT AATAT AATAT A-ATAT -AATAT AATAT AATAT -AATAT AATAT
8410 TTGTTAATAG
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.04
4 10 0.13
5 43 0.57
6 15 0.20
7 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:9016 original size:11 final size:11
Alignment explanation
Indices: 9000--9061 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
8990 AAACACTTAT
9000 ATATTTATATC
1 ATATTTATATC
*
9011 ATATTTATATT
1 ATATTTATATC
* *
9022 AT-TTTTTATT
1 ATATTTATATC
9032 ATATTTATAT-
1 ATATTTATATC
*
9042 -TTTTTATATC
1 ATATTTATATC
9052 ATATTTATAT
1 ATATTTATAT
9062 TGTCTCTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.19
10 9 0.21
11 26 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTTATATC
Found at i:9035 original size:15 final size:14
Alignment explanation
Indices: 9014--9057 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
9004 TTATATCATA
*
9014 TTTATATTATTTTT
1 TTTATATTATATTT
9028 TATTATATTTATATTT
1 T-TTATA-TTATATTT
*
9044 TTTATATCATATTT
1 TTTATATTATATTT
9058 ATATTGTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATATTATATTT
Found at i:9055 original size:20 final size:21
Alignment explanation
Indices: 8996--9062 Score: 95
Period size: 20 Copynumber: 3.3 Consensus size: 21
8986 TTTTAAACAC
8996 TTATA-TA-TTTATATCATAT
1 TTATATTATTTTATATCATAT
* *
9015 TTATATTATTTTTTATTATAT
1 TTATATTATTTTATATCATAT
9036 TTATATT-TTTTATATCATAT
1 TTATATTATTTTATATCATAT
9056 TTATATT
1 TTATATT
9063 GTCTCTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.12
20 20 0.48
21 17 0.40
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATATTATTTTATATCATAT
Found at i:9320 original size:4 final size:4
Alignment explanation
Indices: 9311--9335 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9301 AAAGCAAAAG
9311 CTCC CTCC CTCC CTCC CTCC CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTCC C
9336 CTTTCTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CTCC
Found at i:10401 original size:30 final size:30
Alignment explanation
Indices: 10290--10393 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 30
10280 CCTTTGTGTA
*
10290 CAAATTAAAGGTTAAGGGCTTATTTGGGTG
1 CAAATTAAAGGTTAAAGGCTTATTTGGGTG
* ** *
10320 CATATTAAAGGTTAAAGGCTTATCCGGGTA
1 CAAATTAAAGGTTAAAGGCTTATTTGGGTG
* *
10350 CAAATTAAAGTTTAAAGGCTTATTTGAGTG
1 CAAATTAAAGGTTAAAGGCTTATTTGGGTG
10380 CAAATTAAAGGTTA
1 CAAATTAAAGGTTA
10394 GGGGCTTACT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (30 bp):
CAAATTAAAGGTTAAAGGCTTATTTGGGTG
Done.