Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2353
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: 22469
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:738 original size:27 final size:27
Alignment explanation
Indices: 708--783 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
698 AAAGCCACTC
* *
708 TTGTGTTTGTCAACAATGGTGGTTACT
1 TTGTGTTTGTCAAAAATGATGGTTACT
* *
735 TTGTATTTGTCAAAAATGATGGTTCCT
1 TTGTGTTTGTCAAAAATGATGGTTACT
*
762 TT-TAGTTTGTCAAAAATTATGG
1 TTGT-GTTTGTCAAAAATGATGG
784 CTTATTGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (27 bp):
TTGTGTTTGTCAAAAATGATGGTTACT
Found at i:798 original size:24 final size:24
Alignment explanation
Indices: 740--809 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 24
730 TTACTTTGTA
*
740 TTTGTCAAAAATGATGGTTCCTTTTAG
1 TTTGTCAAAAATTATGG---CTTTTAG
767 TTTGTCAAAAATTATGGCTTATT-G
1 TTTGTCAAAAATTATGGCTT-TTAG
791 TTTGTC-AAAATTAGTGGCT
1 TTTGTCAAAAATTA-TGGCT
810 AATTTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 7 0.17
24 15 0.38
25 2 0.05
27 16 0.40
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (24 bp):
TTTGTCAAAAATTATGGCTTTTAG
Found at i:922 original size:11 final size:13
Alignment explanation
Indices: 888--921 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
878 TCTCTCAAGC
888 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
901 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
914 ATCCCTCT
1 ATCCCTCT
922 TCAATTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.41, G:0.06, T:0.44
Consensus pattern (13 bp):
ATCCCTCTCTTGT
Found at i:1873 original size:17 final size:17
Alignment explanation
Indices: 1847--1883 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1837 CATGCTACGC
1847 TTGAAGTCACGAGCCAT
1 TTGAAGTCACGAGCCAT
*
1864 TTGAATTCACGAGCCAT
1 TTGAAGTCACGAGCCAT
1881 TTG
1 TTG
1884 GGGGTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (17 bp):
TTGAAGTCACGAGCCAT
Found at i:4560 original size:16 final size:16
Alignment explanation
Indices: 4533--4572 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
4523 CGCGCTGTTT
4533 GTTTCA-CCTTATAAA
1 GTTTCAGCCTTATAAA
4548 GTTTCAGCCTTATAAA
1 GTTTCAGCCTTATAAA
*
4564 GTTGCAGCC
1 GTTTCAGCC
4573 CAAACTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (16 bp):
GTTTCAGCCTTATAAA
Found at i:5011 original size:14 final size:14
Alignment explanation
Indices: 4992--5099 Score: 72
Period size: 14 Copynumber: 8.1 Consensus size: 14
4982 TAGACATTAA
4992 ATATTAATATATTT
1 ATATTAATATATTT
5006 ATATT-A-ATATTT
1 ATATTAATATATTT
* *
5018 ATATGTTAT-TAATT
1 ATAT-TAATATATTT
5032 ATATT-ATATA---
1 ATATTAATATATTT
*
5042 ATTTTAATATATTT
1 ATATTAATATATTT
5056 AT-TTAATTATATTT
1 ATATTAA-TATATTT
*
5070 ATTTTAAT-TATTTT
1 ATATTAATATA-TTT
* *
5084 ATTTTATTATATTT
1 ATATTAATATATTT
5098 AT
1 AT
5100 GTATATTATA
Statistics
Matches: 79, Mismatches: 3, Indels: 24
0.75 0.03 0.23
Matches are distributed among these distances:
10 4 0.05
11 5 0.06
12 12 0.15
13 11 0.14
14 41 0.52
15 6 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (14 bp):
ATATTAATATATTT
Found at i:5053 original size:32 final size:30
Alignment explanation
Indices: 4993--5112 Score: 95
Period size: 32 Copynumber: 3.8 Consensus size: 30
4983 AGACATTAAA
4993 TATTAA-TATATTTATATTAATATTTATATGT
1 TATTAATTATA-TTATATTAATATTTATAT-T
*
5024 TATTAATTATATTATA-TAATTTTAATATATT
1 TATTAATTATATTATATTAATATT--TATATT
*
5055 TATTTAATTATATTTATTTTAATTATTT-TATTT
1 TA-TTAATTATA-TTATATTAA-TATTTATA-TT
5088 TATTATATT-TATGTATATTATATAT
1 TATTA-ATTATAT-TATATTA-ATAT
5113 AGCCGTAACA
Statistics
Matches: 74, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
30 6 0.08
31 15 0.20
32 34 0.46
33 13 0.18
34 3 0.04
35 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TATTAATTATATTATATTAATATTTATATT
Found at i:5084 original size:28 final size:28
Alignment explanation
Indices: 5034--5099 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
5024 TATTAATTAT
*
5034 ATTATA-TAATTTTAATATATTTATTTA
1 ATTATATTTATTTTAATATATTTATTTA
*
5061 ATTATATTTATTTTAAT-TATTTTATTTT
1 ATTATATTTATTTTAATATA-TTTATTTA
5089 ATTATATTTAT
1 ATTATATTTAT
5100 GTATATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTATATTTATTTTAATATATTTATTTA
Found at i:5106 original size:15 final size:14
Alignment explanation
Indices: 5004--5110 Score: 73
Period size: 14 Copynumber: 7.8 Consensus size: 14
4994 ATTAATATAT
5004 TTATATTAATATTTA
1 TTATATT-ATATTTA
* *
5019 -TAT-GT-TATTAA
1 TTATATTATATTTA
*
5030 TTATATTATA-TAA
1 TTATATTATATTTA
* *
5043 TTTTAATATATTTA
1 TTATATTATATTTA
5057 TT-TAATTATATTTA
1 TTAT-ATTATATTTA
*
5071 TTTTAATTAT-TTTA
1 TTAT-ATTATATTTA
*
5085 TTTTATTATATTTA
1 TTATATTATATTTA
5099 TGTATATTATAT
1 T-TATATTATAT
5111 ATAGCCGTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.07
12 3 0.04
13 19 0.25
14 33 0.43
15 16 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTATATTATATTTA
Found at i:5108 original size:9 final size:9
Alignment explanation
Indices: 5016--5106 Score: 55
Period size: 9 Copynumber: 9.8 Consensus size: 9
5006 ATATTAATAT
5016 TTATATGTTA
1 TTATAT-TTA
5026 TTA-ATTATA
1 TTATATT-TA
5035 TTATATAATT-
1 TTATAT--TTA
*
5045 TTA-ATATA
1 TTATATTTA
5053 TT-TATTTAA
1 TTATATTT-A
5062 TTATATTTA
1 TTATATTTA
* *
5071 TTTTAATTA
1 TTATATTTA
*
5080 TTTTATTTTA
1 TTATA-TTTA
5090 TTATATTTA
1 TTATATTTA
5099 TGTATATT
1 T-TATATT
5107 ATATATAGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
7 1 0.02
8 6 0.09
9 30 0.46
10 26 0.40
11 1 0.02
12 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TTATATTTA
Found at i:5780 original size:27 final size:27
Alignment explanation
Indices: 5728--5799 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
5718 AACCACTCAT
*
5728 TATTTGTCAAAAATTGTGATTACTTTA
1 TATTTGTCAAAAATGGTGATTACTTTA
* * *
5755 TGTTTGTCAAAAATGGT-AGTTTCTTTT
1 TATTTGTCAAAAATGGTGA-TTACTTTA
5782 TATTTGTC-AAAATGGTGA
1 TATTTGTCAAAAATGGTGA
5800 CATGTTGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 9 0.24
27 29 0.76
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGATTACTTTA
Found at i:10292 original size:27 final size:27
Alignment explanation
Indices: 10257--10324 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
10247 AAGTACCCAT
10257 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATTGTGGTTACTTTG
10284 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATTGTGGTTACTTTG
10311 TGTTTGTCAAAAAT
1 TGTTTGTCAAAAAT
10325 GGTGATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATTGTGGTTACTTTG
Found at i:10342 original size:26 final size:27
Alignment explanation
Indices: 10257--10355 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
10247 AAGTACCCAT
*
10257 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
10284 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* * *
10311 TGTTTGTCAAAAATGGTGATT-TTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
10337 TATTTGCCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
10356 CATGTTGTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 19 0.29
27 46 0.71
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:10883 original size:23 final size:23
Alignment explanation
Indices: 10857--10921 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
10847 TTGATGATTG
10857 ATTGAGTTTATAGATTTTATTTT
1 ATTGAGTTTATAGATTTTATTTT
* *
10880 ATTGAG-TT-T-GA--TGA-TTG
1 ATTGAGTTTATAGATTTTATTTT
10897 ATTGAGTTTATAGATTTTATTTT
1 ATTGAGTTTATAGATTTTATTTT
10920 AT
1 AT
10922 GTTAAAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 8 0.25
18 4 0.12
19 1 0.03
20 4 0.12
21 1 0.03
22 4 0.12
23 10 0.31
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (23 bp):
ATTGAGTTTATAGATTTTATTTT
Found at i:10890 original size:40 final size:40
Alignment explanation
Indices: 10830--10921 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
10820 AATCTTTGAT
* *
10830 ATTTCATTTTAGTGAGTTTGATGATTGATTGAGTTTATAG
1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
10870 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
10910 ATTTTATTTTAT
1 ATTTTATTTTAT
10922 GTTAAAAGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.01, G:0.18, T:0.55
Consensus pattern (40 bp):
ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
Found at i:10912 original size:17 final size:17
Alignment explanation
Indices: 10842--10905 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
10832 TTCATTTTAG
10842 TGAGTTTGATGATTGAT
1 TGAGTTTGATGATTGAT
* *
10859 TGAGTTTATAGATTTTATTTTAT
1 TGAG-TT-T-GA--TGA-TTGAT
10882 TGAGTTTGATGATTGAT
1 TGAGTTTGATGATTGAT
10899 TGAGTTT
1 TGAGTTT
10906 ATAGATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 15 0.41
18 4 0.11
19 1 0.03
20 4 0.11
21 1 0.03
22 4 0.11
23 8 0.22
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (17 bp):
TGAGTTTGATGATTGAT
Found at i:11012 original size:21 final size:20
Alignment explanation
Indices: 10972--11012 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
10962 GATTTTAATG
**
10972 ATTTATTTAATTTTTGTTAT
1 ATTTATTTAATTTTCATTAT
10992 ATTTATGTTAATTTTCATTAT
1 ATTTAT-TTAATTTTCATTAT
11013 GATGATTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTATTTAATTTTCATTAT
Found at i:14816 original size:1 final size:1
Alignment explanation
Indices: 14810--14891 Score: 65
Period size: 1 Copynumber: 82.0 Consensus size: 1
14800 AAATCTTCAC
* * ** * * * ** *
14810 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTGTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
14875 TTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
14892 CCAATTGCCA
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:14833 original size:27 final size:27
Alignment explanation
Indices: 14803--14893 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 27
14793 AAGGAACAAA
14803 TCTTCACTTTTTT-TTTTGTTTTTTTTT
1 TCTTC-CTTTTTTGTTTTGTTTTTTTTT
14830 TCTTTTTCCTTTGTTTGTTTT-TTTTTTTCTT
1 TC---TTCCTTT-TTTGTTTTGTTTTTTT-TT
14861 T-TTCCTTTTTTTTGTTTTGTTTTTTTTT
1 TCTTCC--TTTTTTGTTTTGTTTTTTTTT
14889 T-TTCC
1 TCTTCC
14894 AATTGCCATG
Statistics
Matches: 55, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
27 6 0.11
28 15 0.27
29 14 0.25
30 13 0.24
31 7 0.13
ACGTcount: A:0.01, C:0.12, G:0.05, T:0.81
Consensus pattern (27 bp):
TCTTCCTTTTTTGTTTTGTTTTTTTTT
Found at i:14851 original size:33 final size:32
Alignment explanation
Indices: 14811--14891 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 32
14801 AATCTTCACT
14811 TTTT-TTTTTGTTTTTTTTT-T-CTTTTTCCTTTG
1 TTTTGTTTTT-TTTTTTTTTTTCCTTTTT--TTTG
14843 -TTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTG
1 TTTTGTTTTTTTTTTT-TTTTTCCTTTTTTTTG
14875 TTTTGTTTTTTTTTTTT
1 TTTTGTTTTTTTTTTTT
14892 CCAATTGCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
31 9 0.20
32 13 0.30
33 16 0.36
34 6 0.14
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.86
Consensus pattern (32 bp):
TTTTGTTTTTTTTTTTTTTTTCCTTTTTTTTG
Found at i:14863 original size:28 final size:28
Alignment explanation
Indices: 14812--14893 Score: 116
Period size: 27 Copynumber: 3.0 Consensus size: 28
14802 ATCTTCACTT
*
14812 TTTTTTTTG-TTTTTTTTTTCTTTTTCC
1 TTTTGTTTGTTTTTTTTTTTCTTTTTCC
14839 -TTTGTTTGTTTTTTTTTTTCTTTTTCC
1 TTTTGTTTGTTTTTTTTTTTCTTTTTCC
*
14866 TTTTTTTTGTTTTGTTTTTTT-TTTTTCC
1 TTTTGTTTGTTTT-TTTTTTTCTTTTTCC
14894 AATTGCCATG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
26 7 0.14
27 18 0.36
28 18 0.36
29 7 0.14
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (28 bp):
TTTTGTTTGTTTTTTTTTTTCTTTTTCC
Found at i:14863 original size:37 final size:36
Alignment explanation
Indices: 14810--14891 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 36
14800 AAATCTTCAC
*
14810 TTTTTTTTTTGTTTTTT-TTTTCTTTTTCCTTTGTTT
1 TTTTTTTTTTGTTTTTTCCTTT-TTTTTCCTTTGTTT
**
14846 GTTTTTTTTTT-TCTTTTTCCTTTTTTTTGTTTTGTTT
1 -TTTTTTTTTTGT-TTTTTCCTTTTTTTTCCTTTGTTT
14883 TTTTTTTTT
1 TTTTTTTTT
14892 CCAATTGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 10 0.25
37 27 0.68
38 3 0.08
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (36 bp):
TTTTTTTTTTGTTTTTTCCTTTTTTTTCCTTTGTTT
Found at i:15618 original size:60 final size:62
Alignment explanation
Indices: 15509--15633 Score: 236
Period size: 60 Copynumber: 2.0 Consensus size: 62
15499 AAACACAACT
15509 AAAAAACAAAGCTTAAAAAAAATAAAAAATAAATAAATAACAATAAAAGATATGAACATGCC
1 AAAAAACAAAGCTTAAAAAAAATAAAAAATAAATAAATAACAATAAAAGATATGAACATGCC
15571 AAAAAACAAAGCTTAAAAAAAAT-AAAAA-AAATAAATAACAATAAAAGATATGAACATGCC
1 AAAAAACAAAGCTTAAAAAAAATAAAAAATAAATAAATAACAATAAAAGATATGAACATGCC
15631 AAA
1 AAA
15634 GTCCTCCCCC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
60 35 0.56
61 5 0.08
62 23 0.37
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.15
Consensus pattern (62 bp):
AAAAAACAAAGCTTAAAAAAAATAAAAAATAAATAAATAACAATAAAAGATATGAACATGCC
Done.