Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2002
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: 31460
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1685 original size:15 final size:16
Alignment explanation
Indices: 1665--1694 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1655 AAAATGAAAA
1665 AGAAAAAGAA-ATGAC
1 AGAAAAAGAAGATGAC
1680 AGAAAAAGAAGATGA
1 AGAAAAAGAAGATGA
1695 GTGTGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (16 bp):
AGAAAAAGAAGATGAC
Found at i:2205 original size:16 final size:15
Alignment explanation
Indices: 2186--2215 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2176 AGTATCAATT
2186 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
2202 TTTGATTGGGATGA
1 TTTGATTGGGATGA
2216 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:3123 original size:20 final size:20
Alignment explanation
Indices: 3098--3152 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3088 TGTGGTTCAA
*
3098 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
3118 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
3138 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
3153 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:5062 original size:21 final size:23
Alignment explanation
Indices: 5017--5063 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5007 TCACCTGCAA
* *
5017 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
5040 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
5061 TAA
1 TAA
5064 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:5921 original size:18 final size:18
Alignment explanation
Indices: 5898--5932 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5888 TCTTATGTTC
5898 TTTTCAAATTCTATCTCT
1 TTTTCAAATTCTATCTCT
* *
5916 TTTTCAACTTCTTTCTC
1 TTTTCAAATTCTATCTC
5933 AATTTCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTCAAATTCTATCTCT
Found at i:5941 original size:24 final size:23
Alignment explanation
Indices: 5913--5967 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5903 AAATTCTATC
5913 TCTTTTTCAACTTCTTTCTCAATT
1 TCTTTTTCAACTTCTTTC-CAATT
* * **
5937 TCTTTTTTAACTTTTTTCCTTTT
1 TCTTTTTCAACTTCTTTCCAATT
5960 TCTTTTTC
1 TCTTTTTC
5968 TTTTCGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (23 bp):
TCTTTTTCAACTTCTTTCCAATT
Found at i:6515 original size:20 final size:20
Alignment explanation
Indices: 6492--6545 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
6482 AGTTTTTCCC
*
6492 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
6512 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
6532 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
6546 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:6527 original size:30 final size:30
Alignment explanation
Indices: 6492--6565 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
6482 AGTTTTTCCC
6492 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
6522 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
6552 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
6566 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:6555 original size:20 final size:20
Alignment explanation
Indices: 6492--6556 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
6482 AGTTTTTCCC
* * * *
6492 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
6512 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
6531 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
6552 AGCTC
1 AGCTC
6557 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:12914 original size:17 final size:18
Alignment explanation
Indices: 12892--12932 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12882 CATTTCTTTT
12892 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
12909 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
12927 T-TTTTG
1 TCTTTTG
12933 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:15203 original size:12 final size:13
Alignment explanation
Indices: 15168--15203 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
15158 AGACCGTATG
15168 CAATTTTTTTTCT
1 CAATTTTTTTTCT
*
15181 CGATTTTTTTT-T
1 CAATTTTTTTTCT
15193 CAATTTTTTTT
1 CAATTTTTTTT
15204 GAATCTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (13 bp):
CAATTTTTTTTCT
Found at i:22349 original size:30 final size:30
Alignment explanation
Indices: 22255--22350 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
22245 AGCTCACTCC
22255 TAGCTCATA-TTTAGC-CACGAGCTAAAGCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * **
22284 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
22314 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
22344 TAGCTCA
1 TAGCTCA
22351 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
28 1 0.02
29 15 0.29
30 32 0.63
31 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:25017 original size:5 final size:5
Alignment explanation
Indices: 25007--25068 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
24997 AAGAGAAAAC
* *
25007 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA AAA-GA
25054 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
25069 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 35 0.73
6 10 0.21
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:25037 original size:26 final size:26
Alignment explanation
Indices: 25007--25068 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
24997 AAGAGAAAAC
25007 AAAGAAAAGAAAAGAAAAAGAAA-AA
1 AAAGAAAAGAAAAGAAAAAGAAATAA
* * *
25032 GCAAGAGAAGAAAAGAAAATGAAATAA
1 -AAAGAAAAGAAAAGAAAAAGAAATAA
25059 AAAGAAAAGA
1 AAAGAAAAGA
25069 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAAAAAGAAATAA
Found at i:25069 original size:31 final size:30
Alignment explanation
Indices: 24995--25070 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
24985 TACATTCTTG
* *
24995 TAAAGAGAAAACA-AAGAAAAGAAAAGAAA
1 TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
25024 -AAGAAA-AAGCAAGAGAAGAAAAGAAAATGAAA
1 TAA-AAAGAA--AAGAGAAGAAAAGAAAA-GAAA
25056 TAAAAAGAAAAGAGA
1 TAAAAAGAAAAGAGA
25071 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 3 0.08
31 18 0.47
32 7 0.18
33 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.04
Consensus pattern (30 bp):
TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
Found at i:25148 original size:11 final size:12
Alignment explanation
Indices: 25116--25146 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25106 TTGAGAGAAC
25116 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25128 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25140 TTGAAAA
1 TTGAAAA
25147 GCAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:27323 original size:30 final size:30
Alignment explanation
Indices: 27289--27385 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
27279 AGCTCACTCC
27289 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
27319 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
27349 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
27379 TAGCTCA
1 TAGCTCA
27386 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:29906 original size:12 final size:13
Alignment explanation
Indices: 29873--29906 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
29863 ACCGTATGCA
29873 ATTTTTTTTCTCG
1 ATTTTTTTTCTCG
*
29886 ATTTTTTTT-TTG
1 ATTTTTTTTCTCG
29898 ATTTTTTTT
1 ATTTTTTTT
29907 GAATCTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (13 bp):
ATTTTTTTTCTCG
Done.