Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1288
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: 32911
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:86 original size:13 final size:11
Alignment explanation
Indices: 41--85 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
31 ATCTAGAATA
41 TTGTTTTTTTT
1 TTGTTTTTTTT
*
52 TTGATTTTTTT
1 TTGTTTTTTTT
*
63 TTGTTTTTTTG
1 TTGTTTTTTTT
74 TTGTGTTTTTTT
1 TTGT-TTTTTTT
86 GGGCATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 23 0.79
12 6 0.21
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.84
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:3416 original size:28 final size:28
Alignment explanation
Indices: 3368--3444 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
3358 AAACAACAAG
* *
3368 CCACCATTTTTTAC-AA-ACAAA-AATAA
1 CCACCATATTTGACAAATACAAAGAA-AA
*
3394 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAAGAAAA
3422 CCACCATATTTGACAAATACAAA
1 CCACCATATTTGACAAATACAAA
3445 TGGTGGCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 12 0.27
27 2 0.04
28 30 0.67
29 1 0.02
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.22
Consensus pattern (28 bp):
CCACCATATTTGACAAATACAAAGAAAA
Found at i:7944 original size:24 final size:24
Alignment explanation
Indices: 7916--7961 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
7906 AATAAAAATT
7916 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
7940 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
7962 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:7989 original size:28 final size:28
Alignment explanation
Indices: 7942--8020 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
7932 AAACAACAAG
* * *
7942 CCACCATTTTTTAC-AA-ACAAAAATAA
1 CCACCATATTTGACAAATACAAAAAAAA
*
7968 CCACCATATTTGATAAATACAAAAAAAA
1 CCACCATATTTGACAAATACAAAAAAAA
* *
7996 TCATCATATTTGACAAATACAAAAA
1 CCACCATATTTGACAAATACAAAAA
8021 GTGGTATTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 11 0.25
27 2 0.05
28 31 0.70
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (28 bp):
CCACCATATTTGACAAATACAAAAAAAA
Found at i:8590 original size:2 final size:2
Alignment explanation
Indices: 8583--8621 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8573 TTATAGGTGG
8583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8622 GCAAATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12099 original size:9 final size:9
Alignment explanation
Indices: 12085--12128 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
12075 TTAAAAGTTG
12085 ATATTTAAT
1 ATATTTAAT
12094 ATATTTAAT
1 ATATTTAAT
*
12103 AT-TTAAAT
1 ATATTTAAT
12111 GATATTTAAT
1 -ATATTTAAT
12121 ATATTTAA
1 ATATTTAA
12129 AATTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 5 0.16
9 21 0.68
10 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
ATATTTAAT
Found at i:12113 original size:27 final size:27
Alignment explanation
Indices: 12083--12137 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12073 TCTTAAAAGT
*
12083 TGATATTTAATATATTTAATATTTAAA
1 TGATATTTAATATATTTAAAATTTAAA
12110 TGATATTTAATATATTTAAAATTTAAA
1 TGATATTTAATATATTTAAAATTTAAA
12137 T
1 T
12138 TTTAGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
TGATATTTAATATATTTAAAATTTAAA
Found at i:13096 original size:14 final size:13
Alignment explanation
Indices: 13062--13100 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
13052 AATACGATGC
13062 AAATAAATATAA-
1 AAATAAATATAAT
13074 AAAT-AATATAAT
1 AAATAAATATAAT
13086 AAATAAGATATAAT
1 AAATAA-ATATAAT
13100 A
1 A
13101 TATTTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.29
12 8 0.33
13 1 0.04
14 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAATAAATATAAT
Found at i:13194 original size:33 final size:34
Alignment explanation
Indices: 13134--13199 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
13124 ATATTTAATA
13134 TAAATATTATATTTATGTTTAAAATTTT-TACGT
1 TAAATATTATATTTATGTTTAAAATTTTATACGT
*
13167 TAAATAATT-TATGTTATGTTT-ATATTTTATACG
1 TAAAT-ATTATAT-TTATGTTTAAAATTTTATACG
13200 CCTAAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (34 bp):
TAAATATTATATTTATGTTTAAAATTTTATACGT
Found at i:14101 original size:37 final size:38
Alignment explanation
Indices: 14035--14142 Score: 98
Period size: 38 Copynumber: 2.9 Consensus size: 38
14025 GCATATGTTA
* * * * *
14035 AAACAAAAACCACTATTCTAATTCGGTGACAC-AGTTCAG
1 AAACAAAAACTATTATTCTTATCCAGTGACACGAGTT--G
*
14074 AAA-AAAAA-TCATTATTTTTA-CCAGTGACACGAGTTG
1 AAACAAAAACT-ATTATTCTTATCCAGTGACACGAGTTG
*
14110 AAACAAAAACTATTATTCTTATCCGGTGACACG
1 AAACAAAAACTATTATTCTTATCCAGTGACACG
14143 GCAAAAACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
36 4 0.07
37 22 0.39
38 27 0.48
39 3 0.05
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (38 bp):
AAACAAAAACTATTATTCTTATCCAGTGACACGAGTTG
Found at i:14118 original size:38 final size:38
Alignment explanation
Indices: 14060--14142 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 38
14050 TTCTAATTCG
*
14060 GTGACAC-AGTTCAGAAAAAAAATCATTATTTTTA-CCA
1 GTGACACGAGTTCAGAAAAAAAAT-ATTATTCTTATCCA
*
14097 GTGACACGAGTT--GAAACAAAAACTATTATTCTTATCCG
1 GTGACACGAGTTCAGAAA-AAAAA-TATTATTCTTATCCA
14135 GTGACACG
1 GTGACACG
14143 GCAAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 4 0.10
37 21 0.52
38 15 0.38
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (38 bp):
GTGACACGAGTTCAGAAAAAAAATATTATTCTTATCCA
Found at i:16615 original size:14 final size:14
Alignment explanation
Indices: 16576--16626 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
16566 TAAATTTTTA
16576 TATATTTAAATA-T
1 TATATTTAAATATT
**
16589 TATATTTTTATATT
1 TATATTTAAATATT
*
16603 TATATTTAAATATA
1 TATATTTAAATATT
*
16617 AATATTTAAA
1 TATATTTAAA
16627 AAATCAAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATTTAAATATT
Found at i:18499 original size:18 final size:19
Alignment explanation
Indices: 18476--18515 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
18466 TATAAAAGGT
18476 TTCATCAACCTT-CTCAAC
1 TTCATCAACCTTACTCAAC
**
18494 TTCATCTTCCTTACTCAAC
1 TTCATCAACCTTACTCAAC
18513 TTC
1 TTC
18516 CTTTTGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.40
Consensus pattern (19 bp):
TTCATCAACCTTACTCAAC
Found at i:19816 original size:7 final size:7
Alignment explanation
Indices: 19804--19833 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
19794 CAAATTCTTC
19804 TCAAACA
1 TCAAACA
19811 TCAAACA
1 TCAAACA
19818 TCAAACA
1 TCAAACA
19825 TCAAACA
1 TCAAACA
19832 TC
1 TC
19834 TAGCCATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (7 bp):
TCAAACA
Done.