Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3789
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: 37107
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:831 original size:56 final size:57
Alignment explanation
Indices: 764--884 Score: 226
Period size: 56 Copynumber: 2.1 Consensus size: 57
754 TATTAGTTTA
764 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTC-ATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCAATGACATGTT
*
820 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCAATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCAATGACATGTT
877 TTGCCCAT
1 TTGCCCAT
885 CATCCTTGTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 45 0.71
57 18 0.29
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (57 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCAATGACATGTT
Found at i:12596 original size:44 final size:43
Alignment explanation
Indices: 12463--12608 Score: 168
Period size: 44 Copynumber: 3.4 Consensus size: 43
12453 GCCAACTCCT
* * * * *
12463 AGACGTGGTCTTACATGTAATCAAATATTGATTCCACTGTCCC
1 AGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCC
* * * * *
12506 ATATAAGGTCTTACACGAAATCAAATA-CGATGCCAATGTCCT
1 AGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCC
* *
12548 AGACATGGTCTTACACGTAATCTCAATATCGATGCCAATTTCCC
1 AGACATGGTCTTACACGTAATC-AAATATCGATGCCAATGTCCC
12592 AGACATGGTCTTACACG
1 AGACATGGTCTTACACG
12609 AAAACATATA
Statistics
Matches: 84, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
42 29 0.35
43 25 0.30
44 30 0.36
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
AGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCC
Found at i:12611 original size:86 final size:84
Alignment explanation
Indices: 12451--12611 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 84
12441 AGCTCCTACA
* * * * * * *
12451 ATGCCAACTCCTAGACGTGGTCTTACATGTAATCAAATATTGATTCCACTGTCCCATATAAGGTC
1 ATGCCAACTCCTAGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCCAGACAAGGTC
12516 TTACACGAAATCAAATACG
66 TTACACGAAATCAAATACG
* * * *
12535 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCTCAATATCGATGCCAATTTCCCAGACATGG
1 ATGCCAA-CTCCTAGACATGGTCTTACACGTAATC-AAATATCGATGCCAATGTCCCAGACAAGG
12600 TCTTACACGAAA
64 TCTTACACGAAA
12612 ACATATATTG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 7 0.11
85 24 0.38
86 33 0.52
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (84 bp):
ATGCCAACTCCTAGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCCAGACAAGGTC
TTACACGAAATCAAATACG
Found at i:14993 original size:24 final size:23
Alignment explanation
Indices: 14914--14994 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
14904 GTCGATAACG
*
14914 AAGAGGAAAAAGAAAAGAGA-GAA
1 AAGAGGAAAAAGAAAA-AAATGAA
**
14937 TAAGAATAAAAATGAAAAAAATAAGAA
1 -AAGAGGAAAAA-GAAAAAAAT--GAA
14964 AA-AGGAAAAAGAAAGAAAATGAA
1 AAGAGGAAAAAGAAA-AAAATGAA
14987 AAGAGGAA
1 AAGAGGAA
14995 GAAAAGAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
23 5 0.11
24 20 0.43
25 16 0.35
26 2 0.04
27 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (23 bp):
AAGAGGAAAAAGAAAAAAATGAA
Found at i:14996 original size:17 final size:16
Alignment explanation
Indices: 14922--15000 Score: 52
Period size: 17 Copynumber: 4.6 Consensus size: 16
14912 CGAAGAGGAA
14922 AAAGAAAAGAGAGAATAAG
1 AAAGAAAAG-GA-AA-AAG
* *
14941 AATA-AAAATGAAAAAA
1 AA-AGAAAAGGAAAAAG
14957 ATAAGAAAAAGGAAAAAG
1 A-AAG-AAAAGGAAAAAG
*
14975 AAAGAAAATGAAAAGAG
1 AAAGAAAAGGAAAA-AG
*
14992 GAAGAAAAG
1 AAAGAAAAG
15001 AAGAACATCT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
16 13 0.27
17 15 0.31
18 13 0.27
19 6 0.12
20 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAGGAAAAAG
Found at i:14997 original size:34 final size:36
Alignment explanation
Indices: 14923--15005 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 36
14913 GAAGAGGAAA
* *
14923 AAGAAAAGAGAGAATAAGAATAAAAATGAAAAAAAT
1 AAGAAAAGAGAGAAAAAGAATAAAAATGAAAAAAAG
* *
14959 AAGAAAA-AG-GAAAAAGAA-AGAAAATGAAAAGAGG
1 AAGAAAAGAGAGAAAAAGAATA-AAAATGAAAAAAAG
14993 AAGAAAAGA-AGAA
1 AAGAAAAGAGAGAA
15006 CATCTAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
33 1 0.03
34 26 0.65
35 6 0.15
36 7 0.17
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (36 bp):
AAGAAAAGAGAGAAAAAGAATAAAAATGAAAAAAAG
Found at i:20884 original size:21 final size:21
Alignment explanation
Indices: 20855--20899 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20845 TGTTACACTG
20855 CTTGCTCACACGGACGTGT-C
1 CTTGCTCACACGGACGTGTGC
* *
20875 CTTGCCTCACATGGGCGTGTGC
1 CTTG-CTCACACGGACGTGTGC
20897 CTT
1 CTT
20900 TGACACACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.11, C:0.33, G:0.27, T:0.29
Consensus pattern (21 bp):
CTTGCTCACACGGACGTGTGC
Found at i:24757 original size:20 final size:20
Alignment explanation
Indices: 24691--24757 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
24681 ATTTTAGTAA
*
24691 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
24711 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
24731 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
24751 ACATGAT
1 ACATGAT
24758 GTATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:24890 original size:24 final size:24
Alignment explanation
Indices: 24806--24951 Score: 197
Period size: 25 Copynumber: 6.0 Consensus size: 24
24796 GGAGGAAGTG
24806 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
24830 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
* *
24855 GATAAAGGGCTTATGCCCCAGTAAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
24880 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
24904 TAAAAGGGCTT-TGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
24927 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
24952 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
23 18 0.16
24 39 0.35
25 54 0.49
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:25183 original size:31 final size:31
Alignment explanation
Indices: 25145--25207 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
25135 CGTTTACAGT
25145 AAAGGCTTC-GTCCCAGTAATATGAAATATGA
1 AAAGGCTTCAG-CCCAGTAATATGAAATATGA
**
25176 AAAGGCTTCAGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
25207 A
1 A
25208 GTGTGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATATGA
Found at i:32839 original size:20 final size:20
Alignment explanation
Indices: 32775--32839 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
32765 GATTTAGTAA
*
32775 ACATGGTATGTATGATA--C
1 ACATGATATGTATGATATGC
* *
32793 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
32813 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
32833 ACATGAT
1 ACATGAT
32840 GTATTCATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.35
20 26 0.65
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:32915 original size:24 final size:25
Alignment explanation
Indices: 32883--32964 Score: 141
Period size: 25 Copynumber: 3.4 Consensus size: 25
32873 GAGGAGTGTA
32883 AAAGGGCTTATG-CCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
32907 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
32932 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
32956 AAAGGGCTT
1 AAAGGGCTT
32965 TCCCAGTTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
24 21 0.38
25 35 0.62
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:32996 original size:46 final size:49
Alignment explanation
Indices: 32883--33008 Score: 129
Period size: 49 Copynumber: 2.6 Consensus size: 49
32873 GAGGAGTGTA
*
32883 AAAGGGCTTATG-CCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTAGGCCCCAGTTATGATAAAGGGCTTAT-CCCCAGTTATGAT
* * *
32932 AAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTT-T-CCCAGTTATTA-
1 AAAGGGCTTAGGCCCCAGTTATGATAAAGGGCTTATCCCCAGTTATGAT
32977 AAAGAGGC-TAGGCCTCCAGTTATATGATAAAG
1 AAAG-GGCTTAGGCC-CCAG-T-TATGATAAAG
33009 CAGCTATGCT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
45 9 0.13
46 17 0.25
47 1 0.01
48 5 0.07
49 25 0.37
50 10 0.15
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (49 bp):
AAAGGGCTTAGGCCCCAGTTATGATAAAGGGCTTATCCCCAGTTATGAT
Found at i:33225 original size:29 final size:30
Alignment explanation
Indices: 33192--33251 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
33182 CGTTTACAGT
33192 AAAGGCTTCGGCCCAGT-ATATGAAATATG
1 AAAGGCTTCGGCCCAGTGATATGAAATATG
*
33221 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTGATATGAAATATG
33251 A
1 A
33252 GTGAAAAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGATATGAAATATG
Done.