Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold786
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: 34029
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:885 original size:46 final size:45
Alignment explanation
Indices: 738--954 Score: 198
Period size: 46 Copynumber: 4.8 Consensus size: 45
728 ATGTAACCCC
* * ***
738 CCATAAGCGAACTCGGACTCAACTCAA-G-GCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCAT
*
782 CCATAAGTGAACTCGGA-TCAACTCAA-GAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA---C-A-TTCGCAT
* * *
830 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCGACACTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGACA-TTCGCAT
873 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCAT
*
919 CCATAAGTGAACTCCAGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACT-CGGACTCAACTCAACGAGTTCG
955 GATGCTCAAC
Statistics
Matches: 144, Mismatches: 15, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
42 3 0.02
43 14 0.10
44 22 0.15
45 10 0.07
46 59 0.41
47 31 0.22
48 3 0.02
49 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCAT
Found at i:975 original size:47 final size:45
Alignment explanation
Indices: 842--967 Score: 148
Period size: 46 Copynumber: 2.8 Consensus size: 45
832 CACGAACTTG
* * *
842 GACTCAACTCAACGAGTTC-GACACTTCGCATCCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGA-A-TGCGCAACCATAAGTGAACTCA
* *
888 GACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCCA
1 GACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGTGAACT-CA
*
935 GACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GACTCAACTCAACGAGTTCGGAATGCGCAACCAT
968 CCTAGTGACA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
45 9 0.12
46 39 0.53
47 26 0.35
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (45 bp):
GACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGTGAACTCA
Found at i:7143 original size:10 final size:10
Alignment explanation
Indices: 7128--7153 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
7118 ATACTTAAAT
7128 TTACAAGCCA
1 TTACAAGCCA
7138 TTACAAGCCA
1 TTACAAGCCA
7148 TTACAA
1 TTACAA
7154 AAGTCTTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (10 bp):
TTACAAGCCA
Found at i:7645 original size:46 final size:46
Alignment explanation
Indices: 7587--7808 Score: 281
Period size: 46 Copynumber: 4.8 Consensus size: 46
7577 TGTAACCCGC
* * * * *
7587 CCATAAGCGAACTCGGACTCAACTCAAGGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
7633 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
7683 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
7726 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
7772 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
7809 TGCTCAACCA
Statistics
Matches: 153, Mismatches: 14, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 2 0.01
46 106 0.69
47 28 0.18
48 2 0.01
49 2 0.01
50 3 0.02
51 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:7723 original size:93 final size:93
Alignment explanation
Indices: 7594--7762 Score: 293
Period size: 93 Copynumber: 1.8 Consensus size: 93
7584 CGCCCATAAG
* * *
7594 CGAACTCGGACTCAACTCAAGGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
7659 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
7687 CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
7752 ACGAGTTCGGA
66 ACGAGTTCGGA
7763 CATTCGCATC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:12087 original size:21 final size:20
Alignment explanation
Indices: 12063--12102 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
12053 TGAAATGTAT
12063 GAATAT-ATATAAGCTATGGCC
1 GAATATGAT-TAAGCT-TGGCC
12084 GAATATGATTAAGCTTGGC
1 GAATATGATTAAGCTTGGC
12103 TATTATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
GAATATGATTAAGCTTGGCC
Found at i:18053 original size:29 final size:29
Alignment explanation
Indices: 17980--18055 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
17970 AAGTCTACAT
* *
17980 ACATGCATATGGCCCACTAGGCCCAATCTG
1 ACATTCATATGGCCCATTAGGCCCAATC-G
*
18010 TCATTCATATGGCCCATTAGGCCCAAATC-
1 ACATTCATATGGCCCATTAGGCCC-AATCG
18039 ACATTCATATGGCCCAT
1 ACATTCATATGGCCCAT
18056 CAATTCCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 16 0.39
30 21 0.51
31 4 0.10
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAATCG
Found at i:20115 original size:20 final size:20
Alignment explanation
Indices: 20086--20130 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20076 AGCACATGTA
* *
20086 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
20106 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
20126 TTCAT
1 TTCAT
20131 TTTAGTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:23519 original size:43 final size:42
Alignment explanation
Indices: 23453--23609 Score: 161
Period size: 43 Copynumber: 3.7 Consensus size: 42
23443 AGCTCGTACA
* * *
23453 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAACATTG
1 ATGCCAATGTCCCAGACATGGTCTTACAAGTAATCAAACA-CG
* * * * *
23496 ATGCCACTGTCCCAGACAAGGTCTTACAAGAAATCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACAAGTAATCAAACACG
* ** *
23538 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAAGTCA
1 ATGCCAATGTCCCAGACATGGTCTTACAAGT-AATCA-AACACG
* *
23582 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
23610 CGATAACACA
Statistics
Matches: 94, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
42 28 0.30
43 38 0.40
44 28 0.30
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACAAGTAATCAAACACG
Found at i:29817 original size:40 final size:40
Alignment explanation
Indices: 29641--29863 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
29631 TCCTCGTTCA
* * * * *
29641 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29680 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
29720 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
29760 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
29800 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
29840 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29864 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Done.