Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2343
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: 23901
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:1936 original size:13 final size:13
Alignment explanation
Indices: 1920--1944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1910 AGTCACACGC
1920 CCGTGTGACACAG
1 CCGTGTGACACAG
1933 CCGTGTGACACA
1 CCGTGTGACACA
1945 CATGGGCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.28, T:0.16
Consensus pattern (13 bp):
CCGTGTGACACAG
Found at i:3005 original size:43 final size:43
Alignment explanation
Indices: 2911--3019 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
2901 TAGATGCCTC
* * *
2911 TGTCCCAGACAGGGTCTTACAC-AAAATCAGATACGATGCTGA
1 TGTCCCAGACACGGTCTTACACGAAAATCAGATACAACGCTGA
*
2953 TGTCCCAGACATGGTCTTACACGTAAATATCA-AT-CAACGCTTG-
1 TGTCCCAGACACGGTCTTACACG-AAA-ATCAGATACAACGC-TGA
2996 TGTCCCAGACACGGTCTTACACGA
1 TGTCCCAGACACGGTCTTACACGA
3020 TGTGTCAGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
42 22 0.37
43 26 0.44
44 7 0.12
45 4 0.07
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (43 bp):
TGTCCCAGACACGGTCTTACACGAAAATCAGATACAACGCTGA
Found at i:4836 original size:42 final size:41
Alignment explanation
Indices: 4673--4839 Score: 154
Period size: 42 Copynumber: 4.0 Consensus size: 41
4663 AATCGTACCA
* * * *
4673 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACA-CGAAACTCATAACG
* ** * ** * *
4715 ATGCCAATAGCCCATCTATAGTCTTACACGATTCTTATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAACTCATAACG
* * *
4757 ATGCCATGTCCCAGACATGGTCTTGCACGAAATCTCATAACG
1 ATGCCATATCCCAGATATGGTCTTACACGAAA-CTCATAACG
*
4799 ATGCCATATCCCAAATATGGTCTTACACGTAAACTCATAAC
1 ATGCCATATCCCAGATATGGTCTTACACG-AAACTCATAAC
4840 CTTAATGTCA
Statistics
Matches: 99, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 18 0.18
42 60 0.61
43 21 0.21
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAACTCATAACG
Found at i:7662 original size:40 final size:40
Alignment explanation
Indices: 7479--7662 Score: 216
Period size: 39 Copynumber: 4.7 Consensus size: 40
7469 GCTACTCATT
* *
7479 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
7519 CAAATGCCTTC-GAACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
7558 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
7597 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
7638 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
7663 CATCATTCGA
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.02
39 65 0.53
40 43 0.35
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:14249 original size:107 final size:101
Alignment explanation
Indices: 14069--14272 Score: 338
Period size: 107 Copynumber: 2.0 Consensus size: 101
14059 GGAGCAAGCG
14069 CTACACTCTCAAGATCATCAGCTACTACTCGGTCGGGATCGGGATCCATTACTATAAATAAACAC
1 CTACACTCTCAAGATCATCAGCTACTACTCGGTCGGGATCGGGATCCATTACTATAAATAAACAC
14134 ATTTGCAAATGTCAGAAATCACCACACTATCAGGCA
66 ATTTGCAAATGTCAGAAATCACCACACTATCAGGCA
14170 CTACACTCTCAAGATCATCAGCTACCGCT-CGGTCGGGGTCGGGATCGGGATCCATTACTATAAA
1 CTACACTCTCAAGATCATCAGCTA---CTAC--TC--GGTCGGGATCGGGATCCATTACTATAAA
14234 TAAACACATTTGCAAATGTCAGAAATCACCACACTATCA
59 TAAACACATTTGCAAATGTCAGAAATCACCACACTATCA
14273 AATAATCACA
Statistics
Matches: 96, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
101 24 0.25
103 1 0.01
104 2 0.02
105 2 0.02
107 67 0.70
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (101 bp):
CTACACTCTCAAGATCATCAGCTACTACTCGGTCGGGATCGGGATCCATTACTATAAATAAACAC
ATTTGCAAATGTCAGAAATCACCACACTATCAGGCA
Found at i:16853 original size:41 final size:41
Alignment explanation
Indices: 16796--16938 Score: 170
Period size: 40 Copynumber: 3.6 Consensus size: 41
16786 CGAGCTTGGG
16796 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* *
16837 TTCGAAGGGCTTTTGAGCCAGTG-TCATAACCGGACTTAG-
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * *
16876 TTCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT
*
16917 CTCGAAGGGC-TTTGAGCCAGTG
1 TTCGAAGGGCTTTTGAGCCAGTG
16939 TTAAGAATCG
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
39 21 0.24
40 32 0.36
41 32 0.36
42 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (41 bp):
TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
Found at i:16877 original size:40 final size:40
Alignment explanation
Indices: 16796--16939 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 40
16786 CGAGCTTGGG
* *
16796 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTG-TCATAACCGGACTTAGT
16837 TTCGAAGGGCTTTTGAGCCAGTGTCATAACCGGACTTAG-
1 TTCGAAGGGCTTTTGAGCCAGTGTCATAACCGGACTTAGT
* * * * *
16876 TTCGAAGGGCCTTCGAGCCAGTGGCCTAATCC-GAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGTGTCATAA-CCGGA-CTTAGT
*
16917 CTCGAAGGGC-TTTGAGCCAGTGT
1 TTCGAAGGGCTTTTGAGCCAGTGT
16940 TAAGAATCGT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 27 0.30
40 31 0.34
41 32 0.36
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
TTCGAAGGGCTTTTGAGCCAGTGTCATAACCGGACTTAGT
Found at i:20366 original size:38 final size:39
Alignment explanation
Indices: 20234--20372 Score: 160
Period size: 38 Copynumber: 3.6 Consensus size: 39
20224 GCTACTCGTT
* **
20234 CAAATGCCTTCGGACATAGCCCGTTA-TAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
20272 CAAATGCCTTCGGACTTAACCCGGATTTACTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCA
* *
20311 CCAATG-CTTCGGGCTTAGCCCGGAATTAGTAACTCGC-
1 CAAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCA
*
20348 CAAATG-CTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGA-CTTAGCCCGGA
20373 TATGTTACTT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
37 11 0.13
38 58 0.68
39 16 0.19
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCA
Done.