Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3803
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: 44855
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:5555 original size:29 final size:27
Alignment explanation
Indices: 5537--5606 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
5527 ATATTAAGTC
5537 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
5564 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
5592 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
5607 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:5600 original size:28 final size:28
Alignment explanation
Indices: 5537--5634 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
5527 ATATTAAGTC
*
5537 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
5564 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
5592 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
5621 CGCACACTTAGTGC
1 CGCACACTTAGTGC
5635 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:14772 original size:39 final size:38
Alignment explanation
Indices: 14729--14859 Score: 156
Period size: 39 Copynumber: 3.4 Consensus size: 38
14719 ACCAGCTCGA
* *
14729 AGCCTGCGGGA-CTTTAGCCCAGACGTAATTCCAGCATAT
1 AGCCTGC-GGACCTTAAGCCC-GACATAATTCCAGCATAT
* *
14768 AGCCTGCGGACCTTAAGTCCGAACATAATTCCAACATAT
1 AGCCTGCGGACCTTAAGCCCG-ACATAATTCCAGCATAT
* *
14807 AGCCTACGGACCTTAAGCTCGGACATAATTCCAGCATAT
1 AGCCTGCGGACCTTAAGC-CCGACATAATTCCAGCATAT
*
14846 AGCCTGCGAACCTT
1 AGCCTGCGGACCTT
14860 TAGTCCGGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 4 0.05
39 73 0.92
40 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (38 bp):
AGCCTGCGGACCTTAAGCCCGACATAATTCCAGCATAT
Found at i:14874 original size:39 final size:39
Alignment explanation
Indices: 14754--14876 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
14744 AGCCCAGACG
*
14754 TAATTCCAGCATATAGCCTGCGGACCTTAAGTCCGAACA
1 TAATTCCAGCATATAGCCTGCGGACCTTAAGTCCGGACA
* *
14793 TAATTCCAACATATAGCCTACGGACCTTAAG-CTCGGACA
1 TAATTCCAGCATATAGCCTGCGGACCTTAAGTC-CGGACA
* * *
14832 TAATTCCAGCATATAGCCTGCGAACCTTTAGTCCGGATA
1 TAATTCCAGCATATAGCCTGCGGACCTTAAGTCCGGACA
14871 TAATTC
1 TAATTC
14877 ATCACTGAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 72 0.97
40 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (39 bp):
TAATTCCAGCATATAGCCTGCGGACCTTAAGTCCGGACA
Found at i:25574 original size:45 final size:44
Alignment explanation
Indices: 25407--25576 Score: 179
Period size: 45 Copynumber: 3.9 Consensus size: 44
25397 ATATCATACA
* ** * *
25407 ATGCCAATGTCCCAGACGTGGTCTTACATGCTA-TCTTATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAACACATATATCG
* *
25450 ATGCCACTGTCCCAGACAG-GGTCTTACACGAATCA-A-ATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAACACATATATCG
* * *
25491 ATGCCAATGTTCCAGACATGGTCTTACACGTAACCACATATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAACACATATATCG
*
25536 ATGCCAATGTCCCAAACGTGGTCTTACACGAGAACACATAT
1 ATGCCAATGTCCCAGACGTGGTCTTACACGA-AACACATAT
25577 CAAAAATTCT
Statistics
Matches: 104, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
41 28 0.27
42 7 0.07
43 27 0.26
44 5 0.05
45 37 0.36
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAACACATATATCG
Found at i:34107 original size:40 final size:40
Alignment explanation
Indices: 34052--34197 Score: 265
Period size: 40 Copynumber: 3.6 Consensus size: 40
34042 CGGATGATAA
34052 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
34092 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* **
34132 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
34172 CCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGT
34198 AACACCCCGA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
Found at i:35616 original size:40 final size:40
Alignment explanation
Indices: 35569--35915 Score: 588
Period size: 40 Copynumber: 8.7 Consensus size: 40
35559 CGCAAACACT
* * *
35569 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
35609 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
35649 TTGCCTTCGGGTCATAGCCCGGACATATCAACT-GCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
35688 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
35728 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
35768 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
35808 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
35848 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
35888 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
35916 TCCAATGCTC
Statistics
Matches: 287, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 36 0.13
40 251 0.87
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:44515 original size:40 final size:40
Alignment explanation
Indices: 44467--44814 Score: 549
Period size: 40 Copynumber: 8.7 Consensus size: 40
44457 GCAAACACCT
* * *
44467 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
44507 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
44547 TTGCCTTCGGGTCATAGCCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
44587 TTGCCTTCGGGTCTTAGCCCGGATA-ATTCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATA-TCAACTCGCATAA
* *
44627 TTGCCTTCGGGTCATAGCTCGGACATATAT-AACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGG--ATATATCAACTCGCATAA
44668 TTG-CTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
44707 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
44747 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
44787 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
44815 TCCAATGCTC
Statistics
Matches: 283, Mismatches: 19, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
38 6 0.02
39 15 0.05
40 244 0.86
41 13 0.05
42 4 0.01
43 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Done.