Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold678
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: 10567
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.20
Warning! 4055 characters in sequence are not A, C, G, or T
Found at i:3483 original size:22 final size:22
Alignment explanation
Indices: 3453--3495 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3443 ACAACAAAAC
*
3453 AGGCTTTTAGCGGCACTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
*
3475 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCACTTTTT
3496 AGCACCGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:3655 original size:43 final size:42
Alignment explanation
Indices: 3589--4032 Score: 523
Period size: 43 Copynumber: 10.3 Consensus size: 42
3579 TTCCAGTAAA
* *
3589 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTCCAACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCC-ACAC
* * *
3632 AAATGCCGCCAAAGACCAAGACCTTTAGCGGCGCTTTCCACAT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
** *
3675 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCCTTTTATAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCG-CTTCCACAC
* *
3718 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
*
3761 AAACGCCGCTAAAGACCAAGACCTGTAGCGGCGCTTCCAACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCC-ACAC
* * ** *
3804 AAACGCCGCCAAAAGACCAAAACCTTTAGCGGCGCTTTTAATAC
1 AAACGCCG-CTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
*
3848 AAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
* *
3891 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTCCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-CCACAC
*
3934 AAACGCCGCTAAAGA-CAACGACCATTTAGCGGCGCTTACACTAC
1 AAACGCCGCTAAAGACCAA-GACC-TTTAGCGGCGCTTCCAC-AC
** * * *
3978 AAACGCTTCTAAAGATCGAGACCTTTAGCGGCGCTTTTCC-CAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC--TTCCACAC
4021 AAACGCCGCTAA
1 AAACGCCGCTAA
4033 TTTTGGCGGA
Statistics
Matches: 349, Mismatches: 39, Indels: 26
0.84 0.09 0.06
Matches are distributed among these distances:
42 9 0.03
43 261 0.75
44 72 0.21
45 7 0.02
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCACAC
Found at i:3882 original size:130 final size:128
Alignment explanation
Indices: 3589--4032 Score: 590
Period size: 130 Copynumber: 3.4 Consensus size: 128
3579 TTCCAGTAAA
* * * *
3589 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGC-TTCCAACACAAATGCCGCCAAAGACCAAGA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCC-ACACAAACGCCGCTAAAGACCAAGA
*
3653 CCTTTAGCGGCGCTTTCCACATAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCCTTTT-ATA
65 CCTTTAGCGGCGC-TTCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCG-CTTTTAATA
3717 C
128 C
* *
3718 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCATACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
* * *
3783 CTGTAGCGGCGCTTCCAACACAAACGCCGCCAAAAGACCAAAACCTTTAGCGGCGCTTTTAATAC
66 CTTTAGCGGCGCTTCC-ACACAAACGCCG-CTAAAGACCAAGACCTTTAGCGGCGCTTTTAATAC
* * *
3848 AAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTCCACACAAACGCCGCTATAGATCAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
** *
3913 CTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGA-CAACGACCATTTAGCGGCGCTTACACTA
66 CTTTAGCGGCGCTT-CCACACAAACGCCGCTAAAGACCAA-GACC-TTTAGCGGCGCTTTTAATA
3977 C
128 C
** * * *
3978 AAACGCTTCTAAAGATCGAGACCTTTAGCGGCGCTTTTCC-CAAAAACGCCGCTAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTCCACACAAACGCCGCTAA
4033 TTTTGGCGGA
Statistics
Matches: 279, Mismatches: 28, Indels: 15
0.87 0.09 0.05
Matches are distributed among these distances:
128 7 0.03
129 91 0.33
130 174 0.62
131 7 0.03
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (128 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
CTTTAGCGGCGCTTCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTAATAC
Found at i:10088 original size:16 final size:16
Alignment explanation
Indices: 10077--10116 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
10067 ATTTATGAAG
10077 GTTATGTATTATGTAA
1 GTTATGTATTATGTAA
*
10093 GTTGTGTATTATGTAA
1 GTTATGTATTATGTAA
10109 GTTATGTA
1 GTTATGTA
10117 AGTTAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (16 bp):
GTTATGTATTATGTAA
Found at i:10100 original size:9 final size:9
Alignment explanation
Indices: 10077--10121 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
10067 ATTTATGAAG
10077 GTTATGT-A
1 GTTATGTAA
10085 -TTATGTAA
1 GTTATGTAA
*
10093 GTTGTGT-A
1 GTTATGTAA
10101 -TTATGTAA
1 GTTATGTAA
10109 GTTATGTAA
1 GTTATGTAA
10118 GTTA
1 GTTA
10122 AATATTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
7 11 0.35
8 3 0.10
9 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (9 bp):
GTTATGTAA
Found at i:10199 original size:22 final size:22
Alignment explanation
Indices: 10173--10214 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10163 TAATTTAGTT
*
10173 ATGTACGTTACGTATCATATTA
1 ATGTAAGTTACGTATCATATTA
* *
10195 ATGTAAGTTATGTATTATAT
1 ATGTAAGTTACGTATCATAT
10215 AAGTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (22 bp):
ATGTAAGTTACGTATCATATTA
Found at i:10221 original size:9 final size:9
Alignment explanation
Indices: 10195--10289 Score: 81
Period size: 9 Copynumber: 10.6 Consensus size: 9
10185 TATCATATTA
10195 ATGTAAGTT
1 ATGTAAGTT
10204 ATGT-A-TT
1 ATGTAAGTT
*
10211 ATATAAGTT
1 ATGTAAGTT
*
10220 ATTTAAGTT
1 ATGTAAGTT
10229 ATGTAAGTT
1 ATGTAAGTT
*
10238 GTGTAAGTT
1 ATGTAAGTT
*
10247 ATGTATAATATT
1 ATG--TAA-GTT
*
10259 AACGTAAGTT
1 -ATGTAAGTT
10269 ATGT-A-TT
1 ATGTAAGTT
10276 ATGTAAGTT
1 ATGTAAGTT
10285 ATGTA
1 ATGTA
10290 TAATATTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
7 11 0.16
8 4 0.06
9 42 0.61
10 2 0.03
11 6 0.09
12 2 0.03
13 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:10235 original size:18 final size:18
Alignment explanation
Indices: 10195--10289 Score: 81
Period size: 16 Copynumber: 5.3 Consensus size: 18
10185 TATCATATTA
10195 ATGTAAGTTATGT-A-TT
1 ATGTAAGTTATGTAAGTT
* *
10211 ATATAAGTTATTTAAGTT
1 ATGTAAGTTATGTAAGTT
*
10229 ATGTAAGTTGTGTAAGTT
1 ATGTAAGTTATGTAAGTT
* *
10247 ATGTATAATATTAACGTAAGTT
1 ATG--TAA-GTT-ATGTAAGTT
10269 ATGT-A-TTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
10285 ATGTA
1 ATGTA
10290 TAATATTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
16 23 0.37
17 3 0.05
18 20 0.32
19 1 0.02
20 4 0.06
21 2 0.03
22 10 0.16
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (18 bp):
ATGTAAGTTATGTAAGTT
Found at i:10268 original size:22 final size:21
Alignment explanation
Indices: 10240--10314 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
10230 TGTAAGTTGT
10240 GTAAGTTATGTATAATATTAA
1 GTAAGTTATGTATAATATTAA
10261 CGTAAGTTATGTAT--TA-T--
1 -GTAAGTTATGTATAATATTAA
10278 GTAAGTTATGTATAATATTAA
1 GTAAGTTATGTATAATATTAA
10299 TGTGATAGTTATGTAT
1 -GT-A-AGTTATGTAT
10315 TATGTTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
16 13 0.29
18 2 0.04
19 2 0.04
20 2 0.04
22 15 0.33
23 1 0.02
24 10 0.22
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.45
Consensus pattern (21 bp):
GTAAGTTATGTATAATATTAA
Found at i:10391 original size:69 final size:69
Alignment explanation
Indices: 10316--10453 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
10306 GTTATGTATT
* *
10316 ATGTTAATATTTAGAAAATAGCATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
1 ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAAT
10381 ATAG
66 ATAG
*
10385 ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTTTTGAAAAT
1 ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAAT
10450 ATAG
66 ATAG
10454 GTTACCATGA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (69 bp):
ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAAT
ATAG
Done.