Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1815
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: 22391
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Found at i:1810 original size:79 final size:81
Alignment explanation
Indices: 1686--1869 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
1676 GCTACTCGTT
* *
1686 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
1749 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
1765 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
1828 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
1845 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1870 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:1869 original size:40 final size:40
Alignment explanation
Indices: 1667--1869 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
1657 CGGAATTTAA
** *
1667 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1707 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
1746 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1785 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1825 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1865 CCGGA
1 CCGGA
1870 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:8382 original size:100 final size:100
Alignment explanation
Indices: 8204--8405 Score: 370
Period size: 100 Copynumber: 2.0 Consensus size: 100
8194 TGTATAGCTA
*
8204 GACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCTGATACCAATCAAATGTAA
1 GACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGATCTGATACCAATCAAATGTAA
*
8269 CACCCCGAACCGAGACCGTCACCGGAGTCGAACAC
66 CACCCCGAACCGAGACCGACACCGGAGTCGAACAC
8304 GACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGATCTGATACCAATCAAATGTAA
1 GACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGATCTGATACCAATCAAATGTAA
8369 CA-CCCGAACCCGAGACCGACACCGGAGTCGAACAC
66 CACCCCGAA-CCGAGACCGACACCGGAGTCGAACAC
8404 GA
1 GA
8406 GGTGTTAACG
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
99 6 0.06
100 93 0.94
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.15
Consensus pattern (100 bp):
GACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGATCTGATACCAATCAAATGTAA
CACCCCGAACCGAGACCGACACCGGAGTCGAACAC
Found at i:9835 original size:79 final size:81
Alignment explanation
Indices: 9724--9906 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
9714 AGCTCTCGTT
* **
9724 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
9788 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
9804 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
9867 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
9884 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
9907 GACATCATTC
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
78 3 0.03
79 54 0.61
80 32 0.36
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:9908 original size:40 final size:40
Alignment explanation
Indices: 9724--9908 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
9714 AGCTCTCGTT
* *
9724 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9764 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9804 CAAATGCCTTCGGG-CTTAGCCCAGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
9843 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
9884 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9909 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 79 0.64
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:13538 original size:39 final size:40
Alignment explanation
Indices: 13375--13666 Score: 413
Period size: 39 Copynumber: 7.5 Consensus size: 40
13365 AAACCAAGTA
* * *
13375 CCTTC-GGATTTAG-CCAGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
13413 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
13453 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAGAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13493 CC-TCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13531 CCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
13570 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA-G
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** * * *
13609 CCTTCGGGGTTTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
13649 -CTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
13667 TTATCATCCG
Statistics
Matches: 231, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
38 39 0.17
39 101 0.44
40 91 0.39
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:15315 original size:40 final size:40
Alignment explanation
Indices: 15232--15455 Score: 337
Period size: 40 Copynumber: 5.6 Consensus size: 40
15222 ATTCCAAAAC
* * * *
15232 CAAATACCTTCGGGATTTAG-CCAGATATAGCT-ACTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAG-TAACTCGCA
*
15271 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
15311 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
15351 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
15391 CAAATGCCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
15431 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
15456 TTATCATCCG
Statistics
Matches: 172, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 20 0.12
40 152 0.88
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:18314 original size:47 final size:47
Alignment explanation
Indices: 18245--18506 Score: 479
Period size: 47 Copynumber: 5.6 Consensus size: 47
18235 CCCTTCGGGA
* *
18245 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18292 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18339 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18386 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18433 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
18480 CTGATCACATATATACACTTTCGCATT
1 CTTATCACATATATACACTTTCACATT
18507 TATTCAAATA
Statistics
Matches: 209, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 209 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20012 original size:13 final size:13
Alignment explanation
Indices: 19994--20018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19984 TACTAAATTT
19994 TCATGGATTCAAA
1 TCATGGATTCAAA
20007 TCATGGATTCAA
1 TCATGGATTCAA
20019 TATACCATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:22036 original size:38 final size:39
Alignment explanation
Indices: 21931--22053 Score: 182
Period size: 39 Copynumber: 3.2 Consensus size: 39
21921 ATATGGGAGA
*
21931 TAAGTTCCGAAGAACATTCGTGCTAGTGATGTATCCGG-C
1 TAAGTT-CGAAGAGCATTCGTGCTAGTGATGTATCCGGAC
21970 TTAAGTTCTGAAGAG-ATTCGTGCTAGTGATGTATCCGGAC
1 -TAAGTTC-GAAGAGCATTCGTGCTAGTGATGTATCCGGAC
22010 TAAGTTCGAAGAGCATTCGTGC-AGTGATGTAT-CGGAC
1 TAAGTTCGAAGAGCATTCGTGCTAGTGATGTATCCGGAC
22047 TAAGTTC
1 TAAGTTC
22054 CGAGAGATAT
Statistics
Matches: 79, Mismatches: 1, Indels: 9
0.89 0.01 0.10
Matches are distributed among these distances:
37 12 0.15
38 16 0.20
39 39 0.49
40 12 0.15
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (39 bp):
TAAGTTCGAAGAGCATTCGTGCTAGTGATGTATCCGGAC
Done.