Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2087
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: 44086
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1378 original size:39 final size:40
Alignment explanation
Indices: 1301--1447 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
1291 TAGCTCCTCG
* * *
1301 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
1341 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
1380 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
1420 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
1448 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:1458 original size:80 final size:80
Alignment explanation
Indices: 1347--1527 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
1337 CTCATTCAAT
* * *
1347 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
1410 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
1426 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
1490 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
1507 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
1528 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:1487 original size:40 final size:40
Alignment explanation
Indices: 1344--1527 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
1334 TAACTCATTC
* *
1344 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
1384 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
1424 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
1464 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
1505 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1528 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:9242 original size:39 final size:40
Alignment explanation
Indices: 9165--9311 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
9155 TAGCTCCTCG
* * *
9165 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
9205 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
9244 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
9284 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
9312 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:9322 original size:80 final size:80
Alignment explanation
Indices: 9211--9391 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
9201 CTCATTCAAT
* * *
9211 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
9274 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
9290 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
9354 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
9371 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
9392 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:9351 original size:40 final size:40
Alignment explanation
Indices: 9208--9391 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9198 TAACTCATTC
* *
9208 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
9248 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
9288 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
9328 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
9369 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9392 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:11704 original size:58 final size:57
Alignment explanation
Indices: 11557--11704 Score: 156
Period size: 57 Copynumber: 2.6 Consensus size: 57
11547 CGTATAACAA
* * *
11557 GATTACCAGTCTAGGCTAAATCCTTTATATAACGTAAGCTCAGAGAAGCTCGATTAG
1 GATTACCAGTCCAGGCTAAATCCTTTCTATAACGTAAGCTCAGAGAAGCTAGATTAG
* * * * * *
11614 GATTACTAGTCCAGGCTAAACCCTAATC-ATAACGTATGCTC-GAGAAGTATTATATTAG
1 GATTACCAGTCCAGGCTAAATCCT-TTCTATAACGTAAGCTCAGAGAAG--CTAGATTAG
* *
11672 GATTACCCGTCCAGGCTATATCCTTTCTATAAC
1 GATTACCAGTCCAGGCTAAATCCTTTCTATAAC
11705 AAGGTCAATA
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
56 6 0.08
57 35 0.48
58 32 0.44
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (57 bp):
GATTACCAGTCCAGGCTAAATCCTTTCTATAACGTAAGCTCAGAGAAGCTAGATTAG
Found at i:25926 original size:6 final size:6
Alignment explanation
Indices: 25915--25941 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25905 ATTACGTTTC
25915 TCCATG TCCATG TCCATG TCCATG TCC
1 TCCATG TCCATG TCCATG TCCATG TCC
25942 GTATCCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (6 bp):
TCCATG
Found at i:31259 original size:24 final size:23
Alignment explanation
Indices: 31211--31261 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
31201 GCAAGAACTA
*
31211 TATAACAGGATGCTCGTAAGGGC
1 TATAACAGGATGCTCGTAAGAGC
**
31234 TATAACAGGATTGCTCGTCTGAGC
1 TATAACAGGA-TGCTCGTAAGAGC
31258 TATA
1 TATA
31262 TTTTGTCCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (23 bp):
TATAACAGGATGCTCGTAAGAGC
Found at i:34680 original size:40 final size:40
Alignment explanation
Indices: 34618--34875 Score: 351
Period size: 40 Copynumber: 6.5 Consensus size: 40
34608 AAGCCAAGTA
* * * * *
34618 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
34657 CCTTCGGGACATAGCCCGGATATAGTAACTCACACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
34697 CCTTCGGGACTTATCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
34737 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
34777 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
34817 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
34857 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
34876 TTATCATCCA
Statistics
Matches: 197, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.07
40 184 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39323 original size:26 final size:28
Alignment explanation
Indices: 39292--39344 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
39282 AACTCTTGCA
39292 AACTGAGC-TTCAACTC-TTTAACTCGC
1 AACTGAGCTTTCAACTCTTTTAACTCGC
39318 AACTGAGCTTTCAACTCTTTTAACTCG
1 AACTGAGCTTTCAACTCTTTTAACTCG
39345 GTTGGTGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 8 0.32
27 8 0.32
28 9 0.36
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (28 bp):
AACTGAGCTTTCAACTCTTTTAACTCGC
Found at i:42782 original size:39 final size:40
Alignment explanation
Indices: 42704--42880 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
42694 AAGCCAAGTA
* * * *
42704 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
42743 CCTTCGGGACATAGCCCGGATATAGTAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42782 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
42822 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
42862 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42881 TTATCATCCA
Statistics
Matches: 126, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
39 51 0.40
40 75 0.60
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42837 original size:79 final size:79
Alignment explanation
Indices: 42704--42880 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 79
42694 AAGCCAAGTA
* * * *
42704 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGATA-TA
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGA-ACTA
42767 GTAACT-CGCACAATG
65 GTAACTACGCA-AATG
*
42782 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAACTA
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAGCCCGGAACTA
*
42846 GTCACTAGCGCAAATG
65 GTAACTA-CGCAAATG
42862 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42881 TTATCATCCA
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
78 14 0.16
79 47 0.53
80 23 0.26
81 4 0.05
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGAACTAG
TAACTACGCAAATG
Done.