Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold520
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: 27428
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:1581 original size:94 final size:93
Alignment explanation
Indices: 1452--1623 Score: 265
Period size: 94 Copynumber: 1.8 Consensus size: 93
1442 GCCCCTAAGT
* * *
1452 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAG-TAAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTTAAACTC-GACTCAACTCA
1516 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
* * *
1545 GAACTCGGACTCAACCTCAACGAGTTCAGACATTCGCATCCATAAGTTGAACTCGACTCAACTCA
1 GAACTCAGACTCAA-CTCAACGAGCTCAGACATTCGCATCCATAAGTTAAACTCGACTCAACTCA
1610 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
1624 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
93 13 0.18
94 52 0.73
95 6 0.08
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTTAAACTCGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:10338 original size:40 final size:39
Alignment explanation
Indices: 10240--10462 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
10230 TCCTCGTTCA
* * * *
10240 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
10279 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
**
10318 GAATGCCTTCGGGACTTAACCCGGATTTAGTGTCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
10358 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
10398 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
10439 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
10463 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 40 0.26
40 103 0.66
41 12 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:10471 original size:41 final size:41
Alignment explanation
Indices: 10394--10471 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
10384 TTTGTATCTC
* * *
10394 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
10435 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
10472 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:12222 original size:46 final size:46
Alignment explanation
Indices: 12155--12280 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
12145 AACCCGCCCC
* * * *
12155 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
12201 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
12247 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12281 TGCTCAACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:12299 original size:46 final size:45
Alignment explanation
Indices: 12157--12299 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
12147 CCCGCCCCTA
* * ** * *
12157 AGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
*** *
12202 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
12248 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCT
12295 AGTGA
1 AGTGA
12300 CATGTCACTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
46 81 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCT
Found at i:17251 original size:27 final size:27
Alignment explanation
Indices: 17221--17398 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
17211 ATATTGAGTC
* * * *
17221 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
17248 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17275 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
17303 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
17330 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
17357 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17384 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17399 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:17360 original size:82 final size:81
Alignment explanation
Indices: 17242--17397 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
17232 TGCTATATAA
* *
17242 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
17307 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17324 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17388 CACTTAGTGC
65 CACTTAGTGC
17398 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:25244 original size:27 final size:27
Alignment explanation
Indices: 25214--25391 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
25204 ATATTGAGTC
* * * *
25214 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
25241 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
25268 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
25296 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
25323 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
25350 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
25377 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25392 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:25353 original size:82 final size:81
Alignment explanation
Indices: 25235--25390 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
25225 TGCTATATAA
* *
25235 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
25300 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
25317 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
25381 CACTTAGTGC
65 CACTTAGTGC
25391 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.