Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2130
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: 25167
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:3422 original size:40 final size:40
Alignment explanation
Indices: 3335--3555 Score: 247
Period size: 40 Copynumber: 5.6 Consensus size: 40
3325 TATTCAGATG
* * *
3335 ATATCCGGGCTAAGTCCTGAAGGCA-TGGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
3374 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
* *
3414 ATACCCGGGCTAAGTCCCGAAGGC-GTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCTA-TTGACT
* ** *
3454 ATATCCTGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
* * *
3494 ATATCCGGGCTAAGACCCGAAGG-TGTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCTA-TTGACT
*
3534 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
3556 TACTTGGGTT
Statistics
Matches: 158, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
39 42 0.27
40 111 0.70
41 5 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
Found at i:3471 original size:80 final size:79
Alignment explanation
Indices: 3339--3555 Score: 294
Period size: 80 Copynumber: 2.7 Consensus size: 79
3329 CAGATGATAT
* * * *
3339 CCGGGCTAAGTCCTGAAGGC-ATGGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGGCAGTT
1 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTG-CTATATCC-GGCTAAGTCCCGAAGGCAGTT
*
3402 GTGCTATTGACTATAC
64 GTGCTAGTGACTATAC
**
3418 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCTGGCTAAGTCCCGAAGGCTTTTG
1 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCC-GGCTAAGTCCCGAAGGCAGTTG
*
3483 TGCTAGTGACTATAT
65 TGCTAGTGACTATAC
* * *
3498 CCGGGCTAAGACCCGAAGGTGTTTGTGCGAGTTGCTATATCCGGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGCTAAGTCCCGAAGG
3556 TACTTGGGTT
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
79 34 0.27
80 88 0.71
81 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGCTAAGTCCCGAAGGCAGTTGT
GCTAGTGACTATAC
Found at i:6033 original size:40 final size:40
Alignment explanation
Indices: 5956--6133 Score: 272
Period size: 40 Copynumber: 4.5 Consensus size: 40
5946 AAACCAAGTA
* * *
5956 CCTTC-GGAGCTTAG-CCGGATATAGCT-ACTAGCTCAAATG
1 CCTTCGGGA-CTTAGCCCGGTTATAG-TAACTCGCACAAATG
5995 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
6035 CCTTCGGGACTTAGCCCGGTGATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
6075 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAAAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
6115 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
6134 GTATCAATTC
Statistics
Matches: 130, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
39 11 0.08
40 119 0.92
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:17853 original size:12 final size:12
Alignment explanation
Indices: 17836--17861 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17826 AGCTTGTGAA
17836 AATACTAATAAT
1 AATACTAATAAT
17848 AATACTAATAAT
1 AATACTAATAAT
17860 AA
1 AA
17862 ATAAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AATACTAATAAT
Found at i:18250 original size:12 final size:13
Alignment explanation
Indices: 18235--18263 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18225 GGTTTAAATG
18235 TTTATTTTT-ATT
1 TTTATTTTTAATT
18247 TTTATTTTTAATT
1 TTTATTTTTAATT
18260 TTTA
1 TTTA
18264 ATTGATTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTAATT
Found at i:22381 original size:18 final size:20
Alignment explanation
Indices: 22360--22400 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
22350 TCAACAATTT
22360 AAAAAAAT-AT-GAAATATA
1 AAAAAAATCATAGAAATATA
*
22378 AAAAAAATCATAGAAATTTA
1 AAAAAAATCATAGAAATATA
22398 AAA
1 AAA
22401 CATGACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAAAATCATAGAAATATA
Done.