Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1258
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: 5193
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Found at i:347 original size:25 final size:25
Alignment explanation
Indices: 319--387 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
309 GATTATTCAT
319 ATTTAATATTTATAATTAATAAAAA
1 ATTTAATATTTATAATTAATAAAAA
* ** * * *
344 ATTTAAAATTTATTTTTTATTAATA
1 ATTTAATATTTATAATTAATAAAAA
369 A-TTATATATTTATAATTAA
1 ATTTA-ATATTTATAATTAA
388 ATTTAAATAA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
24 3 0.09
25 30 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAATATTTATAATTAATAAAAA
Found at i:1290 original size:3 final size:3
Alignment explanation
Indices: 1284--1321 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1274 CATCATCATC
*
1284 ATA ATA ATA ATA TATA ACA ATA ATA AT- ATA ATA ATA AT
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT
1322 TGAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2289 original size:82 final size:82
Alignment explanation
Indices: 2177--2408 Score: 371
Period size: 79 Copynumber: 2.9 Consensus size: 82
2167 ATCCATCCCC
** *
2177 ATATATATACATGTATGTATATGTAAGCATGTAGATCATATCTTCACAATCTTCAACAAATCTTG
1 ATATATATTTATGTATGTATATGTAAGCATGTAGATCATATCTTCACAATCTTCAACAAATCTTC
2242 TTAAAAAATATATATAT
66 TTAAAAAATATATATAT
* *
2259 ATATATATTTATGTATGTATATGCAGGCATGTAGATCATATCTTCACAATCTTCAACAAATCTTC
1 ATATATATTTATGTATGTATATGTAAGCATGTAGATCATATCTTCACAATCTTCAACAAATCTTC
*
2324 TT---ATATATATATAT
66 TTAAAAAATATATATAT
* *
2338 ATATATATTTATGTATGTATATGTAAGCGTGTAGATCATATCTTCAGAATCTTCAACAAATCTTC
1 ATATATATTTATGTATGTATATGTAAGCATGTAGATCATATCTTCACAATCTTCAACAAATCTTC
2403 TTAAAA
66 TTAAAA
2409 TCATAAAACA
Statistics
Matches: 137, Mismatches: 10, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
79 74 0.54
82 63 0.46
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (82 bp):
ATATATATTTATGTATGTATATGTAAGCATGTAGATCATATCTTCACAATCTTCAACAAATCTTC
TTAAAAAATATATATAT
Found at i:3293 original size:21 final size:20
Alignment explanation
Indices: 3267--3307 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3257 ATTTAAAAGT
3267 TATTTTT-TATATTAATATTTA
1 TATTTTTCTA-ATTAA-ATTTA
3288 TATTTTTCTAATTAAATTTA
1 TATTTTTCTAATTAAATTTA
3308 AATAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 12 0.63
22 2 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTCTAATTAAATTTA
Found at i:4489 original size:2 final size:2
Alignment explanation
Indices: 4482--4526 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4472 ATAACATGTT
4482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4524 TA T
1 TA T
4527 TAAATTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4946 original size:22 final size:22
Alignment explanation
Indices: 4921--4999 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
4911 TATTTATTTA
4921 TATATTTAAATTTTTATTAATT
1 TATATTTAAATTTTTATTAATT
* * *
4943 TATATAT-ATTTTTTAAAAATAATT
1 TATATTTAAATTTTT---ATTAATT
*
4967 TATA-TTAAATATTTAATTAATT
1 TATATTTAAAT-TTTTATTAATT
*
4989 TAAATTTAAAT
1 TATATTTAAAT
5000 AAATATTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
21 6 0.14
22 15 0.35
23 7 0.16
24 12 0.28
25 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATTTAAATTTTTATTAATT
Found at i:5015 original size:27 final size:29
Alignment explanation
Indices: 4963--5021 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
4953 TTTTAAAAAT
* **
4963 AATTTATATTAAATATTTAATTAATT-TA
1 AATTTATAATAAATATTTAAAAAATTATA
4991 AATTTA-AATAAATATTTAAAAAATTATA
1 AATTTATAATAAATATTTAAAAAATTATA
5019 AAT
1 AAT
5022 ATCCAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTATAATAAATATTTAAAAAATTATA
Done.