Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold602
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: 35920
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:9662 original size:44 final size:44
Alignment explanation
Indices: 9595--10225 Score: 441
Period size: 44 Copynumber: 13.8 Consensus size: 44
9585 GAAAAATTTC
* * *
9595 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* * *
9639 AGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* * ** *
9683 TA-ATCCTATCTCTCTGAAGTTACAGTGGAGCGGATT-AAAATAA
1 -AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
*
9726 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAG
1 A-GATCTTATCTCTCTGAAGTTACAGT-G-G-AG-------CAGATTGAAGCTAG
* * ** ** **
9781 AGATCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAAAATTTC
1 AGATCTTATCTCTCTGAAG-TTACAGTGGAGCAGATTG--AAGCTAG
* * *
9827 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* * *
9871 AGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* * ** *
9915 TA-ATCCTATCTCTCTGAAGTTACAGTGGAGCGGATT-AAAATAA
1 -AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
*
9958 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAG
1 A-GATCTTATCTCTCTGAAGTTACAGT-G-G-AG-------CAGATTGAAGCTAG
* * ** ** **
10013 AGATCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAAAATTTC
1 AGATCTTATCTCTCTGAAG-TTACAGTGGAGCAGATTG--AAGCTAG
* * *
10059 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* * *
10103 AGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* * ** *
10147 TA-ATCCTATCTCTCTGAAGTTACAGTGGAGCGGATT-AAAATAA
1 -AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
* *
10190 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 A-GATCTTATCTCTCTGAAGTTACAGTGGAGCAGAT
10226 CACATCAGAT
Statistics
Matches: 454, Mismatches: 94, Indels: 78
0.73 0.15 0.12
Matches are distributed among these distances:
42 3 0.01
43 12 0.03
44 290 0.64
45 5 0.01
46 68 0.15
47 6 0.01
51 2 0.00
52 2 0.00
53 6 0.01
54 52 0.11
55 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGCTAG
Found at i:9958 original size:232 final size:232
Alignment explanation
Indices: 9552--10285 Score: 1407
Period size: 232 Copynumber: 3.2 Consensus size: 232
9542 ATTATACAGG
**
9552 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
9617 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
66 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
9682 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
131 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
9747 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
196 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
9784 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
9849 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
66 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
9914 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
131 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
9979 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
196 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
10016 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
10081 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
66 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
10146 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
131 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
10211 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
196 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
* * *
10248 TCTTATCTCCCAGATG-TTGCAGTGGAACAGACTGAAAA
1 TCTTATCTCCCTGA-GATTACAGTGGAACAGACCGAAAA
10286 CATAAATTTC
Statistics
Matches: 496, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
232 495 1.00
233 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (232 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
Found at i:11947 original size:3 final size:3
Alignment explanation
Indices: 11939--11967 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11929 GATTTAGTCC
11939 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
11968 CCTATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14372 original size:16 final size:16
Alignment explanation
Indices: 14341--14377 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
14331 ATGTGAAGAA
14341 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
14357 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
14373 TATTA
1 TATTA
14378 AAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:18517 original size:26 final size:26
Alignment explanation
Indices: 18487--18537 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
18477 ATGTTCATGC
*
18487 TATTTTTTCAT-ATATTTAAAATATTA
1 TATTTTTT-ATAAAATTTAAAATATTA
*
18513 TATTTTTTATAAAATTTAACATATT
1 TATTTTTTATAAAATTTAAAATATT
18538 GATTATTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTTTTATAAAATTTAAAATATTA
Found at i:22278 original size:3 final size:3
Alignment explanation
Indices: 22270--22303 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
22260 ATCAAGATAA
22270 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
22304 GATGAATGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.