Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1545
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: 24291
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:742 original size:19 final size:21
Alignment explanation
Indices: 718--758 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
708 ATCATATATT
*
718 AAATATAATTAT-A-ATAAAA
1 AAATATAAATATGACATAAAA
737 AAATATAAATATGACATAAAA
1 AAATATAAATATGACATAAAA
758 A
1 A
759 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 1 0.05
21 7 0.37
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATATAAATATGACATAAAA
Found at i:2551 original size:17 final size:18
Alignment explanation
Indices: 2530--2571 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2520 AAACTAACCA
2530 ATAATAT-TAATTTATTT
1 ATAATATATAATTTATTT
* *
2547 TTAAT-TATATTTTATTT
1 ATAATATATAATTTATTT
2564 ATAATATA
1 ATAATATA
2572 GAAATACAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.85
18 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATATATAATTTATTT
Found at i:2998 original size:21 final size:21
Alignment explanation
Indices: 2972--3011 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2962 AGTTGTTGTC
2972 ATTGTTGACTATCATTCACCA
1 ATTGTTGACTATCATTCACCA
*
2993 ATTGTTGACTATCCTTCAC
1 ATTGTTGACTATCATTCAC
3012 TAACCTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (21 bp):
ATTGTTGACTATCATTCACCA
Found at i:3067 original size:50 final size:50
Alignment explanation
Indices: 2992--3101 Score: 177
Period size: 50 Copynumber: 2.2 Consensus size: 50
2982 ATCATTCACC
* *
2992 AATTGTTGACTATCCTTCACTAACCTTTGACAATAGA-AGGAGGTGGCCAT
1 AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCAT
*
3042 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCAT
1 AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCAT
3092 AATTGTTGAC
1 AATTGTTGAC
3102 TCTAAGTATA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 55 0.98
51 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (50 bp):
AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCAT
Found at i:7567 original size:50 final size:50
Alignment explanation
Indices: 7498--7606 Score: 191
Period size: 50 Copynumber: 2.2 Consensus size: 50
7488 AGTTGTTGCC
*
7498 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
* *
7548 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
7598 ATTGTTGAC
1 ATTGTTGAC
7607 TCTAAGTATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (50 bp):
ATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:18121 original size:21 final size:20
Alignment explanation
Indices: 18095--18136 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
18085 TCATTTGAAC
*
18095 AATAAAATATTTTTTTAAAAA
1 AATAAAAT-TATTTTTAAAAA
*
18116 AATAAACTTATTTTTAAAAA
1 AATAAAATTATTTTTAAAAA
18136 A
1 A
18137 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAATTATTTTTAAAAA
Found at i:18498 original size:76 final size:76
Alignment explanation
Indices: 18367--18522 Score: 213
Period size: 76 Copynumber: 2.1 Consensus size: 76
18357 TGAAGTTTGA
* * * * * * *
18367 ATCATTATATGGGTGTTTCCGTTGTCGCCTCTTTGGATCTGGACCATGCATCTTGAAATAATACC
1 ATCATTACACGGGTGTTGCCATTGTCGCATCTCTGGATCTGGACCATGCACCTTGAAATAATACC
*
18432 CACTTTTATTC
66 CACTTTTATCC
* * *
18443 ATCATTACACGGGTGTTGCCATTGTTGCATCTCTGGGTCTGGACCATGCACCTTGAAATGATACC
1 ATCATTACACGGGTGTTGCCATTGTCGCATCTCTGGATCTGGACCATGCACCTTGAAATAATACC
18508 CACTTTTATCC
66 CACTTTTATCC
18519 ATCA
1 ATCA
18523 GCACTAGTAG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (76 bp):
ATCATTACACGGGTGTTGCCATTGTCGCATCTCTGGATCTGGACCATGCACCTTGAAATAATACC
CACTTTTATCC
Found at i:18788 original size:2 final size:2
Alignment explanation
Indices: 18781--18813 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18771 CCAACCAACC
18781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18814 CAGTTCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20801 original size:18 final size:20
Alignment explanation
Indices: 20778--20818 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
20768 ATGAATATTG
20778 AAATTTATTT-TATTTTA-A
1 AAATTTATTTGTATTTTATA
20796 AAATTTATTTGTATTTTATA
1 AAATTTATTTGTATTTTATA
20816 AAA
1 AAA
20819 GTTTTATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 7 0.33
20 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTTATTTGTATTTTATA
Found at i:23023 original size:6 final size:6
Alignment explanation
Indices: 23012--23106 Score: 97
Period size: 6 Copynumber: 15.5 Consensus size: 6
23002 ATTCGTAATC
* *
23012 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAT AT-TTA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
23059 ATATAA TTATATTAA AT-T-T ATATCAA ATATAA ATAATAA ATATAA ATA
1 ATATAA --ATA-TAA ATATAA ATAT-AA ATATAA AT-ATAA ATATAA ATA
23107 AAAAAAATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
4 2 0.03
5 5 0.07
6 50 0.67
7 12 0.16
8 3 0.04
9 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Done.