Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1805
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: 11503
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Found at i:223 original size:19 final size:20
Alignment explanation
Indices: 171--226 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
161 TTTTCACAAT
*
171 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTCCA
*
191 TTATATCGATACATTGTCCA
1 TTGTATCGATACATTGTCCA
211 TTGTATC-ATACATTGT
1 TTGTATCGATACATTGT
227 ATCGATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGTCCA
Found at i:226 original size:12 final size:13
Alignment explanation
Indices: 209--237 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
199 ATACATTGTC
209 CATTGTATC-ATA
1 CATTGTATCGATA
221 CATTGTATCGATA
1 CATTGTATCGATA
234 CATT
1 CATT
238 CTGGGTTTAC
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:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:299 original size:20 final size:20
Alignment explanation
Indices: 252--306 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
242 GTTTACCCAG
* * *
252 ATGTATCAATACATTTTGCA
1 ATGTATCGATATATTTTACA
*
272 TTGTATCGATATATTTTACA
1 ATGTATCGATATATTTTACA
292 ATGTATCGATATATT
1 ATGTATCGATATATT
307 CAGGCATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (20 bp):
ATGTATCGATATATTTTACA
Found at i:1534 original size:20 final size:20
Alignment explanation
Indices: 1486--1534 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1476 CATGTTGTTT
1486 TGTGCCAACATGCTTATTTA
1 TGTGCCAACATGCTTATTTA
* *
1506 TGTTGCCAAGATGCTTATTTG
1 TG-TGCCAACATGCTTATTTA
1527 TGTGCCAA
1 TGTGCCAA
1535 AATCAGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTGCCAACATGCTTATTTA
Found at i:2658 original size:28 final size:28
Alignment explanation
Indices: 2625--2696 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
2615 TTTCACAACT
* **
2625 GGGGATACTCCAA-CCTCGTTATTTCATC
1 GGGGATACTCTAACCCT-GTTATTTCAGA
*
2653 GGGGATACTCTAACCCTGTTATTTCCGA
1 GGGGATACTCTAACCCTGTTATTTCAGA
2681 GGGGATACTCTAACCC
1 GGGGATACTCTAACCC
2697 CGGCTTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (28 bp):
GGGGATACTCTAACCCTGTTATTTCAGA
Found at i:2769 original size:28 final size:27
Alignment explanation
Indices: 2729--2805 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 27
2719 ATTTTTCATA
*
2729 ATCG-GGGGTACTCCAACCCCGTTATGT
1 ATCGAGGGATACTCCAACCCCGTTAT-T
*
2756 CATCGA-GGATACTCCAATCCCGTTATT
1 -ATCGAGGGATACTCCAACCCCGTTATT
*
2783 TTCGAGGGGATACTCCAACCCCG
1 ATCGA-GGGATACTCCAACCCCG
2806 ATTTTATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 4 0.10
27 1 0.02
28 37 0.88
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (27 bp):
ATCGAGGGATACTCCAACCCCGTTATT
Found at i:2803 original size:107 final size:107
Alignment explanation
Indices: 2611--2852 Score: 317
Period size: 107 Copynumber: 2.3 Consensus size: 107
2601 TAAATTTCTA
* * * *
2611 AATTTTTCACAA-CTGGGGATACTCCAACCTCGTTATTTCATCGGGGATACTCTAACCCTGTTAT
1 AATTTTTCACAATC-GGGGATACTCCAACCCCGTTATGTCATCGAGGATACTCCAACCCTGTTAT
* * **
2675 TTCCGAGGGGATACTCTAACCCCGGCTTTATATCTAAAATATT
65 TTCCGAGGGGATACTCCAACCCCGACTTTATATCTAAAATACC
* * *
2718 GATTTTTCATAATCGGGGGTACTCCAACCCCGTTATGTCATCGAGGATACTCCAATCCC-GTTAT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATGTCATCGAGGATACTCCAA-CCCTGTTAT
* * *
2782 TTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAATACC
65 TTCCGAGGGGATACTCCAACCCCGACTTTATATCTAAAATACC
*
2825 AATTTTCCACAATCGGGGATACTCCAAC
1 AATTTTTCACAATCGGGGATACTCCAAC
2853 TCCGATTTTA
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
107 111 0.97
108 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (107 bp):
AATTTTTCACAATCGGGGATACTCCAACCCCGTTATGTCATCGAGGATACTCCAACCCTGTTATT
TCCGAGGGGATACTCCAACCCCGACTTTATATCTAAAATACC
Found at i:2851 original size:51 final size:51
Alignment explanation
Indices: 2788--2951 Score: 206
Period size: 51 Copynumber: 3.2 Consensus size: 51
2778 TTATTTTCGA
*
2788 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATC
* *
2839 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTC-CACAATC
*** * * * *
2890 -GGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCGATTTTCCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATC
*
2940 GGAGATACTCCA
1 GGGGATACTCCA
2952 GCCCTGTTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
50 40 0.41
51 57 0.59
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATC
Found at i:7363 original size:20 final size:21
Alignment explanation
Indices: 7338--7382 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
7328 TACTTCTATC
7338 GATACTTTGAA-GCATGTATT
1 GATACTTTGAAGGCATGTATT
* *
7358 GATACTTTTAAGGCTTGTATT
1 GATACTTTGAAGGCATGTATT
7379 GATA
1 GATA
7383 TAGTAGCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (21 bp):
GATACTTTGAAGGCATGTATT
Found at i:7537 original size:19 final size:17
Alignment explanation
Indices: 7486--7539 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
7476 TATCTGATGG
7486 ATTTGTATCGATACACT
1 ATTTGTATCGATACACT
*
7503 AGCTTGTGTATTGATACATTCT
1 A--TT-TGTATCGATACA--CT
7525 ATTTGTATCGATACA
1 ATTTGTATCGATACA
7540 ACCATGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 1 0.03
19 13 0.43
20 13 0.43
22 3 0.10
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (17 bp):
ATTTGTATCGATACACT
Done.