Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1330
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: 36758
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Found at i:2373 original size:16 final size:16
Alignment explanation
Indices: 2352--2387 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2342 GACCATCTAA
2352 ACGATAGAATTTCTTC
1 ACGATAGAATTTCTTC
*
2368 ACGATAGGATTTCTTC
1 ACGATAGAATTTCTTC
2384 ACGA
1 ACGA
2388 AATTTTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (16 bp):
ACGATAGAATTTCTTC
Found at i:5723 original size:23 final size:23
Alignment explanation
Indices: 5697--5743 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5687 TATTTTGATG
5697 TCTAATGATAGAAGATGCATGTT
1 TCTAATGATAGAAGATGCATGTT
5720 TCTAATGATAGAAGATGCATGTT
1 TCTAATGATAGAAGATGCATGTT
5743 T
1 T
5744 GGTGTTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (23 bp):
TCTAATGATAGAAGATGCATGTT
Found at i:8584 original size:20 final size:22
Alignment explanation
Indices: 8543--8590 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
8533 AACAATGAAA
8543 GTCTGTCGTATGGCACAGTTTT
1 GTCTGTCGTATGGCACAGTTTT
*
8565 GTCTG-CGTAT-GCATAGTTTT
1 GTCTGTCGTATGGCACAGTTTT
8585 GTCTGT
1 GTCTGT
8591 TTTGCACGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 14 0.58
21 5 0.21
22 5 0.21
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (22 bp):
GTCTGTCGTATGGCACAGTTTT
Found at i:14085 original size:55 final size:55
Alignment explanation
Indices: 14014--14119 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
14004 ACATTAGGCA
*
14014 ACACTGACTTATTAACACGGCCATGGCACACACCCGTGCT-GCCTGCCCGTGGATG
1 ACACTGACTTATTAACACGGCCATGGCACACACCCGTG-TGGCCTACCCGTGGATG
* * * *
14069 ACACTGTCTTTTTAACACGGCCATGGCGCACGCCCGTGTGGCCTACCCGTG
1 ACACTGACTTATTAACACGGCCATGGCACACACCCGTGTGGCCTACCCGTG
14120 TACATCTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
54 1 0.02
55 44 0.98
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.22
Consensus pattern (55 bp):
ACACTGACTTATTAACACGGCCATGGCACACACCCGTGTGGCCTACCCGTGGATG
Found at i:20506 original size:22 final size:22
Alignment explanation
Indices: 20463--20509 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
20453 CACTAAGTCA
* *
20463 ACAAGACGACTCAATGTCGTAG
1 ACAAGAAGACTCAATCTCGTAG
20485 ACAAGAAGACTCAA-CTCTGTAG
1 ACAAGAAGACTCAATCTC-GTAG
20507 ACA
1 ACA
20510 GGTCGGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (22 bp):
ACAAGAAGACTCAATCTCGTAG
Found at i:23772 original size:27 final size:27
Alignment explanation
Indices: 23726--23777 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
23716 CAGTAACAGT
*
23726 TGGGCCTAACCCATTAACAGAATCAAA
1 TGGGCCTAACCCAGTAACAGAATCAAA
23753 TGGGCCTAAGCCCAGT-ACAGAATCA
1 TGGGCCTAA-CCCAGTAACAGAATCA
23778 GTATCAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (27 bp):
TGGGCCTAACCCAGTAACAGAATCAAA
Found at i:27202 original size:21 final size:22
Alignment explanation
Indices: 27157--27202 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
27147 ACTAAAATAA
* *
27157 ATAATAAAAAATAGTAATAATT
1 ATAATAAAAAATAGTAAGAAAT
27179 ATAA-AAAAAATAGTAAGAAAT
1 ATAATAAAAAATAGTAAGAAAT
27200 ATA
1 ATA
27203 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
ATAATAAAAAATAGTAAGAAAT
Found at i:30215 original size:31 final size:31
Alignment explanation
Indices: 30172--30234 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
30162 CTTTTCACAC
30172 TTCATATGTCATAACACTGAGCCGAAGCCTT
1 TTCATATGTCATAACACTGAGCCGAAGCCTT
* ** *
30203 TTCATATTTCATATTACTGGGCCGAAGCCTT
1 TTCATATGTCATAACACTGAGCCGAAGCCTT
30234 T
1 T
30235 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (31 bp):
TTCATATGTCATAACACTGAGCCGAAGCCTT
Found at i:30472 original size:24 final size:24
Alignment explanation
Indices: 30444--30520 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
30434 AGCCTATCCT
*
30444 CTTTTAATAACAGGGGCAAAAGCC
1 CTTTTAATAACTGGGGCAAAAGCC
*
30468 CTTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCAAAAGCC
* *
30492 CTTTTGATAATTGGGGCATAAA-CC
1 CTTTTAATAACTGGGGCA-AAAGCC
30516 CTTTT
1 CTTTT
30521 GCACTTCCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCAAAAGCC
Found at i:30595 original size:20 final size:20
Alignment explanation
Indices: 30570--30636 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
30560 TTATGAACAC
*
30570 ATCATGTGCATATCATTCAT
1 ATCATGTGCATATCATACAT
* *
30590 ATCATGTGCATAGCATACAC
1 ATCATGTGCATATCATACAT
*
30610 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
30630 ACCATGT
1 ATCATGT
30637 TTACTAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:30601 original size:11 final size:11
Alignment explanation
Indices: 30570--30601 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
30560 TTATGAACAC
30570 ATCATGTGCAT
1 ATCATGTGCAT
30581 ATCAT-T-CAT
1 ATCATGTGCAT
30590 ATCATGTGCAT
1 ATCATGTGCAT
30601 A
1 A
30602 GCATACACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.42
10 2 0.11
11 9 0.47
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Done.