Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1290
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: 20001
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Found at i:1593 original size:23 final size:23
Alignment explanation
Indices: 1552--1595 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1542 AATATATATA
*
1552 TATATATATAACATGTTAAATTT
1 TATATATATAACATCTTAAATTT
* *
1575 TATATATTTAATATCTTAAAT
1 TATATATATAACATCTTAAAT
1596 ATAATTATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATATATAACATCTTAAATTT
Found at i:2817 original size:5 final size:5
Alignment explanation
Indices: 2807--2839 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2797 CATAACTGGT
*
2807 TCTCC TCTCC TCTCC TCTCG TCTCC TCTCC TCT
1 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC TCT
2840 TGTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.55, G:0.03, T:0.42
Consensus pattern (5 bp):
TCTCC
Found at i:7521 original size:28 final size:28
Alignment explanation
Indices: 7440--7513 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
7430 GAAAATTAAT
7440 ACTGCTTCCATTTGAATAGCATCATAAA
1 ACTGCTTCCATTTGAATAGCATCATAAA
* *
7468 TCTGTTTCCATTTGAATAGCATCATAAA
1 ACTGCTTCCATTTGAATAGCATCATAAA
7496 ACTGCTTCCATTTGAATA
1 ACTGCTTCCATTTGAATA
7514 CTGTCATACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (28 bp):
ACTGCTTCCATTTGAATAGCATCATAAA
Found at i:9897 original size:21 final size:21
Alignment explanation
Indices: 9873--9913 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9863 TTTTAAAAAA
9873 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
9894 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
9914 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:11470 original size:13 final size:13
Alignment explanation
Indices: 11452--11477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11442 CAATTTTTTG
11452 TGTATCGATACAT
1 TGTATCGATACAT
11465 TGTATCGATACAT
1 TGTATCGATACAT
11478 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11542 original size:21 final size:21
Alignment explanation
Indices: 11516--11591 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
11506 CTGCCAAGAA
*
11516 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
11537 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
11557 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
11578 ATGTATCGATACAT
1 ATGTATCGATACAT
11592 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:11562 original size:20 final size:20
Alignment explanation
Indices: 11537--11609 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
11527 CATCTTTTTT
11537 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
11557 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
11578 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
11598 ATGTATCGATAC
1 ATGTATCGATAC
11610 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:11573 original size:41 final size:41
Alignment explanation
Indices: 11516--11609 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
11506 CTGCCAAGAA
*
11516 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
11557 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
11598 ATGTATCGATAC
1 ATGTATCGATAC
11610 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:14066 original size:13 final size:13
Alignment explanation
Indices: 14048--14112 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
14038 ATAATCACCC
*
14048 TGTATCGATACAG
1 TGTATCGATACAA
14061 TGTATCGATACAA
1 TGTATCGATACAA
*
14074 TGTATCGATACAG
1 TGTATCGATACAA
14087 TGTATCGATACAA
1 TGTATCGATACAA
14100 TGTATCGATACAA
1 TGTATCGATACAA
14113 AGAAAAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14077 original size:26 final size:26
Alignment explanation
Indices: 14048--14111 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
14038 ATAATCACCC
14048 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
14074 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
14100 TGTATCGATACA
1 TGTATCGATACA
14112 AAGAAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAA
Found at i:14123 original size:20 final size:20
Alignment explanation
Indices: 14098--14176 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
14088 GTATCGATAC
14098 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
14118 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
14143 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
14163 CATGTATCGATACA
1 AATGTATCGATACA
14177 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:16211 original size:15 final size:15
Alignment explanation
Indices: 16191--16221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16181 ATTTCGTTTG
*
16191 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
16206 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
16221 G
1 G
16222 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:18044 original size:20 final size:21
Alignment explanation
Indices: 18017--18061 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18007 AAGTTTTCAT
*
18017 TTTC-TTAGCTAAC-TCATTA
1 TTTCATTAGCCAACTTCATTA
*
18036 TTTCATTAGCCAACTTCTTTA
1 TTTCATTAGCCAACTTCATTA
18057 TTTCA
1 TTTCA
18062 ACTTGCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 8 0.36
21 10 0.45
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTCATTAGCCAACTTCATTA
Done.