Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1585
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: 26276
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1539 original size:13 final size:13
Alignment explanation
Indices: 1521--1546 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1511 CAATTTTTTG
1521 TGTATCGATACAT
1 TGTATCGATACAT
1534 TGTATCGATACAT
1 TGTATCGATACAT
1547 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:1611 original size:21 final size:21
Alignment explanation
Indices: 1585--1660 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1575 CTGCCAAGAA
*
1585 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1606 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1626 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1647 ATGTATCGATACAT
1 ATGTATCGATACAT
1661 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:1631 original size:20 final size:20
Alignment explanation
Indices: 1606--1678 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1596 CATCTTTTTT
1606 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1626 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1647 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1667 ATGTATCGATAC
1 ATGTATCGATAC
1679 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:1642 original size:41 final size:41
Alignment explanation
Indices: 1585--1678 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1575 CTGCCAAGAA
*
1585 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1626 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1667 ATGTATCGATAC
1 ATGTATCGATAC
1679 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:4134 original size:13 final size:13
Alignment explanation
Indices: 4116--4154 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4106 ATAATCACCC
*
4116 TGTATCGATACAG
1 TGTATCGATACAA
4129 TGTATCGATACAA
1 TGTATCGATACAA
4142 TGTATCGATACAA
1 TGTATCGATACAA
4155 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4165 original size:20 final size:20
Alignment explanation
Indices: 4140--4218 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
4130 GTATCGATAC
4140 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
4160 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
4185 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
4205 CATGTATCGATACA
1 AATGTATCGATACA
4219 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:6253 original size:15 final size:15
Alignment explanation
Indices: 6233--6263 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6223 ATTTCGTTTG
*
6233 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
6248 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
6263 G
1 G
6264 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:10338 original size:13 final size:13
Alignment explanation
Indices: 10320--10345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10310 CAATTTTTTG
10320 TGTATCGATACAT
1 TGTATCGATACAT
10333 TGTATCGATACAT
1 TGTATCGATACAT
10346 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:10410 original size:21 final size:21
Alignment explanation
Indices: 10384--10459 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
10374 CTGCCAAGAA
*
10384 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
10405 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
10425 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
10446 ATGTATCGATACAT
1 ATGTATCGATACAT
10460 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:10430 original size:20 final size:20
Alignment explanation
Indices: 10405--10477 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
10395 CATCTTTTTT
10405 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
10425 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
10446 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
10466 ATGTATCGATAC
1 ATGTATCGATAC
10478 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:10441 original size:41 final size:41
Alignment explanation
Indices: 10384--10477 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
10374 CTGCCAAGAA
*
10384 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
10425 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
10466 ATGTATCGATAC
1 ATGTATCGATAC
10478 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:12229 original size:20 final size:20
Alignment explanation
Indices: 12204--12253 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
12194 CATGGTCCAA
12204 TATCGATACATTTCA-AGATG
1 TATCGATACA-TTCACAGATG
**
12224 TATCGATACATTCACTTATG
1 TATCGATACATTCACAGATG
12244 TATCGATACA
1 TATCGATACA
12254 GTAACTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (20 bp):
TATCGATACATTCACAGATG
Found at i:12260 original size:20 final size:20
Alignment explanation
Indices: 12221--12267 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
12211 ACATTTCAAG
* *
12221 ATGTATCGATACATTCACTT
1 ATGTATCGATACAGTAACTT
12241 ATGTATCGATACAGTAACTT
1 ATGTATCGATACAGTAACTT
12261 ATTGTAT
1 A-TGTAT
12268 TTATACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAGTAACTT
Found at i:21937 original size:20 final size:20
Alignment explanation
Indices: 21912--21965 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
21902 ATTTAAAGCA
21912 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
**
21932 ATGTATTAATACAATGTGCC
1 ATGTATCGATACAATGTGCC
21952 ATGTATCGATACAA
1 ATGTATCGATACAA
21966 ACAGTGGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 26 0.93
21 1 0.04
22 1 0.04
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:22019 original size:20 final size:20
Alignment explanation
Indices: 21994--22051 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
21984 TTGCCAGTTT
*
21994 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
22014 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
*
22033 CATGTATCAATAC-ATTGTA
1 CATGTATCGATACAATTGTA
22052 TCGATACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
20 15 0.45
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:22057 original size:32 final size:33
Alignment explanation
Indices: 22016--22080 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22006 CAATTGTCCA
*
22016 TGTATCGATACAATG-A-ACATGTATCAATACAT
1 TGTATCGATACAAAGCATA-ATGTATCAATACAT
22048 TGTATCGATACAAAGCATAATGTATCAATACAT
1 TGTATCGATACAAAGCATAATGTATCAATACAT
22081 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAAAGCATAATGTATCAATACAT
Found at i:22658 original size:21 final size:23
Alignment explanation
Indices: 22632--22676 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
22622 GGCTCTCGTT
*
22632 AAAAAATTT-T-CCCTTTGATAA
1 AAAAAATTTCTCCCCCTTGATAA
22653 AAAAAATTTCTCCCCCTTGATAA
1 AAAAAATTTCTCCCCCTTGATAA
22676 A
1 A
22677 CGATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
23 11 0.52
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAAATTTCTCCCCCTTGATAA
Found at i:24466 original size:22 final size:21
Alignment explanation
Indices: 24431--24480 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
24421 TTTATTGATG
*
24431 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
24451 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
24472 AATTTGAAG
1 ATTTTGAAG
24481 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:24477 original size:21 final size:22
Alignment explanation
Indices: 24438--24480 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
24428 ATGATTTTGA
* *
24438 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
24460 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
24481 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:24616 original size:13 final size:13
Alignment explanation
Indices: 24595--24627 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
24585 CCCTTATATT
24595 GATACAATGTATC
1 GATACAATGTATC
*
24608 GATATAATGTATC
1 GATACAATGTATC
24621 GATACAA
1 GATACAA
24628 AGAATATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (13 bp):
GATACAATGTATC
Done.