Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold8126.1
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: 5520
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:628 original size:132 final size:132
Alignment explanation
Indices: 440--1084 Score: 1076
Period size: 132 Copynumber: 4.9 Consensus size: 132
430 CAAATACAGG
* * * * *
440 GACAATATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCGTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
* *
505 TCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
570 AA
131 AA
*
572 GACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
*
637 TCCACTTCCTACCAATATAGGAAGATAGGATCTACTA-CTTTCGATCTACTTCACGCCAATACAT
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATC-TTCGATCTACTTCACGCCAATACAT
701 GAA
130 GAA
* * *
704 GACAATATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGTCAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
* * * *
769 TCCACTTCCTACCAATATAGGAAGATAAGATCTACTACCTTCGATCTACTTCACGCCAATGCATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
834 AA
131 AA
836 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
* *
901 TCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
966 AA
131 AA
*
968 GACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
* * *
1033 TCTATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTC
1085 TTGCCCCGGG
Statistics
Matches: 487, Mismatches: 24, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 485 1.00
133 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
AA
Found at i:1541 original size:135 final size:134
Alignment explanation
Indices: 1235--1604 Score: 659
Period size: 135 Copynumber: 2.7 Consensus size: 134
1225 GCCATCTTTG
1235 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1300 TGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
66 TGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
*
1365 TGTA
131 TGCA
* *
1369 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAGTGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1434 TGGTCAGGGAGGTAAAATCTGCCATCTTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
66 TGGTCAGGGAGGTAAAATCTGCCATC-TTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
1499 CTGCA
130 CTGCA
*
1504 ATCTTCAATCTATTCCACTGCCAAATACTGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
1569 TAGTCACATGGAGGTAAAATCTGCCATCTTTGATCT
66 TGGT--CAGGGAGGTAAAATCTGCCATCTTTGATCT
1605 TCAATCTATT
Statistics
Matches: 225, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
134 89 0.40
135 107 0.48
136 8 0.04
137 21 0.09
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (134 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
TGCA
Found at i:1821 original size:95 final size:95
Alignment explanation
Indices: 1504--1986 Score: 858
Period size: 95 Copynumber: 5.0 Consensus size: 95
1494 AAGATCTGCA
* *
1504 ATCTTCAATCTATTCCACTGCCAAATACTGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1569 TAGTCACATGGAGGTAAAATCTGCCATCTTTG
66 TAGT--CAGGGAGGTAAAATCTGCCATCTTTG
*
1601 ATCTTCAATCTATTCCACTGCCAGATGCAGGGAGATAGAGTTATCGGCTTCAATGTATACTCCAC
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATG--TACTCCAC
1666 TGTAGTCAGGGAGGTAAAATCTGCCATCTTTG
64 TGTAGTCAGGGAGGTAAAATCTGCCATCTTTG
*
1698 ATCTTCAATCTATTCCACTGCCAGATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1763 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
*
1793 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCCCTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1858 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
*
1888 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1953 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
1983 ATCT
1 ATCT
1987 GCTTCGCTGC
Statistics
Matches: 374, Mismatches: 10, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
95 228 0.61
97 132 0.35
99 14 0.04
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTTG
Found at i:1868 original size:42 final size:42
Alignment explanation
Indices: 1820--1963 Score: 108
Period size: 42 Copynumber: 3.2 Consensus size: 42
1810 CTGCCAAATG
*
1820 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCCCTGTAGT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT
* * * * * * * *
1862 CAGGGAGGTAAAATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAAAT
1 CAGGGAGATAGAGT-T---A---TCG-GCTTCAATGTACTCCACTG--TAGT
1914 ACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT
1 -CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT
1957 CAGGGAG
1 CAGGGAG
1964 GTAAAATCTG
Statistics
Matches: 74, Mismatches: 17, Indels: 22
0.65 0.15 0.19
Matches are distributed among these distances:
42 18 0.24
43 3 0.04
45 16 0.22
46 4 0.05
49 4 0.05
50 15 0.20
52 3 0.04
53 11 0.15
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (42 bp):
CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT
Found at i:2981 original size:7 final size:7
Alignment explanation
Indices: 2965--3014 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
2955 TGGCCTCTCC
2965 TTTTTC-
1 TTTTTCT
2971 TTTTTCT
1 TTTTTCT
2978 TTTTTC-
1 TTTTTCT
2984 -TTTTCT
1 TTTTTCT
2990 TTTTTCAT
1 TTTTTC-T
*
2998 TTTTTCA
1 TTTTTCT
3005 TTTTTCT
1 TTTTTCT
3012 TTT
1 TTT
3015 CGTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.13
6 6 0.16
7 20 0.53
8 7 0.18
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:3021 original size:7 final size:6
Alignment explanation
Indices: 2964--3026 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
2954 TTGGCCTCTC
2964 CTTTTT CTTTTT CTTTTT -TCTTTT CTTTTTT CATTTTTT CATTTTT C-TTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT C-TTTTT C--TTTTT C-TTTTT CTTTTT
*
3015 CGTTTT -TTTTT C
1 CTTTTT CTTTTT C
3027 AAGTGAAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 10 0.20
6 20 0.41
7 11 0.22
8 8 0.16
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:3461 original size:11 final size:11
Alignment explanation
Indices: 3442--3519 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
3432 GAGGTTTTTC
* *
3442 TTTTATTTGGT
1 TTTTTTTTGCT
3453 TTTTTTTTGCT
1 TTTTTTTTGCT
3464 TTTTATTTT-CT
1 TTTT-TTTTGCT
* *
3475 CGTTTTTTTAC-
1 -TTTTTTTTGCT
*
3486 CTTTTTTTGTCT
1 TTTTTTTTG-CT
*
3498 TTTTTTTGTCCT
1 TTTTTTT-TGCT
3510 TTTTTTTTGC
1 TTTTTTTTGC
3520 CTCCACTGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 7 0.13
11 22 0.42
12 23 0.43
13 1 0.02
ACGTcount: A:0.04, C:0.12, G:0.09, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGCT
Found at i:3467 original size:12 final size:11
Alignment explanation
Indices: 3452--3517 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
3442 TTTTATTTGG
*
3452 TTTTTTTTTGC
1 TTTTTTTTTTC
*
3463 TTTTTATTTTC
1 TTTTTTTTTTC
* *
3474 TCGTTTTTTTAC
1 T-TTTTTTTTTC
* *
3486 CTTTTTTTGTC
1 TTTTTTTTTTC
*
3497 TTTTTTTTGTCC
1 TTTTTTTT-TTC
3509 TTTTTTTTT
1 TTTTTTTTT
3518 GCCTCCACTG
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
11 25 0.61
12 16 0.39
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:4904 original size:62 final size:62
Alignment explanation
Indices: 4802--4926 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
4792 CTAAACTCGA
* * *
4802 CGTACTTTTGGATTTTAGGAAATTTACTGTATGCAATGAAACGTAGTGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGAAGCATGAATG
* * * *
4864 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGAAGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGAAGCATGAATG
4926 C
1 C
4927 AAAAAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.38
Consensus pattern (62 bp):
CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGAAGCATGAATG
Done.