Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold626
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: 16109
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.22
Warning! 5176 characters in sequence are not A, C, G, or T
Found at i:120 original size:44 final size:42
Alignment explanation
Indices: 70--208 Score: 102
Period size: 44 Copynumber: 3.2 Consensus size: 42
60 CAACCGATGG
70 AGGCAAGGTTTGTGTCTTCGACCTGTTTCGCTGTCAATGTAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTG-TTCGCTGTCAATG-AGGA
* * * * * ** *
114 AGGCAAGATCTTTTGTCTTCAACCAGCTC-CATCACAACCGA-GA
1 AGGCAAGGT-TTGTGTCTTCGACCTGTTCGC-TGTCAA-TGAGGA
* *
157 GAGGCAATGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTG-TTCGCTGTCAAT-GAGGA
202 AGGCAAG
1 AGGCAAG
209 ATCTATTGTC
Statistics
Matches: 68, Mismatches: 19, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
43 16 0.24
44 35 0.51
45 17 0.25
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (42 bp):
AGGCAAGGTTTGTGTCTTCGACCTGTTCGCTGTCAATGAGGA
Found at i:202 original size:88 final size:88
Alignment explanation
Indices: 60--222 Score: 265
Period size: 88 Copynumber: 1.9 Consensus size: 88
50 AGCTCCACTG
* **
60 CAACCGATGGAGGCAAGGTTTGTGTCTTCGACCTGTTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGATGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCT
*
125 TTTGTCTTCAACCAGCTCCATCA
66 ATTGTCTTCAACCAGCTCCATCA
*
148 CAACCGA-GAGAGGCAATGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATC
1 CAACCGATG-GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATC
212 TATTGTCTTCA
65 TATTGTCTTCA
223 CTGATCTGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
87 1 0.01
88 68 0.99
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (88 bp):
CAACCGATGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCT
ATTGTCTTCAACCAGCTCCATCA
Found at i:221 original size:45 final size:44
Alignment explanation
Indices: 82--221 Score: 112
Period size: 45 Copynumber: 3.2 Consensus size: 44
72 GCAAGGTTTG
* **
82 TGTCTTCGACCTGTTTCGCTGTCAATGTAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATC-TT
* * * *
127 TGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAATG-T-TT
1 TGTCTTCGACCTGCTTCGCTGTCA-ATACAG-GA-AGGCAA-GATCTT
169 GTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTAT
1 -TGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCT-T
215 TGTCTTC
1 TGTCTTC
222 ACTGATCTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 24
0.67 0.10 0.22
Matches are distributed among these distances:
42 6 0.08
43 17 0.24
44 18 0.25
45 24 0.33
46 7 0.10
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
TGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTT
Found at i:2517 original size:6 final size:6
Alignment explanation
Indices: 2506--2561 Score: 71
Period size: 6 Copynumber: 9.3 Consensus size: 6
2496 TTGACCTCTC
*
2506 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTTT CTTTTT -TTTCTT CTCTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT CTTTTT CTTT-TT CTTTTT
2555 -TTTTT CT
1 CTTTTT CT
2562 CCTATTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 7 0.16
6 29 0.66
7 8 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:2529 original size:19 final size:19
Alignment explanation
Indices: 2506--2556 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2496 TTGACCTCTC
2506 CTTTTTC-TTTTTCTTTTT
1 CTTTTTCTTTTTTCTTTTT
2524 CTTTTTCTTTTTTCTTTTT
1 CTTTTTCTTTTTTCTTTTT
2543 -TTTCTTCTCTTTTT
1 CTTT-TTCT-TTTTT
2557 TTTCTCCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.33
19 15 0.50
20 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
CTTTTTCTTTTTTCTTTTT
Found at i:2558 original size:14 final size:13
Alignment explanation
Indices: 2509--2561 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
2499 ACCTCTCCTT
*
2509 TTTCTTTTTCTT-
1 TTTCTTTTTTTTC
2521 TTTCTTTTTCTTT-
1 TTTCTTTTT-TTTC
2534 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
2547 TTCTCTTTTTTTTC
1 TT-TCTTTTTTTTC
2561 T
1 T
2562 CCTATTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 12 0.32
13 13 0.35
14 12 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:2570 original size:13 final size:14
Alignment explanation
Indices: 2513--2561 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2503 CTCCTTTTTC
*
2513 TTTTTCTTTTTCTTT
1 TTTTTC-TTCTCTTT
2528 TTCTTT-TT-TCTTT
1 TT-TTTCTTCTCTTT
2541 TTTTTCTTCTCTTT
1 TTTTTCTTCTCTTT
2555 TTTTTCT
1 TTTTTCT
2562 CCTATTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.10
13 9 0.29
14 14 0.45
15 2 0.06
16 3 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTCTCTTT
Found at i:2584 original size:15 final size:16
Alignment explanation
Indices: 2566--2616 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
2556 TTTTCTCCTA
2566 TTTTTGACTTTT-ATT
1 TTTTTGACTTTTGATT
*
2581 TTTTTGATTTTTGA-T
1 TTTTTGACTTTTGATT
* *
2596 TTTTTAATTTTTGATT
1 TTTTTGACTTTTGATT
2612 TTTTT
1 TTTTT
2617 TTGAGTCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (16 bp):
TTTTTGACTTTTGATT
Found at i:2590 original size:22 final size:21
Alignment explanation
Indices: 2565--2614 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
2555 TTTTTCTCCT
2565 ATTTTTGACTTTTATT-TTTTTG
1 ATTTTTGA-TTTT-TTATTTTTG
2587 ATTTTTGATTTTTTAATTTTTG
1 ATTTTTGATTTTTT-ATTTTTG
2609 ATTTTT
1 ATTTTT
2615 TTTTGAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.08
21 4 0.15
22 20 0.77
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.74
Consensus pattern (21 bp):
ATTTTTGATTTTTTATTTTTG
Found at i:2591 original size:6 final size:7
Alignment explanation
Indices: 2581--2614 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2571 GACTTTTATT
2581 TTTTTGA
1 TTTTTGA
2588 TTTTTGA
1 TTTTTGA
*
2595 TTTTTTAA
1 -TTTTTGA
2603 TTTTTGA
1 TTTTTGA
2610 TTTTT
1 TTTTT
2615 TTTTGAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (7 bp):
TTTTTGA
Found at i:6666 original size:3 final size:3
Alignment explanation
Indices: 6631--6720 Score: 67
Period size: 3 Copynumber: 29.3 Consensus size: 3
6621 ATAAGAAAAC
* * * * * *
6631 ATA ATA CTA ACA ATA GTA TTA ATA A-A TATA ATA ATA AAA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
6676 A-A GATA ATA ATG ATA ATA ATA ATA ATA ACTAA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA ATA A
6721 AAAATGCTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
2 2 0.03
3 60 0.88
4 4 0.06
5 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:7623 original size:20 final size:20
Alignment explanation
Indices: 7598--7636 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7588 GACGGCGCAA
**
7598 GTGGTGGTGGTGACGTGACC
1 GTGGTGGTGACGACGTGACC
7618 GTGGTGGTGACGACGTGAC
1 GTGGTGGTGACGACGTGAC
7637 GTTGGCGGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.15, G:0.49, T:0.23
Consensus pattern (20 bp):
GTGGTGGTGACGACGTGACC
Found at i:13672 original size:70 final size:70
Alignment explanation
Indices: 13593--13735 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
13583 ATACAATATC
13593 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
1 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
13658 AAATA
66 AAATA
*
13663 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGTT
1 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
13728 AAATA
66 AAATA
13733 TAA
1 TAA
13736 GTCTTGATAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (70 bp):
TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
AAATA
Found at i:13711 original size:35 final size:35
Alignment explanation
Indices: 13602--13713 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
13592 CTAAAAATTA
13602 TTTATATCATAATTTAATTCTTATTAACATAATAT
1 TTTATATCATAATTTAATTCTTATTAACATAATAT
** * * ** *
13637 TTTATATTTTAAATAAAAGCTAAATATAA-A-AAT-T
1 TTTATATCATAATTTAATTCT-TAT-TAACATAATAT
13671 ATTTATATCATAATTTAATTCTTATTAACATAATAT
1 -TTTATATCATAATTTAATTCTTATTAACATAATAT
13707 TTTATAT
1 TTTATAT
13714 TTTAAATAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
33 3 0.05
34 4 0.07
35 43 0.75
36 4 0.07
37 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (35 bp):
TTTATATCATAATTTAATTCTTATTAACATAATAT
Found at i:16080 original size:26 final size:27
Alignment explanation
Indices: 16041--16092 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
16031 AGTTTTTCAT
16041 TGCTTTTGAAAAGTGC-TGTGAAAAAG
1 TGCTTTTGAAAAGTGCTTGTGAAAAAG
*
16067 TGCTTTT-AAGAAGTGCTTTTGAAAAA
1 TGCTTTTGAA-AAGTGCTTGTGAAAAA
16093 TTTGAGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 13 0.57
27 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (27 bp):
TGCTTTTGAAAAGTGCTTGTGAAAAAG
Done.