Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3261
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: 35759
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:6222 original size:27 final size:27
Alignment explanation
Indices: 6192--6369 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
6182 ATATTGAGCC
* * *
6192 CGCACACTCAGTGCTATATATTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * * *
6219 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
6246 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
** * *
6274 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
6301 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
6328 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
6355 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6370 GTACAATTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.80
28 25 0.20
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:6331 original size:82 final size:81
Alignment explanation
Indices: 6213--6368 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
6203 TGCTATATAT
* * *
6213 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
6278 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
6295 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
6359 CACTTAGTGC
65 CACTTAGTGC
6369 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 19 0.29
82 47 0.71
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:8580 original size:35 final size:35
Alignment explanation
Indices: 8541--8613 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
8531 CAAGTATGTG
8541 ATATATATTATTTATGTGAGATTGATCTGACGAGA
1 ATATATATTATTTATGTGAGATTGATCTGACGAGA
*
8576 ATATATATTATTTATGTGAGATTGATCTTACGAGA
1 ATATATATTATTTATGTGAGATTGATCTGACGAGA
8611 ATA
1 ATA
8614 AAGAATGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (35 bp):
ATATATATTATTTATGTGAGATTGATCTGACGAGA
Found at i:20248 original size:21 final size:22
Alignment explanation
Indices: 20210--20250 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20200 CTTTTTGTTT
**
20210 TCATTTTTATTTTCTCCTCCTC
1 TCATTTTTATCGTCTCCTCCTC
20232 TCATTTTTATCGT-TCCTCC
1 TCATTTTTATCGTCTCCTCC
20251 CTTTGATCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.10, C:0.32, G:0.02, T:0.56
Consensus pattern (22 bp):
TCATTTTTATCGTCTCCTCCTC
Found at i:25431 original size:29 final size:29
Alignment explanation
Indices: 25395--25453 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
25385 CTATGAATTG
*
25395 AGTAGTTTAGCATAGTTTAAAGGTTGAAA
1 AGTAGTTTAACATAGTTTAAAGGTTGAAA
25424 AGTAGTTTAACATAGTTTAAAGGTTGAAA
1 AGTAGTTTAACATAGTTTAAAGGTTGAAA
25453 A
1 A
25454 TTAATTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
AGTAGTTTAACATAGTTTAAAGGTTGAAA
Found at i:27405 original size:27 final size:26
Alignment explanation
Indices: 27374--27550 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
27364 TAAATTGTAC
27374 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
27401 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
27427 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
27455 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
27483 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
27510 GGCACTAAGTGTGCGAGTTGA-TATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
27536 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
27551 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
26 17 0.14
27 83 0.66
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:27490 original size:82 final size:81
Alignment explanation
Indices: 27375--27530 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
27365 AAATTGTACA
* * *
27375 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
27439 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
27456 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
27521 TGCGAGTTGA
65 TGCGAATTGA
27531 TATATAGCAC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:27498 original size:55 final size:53
Alignment explanation
Indices: 27374--27550 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 53
27364 TAAATTGTAC
* **
27374 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCGAGTTG-ATATGT
* *
27427 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTGACTATGT
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-TGA-TATGT
* * * *
27483 AGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGTTGATATAT
1 AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTTGATATGT
*
27536 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
27551 GGCTCAATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
53 19 0.18
54 39 0.36
55 48 0.45
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (53 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTTGATATGT
Found at i:35468 original size:27 final size:26
Alignment explanation
Indices: 35438--35614 Score: 160
Period size: 27 Copynumber: 6.5 Consensus size: 26
35428 AAATTGTACA
35438 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTT
* * *
35465 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCG-ATTGACTATGTT
* *
35492 GCACTAAGTGTGCGAATTGACCATG-C
1 GCACTAAGTGTGCG-ATTGACTATGTT
*
35518 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTT
* * *
35546 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTT
*
35573 GCACTAAGTGTGCGAGTTGAATAT-TAT
1 GCACTAAGTGTGCGA-TTGACTATGT-T
*
35600 AGCACTGAGTGTGCG
1 -GCACTAAGTGTGCG
35615 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.01
26 16 0.13
27 78 0.62
28 31 0.25
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTT
Found at i:35498 original size:54 final size:54
Alignment explanation
Indices: 35437--35614 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 54
35427 TAAATTGTAC
*
35437 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-GACTATGTCGCACTAAGTGTGCGAAATGAATATGAT
* ** *
35492 -GCACTAAGTGTGCGAATTGACCATG-CGCACTAAGTGTGCGAGTCTGACTATG-T
1 AGCACTAAGTGTGCG-ATTGACTATGTCGCACTAAGTGTGCGA-AATGAATATGAT
* * * ** *
35545 AGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGTTGAATATTAT
1 AGCACTAAGTGTGCGA-TTGACTATGTCGCACTAAGTGTGCGAAATGAATATGAT
*
35600 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35615 GGCTCAATAT
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
53 17 0.17
54 53 0.51
55 33 0.32
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACTATGTCGCACTAAGTGTGCGAAATGAATATGAT
Found at i:35552 original size:81 final size:80
Alignment explanation
Indices: 35438--35592 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 80
35428 AAATTGTACA
* * *
35438 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
35502 TGCGAATTGACCATGC
65 TGCGAATTGACCATGC
** *
35518 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
35583 TGCGAGTTGA
65 TGCGAATTGA
35593 ATATTATAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
80 18 0.27
81 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (80 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGC
Done.