Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2529
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: 35274
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:1720 original size:40 final size:40
Alignment explanation
Indices: 1667--1897 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
1657 TATTACCACA
* * * * *
1667 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
* * *
1707 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
*
1747 CGCACAAATGCCTTCGGGTCTTAGCCCGGATC-AATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1786 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
*
1826 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
*
1866 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATC
1898 TCATTCAAAT
Statistics
Matches: 178, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 34 0.19
40 144 0.81
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
Found at i:1850 original size:119 final size:119
Alignment explanation
Indices: 1667--1897 Score: 331
Period size: 119 Copynumber: 1.9 Consensus size: 119
1657 TATTACCACA
* * * * *
1667 AGCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 AGCACAAATGCCTTCGGGTCTTAACCCGGGCAAAGCAACTAGCACAAATGCCTTCGGGACTTAGC
* * *
1732 CCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATCAATCACT
66 CCGGATCAAATC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATCAATCACT
* * *
1786 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACTAGCACAAATGCCTTCGGGACTTAG
1 AGCACAAATGCCTTCGGGTCTTAACCCGG-GCAAAGCAACTAGCACAAATGCCTTCGGGACTTAG
1850 CCCGGATCAAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATC
65 CCCGGATCAAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATC
1898 TCATTCAAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
119 91 0.92
120 8 0.08
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (119 bp):
AGCACAAATGCCTTCGGGTCTTAACCCGGGCAAAGCAACTAGCACAAATGCCTTCGGGACTTAGC
CCGGATCAAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATCAATCACT
Found at i:10112 original size:40 final size:40
Alignment explanation
Indices: 10059--10290 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
10049 TATTACCACA
* * * * * *
10059 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* * * *
10099 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* *
10139 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
10179 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
10219 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
10259 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
10291 TCATTCAAAT
Statistics
Matches: 180, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 176 0.98
41 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
Found at i:16232 original size:27 final size:27
Alignment explanation
Indices: 16202--16379 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16192 ATATTGAGTC
* * * *
16202 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16229 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16256 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16284 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16311 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16338 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16365 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16380 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16341 original size:82 final size:81
Alignment explanation
Indices: 16223--16378 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16213 TGCTATATAA
* *
16223 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16288 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16305 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16369 CACTTAGTGC
65 CACTTAGTGC
16379 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:24353 original size:27 final size:27
Alignment explanation
Indices: 24323--24500 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
24313 ATATTGAGTC
* * * *
24323 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
24350 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24377 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
24405 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
24432 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
24459 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24486 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24501 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:24462 original size:82 final size:81
Alignment explanation
Indices: 24344--24499 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
24334 TGCTATATAA
* *
24344 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
24409 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
24426 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
24490 CACTTAGTGC
65 CACTTAGTGC
24500 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31951 original size:19 final size:22
Alignment explanation
Indices: 31901--31957 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
31891 TTAGATATTG
31901 ATATGCAATCTTAGATTATGAT
1 ATATGCAATCTTAGATTATGAT
31923 ATATTGCAATCTT-GA-TA-GAT
1 ATA-TGCAATCTTAGATTATGAT
*
31943 TTATGCAATCTTAGA
1 ATATGCAATCTTAGA
31958 ATATATAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.28
20 7 0.22
21 2 0.06
22 5 0.16
23 9 0.28
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (22 bp):
ATATGCAATCTTAGATTATGAT
Done.