Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold465
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: 26365
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:6625 original size:40 final size:40
Alignment explanation
Indices: 6594--6723 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
6584 GGACTAAGAT
*
6594 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGAATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* *
6634 CCGAAGGAAGGCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGAA---TTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
6677 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGAATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
6717 CCGAAGG
1 CCGAAGG
6724 CATTGAATGA
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 40 0.51
43 37 0.47
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGAAGGAATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Found at i:6748 original size:39 final size:39
Alignment explanation
Indices: 6664--6774 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 39
6654 AGATACTAAT
** *
6664 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* *
6704 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
6744 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
6775 GAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 25 0.41
40 36 0.59
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:6782 original size:40 final size:39
Alignment explanation
Indices: 6665--6787 Score: 97
Period size: 40 Copynumber: 3.1 Consensus size: 39
6655 GATACTAATT
* ** ** *
6665 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
6704 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
6744 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
6784 CCGG
1 CCGG
6788 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.36
40 44 0.64
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Found at i:9291 original size:45 final size:44
Alignment explanation
Indices: 9227--9397 Score: 140
Period size: 45 Copynumber: 3.9 Consensus size: 44
9217 TAGGATTTTT
* *
9227 TATATGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCATCGA
1 TATATGTG-ATTCGTGTAAGACCACGTCTGGGACGTTGGCATCGA
* * * *
9272 TATATGTGGTTACGTGTAAGACCATGTCTGTGACATTGGCATCG-
1 TATATGTGATT-CGTGTAAGACCACGTCTGGGACGTTGGCATCGA
*
9316 TAT-T-TAATTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA
1 TATATGTGATTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGA
* * * * *
9358 TATGAGGT-A-TCATGTAGGACCACATCTGGGATGTTGGCAT
1 TAT-ATGTGATTCGTGTAAGACCACGTCTGGGACGTTGGCAT
9398 TGTACAATAC
Statistics
Matches: 102, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
41 27 0.26
42 7 0.07
43 24 0.24
44 7 0.07
45 37 0.36
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (44 bp):
TATATGTGATTCGTGTAAGACCACGTCTGGGACGTTGGCATCGA
Found at i:16707 original size:30 final size:30
Alignment explanation
Indices: 16673--16733 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
16663 TCCTTAACTC
16673 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
16703 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
16733 A
1 A
16734 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:20376 original size:28 final size:28
Alignment explanation
Indices: 20344--20413 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
20334 TATGGTACTC
*
20344 AGTGTACGAAATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
* *
20372 AGTGTGCGAGATATTGAGAATGGCACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
20400 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
20414 CGAATGATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:22297 original size:28 final size:28
Alignment explanation
Indices: 22266--22420 Score: 100
Period size: 28 Copynumber: 5.5 Consensus size: 28
22256 GTGAACATAG
*
22266 GCACTGTGTGTGTGAGTTTCGTAACTGA
1 GCACTGTGTGTGCGAGTTTCGTAACTGA
* * ***
22294 GCACTCTGTGTGCGAG-ATCAGTTGTTGA
1 GCACTGTGTGTGCGAGTTTC-GTAACTGA
* *
22322 GGCACTGTGTGTGCGAGTTCCGTAACCGA
1 -GCACTGTGTGTGCGAGTTTCGTAACTGA
* * ***
22351 GCACTGTATGTGCGAG-ATCGATTGTTGA
1 GCACTGTGTGTGCGAGTTTCG-TAACTGA
* **
22379 GGCACTGTGTATGCGAG-TTCTGTAACCAA
1 -GCACTGTGTGTGCGAGTTTC-GTAACTGA
22408 GCACTGTGTGTGC
1 GCACTGTGTGTGC
22421 AAGATCGGTT
Statistics
Matches: 92, Mismatches: 29, Indels: 12
0.69 0.22 0.09
Matches are distributed among these distances:
27 4 0.04
28 49 0.53
29 37 0.40
30 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (28 bp):
GCACTGTGTGTGCGAGTTTCGTAACTGA
Found at i:22333 original size:29 final size:28
Alignment explanation
Indices: 22294--22395 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 28
22284 TCGTAACTGA
*
22294 GCACTCTGTGTGCGAGATCAGTTGTTGAG
1 GCACTGTGTGTGCGAGATC-GTTGTTGAG
* ****
22323 GCACTGTGTGTGCGAGTTCCGTAACCGA-
1 GCACTGTGTGTGCGAGAT-CGTTGTTGAG
*
22351 GCACTGTATGTGCGAGATCGATTGTTGAG
1 GCACTGTGTGTGCGAGATCG-TTGTTGAG
*
22380 GCACTGTGTATGCGAG
1 GCACTGTGTGTGCGAG
22396 TTCTGTAACC
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
27 2 0.04
28 19 0.34
29 34 0.61
30 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (28 bp):
GCACTGTGTGTGCGAGATCGTTGTTGAG
Found at i:22333 original size:57 final size:56
Alignment explanation
Indices: 22264--22450 Score: 232
Period size: 57 Copynumber: 3.2 Consensus size: 56
22254 AAGTGAACAT
* * *
22264 AGGCACTGTGTGTGTGAGTTTCGTAACTGAGCACTCTGTGTGCGAGATCAGTTGTTG
1 AGGCACTGTGTGTGCGAGTTTCGTAACCGAGCACTGTGTGTGCGAGATC-GTTGTTG
* *
22321 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTATGTGCGAGATCGATTGTTG
1 AGGCACTGTGTGTGCGAGTTTCGTAACCGAGCACTGTGTGTGCGAGATCG-TTGTTG
* * *
22378 AGGCACTGTGTATGCGAG-TTCTGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTTC-GTAACCGAGCACTGTGTGTGCGAGATC-GTTGTTG
*
22435 GGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
22451 AAATGAGATC
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
56 3 0.03
57 103 0.91
58 1 0.01
59 6 0.05
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (56 bp):
AGGCACTGTGTGTGCGAGTTTCGTAACCGAGCACTGTGTGTGCGAGATCGTTGTTG
Done.