Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2055
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: 16786
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4302 original size:52 final size:52
Alignment explanation
Indices: 4159--4309 Score: 207
Period size: 53 Copynumber: 2.9 Consensus size: 52
4149 CCGAAATATG
4159 AAATTTTGCC-TCATGTAATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTTGCCTTCATGT-ATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
4212 AAATTTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTTGCCTTCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
4265 AAA-TTTGCCTTCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTTGCCTTCATGTATCGATACATTGAT-AGTGTATCGATACA
4310 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
51 2 0.02
52 34 0.39
53 44 0.51
54 7 0.08
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTTGCCTTCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:4316 original size:13 final size:13
Alignment explanation
Indices: 4298--4322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4288 CAAAGATCAG
4298 TGTATCGATACAA
1 TGTATCGATACAA
4311 TGTATCGATACA
1 TGTATCGATACA
4323 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4402 original size:13 final size:13
Alignment explanation
Indices: 4384--4408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4374 ACAAAAAAAA
4384 TGTATCGATACAT
1 TGTATCGATACAT
4397 TGTATCGATACA
1 TGTATCGATACA
4409 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10372 original size:9 final size:9
Alignment explanation
Indices: 10358--10418 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
10348 GGGGGTGTGA
10358 AAAAAAATT
1 AAAAAAATT
10367 -AAAAAATCAT
1 AAAAAAAT--T
*
10377 AAAAATAAAT
1 AAAAA-AATT
*
10387 AATAAAAATG
1 AA-AAAAATT
10397 AAAAAAATT
1 AAAAAAATT
10406 AAAAAAATT
1 AAAAAAATT
10415 AAAA
1 AAAA
10419 TTAAATGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.16
9 19 0.44
10 8 0.19
11 7 0.16
12 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (9 bp):
AAAAAAATT
Found at i:10372 original size:10 final size:9
Alignment explanation
Indices: 10357--10418 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
10347 TGGGGGTGTG
10357 AAAAAAAATT
1 AAAAAAAA-T
*
10367 AAAAAATCAT
1 AAAAAA-AAT
10377 AAAAATAAAT
1 AAAAA-AAAT
*
10387 AATAAAAAT
1 AAAAAAAAT
*
10396 GAAAAAAATT
1 -AAAAAAAAT
*
10406 AAAAAAATT
1 AAAAAAAAT
10415 AAAA
1 AAAA
10419 TTAAATGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 17 0.39
10 25 0.57
11 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:12430 original size:33 final size:32
Alignment explanation
Indices: 12357--12432 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
12347 TAGAATTCAA
12357 AAACCTCTCTTGAGGAATTTTTAGAGATTTTG
1 AAACCTCTCTTGAGGAATTTTTAGAGATTTTG
*
12389 AAACCTCTCTTGA-GAATGATTTTTGAGATTGTT-
1 AAACCTCTCTTGAGGAAT--TTTTAGAGATT-TTG
*
12422 AAAGCTCTCTT
1 AAACCTCTCTT
12433 TTAGAGAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.10
32 13 0.33
33 20 0.51
34 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
AAACCTCTCTTGAGGAATTTTTAGAGATTTTG
Found at i:12749 original size:20 final size:20
Alignment explanation
Indices: 12721--12796 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
12711 TCATACCCTG
12721 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
12741 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
12761 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
12781 ATGTATCGATTACATT
1 ATGTATCGA-TACATT
12797 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 38 0.88
21 5 0.12
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:12788 original size:40 final size:40
Alignment explanation
Indices: 12721--12799 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
12711 TCATACCCTG
* *
12721 ATGTATCGATACATTTTTCAATATATCGA-TACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATTACAT-TATGA
* *
12761 ATGTATCGATATATTCTACAATGTATCGATTACATTATG
1 ATGTATCGATACATTCTACAATATATCGATTACATTATG
12800 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 29 0.85
41 5 0.15
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATTCTACAATATATCGATTACATTATGA
Found at i:16076 original size:31 final size:34
Alignment explanation
Indices: 16031--16258 Score: 86
Period size: 34 Copynumber: 6.8 Consensus size: 34
16021 ACGTTGCGAC
* * *
16031 ACCTCTTTTGAGGATATTTTTAAA-ATT-TTAAA
1 ACCTCTCTTGAGGATAATTTCAAAGATTGTTAAA
*
16063 GCCTCTCTT-AGGATAATTTCAAAGATTGTTAAA
1 ACCTCTCTTGAGGATAATTTCAAAGATTGTTAAA
* * * *
16096 A-C-CTCTTAAGAAT-GTCTT-AAGAGATT-TTATA
1 ACCTCTCTTGAGGATAAT-TTCAA-AGATTGTTAAA
* * * * *
16127 AGCTCTATTGAGTATACTTTTCAAGAGA-TGTCAAA
1 ACCTCTCTTGAGGATA-ATTTCAA-AGATTGTTAAA
* * *
16162 AGCCTCTCTTAAGGATACTTTCAAAGATT-TTATGA
1 A-CCTCTCTTGAGGATAATTTCAAAGATTGTTA-AA
* * *
16197 GCC-CTTCTTAAGGATACTTTCAAGAGA-TGTTAAA
1 ACCTC-TCTTGAGGATAATTTCAA-AGATTGTTAAA
** *
16231 AGCCTCT-TTGACAATATTTTCAAAGATT
1 A-CCTCTCTTGAGGATAATTTCAAAGATT
16259 TTATAATCCT
Statistics
Matches: 148, Mismatches: 28, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
31 25 0.17
32 23 0.16
33 17 0.11
34 43 0.29
35 28 0.19
36 12 0.08
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (34 bp):
ACCTCTCTTGAGGATAATTTCAAAGATTGTTAAA
Found at i:16184 original size:35 final size:35
Alignment explanation
Indices: 16060--16237 Score: 142
Period size: 34 Copynumber: 5.3 Consensus size: 35
16050 TTAAAATTTT
*
16060 AAAGCCTCTCTT-AGGATAATTTCAA-AGATTGTTA
1 AAAGCCTCTCTTAAGGATACTTTCAAGAGA-TGTTA
* * *
16094 AAA--C-CTCTTAAGAAT-GTCTT-AAGAGATTTTA
1 AAAGCCTCTCTTAAGGATACT-TTCAAGAGATGTTA
* * * * *
16125 TAAG-CTCTATTGAGTATACTTTTCAAGAGATGTCA
1 AAAGCCTCTCTTAAGGATAC-TTTCAAGAGATGTTA
*
16160 AAAGCCTCTCTTAAGGATACTTTCAA-AGATTTTA
1 AAAGCCTCTCTTAAGGATACTTTCAAGAGATGTTA
**
16194 TGAGCC-CTTCTTAAGGATACTTTCAAGAGATGTTA
1 AAAGCCTC-TCTTAAGGATACTTTCAAGAGATGTTA
16229 AAAGCCTCT
1 AAAGCCTCT
16238 TTGACAATAT
Statistics
Matches: 111, Mismatches: 21, Indels: 23
0.72 0.14 0.15
Matches are distributed among these distances:
31 14 0.13
32 11 0.10
33 9 0.08
34 33 0.30
35 31 0.28
36 13 0.12
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (35 bp):
AAAGCCTCTCTTAAGGATACTTTCAAGAGATGTTA
Found at i:16276 original size:68 final size:68
Alignment explanation
Indices: 16044--16279 Score: 229
Period size: 69 Copynumber: 3.5 Consensus size: 68
16034 TCTTTTGAGG
* *
16044 ATATTTTTAAA-ATTTTA-AAGCCTCTCTT-AGGATAATTTCAA-AGATTGTTAAAA-CCTC-TT
1 ATATTTTCAAAGATTTTATAAGCCTCTCTTAAGGATACTTTCAAGAGA-TGTTAAAAGCCTCTTT
16103 AAGA
65 AAGA
* * * * * *
16107 ATGTCTT-AAGAGATTTTATAAG-CTCTATTGAGTATACTTTTCAAGAGATGTCAAAAGCCTCTC
1 ATATTTTCAA-AGATTTTATAAGCCTCTCTTAAGGATAC-TTTCAAGAGATGTTAAAAGCCTCT-
*
16170 TTAAGG
63 TTAAGA
* *
16176 ATACTTTCAAAGATTTTATGAGCC-CTTCTTAAGGATACTTTCAAGAGATGTTAAAAGCCTCTTT
1 ATATTTTCAAAGATTTTATAAGCCTC-TCTTAAGGATACTTTCAAGAGATGTTAAAAGCCTCTTT
* *
16240 GACA
65 AAGA
* *
16244 ATATTTTCAAAGATTTTATAATCCTTTCTTAAGGAT
1 ATATTTTCAAAGATTTTATAAGCCTCTCTTAAGGAT
16280 GTTTTACTAA
Statistics
Matches: 138, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
62 2 0.01
63 6 0.04
64 12 0.09
65 8 0.06
66 13 0.09
67 7 0.05
68 34 0.25
69 44 0.32
70 12 0.09
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (68 bp):
ATATTTTCAAAGATTTTATAAGCCTCTCTTAAGGATACTTTCAAGAGATGTTAAAAGCCTCTTTA
AGA
Found at i:16329 original size:68 final size:67
Alignment explanation
Indices: 16229--16366 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 67
16219 AGAGATGTTA
* *
16229 AAAGCCTCTTTGACAATATTTTCAAAGATTTTATAATCCTTTCTTAAGGATGT-TTT-ACTAATT
1 AAAGCCTCTTTGACAATATTTTCAAAGATTTTAAAAACCTTTCTTAAGGATGTGTTTCA-TAATT
16292 TTG
65 TTG
** * * * *
16295 AAAGCCTCTTTAGAGGATATTTTCTAAAGGTTTTAAAAACCTTTTTTGAGGATGTGTTTCATAGT
1 AAAGCCTCTTT-GACAATATTTTC-AAAGATTTTAAAAACCTTTCTTAAGGATGTGTTTCATAAT
16360 TTTG
64 TTTG
16364 AAA
1 AAA
16367 ATCTCTCTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
66 11 0.18
67 10 0.17
68 25 0.42
69 13 0.22
70 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (67 bp):
AAAGCCTCTTTGACAATATTTTCAAAGATTTTAAAAACCTTTCTTAAGGATGTGTTTCATAATTT
TG
Done.