Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1436
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: 29072
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Found at i:1234 original size:15 final size:15
Alignment explanation
Indices: 1210--1254 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1200 TTCACAATTT
1210 TTTTTCAAATTTTTTC
1 TTTTT-AAATTTTTTC
1226 TTTTTAAATTTTTT-
1 TTTTTAAATTTTTTC
1240 TTTTT--ATTTTTTC
1 TTTTTAAATTTTTTC
1253 TT
1 TT
1255 CTTTTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.25
13 2 0.07
14 5 0.18
15 9 0.32
16 5 0.18
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTAAATTTTTTC
Found at i:2337 original size:39 final size:41
Alignment explanation
Indices: 2242--2342 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
2232 AACTCTTTTT
* * * *
2242 TTGATAAGGCGTGGGCATGTTAAGAAACTAAAAGCTCTTGT
1 TTGATAAGGCGTGGGTACGCTAAGAAACTAAAAGCTCTTGA
* * *
2283 TTGATAAGGCATGGGTACGCTAAGAAAC-AGAAGTTCTT-A
1 TTGATAAGGCGTGGGTACGCTAAGAAACTAAAAGCTCTTGA
*
2322 TTGATAAAGCGTGGGTACGCT
1 TTGATAAGGCGTGGGTACGCT
2343 CTATGAAAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 19 0.37
40 8 0.16
41 24 0.47
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.28
Consensus pattern (41 bp):
TTGATAAGGCGTGGGTACGCTAAGAAACTAAAAGCTCTTGA
Found at i:7493 original size:2 final size:2
Alignment explanation
Indices: 7486--7527 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
7476 CTACTCAAAC
*
7486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7528 GAAGGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10111 original size:2 final size:2
Alignment explanation
Indices: 10104--10139 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10094 ATAACCAAAG
10104 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
10140 TATATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:18977 original size:87 final size:87
Alignment explanation
Indices: 18831--19016 Score: 277
Period size: 87 Copynumber: 2.1 Consensus size: 87
18821 AAAATCCCTT
*
18831 GTATTATACCATTTTTATTATTTAAATTCTTTATAAATTTTCATTCCTTGTTGAGTACTTATTGT
1 GTATTATACCATTTTTATTATTTAAATTCTTTATAAATTTTCATTCCTTGTTGAATACTTATTGT
*
18896 ATAATTTCATCAGAACAACTTA
66 ATAATTTCATCAAAACAACTTA
*
18918 GTATTATACCATTTTTATTATTTAGATAT-TTTATAAATTTTCATT-CTTAGTTGAATACTTATT
1 GTATTATACCATTTTTATTATTTAAAT-TCTTTATAAATTTTCATTCCTT-GTTGAATACTTATT
** *
18981 GTATAATTTTGTTAAAACAACTTA
64 GTATAATTTCATCAAAACAACTTA
*
19005 GTATTTTACCAT
1 GTATTATACCAT
19017 AATACTGTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
86 3 0.03
87 86 0.96
88 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (87 bp):
GTATTATACCATTTTTATTATTTAAATTCTTTATAAATTTTCATTCCTTGTTGAATACTTATTGT
ATAATTTCATCAAAACAACTTA
Found at i:19200 original size:29 final size:29
Alignment explanation
Indices: 19106--19213 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 29
19096 AAAGTTTAAA
* *
19106 TTAAAAATATATAAAATTTAAATAAATTCATTTT
1 TTAAAAATATATAAAATTT-TA-AAATACA---T
* *
19140 TTAAAAATATCTAAAATTTTAAAATACTT
1 TTAAAAATATATAAAATTTTAAAATACAT
*
19169 TTAAAAATATGTAAAATTTTATATAA-A-AT
1 TTAAAAATATATAAAATTTTA-A-AATACAT
19198 TTAAAAAGTATATAAA
1 TTAAAAA-TATATAAA
19214 CAATGAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
29 29 0.45
30 9 0.14
31 2 0.03
32 5 0.08
33 1 0.02
34 18 0.28
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (29 bp):
TTAAAAATATATAAAATTTTAAAATACAT
Found at i:20121 original size:16 final size:16
Alignment explanation
Indices: 20100--20131 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20090 CCAACTGCCT
20100 TTTGTGTAGACAAAGC
1 TTTGTGTAGACAAAGC
20116 TTTGTGTAGACAAAGC
1 TTTGTGTAGACAAAGC
20132 CCTATCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
TTTGTGTAGACAAAGC
Found at i:25264 original size:6 final size:6
Alignment explanation
Indices: 25253--25296 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
25243 CATATAATTG
* *
25253 GTATAT GTATAT GTATAT GTATGTAT GTATAT ATATAT ATATAT
1 GTATAT GTATAT GTATAT GTA--TAT GTATAT GTATAT GTATAT
25297 ATATTGACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
6 29 0.83
8 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:26203 original size:1 final size:1
Alignment explanation
Indices: 26197--26226 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
26187 TAAAACTCAG
26197 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26227 CTTACAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26851 original size:1 final size:1
Alignment explanation
Indices: 26845--26934 Score: 180
Period size: 1 Copynumber: 90.0 Consensus size: 1
26835 AGAAGAAGTT
26845 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
26910 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
26935 ATAAAGACAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:28074 original size:19 final size:19
Alignment explanation
Indices: 28052--28095 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28042 TGTATATATA
* **
28052 TTATATTTATTTTTTATTT
1 TTATATTTATTATAAATTT
28071 TTATATTTATTATAAATTT
1 TTATATTTATTATAAATTT
28090 TTATAT
1 TTATAT
28096 ATTAATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATATTTATTATAAATTT
Found at i:28139 original size:30 final size:29
Alignment explanation
Indices: 28034--28141 Score: 82
Period size: 30 Copynumber: 3.6 Consensus size: 29
28024 AGACGAATAA
*
28034 ATAATTTATGTATATATATTATATTTATTTTTT
1 ATAATTT-TATAT-TATATTATA--TATTTTTT
*
28067 AT--TTTTATATT-TATTATA-AATTTTT
1 ATAATTTTATATTATATTATATATTTTTT
*
28092 AT-ATATTAATAATTTATATTATATATTTTTT
1 ATAAT-TTTAT-A-TTATATTATATATTTTTT
28123 ATACATTTTATATTATATT
1 ATA-ATTTTATATTATATT
28142 CGTATTTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
25 8 0.13
26 1 0.02
27 4 0.06
28 8 0.13
29 3 0.05
30 18 0.29
31 12 0.19
32 4 0.06
33 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
ATAATTTTATATTATATTATATATTTTTT
Found at i:28991 original size:15 final size:16
Alignment explanation
Indices: 28971--29016 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
28961 ATAAATTTTT
28971 ATATATTA-ATAATTA
1 ATATATTATATAATTA
*
28986 ATATA-TATATATTTA
1 ATATATTATATAATTA
*
29001 ATATA-TATATATTTA
1 ATATATTATATAATTA
29016 A
1 A
29017 AAATATGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 2 0.07
15 27 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATATTATATAATTA
Done.