Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2565
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: 31577
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:2486 original size:59 final size:59
Alignment explanation
Indices: 2414--2543 Score: 235
Period size: 59 Copynumber: 2.2 Consensus size: 59
2404 ATAAATGAAT
*
2414 GTATCGATACATGCTTAAAATG-TTTGAGACAAAACTACCCTGCATATTGCCAAGGAAAA
1 GTATCGATACATGCTTAAAATGTTTTGAGACAAAAC-ACCCTGCATACTGCCAAGGAAAA
2473 GTATCGATACATGCTTAAAATGTTTTGAGACAAAACACCCTGCATACTGCCAAGGAAAA
1 GTATCGATACATGCTTAAAATGTTTTGAGACAAAACACCCTGCATACTGCCAAGGAAAA
2532 GTATCGATACAT
1 GTATCGATACAT
2544 AAGTAAATGT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
59 56 0.81
60 13 0.19
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (59 bp):
GTATCGATACATGCTTAAAATGTTTTGAGACAAAACACCCTGCATACTGCCAAGGAAAA
Found at i:5038 original size:79 final size:79
Alignment explanation
Indices: 4934--5241 Score: 313
Period size: 79 Copynumber: 3.9 Consensus size: 79
4924 CTAACTCGTA
* * * *
4934 TTTATTTCAAAAATATTAAAATTTTCATCTCGGGGATACTCCTACCTCATCAATTTCAAGGGGAT
1 TTTATTTCTAAAATATTTAAATTTTCATCTCGGGGATACTCCTACCTCATTAATTTCGAGGGGAT
4999 ACTCCAACCCCATT
66 ACTCCAACCCCATT
* * * * * *
5013 TTTATTTCTAAAATATTTAATTTTTCATCCCGGGGATCCT-CTAACCCCGTTATTTTCGAGGGGA
1 TTTATTTCTAAAATATTTAAATTTTCATCTCGGGGATACTCCT-ACCTCATTAATTTCGAGGGGA
*
5077 TACTCAAACCCCATT
65 TACTCCAACCCCATT
* * * * * *
5092 TTTCTTTCCAAAATA-TTAAAATTTCATCTTGGGGATACTCC-AACTCCATTAATTCCGAGGGGA
1 TTTATTTCTAAAATATTTAAATTTTCATCTCGGGGATACTCCTACCT-CATTAATTTCGAGGGGA
*
5155 TACTCCAACCCCTTT
65 TACTCCAACCCCATT
* * * ** * * *
5170 TTTATTT-TCAAAATATTGAATTTTTTATCT-TAGGATACTCCAACCTC-GTATTTTCGAGGGGA
1 TTTATTTCT-AAAATATTTAAATTTTCATCTCGGGGATACTCCTACCTCATTAATTTCGAGGGGA
5232 TACTCCAACC
65 TACTCCAACC
5242 TCGTTATTTC
Statistics
Matches: 186, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
77 24 0.13
78 70 0.38
79 92 0.49
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (79 bp):
TTTATTTCTAAAATATTTAAATTTTCATCTCGGGGATACTCCTACCTCATTAATTTCGAGGGGAT
ACTCCAACCCCATT
Found at i:5153 original size:157 final size:156
Alignment explanation
Indices: 4938--5241 Score: 407
Period size: 157 Copynumber: 1.9 Consensus size: 156
4928 CTCGTATTTA
* *
4938 TTTCAAAAATATTAAAATTTTCATCTCGGGGATACTCCTACCTCATCAATTTCAAGGGGATACTC
1 TTTCAAAAATATTAAAATTTTCATCTCGGGGATACTCCAACCTCATCAATTCCAAGGGGATACTC
* * * *
5003 CAACCCCATTTTTA-TTTCTAAAATATTTAATTTTTCATCCCGGGGATCCTCTAACCCCGTTATT
66 CAACCCCATTTTTATTTTC-AAAATATTGAATTTTTCAT-CCGAGGATACTCCAACCCCG-TATT
5067 TTCGAGGGGATACTCAAACCCCATTTTTC
128 TTCGAGGGGATACTCAAACCCCATTTTTC
* * * *
5096 TTTCCAAAATATTAAAA-TTTCATCTTGGGGATACTCCAA-CTCCATTAATTCCGAGGGGATACT
1 TTTCAAAAATATTAAAATTTTCATCTCGGGGATACTCCAACCT-CATCAATTCCAAGGGGATACT
* * ** *
5159 CCAACCCCTTTTTTATTTTCAAAATATTGAATTTTTTATCTTAGGATACTCCAACCTCGTATTTT
65 CCAACCCCATTTTTATTTTCAAAATATTGAATTTTTCATCCGAGGATACTCCAACCCCGTATTTT
*
5224 CGAGGGGATACTCCAACC
130 CGAGGGGATACTCAAACC
5242 TCGTTATTTC
Statistics
Matches: 128, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
155 23 0.18
156 16 0.12
157 69 0.54
158 20 0.16
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (156 bp):
TTTCAAAAATATTAAAATTTTCATCTCGGGGATACTCCAACCTCATCAATTCCAAGGGGATACTC
CAACCCCATTTTTATTTTCAAAATATTGAATTTTTCATCCGAGGATACTCCAACCCCGTATTTTC
GAGGGGATACTCAAACCCCATTTTTC
Found at i:5233 original size:27 final size:28
Alignment explanation
Indices: 5202--5269 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
5192 TTTTATCTTA
5202 GGATACTCCAACCTCG-TATTT-TCGAGG
1 GGATACTCCAACCTCGTTATTTCT-GAGG
5229 GGATACTCCAACCTCGTTATTTCTGAGG
1 GGATACTCCAACCTCGTTATTTCTGAGG
*
5257 GGAAACTCCAACC
1 GGATACTCCAACC
5270 CTGTTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 16 0.42
28 21 0.55
29 1 0.03
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (28 bp):
GGATACTCCAACCTCGTTATTTCTGAGG
Found at i:5546 original size:25 final size:24
Alignment explanation
Indices: 5500--5556 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
5490 AGCGATTAAT
* *
5500 AAAAGCAAATTATTAATATAAAATA
1 AAAATCAAATTATCAATAT-AAATA
*
5525 AAAATCAAATTATCAAGT-TAAATG
1 AAAATCAAATTATCAA-TATAAATA
5549 AAAATCAA
1 AAAATCAA
5557 TCTTACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.43
25 15 0.54
26 1 0.04
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26
Consensus pattern (24 bp):
AAAATCAAATTATCAATATAAATA
Found at i:15765 original size:78 final size:77
Alignment explanation
Indices: 15534--15811 Score: 285
Period size: 79 Copynumber: 3.6 Consensus size: 77
15524 TAACCTGTCA
* *
15534 TGGGGATACTCCAACCCCATCAATTTCGAGGGGATACTCCAACCTTGCTTTTATTTCTAAAATAT
1 TGGGGATACTCCAACCCCAT-TATTTCGAGGGGATACTCCAACC-CGCTTTTATTTCTAAAATAT
*
15599 TAATTTTTTCA-CC
64 TAAATTTTTCATCC
* * * * * ** **
15612 TTGAGAATATTCTAACCTCATTATTTTTAAGGGGATACTCCAACCCAATTTTTATTTCTAAAATA
1 -TGGGGATACTCCAACCCCATTA-TTTCGAGGGGATACTCCAACCC-GCTTTTATTTCTAAAATA
*
15677 TTAAAATTTTCATCC
63 TTAAATTTTTCATCC
* * * *
15692 TGGGGATACTCCAACCCCATTATTTCGAGGGGATACTCTAATCCCGCTCTTATTTCCAAAATACT
1 TGGGGATACTCCAACCCCATTATTTCGAGGGGATACTCCAA-CCCGCTTTTATTTCTAAAATATT
15757 AAATTTTTCAT-C
65 AAATTTTTCATCC
* * *
15769 TCGGGATACTCCAACCCC-CTA-TTCAGAGGGGATACTCTAACCC
1 TGGGGATACTCCAACCCCATTATTTC-GAGGGGATACTCCAACCC
15812 TGTTTCTTTT
Statistics
Matches: 165, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
75 6 0.04
76 17 0.10
77 18 0.11
78 42 0.25
79 80 0.48
80 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (77 bp):
TGGGGATACTCCAACCCCATTATTTCGAGGGGATACTCCAACCCGCTTTTATTTCTAAAATATTA
AATTTTTCATCC
Found at i:19127 original size:20 final size:20
Alignment explanation
Indices: 19104--19154 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
19094 AAGTACCTAG
*
19104 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
19124 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
*
19144 ATGTAACGATA
1 ATGTATCGATA
19155 TATTTAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:19159 original size:20 final size:20
Alignment explanation
Indices: 19111--19159 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
19101 TAGATGTATT
* *
19111 GATACATTCTTCAATGTATC
1 GATACATTTTTCAATGTAAC
19131 GATACATTTTTCAATGTAAC
1 GATACATTTTTCAATGTAAC
*
19151 GATATATTT
1 GATACATTT
19160 AGTTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
GATACATTTTTCAATGTAAC
Found at i:20054 original size:20 final size:21
Alignment explanation
Indices: 20017--20055 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20007 AGCCTTTGAC
**
20017 CATGCATTTTTTTTTATGTTT
1 CATGCATTTTTTAATATGTTT
20038 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
20056 CCAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:21464 original size:97 final size:95
Alignment explanation
Indices: 21305--21544 Score: 313
Period size: 97 Copynumber: 2.5 Consensus size: 95
21295 AATTTTATTT
* * *
21305 ATCGAGGATACTCCAACCCTATTCCTCCGAGGGGATACTCTAACCCCACTTTTAAACACATCAAA
1 ATCGAGGACACTCCAACCC-ATTCCTCCAAGGGGATACTCCAA-CCCACTTTTAAACACATCAAA
*
21370 GTTTAAATCTTATTC-CGACTTAAATTGTCATC
64 ATTTAAATCTTATTCTC-ACTTAAATTGTCATC
* *
21402 ATCGAGGACACTTCAACTCCATTCCTCCAAGGGGATACTCCAACCCAGCTTTTAAACGCATCAAA
1 ATCGAGGACACTCCAAC-CCATTCCTCCAAGGGGATACTCCAACCCA-CTTTTAAACACATCAAA
*
21467 ATTTAAATTTTATTCTCACTTAAATTGTCATC
64 ATTTAAATCTTATTCTCACTTAAATTGTCATC
* * *
21499 ATCGGGGACACTCCAACCCCATTCCTTCGAA-GGAATACTCCAACCC
1 ATCGAGGACACTCCAA-CCCATTCC-TCCAAGGGGATACTCCAACCC
21545 CGTTTTTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
96 4 0.03
97 115 0.91
98 8 0.06
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.28
Consensus pattern (95 bp):
ATCGAGGACACTCCAACCCATTCCTCCAAGGGGATACTCCAACCCACTTTTAAACACATCAAAAT
TTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:23173 original size:19 final size:19
Alignment explanation
Indices: 23131--23206 Score: 118
Period size: 19 Copynumber: 4.0 Consensus size: 19
23121 TTTCAATGAT
23131 TTGTATCGATACATAAAGTA
1 TTGTATCGATACAT-AAGTA
*
23151 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
*
23170 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
23189 TTGTATCGATACA-AAGTA
1 TTGTATCGATACATAAGTA
23207 AGCTACTGCC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
18 4 0.08
19 35 0.66
20 14 0.26
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:23262 original size:13 final size:13
Alignment explanation
Indices: 23244--23268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23234 AATACTCAAA
23244 TGTATCGATACAT
1 TGTATCGATACAT
23257 TGTATCGATACA
1 TGTATCGATACA
23269 CTGATCTTTG
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:23370 original size:52 final size:52
Alignment explanation
Indices: 23277--23404 Score: 195
Period size: 52 Copynumber: 2.5 Consensus size: 52
23267 CACTGATCTT
23277 TGTATCGATACAT-CAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
23328 TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
23380 TGTATCGACACATGTAGACAAATTT
1 TGTATCGATACATGCAGGCAAATTT
23405 TCATATTTCG
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 12 0.17
52 57 0.83
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:27194 original size:20 final size:20
Alignment explanation
Indices: 27169--27292 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
27159 TTTTTCCTAG
27169 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
27189 ATGTATCGATACATTCTGTCTTTTACCCA
1 ATGTATCGATACA-----T-TTTT---CA
*
27218 GATGTATCAATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
27239 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
27259 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
27279 ATGTATCGATACAT
1 ATGTATCGATACAT
27293 CTAGTTAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
20 57 0.69
21 2 0.02
24 4 0.05
25 2 0.02
26 4 0.05
29 2 0.02
30 12 0.14
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:31498 original size:60 final size:59
Alignment explanation
Indices: 31425--31555 Score: 244
Period size: 60 Copynumber: 2.2 Consensus size: 59
31415 ATAAATGAAT
*
31425 GTATCGATACATGCTTAAAATGTTTTGAGACAAAACTACCCTGCATATTGCCAAGGAAAA
1 GTATCGATACATGCTTAAAATGTTTTGAGACAAAACTACCCTGCATACTGCCAAGG-AAA
31485 GTATCGATACATGCTTAAAATGTTTTGAGACAAAACTACCCTGCATACTGCCAAGGAAA
1 GTATCGATACATGCTTAAAATGTTTTGAGACAAAACTACCCTGCATACTGCCAAGGAAA
31544 GTATCGATACAT
1 GTATCGATACAT
31556 AATTAAAGTA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 15 0.21
60 55 0.79
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (59 bp):
GTATCGATACATGCTTAAAATGTTTTGAGACAAAACTACCCTGCATACTGCCAAGGAAA
Done.