Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2090
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: 42578
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5191 original size:13 final size:13
Alignment explanation
Indices: 5173--5197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5163 GAAATATTAA
5173 TTATAATAATTTG
1 TTATAATAATTTG
5186 TTATAATAATTT
1 TTATAATAATTT
5198 TAGTAAACTA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTATAATAATTTG
Found at i:8009 original size:26 final size:27
Alignment explanation
Indices: 7963--8028 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
7953 AAAATAATGA
* *
7963 ATTTTA-CCCTAAGTATGAAAATTACC
1 ATTTTACCCCTAGGTATGAAAATGACC
*
7989 ATTTTACCCCTAGGTGT-AAAATGACC
1 ATTTTACCCCTAGGTATGAAAATGACC
* * *
8015 GTTATACCCTTAGG
1 ATTTTACCCCTAGG
8029 GTTAATTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 25 0.76
27 8 0.24
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (27 bp):
ATTTTACCCCTAGGTATGAAAATGACC
Found at i:8360 original size:20 final size:20
Alignment explanation
Indices: 8330--8374 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
8320 CTGTTTTGTT
8330 ATGGG-CCAACTGTATTGAA
1 ATGGGCCCAACTGTATTGAA
* *
8349 ATGGGCCCAACTGTGTTGAT
1 ATGGGCCCAACTGTATTGAA
8369 ATGGGC
1 ATGGGC
8375 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTGAA
Found at i:12352 original size:13 final size:13
Alignment explanation
Indices: 12334--12358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12324 ACAACTGCTA
12334 AAACATATTTGTT
1 AAACATATTTGTT
12347 AAACATATTTGT
1 AAACATATTTGT
12359 ATTTGGCTAA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
AAACATATTTGTT
Found at i:15630 original size:102 final size:104
Alignment explanation
Indices: 15453--15716 Score: 426
Period size: 102 Copynumber: 2.5 Consensus size: 104
15443 ACCGTTATTG
* *
15453 GTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
15518 TCAGCACATAGCAACCCCCTTTT-CATTTCAAAGATACA
66 TCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACA
15556 GTGGATATCGCACTTAGCACCACCAATGAA-CGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
**
15620 TCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
66 TCAGCACATAGCAACCCCCTTTT-ACATTTCAAAGATACA
* **
15660 GTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
15717 TTATATACAA
Statistics
Matches: 150, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
102 57 0.38
103 28 0.19
104 40 0.27
105 25 0.17
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (104 bp):
GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACA
Found at i:16074 original size:29 final size:29
Alignment explanation
Indices: 16041--16104 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
16031 TAATCCACCA
16041 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
16070 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
16100 CCCAA
1 CCCAA
16105 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:16078 original size:30 final size:30
Alignment explanation
Indices: 16048--16104 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16038 CCACCCAACT
16048 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
16077 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
16105 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:20719 original size:50 final size:50
Alignment explanation
Indices: 20650--20753 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
20640 ACTTTATAAG
20650 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
1 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
20700 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
1 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
20750 TTGA
1 TTGA
20754 TTGAGTATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (50 bp):
TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
Found at i:24393 original size:27 final size:26
Alignment explanation
Indices: 24361--24638 Score: 235
Period size: 27 Copynumber: 10.3 Consensus size: 26
24351 GTAGGGCAAA
*
24361 TCAGTCATTTTACCTTACAGGGGTATT
1 TCAGTCATTTTACC-TATAGGGGTATT
* *
24388 ACAGTCATTTTACCTTATAGAGGTATT
1 TCAGTCATTTTACC-TATAGGGGTATT
* * *
24415 TTAGTCATTTTATCCCATGGGGGTATT
1 TCAGTCATTTTA-CCTATAGGGGTATT
*
24442 TCAATCATTTTATCCTAT-GAGGGTATT
1 TCAGTCATTTTA-CCTATAG-GGGTATT
24469 TCAGTCATTTTACCCTAT-GAGGGTATT
1 TCAGTCATTTTA-CCTATAG-GGGTATT
* * *
24496 TCGGTTATTTTACCCTATGGGAGGTATT
1 TCAGTCATTTTA-CCTATAGG-GGTATT
* *
24524 TCGGTCATTTTACCCTATGGGGGTATT
1 TCAGTCATTTTA-CCTATAGGGGTATT
** *
24551 TTGGTCATTTTATCATATAGGGGTATT
1 TCAGTCATTTTA-CCTATAGGGGTATT
24578 T-AGGTCA-TTTACCCTAT-GAGGGTATT
1 TCA-GTCATTTTA-CCTATAG-GGGTATT
*
24604 TC-GATCATTTTACCTATGGGGGTATT
1 TCAG-TCATTTTACCTATAGGGGTATT
24630 TCAGTCATT
1 TCAGTCATT
24639 ATTTTGACCC
Statistics
Matches: 217, Mismatches: 23, Indels: 23
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.01
26 39 0.18
27 147 0.68
28 29 0.13
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (26 bp):
TCAGTCATTTTACCTATAGGGGTATT
Found at i:24643 original size:109 final size:109
Alignment explanation
Indices: 24361--24649 Score: 301
Period size: 108 Copynumber: 2.7 Consensus size: 109
24351 GTAGGGCAAA
* * * * * *
24361 TCAGTCATTTTACCTTA-CAGGGGTATTAC-AGTCATTTTACCTTATAGAGGTATTTTAGTCATT
1 TCAGTCATTTTACCCTATGA-GGGTATTTCGA-TCATTTTACC-TATGGGGGTATTTCAGTCATT
* *
24424 -TTAT-CCCATGGGGGTATTTCAATCATTTTATCCTATGAGGGTATT
63 ATTTTACCCATGGGGGTATTTCAATCATTTTATCATATGAGGGTATT
* * *
24469 TCAGTCATTTTACCCTATGAGGGTATTTCGGTTATTTTACCCTATGGGAGGTATTTCGGTC---A
1 TCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTA-CCTATGGG-GGTATTTCAGTCATTA
***
24531 TTTTACCCTATGGGGGTATTTTGGTCATTTTATCATAT-AGGGGTATT
64 TTTTACCC-ATGGGGGTATTTCAATCATTTTATCATATGA-GGGTATT
24578 T-AGGTCA-TTTACCCTATGAGGGTATTTCGATCATTTTACCTATGGGGGTATTTCAGTCATTAT
1 TCA-GTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTATGGGGGTATTTCAGTCATTAT
24641 TTTGACCCA
65 TTT-ACCCA
24650 ACATGGCCCA
Statistics
Matches: 151, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
106 11 0.07
107 11 0.07
108 69 0.46
109 56 0.37
110 4 0.03
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (109 bp):
TCAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTATGGGGGTATTTCAGTCATTATT
TTACCCATGGGGGTATTTCAATCATTTTATCATATGAGGGTATT
Found at i:28680 original size:20 final size:20
Alignment explanation
Indices: 28655--28695 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28645 TTGTGGAATT
28655 GAGAAAGTATGATGATAATA
1 GAGAAAGTATGATGATAATA
28675 GAGAAAGTATGATGATAATA
1 GAGAAAGTATGATGATAATA
28695 G
1 G
28696 TTGAATTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (20 bp):
GAGAAAGTATGATGATAATA
Found at i:33108 original size:28 final size:28
Alignment explanation
Indices: 33044--33115 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
33034 ATCTTCGATG
*
33044 TCTCGCACACTAAGTTTCATACTCAATA
1 TCTCGCACACTAAGTGTCATACTCAATA
* *
33072 TCT-GACACACCAAGTGTCATTCTCAATA
1 TCTCG-CACACTAAGTGTCATACTCAATA
*
33100 TTTCGCACACTAAGTG
1 TCTCGCACACTAAGTG
33116 CCACATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 35 0.95
29 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (28 bp):
TCTCGCACACTAAGTGTCATACTCAATA
Found at i:33162 original size:44 final size:40
Alignment explanation
Indices: 33102--33202 Score: 130
Period size: 40 Copynumber: 2.4 Consensus size: 40
33092 TCTCAATATT
33102 TCGCACACTAAGTGCCACATATATATAGTCGAAGCTATCTCAAA
1 TCGCACACTAAGTGCCAC--AT-T-TAGTCGAAGCTATCTCAAA
* * *
33146 TCGCACACCAAATGCCACATTTAGTCGAAGCTATTTCAAA
1 TCGCACACTAAGTGCCACATTTAGTCGAAGCTATCTCAAA
*
33186 CCGCACACTAAGTGCCA
1 TCGCACACTAAGTGCCA
33203 TTCTTAGTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
40 32 0.63
41 1 0.02
42 2 0.04
44 16 0.31
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.23
Consensus pattern (40 bp):
TCGCACACTAAGTGCCACATTTAGTCGAAGCTATCTCAAA
Found at i:37524 original size:50 final size:50
Alignment explanation
Indices: 37455--37558 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
37445 ACTTTATAAG
37455 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
1 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
37505 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
1 TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
37555 TTGA
1 TTGA
37559 TTGAGTATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (50 bp):
TTGAATTCTAACTTATGGCATGTATAGACTAGCCTTTGTGTTAGTTTATT
Done.