Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold309
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: 161035
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
File 2 of 2
Found at i:142106 original size:98 final size:97
Alignment explanation
Indices: 141754--142243 Score: 439
Period size: 92 Copynumber: 5.2 Consensus size: 97
141744 ATATGCGGCT
* * * * * * * *
141754 AGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGTGTTGATTCATGGCCAGCGACATTAGAC
1 AGCGATATTGGACTTAAAGAT--GAAG-ATGCCAATATGCTGATTCAAGGCCA-CGATATTGGAC
* * * **
141819 TTGAAGAAG-A-ATGCCAATGTGCTGAGACAAGGCC
62 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * * * * **
141853 AGCGACATTGGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCTAACGATATCAGAC
1 AGCGATATTGGACTTA--AA-GATGAAGATGCCAATATGCTGATTCAAGGC-CACGATATTGGAC
* *
141918 TTAAAGATGAAGATACCAATGTGCTGATTCAAGGCC
62 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
141954 GGTGATATTGGACTT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCA-CGATATTGGACTTA
142013 AAGATGAAGATGCCAATATGCTGATTCAAGGCC
65 AAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
142046 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCACTGATATTGGACTAA
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAC-GATATTGGACTTA
* *
142111 AAGATGAAGATACCAATCTGCTGATTCAAGGCC
65 AAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * * *
142144 AGCGACATTGG--TTTAA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGTGATATTGG--TTT
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCA-CGATATTGGACTTA
142200 AA-A-G--G-TGCCAATATGCTGATTCAAGGCC
65 AAGATGAAGATGCCAATATGCTGATTCAAGGCC
142228 AGCGATATTGGACTTA
1 AGCGATATTGGACTTA
142244 GAAAAAGATG
Statistics
Matches: 331, Mismatches: 43, Indels: 47
0.79 0.10 0.11
Matches are distributed among these distances:
84 31 0.09
85 1 0.00
86 2 0.01
87 1 0.00
88 1 0.00
89 3 0.01
91 32 0.10
92 79 0.24
93 3 0.01
94 2 0.01
95 2 0.01
96 4 0.01
97 2 0.01
98 78 0.24
99 49 0.15
100 5 0.02
101 34 0.10
102 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (97 bp):
AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCACGATATTGGACTTAA
AGATGAAGATGCCAATATGCTGATTCAAGGCC
Found at i:142182 original size:42 final size:42
Alignment explanation
Indices: 142123--142238 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
142113 GATGAAGATA
* *
142123 CCAATCTGCTGATTCAAGGCCAGCGACATTGGTTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTTTAAAGGTG
*
142165 CCAATATGCTGATTCAAGGCCAGTGATATTGGTTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTTTAAAGGTG
142207 CCAATATGCTGATTCAAGGCCAGCGATATTGG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGG
142239 ACTTAGAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (42 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGTTTAAAGGTG
Found at i:142183 original size:21 final size:21
Alignment explanation
Indices: 142159--142225 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
142149 CATTGGTTTA
142159 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* ** * *
142180 AA-G-GCCAGTGATATTGGTTTA
1 AAGGTGCCAAT-ATGCT-GATTC
142201 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
142222 AAGG
1 AAGG
142226 CCAGCGATAT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 14 0.44
22 4 0.12
23 5 0.16
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:142293 original size:31 final size:30
Alignment explanation
Indices: 142255--142335 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 30
142245 AAAAAGATGC
142255 CACCAACTTGTGTGGGCTTTTGATAGGGTT-G
1 CACCAACTTGTGTGGGCTTTTGA-A-GGTTGG
142286 CACCAACTTGTGT--GCTTTTGAAGGTTGG
1 CACCAACTTGTGTGGGCTTTTGAAGGTTGG
*
142314 CACTAAC-T-TGTGGGCTTTTGAA
1 CACCAACTTGTGTGGGCTTTTGAA
142336 AAGATACCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
26 3 0.07
27 5 0.11
28 17 0.37
29 8 0.17
31 13 0.28
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (30 bp):
CACCAACTTGTGTGGGCTTTTGAAGGTTGG
Found at i:142352 original size:57 final size:57
Alignment explanation
Indices: 142291--142682 Score: 475
Period size: 57 Copynumber: 6.8 Consensus size: 57
142281 GGTTGCACCA
* * * * * *
142291 ACTTGTGTGCTTTTGAAGGTTGGCACTAACTTGTGGGCTTTTGAAAAGATACCATTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
* ** * * * *
142348 ACTTGTGGGC-TTTGAAAAAGGGTGTTATTGACTTGTGGGCTTTTG-AAGGTTGCCACTG
1 ACTTGTGGGCTTTTG---AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
*
142406 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
*
142463 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
142520 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
* * * * * * * *
142577 GCTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGCTTTTG-AAGGTTGCCACTG
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
* * * *
142634 ACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGGGCTTTGGAAAAG
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAG
142683 GTGAGGAATG
Statistics
Matches: 296, Mismatches: 32, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
56 27 0.09
57 196 0.66
58 46 0.16
59 27 0.09
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (57 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
Found at i:142523 original size:86 final size:85
Alignment explanation
Indices: 142291--142682 Score: 462
Period size: 86 Copynumber: 4.6 Consensus size: 85
142281 GGTTGCACCA
* * * * * **
142291 ACTTGTGTGCTTTTGAAGGTTGGCACTAACTTGTGGGCTTTTGAAAAGATACCATTGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
* * ** *
142356 GCTTTGAAAAAGGGTGTTATTG
66 GCTTTG-GAAA-GTTGCCACTG
* * * *
142378 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
* *
142442 GCTTTGGAAAAGATGCCACGG
66 GCTTTGG-AAAGTTGCCACTG
142463 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
* *
142528 GCTTTTGAAGGTTGCCACTG
66 GCTTTGGAAAGTTGCCACTG
* * * *
142548 ACTTGTGGGCTTTGGAAAAGATGCCACTGGCTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTG
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTG
* *
142613 GGCTTTTGAAGGTTGCCACTG
65 GGCTTTGGAAAGTTGCCACTG
* * * *
142634 ACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGGGCTTTGGAAAAG
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAG
142683 GTGAGGAATG
Statistics
Matches: 275, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
85 71 0.26
86 164 0.60
87 40 0.15
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (85 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
GCTTTGGAAAGTTGCCACTG
Found at i:142582 original size:143 final size:142
Alignment explanation
Indices: 142319--142675 Score: 552
Period size: 143 Copynumber: 2.5 Consensus size: 142
142309 GTTGGCACTA
* * * * * * ** *
142319 ACTTGTGGGCTTTTGAAAAGATACCATTGACTTGTGGGCTTTGAAAAAGGGTGTTATTGACTTGT
1 ACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACTGACTTGT
* * *
142384 GGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG
64 GGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGATGCCACTGACTTGTGGGCTTTGG
142449 AAAAGATGCCACGG
129 AAAAGATGCCACGG
*
142463 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGG
*
142528 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGGCTTGTGGGCTTTGGA
66 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGATGCCACTGACTTGTGGGCTTTGGA
142593 AAAGATGCCACGG
130 AAAGATGCCACGG
*
142606 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGG
142671 GCTTT
66 GCTTT
142676 GGAAAAGGTG
Statistics
Matches: 196, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
142 47 0.24
143 134 0.68
144 15 0.08
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (142 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGG
GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGATGCCACTGACTTGTGGGCTTTGGAA
AAGATGCCACGG
Found at i:144139 original size:13 final size:12
Alignment explanation
Indices: 144117--144161 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
144107 ATCCGGACCC
*
144117 TTTTTGTTGTTAT
1 TTTTTTTTGTT-T
*
144130 TTTTTTTTGTGT
1 TTTTTTTTGTTT
144142 TTTTTTTTGTTT
1 TTTTTTTTGTTT
144154 TTTTTTTT
1 TTTTTTTT
144162 TTTGCGGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:157470 original size:13 final size:13
Alignment explanation
Indices: 157452--157479 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
157442 ATACAAAGAT
157452 CAATGTATCGATA
1 CAATGTATCGATA
157465 CAATGTATCGATA
1 CAATGTATCGATA
157478 CA
1 CA
157480 TTTCCTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:157535 original size:19 final size:19
Alignment explanation
Indices: 157511--157558 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
157501 AGCGATACAT
*
157511 TGTATCGATACAACATTTA
1 TGTATCGATACAACACTTA
157530 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
157549 TGTATCGATA
1 TGTATCGATA
157559 TAGTTACTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:159790 original size:10 final size:9
Alignment explanation
Indices: 159771--159807 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
159761 ACTAGCTTAG
159771 TTTTTTCTA
1 TTTTTTCTA
159780 TTTTTTCCTA
1 TTTTTT-CTA
159790 TTTTCTTCTA
1 TTTT-TTCTA
159800 TTTTTTCT
1 TTTTTTCT
159808 TACCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 10 0.38
10 14 0.54
11 2 0.08
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTCTA
Done.