Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold13
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 13776
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:149 original size:6 final size:6
Alignment explanation
Indices: 138--223 Score: 100
Period size: 6 Copynumber: 13.0 Consensus size: 6
128 TCTTATTGGT
138 GTGTTG GTGTTGG AGTGTTG GTGTTGG TGTGTTG GTGTTG GTGTTG GTGTTGG
1 GTGTTG GTGTT-G -GTGTTG GTGTT-G -GTGTTG GTGTTG GTGTTG GTGTT-G
191 TGTGTTG GTGTTGG TGTGTTG GTGTTG GTGTTG
1 -GTGTTG GTGTT-G -GTGTTG GTGTTG GTGTTG
224 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
6 44 0.61
7 8 0.11
8 20 0.28
ACGTcount: A:0.01, C:0.00, G:0.50, T:0.49
Consensus pattern (6 bp):
GTGTTG
Left flanking sequence: Indices 1 -- 137
TAGCGTCAGGATGGGCGGTATCGCCACAGAACCATCCCGTGGTCGGCGCGGGGAGTTGCAAGCCT
CTGGGCTTCGCTTCCTTTGCCATATGGGAGACGAAATCAGAAGTACTAGCAGTACCACCCCCTCT
TATTGGT
Right flanking sequence: Indices 224 -- 723
NNNNNNNNNNNNNNNNNNNNNTGTTGTTGTTGTTGTTGCTGGAGGTTGTTTAAGGGTTGGATGCC
AATGGCTCCTTTTCCCCCTGTTGGTGGTGTCAGTGGTATCCGATTCGATTTGTTGGATCGGGTGC
CATTGGCGCCGTTTTTTCCCCTGTTGGTTGTGCCATTGGTATCCAATCCGGGTTTCTATAATTGT
TTAGTTAAGCACTGGGTGCGCCTTCGGAGTAGCCTGCATGAGCGGGCTACCCTGAAGCCGTACTG
GGGGCTTATATTGTAGTATATAGGATATATAGGATATATAGGATATATACAGGTTCGCCATAATC
AACGCTATCTACGGTATCAACAGTAAAGTCACGTGACATATATCACCTGCCATCAGTGAGCCGCA
CCAGTATATTAGGTCAGCTCGTAAAGCGGCTAACATAACGTGTTATGTAATGCTCGTAAAGTCTT
TGGCAAATGTTGAATGGTCGTCGTATAGCTCGTCGTTTAGTGGGG
Found at i:155 original size:14 final size:14
Alignment explanation
Indices: 133--221 Score: 155
Period size: 14 Copynumber: 6.5 Consensus size: 14
123 CCCCCTCTTA
133 TTGGTGTGTTGGTG
1 TTGGTGTGTTGGTG
*
147 TTGGAGTGTTGGTG
1 TTGGTGTGTTGGTG
161 TTGGTGTGTTGGTG
1 TTGGTGTGTTGGTG
175 TT-G-GTGTTGGTG
1 TTGGTGTGTTGGTG
187 TTGGTGTGTTGGTG
1 TTGGTGTGTTGGTG
201 TTGGTGTGTTGGTG
1 TTGGTGTGTTGGTG
215 TTGGTGT
1 TTGGTGT
222 TGNNNNNNNN
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
12 11 0.15
13 2 0.03
14 58 0.82
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.49
Consensus pattern (14 bp):
TTGGTGTGTTGGTG
Left flanking sequence: Indices 1 -- 132
TAGCGTCAGGATGGGCGGTATCGCCACAGAACCATCCCGTGGTCGGCGCGGGGAGTTGCAAGCCT
CTGGGCTTCGCTTCCTTTGCCATATGGGAGACGAAATCAGAAGTACTAGCAGTACCACCCCCTCT
TA
Right flanking sequence: Indices 222 -- 721
TGNNNNNNNNNNNNNNNNNNNNNTGTTGTTGTTGTTGTTGCTGGAGGTTGTTTAAGGGTTGGATG
CCAATGGCTCCTTTTCCCCCTGTTGGTGGTGTCAGTGGTATCCGATTCGATTTGTTGGATCGGGT
GCCATTGGCGCCGTTTTTTCCCCTGTTGGTTGTGCCATTGGTATCCAATCCGGGTTTCTATAATT
GTTTAGTTAAGCACTGGGTGCGCCTTCGGAGTAGCCTGCATGAGCGGGCTACCCTGAAGCCGTAC
TGGGGGCTTATATTGTAGTATATAGGATATATAGGATATATAGGATATATACAGGTTCGCCATAA
TCAACGCTATCTACGGTATCAACAGTAAAGTCACGTGACATATATCACCTGCCATCAGTGAGCCG
CACCAGTATATTAGGTCAGCTCGTAAAGCGGCTAACATAACGTGTTATGTAATGCTCGTAAAGTC
TTTGGCAAATGTTGAATGGTCGTCGTATAGCTCGTCGTTTAGTGG
Found at i:163 original size:20 final size:20
Alignment explanation
Indices: 138--223 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
128 TCTTATTGGT
138 GTGTTGGTGT-TGGAGTGTTG
1 GTGTTGGTGTGTGG-GTGTTG
*
158 GTGTTGGTGTGTTGGTGTTG
1 GTGTTGGTGTGTGGGTGTTG
178 GTGTTGGTGT-TGGTGTGTTG
1 GTGTTGGTGTGTGG-GTGTTG
*
198 GTGTTGGTGTGTTGGTGTTG
1 GTGTTGGTGTGTGGGTGTTG
218 GTGTTG
1 GTGTTG
224 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.03
20 54 0.90
21 4 0.07
ACGTcount: A:0.01, C:0.00, G:0.50, T:0.49
Consensus pattern (20 bp):
GTGTTGGTGTGTGGGTGTTG
Left flanking sequence: Indices 1 -- 137
TAGCGTCAGGATGGGCGGTATCGCCACAGAACCATCCCGTGGTCGGCGCGGGGAGTTGCAAGCCT
CTGGGCTTCGCTTCCTTTGCCATATGGGAGACGAAATCAGAAGTACTAGCAGTACCACCCCCTCT
TATTGGT
Right flanking sequence: Indices 224 -- 723
NNNNNNNNNNNNNNNNNNNNNTGTTGTTGTTGTTGTTGCTGGAGGTTGTTTAAGGGTTGGATGCC
AATGGCTCCTTTTCCCCCTGTTGGTGGTGTCAGTGGTATCCGATTCGATTTGTTGGATCGGGTGC
CATTGGCGCCGTTTTTTCCCCTGTTGGTTGTGCCATTGGTATCCAATCCGGGTTTCTATAATTGT
TTAGTTAAGCACTGGGTGCGCCTTCGGAGTAGCCTGCATGAGCGGGCTACCCTGAAGCCGTACTG
GGGGCTTATATTGTAGTATATAGGATATATAGGATATATAGGATATATACAGGTTCGCCATAATC
AACGCTATCTACGGTATCAACAGTAAAGTCACGTGACATATATCACCTGCCATCAGTGAGCCGCA
CCAGTATATTAGGTCAGCTCGTAAAGCGGCTAACATAACGTGTTATGTAATGCTCGTAAAGTCTT
TGGCAAATGTTGAATGGTCGTCGTATAGCTCGTCGTTTAGTGGGG
Found at i:514 original size:9 final size:9
Alignment explanation
Indices: 500--532 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
490 TATATTGTAG
500 TATATAGGA
1 TATATAGGA
509 TATATAGGA
1 TATATAGGA
518 TATATAGGA
1 TATATAGGA
527 TATATA
1 TATATA
533 CAGGTTCGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (9 bp):
TATATAGGA
Left flanking sequence: Indices 1 -- 499
TAGCGTCAGGATGGGCGGTATCGCCACAGAACCATCCCGTGGTCGGCGCGGGGAGTTGCAAGCCT
CTGGGCTTCGCTTCCTTTGCCATATGGGAGACGAAATCAGAAGTACTAGCAGTACCACCCCCTCT
TATTGGTGTGTTGGTGTTGGAGTGTTGGTGTTGGTGTGTTGGTGTTGGTGTTGGTGTTGGTGTGT
TGGTGTTGGTGTGTTGGTGTTGGTGTTGNNNNNNNNNNNNNNNNNNNNNTGTTGTTGTTGTTGTT
GCTGGAGGTTGTTTAAGGGTTGGATGCCAATGGCTCCTTTTCCCCCTGTTGGTGGTGTCAGTGGT
ATCCGATTCGATTTGTTGGATCGGGTGCCATTGGCGCCGTTTTTTCCCCTGTTGGTTGTGCCATT
GGTATCCAATCCGGGTTTCTATAATTGTTTAGTTAAGCACTGGGTGCGCCTTCGGAGTAGCCTGC
ATGAGCGGGCTACCCTGAAGCCGTACTGGGGGCTTATATTGTAG
Right flanking sequence: Indices 533 -- 1032
CAGGTTCGCCATAATCAACGCTATCTACGGTATCAACAGTAAAGTCACGTGACATATATCACCTG
CCATCAGTGAGCCGCACCAGTATATTAGGTCAGCTCGTAAAGCGGCTAACATAACGTGTTATGTA
ATGCTCGTAAAGTCTTTGGCAAATGTTGAATGGTCGTCGTATAGCTCGTCGTTTAGTGGGGTGGT
TGTTTGTTAGAGGGGGCCGTTTTTACATGCAGACGTCTCTGAAATTTGTTAGAGGGGGCCGGTAT
GCAATGTCACGTGATCAGAGTCACACTATAATGTAAACTCGTAAAGTGATGTTCGTAAAGTCTTA
TTGGATTTTTGAATTGACGTCGTATAGCTCGTCGTTTAATGGGTGTTTGGTAAGAAATATAAACT
AGAATAACTCCTCAAATAATGGTCCAAACAAGCCATTGAGTACTGACATCGATACAGACAGCACT
AATTTACCTCTCTTAAGTACTACCAGGTCGATTGGTGGCGAATTG
Found at i:4492 original size:18 final size:18
Alignment explanation
Indices: 4469--4525 Score: 105
Period size: 18 Copynumber: 3.2 Consensus size: 18
4459 GTGAACAGGA
4469 CCGGGCAAAGACCTAACT
1 CCGGGCAAAGACCTAACT
4487 CCGGGCAAAGACCTAACT
1 CCGGGCAAAGACCTAACT
*
4505 CCGGGCAAAGTCCTAACT
1 CCGGGCAAAGACCTAACT
4523 CCG
1 CCG
4526 TTATCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (18 bp):
CCGGGCAAAGACCTAACT
Left flanking sequence: Indices 3969 -- 4468
GGATCGATAGTGTAGAAGTAGTCCTGGCCAATTCTAGCTCCAAAAGCACCGTTTCCAGGCATGAC
TCCCCCGGGAAACGCAAATGACTCTATTGGCACCTTCCCCTGACACTCACGATACAATGCTTTGT
ATATATCCCTAAATTCGACACAATCATAACGACATTTAAAGCTCCCAGGGGCAACTGTGAAAGTG
AAAGTGTCATTGTTCCAGACTCCCAATGTATTCATCTCGGCGTCTCCACGACTTATCTCCAGGCC
GTGGTCATCGGAGTAGGAAAGGTCGTCGTACAGGGCCGCGACAGTTAGCGTTAGTAATAGTAACA
ATCTGAACATGTCAGCACTTGTGCTGAAAATGCATTATATGTTAAAAAAGAATGGGCACCACCAC
AAGCATTATTTTTTTACATCGTTGTCCCGACATGACGCAACGGGGCATCGTGGTGGTAGAAAACA
TGGGGTAAACCTGTAAGGAGTGGGGTGCTGGCGCAGTGAACAGGA
Right flanking sequence: Indices 4526 -- 5025
TTATCAAATTCTGGATTGCAAATACAAACCTGAGCGATCATTCCTATGGGCTGATTCAAACGGTT
TAACGGCGCCAACGTTGCATTGTTAGTCTCGTAAACCTTAATGATGGCAGACATTTTCTGTATGG
CGTCTTCGGGTTATTGACGCACACGCTGGTTTGGAGCATCCATTTGGGGTGCGACTGTCCCTAGC
CATGCTTCTATATTGCAGCTGCTTGCGTGTTTACCTTCCCGCCGGTTTTGATCGATTGTTTGCGC
GTATTCTGTCGTATTTTCAAGTGACAGTTACATCCGTGAAACGTTCCGGACACACCACTAACGTC
AGCGTGGGTTAAAGGCATATGTGTGTTACTATTTTTGCTTACGGGGGCCTCTCTCATAGGTGCCC
TTCTGTGCACATGTTTAAGAGACAAGAAATAATCCTATCGATCAGGGCGGACCAAGGATGGCCAG
GTGGTGCCTACCTTCCGGGTCGAATAGCTCCGCCCGTTTACCCGG
Done.