Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: C7673
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: 5372
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Found at i:500 original size:138 final size:138
Alignment explanation
Indices: 1--500 Score: 713
Period size: 138 Copynumber: 3.6 Consensus size: 138
*
1 ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCTAACGG
1 ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGG
* * * *
66 CTCGCTGGGCACTTCGACGTCCGTG--TTTCCTCATTTG-ACGTCTGGT-TCGTTGACTGAGTAC
66 CTCGCTGGGCACTTCTAC--CC-TGACCTTCC-C----GCAC-TCCGGTCCCG-TGACTGAGTAC
127 ACCACCACCTGGACCACC
121 ACCACCACCTGGACCACC
* * * *
145 ACTGGTGACGATGGTAAGCCTACCACCGACTCAGGTCTTGTTGATGTGACCACCGACTCCGATGG
1 ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGG
* **
210 CTCGTTGACCACTTCTACCCTGACCTTCCCGCACTCCGGTCCCGTGACTGAGTACACCACCACCT
66 CTCGCTGGGCACTTCTACCCTGACCTTCCCGCACTCCGGTCCCGTGACTGAGTACACCACCACCT
275 GGACCACC
131 GGACCACC
* * *
283 ACTGGTCACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCGATGG
1 ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGG
* *
348 CTTGCT-GACAACTTCTACCCTGACCTTCCCGCACTCCGGTCCCGTGACTGAGTACACCACCACC
66 CTCGCTGGGC-ACTTCTACCCTGACCTTCCCGCACTCCGGTCCCGTGACTGAGTACACCACCACC
412 TGGACCACC
130 TGGACCACC
421 ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGG
1 ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGG
486 CTCGCTGGGCACTTC
66 CTCGCTGGGCACTTC
501 GACATCCGTG
Statistics
Matches: 326, Mismatches: 24, Indels: 18
0.89 0.07 0.05
Matches are distributed among these distances:
137 1 0.00
138 236 0.72
139 6 0.02
141 2 0.01
142 3 0.01
143 4 0.01
144 74 0.23
ACGTcount: A:0.19, C:0.34, G:0.24, T:0.24
Consensus pattern (138 bp):
ACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGG
CTCGCTGGGCACTTCTACCCTGACCTTCCCGCACTCCGGTCCCGTGACTGAGTACACCACCACCT
GGACCACC
Left flanking sequence: None
Right flanking sequence: Indices 501 -- 1000
GACATCCGTGTTCCCCGATTTGACAATCACTTCCTCGCCTTTGATCTCCGGCTCCACCACATTAA
TTACTGTGACCCCTCCTAATAGTAACGGGGTATCTGTTAACTATCATACCGACACCGTCACATTC
ATCCCGGAGCTTCCTCATCCCACAACTCCAATCCCCACTGGCTGTCGTACAGTCTTCGCCACAGC
TACTGTGACCCCAACGATTTACTTCGTTTTAAACCCGTACTAATACCCCCCTATACCGTTTCGGT
TAAATCCTTCACTTCGGTTTTTTCTCTGGGCAGAGCCCTTATGTTTGAATATTGAATTCATGGCT
GTTATAGAATGTTTTAACTCCTTAAGTCTTGTAAGTTCTCCTATCTGGATATAAAGTGAATTTAT
GCCTCGCACTAGGCGCGTCACCTCCTTACATAACGAGTACCTGTCATCAAATTTTCCAGCTATGA
TGGAATACGAGTGTTGAAAACAAAAAATCAATTGAGATCTTGGAG
Found at i:4656 original size:12 final size:12
Alignment explanation
Indices: 4639--4664 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4629 GAGACGTGGG
4639 GGATTAATCGGA
1 GGATTAATCGGA
4651 GGATTAATCGGA
1 GGATTAATCGGA
4663 GG
1 GG
4665 TTGGCTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (12 bp):
GGATTAATCGGA
Left flanking sequence: Indices 4139 -- 4638
AGGCACCCAGAGTCAGTATCCGTACCTCAGTGATGAGAAACCAAGGGATCATTTCCGTGTTCCAA
GATGCAACAGCTGAAGGCACTCTTACAATGGGTGGCAGTGGAAACGGTTTGGTGAACGATGGCGT
AGTGTGTTTGAGTAAGTTTACCTGGGAGCAGGAGTCTCAGGTCACCGGTAAGGGGTGTATTCGTG
CCGGGGAAAATTCGGTGGTTCATATCAAACAAACGCTTCTGCCCATTTCGCAAACCATTTCTTTA
GACGGGCCCAATGCAGGTGTTCGTGTTGCGGATATCAATGTGGCTGATGCGTTCCGAGTTGCAGG
ACTTGGCAATGGCAATTTCGTAGCCACTGATGGTAAGATTCAGTACTACGACTACGATGAAAAAA
AGGGTATTCTTACTATCTCGGCCGACCCCCTAGGTCTTCAAAAGGTCAAATTCAACATCGGATTA
GGCTATGATAGAGACAAGTTCACTATTGGAACTGAGAGACGTGGG
Right flanking sequence: Indices 4665 -- 5164
TTGGCTCCCAGAAATCGACAGAATCCTTTATTATGACTATCCTGTGCCGGAAGGGGCCAATCTGA
ACGCTCACTGCTTAGCATGCCCTCTGCCACCTGCCCACCCTGGTTGGGATAAAATTCCTGACGAG
TCTGAGATTGTGGATAAAGAGCCAGCAACCATATACATCTCGGGTCTGGAAGGCACAGTCACTGA
ATGGTACCCAACTATAGTATTCACCGGTCCCAATCCATTTAAGGACAGTTCTGATATTGCTCCTA
CCACTCTGAAAGCAGCCAATGTTAGTACAACTCCTTACGATGCGCAACCCATTGAAACTGGACTG
CTTTCTGACGATTGTATTTTCTGTACACGATATCTGTCTATTTGGACATCTTTGGGCCCCGATGA
TAAAGCATTAACGGGAACGGCAGTTGTGGTTGTAACCACCGACTCTATCGGGTCGTTGTACACGT
CAACGAACTTTTGTCCAGAGTGCACTCAGTACACCACCACTTGGA
Found at i:5270 original size:129 final size:128
Alignment explanation
Indices: 5089--5372 Score: 385
Period size: 129 Copynumber: 2.2 Consensus size: 128
5079 TGTGGTTGTA
** ** *
5089 ACCACCGACTCTATCGGGTCGTTGTACACGTCAACGAACTTTTGTCCAGAGTGCACTCAGTACAC
1 ACCACCGACTCTA-CGGGTCGTTGTACACAACAACGAACTACTGTCCAGAGTGCACTCAATACAC
** * * *
5154 CACCACTTGGACTTCGACGGATGAA-AATGGCCAAGCGAGCACTGGTACGGGTATTGTTGATGTG
65 CACCACTTGGACCACGACGGAT-AAGAATGGCCAAGCGAGCACTGGTACGGGCATCGTTGACGTG
5218 ACCACCGACTCTTACGGGTCGTTGTACACAACAACGAA-TGACTGTCTC-GAGTGCACTCAATAC
1 ACCACCGACTC-TACGGGTCGTTGTACACAACAACGAACT-ACTGTC-CAGAGTGCACTCAATAC
* *
5281 ACCACTACTTGGACCACGACGGATAAGAATGGCCAAGCGAGCACTGGTACGGGCATCGTTGCCGT
63 ACCACCACTTGGACCACGACGGATAAGAATGGCCAAGCGAGCACTGGTACGGGCATCGTTGACGT
5346 G
128 G
5347 ACCACCGACTCGTACGGGTCGTTGTA
1 ACCACCGACTC-TACGGGTCGTTGTA
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
128 3 0.02
129 132 0.96
130 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (128 bp):
ACCACCGACTCTACGGGTCGTTGTACACAACAACGAACTACTGTCCAGAGTGCACTCAATACACC
ACCACTTGGACCACGACGGATAAGAATGGCCAAGCGAGCACTGGTACGGGCATCGTTGACGTG
Left flanking sequence: Indices 4589 -- 5088
GATTAGGCTATGATAGAGACAAGTTCACTATTGGAACTGAGAGACGTGGGGGATTAATCGGAGGA
TTAATCGGAGGTTGGCTCCCAGAAATCGACAGAATCCTTTATTATGACTATCCTGTGCCGGAAGG
GGCCAATCTGAACGCTCACTGCTTAGCATGCCCTCTGCCACCTGCCCACCCTGGTTGGGATAAAA
TTCCTGACGAGTCTGAGATTGTGGATAAAGAGCCAGCAACCATATACATCTCGGGTCTGGAAGGC
ACAGTCACTGAATGGTACCCAACTATAGTATTCACCGGTCCCAATCCATTTAAGGACAGTTCTGA
TATTGCTCCTACCACTCTGAAAGCAGCCAATGTTAGTACAACTCCTTACGATGCGCAACCCATTG
AAACTGGACTGCTTTCTGACGATTGTATTTTCTGTACACGATATCTGTCTATTTGGACATCTTTG
GGCCCCGATGATAAAGCATTAACGGGAACGGCAGTTGTGGTTGTA
Right flanking sequence: None
Done.