Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2467
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: 36856
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Found at i:7405 original size:40 final size:40
Alignment explanation
Indices: 7347--7564 Score: 334
Period size: 40 Copynumber: 5.5 Consensus size: 40
7337 CAGATGATAA
* *
7347 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
7387 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
7427 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
7467 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
7507 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
7547 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
7565 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 17 0.10
40 148 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:13810 original size:20 final size:20
Alignment explanation
Indices: 13785--13825 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13775 ATATATCATA
13785 AAACATAAAATAAAATTATT
1 AAACATAAAATAAAATTATT
13805 AAACATAAAATAAAATTATT
1 AAACATAAAATAAAATTATT
13825 A
1 A
13826 TATGTGTTAT
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:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAACATAAAATAAAATTATT
Found at i:15621 original size:21 final size:20
Alignment explanation
Indices: 15597--15635 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15587 GTGTAAATGT
15597 AGTAACATAATTGTTATTTTA
1 AGTAACATAA-TGTTATTTTA
**
15618 AGTAATTTAATGTTATTT
1 AGTAACATAATGTTATTT
15636 ATATGATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
AGTAACATAATGTTATTTTA
Found at i:18314 original size:27 final size:27
Alignment explanation
Indices: 18276--18328 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
18266 AGTAAATTGG
18276 TACTTATTTCAAATTATGCATAATGCT
1 TACTTATTTCAAATTATGCATAATGCT
18303 TACTTATTTCAAATTATGCATAATGC
1 TACTTATTTCAAATTATGCATAATGC
18329 AATTGATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (27 bp):
TACTTATTTCAAATTATGCATAATGCT
Found at i:19829 original size:23 final size:23
Alignment explanation
Indices: 19799--19844 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19789 CGTTTTATGC
19799 GTGTATAGTATTAGAGAAAGACA
1 GTGTATAGTATTAGAGAAAGACA
19822 GTGTATAGTATTAGAGAAAGACA
1 GTGTATAGTATTAGAGAAAGACA
19845 ACGTTGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.26
Consensus pattern (23 bp):
GTGTATAGTATTAGAGAAAGACA
Found at i:23258 original size:50 final size:50
Alignment explanation
Indices: 23054--23286 Score: 214
Period size: 50 Copynumber: 4.8 Consensus size: 50
23044 GGTGTCGACA
* * * * *
23054 CCATGTCCCGGACATGGTCTTACACTAGCT-T-ACA-CATCAAAGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-TCGAGGCCGATG
* * * * *
23102 CCATGTCCTAGACATGGTCTTACACTGGCTTTCATTTATCG-GTGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG-GCCGATG
* * * * * *
23152 CCATATCCTAGACATGGTCTTACACT-G-ACACATA--TC-AAGCCAATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCCGATG
* * *
23197 TCATGTCCCAGACATGGCCTTACACTATCTCTCATATCTCGAGGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCCGATG
23247 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTC
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTC
23287 CCTAGCATCA
Statistics
Matches: 147, Mismatches: 28, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
45 28 0.19
46 2 0.01
47 5 0.03
48 30 0.20
49 4 0.03
50 78 0.53
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCCGATG
Found at i:33502 original size:25 final size:26
Alignment explanation
Indices: 33461--33515 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
33451 TTGATAAAAT
33461 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
33487 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
33512 TGAT
1 TGAT
33516 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Done.