Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2026
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: 17939
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:700 original size:3 final size:3
Alignment explanation
Indices: 692--729 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
682 CCGTAAGTAC
*
692 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
730 GGCTTGATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:850 original size:2 final size:2
Alignment explanation
Indices: 843--871 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
833 TGTAAGCTTG
843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
872 GGCAACTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1937 original size:3 final size:3
Alignment explanation
Indices: 1931--1992 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
1921 AGCAGCATGG
*
1931 ATT ATT AGT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1978 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
1993 TTCCATTTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7564 original size:90 final size:90
Alignment explanation
Indices: 7406--7575 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 90
7396 GACTTTCTTG
* * * *
7406 ATTTTTTCTTTTTGTGATTTTTGATTTGCGCCGTAGTAGATTTGGAGGGAATGGAGGAACTTAGT
1 ATTTTTTCTCTTTGTGATTCTTGA-TTGCGCCATAGTAGATTTGGAGGGAATGGAAGAACTTAGT
7471 AGTCCTCCTCCATAGTTGCCCACTTA
65 AGTCCTCCTCCATAGTTGCCCACTTA
* * *
7497 ATTTTTTCTCTTTGTGATTCTTGA-TGTGCCATAGTTGGATTTGGAGGTAATGGAAGAACTTCA-
1 ATTTTTTCTCTTTGTGATTCTTGATTGCGCCATAG-TAGATTTGGAGGGAATGGAAGAACTT-AG
* *
7560 TAGTCTTTCTCCATAG
64 TAGTCCTCCTCCATAG
7576 CTTTCCAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
89 8 0.12
90 37 0.54
91 23 0.34
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (90 bp):
ATTTTTTCTCTTTGTGATTCTTGATTGCGCCATAGTAGATTTGGAGGGAATGGAAGAACTTAGTA
GTCCTCCTCCATAGTTGCCCACTTA
Found at i:11979 original size:2 final size:2
Alignment explanation
Indices: 11972--11996 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11962 TGTATATGTG
11972 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11997 GAAGATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13518 original size:2 final size:2
Alignment explanation
Indices: 13469--13499 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13459 TATTGAAAGG
*
13469 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13500 AAAGGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13643 original size:2 final size:2
Alignment explanation
Indices: 13631--13668 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
13621 ATTGTCAGAG
*
13631 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13669 GCTCCTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14091 original size:108 final size:107
Alignment explanation
Indices: 13886--14111 Score: 319
Period size: 108 Copynumber: 2.1 Consensus size: 107
13876 AAATATTTAT
* * * *
13886 GTTAAAAAAATTTAAAAGAGTAATTGGATAATATTTAGCTGGTGTTTATATATACTTGTGAAATC
1 GTTAAAAAAATTTAAAAGAGTAATTAGATAATATTTAACTGGTGCTTATATACACTTGTGAAATC
* **
13951 AACCCAAAGCAAGGGAATTGTTGGATTTTTTTTTCAATAAAAAG
66 AACCAAAAAAAAGGGAATTGTTGGA--TTTTTTTCAATAAAAAG
13995 GTTAAAAAAA-TTAAAAGAGTAATTAGATAATATTTAACTGGTGCTTATATACACTTGTGAAATC
1 GTTAAAAAAATTTAAAAGAGTAATTAGATAATATTTAACTGGTGCTTATATACACTTGTGAAATC
14059 AACACAAAAAAAAGGGAATTGGGTTGGATTTTTTTTTCAATAAAAAG
66 AAC-CAAAAAAAAGGGAATT--GTTGGA--TTTTTTTCAATAAAAAG
14106 GTTAAA
1 GTTAAA
14112 TAGTTGACAT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
108 53 0.50
109 23 0.21
111 31 0.29
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (107 bp):
GTTAAAAAAATTTAAAAGAGTAATTAGATAATATTTAACTGGTGCTTATATACACTTGTGAAATC
AACCAAAAAAAAGGGAATTGTTGGATTTTTTTCAATAAAAAG
Done.