Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g00455.F5
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: 4517
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Found at i:1005 original size:84 final size:84
Alignment explanation
Indices: 864--1033 Score: 243
Period size: 84 Copynumber: 2.0 Consensus size: 84
854 TAATGAAGAG
* * * *
864 TGGGTGCAAGATTCTCCTTTCTTTTAATATTTTAAAATCCAATTATTTCATGGAAATGATTTGAA
1 TGGGTACAAGATTCTCCTTTCTTTTAATATATTAAAATCCAATCATTTCATGGAAATGATTTAAA
*
929 CAG-TGTCCTATTTGTGTTA
66 C-GTTGTACTATTTGTGTTA
* * *
948 TGGGTACAGGATTCTCCTTTCTTTTAATATATTAAAATTCAATCATTTCATGGAAATGTTTTAAA
1 TGGGTACAAGATTCTCCTTTCTTTTAATATATTAAAATCCAATCATTTCATGGAAATGATTTAAA
*
1013 CGTTGTAGTATTTGTGTTA
66 CGTTGTACTATTTGTGTTA
1032 TG
1 TG
1034 CACATGCTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
83 1 0.01
84 75 0.99
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (84 bp):
TGGGTACAAGATTCTCCTTTCTTTTAATATATTAAAATCCAATCATTTCATGGAAATGATTTAAA
CGTTGTACTATTTGTGTTA
Found at i:1575 original size:374 final size:378
Alignment explanation
Indices: 1046--1773 Score: 954
Period size: 387 Copynumber: 1.9 Consensus size: 378
1036 CATGCTTTTG
* * *
1046 TTGTTTGTAATTACTCTCTGTTCATGGAAAATTAATAATATTCTAACTAGATTATAATCTGTGTA
1 TTGTTTGTAATTACTATCTGTGCATGGAAAATTAATAATATTCTAACTAGATTATAATCTCTGTA
** * *
1111 CATGATGGAAGTGGTCATGGATGCTAATATAAGTAGTATTGTATCCTTCTTAAGTGATCAAAATC
66 CATGATGGAAGTGGTCATACATGCTAATATAAGTAGTATTGTATCCTCCATAAGTGATCAAAATC
1176 TCTAATTTTGTTACCAAGTTATAATTGTGTTGCTAATGCA-TG-TG-TTTATATT-C-TTGTGAA
131 TCTAATTTTGTTACCAAGTTATAATTGTGTTGCTAATGCAGTGATGATTTATATTACTTTGTGAA
* * * * *
1236 TTGGTCAAAATATCAAAACTTTATTTTTAATTTATATTTTGTTTCTATATAATATGGAATTTGTC
196 TTGGTCAAAATATC-AAACTTTATCTTCAATTTATAATTTGTTGCTATATAATATGGAATTTATC
* * * * *
1301 AATTTGTTTTGGACCTGACTTCAGGTTTGGTATTAGGGTTATATATACCGGGATCACATTGTATT
260 AATTTATTTTGGACCTAACTTCAGGTTAGGTATTAGGGTTATATATACCGGGATAACATTGTAAT
1366 AAGTTCTTTCCCTTGGCTCTAGGAACTTTTTACTATTTGTGTTACTTACATGCTT
325 AAGTTCTTT-CCTTGGCTCTAGGAACTTTTTACTATTTGTGTTACTTACATGCTT
*
1421 TTGTTTGTAATTACTATTTGTGCAT-GAAAATTTAATAATATTCTAACTAGATTATAATC-CTGT
1 TTGTTTGTAATTACTATCTGTGCATGGAAAA-TTAATAATATTCTAACTAGATTATAATCTCTGT
* * *
1484 ACGTGATGGAAGTGGTCATACATGCTAATATACA-TAGTATTGTA-CTCTCCATAAGTTATTAAA
65 ACATGATGGAAGTGGTCATACATGCTAATATA-AGTAGTATTGTATC-CTCCATAAGTGATCAAA
* *
1547 ATTTCTAATGTTT-TTATCAAGTTATAATTGTGTTGCTAATGCATGTGTCTTAAATGTATTTATA
128 ATCTCTAAT-TTTGTTACCAAGTTATAATTGTGTTGCTAATGCA-GTG------ATG-ATTTATA
** * * *
1611 TTCACTTTGTGCGTTGGTCAAAATCTCAATCTTTATCTTCAATTTTTAATTTGTTGCTATATAAT
184 TT-ACTTTGTGAATTGGTCAAAATATCAAACTTTATCTTCAATTTATAATTTGTTGCTATATAAT
* * * *
1676 ATGGAATTTATCAATTTATTTTGGACCTAATTTCAGGTTAGGTGTTAGGGTTATTTATACCTGGA
248 ATGGAATTTATCAATTTATTTTGGACCTAACTTCAGGTTAGGTATTAGGGTTATATATACCGGGA
*
1741 TAACATTGTAATAGGTTCTTTCCTTGGCTCTAG
313 TAACATTGTAATAAGTTCTTTCCTTGGCTCTAG
1774 ATTTGGGCAT
Statistics
Matches: 302, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
373 1 0.00
374 97 0.32
375 54 0.18
376 2 0.01
383 2 0.01
385 8 0.03
386 12 0.04
387 108 0.36
388 18 0.06
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (378 bp):
TTGTTTGTAATTACTATCTGTGCATGGAAAATTAATAATATTCTAACTAGATTATAATCTCTGTA
CATGATGGAAGTGGTCATACATGCTAATATAAGTAGTATTGTATCCTCCATAAGTGATCAAAATC
TCTAATTTTGTTACCAAGTTATAATTGTGTTGCTAATGCAGTGATGATTTATATTACTTTGTGAA
TTGGTCAAAATATCAAACTTTATCTTCAATTTATAATTTGTTGCTATATAATATGGAATTTATCA
ATTTATTTTGGACCTAACTTCAGGTTAGGTATTAGGGTTATATATACCGGGATAACATTGTAATA
AGTTCTTTCCTTGGCTCTAGGAACTTTTTACTATTTGTGTTACTTACATGCTT
Found at i:3292 original size:18 final size:18
Alignment explanation
Indices: 3269--3317 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3259 GGAGGACTCA
3269 TAGCCGGAGCCCAAGTCT
1 TAGCCGGAGCCCAAGTCT
* * *
3287 TAGCCGAAGCCGAAGTGT
1 TAGCCGGAGCCCAAGTCT
* *
3305 GAGCAGGAGCCCA
1 TAGCCGGAGCCCA
3318 GTTGCAAGTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.29, G:0.33, T:0.12
Consensus pattern (18 bp):
TAGCCGGAGCCCAAGTCT
Found at i:3609 original size:33 final size:35
Alignment explanation
Indices: 3569--3652 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 35
3559 GACTTTCAAA
*
3569 GAGAAGCACAAGTAGAAGTCCTGCAAGATC-TC-G
1 GAGAAGCATAAGTAGAAGTCCTGCAAGATCTTCAG
* ** *
3602 GAGAAGCATTAGCGGAAGTCCTGTAAGATCTTCTAG
1 GAGAAGCATAAGTAGAAGTCCTGCAAGATCTTC-AG
3638 GAGAAGCATAAGTAG
1 GAGAAGCATAAGTAG
3653 GAGCTCTGCT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 25 0.62
34 2 0.05
36 13 0.32
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (35 bp):
GAGAAGCATAAGTAGAAGTCCTGCAAGATCTTCAG
Found at i:4173 original size:36 final size:36
Alignment explanation
Indices: 4095--4173 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
4085 TGGTCATGGC
* *
4095 CGCAGCCGTAGTCCAAGTCGAAGTCGAACCTCTATT
1 CGCAGCCGTAGTCCAAGTCAAAGTCGAACCCCTATT
* *
4131 CACAGCCGTAG-CTCAAGTCAAAGTCGAACCCCTGTT
1 CGCAGCCGTAGTC-CAAGTCAAAGTCGAACCCCTATT
4167 CGCAGCC
1 CGCAGCC
4174 ATATTGCAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (36 bp):
CGCAGCCGTAGTCCAAGTCAAAGTCGAACCCCTATT
Done.