Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g02514.M1
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: 8257
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Found at i:1539 original size:161 final size:161
Alignment explanation
Indices: 1274--1728 Score: 662
Period size: 161 Copynumber: 2.8 Consensus size: 161
1264 CAGGAGTGCT
* * * * * *
1274 GAATTGGAGGCAATTGTTGAAGAGAGTAGTGAGGTTGAGAAGGTCAAGTGTGTC-GTTACTTCAC
1 GAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATG-CAGCTACTTCAC
*
1338 AACAACAAGCCCCTCGAGGAGGAGCAGACGCAAGACTGTGGCTCTTACCGCTCCAGCTGCCGATT
65 AACAAGAAGCCCCTCGAGGAGGAGCAGACGCAAGACTGTGGCTCTTACCGCTCCAGCTGCCGATT
* * *
1403 TGGCACCGGCTGTAGGGAAGGGCTCGACTGAC
130 TGGCACCGGCTGGAGGGAAGGGCTCGACCGAA
* *
1435 GAATTGGATGCAATTATTGAAGATAGTAGTGAGGTTGAG-GGGCCAAGTATGCAGCAACTTCACA
1 GAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
* * *
1499 ACAAGAAGCCCACTCGAGGAGGAGCAGACGCAAGACTGTGGCTCTTACCGATCTAGCTTCCGATT
66 ACAAGAAGCCC-CTCGAGGAGGAGCAGACGCAAGACTGTGGCTCTTACCGCTCCAGCTGCCGATT
* *
1564 TGGCATCGGTTGGAGGGAAGGGCTCGACCGAA
130 TGGCACCGGCTGGAGGGAAGGGCTCGACCGAA
*
1596 GAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCAGCTACTTCACA
1 GAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
* * * * *
1661 ACAAGCAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAGCTGTCGATT
66 ACAAGAAG-CCCCTCGAGGAGGAGCAGACGCAAGACTGTGGCTCTTACCGCTCCAGCTGCCGATT
1726 TGG
130 TGG
1729 TCAATAAGGA
Statistics
Matches: 262, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
159 1 0.00
160 28 0.11
161 150 0.57
162 80 0.31
163 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (161 bp):
GAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
ACAAGAAGCCCCTCGAGGAGGAGCAGACGCAAGACTGTGGCTCTTACCGCTCCAGCTGCCGATTT
GGCACCGGCTGGAGGGAAGGGCTCGACCGAA
Found at i:1942 original size:200 final size:200
Alignment explanation
Indices: 1588--2559 Score: 1282
Period size: 200 Copynumber: 4.9 Consensus size: 200
1578 GGGAAGGGCT
* * *
1588 CGACCGAAGAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCAGCT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCACCT
* ** *
1653 ACTTCACAACAAGCAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAGC
66 ACTTCACAACAAGAAG-CCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
* * * *
1718 TGTCGATTTGGTCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGGTTGTAGGGA
130 TGCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAA
1783 AAGGCA
195 AAGGCA
* * * *
1789 CGACTGAAGAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAAAAGGCCAAGTATGCAGCT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCACCT
** * *
1854 ACTTCACAACAAGAAGCCCCTCGAGGAGGGGCAGACGCAAAACTGTGGTTCTTACTGCTCCAGCT
66 ACTTCACAACAAGAAGCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCT
1919 GCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAAA
131 GCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAAA
1984 AGGCA
196 AGGCA
* **
1989 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTAGAGAGGGCCAAGGGTGC-CCT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCACC-
* *
2053 TTCTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
65 TACTTCACAACAAGAAG-CCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
* * *
2118 TTGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGT----
129 CTGCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGA
2179 --AGGCA
194 AAAGGCA
* * **
2184 CGAATGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGGTGC-CCT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCACC-
* *
2248 TTCTTCACAACAAGATGCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
65 TACTTCACAACAAGAAGCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
* * * **
2313 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGTACGGAGCAGTT-GAAGGCACCGCTTCAAGGA
130 TGCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAG-AGGCACCGCTTGTAGGA
2377 AAAGGCA
194 AAAGGCA
* ** * * * *
2384 CAACTGAAGAATTGGATGCAATTGTACAAGATAGGAGTGAGGTTGAGAGGGCCAAGTCTGC-CAT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCACCT
* ** * * * * *
2448 CACTTCAGAACACCAATCCCCCTTGAGGAAGAATAGACGCAAGACTGTGATTCTCACTGCTCCAG
66 -ACTTCACAACAAGAA-GCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
* * * *
2513 CTGCCGAGTT-GCCAATTAGGGAAGATATTAGTAGAATGGAGCAGTTA
129 CTGCCGATTTGGCCAA-TAAGGAAGATATTGGTAGAACGGAGCAGTTA
2560 AGATCACCGC
Statistics
Matches: 700, Mismatches: 58, Indels: 25
0.89 0.07 0.03
Matches are distributed among these distances:
193 1 0.00
194 101 0.14
195 83 0.12
199 2 0.00
200 259 0.37
201 254 0.36
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.21
Consensus pattern (200 bp):
CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCACCT
ACTTCACAACAAGAAGCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCT
GCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAAA
AGGCA
Found at i:2174 original size:201 final size:201
Alignment explanation
Indices: 1588--2559 Score: 1295
Period size: 201 Copynumber: 4.9 Consensus size: 201
1578 GGGAAGGGCT
* * *
1588 CGACCGAAGAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCAGC-
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGC-CCT
* ** *
1652 TACTTCACAACAAGCAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAG
65 TACTTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
*
1717 CTGTC-GATTTGGTC-AATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGGTTGTAG
130 CTG-CAGATTTGG-CAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAG
*
1780 GGAAAGGCA
193 GAAAAGGCA
* * * *
1789 CGACTGAAGAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAAAAGGCCAAGTATGCAGC-
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGC-CCT
** * *
1853 TACTTCACAACAAGAAG-CCCCTCGAGGAGGGGCAGACGCAAAACTGTGGTTCTTACTGCTCCAG
65 TACTTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
* *
1917 CTGCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGA
130 CTGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGA
1982 AAAGGCA
195 AAAGGCA
* **
1989 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTAGAGAGGGCCAAGGGTGCCCTT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCCCTT
* * *
2054 TCTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGT
66 ACTTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
2119 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGT-----
131 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAA
2179 -AGGCA
196 AAGGCA
* * **
2184 CGAATGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGGTGCCCTT
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCCCTT
* *
2249 TCTTCACAACAAGATG-CCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
66 ACTTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
* **
2313 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGTACGGAGCAGTT-GAAGGCACCGCTTCAAGGA
131 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAG-AGGCACCGCTTGTAGGA
2377 AAAGGCA
195 AAAGGCA
* ** * * * * *
2384 CAACTGAAGAATTGGATGCAATTGTACAAGATAGGAGTGAGGTTGAGAGGGCCAAGTCTGCCATC
1 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCCCTT
* ** * * * * *
2449 ACTTCAGAACACCAATCCCCCTTGAGGAAGAATAGACGCAAGACTGTGATTCTCACTGCTCCAGC
66 ACTTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
* * * * * * *
2514 TGCCGAGTTGCCAATTAGGGAAGATATTAGTAGAATGGAGCAGTTA
131 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTA
2560 AGATCACCGC
Statistics
Matches: 700, Mismatches: 58, Indels: 25
0.89 0.07 0.03
Matches are distributed among these distances:
193 1 0.00
194 101 0.14
195 83 0.12
199 3 0.00
200 254 0.36
201 258 0.37
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.21
Consensus pattern (201 bp):
CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCCCTT
ACTTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
TGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAA
AAGGCA
Found at i:2379 original size:395 final size:395
Alignment explanation
Indices: 1588--2559 Score: 1315
Period size: 395 Copynumber: 2.4 Consensus size: 395
1578 GGGAAGGGCT
* * * *
1588 CGACCGAAGAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCAGC-
1 CGACTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTAGAGAGGGCCAAGTATGC-CCT
* * ** *
1652 TACTTCACAACAAGCAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAG
65 TACTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
*
1717 CTGTCGATTTGGTC-AATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGGTTGTAGG
130 CTG-CGATTTGG-CAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGT---
* * *
1781 GAAAGGCACGACTGAAGAATTGGATGCAATTGTTGAAGATAGTAGTGAGGTCGAAAAGGCCAAGT
190 --AAGGCACGAATGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAAAAGGCCAAGG
* ** *
1846 ATGCAGCTACTTCACAACAAGAAGCCCCTCGAGGAGGGGCAGACGCAAAACTGTGGTTCTTACTG
253 ATGCACCTACTTCACAACAAGAAGCCCCTCGAGGAGGAACAGACGCAAAACTGTGATTCTTACTG
* *
1911 CTCCAGCTGCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTT
318 CTCCAGCTGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTT
**
1976 GTAGGAAAAGGCA
383 CAAGGAAAAGGCA
* **
1989 CGACTGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTAGAGAGGGCCAAGGGTGCCCTT
1 CGACTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTAGAGAGGGCCAAGTATGCCCTT
* *
2054 TCTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGT
66 ACTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
2119 TGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGT-AGGC
131 TGC-GATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAAGGC
* * * *
2183 ACGAATGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGGTGC-CC
195 ACGAATGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAAAAGGCCAAGGATGCACC
* * *
2247 TTTCTTCACAACAAGATGCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAG
260 -TACTTCACAACAAGAAGCCCCTCGAGGAGGAACAGACGCAAAACTGTGATTCTTACTGCTCCAG
*
2312 CTGCAGATTTGGCAAATAAGGAAGATATTGGTAGTACGGAGCAGTT-GAAGGCACCGCTTCAAGG
324 CTGCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAG-AGGCACCGCTTCAAGG
2376 AAAAGGCA
388 AAAAGGCA
* * * * * * *
2384 CAACTGAAGAATTGGATGCAATTGTACAAGATAGGAGTGAGGTTGAGAGGGCCAAGTCTGCCATC
1 CGACTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTAGAGAGGGCCAAGTATGCCCTT
* ** * * * *
2449 ACTTCAGAACACCAATCCCCCTTGAGGAAGAATAGACGCAAGACTGTGATTCTCACTGCTCCAGC
66 ACTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
* * * * * *
2514 TGCCGAGTTGCCAATTAGGGAAGATATTAGTAGAATGGAGCAGTTA
131 TG-CGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTA
2560 AGATCACCGC
Statistics
Matches: 508, Mismatches: 57, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
394 2 0.00
395 332 0.65
396 1 0.00
400 3 0.01
401 170 0.33
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.21
Consensus pattern (395 bp):
CGACTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTAGAGAGGGCCAAGTATGCCCTT
ACTTCACAACAAGAAGCCCCCTTGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGC
TGCGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAAGGCA
CGAATGAAGAATTGGATGCAATTGTGGAAGATAGTAGTGAGGTCGAAAAGGCCAAGGATGCACCT
ACTTCACAACAAGAAGCCCCTCGAGGAGGAACAGACGCAAAACTGTGATTCTTACTGCTCCAGCT
GCAGATTTGGCAAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTCAAGGAAA
AGGCA
Found at i:3960 original size:18 final size:18
Alignment explanation
Indices: 3937--3973 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3927 TGTATTGGAG
3937 ACACAAGAACTTTCTGAA
1 ACACAAGAACTTTCTGAA
3955 ACACAAGAACTTTCTGAA
1 ACACAAGAACTTTCTGAA
3973 A
1 A
3974 ACATGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ACACAAGAACTTTCTGAA
Done.