Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g01372.F3
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: 4200
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:2294 original size:28 final size:27
Alignment explanation
Indices: 2239--2357 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 27
2229 CTTGATTTAC
* *
2239 AAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACTAAAATACCCCCGATTTGT
2266 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATACCCCC-GATTTGT
* *
2294 AAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCCCGATTTGT
* * * *
2321 AAAAATTACCAAAGTACCCTCGATTTAT
1 -AAAATTACTAAAATACCCCCGATTTGT
*
2349 AGAATTACT
1 AAAATTACT
2358 GTTTTACCCT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 32 0.40
28 48 0.60
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCCGATTTGT
Found at i:2389 original size:27 final size:27
Alignment explanation
Indices: 2144--2426 Score: 171
Period size: 27 Copynumber: 10.4 Consensus size: 27
2134 ATTACCAAAG
*
2144 TACCCTCGATTTACAGAATTA-TAGTTC
1 TACCCTCGATTTACAGAATTACTA-TTT
* *
2171 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
* * *
2198 TACCCTCAATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
* * ***
2225 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAGAATTACTATTT
* * ***
2252 TACCCCTGGTTTGTA-A-AATTACTAAAA
1 TA-CCCTCGATT-TACAGAATTACTATTT
* ** * ***
2279 TACCCCCTGATTTGTAAAATTACTAAAA
1 TACCCTC-GATTTACAGAATTACTATTT
* * ***
2307 TACCCTCGACTTGTA-AAAATTACCAAAG
1 TACCCTCGA-TT-TACAGAATTACTATTT
* *
2335 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
*
2362 TACCCTCGATTTACAGAATTAGTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
2389 TACCC-CTGATTTACAAAATTACCATTT
1 TACCCTC-GATTTACAGAATTACTATTT
2416 TACCCTCGATT
1 TACCCTCGATT
2427 GTGAAATTAC
Statistics
Matches: 211, Mismatches: 34, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
26 7 0.03
27 152 0.72
28 49 0.23
29 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:2420 original size:137 final size:135
Alignment explanation
Indices: 2198--2446 Score: 309
Period size: 137 Copynumber: 1.8 Consensus size: 135
2188 ATTACCATTT
* *
2198 TACCCTCAATTTATAGAATTACCATTTTACCCTTGATTTACAAAATTACTAAAATACCCCTGGTT
1 TACCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCCTGATT
** *
2263 TGTAAAATTACTAAAATACCCCCTGATTTGTAAAATTACTAAAATACCCTCGACTTGTAAAAATT
66 TACAAAATTACCAAAATACCCCC-GA-TTGTAAAATTACTAAAATACCCTCGACTTGTAAAAATT
2328 ACCAAAG
129 ACCAAAG
* ** * * ***
2335 TACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTAGTATTTTACCCCTGATT
1 TACCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCCTGATT
*** * * *
2400 TACAAAATTACCATTTTACCCTCGATTGTGAAATTACTGAAATACCC
66 TACAAAATTACCAAAATACCCCCGATTGTAAAATTACTAAAATACCC
2447 CTATAGGATA
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
135 20 0.22
136 2 0.02
137 71 0.76
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (135 bp):
TACCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCCTGATT
TACAAAATTACCAAAATACCCCCGATTGTAAAATTACTAAAATACCCTCGACTTGTAAAAATTAC
CAAAG
Found at i:2488 original size:27 final size:27
Alignment explanation
Indices: 2458--2608 Score: 124
Period size: 27 Copynumber: 5.6 Consensus size: 27
2448 TATAGGATAG
* * *
2458 AATTACTAAAACACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* ** *
2485 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
* * *
2512 AATTATCGAAATACCCTTAATTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
**
2539 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCCTAATTTGTAA
** * *
2566 AATTA-CAGAAATACCTTTGATTTGTAG
1 AATTACCA-AAATACCCCTAATTTGTAA
* *
2593 ATTTACCAAAACACCC
1 AATTACCAAAATACCC
2609 TTGTAGGATG
Statistics
Matches: 96, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
26 2 0.02
27 92 0.96
28 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:2569 original size:54 final size:54
Alignment explanation
Indices: 2478--2608 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 54
2468 ACACCCCTAG
* ** ***
2478 TTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTATC-GAAATACCCTTAA
1 TTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTA-CAGAAATACCCTTAA
* *
2532 TTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAATACCTTTGA
1 TTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAATACCCTTAA
* * *
2586 TTTGTAGATTTACCAAAACACCC
1 TTTGTAAAATTACCAAAATACCC
2609 TTGTAGGATG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.02
54 64 0.98
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAATACCCTTAA
Found at i:3437 original size:20 final size:20
Alignment explanation
Indices: 3412--3498 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
3402 GATATGATAT
*
3412 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
3432 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
*
3452 ACAAGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
3472 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
3492 ACATGAT
1 ACATGAT
3499 GTATTCATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:3798 original size:42 final size:42
Alignment explanation
Indices: 3739--3830 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
3729 TAGTCTCCCC
* ** *
3739 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
3781 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
3823 AAATGGGC
1 AAATGGGC
3831 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:3889 original size:31 final size:31
Alignment explanation
Indices: 3854--3932 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
3844 CATTTACAGT
3854 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
3885 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
3916 AAATGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
3933 ATATGTCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Done.