Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00576.N1
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, 574
Length: 958
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Found at i:142 original size:3 final size:3
Alignment explanation
Indices: 134--160 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
124 CTAGACATAA
134 TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG
161 AGCAATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:270 original size:57 final size:57
Alignment explanation
Indices: 169--300 Score: 174
Period size: 57 Copynumber: 2.3 Consensus size: 57
159 GGAGCAATTG
* * * * **
169 CACATGCTGCTGCTGATAGAGCAGCTGCTGTCCGTTCTGCTTTTCATAAAGCAGCTT
1 CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGCTT
* *
226 CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGGTTTTCGTAAAGCAGCTT
1 CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGCTT
* *
283 CACAAGTTGCTTCTGATG
1 CACAAGCTGCTGCTGATG
301 TAGCTGCTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (57 bp):
CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGCTT
Found at i:369 original size:24 final size:24
Alignment explanation
Indices: 339--419 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
329 AGGTGGCATT
339 GGTGGAGGTAGTTTAAGAGGTGGA
1 GGTGGAGGTAGTTTAAGAGGTGGA
* * *
363 GGAGGAGGCAGTTTAATAGGTGGA
1 GGTGGAGGTAGTTTAAGAGGTGGA
* *
387 GGTGGAAGTAGTTTTAGAGGTGGA
1 GGTGGAGGTAGTTTAAGAGGTGGA
411 GGTGGAGGT
1 GGTGGAGGT
420 GGAAGCAGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.01, G:0.49, T:0.25
Consensus pattern (24 bp):
GGTGGAGGTAGTTTAAGAGGTGGA
Found at i:414 original size:30 final size:30
Alignment explanation
Indices: 380--437 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
370 GCAGTTTAAT
*
380 AGGTGGAGGTGGAAGTAGTTTTAGAGGTGG
1 AGGTGGAGGTGGAAGCAGTTTTAGAGGTGG
*
410 AGGTGGAGGTGGAAGCAGTTTTGGAGGT
1 AGGTGGAGGTGGAAGCAGTTTTAGAGGT
438 AGTGCTACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.02, G:0.50, T:0.26
Consensus pattern (30 bp):
AGGTGGAGGTGGAAGCAGTTTTAGAGGTGG
Found at i:482 original size:66 final size:66
Alignment explanation
Indices: 411--575 Score: 258
Period size: 66 Copynumber: 2.5 Consensus size: 66
401 TAGAGGTGGA
* *
411 GGTGGAGGTGGAAGCAGTTTTGGAGGTAGTGCTACCGGTTCCGTTGGTGGACGTGGTGCTACCGT
1 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTACCGT
476 T
66 T
* *
477 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTGCTGT
1 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTACCGT
542 T
66 T
* * * *
543 GGTGGAGGTGGAGGTAGTGTTGGGGGTAGTGCT
1 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCT
576 GGCGGTAGTT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 91 1.00
ACGTcount: A:0.13, C:0.13, G:0.45, T:0.28
Consensus pattern (66 bp):
GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTACCGT
T
Found at i:606 original size:24 final size:24
Alignment explanation
Indices: 543--611 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
533 TGCTGCTGTT
**
543 GGTGGAGGTGGAGGTAGTGTTGGG
1 GGTGGAGGTGGAGGTAGTGTTAAG
* * * *
567 GGTAGTGCTGGCGGTAGT-TTAAAG
1 GGTGGAGGTGGAGGTAGTGTT-AAG
591 GGTGGAGGTGGAGGTAGTGTT
1 GGTGGAGGTGGAGGTAGTGTT
612 GGAAGTGGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
23 2 0.06
24 29 0.88
25 2 0.06
ACGTcount: A:0.16, C:0.03, G:0.54, T:0.28
Consensus pattern (24 bp):
GGTGGAGGTGGAGGTAGTGTTAAG
Found at i:607 original size:36 final size:36
Alignment explanation
Indices: 567--638 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
557 TAGTGTTGGG
**
567 GGTAGTGCTGGCGGTAGTTTAAAGGGTGGAGGTGGA
1 GGTAGTGCTGGAAGTAGTTTAAAGGGTGGAGGTGGA
* * *
603 GGTAGTGTTGGAAGTGGTTTAAGGGGTGGAGGTGGA
1 GGTAGTGCTGGAAGTAGTTTAAAGGGTGGAGGTGGA
639 TATGGAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.19, C:0.03, G:0.51, T:0.26
Consensus pattern (36 bp):
GGTAGTGCTGGAAGTAGTTTAAAGGGTGGAGGTGGA
Found at i:619 original size:24 final size:24
Alignment explanation
Indices: 544--619 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
534 GCTGCTGTTG
**
544 GTGGAGGTGGAGGTAGTGTTGGGG
1 GTGGAGGTGGAGGTAGTGTTGGAA
* * * * *
568 GTAGTGCTGGCGGTAGT-TT-AAA
1 GTGGAGGTGGAGGTAGTGTTGGAA
590 GGGTGGAGGTGGAGGTAGTGTTGGAA
1 --GTGGAGGTGGAGGTAGTGTTGGAA
616 GTGG
1 GTGG
620 TTTAAGGGGT
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
23 2 0.06
24 30 0.83
25 2 0.06
26 2 0.06
ACGTcount: A:0.17, C:0.03, G:0.54, T:0.26
Consensus pattern (24 bp):
GTGGAGGTGGAGGTAGTGTTGGAA
Done.