Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g00672.C1
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: 4147
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:2150 original size:24 final size:24
Alignment explanation
Indices: 2121--2172 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2111 CATATACTTG
2121 TGATAATGCCTCAGCAGTTTTTGA
1 TGATAATGCCTCAGCAGTTTTTGA
2145 TGATAATGCCTCAGCAGTTTTTGA
1 TGATAATGCCTCAGCAGTTTTTGA
2169 TGAT
1 TGAT
2173 GAAGGTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATAATGCCTCAGCAGTTTTTGA
Found at i:3371 original size:102 final size:102
Alignment explanation
Indices: 3192--3390 Score: 362
Period size: 102 Copynumber: 2.0 Consensus size: 102
3182 ATTTTGGTCC
*
3192 AGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAAAGGCTCGTTCAAGCACAATTT
1 AGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAAAGACTCGTTCAAGCACAATTT
*
3257 TTTCTCATAGGACAACTGCCTCTCCAAATGCACAAAA
66 TTTCTCAGAGGACAACTGCCTCTCCAAATGCACAAAA
**
3294 AGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAAAGACTCGTTCAAGCATGATTT
1 AGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAAAGACTCGTTCAAGCACAATTT
3359 TTTCTCAGAGGACAACTGCCTCTCCAAATGCA
66 TTTCTCAGAGGACAACTGCCTCTCCAAATGCA
3391 AGAAGAGGTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (102 bp):
AGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAAAGACTCGTTCAAGCACAATTT
TTTCTCAGAGGACAACTGCCTCTCCAAATGCACAAAA
Found at i:3511 original size:276 final size:276
Alignment explanation
Indices: 3018--3541 Score: 753
Period size: 276 Copynumber: 1.9 Consensus size: 276
3008 ATTTTGATTC
* **
3018 AGGAAATAGTGATTCCGATGAAGAACTTCCTAAAACACGTTCAAAGGTTCATTCAAGCATTGGTT
1 AGGAAATAGTGATTCCGATGAAGAACTTCCTAAAACAAGTTCAAAGACTCATTCAAGCATTGGTT
* * * *
3083 TTTCTCACAAGACAACTGCCTCCCCGAATTCAGGAAAAGGTTCCACTCTTAAAGCTACAGTTTCC
66 TTTCTCACAAGACAACTGCCTCCCCAAATGCAAGAAAAGGTTCCACTCTTAAAACTACAGTTTCC
** * * *
3148 TCCGAATTGACGCTAGTTTCTAACCCCATACCATATTTTGGTCCAGGAAATAGTGATTCTGATGA
131 TCCGAATCAAAGCTAGTTTCTAACCCCATACCATATTTAGGTCCAGGAAACAGTGATTCTGATGA
* * *
3213 AGATCTTCCTAAAACAAGTTCAAAGGCTCGTTCAAGCACAATTTTTTCTCATAGGACAACTGCCT
196 AGATCTTCCGAAAACAAGTTCAAAGGCTCATTCAAGCACAAGTTTTTCTCATAGGACAACTGCCT
3278 CTCCAAATGCACAAAA
261 CTCCAAATGCACAAAA
* * * *
3294 AGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAAAGACTCGTTCAAGCA-TGATT
1 AGGAAATAGTGATTCCGATGAAGAACTTCCTAAAACAAGTTCAAAGACTCATTCAAGCATTG-GT
* * * *
3358 TTTTCTCAGAGGACAACTGCCTCTCCAAATGCAAGAAGAGGTTCCACTCTTAAAACTACAGTTTC
65 TTTTCTCACAAGACAACTGCCTCCCCAAATGCAAGAAAAGGTTCCACTCTTAAAACTACAGTTTC
* * * * *
3423 CTCTGAATCAAAGGTAGTTTCTGACCCCATGCCATATTTAGGTCCAGGAAACAGTGGTTCTGATG
130 CTCCGAATCAAAGCTAGTTTCTAACCCCATACCATATTTAGGTCCAGGAAACAGTGATTCTGATG
* **
3488 AAGATCTTCCGGAAACAAGTTCAAAGGCTCATTCAAGCACTGGTTTTTCTCATA
195 AAGATCTTCCGAAAACAAGTTCAAAGGCTCATTCAAGCACAAGTTTTTCTCATA
3542 AGAGAAAAGA
Statistics
Matches: 216, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
275 2 0.01
276 214 0.99
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (276 bp):
AGGAAATAGTGATTCCGATGAAGAACTTCCTAAAACAAGTTCAAAGACTCATTCAAGCATTGGTT
TTTCTCACAAGACAACTGCCTCCCCAAATGCAAGAAAAGGTTCCACTCTTAAAACTACAGTTTCC
TCCGAATCAAAGCTAGTTTCTAACCCCATACCATATTTAGGTCCAGGAAACAGTGATTCTGATGA
AGATCTTCCGAAAACAAGTTCAAAGGCTCATTCAAGCACAAGTTTTTCTCATAGGACAACTGCCT
CTCCAAATGCACAAAA
Done.