Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g02326.C2
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: 4881
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:1415 original size:150 final size:151
Alignment explanation
Indices: 905--1717 Score: 614
Period size: 150 Copynumber: 5.3 Consensus size: 151
895 TTTTCGCTTG
* * * * * *
905 AGCATCATGCCTTAGCTTTCTTGGTATTGTCC-GCCTTTCCATTAGTCATTGAACATTGTAGAGC
1 AGCATCATGCCTGAGATTTATTGGTAGTG-CCTGCCTTTCCATTAGTCATTGAGCATTGTAGAAC
* * * * *
969 TGGAATAGAAGTAAA-GAAACATTGAACTTGAAACCAGCCATGTGAACCA-ATTAGCTTATAA-A
65 TGAAATAGAAG-AAATGAAAGATTGAACTTGAAAGCAGCCATATGAACCATA-TAGCATATAACA
** * * * * *
1031 CGACATGTTCAGATTAAATC-CTT
128 ATACATTTTCAAAGTGAATCTGTT
* * * * * *
1054 AACATCGTGCCTAAGA-TTATTTTGTAGTGCCTGCCTTTTTGGTTTCCATTAGTCATCGAACATT
1 AGCATCATGCCTGAGATTTA-TTGGTAGTGCCTGCC-------TTTCCATTAGTCATTGAGCATT
* * *
1118 GTAGAGCTGAAATAGAAGCAATG-AAGCATTGAACTTGAAAGCATCCATATGAAGCCAT-TAGCA
58 GTAGAACTGAAATAGAAGAAATGAAAG-ATTGAACTTGAAAGCAGCCATATGAA-CCATATAGCA
*
1181 TTATAACAAGACATTTTCAAAGTGAATCTGTT
121 -TATAACAATACATTTTCAAAGTGAATCTGTT
* *
1213 AGCATCAAGCCTGAGATTTATTGGTAGTGCCTGCCTTTCCATTAGCCATTGAGCATTGTAGAACT
1 AGCATCATGCCTGAGATTTATTGGTAGTGCCTGCCTTTCCATTAGTCATTGAGCATTGTAGAACT
* * * *
1278 GAAATAGAAGAAATGAAAGAGTGAACTTGAAAGCAGCTACATGAACCGTATAGCATATAACAATA
66 GAAATAGAAGAAATGAAAGATTGAACTTGAAAGCAGCCATATGAACCATATAGCATATAACAATA
1343 CATTTT-AAAGTGAATCTGTT
131 CATTTTCAAAGTGAATCTGTT
* * * * * *
1363 AGCATCATGCTTGAGATTTCTTTGT-TTGGCCTGCTTTTCCATTAGTCATTGAG-ATTCTAGAAC
1 AGCATCATGCCTGAGATTTATTGGTAGT-GCCTGCCTTTCCATTAGTCATTGAGCATTGTAGAAC
* * * * *
1426 TGAAACAGAAGTAATGAAACG-TTGAACTCAGAAGGCAGCCATATGAACCAAATAGCATATAAC-
65 TGAAATAGAAGAAATGAAA-GATTGAACT-TGAAAGCAGCCATATGAACCATATAGCATATAACA
* * **
1489 ATAACATTTTCAGAGTGAGTCCATT
128 AT-ACATTTTCAAAGTGAATCTGTT
* * * * * ** *
1514 AGCATCATGCCTAAGA-TTATTTCGTAGTGCTTGTCTTTCTGTTTTCATTAGTCGTCAAACATTG
1 AGCATCATGCCTGAGATTTA-TTGGTAGTGCCTG-C---C--TTTCCATTAGTCATTGAGCATTG
* ** * * *
1578 TATAACTGAAATAGAAGCGATGAAACATTGAACTTAAAAGTAGCCATATGAACCCA-ATAGCATA
59 TAGAACTGAAATAGAAGAAATGAAAGATTGAACTTGAAAGCAGCCATATGAA-CCATATAGCATA
* *
1642 TAACATAACAGGGCATTTTCAAAATGAATCTGTT
123 TAAC--AATA---CATTTTCAAAGTGAATCTGTT
* * * *
1676 AGCATCATGCCTAAGATTTGTTGGTAG-ACCTGCTTTTCCATT
1 AGCATCATGCCTGAGATTTATTGGTAGTGCCTGCCTTTCCATT
1718 TCCATTAGTA
Statistics
Matches: 530, Mismatches: 92, Indels: 78
0.76 0.13 0.11
Matches are distributed among these distances:
148 4 0.01
149 57 0.11
150 96 0.18
151 50 0.09
152 69 0.13
153 3 0.01
155 11 0.02
156 66 0.12
157 47 0.09
158 50 0.09
159 29 0.05
160 5 0.01
161 3 0.01
162 38 0.07
163 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (151 bp):
AGCATCATGCCTGAGATTTATTGGTAGTGCCTGCCTTTCCATTAGTCATTGAGCATTGTAGAACT
GAAATAGAAGAAATGAAAGATTGAACTTGAAAGCAGCCATATGAACCATATAGCATATAACAATA
CATTTTCAAAGTGAATCTGTT
Found at i:3463 original size:51 final size:51
Alignment explanation
Indices: 3403--3504 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
3393 GAAGTAGTTC
* *
3403 CCCTTTGCAGGTTTCTTCTTCTATCTTGAATCATTATCCAGACTCGAACTA
1 CCCTTTGCAGGTTTCTTCCTCTATCTTCAATCATTATCCAGACTCGAACTA
3454 CCCTTTGCAGGTTTCTTCCTCTATCTTCAATCATTATCCAGACTCGAACTA
1 CCCTTTGCAGGTTTCTTCCTCTATCTTCAATCATTATCCAGACTCGAACTA
3505 GTGTTGAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (51 bp):
CCCTTTGCAGGTTTCTTCCTCTATCTTCAATCATTATCCAGACTCGAACTA
Done.