Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011486.1 Corchorus olitorius cultivar O-4 contig11519, whole genome shotgun sequence
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: 2118
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Found at i:285 original size:147 final size:147
Alignment explanation
Indices: 39--334 Score: 513
Period size: 147 Copynumber: 2.0 Consensus size: 147
29 CTTTCAATTG
39 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGGA
1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGGA
* *
104 ACACTTGTTATTTTGGGCTTATCAGGACCTATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAA
66 ACACTTGTTATTTTGGGCCTATCAGGACCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAA
*
169 CCCTCAATGCTTTTCTT
131 ACCTCAATGCTTTTCTT
*
186 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGGA
* *
251 ACACTTGTTATTTTGGGCCTAT-AGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
66 ACACTTGTTATTTTGGGCCTATCA-GGACCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCA
*
315 AACCTCAATGGTTTTCTT
130 AACCTCAATGCTTTTCTT
333 TT
1 TT
335 GATACGGGGA
Statistics
Matches: 141, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
146 1 0.01
147 140 0.99
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (147 bp):
TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTAGCTCATTTGGA
ACACTTGTTATTTTGGGCCTATCAGGACCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAA
ACCTCAATGCTTTTCTT
Found at i:697 original size:68 final size:68
Alignment explanation
Indices: 588--733 Score: 258
Period size: 68 Copynumber: 2.1 Consensus size: 68
578 AACACTACTT
* *
588 GATACAGATTTCACTGCAAGGAGAATTCAATGGATGAACAAGCTTCGATTAATCCCAAATCAATA
1 GATACAGATTTCACTACAAGGAGAATTCAATGGATGAACAAGCTTCGATTAATCCCAAATCAACA
653 AGA
66 AGA
656 GATACAGATTTCAGC-ACAAGGAGAATTCAATGGATGAACAAGCTTCGATTAATCCCAAATCAAC
1 GATACAGATTTCA-CTACAAGGAGAATTCAATGGATGAACAAGCTTCGATTAATCCCAAATCAAC
720 AAGA
65 AAGA
724 GATACAGATT
1 GATACAGATT
734 ACACCACTCA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 74 0.99
69 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (68 bp):
GATACAGATTTCACTACAAGGAGAATTCAATGGATGAACAAGCTTCGATTAATCCCAAATCAACA
AGA
Found at i:1800 original size:155 final size:154
Alignment explanation
Indices: 1368--1900 Score: 809
Period size: 154 Copynumber: 3.5 Consensus size: 154
1358 TCCCGTGTCA
* * *
1368 TCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTCAGATTAGTCCACTGCA-ATGTTTTT
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG-AGAAGTTTTT
* * *
1432 AGCGCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCTTTAGTGACGTTTTGAATCGTCT
65 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCT
1497 TCGATTGGGCAAACCTCAATGCTTT
130 TCGATTGGGCAAACCTCAATGCTTT
* * *
1522 TCTTTCCATTGTTTATGGCCTAACTATAATAATTTTGGTGACATTAGTCCACTGTGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGAGAAGTTTTTA
* * * ** * *
1587 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGTGGCTCATTTGTTCCGTTTTGAATCATTTT
66 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTT
* *
1652 CGATTTGGCAACCCTCAATGCTTT
131 CGATTGGGCAAACCTCAATGCTTT
* *
1676 TCTTTCCATCGTTTATGGCCTAACTATAATCATTTTGGTTGAGATTAGTCCACTGAGAAGTTTTG
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG-TGAGATTAGTCCACTGAGAAGTTTTT
* *
1741 AGCTCATTTGGAACACTTCTTATTTTGGGCATATCGGGGCCCATTAGTGACGTTTTGAATCGTCT
65 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCT
*
1806 TCAATTGGGCAAACCTCAATGCTTT
130 TCGATTGGGCAAACCTCAATGCTTT
*
1831 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTT
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGAGAA-GTTTTT
1896 -GCTCA
65 AGCTCA
1901 CATGGCAAGG
Statistics
Matches: 338, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
154 195 0.58
155 143 0.42
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGAGAAGTTTTTA
GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTT
CGATTGGGCAAACCTCAATGCTTT
Done.