Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010978.1 Corchorus olitorius cultivar O-4 contig11010, 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: 1844
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Found at i:1794 original size:153 final size:154
Alignment explanation
Indices: 1214--1844 Score: 868
Period size: 153 Copynumber: 4.1 Consensus size: 154
1204 GTTGCTTTTT
*
1214 CTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCC
1 CTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCC
* *
1279 TCAATG-TTTTCTTTCCATTGTATAAGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
66 TCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
*
1343 GAAGTTTTTAGCTCATTTGGAACA
131 GAAGTTTTTAGCTCATTTGAAACA
* * *
1367 CTTGTTATTTTGGGCTTATCGGGGCCAATTAGTTTTGTTTTGAATTGTCTTCGATTTGGCAACCC
1 CTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCC
* *
1432 TCAATGCTTTTCTTTCCATTGTTTATGCCCAAACTATAATCATTTTGGTGAGATTAGTCCAATGT
66 TCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
1497 GAAGTTTTTAGCTCATTTTG-AACA
131 GAAGTTTTTAGCTCA-TTTGAAACA
* * *** * **
1521 CTTGTTA-----AGCCTATCAGGGCCCATTAGTTCCATTTGGAATCAACTTCGATTTGGCAACCC
1 CTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCC
* * * *
1581 TCAATGTCTTTTCTTTCCAATGTTTATCGACCTAACTATAATCGTTTTGGTAAGATTAGTCCACT
66 TCAATG-CTTTTCTTTCCATTGTTTAT-GCCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* *
1646 TTGAAGTTTTTAGCTCATTTAAAACA
129 GTGAAGTTTTTAGCTCATTTGAAACA
* * *
1672 CTAT-TTATTTTGGCCCTATCGGGGCCCATTAGTGATT-TTTTGAATCGTCTTCTATTT-GCAAC
1 CT-TGTTATTTTGGGCCTATCGGGGCCCATTAGT-TTTGTTTTGAATCGTCTTCGATTTGGCAAC
* *
1734 CTTCAATGCGTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
64 CCTCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * *
1799 ATTAAGTTTTTAGCTCAATTGAAACA
129 GTGAAGTTTTTAGCTCATTTGAAACA
1825 CTTGTTATTTTGGGCCTATC
1 CTTGTTATTTTGGGCCTATC
Statistics
Matches: 417, Mismatches: 48, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
149 48 0.12
150 22 0.05
151 57 0.14
152 2 0.00
153 140 0.34
154 98 0.24
155 16 0.04
156 34 0.08
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (154 bp):
CTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCC
TCAATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
GAAGTTTTTAGCTCATTTGAAACA
Found at i:1810 original size:304 final size:302
Alignment explanation
Indices: 1262--1831 Score: 860
Period size: 304 Copynumber: 1.9 Consensus size: 302
1252 TTTGAATCGT
* *
1262 CTTCGATTTGGCAACCCTCAATGTTTTCTTTCCATTGTATAAGCCCTAACTATAATCATTTTGGT
1 CTTCGATTTGGCAACCCTCAATGTTTTCTTTCCAATGTATAAGACCTAACTATAATCATTTTGGT
* ** * *
1327 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGC
66 AAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAAAACACTTGTTATTTTGGCCCTATCGGGGC
* * *
1392 CAATTAGTTTTGTTTTGAATTGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTA
131 CAATTAGTATTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTA
* *
1457 TGCCCAAACTATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAGCTCATTTTG-AACA
196 TGCCCAAACTATAATCATTTTGGTGAGATTAGTCCAATATGAAGTTTTTAGCTCA-ATTGAAACA
1521 CTTGTTAAGCCTATCAGGGCCCATTAGTTCCATTTGGAATCAA
260 CTTGTTAAGCCTATCAGGGCCCATTAGTTCCATTTGGAATCAA
* * *
1564 CTTCGATTTGGCAACCCTCAATGTCTTTTCTTTCCAATGTTTATCGACCTAACTATAATCGTTTT
1 CTTCGATTTGGCAACCCTCAATG--TTTTCTTTCCAATGTATA-AGACCTAACTATAATCATTTT
*
1629 GGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTAAAACACTAT-TTATTTTGGCCCTATCG
63 GGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAAAACACT-TGTTATTTTGGCCCTATCG
* * *
1693 GGGCCCATTAGTGATT-TTTTGAATCGTCTTCTATTT-GCAACCTTCAATGCGTTTCTTTCCATT
127 GGGCCAATTAGT-ATTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATT
* * *
1756 GTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATTAAGTTTTTAGCTCAATTGA
191 GTTTATGCCCAAACTATAATCATTTTGGTGAGATTAGTCCAATATGAAGTTTTTAGCTCAATTGA
1821 AACACTTGTTA
256 AACACTTGTTA
1832 TTTTGGGCCT
Statistics
Matches: 240, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
302 23 0.10
303 3 0.01
304 108 0.45
305 103 0.43
306 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (302 bp):
CTTCGATTTGGCAACCCTCAATGTTTTCTTTCCAATGTATAAGACCTAACTATAATCATTTTGGT
AAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAAAACACTTGTTATTTTGGCCCTATCGGGGC
CAATTAGTATTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCGTTTCTTTCCATTGTTTA
TGCCCAAACTATAATCATTTTGGTGAGATTAGTCCAATATGAAGTTTTTAGCTCAATTGAAACAC
TTGTTAAGCCTATCAGGGCCCATTAGTTCCATTTGGAATCAA
Done.