Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011687.1 Corchorus olitorius cultivar O-4 contig11720, 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, 806
Length: 1344
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Found at i:276 original size:154 final size:154
Alignment explanation
Indices: 1--1343 Score: 2047
Period size: 154 Copynumber: 8.8 Consensus size: 154
* * *
1 CATTTTGGTGAGATTAGTCCACTGTGAAG-----AGCTCATTTGGAACACTCGTTATTTTGGGCA
1 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
**
61 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGTTAACCCTCAATGCTTTTCTTTC
66 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
126 CAATGTTTATGGCCTAACTATAAT
131 CAATGTTTATGGCCTAACTATAAT
* * *
150 CATTTTGGTAAGATTAGACCACTTTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGGGCC
1 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
* *
215 TATCGGGGTCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
66 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
*
280 CATTGTTTATGGCCTAACTATAAT
131 CAATGTTTATGGCCTAACTATAAT
* *
304 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
1 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
369 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
66 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
*
434 CATTGTTTATGGCCTAACTATAAT
131 CAATGTTTATGGCCTAACTATAAT
*
458 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
1 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
* *
523 TATC-AGGGCCCATTAGTTCCG-TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
66 TATCGA-GGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
*
586 CCATTGTTTATGGCCTAACTATAAT
130 CCAATGTTTATGGCCTAACTATAAT
* * *
611 CATTTTGG-AGAGATTAGTCCACTGTGAAGTTTTTAGCTTCACTTGCAACACTTGTTA-TTTGGG
1 CATTTTGGTA-AGATTAGTCCACTTTGAAGTTTTTAGC-TCATTTGGAACACTTGTTATTTTGGG
674 CATATCGAGGACCATTAG-TCCG-TTTGAATCGTCTTCGATTTGGCAA-CCTCAATGC-TTTC-T
64 CATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTT
734 TCCAATG-TTATGGCCTAACTATAAT
129 TCCAATGTTTATGGCCTAACTATAAT
* *
759 CA-TTTGGTAAGATTAGTCCACTTTGAAG-TTTTAGCTCAATTGGAACACTTGTTA-TTTGGGCC
1 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
* *
821 TATCGGGGTCCATTAG-TCCG-TTTGAATCGTCTTCGATTTGGCAACCCTCAATGC-TTTCTTTC
66 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
*
883 CATTGTTTATGGCCTAACTATAAT
131 CAATGTTTATGGCCTAACTATAAT
* * *
907 CA-TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTT-GGCA
1 CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
970 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
66 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
1035 CAATGTTTATGGCCTAACTATAAT
131 CAATGTTTATGGCCTAACTATAAT
*
1059 CATTTTTGGTAGAGTATTTACGTCCTACTGTT-AAGTTTTTAGCTCATTTGGAACACTCGTTATT
1 CA-TTTTGGTA-AG-A-TTA-GTCC-ACT-TTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
1123 TTGGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCT-AATGCT
59 TT-GGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCT
*
1187 TTTC-TTCCAATGTTTATAGCCTAACTATAAT
123 TTTCTTTCCAATGTTTATGGCCTAACTATAAT
* * * *
1218 CTATTTTGGTAAGATAAGTCCACTTTGTAAGTTTTTAGCTCAATTAGAATACTTGTTATTTTGGG
1 C-ATTTTGGTAAGATTAGTCCACTTTG-AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
*
1283 CATATCGAGGACCATTAGTTCCGGTTTGAATCGTCTTCGATTTGGCAA-CCTCAATGTCTTT
64 CATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATG-CTTT
1344 C
Statistics
Matches: 1108, Mismatches: 53, Indels: 60
0.91 0.04 0.05
Matches are distributed among these distances:
145 66 0.06
146 20 0.02
147 30 0.03
148 65 0.06
149 74 0.07
150 11 0.01
151 43 0.04
152 62 0.06
153 126 0.11
154 420 0.38
155 40 0.04
156 3 0.00
157 4 0.00
158 6 0.01
159 72 0.06
160 12 0.01
161 54 0.05
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (154 bp):
CATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTC
CAATGTTTATGGCCTAACTATAAT
Done.