Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011631.1 Corchorus olitorius cultivar O-4 contig11664, 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, 899
Length: 1499
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Found at i:575 original size:306 final size:305
Alignment explanation
Indices: 1--751 Score: 1175
Period size: 306 Copynumber: 2.4 Consensus size: 305
* * *
1 CATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTATG
1 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTT-TA
*
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTGTTGCTC-ATTCGGAACA
65 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTT-TAGCTCAATTC-GAACA
* *
130 CTTGTTATTTTGGGCCTATCGAGGCTCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACC
127 CTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTAAATCGACTTCGATTTGGCAAACC
195 TCAATGCTTTTCTTCCATTGTTTATGGCCTAACTAAAATCATTTTGGTGAGATTAGTCCACTGTG
192 TCAATGCTTTTCTTCCATTGTTTATGGCCTAACTAAAATCATTTTGGTGAGATTAGTCCACTGTG
* * *
260 AAATTTTTAGCCCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCC
257 AAATTTTTAGCCCATTCGGAACACTTGTTATTCTGGGCCTATCGAGGAC
*
309 CATTAGT-CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAG
1 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAG
*
373 CCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTCGAACACTTG
66 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTCGAACACTTG
* * *
438 TTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGTTTTAAAATCGTCTTCGATTTGGCAAACAC-C
131 TTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT-AAATCGACTTCGATTTGGCAAAC-CTC
*
502 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
194 AATGCTTTTC-TTCCATTGTTTATGGCCTAACTAAAATCATTTTGGTGAGATTAGTCCACTGTGA
* * *
567 AGTTTTTAGCTCATTCGGAACACTTGTTATTCTGGGCCTATCGGGGAC
258 AATTTTTAGCCCATTCGGAACACTTGTTATTCTGGGCCTATCGAGGAC
* * * *
615 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGTTTTTCTTTACAATGTTTAT
1 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTA-
* * *
680 GGCCTAACTATTATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACT
65 -GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTCGAACACT
745 TGTTATT
129 TGTTATT
752 GGTCCACTGT
Statistics
Matches: 409, Mismatches: 27, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
304 48 0.12
305 40 0.10
306 145 0.35
307 102 0.25
308 7 0.02
309 67 0.16
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (305 bp):
CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAG
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTCGAACACTTG
TTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTAAATCGACTTCGATTTGGCAAACCTCAA
TGCTTTTCTTCCATTGTTTATGGCCTAACTAAAATCATTTTGGTGAGATTAGTCCACTGTGAAAT
TTTTAGCCCATTCGGAACACTTGTTATTCTGGGCCTATCGAGGAC
Found at i:705 original size:154 final size:154
Alignment explanation
Indices: 1--751 Score: 1158
Period size: 155 Copynumber: 4.9 Consensus size: 154
* * *
1 CATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTG-TTAT
1 CATTAGTGCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
*
65 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTGTTGCTCATTCGGAACA
66 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTT-TAGCTCATTCGGAACA
*
130 CTTGTTATTTTGGGCCTATCGAGGCT
129 CTTGTTATTTTGGGCCTATCGAGGCC
* *
156 CATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTC-TTCCATTGTTTAT
1 CATTAGTGCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
* * * *
220 GGCCTAACTAAAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCCCATTTGGAACACT
66 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACT
285 TGTTATTTTGGGCCTATCGAGGCC
131 TGTTATTTTGGGCCTATCGAGGCC
*
309 CATTAGT-CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTA-
1 CATTAGTGCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
*
372 -GCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTC-GAACAC
66 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTCGGAACAC
* *
435 TTGTTATTTTGGGCCTTTCGGGGCC
130 TTGTTATTTTGGGCCTATCGAGGCC
* *
460 CATTAGTTCCGTTTTAAAATCGTCTTCGATTTGGCAAACAC-CAATGCTTTTCTTTCCATTGTTT
1 CATTAGTGCCGTTTT-GAATCGTCTTCGATTTGGCAAAC-CTCAATGCTTTTCTTTCCATTGTTT
524 ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACA
64 ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACA
* * *
589 CTTGTTATTCTGGGCCTATCGGGGAC
129 CTTGTTATTTTGGGCCTATCGAGGCC
* * * *
615 CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGTTTTTCTTTACAATGTTTAT
1 CATTAGTGCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
* *
680 GGCCTAACTATTATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCAATT-GGAACAC
66 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTCGGAACAC
744 TTGTTATT
130 TTGTTATT
752 GGTCCACTGT
Statistics
Matches: 551, Mismatches: 34, Indels: 23
0.91 0.06 0.04
Matches are distributed among these distances:
151 84 0.15
152 51 0.09
153 103 0.19
154 127 0.23
155 186 0.34
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
CATTAGTGCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACT
TGTTATTTTGGGCCTATCGAGGCC
Found at i:771 original size:43 final size:43
Alignment explanation
Indices: 710--791 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
700 GGTGAGATTT
*
710 GTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTG
1 GTCCACTGTGAAGTTTTTAACTCAATTGGAACACTTGTTATTG
*
753 GTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTT
1 GTCCACTGTGAAGTTTTTAACTCAATTGGAACACTTGTT
792 TTTTTGGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (43 bp):
GTCCACTGTGAAGTTTTTAACTCAATTGGAACACTTGTTATTG
Done.