Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000016.1 Corchorus olitorius cultivar O-4 contig00016, 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, 666
Length: 1110
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Found at i:659 original size:7 final size:7
Alignment explanation
Indices: 641--677 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
631 TGTTATCATT
641 ATATAT-
1 ATATATG
647 ATATATG
1 ATATATG
654 ATATATG
1 ATATATG
661 ATATATG
1 ATATATG
668 ATATTATG
1 ATA-TATG
676 AT
1 AT
678 TCTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (7 bp):
ATATATG
Found at i:846 original size:228 final size:229
Alignment explanation
Indices: 448--1093 Score: 869
Period size: 209 Copynumber: 2.9 Consensus size: 229
438 AATTATTAAT
* *
448 TTCTTTATTTTTCAATTAAAATCTTAAAAGTTTGTAAGAGAAATTATTGTTCTTTCTTAAAATAT
1 TTCTTTATTTTTCAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAACAT
*
513 ACCAAAGGCTTTTTTCTAATCAAAATATCAATATAATGAATATTAGAATTAATTAGAGACACGTG
66 ACCAAAGACTTTTTTCTAATCAAAATATCAATATAATGAATATTAGAATTAATTAGAGACACGTG
*
578 TCGTGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTAT
131 TCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTAT
643 ATATATATATGATATATGATATATGATATTATGA
196 ATATATATATGATATATGATATATGATATTATGA
*
677 TTCTTTATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAACAT
1 TTCTTTATTTTTCAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAACAT
*
742 ACCAAAGAC-TTTTTCTAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGACACGTG
66 ACCAAAGACTTTTTTCTAATCAAAATATCAATATAATGAATATTAGAATTAATTAGAGACACGTG
806 TCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATC-----
131 TCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTAT
866 ----AT-TAT-ATATAT-ATATATG-----AT--
196 ATATATATATGATATATGATATATGATATTATGA
* ** * * * *
886 TTCTTTATTTTT-AATTAAAATCTTACAAATTTGTAAGAGA-AATTATTGTTCTT-TCT-TAAAA
1 TTCTTTATTTTTCAATTAAAATCTTAAAAATTT-GTA-AGAGAA--ATTATTGTTCTTTCTTAAA
* * * * ** * *
947 TATA-CCAAAGGCTTTTTTC-TAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGAC
62 -ACATACCAAAGACTTTTTTCTAATCAAAATATCAATATAATGAATATTAGAATTAATTAGAGAC
1010 ACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATC
126 ACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATC
1075 ATTATATATATATAT-ATAT
191 ATTATATATATATATGATAT
1094 GATTTCTTTA
Statistics
Matches: 381, Mismatches: 20, Indels: 42
0.86 0.05 0.09
Matches are distributed among these distances:
208 19 0.05
209 132 0.35
210 11 0.03
211 9 0.02
216 7 0.02
217 6 0.02
218 5 0.01
219 9 0.02
228 113 0.30
229 70 0.18
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (229 bp):
TTCTTTATTTTTCAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAACAT
ACCAAAGACTTTTTTCTAATCAAAATATCAATATAATGAATATTAGAATTAATTAGAGACACGTG
TCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCATTAT
ATATATATATGATATATGATATATGATATTATGA
Done.