Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002503.1 Corchorus olitorius cultivar O-4 contig02503, 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, 621
Length: 1035
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Found at i:762 original size:17 final size:17
Alignment explanation
Indices: 742--792 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
732 AACCAATTAA
742 CAATCTAAATTATATAT
1 CAATCTAAATTATATAT
759 CAAT-TCAAA-T-TA-A-
1 CAATCT-AAATTATATAT
772 CAATCTAAATTATATAT
1 CAATCTAAATTATATAT
789 CAAT
1 CAAT
793 TCAAATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.25
14 3 0.11
15 4 0.14
16 3 0.11
17 11 0.39
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATCTAAATTATATAT
Found at i:770 original size:30 final size:30
Alignment explanation
Indices: 736--798 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
726 CTACTAAACC
736 AATTAACAATCTAAATTATATATCAATTCA
1 AATTAACAATCTAAATTATATATCAATTCA
766 AATTAACAATCTAAATTATATATCAATTCA
1 AATTAACAATCTAAATTATATATCAATTCA
796 AAT
1 AAT
799 GATTATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (30 bp):
AATTAACAATCTAAATTATATATCAATTCA
Found at i:798 original size:17 final size:17
Alignment explanation
Indices: 748--810 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 17
738 TTAACAATCT
748 AAATTATATATCAATTC
1 AAATTATATATCAATTC
765 AAA-T-TA-A-CAA-TC
1 AAATTATATATCAATTC
777 TAAATTATATATCAATTC
1 -AAATTATATATCAATTC
*
795 AAATGAT-TATCAATTC
1 AAATTATATATCAATTC
811 TTACTATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 2 0.05
15 4 0.10
16 11 0.28
17 12 0.31
18 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTATATATCAATTC
Found at i:823 original size:18 final size:18
Alignment explanation
Indices: 800--835 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
790 AATTCAAATG
800 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
818 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
836 CAATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATCAATTCTTACTAT
Found at i:867 original size:20 final size:20
Alignment explanation
Indices: 839--949 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
829 TTACTATCAA
839 TTATTATTAATTTATATTAG
1 TTATTATTAATTTATATTAG
* * *
859 TTGTTATTAATTTCTATT-T
1 TTATTATTAATTTATATTAG
* * *
878 TTATT-CTACTTT-T-TT-T
1 TTATTATTAATTTATATTAG
* *
894 TTATTATTAAATTTTTATATCAA
1 TTATTATT-AA--TTTATATTAG
917 TTATTATTAATTTATATTAG
1 TTATTATTAATTTATATTAG
*
937 TTGTTATTAATTT
1 TTATTATTAATTT
950 CTAATTTTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
16 8 0.11
17 2 0.03
18 6 0.08
19 4 0.06
20 39 0.55
21 1 0.01
22 3 0.04
23 8 0.11
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
TTATTATTAATTTATATTAG
Found at i:920 original size:78 final size:78
Alignment explanation
Indices: 824--1005 Score: 312
Period size: 78 Copynumber: 2.3 Consensus size: 78
814 CTATATTATC
*
824 AATTCTTACTATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCT-ATTTTTATTCTACT
1 AATTTTTA-TATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTAATTTTTATTCTAC-
888 TTTTTTTTATTATTA
64 TTTTTTTTATTATTA
903 AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTAATTTTTATTCTACTT
1 AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTAATTTTTATTCTACTT
968 TTTTTTATTATTA
66 TTTTTTATTATTA
* *
981 AATTTTTATATTATTTATTATTAAT
1 AATTTTTATATCAATTATTATTAAT
1006 ACTTCTATTT
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
78 79 0.80
79 20 0.20
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (78 bp):
AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTAATTTTTATTCTACTT
TTTTTTATTATTA
Found at i:1000 original size:20 final size:20
Alignment explanation
Indices: 897--1000 Score: 53
Period size: 20 Copynumber: 5.3 Consensus size: 20
887 TTTTTTTTTA
* *
897 TTATTAAATTTTTATATCAA
1 TTATTAAATTTTTATATTAT
917 TTATT--ATTAATTTATATTAGTT
1 TTATTAAATT--TTTATATTA--T
*
939 GTTATT-AATTTCTA-ATT-T
1 -TTATTAAATTTTTATATTAT
* *
957 TTATTCTACTTTTT-T-TTA-
1 TTATT-AAATTTTTATATTAT
975 TTATTAAATTTTTATATTAT
1 TTATTAAATTTTTATATTAT
995 TTATTA
1 TTATTA
1001 TTAATACTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
17 11 0.17
18 12 0.19
19 8 0.12
20 19 0.30
21 3 0.05
22 3 0.05
23 5 0.08
24 3 0.05
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATTAAATTTTTATATTAT
Done.