Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010401.1 Corchorus olitorius cultivar O-4 contig10433, 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: 3943
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Found at i:90 original size:28 final size:28
Alignment explanation
Indices: 39--92 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
29 TCATGAATTT
*
39 ATAAGACTATAATCAATTTTTTTGAAAA
1 ATAAGACTATAATCAATTTATTTGAAAA
67 ATAAGACTATAATC-ATTCTATTTGAA
1 ATAAGACTATAATCAATT-TATTTGAA
93 CATGAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (28 bp):
ATAAGACTATAATCAATTTATTTGAAAA
Found at i:714 original size:26 final size:26
Alignment explanation
Indices: 685--751 Score: 93
Period size: 25 Copynumber: 2.6 Consensus size: 26
675 CAAAAATTAT
**
685 TTTTCAAATTATTATTTTCAAG-TAAA
1 TTTTCAAATT-TTATTTGAAAGATAAA
711 TTTTCAAATTTT-TTTGAAAGATAAA
1 TTTTCAAATTTTATTTGAAAGATAAA
736 TTTTCAAATTTTATTT
1 TTTTCAAATTTTATTT
752 ACAAATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 6 0.16
25 18 0.49
26 13 0.35
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTTCAAATTTTATTTGAAAGATAAA
Found at i:1009 original size:2 final size:2
Alignment explanation
Indices: 997--1060 Score: 76
Period size: 2 Copynumber: 30.0 Consensus size: 2
987 TATCATTATC
997 AT AT AT CAT AT AT CAT AT AT AT CAT AT CAT AT AT CAT AT AT AT AT
1 AT AT AT -AT AT AT -AT AT AT AT -AT AT -AT AT AT -AT AT AT AT AT
1042 AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT
1061 GATAACAATG
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 1 0.02
2 45 0.80
3 10 0.18
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1012 original size:14 final size:14
Alignment explanation
Indices: 987--1060 Score: 95
Period size: 14 Copynumber: 5.6 Consensus size: 14
977 CCAAATCAAT
987 TATCAT-TATCATA
1 TATCATATATCATA
1000 TATCATATATCATA
1 TATCATATATCATA
1014 TAT-ATCATATCATA
1 TATCAT-ATATCATA
1028 TATCATATAT-ATA
1 TATCATATATCATA
1041 TAT-ATATAT-ATA
1 TATCATATATCATA
*
1053 TATAATAT
1 TATCATAT
1061 GATAACAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.21
13 18 0.32
14 25 0.44
15 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (14 bp):
TATCATATATCATA
Found at i:1025 original size:21 final size:20
Alignment explanation
Indices: 987--1060 Score: 102
Period size: 21 Copynumber: 3.8 Consensus size: 20
977 CCAAATCAAT
987 TATCAT-TATCATATATCATA
1 TATCATATAT-ATATATCATA
1007 TATCATATATATCATATCATA
1 TATCATATATAT-ATATCATA
1028 TATCATATATATATAT-ATA
1 TATCATATATATATATCATA
1047 TAT-ATATATA-ATAT
1 TATCATATATATATAT
1061 GATAACAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.08
18 7 0.13
19 6 0.12
20 12 0.23
21 23 0.44
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (20 bp):
TATCATATATATATATCATA
Found at i:1065 original size:8 final size:7
Alignment explanation
Indices: 997--1065 Score: 56
Period size: 7 Copynumber: 10.1 Consensus size: 7
987 TATCATTATC
*
997 ATATATC
1 ATATATA
*
1004 ATATATC
1 ATATATA
1011 ATATAT-
1 ATATATA
*
1017 ATCATATC
1 AT-ATATA
*
1025 ATATATC
1 ATATATA
1032 ATATAT-
1 ATATATA
1038 ATATAT-
1 ATATATA
1044 ATATAT-
1 ATATATA
1050 ATATATA
1 ATATATA
1057 ATATGATA
1 ATAT-ATA
1065 A
1 A
1066 CAATGTACAC
Statistics
Matches: 58, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
6 20 0.34
7 32 0.55
8 6 0.10
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:1184 original size:7 final size:7
Alignment explanation
Indices: 1172--1244 Score: 96
Period size: 7 Copynumber: 10.1 Consensus size: 7
1162 TATTAAAAAA
1172 ATCATAT
1 ATCATAT
1179 ATCATAT
1 ATCATAT
1186 ATCATAT
1 ATCATAT
1193 CAT-ATAT
1 -ATCATAT
1200 ATCATATCAT
1 ATC--AT-AT
1210 ATCATAT
1 ATCATAT
1217 ATCATAT
1 ATCATAT
1224 ATCATAT
1 ATCATAT
1231 ATCATAT
1 ATCATAT
1238 AT-ATAT
1 ATCATAT
1244 A
1 A
1245 ATGATAGCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
6 7 0.11
7 43 0.70
8 4 0.07
9 2 0.03
10 5 0.08
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (7 bp):
ATCATAT
Found at i:1196 original size:19 final size:18
Alignment explanation
Indices: 1172--1243 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 18
1162 TATTAAAAAA
1172 ATCATATATCATATATCAT
1 ATCATATAT-ATATATCAT
1191 ATCATATATATCATATCAT
1 ATCATATATAT-ATATCAT
1210 ATCATATATCATATATCAT
1 ATCATATAT-ATATATCAT
1229 AT-ATCATATATATAT
1 ATCAT-ATATATATAT
1244 AATGATAGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.20
19 38 0.76
20 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (18 bp):
ATCATATATATATATCAT
Done.