Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020054.1 Corchorus olitorius cultivar O-4 contig20087, 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: 10203
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:610 original size:29 final size:29
Alignment explanation
Indices: 576--636 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
566 CCATCCTTAA
*
576 TATGACAATTTCGGGTGTCAAAATAATAC
1 TATGACAACTTCGGGTGTCAAAATAATAC
*
605 TATGACAACTTCGGGTGTCAAAGTAATAC
1 TATGACAACTTCGGGTGTCAAAATAATAC
634 TAT
1 TAT
637 ATTTTTGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAATAATAC
Found at i:771 original size:32 final size:33
Alignment explanation
Indices: 705--777 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
695 AATTTTTTTA
*
705 ATGATAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGAAGGAGATTATGC
738 ATGATAAAGAAAGGTAGAAGAAGG-GATTATGC
1 ATGATAAAGAAAGGTAGAAGAAGGAGATTATGC
*
770 ATGTTAAA
1 ATGATAAA
778 TAAACTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.39
33 23 0.61
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.21
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGAAGGAGATTATGC
Found at i:979 original size:22 final size:23
Alignment explanation
Indices: 953--998 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
943 GGGAGTAGAA
*
953 AATTGAAGTATGAAAA-GACAAG
1 AATTGAACTATGAAAAGGACAAG
975 AATTGAACTATGAAAAGGACAAG
1 AATTGAACTATGAAAAGGACAAG
998 A
1 A
999 GAATGTAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (23 bp):
AATTGAACTATGAAAAGGACAAG
Found at i:1121 original size:21 final size:21
Alignment explanation
Indices: 1095--1136 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1085 GGCACATAGA
1095 TACATCA-CAATAAATACAAGG
1 TACATCATC-ATAAATACAAGG
1116 TACATCATCATAAATACAAGG
1 TACATCATCATAAATACAAGG
1137 GGATGAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (21 bp):
TACATCATCATAAATACAAGG
Found at i:1248 original size:15 final size:15
Alignment explanation
Indices: 1230--1262 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1220 CACATTATAT
1230 ACATGTATATTCATA
1 ACATGTATATTCATA
1245 ACATGTATATTCATA
1 ACATGTATATTCATA
1260 ACA
1 ACA
1263 ATATGATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (15 bp):
ACATGTATATTCATA
Found at i:1598 original size:2 final size:2
Alignment explanation
Indices: 1591--1654 Score: 54
Period size: 2 Copynumber: 35.5 Consensus size: 2
1581 AATGGTTTTC
*
1591 TA TA TA TA T- TA CTA T- TA GA TA T- TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1628 TA TA T- TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1655 TAAGAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
1 8 0.16
2 41 0.80
3 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1619 original size:5 final size:5
Alignment explanation
Indices: 1591--1656 Score: 80
Period size: 5 Copynumber: 12.4 Consensus size: 5
1581 AATGGTTTTC
1591 TATA- TATAT TACTAT TAGATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TA-TAT T--ATAT TATAT TATAT TATAT TATAT TATAT
1638 TATAT ATATAT ATATAT TA
1 TATAT -TATAT -TATAT TA
1657 AGAACACTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.07
5 33 0.58
6 15 0.26
7 4 0.07
8 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:3975 original size:22 final size:22
Alignment explanation
Indices: 3947--3988 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3937 AAGAGAATCA
3947 TCACAACCATAAATACATTGGC
1 TCACAACCATAAATACATTGGC
3969 TCACAACCATAAATACATTG
1 TCACAACCATAAATACATTG
3989 TCAAGACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (22 bp):
TCACAACCATAAATACATTGGC
Found at i:8456 original size:23 final size:22
Alignment explanation
Indices: 8401--8456 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
8391 TTTAATGTAG
8401 ATATTTATTTTATCATTTTATAT
1 ATATTT-TTTTATCATTTTATAT
* *
8424 TTCA-TTTTTTATTATTTTTATAT
1 AT-ATTTTTTTATCA-TTTTATAT
8447 ATATTTTTTT
1 ATATTTTTTT
8457 TAAATTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
22 8 0.30
23 18 0.67
24 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (22 bp):
ATATTTTTTTATCATTTTATAT
Found at i:8464 original size:23 final size:23
Alignment explanation
Indices: 8408--8455 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
8398 TAGATATTTA
* *
8408 TTTTATCA-TTTTATATTTCATT
1 TTTTATTATTTTTATATATCATT
8430 TTTTATTATTTTTATATAT-ATT
1 TTTTATTATTTTTATATATCATT
8452 TTTT
1 TTTT
8456 TTAAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTATTATTTTTATATATCATT
Done.