Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005241.1 Corchorus capsularis cultivar CVL-1 contig05259, 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, 977
Length: 1629
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Found at i:536 original size:42 final size:42
Alignment explanation
Indices: 480--626 Score: 267
Period size: 42 Copynumber: 3.5 Consensus size: 42
470 AACGGAGTGC
480 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
* *
522 TGAAATGCAGGTTTTGAATTTTGAGTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
564 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
606 TGAAATGCAGGTTTTGAATTT
1 TGAAATGCAAGTTTTGAATTT
627 CGAACCATGA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (42 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
Found at i:631 original size:28 final size:28
Alignment explanation
Indices: 600--654 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
590 TTTGAAGAAT
* *
600 GAACCGTGAAATGCAGGTTTTGAATTTC
1 GAACCATGAAATGCAGATTTTGAATTTC
* *
628 GAACCATGAGATGCTGATTTTGAATTT
1 GAACCATGAAATGCAGATTTTGAATTT
655 TGATTTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (28 bp):
GAACCATGAAATGCAGATTTTGAATTTC
Found at i:656 original size:35 final size:35
Alignment explanation
Indices: 617--700 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
607 GAAATGCAGG
* * **
617 TTTTGAATTTCGAACCATGAGATGCTGATTTTGAA
1 TTTTGATTTTCGAACCATGAAATGCAAATTTTGAA
* *
652 TTTTGATTTTTGAATCATGAAATGCAAATTTTGAA
1 TTTTGATTTTCGAACCATGAAATGCAAATTTTGAA
*
687 CTTTGATTTTCGAA
1 TTTTGATTTTCGAA
701 GAATAGAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTTGATTTTCGAACCATGAAATGCAAATTTTGAA
Found at i:975 original size:37 final size:37
Alignment explanation
Indices: 933--1295 Score: 328
Period size: 37 Copynumber: 9.8 Consensus size: 37
923 TGGTTCTCGA
*
933 ACACCTAAACAGGGATCATT-AACAAGATTTTGATGAG
1 ACACCTAAACAGGGATC-TTAAACAAGATTTTGATAAG
* *
970 ACACCTAAATAGGGA-CTTTAAATAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATC-TTAAACAA-GATTTTGATAAG
* * * * * * *
1007 AAACCTAAACAGGCATCTTGAAGAAGGTTTTGATGAC
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
* * *
1044 ACACCTAAACAGGTACCTTAAATAAAGATTTTGATAAG
1 ACACCTAAACAGGGATCTTAAA-CAAGATTTTGATAAG
* * * *
1082 AAACCTAAATAGGAATCTTGAACAAGATTTTGAT--G
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
* *
1117 ACACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATAAG
* * * *
1154 AAACCTAAACAGGAATCTTGAACAAGATTTTGATGAG
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
*
1191 ACACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATAAG
* * * *
1228 AAATCTAAACAGGAATCTTGAACAAGATTTTGATGAA-
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGAT-AAG
* *
1265 ACACCTAAACAGGGACCTTAAATAAGGATTT
1 ACACCTAAACAGGGATCTTAAACAA-GATTT
1296 GTCATGAAAA
Statistics
Matches: 259, Mismatches: 54, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
35 26 0.10
36 10 0.04
37 183 0.71
38 40 0.15
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (37 bp):
ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
Found at i:1065 original size:74 final size:74
Alignment explanation
Indices: 935--1296 Score: 550
Period size: 74 Copynumber: 4.9 Consensus size: 74
925 GTTCTCGAAC
* * *
935 ACCTAAACAGGGATCATT-AACAAGATTTTGATGAGACACCTAAATAGGGACTTTAAATAAGGAT
1 ACCTAAACAGGAATC-TTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
999 TTGATAAGAA
65 TTGATAAGAA
* * * * * *
1009 ACCTAAACAGGCATCTTGAAGAAGGTTTTGATGACACACCTAAACAGGTACCTTAAATAAAGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-T
1074 TTGATAAGAA
65 TTGATAAGAA
* *
1084 ACCTAAATAGGAATCTTGAACAAGATTTTGAT--GACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
*
1147 TAATAAGAA
66 TGATAAGAA
*
1156 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1221 TGATAAGAA
66 TGATAAGAA
* *
1230 ATCTAAACAGGAATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1295 TG
66 TG
1297 TCATGAAAAA
Statistics
Matches: 262, Mismatches: 22, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
72 41 0.16
73 27 0.10
74 155 0.59
75 39 0.15
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
TGATAAGAA
Done.