Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014153.1 Corchorus capsularis cultivar CVL-1 contig14174, 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: 16656
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:8586 original size:30 final size:30
Alignment explanation
Indices: 8542--8610 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
8532 GTAGAAAAAA
8542 ATAGTACAGAGACCAAAATCAACATTTCGT
1 ATAGTACAGAGACCAAAATCAACATTTCGT
* *
8572 ATAGTATAGGGACCAAAATCAACATTTCGT
1 ATAGTACAGAGACCAAAATCAACATTTCGT
8602 ATAGTACAG
1 ATAGTACAG
8611 GAACTCCGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (30 bp):
ATAGTACAGAGACCAAAATCAACATTTCGT
Found at i:8670 original size:13 final size:13
Alignment explanation
Indices: 8652--8685 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
8642 CACACCAGCA
8652 CTCACGGTCTCAC
1 CTCACGGTCTCAC
8665 CTCACGCGGTCTCAC
1 CTCA--CGGTCTCAC
8680 CTCACG
1 CTCACG
8686 CGCCCATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.15, C:0.47, G:0.18, T:0.21
Consensus pattern (13 bp):
CTCACGGTCTCAC
Found at i:8676 original size:15 final size:15
Alignment explanation
Indices: 8656--8687 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8646 CCAGCACTCA
8656 CGGTCTCACCTCACG
1 CGGTCTCACCTCACG
8671 CGGTCTCACCTCACG
1 CGGTCTCACCTCACG
8686 CG
1 CG
8688 CCCATCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.47, G:0.22, T:0.19
Consensus pattern (15 bp):
CGGTCTCACCTCACG
Found at i:10274 original size:205 final size:205
Alignment explanation
Indices: 9941--10351 Score: 822
Period size: 205 Copynumber: 2.0 Consensus size: 205
9931 CTTTAAGTCC
9941 TGTGGAAGCTCAACAAATTAACATCTTCCTGAATCCACCAAAAATTCTATGTGACAGACAGTTAA
1 TGTGGAAGCTCAACAAATTAACATCTTCCTGAATCCACCAAAAATTCTATGTGACAGACAGTTAA
10006 GCATTAGATTGGGTCTCATCAACGAAATTTCGATGCAAAGAATGAAAGAAAGGTAGGTTGTAGTT
66 GCATTAGATTGGGTCTCATCAACGAAATTTCGATGCAAAGAATGAAAGAAAGGTAGGTTGTAGTT
10071 TGGACTTTACTTACCTTATGGATTGCGCCAACTCCACAGTCCTTGTGCCATTGAAGATAATACAG
131 TGGACTTTACTTACCTTATGGATTGCGCCAACTCCACAGTCCTTGTGCCATTGAAGATAATACAG
10136 AAACATTTAT
196 AAACATTTAT
10146 TGTGGAAGCTCAACAAATTAACATCTTCCTGAATCCACCAAAAATTCTATGTGACAGACAGTTAA
1 TGTGGAAGCTCAACAAATTAACATCTTCCTGAATCCACCAAAAATTCTATGTGACAGACAGTTAA
10211 GCATTAGATTGGGTCTCATCAACGAAATTTCGATGCAAAGAATGAAAGAAAGGTAGGTTGTAGTT
66 GCATTAGATTGGGTCTCATCAACGAAATTTCGATGCAAAGAATGAAAGAAAGGTAGGTTGTAGTT
10276 TGGACTTTACTTACCTTATGGATTGCGCCAACTCCACAGTCCTTGTGCCATTGAAGATAATACAG
131 TGGACTTTACTTACCTTATGGATTGCGCCAACTCCACAGTCCTTGTGCCATTGAAGATAATACAG
10341 AAACATTTAT
196 AAACATTTAT
10351 T
1 T
10352 TTGCTCTTGA
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 206 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (205 bp):
TGTGGAAGCTCAACAAATTAACATCTTCCTGAATCCACCAAAAATTCTATGTGACAGACAGTTAA
GCATTAGATTGGGTCTCATCAACGAAATTTCGATGCAAAGAATGAAAGAAAGGTAGGTTGTAGTT
TGGACTTTACTTACCTTATGGATTGCGCCAACTCCACAGTCCTTGTGCCATTGAAGATAATACAG
AAACATTTAT
Found at i:11928 original size:1 final size:1
Alignment explanation
Indices: 11922--11953 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
11912 TGTGTTTGTG
11922 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11954 ATGGGAGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15469 original size:51 final size:51
Alignment explanation
Indices: 15406--15515 Score: 175
Period size: 51 Copynumber: 2.2 Consensus size: 51
15396 AAATTTTTCC
* * * *
15406 ATTTCTTTAACACTTTCTATCAATTCTTTGTAAACTAATTTTGGCTAGTTG
1 ATTTTTTTAACACTTTCTATCAACTCTTTATAAACTAATTTTGGCAAGTTG
*
15457 ATTTTTTTAACACTTTTTATCAACTCTTTATAAACTAATTTTGGCAAGTTG
1 ATTTTTTTAACACTTTCTATCAACTCTTTATAAACTAATTTTGGCAAGTTG
15508 ATTTTTTT
1 ATTTTTTT
15516 TTCTAACACC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (51 bp):
ATTTTTTTAACACTTTCTATCAACTCTTTATAAACTAATTTTGGCAAGTTG
Done.