Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006079.1 Corchorus capsularis cultivar CVL-1 contig06097, 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: 25301
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:166 original size:1 final size:1
Alignment explanation
Indices: 160--185 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
150 ACTGCTAAGC
160 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
186 GTCTACAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:7418 original size:30 final size:30
Alignment explanation
Indices: 7288--7411 Score: 167
Period size: 30 Copynumber: 4.1 Consensus size: 30
7278 CCCTCTTCAA
*
7288 CATTGTTATCTCCCACTTGCTGCTGGTTTC
1 CATTGTTATCTTCCACTTGCTGCTGGTTTC
* *
7318 CATTGTTATCTCCCACTTGCTGCTAGTTTC
1 CATTGTTATCTTCCACTTGCTGCTGGTTTC
** **
7348 CATTGTTATCTTCCACTTGCTGCTCATGAC
1 CATTGTTATCTTCCACTTGCTGCTGGTTTC
* *
7378 CATTGTTGTCTTCCACTTGTTGCTGGTTTC
1 CATTGTTATCTTCCACTTGCTGCTGGTTTC
7408 CATT
1 CATT
7412 ATTGTCTACT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.12, C:0.28, G:0.15, T:0.44
Consensus pattern (30 bp):
CATTGTTATCTTCCACTTGCTGCTGGTTTC
Found at i:7903 original size:35 final size:35
Alignment explanation
Indices: 7853--7935 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
7843 TACATTAGAT
*
7853 ATGCTCAAACATAGTCACAAAACAAAATTAGAAAC
1 ATGCTCAAACATAGTCACAAAACAAAATCAGAAAC
* * * *
7888 ATGGTCAAATATAGTCACAAAGCCAAATCAGAAAC
1 ATGCTCAAACATAGTCACAAAACAAAATCAGAAAC
7923 ATGCTCAAACATA
1 ATGCTCAAACATA
7936 CAGAAACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (35 bp):
ATGCTCAAACATAGTCACAAAACAAAATCAGAAAC
Found at i:8084 original size:41 final size:40
Alignment explanation
Indices: 8036--8130 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
8026 ACACAAGCAT
* *
8036 TCAATAATTTACTCAATA-AATTAACAAAAACCAACTGCAAA
1 TCAATAATTCAATCAATATAA--AACAAAAACCAACTGCAAA
** *
8077 TCAATAATTCAATCTGTATAACACAAAAACCAACTGCAAA
1 TCAATAATTCAATCAATATAAAACAAAAACCAACTGCAAA
8117 TCAATAATTCAATC
1 TCAATAATTCAATC
8131 TGTATAACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 32 0.67
41 14 0.29
42 2 0.04
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.25
Consensus pattern (40 bp):
TCAATAATTCAATCAATATAAAACAAAAACCAACTGCAAA
Found at i:8107 original size:40 final size:40
Alignment explanation
Indices: 8059--8139 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
8049 CAATAAATTA
8059 ACAAAAACCAACTGCAAATCAATAATTCAATCTGTATAAC
1 ACAAAAACCAACTGCAAATCAATAATTCAATCTGTATAAC
8099 ACAAAAACCAACTGCAAATCAATAATTCAATCTGTATAAC
1 ACAAAAACCAACTGCAAATCAATAATTCAATCTGTATAAC
8139 A
1 A
8140 TAACAAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (40 bp):
ACAAAAACCAACTGCAAATCAATAATTCAATCTGTATAAC
Found at i:10108 original size:53 final size:53
Alignment explanation
Indices: 10044--10150 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
10034 CGGCTGTTTT
*
10044 ATTTTAGAAATTCTTTTAAGAAAATCCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTAGAAATTCTCTTAAGAAAATCCAGTTAAGAAATCAAATTTTGTTGTGA
* *
10097 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTAGAAATTCTCTTAAGAAAATCCAGTTAAGAAATCAAATTTTGTTGTGA
10150 A
1 A
10151 ATGATAACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (53 bp):
ATTTTAGAAATTCTCTTAAGAAAATCCAGTTAAGAAATCAAATTTTGTTGTGA
Found at i:13062 original size:15 final size:15
Alignment explanation
Indices: 13042--13072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13032 TGAATTTGAA
*
13042 TAAAATTTTGACTAT
1 TAAAATTTTGAATAT
13057 TAAAATTTTGAATAT
1 TAAAATTTTGAATAT
13072 T
1 T
13073 CTAGAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TAAAATTTTGAATAT
Found at i:13838 original size:15 final size:15
Alignment explanation
Indices: 13814--13859 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
13804 TTTGGTTGAA
*
13814 GGTGGTGTGGGGAGG
1 GGTGGGGTGGGGAGG
13829 GGTGGGGTGGGGAGG
1 GGTGGGGTGGGGAGG
13844 GGTAGGGAG-GGGGAGG
1 GGT-GGG-GTGGGGAGG
13860 AGAGTGGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 17 0.61
16 10 0.36
17 1 0.04
ACGTcount: A:0.11, C:0.00, G:0.76, T:0.13
Consensus pattern (15 bp):
GGTGGGGTGGGGAGG
Found at i:16837 original size:13 final size:13
Alignment explanation
Indices: 16819--16854 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
16809 TATAATATAT
16819 ATTAATTTTCTTA
1 ATTAATTTTCTTA
*
16832 ATTAATTTCCTTA
1 ATTAATTTTCTTA
16845 ATTTAATTTT
1 A-TTAATTTT
16855 AATAGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTAATTTTCTTA
Found at i:18850 original size:40 final size:40
Alignment explanation
Indices: 18774--18855 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
18764 TAGATTCTCC
*
18774 TGCACCTACAATCTTGGGAATCCAATCCACCTTATTATGCT
1 TGCAACTACAATCTTGGGAAT-CAATCCACCTTATTATGCT
*
18815 TGCAACTACAATGTTGGGAAAT-AATCCACCTTATTATGCT
1 TGCAACTACAATCTTGGG-AATCAATCCACCTTATTATGCT
18855 T
1 T
18856 ACAATACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 19 0.50
41 16 0.42
42 3 0.08
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (40 bp):
TGCAACTACAATCTTGGGAATCAATCCACCTTATTATGCT
Found at i:19776 original size:3 final size:3
Alignment explanation
Indices: 19762--19808 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
19752 GCATCACCCA
*
19762 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19809 CAACAACAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20747 original size:3 final size:3
Alignment explanation
Indices: 20741--20765 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20731 TGTATTATAT
20741 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
20766 GAGTTGGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.