Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023467.1 Corchorus olitorius cultivar O-4 contig23500, 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: 4789
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Found at i:221 original size:103 final size:103
Alignment explanation
Indices: 42--247 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
32 GGAGAGGGGA
* *
42 TGATGCGCTAAGGACTCATCATGGTCTTGAAGAGCACAATGGAGATCATGGAGAGGATGTGCATA
1 TGATGCGCCAAGGACTCATCATGGTCTTGAAGAGCACAATGGAGATCATGGAGAAGATGTGCATA
107 TGCGGCAAGGAGGCTTGGAGAAGCTTGAAGATGCTAAG
66 TGCGGCAAGGAGGCTTGGAGAAGCTTGAAGATGCTAAG
*
145 TGATGCGCCAAGGACTCATCATGGTCTTGAAGAGCACAATGGAGATCATGGAGAAGATGTGCATT
1 TGATGCGCCAAGGACTCATCATGGTCTTGAAGAGCACAATGGAGATCATGGAGAAGATGTGCATA
*
210 TGCGGCAAGGAGGCTTGGGGAAGCTTGAAGATGCTAAG
66 TGCGGCAAGGAGGCTTGGAGAAGCTTGAAGATGCTAAG
248 GAAGAAGTTT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (103 bp):
TGATGCGCCAAGGACTCATCATGGTCTTGAAGAGCACAATGGAGATCATGGAGAAGATGTGCATA
TGCGGCAAGGAGGCTTGGAGAAGCTTGAAGATGCTAAG
Found at i:680 original size:11 final size:11
Alignment explanation
Indices: 640--673 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
630 AGGAGTAGGG
640 TCCTTCCTAGC
1 TCCTTCCTAGC
651 TCCTTCCTAGC
1 TCCTTCCTAGC
662 TCCTTCCTAGC
1 TCCTTCCTAGC
673 T
1 T
674 TTTTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Found at i:3999 original size:66 final size:66
Alignment explanation
Indices: 3812--4001 Score: 283
Period size: 66 Copynumber: 2.9 Consensus size: 66
3802 AATTCTGAAC
* * * *
3812 CTAATTTGAGTGTTGTTTGCAATGACACGAAATTTGTTTT-GAGTGTTGTTAGTGACGATACTAA
1 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAG-GTGTTGTTAGTGATGATACTAA
*
3876 AC
65 AA
* *
3878 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACTAAA
1 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTAGTGATGATACTAAA
3943 A
66 A
* *
3944 CTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTAGTGATGA
4002 AACAAATTCT
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
66 111 0.99
67 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (66 bp):
CTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTAGTGATGATACTAAA
A
Found at i:4013 original size:33 final size:32
Alignment explanation
Indices: 3816--4044 Score: 147
Period size: 33 Copynumber: 6.9 Consensus size: 32
3806 CTGAACCTAA
** * * *
3816 TTTGAGTGTTGTTTGCAATGACACGAAATTTGT
1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT
* * * * **
3849 TTTGAGTGTTGTTAGTGACGATACTAAACCTAA
1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT
* *
3882 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT
1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT
* * * * * **
3915 TCTAGATGTTGTTAGTGATGATACTAAAACTAA
1 T-TTGGTGTTGTTTGTGATGAAACTAAATCTGT
*
3948 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
1 TTTG-GTGTTGTTTGTGATGAAACTAAATCTGT
3981 TTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGT
1 TTT-GGTGTTGTTTGTGATGAAACTAAA-TCTGT
* **
4014 TTTGGATGCTAATTGTGATGAAAAC-AAATCT
1 TTTGG-TGTTGTTTGTGATG-AAACTAAATCT
4045 CTTGAAAATA
Statistics
Matches: 154, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
32 7 0.05
33 137 0.89
34 10 0.06
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.41
Consensus pattern (32 bp):
TTTGGTGTTGTTTGTGATGAAACTAAATCTGT
Found at i:4030 original size:66 final size:66
Alignment explanation
Indices: 3833--4034 Score: 176
Period size: 66 Copynumber: 3.1 Consensus size: 66
3823 GTTGTTTGCA
* * * * * * * **
3833 ATGACACGAAATTTGTT-TTGAGTGTTGTTAGTGACGATACTAAACCTAATTTGAGTGTTGTTTG
1 ATGACACTAAATCTGTTCTAGA-TGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTG
*
3897 CG
65 TG
* * **
3899 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGT
1 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTGT
3964 G
66 G
* * * * **
3965 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATT
1 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGAAACTAAA-ACTAATTTGAG-TGCTAATT
4028 GTG
64 GTG
4031 ATGA
1 ATGA
4035 AAACAAATCT
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
65 4 0.03
66 110 0.94
67 3 0.03
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (66 bp):
ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTGT
G
Found at i:4032 original size:99 final size:99
Alignment explanation
Indices: 3849--4034 Score: 216
Period size: 99 Copynumber: 1.9 Consensus size: 99
3839 CGAAATTTGT
* *
3849 TTTGAGTGTTGTTAGTGACGATACTAAACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTG
1 TTTGAGTGTTGTTAGTGACGACACTAAACCTAATTTGAGTGTTGTTTGCGATGAAACTAAATCTG
**
3914 TTCTAGATGTTGTTAGTGATGATACTAAAACTAA
66 TTCTAGATGTAATTAGTGATGATACTAAAACTAA
* * * * * *
3948 TTTGAGTGTTGTTTGTGATGACACTAAATCT-GTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TTTGAGTGTTGTTAGTGACGACACTAAACCTAATTTGA-GTGTTGTTTGCGATGAAACTAAA-TC
* *
4011 TGTTTTGGATGCTAATT-GTGATGA
64 TGTTCTAGATG-TAATTAGTGATGA
4035 AAACAAATCT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
98 7 0.10
99 62 0.86
100 3 0.04
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.41
Consensus pattern (99 bp):
TTTGAGTGTTGTTAGTGACGACACTAAACCTAATTTGAGTGTTGTTTGCGATGAAACTAAATCTG
TTCTAGATGTAATTAGTGATGATACTAAAACTAA
Done.