Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023565.1 Corchorus olitorius cultivar O-4 contig23598, 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: 27301
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2582 original size:67 final size:67
Alignment explanation
Indices: 2499--2994 Score: 750
Period size: 67 Copynumber: 7.4 Consensus size: 67
2489 AAGTTTTATT
* *
2499 TTTTC-TTTCCAGAAATACCCTTTTGGTCAAAGGGTCGATTTCGTCTTTTTGCATCCAAGTTTAG
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCATCCAAGTTTAG
2563 TA
66 TA
* *
2565 TTTTCATTTCCAAAAATACCCTTTCGGTCAAAGGGTC-AGTTTTGTCTGTTTGCATCCAAGTTTA
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGA-TTTTGTCTTTTTGCATCCAAGTTTA
*
2629 TTA
65 GTA
*
2632 TTTTCATTTCCAGAAATACCATTTCGGTCAAAGGGTCGAATTTT-TCTTTTTGCATCCAAGTTTA
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCG-ATTTTGTCTTTTTGCATCCAAGTTTA
2696 GTA
65 GTA
*
2699 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCACCCAAGTTTAG
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCATCCAAGTTTAG
2764 TA
66 TA
*
2766 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTTGATTTTGTCTTTTTGCATCCAAGTTTAG
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCATCCAAGTTTAG
2831 TA
66 TA
* *
2833 TTTTCATTTCCATAAATACCCTTTCGGTCAAAGGTTCGATTTTGTCTTTTTGCATCCAAGTTTAG
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCATCCAAGTTTAG
2898 TA
66 TA
* * * ** * *
2900 TTTTCATTTCCAAAAATACCCTTTCGATCAAAGGGTCGGTTTCATCTTTTTGCATTCAAGTCTAG
1 TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCATCCAAGTTTAG
2965 T-
66 TA
* * *
2966 CTCTC-TTTCCAAAGAATACCCTTTCGGTC
1 TTTTCATTTCCAGA-AATACCCTTTCGGTC
2995 GATGGGTCAA
Statistics
Matches: 397, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
65 8 0.02
66 28 0.07
67 356 0.90
68 4 0.01
69 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (67 bp):
TTTTCATTTCCAGAAATACCCTTTCGGTCAAAGGGTCGATTTTGTCTTTTTGCATCCAAGTTTAG
TA
Found at i:17486 original size:42 final size:43
Alignment explanation
Indices: 17439--17526 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 43
17429 ATTACCCGAA
* *
17439 TCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATAT
1 TCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
*
17481 TCTACTCCTCCATCTCTAGATTATTCATCAAAATAAAACTAATAT
1 TCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
17526 T
1 T
17527 AATTGTTGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 4 0.10
45 36 0.90
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (43 bp):
TCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
Found at i:21744 original size:13 final size:13
Alignment explanation
Indices: 21726--21750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21716 AAATCAACAT
21726 ATATATATATATG
1 ATATATATATATG
21739 ATATATATATAT
1 ATATATATATAT
21751 AGCTAGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATATATATATG
Found at i:22397 original size:32 final size:32
Alignment explanation
Indices: 22337--22398 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
22327 CGTGCTCCCT
**** *
22337 TAAATAATGCATATACTCTTTTTTTATATATA
1 TAAATAATGCATATACTCAAAGTATATATATA
22369 TAAATAATGCATATACTCAAAGTATATATA
1 TAAATAATGCATATACTCAAAGTATATATA
22399 GATGTGATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.42
Consensus pattern (32 bp):
TAAATAATGCATATACTCAAAGTATATATATA
Found at i:24141 original size:7 final size:7
Alignment explanation
Indices: 24131--24161 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
24121 CCTAATTTAG
24131 ACTGCAA
1 ACTGCAA
24138 ACTGCAA
1 ACTGCAA
24145 ACTGCAA
1 ACTGCAA
24152 ACTGCAA
1 ACTGCAA
24159 ACT
1 ACT
24162 TACTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (7 bp):
ACTGCAA
Found at i:26315 original size:13 final size:13
Alignment explanation
Indices: 26297--26321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26287 GTTATCAAAT
26297 TTACAGTAATTAG
1 TTACAGTAATTAG
26310 TTACAGTAATTA
1 TTACAGTAATTA
26322 CTGAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAG
Done.