Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01003025.1 Corchorus olitorius cultivar O-4 contig03030, 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: 1800
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Found at i:494 original size:22 final size:22
Alignment explanation
Indices: 469--619 Score: 144
Period size: 22 Copynumber: 6.9 Consensus size: 22
459 AAAAATGAGT
* *
469 TTATTAAAATTTCATATTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
491 TTATC-AAATTTTATAGTGTAG
1 TTATCAAAATTTCATAGTGTGG
* * *
512 TTATCAAAATTTCATACTGAGA
1 TTATCAAAATTTCATAGTGTGG
534 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * * *
556 TTATCACAATTTTATAATGCGA
1 TTATCAAAATTTCATAGTGTGG
* *
578 TTATCAAAATTCCATAG-GAAGG
1 TTATCAAAATTTCATAGTG-TGG
*
600 TTATCAAAATTTTATAGTGT
1 TTATCAAAATTTCATAGTGT
620 AAAAACTAAA
Statistics
Matches: 100, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
21 19 0.19
22 80 0.80
23 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:604 original size:66 final size:65
Alignment explanation
Indices: 469--619 Score: 189
Period size: 66 Copynumber: 2.3 Consensus size: 65
459 AAAAATGAGT
* * * * * *
469 TTATTAAAATTTCATATTGTGGTTATCAAATTTTATAGTGTAGTTATCAAAATTTCATACTGAGA
1 TTATCAAAATTTCATAGTGTGGTTATCAAATTTTATAATGGAGTTATCAAAATTCCATACGGAGA
534 TTATCAAAATTTCATAGTGTGGTTATCACAATTTTATAATGCGA-TTATCAAAATTCCATA-GGA
1 TTATCAAAATTTCATAGTGTGGTTATCA-AATTTTATAATG-GAGTTATCAAAATTCCATACGG-
*
597 AGG
63 AGA
*
600 TTATCAAAATTTTATAGTGT
1 TTATCAAAATTTCATAGTGT
620 AAAAACTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 27 0.36
66 47 0.63
67 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (65 bp):
TTATCAAAATTTCATAGTGTGGTTATCAAATTTTATAATGGAGTTATCAAAATTCCATACGGAGA
Found at i:725 original size:21 final size:21
Alignment explanation
Indices: 699--770 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
689 TTTGGTTATG
699 AAAATTTCATAGGGAGGTATC
1 AAAATTTCATAGGGAGGTATC
* *
720 AAAATTTCATAGTGTAGTTATC
1 AAAATTTCATAG-GGAGGTATC
*
742 -AAATCTTTATTA-GGAGGTTATC
1 AAAAT-TTCA-TAGGGAGG-TATC
764 AAAATTT
1 AAAATTT
771 TATTGTGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 19 0.46
22 16 0.39
23 6 0.15
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (21 bp):
AAAATTTCATAGGGAGGTATC
Found at i:740 original size:43 final size:44
Alignment explanation
Indices: 678--770 Score: 102
Period size: 43 Copynumber: 2.1 Consensus size: 44
668 GATGTTATTC
* * *
678 AAATTTTATAGTTTGGTTATGAAAAT-TTCA-TAGGGAGG-TATCA
1 AAATTTCATAGTGTAGTTAT-AAAATCTTCATTA-GGAGGTTATCA
* *
721 AAATTTCATAGTGTAGTTATCAAATCTTTATTAGGAGGTTATCA
1 AAATTTCATAGTGTAGTTATAAAATCTTCATTAGGAGGTTATCA
765 AAATTT
1 AAATTT
771 TATTGTGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
42 4 0.10
43 25 0.60
44 13 0.31
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.41
Consensus pattern (44 bp):
AAATTTCATAGTGTAGTTATAAAATCTTCATTAGGAGGTTATCA
Found at i:780 original size:22 final size:22
Alignment explanation
Indices: 678--805 Score: 93
Period size: 22 Copynumber: 5.9 Consensus size: 22
668 GATGTTATTC
** *
678 AAATTTTATAGTTTGGTTATGA
1 AAATTTTATAGTGAGGTTATCA
* *
700 AAATTTCATAGGGAGG-TATCA
1 AAATTTTATAGTGAGGTTATCA
*
721 AAATTTCATAGTGTA-GTTATC-
1 AAATTTTATAGTG-AGGTTATCA
742 AAATCTTTATTAG-GAGGTTATCA
1 AAAT-TTTA-TAGTGAGGTTATCA
* * *
765 AAATTTTATTGTGAGGCTATCG
1 AAATTTTATAGTGAGGTTATCA
* * *
787 ATATTTTGTAGTGTGGTTA
1 AAATTTTATAGTGAGGTTA
806 ATTATCGAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
21 24 0.29
22 53 0.63
23 7 0.08
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.42
Consensus pattern (22 bp):
AAATTTTATAGTGAGGTTATCA
Found at i:1586 original size:3 final size:3
Alignment explanation
Indices: 1578--1627 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1568 AACCCTATAT
1578 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1626 AT
1 AT
1628 TATCACATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.