Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022302.1 Corchorus olitorius cultivar O-4 contig22335, 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, 976
Length: 1627
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:229 original size:128 final size:128
Alignment explanation
Indices: 1--409 Score: 764
Period size: 128 Copynumber: 3.2 Consensus size: 128
*
1 CTTAAACTAACTCGTATGGAAACGAGTTTGGACTTGAAGGACTGAACTATCTTCAAATCAAATTG
1 CTTAAACTAACTCGTATGGAAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTG
*
66 TATACTCGCATGGAAGCGGACTTGACTTATGGAAAAGCTCCAAATGCTTGGATGGAACCAAAG
66 TATACTCGCATGGAAGCGAACTTGACTTATGGAAAAGCTCCAAATGCTTGGATGGAACCAAAG
129 CTTAAACTAACTCGTATGGAAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTG
1 CTTAAACTAACTCGTATGGAAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTG
194 TATACTCGCATGGAAGCGAACTTGACTTATGGAAAAGCTCCAAATGCTTGGATGGAACCAAAG
66 TATACTCGCATGGAAGCGAACTTGACTTATGGAAAAGCTCCAAATGCTTGGATGGAACCAAAG
257 CTTAAACTAACTCGTATGGAAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTG
1 CTTAAACTAACTCGTATGGAAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTG
* * *
322 TATACTCGCATGGAAGCGAACTTGGCTTATGGAAAAGCCCCAAATGCTTGGATGGAATCAAAG
66 TATACTCGCATGGAAGCGAACTTGACTTATGGAAAAGCTCCAAATGCTTGGATGGAACCAAAG
*
385 CTTAAACCAACTCGTATGGAAACGA
1 CTTAAACTAACTCGTATGGAAACGA
410 ACTTTGGCTT
Statistics
Matches: 275, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 275 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (128 bp):
CTTAAACTAACTCGTATGGAAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTG
TATACTCGCATGGAAGCGAACTTGACTTATGGAAAAGCTCCAAATGCTTGGATGGAACCAAAG
Found at i:425 original size:70 final size:69
Alignment explanation
Indices: 325--479 Score: 204
Period size: 70 Copynumber: 2.2 Consensus size: 69
315 CAAATTGTAT
* * *
325 ACTCGCATGGAAGCGAACTTGGCTTATGGAAAAGCCCCA-AATGCTTGGATGGAATCAAAGCTTA
1 ACTCGTATGGAAACGAACTTGGCTTATGGAAAAG-CCCATAATGCTTGGATGGAACCAAAGCTTA
389 AACCA
65 AACCA
* ** *
394 ACTCGTATGGAAACGAACTTTGGCTTATGGAAAAGCGCATGTTGCTTGGATGGAACCAAGGCTTA
1 ACTCGTATGGAAACGAAC-TTGGCTTATGGAAAAGCCCATAATGCTTGGATGGAACCAAAGCTTA
**
459 AACTT
65 AACCA
464 ACTCGTATGGAAACGA
1 ACTCGTATGGAAACGA
480 GCTTAGTCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
69 19 0.25
70 56 0.75
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (69 bp):
ACTCGTATGGAAACGAACTTGGCTTATGGAAAAGCCCATAATGCTTGGATGGAACCAAAGCTTAA
ACCA
Found at i:526 original size:102 final size:101
Alignment explanation
Indices: 413--992 Score: 1061
Period size: 102 Copynumber: 5.7 Consensus size: 101
403 GAAACGAACT
* *
413 TTGGCTTATGGAAAAGCGCATGTTGCTTGGATGGAACCAAGGCTTAAACTTACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
478 GAGCTTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAG-TTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
515 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
580 GAGTTTAGTCTTGGAAGACTGAATTCATATGGAAAAC
66 GAG-TTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
*
617 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACCGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
682 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAGT-TAGTCTTGGAAGACTGAATTCATGTGGAAAAC
719 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
784 GAGTTTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAG-TTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
*
821 TTGGCTTATGGAGAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
886 GAGTATATTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAGT-TAGTCTTGGAAGACTGAATTCATGTGGAAAAC
923 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
988 GAGTT
66 GAGTT
993 TGACTTATGG
Statistics
Matches: 465, Mismatches: 10, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
101 3 0.01
102 461 0.99
103 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (101 bp):
TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGTTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
Found at i:593 original size:49 final size:49
Alignment explanation
Indices: 540--798 Score: 112
Period size: 49 Copynumber: 5.1 Consensus size: 49
530 GCCCATGTTG
540 CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTAGT
1 CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTAGT
* * * * *
589 CTTGGAAGACTGAATTCATATGG--AAAACTTGGCT--TATGGAAAAGCCCA-TGTT-G-
1 CTTGGATG---GAA-CCA-A-GGCTTAAAC-TGACTCGTATGG-AAA--CGAGT-TTAGT
* *
642 CTTGGATGGAACCAAGGCTTAAACCGACTCGTATGGAAACGAGTATAGT
1 CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTAGT
* * * ** * *
691 CTTGGAAGACTGAATTCATGTG-GAAAACTTGGCT--TATGGAAAAGCCCA-TGTT-G-
1 CTTGGATG---GAA-CCAAG-GCTTAAAC-TGACTCGTATGG-AAA--CGAGT-TTAGT
744 CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTAGT
1 CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTAGT
793 CTTGGA
1 CTTGGA
799 AGACTGAATT
Statistics
Matches: 148, Mismatches: 28, Indels: 68
0.61 0.11 0.28
Matches are distributed among these distances:
47 9 0.06
48 13 0.09
49 39 0.26
50 16 0.11
52 16 0.11
53 33 0.22
54 13 0.09
55 9 0.06
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (49 bp):
CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTAGT
Done.