Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019840.1 Corchorus olitorius cultivar O-4 contig19873, 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: 21479
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:525 original size:58 final size:57
Alignment explanation
Indices: 460--654 Score: 264
Period size: 58 Copynumber: 3.4 Consensus size: 57
450 ACTTAGAGTA
** *
460 TGCAAAAACAACCAAAATGCCCCAGAACATGCAAAAATGACCATAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCAG-ACGTGCAAAAATGACCATAATGCCCCTAGATG
* *
518 TGCAAAAATGACCATAATGCCCCTAGATGTGCAAAAATGACCATAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCC-AGACGTGCAAAAATGACCATAATGCCCCTAGATG
* * * * * *
576 TGCAAAAATGACCAAAATACCCCTGGAGGTGCTAAAATGACCATAATGCCCCTGGAAG
1 TGCAAAAATGACCAAAATGCCCC-AGACGTGCAAAAATGACCATAATGCCCCTAGATG
634 TGCAAAAATGACCAAAATGCC
1 TGCAAAAATGACCAAAATGCC
655 TTTGGACGTG
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
58 121 0.98
59 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (57 bp):
TGCAAAAATGACCAAAATGCCCCAGACGTGCAAAAATGACCATAATGCCCCTAGATG
Found at i:613 original size:87 final size:87
Alignment explanation
Indices: 460--654 Score: 266
Period size: 87 Copynumber: 2.2 Consensus size: 87
450 ACTTAGAGTA
** ** * * *
460 TGCAAAAACAACCAAAATGCCCC-AGAACATGCAAAAATGACCATAATGCCCCTAGATGTGCAAA
1 TGCAAAAATGACCAAAATGCCCCTAG-ATGTGCAAAAATGACCAAAATACCCCTAGAGGTGCAAA
*
524 AATGACCATAATGCCCCTAGATG
65 AATGACCATAATGCCCCTAGAAG
* * *
547 TGCAAAAATGACCATAATGCCCCTAGATGTGCAAAAATGACCAAAATACCCCTGGAGGTGCTAAA
1 TGCAAAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATACCCCTAGAGGTGCAAAA
*
612 ATGACCATAATGCCCCTGGAAG
66 ATGACCATAATGCCCCTAGAAG
634 TGCAAAAATGACCAAAATGCC
1 TGCAAAAATGACCAAAATGCC
655 TTTGGACGTG
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 92 0.98
88 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (87 bp):
TGCAAAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATACCCCTAGAGGTGCAAAA
ATGACCATAATGCCCCTAGAAG
Found at i:660 original size:29 final size:29
Alignment explanation
Indices: 489--654 Score: 260
Period size: 29 Copynumber: 5.7 Consensus size: 29
479 CCCCAGAACA
489 TGCAAAAATGACCATAATGCCCCTAGATG
1 TGCAAAAATGACCATAATGCCCCTAGATG
518 TGCAAAAATGACCATAATGCCCCTAGATG
1 TGCAAAAATGACCATAATGCCCCTAGATG
547 TGCAAAAATGACCATAATGCCCCTAGATG
1 TGCAAAAATGACCATAATGCCCCTAGATG
* * * *
576 TGCAAAAATGACCAAAATACCCCTGGAGG
1 TGCAAAAATGACCATAATGCCCCTAGATG
* * *
605 TGCTAAAATGACCATAATGCCCCTGGAAG
1 TGCAAAAATGACCATAATGCCCCTAGATG
*
634 TGCAAAAATGACCAAAATGCC
1 TGCAAAAATGACCATAATGCC
655 TTTGGACGTG
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 127 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (29 bp):
TGCAAAAATGACCATAATGCCCCTAGATG
Found at i:5038 original size:59 final size:60
Alignment explanation
Indices: 4781--5057 Score: 414
Period size: 60 Copynumber: 4.6 Consensus size: 60
4771 ATCCTTTATT
* *
4781 ATATAGCGGCGTTTAAACGCCACTATATTTAATTTGAGATTTATTTTAAAATATCCTTAA
1 ATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAGATTTATTTTAAAATACCCTTAA
* * * *
4841 ATATAGCGGCGTTTAAACGCCGTTATATTTAATTTGATATTT-TTTTAAAACACTCTTAAA
1 ATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAGATTTATTTTAAAATACCCTT-AA
* *
4901 ATATAGCGGCGTTTAAACACCACTATATTTAATTTGAGATTTATTTTAAAATACCCTTAA
1 ATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAGATTTATTTTAAAATACCCTTAA
* *
4961 ATATAGCGACGTTTAAACGCCGCTATATTTAATTTGAGATTT-TTTAAAAATACCCTTAA
1 ATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAGATTTATTTTAAAATACCCTTAA
* * *
5020 ATATAGCGGCGCTGAAACGCCGCTATATATAATTTGAG
1 ATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAG
5058 GTAGCGACGT
Statistics
Matches: 195, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
59 62 0.32
60 120 0.62
61 13 0.07
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (60 bp):
ATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAGATTTATTTTAAAATACCCTTAA
Found at i:7445 original size:15 final size:16
Alignment explanation
Indices: 7412--7451 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7402 TTACTTTGCT
7412 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
7428 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
7443 TTGCTTTCT
1 TTGTTTTCT
7452 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:13359 original size:15 final size:15
Alignment explanation
Indices: 13341--13382 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
13331 TGGAAACGTC
13341 TTCGATTGTCTCAG-A
1 TTCGATTGTCTC-GTA
13356 TTCGATTGTCTCGTA
1 TTCGATTGTCTCGTA
*
13371 TTCGATTTTCTC
1 TTCGATTGTCTC
13383 TTCAATCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 1 0.04
15 24 0.96
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (15 bp):
TTCGATTGTCTCGTA
Found at i:19028 original size:23 final size:21
Alignment explanation
Indices: 18998--19039 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
18988 TTTGTTTTAT
18998 GTTTTTGCGTCATAAAAAAAAGA
1 GTTTTTGCGT-A-AAAAAAAAGA
19021 GTTTTTGCGTAAAAAAAAA
1 GTTTTTGCGTAAAAAAAAA
19040 TTCGTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (21 bp):
GTTTTTGCGTAAAAAAAAAGA
Done.