Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024859.1 Corchorus olitorius cultivar O-4 contig24892, 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: 11007
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:4602 original size:13 final size:14
Alignment explanation
Indices: 4565--4603 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
4555 GCTTTTAAAG
*
4565 GATTTTTCAAAAAT
1 GATTTCTCAAAAAT
4579 GATTTCTCAAAAAT
1 GATTTCTCAAAAAT
4593 GATTTC-CAAAA
1 GATTTCTCAAAA
4604 TTTGTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (14 bp):
GATTTCTCAAAAAT
Found at i:4935 original size:29 final size:29
Alignment explanation
Indices: 4903--4967 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
4893 AATCAAAGGT
4903 ATAAGATGTAGCAAAGGGCAATTGGTATG
1 ATAAGATGTAGCAAAGGGCAATTGGTATG
4932 ATAAGATGTAGCAAAGGGCAATTGGTATG
1 ATAAGATGTAGCAAAGGGCAATTGGTATG
4961 ATAAGAT
1 ATAAGAT
4968 CTTCACATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.29, T:0.25
Consensus pattern (29 bp):
ATAAGATGTAGCAAAGGGCAATTGGTATG
Found at i:6287 original size:35 final size:35
Alignment explanation
Indices: 6247--7025 Score: 794
Period size: 35 Copynumber: 21.9 Consensus size: 35
6237 CATTTAGTAA
** *
6247 ATTTCAATCAACCCAGGGTGGTCTTTCTTCGGTTGT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTT-T
* * * * * *
6283 -TTTCAAGTTGATCTAGGGCGATCATTCTTCAGTCT
1 ATTTCAA-TTGACCCAGGGTGGTCTTTCTTCAGTTT
* *
6318 ACTTCAATTGACCCAGGGCGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* *
6353 ATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTC-TTTCTTCAGTTT
* *
6389 ATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
*
6424 ATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* * *
6459 ATTGT-AGTTGACCTAAGGTGGTCTTTTCTTCAGTTT
1 ATT-TCAATTGACCCAGGGTGGTC-TTTCTTCAGTTT
* *
6495 ATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* **
6530 ATTTCAGTTGACCCAGGACGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* *
6565 ATTGT-AGTTGACCCAAGGTGGTCTTTTCTTCAGTTT
1 ATT-TCAATTGACCCAGGGTGGTC-TTTCTTCAGTTT
* *
6601 ATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* * *
6636 ATTTCAGTTGACCCAGGGCGGTTTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* *
6671 ATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTC-TTTCTTCAGTTT
* * *
6707 ATGTCAGTTGACCCAGGGTGGTCTTTCTTCAATTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* *
6742 ATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* * *
6777 ATTGCAGTTGACCCAGGGTGGTCCTTTCTTCAGTAT
1 ATTTCAATTGACCCAGGGTGGT-CTTTCTTCAGTTT
* * * * *
6813 ATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGTTTTTTT
1 ATTTCA-ATTGACCCAGGGTGGTCTTTCTTCAG----TTT
* * *
6853 TTTTCAATTGACCCAGGGCGTTCTTTCTTCAGTTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
6888 ACTTT-AGA-TGACCCAGGGTGGTCTTTTCTTCAGTTT
1 A-TTTCA-ATTGACCCAGGGTGGTC-TTTCTTCAGTTT
* * * * *
6924 ATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGTTT
1 ATTTCA-ATTGACCCAGGGTGGTCTTTCTTCAGTTT
* * * * *
6960 ATTTCAGTTGACCAAGGGAGGTCTTGCTTCAATTT
1 ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
* * *
6995 ATCTCAGAATGATCCAGGGTGGTCTTTCTTC
1 ATTTCA-ATTGACCCAGGGTGGTCTTTCTTC
7026 TTTCTTCAAT
Statistics
Matches: 632, Mismatches: 89, Indels: 44
0.83 0.12 0.06
Matches are distributed among these distances:
35 350 0.55
36 231 0.37
37 25 0.04
39 20 0.03
40 6 0.01
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (35 bp):
ATTTCAATTGACCCAGGGTGGTCTTTCTTCAGTTT
Found at i:6333 original size:71 final size:69
Alignment explanation
Indices: 6257--7025 Score: 876
Period size: 71 Copynumber: 10.8 Consensus size: 69
6247 ATTTCAATCA
* * * * * * *
6257 ACCCAGGGTGGTCTTTCTTCGGTTGT-TTTCAAGTTGATCTAGGGCGATCATTCTTCAGTCTACT
1 ACCCAGGGTGGTCTTTCTTCAGTT-TATTTC-AGTTGACCCAGGGTGGTCTTTCTTCAGTTTA-T
*
6321 TCAATTG
63 TCAGTTG
* *
6328 ACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGT
1 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGTTTAT-T
6393 CAGTTG
64 CAGTTG
*
6399 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTGT
1 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATT-C
6464 AGTTG
65 AGTTG
* * *
6469 ACCTAAGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
1 ACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA-TT
6534 CAGTTG
64 CAGTTG
** *
6540 ACCCAGGACGGTCTTTCTTCAGTTTATTGT-AGTTGACCCAAGGTGGTCTTTTCTTCAGTTTATG
1 ACCCAGGGTGGTCTTTCTTCAGTTTATT-TCAGTTGACCCAGGGTGGTC-TTTCTTCAGTTTAT-
6604 TCAGTTG
63 TCAGTTG
* *
6611 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTTTTTCTTCAGTTTATTGC
1 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATT-C
6676 AGTTG
65 AGTTG
* *
6681 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAATTTATTT
1 ACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA-TT
6746 CAGTTG
64 CAGTTG
* * *
6752 ACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCCTTTCTTCAGTATATGT
1 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGT-CTTTCTTCAGTTTAT-T
*
6817 CAGAATG
64 CAG-TTG
* * * * * * *
6824 ATCGAGGGTGGTCGTTCTTCAGTTTTTTTTTTTCAATTGACCCAGGGCGTTCTTTCTTCAGTTTA
1 ACCCAGGGTGGTCTTTCTTCAG----TTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
6889 CTTTAGATG
62 -TTCAGTTG
* * * * *
6898 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGTTTATT
1 ACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTCTTCAGTTTA-T
6963 TCAGTTG
63 TCAGTTG
* * * * * * *
6970 ACCAAGGGAGGTCTTGCTTCAATTTATCTCAGAATGATCCAGGGTGGTCTTTCTTC
1 ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTCTTC
7026 TTTCTTCAAT
Statistics
Matches: 604, Mismatches: 71, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
69 2 0.00
70 145 0.24
71 334 0.55
72 64 0.11
74 14 0.02
75 24 0.04
76 21 0.03
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (69 bp):
ACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTCA
GTTG
Found at i:6417 original size:106 final size:106
Alignment explanation
Indices: 6257--7025 Score: 1044
Period size: 106 Copynumber: 7.2 Consensus size: 106
6247 ATTTCAATCA
* * * * * * * * *
6257 ACCCAGGGTGGTC-TTTCTTCGGTTGT-TTTCAAGTTGATCTAGGGCGATCATTCTTCAGTCTAC
1 ACCCAGGGTGGTCTTTTCTTCAGTT-TATGTC-AGTTGACCCAGGGTGGTCTTTCTTCAGTTTAT
*
6320 TTCAATTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
64 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
6363 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
1 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
* *
6428 CAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTGTAGTTG
66 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
* *
6469 ACCTAAGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
1 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
* *
6534 CAGTTGACCCAGGACGGTCTTTCTTCAGTTTATTGTAGTTG
66 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
*
6575 ACCCAAGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
1 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
*
6640 CAGTTGACCCAGGGCGGTTTTTCTTCAGTTTATTGCAGTTG
66 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
*
6681 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAATTTATTT
1 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
6746 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
66 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
* * * * * *
6787 ACCCAGGGTGGTCCTTTCTTCAGTATATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGTTTTTT
1 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAG-TTGACCCAGGGTGGTCTTTCTTCAG----TT
* * * * *
6852 TTTTTCAATTGACCCAGGGCGTTCTTTCTTCAGTTTACTT-TAGATG
61 TATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTGCAGTTG
* * * *
6898 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGTTTATT
1 ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAG-TTGACCCAGGGTGGTCTTTCTTCAGTTTATT
* * * * *
6963 TCAGTTGACCAAGGGAGGTCTTGCTTCAATTTATCT-CAGAATG
65 TCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT-TGCAG-TTG
*
7006 ATCCAGGGTGGTC-TTTCTTC
1 ACCCAGGGTGGTCTTTTCTTC
7026 TTTCTTCAAT
Statistics
Matches: 607, Mismatches: 46, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
106 418 0.69
107 75 0.12
108 15 0.02
111 97 0.16
112 2 0.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (106 bp):
ACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTT
CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTGCAGTTG
Done.