Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011903.1 Corchorus olitorius cultivar O-4 contig11936, 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: 50116
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:3006 original size:12 final size:12
Alignment explanation
Indices: 2985--3063 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
2975 AGACCGTTTA
2985 ATAATTATATAT
1 ATAATTATATAT
**
2997 ATTTTTATATAT
1 ATAATTATATAT
*
3009 GTAATTATATAT
1 ATAATTATATAT
3021 ATCTAA-TAT-TAT
1 A--TAATTATATAT
3033 -TACATATATATAT
1 ATA-AT-TATATAT
3046 ATAA-TATA-AT
1 ATAATTATATAT
3056 -TAATTATA
1 ATAATTATA
3064 AAAATTACTA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
9 5 0.09
10 7 0.13
11 4 0.08
12 25 0.47
13 7 0.13
14 5 0.09
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:3063 original size:23 final size:22
Alignment explanation
Indices: 2986--3063 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
2976 GACCGTTTAA
**
2986 TAATTATATATATTTTTATATAT
1 TAATTATATATATTAATATA-AT
*
3009 GTAATTATATATATCTAATATTAT
1 -TAATTATATATAT-TAATATAAT
3033 TACA-TATATATATATAATATAAT
1 TA-ATTATATATAT-TAATATAAT
3056 TAATTATA
1 TAATTATA
3064 AAAATTACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 25 0.54
24 16 0.35
25 4 0.09
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (22 bp):
TAATTATATATATTAATATAAT
Found at i:18406 original size:22 final size:22
Alignment explanation
Indices: 18378--18429 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
18368 CCAGGCTGCT
18378 TGGGCCTGAGCTGCTAGCCGCC
1 TGGGCCTGAGCTGCTAGCCGCC
* * *
18400 TGGGCCTGCGCTGCTAGCCTCT
1 TGGGCCTGAGCTGCTAGCCGCC
18422 TGGGCCTG
1 TGGGCCTG
18430 TGCGCGGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.06, C:0.35, G:0.37, T:0.23
Consensus pattern (22 bp):
TGGGCCTGAGCTGCTAGCCGCC
Found at i:18559 original size:11 final size:11
Alignment explanation
Indices: 18545--18570 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18535 TAAAAGAAAG
18545 AAAAAAATAAA
1 AAAAAAATAAA
18556 AAAAAAATAAA
1 AAAAAAATAAA
18567 AAAA
1 AAAA
18571 GAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:18561 original size:13 final size:13
Alignment explanation
Indices: 18532--18578 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
18522 GCCCAATGTG
18532 AAATAAAAGAAAGAA
1 AAATAAAA-AAA-AA
18547 AAA-AATAAAAAAA
1 AAATAA-AAAAAAA
*
18560 AAATAAAAAAAGA
1 AAATAAAAAAAAA
18573 AAATAA
1 AAATAA
18579 TACGAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 17 0.59
14 7 0.24
15 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (13 bp):
AAATAAAAAAAAA
Found at i:24772 original size:23 final size:23
Alignment explanation
Indices: 24736--24779 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
24726 GAGTCCAGAC
24736 CCAGCAACAATGGCTGATACTCA
1 CCAGCAACAATGGCTGATACTCA
* *
24759 CCAGCAATAGTGGCTGATACT
1 CCAGCAACAATGGCTGATACT
24780 ATCCAACAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CCAGCAACAATGGCTGATACTCA
Found at i:32705 original size:22 final size:22
Alignment explanation
Indices: 32675--32894 Score: 153
Period size: 22 Copynumber: 10.0 Consensus size: 22
32665 TCCAACGTAG
*
32675 AAATATTGATAACCACACTATGA
1 AAAT-TTGATAACCTCACTATGA
*
32698 AAATTTGATAACCTCATTATG-
1 AAATTTGATAACCTCACTATGA
* *
32719 AAATTTCAATAACCTCCCTATGA
1 AAATTT-GATAACCTCACTATGA
*
32742 AAATTTGATAACCACACTATG-
1 AAATTTGATAACCTCACTATGA
* * * *
32763 AAATTGTGATAACCTTAATGTGG
1 AAATT-TGATAACCTCACTATGA
* * *
32786 AATTTTGATAATCTCCCTAT-A
1 AAATTTGATAACCTCACTATGA
* * *
32807 CAATTTTGATAATCACACTAT--
1 -AAATTTGATAACCTCACTATGA
* * * *
32828 ATAGTTGGTAACCGCACTATGA
1 AAATTTGATAACCTCACTATGA
* * *
32850 AAATTTTAATAACCACACCATGA
1 AAA-TTTGATAACCTCACTATGA
*
32873 AAATTTGATAACCTCCCTATGA
1 AAATTTGATAACCTCACTATGA
32895 GAATGAAACT
Statistics
Matches: 152, Mismatches: 37, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
20 14 0.09
21 11 0.07
22 96 0.63
23 31 0.20
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACCTCACTATGA
Found at i:32762 original size:66 final size:65
Alignment explanation
Indices: 32675--32894 Score: 212
Period size: 66 Copynumber: 3.3 Consensus size: 65
32665 TCCAACGTAG
* *
32675 AAATATTGATAACCACACTATGAAAATTTGATAACCTCATTATGAAATTTCAATAACCTCCCTAT
1 AAAT-TTGATAACCACACTATG-AAATTTGATAACCTCAATATGAAATTTTAATAACCTCCCTAT
32740 GA
64 GA
* * * * *
32742 AAATTTGATAACCACACTATGAAATTGTGATAACCTTAATGTGGAATTTTGATAATCTCCCTAT-
1 AAATTTGATAACCACACTATGAAATT-TGATAACCTCAATATGAAATTTTAATAACCTCCCTATG
32806 A
65 A
* * * * * * * *
32807 CAATTTTGATAATCACACTAT-ATAGTTGGTAACCGCACTATGAAAATTTTAATAACCACACC-A
1 -AAATTTGATAACCACACTATGAAATTTGATAACCTCAATATG-AAATTTTAATAACCTC-CCTA
32870 TGA
63 TGA
* *
32873 AAATTTGATAACCTCCCTATGA
1 AAATTTGATAACCACACTATGA
32895 GAATGAAACT
Statistics
Matches: 123, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
64 11 0.09
65 39 0.32
66 69 0.56
67 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (65 bp):
AAATTTGATAACCACACTATGAAATTTGATAACCTCAATATGAAATTTTAATAACCTCCCTATGA
Found at i:32944 original size:20 final size:21
Alignment explanation
Indices: 32915--32959 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
32905 GTGATATCTT
* *
32915 CTCTATAT-AATTTTGATAAC
1 CTCTACATAAATTTTCATAAC
32935 CTCTACATAAAATTTTCATAAC
1 CTCTACAT-AAATTTTCATAAC
32957 CTC
1 CTC
32960 CTTATGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (21 bp):
CTCTACATAAATTTTCATAAC
Found at i:33248 original size:22 final size:22
Alignment explanation
Indices: 33025--33255 Score: 114
Period size: 22 Copynumber: 10.5 Consensus size: 22
33015 AATTCCCTCC
** *
33025 CTATGAAATTCGGTTAACC-TT
1 CTATGAAATTTTGATAACCTTT
***
33046 CTTATGAAATTTTGATAACCAAG
1 C-TATGAAATTTTGATAACCTTT
* *
33069 CTATAAAATTTCGATAA-CTTT
1 CTATGAAATTTTGATAACCTTT
* **
33090 CGTATAAAATTTT-ATTAACCTCC
1 C-TATGAAATTTTGA-TAACCTTT
* * *
33113 CTACGAAATTTTAATAATCTTT
1 CTATGAAATTTTGATAACCTTT
* * * *
33135 TTATGAAAATTTGGTAACATTT
1 CTATGAAATTTTGATAACCTTT
* * *
33157 GTATGAAGTTTTGATAA--TTACA
1 CTATGAAATTTTGATAACCTT--T
* *
33179 CTATGAAGTTTTGATAATC-TT
1 CTATGAAATTTTGATAACCTTT
* * * *
33200 CATATGAAATTTTGGTCACCATA
1 C-TATGAAATTTTGATAACCTTT
33223 CTATGAAATTTTGATAACCTTT
1 CTATGAAATTTTGATAACCTTT
*
33245 CTATGTAATTT
1 CTATGAAATTT
33256 AATTTGGTTT
Statistics
Matches: 156, Mismatches: 42, Indels: 23
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.01
21 5 0.03
22 141 0.90
23 8 0.05
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTTT
Found at i:34907 original size:3 final size:3
Alignment explanation
Indices: 34899--34990 Score: 175
Period size: 3 Copynumber: 30.7 Consensus size: 3
34889 TAATTATCAA
*
34899 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34947 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34991 AACATACAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39866 original size:15 final size:15
Alignment explanation
Indices: 39836--39877 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
39826 TTACTTTGCT
39836 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
39852 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
39867 TTGCTTTCTGT
1 TTGTTTTCTGT
39878 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:42687 original size:21 final size:19
Alignment explanation
Indices: 42662--42720 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
42652 CGCTGCTCTA
*
42662 ATAATTTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
42681 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
42702 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
42721 TGCTAAACAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:44618 original size:81 final size:81
Alignment explanation
Indices: 44468--44628 Score: 223
Period size: 81 Copynumber: 2.0 Consensus size: 81
44458 ACTTTCATCT
* *
44468 TGTTTATACCTCAATTTACAATTGAGGGTAAATTGATCTTCACACAAATAATATCAAGATAAGTA
1 TGTTTATACATCAATTTACAATTGAGAGTAAATTGATCTTCACACAAATAATATCAAGATAAGTA
* *
44533 GTCAAGGTTTGATTAC
66 GTCAAGATTTAATTAC
* * * * ** *
44549 TGTTTATACATCAATTTACAATTGAGAGTAAATTGATCTTCACATATATATTATTAAGATGTGTG
1 TGTTTATACATCAATTTACAATTGAGAGTAAATTGATCTTCACACAAATAATATCAAGATAAGTA
44614 GTCAAGATTTAATTA
66 GTCAAGATTTAATTA
44629 AAAATCCTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (81 bp):
TGTTTATACATCAATTTACAATTGAGAGTAAATTGATCTTCACACAAATAATATCAAGATAAGTA
GTCAAGATTTAATTAC
Found at i:44752 original size:18 final size:18
Alignment explanation
Indices: 44718--44761 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
44708 TGAAATTTAT
*
44718 TAATTATTTATTAAATAA
1 TAATTATTTATCAAATAA
44736 TAATTATTT-TCAGAATAA
1 TAATTATTTATCA-AATAA
*
44754 TTATTATT
1 TAATTATT
44762 AATATTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTTATCAAATAA
Done.