Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021254.1 Corchorus olitorius cultivar O-4 contig21287, 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: 57163
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4947 original size:28 final size:28
Alignment explanation
Indices: 4853--4955 Score: 147
Period size: 29 Copynumber: 3.7 Consensus size: 28
4843 AAGTGAACCT
* *
4853 AAAATGACCAAAATG-CCCTTAGTGT-A
1 AAAATGACCAAAATGCCCCTGAATGTGA
**
4879 AAAATGACCAAAATGCTGCTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTG-A
4908 AAAATGACCAAAATGCCCCTGAATGTGA
1 AAAATGACCAAAATGCCCCTGAATGTGA
4936 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
4956 AGGTGACCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 15 0.22
27 6 0.09
28 21 0.31
29 26 0.38
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATGTGA
Found at i:9135 original size:17 final size:17
Alignment explanation
Indices: 9094--9135 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
9084 ATTAAAATTG
*
9094 ATTTTTGCTTGCATGTT
1 ATTTTTGCTTGAATGTT
*
9111 ATTATTGCTTGAAT-TT
1 ATTTTTGCTTGAATGTT
9127 AGTTTTTGC
1 A-TTTTTGC
9136 ATTTAGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (17 bp):
ATTTTTGCTTGAATGTT
Found at i:15145 original size:76 final size:76
Alignment explanation
Indices: 15008--15159 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
14998 ACAAGGACTT
* *
15008 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
15073 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * **
15084 CGACTCCAGCTGGGTGCCCATATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
15146 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
15160 TAGCTTATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:16372 original size:21 final size:21
Alignment explanation
Indices: 16346--16386 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
16336 ACTCATAAAG
16346 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
16367 AAGTTTCAAGCTCATTGGAG
1 AAGTTTCAAGCTCATTGGAG
16387 TTGCCTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (21 bp):
AAGTTTCAAGCTCATTGGAGA
Found at i:17437 original size:10 final size:11
Alignment explanation
Indices: 17412--17441 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
17402 TAGTTTAATC
17412 AAAAAATATAA
1 AAAAAATATAA
17423 AAAAAATA-AA
1 AAAAAATATAA
17433 AAAAAATAT
1 AAAAAATAT
17442 TTCGACCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAATATAA
Found at i:19783 original size:22 final size:21
Alignment explanation
Indices: 19758--19811 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
19748 GAAGTTCGTG
19758 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
19780 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
19799 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
19812 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:28499 original size:46 final size:45
Alignment explanation
Indices: 28423--28512 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 45
28413 CTTTTTCAAA
*
28423 GACGCAAGACAAAAATTTTAAAAACGCAAAA-ATCAAATTTTTTTAT
1 GACGCAAGACAAAAA-TTTAAAAACGCAAAACA-AAAATTTTTTTAT
28469 GACGCAA-ACACAAAA-TTAAAAACGGACAAAACAAAAATTTTTTT
1 GACGCAAGACA-AAAATTTAAAAAC-G-CAAAACAAAAATTTTTTT
28513 TTTTAGGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
44 8 0.21
45 4 0.10
46 26 0.67
47 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.24
Consensus pattern (45 bp):
GACGCAAGACAAAAATTTAAAAACGCAAAACAAAAATTTTTTTAT
Found at i:28865 original size:15 final size:16
Alignment explanation
Indices: 28841--28880 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
28831 AGAAGTTGAA
*
28841 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
28856 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
28872 AGAAAACAA
1 AGAAAACAA
28881 AACAAAGTAA
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:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:37919 original size:2 final size:2
Alignment explanation
Indices: 37912--37956 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
37902 TTTTTATTAG
37912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37954 TA T
1 TA T
37957 CAGCTGCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42100 original size:38 final size:38
Alignment explanation
Indices: 42044--42120 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
42034 TTTGTTGCCC
*
42044 TTGAGGTAATTTACACTTCAATTATTATTGATGTTTTT
1 TTGAGGTAATTTACACTTCAATTATTACTGATGTTTTT
**
42082 TTGAGGTAATTTGTACTTCAATTATTACTGATGTTTTT
1 TTGAGGTAATTTACACTTCAATTATTACTGATGTTTTT
42120 T
1 T
42121 CATGGTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (38 bp):
TTGAGGTAATTTACACTTCAATTATTACTGATGTTTTT
Found at i:44358 original size:23 final size:23
Alignment explanation
Indices: 44326--44377 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
44316 TTGAAGAGCC
44326 TAAATACAATT-AAGATTCAAGT
1 TAAATACAATTAAAGATTCAAGT
*
44348 TAAATGACAATTAAAGATTCAA-A
1 TAAAT-ACAATTAAAGATTCAAGT
44371 TAAATAC
1 TAAATAC
44378 CTTCGCTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 9 0.33
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (23 bp):
TAAATACAATTAAAGATTCAAGT
Found at i:45537 original size:2 final size:2
Alignment explanation
Indices: 45530--45599 Score: 63
Period size: 2 Copynumber: 33.5 Consensus size: 2
45520 ATTGCTTGTC
* *
45530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TGA GTA GTT TA GCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA -TA TA -TA
45573 CT- TA TA TA TA TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA T
45600 TTTTTTTAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
1 2 0.03
2 51 0.88
3 4 0.07
4 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48442 original size:24 final size:24
Alignment explanation
Indices: 48415--48474 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 24
48405 ATAAGCAACA
*
48415 AATAAGCAACGACAATTTTTCAAG
1 AATAAGCAACGACAATTCTTCAAG
*
48439 AATAATCAGCAGCGACAATTCTTCAAG
1 AAT-A--AGCAACGACAATTCTTCAAG
*
48466 AATATGCAA
1 AATAAGCAA
48475 AAGTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
24 6 0.21
25 1 0.03
26 1 0.03
27 21 0.72
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (24 bp):
AATAAGCAACGACAATTCTTCAAG
Found at i:51800 original size:30 final size:30
Alignment explanation
Indices: 51766--51825 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
51756 TCAATTCTTC
*
51766 CTCTTGAAATAAATCTTC-AATGGTCTTCAA
1 CTCTTCAAAT-AATCTTCAAATGGTCTTCAA
*
51796 CTCTTCAAATTATCTTCAAATGGTCTTCAA
1 CTCTTCAAATAATCTTCAAATGGTCTTCAA
51826 ACACGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (30 bp):
CTCTTCAAATAATCTTCAAATGGTCTTCAA
Done.