Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024581.1 Corchorus olitorius cultivar O-4 contig24614, 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: 9122
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 ACCCCAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2253 original size:36 final size:36
Alignment explanation
Indices: 2208--3091 Score: 1222
Period size: 36 Copynumber: 24.8 Consensus size: 36
2198 CTGAAGAATC
* * *
2208 GAAG-AAAGACCACCCCGGGTCATTCTGAAATAAGCT
1 GAAGAAAAGACCACCCTGGGTCA-ACTGAAATAAACT
* *
2244 GAAG-CAAGACCACCCTGGGT-TACTTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAAC-TGAAATAAACT
* * * * * *
2279 GAA-AAATGACCACCCTCGATC-ATTCCAACACAAACT
1 GAAGAAAAGACCACCCTGGGTCAACT-GAA-ATAAACT
*
2315 AAAG-AAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* * * *
2350 GAAGAACA-ACCACCCTCGGTTAACTGACATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2385 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
*
2421 GAAG-AAAGACCACCCTGGGTCAACTGACATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* *
2456 GAAGAAAAGACCGCCTTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* *
2492 GAAG-AAAGACCACCCTGGGTCAACTGACATAAATT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
*
2527 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* *
2563 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAATT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
*
2599 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAATT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2635 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2671 GAAG-AAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* * *
2706 AAAG-AAAGACCACCCTAGGTCAACTGACATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* * *
2741 GAAGAAAAGACCGCCCTGGGTCAACTGACATAAATT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* ** *
2777 GAAGAAAAGATCGGCCTGGGTCAACTGAAATAAACC
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* *
2813 GAAGAAAAGACCACCCTGGGTCAACTGACATAAATT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2849 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2885 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2921 GAAG-AAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
*
2956 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
2992 GAAGAAAA-ACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* **
3027 GAAGAAAAGACCACCCTGGGCCAACTGAAATTTACT
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
* * *
3063 GAATG--GAGACCGCCCTGAGTCAACTGAAA
1 GAA-GAAAAGACCACCCTGGGTCAACTGAAA
3092 CTTTGAACAT
Statistics
Matches: 762, Mismatches: 71, Indels: 31
0.88 0.08 0.04
Matches are distributed among these distances:
34 2 0.00
35 288 0.38
36 469 0.62
37 3 0.00
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (36 bp):
GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACT
Found at i:2303 original size:71 final size:72
Alignment explanation
Indices: 2208--3091 Score: 1222
Period size: 71 Copynumber: 12.4 Consensus size: 72
2198 CTGAAGAATC
* * * * *
2208 GAAG-AAAGACCACCCCGGGTCATTCTGAAATAAGCTGAAG-CAAGACCACCCTGGGT-TACTTG
1 GAAGAAAAGACCACCCTGGGTCA-ACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAAC-TG
2270 AAATAAACT
64 AAATAAACT
* * * * * * *
2279 GAA-AAATGACCACCCTCGATC-ATTCCAACACAAACTAAAG-AAAGACCACCCTGGGTCAACTG
1 GAAGAAAAGACCACCCTGGGTCAACT-GAA-ATAAACTGAAGAAAAGACCACCCTGGGTCAACTG
2341 AAATAAACT
64 AAATAAACT
* * * *
2350 GAAGAACA-ACCACCCTCGGTTAACTGACATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
2414 ATAAACT
66 ATAAACT
* * *
2421 GAAG-AAAGACCACCCTGGGTCAACTGACATAAACTGAAGAAAAGACCGCCTTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
2485 ATAAACT
66 ATAAACT
* * *
2492 GAAG-AAAGACCACCCTGGGTCAACTGACATAAATTGAAGAAAAGACCGCCCTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
2556 ATAAACT
66 ATAAACT
* *
2563 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
*
2628 ATAAATT
66 ATAAACT
2635 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
2699 ATAAACT
66 ATAAACT
* * * * *
2706 AAAG-AAAGACCACCCTAGGTCAACTGACATAAACTGAAGAAAAGACCGCCCTGGGTCAACTGAC
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
*
2770 ATAAATT
66 ATAAACT
* ** * *
2777 GAAGAAAAGATCGGCCTGGGTCAACTGAAATAAACCGAAGAAAAGACCACCCTGGGTCAACTGAC
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
*
2842 ATAAATT
66 ATAAACT
2849 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
2914 ATAAACT
66 ATAAACT
*
2921 GAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGGTCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
2985 ATAAACT
66 ATAAACT
*
2992 GAAGAAAA-ACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGCCAACTGAA
1 GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
**
3056 ATTTACT
66 ATAAACT
* * *
3063 GAATG--GAGACCGCCCTGAGTCAACTGAAA
1 GAA-GAAAAGACCACCCTGGGTCAACTGAAA
3092 CTTTGAACAT
Statistics
Matches: 736, Mismatches: 63, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
69 1 0.00
70 47 0.06
71 447 0.61
72 241 0.33
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (72 bp):
GAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
ATAAACT
Found at i:2667 original size:250 final size:249
Alignment explanation
Indices: 2208--3091 Score: 1251
Period size: 250 Copynumber: 3.5 Consensus size: 249
2198 CTGAAGAATC
* * * * * *
2208 GAAG-AAAGACCACCCCGGGTCATTCTGAAATAAGCTGAAGCAAGACCACCCTGGGT-TACTTGA
1 GAAGAAAAGACCGCCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAAC-TGA
* * * * * * *
2271 AATAAACTGAA-AAATGACCACCCTCGATC-ATTCCAACACAAACTAAAGAAAGACCACCCTGGG
64 AATAAACTGAAGAAAAGACCACCCTGGGTCAACT-GAA-ATAAACTGAAGAAAGACCACCCTGGG
* * * * *
2334 TCAACTGAAATAAACTGAAGAACA-ACCACCCTCGGTTAACTGACATAAACTGAAGAAAAGACCA
127 TCAACTGAAATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCA
*
2398 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGACATAAACT
192 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
* *
2456 GAAGAAAAGACCGCCTTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGACA
1 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
* * *
2521 TAAATTGAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGGTCA
66 TAAACTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCA
*
2586 ACTGAAATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAATTGAAGAAAAGACCACCC
130 ACTGAAATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCC
2651 TGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
195 TGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
* * * * * *
2706 AAAG-AAAGACCACCCTAGGTCAACTGACATAAACTGAAGAAAAGACCGCCCTGGGTCAACTGAC
1 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAA
* * ** *
2770 ATAAATTGAAGAAAAGATCGGCCTGGGTCAACTGAAATAAACCGAAGAAAAGACCACCCTGGGTC
65 ATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTC
*
2835 AACTGACATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACC
129 AACTGAAATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACC
2900 CTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
194 CTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
*
2956 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAAACCACCCTGGGTCAACTGAAA
1 GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
* ** * * *
3021 TAAACTGAAGAAAAGACCACCCTGGGCCAACTGAAATTTACTGAATG-GAGACCGCCCTGAGTCA
66 TAAACTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAA-GAAAGACCACCCTGGGTCA
3085 ACTGAAA
130 ACTGAAA
3092 CTTTGAACAT
Statistics
Matches: 571, Mismatches: 56, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
248 55 0.10
249 120 0.21
250 363 0.64
251 33 0.06
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (249 bp):
GAAGAAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
TAAACTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
CTGAAATAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCT
GGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
Found at i:4416 original size:19 final size:17
Alignment explanation
Indices: 4382--4433 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
4372 CTTCTTCTTA
4382 CTCTTCTTTTTCTTTCTTT
1 CTCTTCTTTTT-TTT-TTT
* *
4401 C-CTT-TTGTTTATTTT
1 CTCTTCTTTTTTTTTTT
4416 CTCTTCTTTTTTTTTTT
1 CTCTTCTTTTTTTTTTT
4433 C
1 C
4434 AAGCTCTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 14 0.52
18 3 0.11
19 1 0.04
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (17 bp):
CTCTTCTTTTTTTTTTT
Found at i:4795 original size:14 final size:14
Alignment explanation
Indices: 4773--4805 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4763 TGAAAACAAA
4773 TTTTG-GAAACCAT
1 TTTTGAGAAACCAT
*
4786 TTTTGAGAAATCAT
1 TTTTGAGAAACCAT
4800 TTTTGA
1 TTTTGA
4806 AAAATCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (14 bp):
TTTTGAGAAACCAT
Done.