Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022976.1 Corchorus olitorius cultivar O-4 contig23009, 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: 33167
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1057 original size:27 final size:28
Alignment explanation
Indices: 998--1055 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
988 AGTGAACTTA
*
998 AAATGACCAAAATGCCCCCTGACTGTGC
1 AAATGACCAAAATGCCCCCCGACTGTGC
**
1026 AAATGACCAAAATGCCCCCCGGGTGTGC
1 AAATGACCAAAATGCCCCCCGACTGTGC
1054 AA
1 AA
1056 TGCCAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.16
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCCCGACTGTGC
Found at i:2282 original size:10 final size:10
Alignment explanation
Indices: 2267--2296 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2257 GTGAATTCAC
*
2267 TGGAAAGTGT
1 TGGAAAATGT
2277 TGGAAAATGT
1 TGGAAAATGT
2287 TGGAAAATGT
1 TGGAAAATGT
2297 CTTTCTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (10 bp):
TGGAAAATGT
Found at i:3162 original size:168 final size:168
Alignment explanation
Indices: 2817--3325 Score: 670
Period size: 168 Copynumber: 3.0 Consensus size: 168
2807 GGTTGTTGCA
* ** *
2817 AAGATATTAATATAGATATTTTTGAAGGGGAAATCAACAATAAATCCATGGAAGCTGATTTGGTG
1 AAGATATTAATATAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTATGGAAGCTGATTTGGTG
* ** ** * *
2882 GTGAATAATTTGAATTAAAAAAAAAAGTGATGTTCCTAATGGAGATTTGGTTCTTTATGATAGCA
66 GTGAATAATTTGAATT-CAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCA
*
2947 TTGACTCTAGAAAAGAGGAGTTTGTTGCAAAATC-AACTG
130 TTGACTCTAGTAAAGAGGAGTTTGTTGCAAAATCTAA-TG
* * *
2986 ATGATATTAAT-TCAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAACCTGATTTGGT
1 AAGATATTAATAT-AGAGATTTTTGAAGGGGAAATCGGCAATAAATCTATGGAAGCTGATTTGGT
*
3050 GGTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAGTGGAGATTTGGTTATTTATGATAGCA
65 GGTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCA
* * *
3115 TTGACTCTAGTAAAGAGGAATGTGTTGCAGAATCTAATG
130 TTGACTCTAGTAAAGAGGAGTTTGTTGCAAAATCTAATG
* * * *
3154 AAGATATTAATGTAGAGATTTTCGTAGGGGAAATCGGCAATATATCTATGGAAGCTGATTTGGTG
1 AAGATATTAATATAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTATGGAAGCTGATTTGGTG
* * * **
3219 GTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAAATTTGGCTAATTATGATTCCA-
66 GTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCAT
* *
3283 T---TCTAGTAAAGAGGTGTTTGTTGCATAATCTAATG
131 TGACTCTAGTAAAGAGGAGTTTGTTGCAAAATCTAATG
*
3318 ATGATATT
1 AAGATATT
3326 CAGGGCTTAG
Statistics
Matches: 301, Mismatches: 36, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
164 37 0.12
167 1 0.00
168 188 0.62
169 75 0.25
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (168 bp):
AAGATATTAATATAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTATGGAAGCTGATTTGGTG
GTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCAT
TGACTCTAGTAAAGAGGAGTTTGTTGCAAAATCTAATG
Found at i:3439 original size:12 final size:12
Alignment explanation
Indices: 3422--3451 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3412 TAGAGTTTTG
3422 GAGGATATTGAA
1 GAGGATATTGAA
*
3434 GAGGATATTGAG
1 GAGGATATTGAA
3446 GAGGAT
1 GAGGAT
3452 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (12 bp):
GAGGATATTGAA
Found at i:9936 original size:9 final size:8
Alignment explanation
Indices: 9911--9935 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9901 TCGATCATTT
9911 ATAAAAAA
1 ATAAAAAA
9919 ATAAAAAA
1 ATAAAAAA
9927 ATAAAAAA
1 ATAAAAAA
9935 A
1 A
9936 AACTTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:13529 original size:34 final size:34
Alignment explanation
Indices: 13486--13553 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
13476 CTCAACTTGT
* *
13486 AAAGGCGTGATGAAGGCCCGTTTAACATCATTGG
1 AAAGGCGTGAAGAAGGCCCGTGTAACATCATTGG
*
13520 AAAGGCGTGAAGAAGGCCCGTGTAACTTCATTGG
1 AAAGGCGTGAAGAAGGCCCGTGTAACATCATTGG
13554 TGTAAGAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (34 bp):
AAAGGCGTGAAGAAGGCCCGTGTAACATCATTGG
Found at i:22080 original size:11 final size:11
Alignment explanation
Indices: 22066--22103 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22056 ATTCATAACA
22066 AATTTATAATT
1 AATTTATAATT
22077 AATTTATAATT
1 AATTTATAATT
22088 -ATTTGATAATT
1 AATTT-ATAATT
*
22099 TATTT
1 AATTT
22104 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:25104 original size:11 final size:11
Alignment explanation
Indices: 25090--25114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25080 TCTGTGTTTC
25090 ATTATGAAGTT
1 ATTATGAAGTT
25101 ATTATGAAGTT
1 ATTATGAAGTT
25112 ATT
1 ATT
25115 GTTGTCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTATGAAGTT
Found at i:27545 original size:2 final size:2
Alignment explanation
Indices: 27538--27572 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27528 ATTCTAGGAC
27538 TA TA TA TA TA 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 TA TA TA TA T
27573 GACAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28338 original size:2 final size:2
Alignment explanation
Indices: 28331--28366 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28321 TAAGATACAA
*
28331 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28367 CTTCTTGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.