Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022135.1 Corchorus olitorius cultivar O-4 contig22168, 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: 34247
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:16318 original size:32 final size:32
Alignment explanation
Indices: 16282--16369 Score: 140
Period size: 32 Copynumber: 2.8 Consensus size: 32
16272 TGCCTGCCTA
*
16282 TTAATTGTTTCTTCAATCTGATCTATTCTGCT
1 TTAATTGCTTCTTCAATCTGATCTATTCTGCT
* *
16314 TTAATTGCTTCTTCAATCTGATTTGTTCTGCT
1 TTAATTGCTTCTTCAATCTGATCTATTCTGCT
*
16346 TTAATTGCTACTTCAATCTGATCT
1 TTAATTGCTTCTTCAATCTGATCT
16370 TTCAGAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.51
Consensus pattern (32 bp):
TTAATTGCTTCTTCAATCTGATCTATTCTGCT
Found at i:17270 original size:17 final size:17
Alignment explanation
Indices: 17250--17288 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
17240 AATAATAATA
17250 ATTATAAAATTATTATT
1 ATTATAAAATTATTATT
17267 ATTATAAAATTATTATT
1 ATTATAAAATTATTATT
17284 ATTAT
1 ATTAT
17289 TGATCTAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATAAAATTATTATT
Found at i:21223 original size:28 final size:28
Alignment explanation
Indices: 21168--21223 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
21158 TGGAAAATGG
** * *
21168 AATTACTATTTTACCCTTGGATGGGTAA
1 AATTACTAAATTACCCTTGGAAGAGTAA
*
21196 AATTACTAAATTACCCTTTGAAGAGTAA
1 AATTACTAAATTACCCTTGGAAGAGTAA
21224 TTTTAAGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
AATTACTAAATTACCCTTGGAAGAGTAA
Found at i:22236 original size:13 final size:13
Alignment explanation
Indices: 22220--22244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22210 CTGACTGTTT
22220 TGGTTTATTATTC
1 TGGTTTATTATTC
22233 TGGTTTATTATT
1 TGGTTTATTATT
22245 TTGATTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TGGTTTATTATTC
Found at i:24364 original size:7 final size:7
Alignment explanation
Indices: 24353--24393 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
24343 TACTAGCTCT
*
24353 TTTGTAT
1 TTTGTAC
24360 TTTGTAC
1 TTTGTAC
24367 TTTGTAC
1 TTTGTAC
24374 TTTGTAC
1 TTTGTAC
24381 TTTGTAC
1 TTTGTAC
24388 TTTGTA
1 TTTGTA
24394 AGCAGTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (7 bp):
TTTGTAC
Found at i:25309 original size:178 final size:178
Alignment explanation
Indices: 24939--25325 Score: 444
Period size: 178 Copynumber: 2.2 Consensus size: 178
24929 TCCATATATA
* * * ** * *
24939 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTTCTTTAACCAAAATAACTAATTCTTTGA
1 AGCAAAAATTATATAATATTAAGTAGATCGTCTATTCCCGTTAACCAAAACAACTAATTCTTTGA
25004 AAGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTCCATGAAAGTTGTAGATCAT
66 AAGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTCCATGAAAGTTGTAGATCAT
* * * * *
25069 GGAACAACCTTTAAAGAGACACTTGAATCATCTCAATTAGACATCTGG
131 GGAACAACCTTTAAAGAGACACTTAAATCACCTCAATCAGACAACCGG
* * *
25117 AGCAAAAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAA-TAAATT-TTTC
1 AGCAAAAATTATATAATATTAAGTAGATCGTCTATTCCCGTTAACCAAAACAACT-AATTCTTT-
* * *
25180 GGAAGC-ATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGA-CTCCTTCATGAAAGTTGTAG
64 GAAAGCAATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCGAGC-CCTCCATGAAAGTTGTAG
* * * * * *
25242 ATGATGGAACAATCTTTTAATAGACACTTAAATCACCTCAATCGGATAACCGG
126 ATCATGGAACAACCTTTAAAGAGACACTTAAATCACCTCAATCAGACAACCGG
* *
25295 AG-AAAACATTATATAATGTTAAATAGATCGT
1 AGCAAAA-ATTATATAATATTAAGTAGATCGT
25326 TTAGTCAAAC
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
177 18 0.10
178 157 0.90
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (178 bp):
AGCAAAAATTATATAATATTAAGTAGATCGTCTATTCCCGTTAACCAAAACAACTAATTCTTTGA
AAGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTCCATGAAAGTTGTAGATCAT
GGAACAACCTTTAAAGAGACACTTAAATCACCTCAATCAGACAACCGG
Found at i:26076 original size:43 final size:41
Alignment explanation
Indices: 25991--26077 Score: 102
Period size: 43 Copynumber: 2.1 Consensus size: 41
25981 GATTGTTAAG
* * * * *
25991 AAACCTTATAACATTACTAAAAAAATCTTATATGATTTCTA
1 AAACCTTATAAAATTAATAAAAAAAGCTTATAAGATTACTA
*
26032 AAACCTTATAAAATTAATAAAAAAAAAGCTTTTAAGATTACTA
1 AAACCTTATAAAATTAAT--AAAAAAAGCTTATAAGATTACTA
26075 AAA
1 AAA
26078 GAGTTATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 16 0.42
43 22 0.58
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.32
Consensus pattern (41 bp):
AAACCTTATAAAATTAATAAAAAAAGCTTATAAGATTACTA
Found at i:26522 original size:21 final size:20
Alignment explanation
Indices: 26498--26552 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
26488 AAAAAAAGTG
*
26498 TTAAAAATTTTATAAGATTA
1 TTAAAAATCTTATAAGATTA
*
26518 TTTAAAAAAACTTATAAGATTA
1 -TT-AAAAATCTTATAAGATTA
*
26540 CTAAAAATGCTTA
1 TTAAAAAT-CTTA
26553 AAAACTTCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 16 0.57
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TTAAAAATCTTATAAGATTA
Found at i:30181 original size:22 final size:22
Alignment explanation
Indices: 30153--30206 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
30143 ACATTAAAAA
30153 TGGGTCGTGCTGCGTCT-GCACG
1 TGGGTCGTGCTGCG-CTGGCACG
* *
30175 TGGGTCGTACTGTGCTGGCACG
1 TGGGTCGTGCTGCGCTGGCACG
30197 TGGGTCGTGC
1 TGGGTCGTGC
30207 CGTTCCATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.06, C:0.24, G:0.43, T:0.28
Consensus pattern (22 bp):
TGGGTCGTGCTGCGCTGGCACG
Found at i:31619 original size:28 final size:27
Alignment explanation
Indices: 31588--31649 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
31578 TCCTCATTGT
* *
31588 AGGGGTAAAATCGTAAGTTTTATCAATC
1 AGGGGTAAAATAGTAA-ATTTATCAATC
* *
31616 AGGGGTAATATAGTAAATTTATCCATC
1 AGGGGTAAAATAGTAAATTTATCAATC
*
31643 ACGGGTA
1 AGGGGTA
31650 TTTTGGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCAATC
Found at i:33002 original size:2 final size:2
Alignment explanation
Indices: 32995--33040 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
32985 GCCGGTTAAG
*
32995 AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT AT AT
33037 AT AT
1 AT AT
33041 TAATTAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Done.