Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015092.1 Corchorus olitorius cultivar O-4 contig15125, 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: 8104
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:3781 original size:18 final size:16
Alignment explanation
Indices: 3758--3791 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
3748 AGCATTGATT
3758 ATTAAACACATTGAAAAA
1 ATTAAA-ACATT-AAAAA
3776 ATTAAAACATTAAAAA
1 ATTAAAACATTAAAAA
3792 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (16 bp):
ATTAAAACATTAAAAA
Found at i:3791 original size:17 final size:18
Alignment explanation
Indices: 3758--3791 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3748 AGCATTGATT
*
3758 ATTAAACACATTGAAAAA
1 ATTAAACACATTAAAAAA
3776 ATTAAA-ACATTAAAAA
1 ATTAAACACATTAAAAA
3792 TTTTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (18 bp):
ATTAAACACATTAAAAAA
Found at i:4319 original size:14 final size:15
Alignment explanation
Indices: 4291--4321 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4281 GTATAGATTT
4291 AAGATAAAAATACAC
1 AAGATAAAAATACAC
4306 AAGATAAAAA-ACAC
1 AAGATAAAAATACAC
4320 AA
1 AA
4322 AACGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.71, C:0.13, G:0.06, T:0.10
Consensus pattern (15 bp):
AAGATAAAAATACAC
Found at i:4516 original size:2 final size:2
Alignment explanation
Indices: 4509--4555 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
4499 TCAACGTTAA
*
4509 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4549 AT AT AT A
1 AT AT AT A
4556 AAAGTATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4881 original size:22 final size:21
Alignment explanation
Indices: 4839--4879 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4829 TAAATAAGTA
4839 AAATTTTATTATAATCAAAAT
1 AAATTTTATTATAATCAAAAT
*
4860 AAATCTTTA-TATATTCAAAA
1 AAAT-TTTATTATAATCAAAA
4880 ATTTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTTTATTATAATCAAAAT
Found at i:7815 original size:294 final size:292
Alignment explanation
Indices: 7184--8063 Score: 1367
Period size: 294 Copynumber: 3.0 Consensus size: 292
7174 AATCTTGATT
* * * * *
7184 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACTAATCCTATGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* * *
7249 GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
7314 CATAAATATAAAAATAGTAAATTACAAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATC
131 CATAAATATAAAAATAGTAAATTAC-AAAAAAGGGCAGCAGGAAAAGT-A---AGAAAATTCATC
7379 GAAGGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAGGCAAAAGGAAGCACCAC
191 GAAGGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAGGCAAAAGGAAGCACCAC
7444 ATTAATTCTCAATTTGGCCTTTTAGGTAATTTCTAAA
256 ATTAATTCTCAATTTGGCCTTTTAGGTAATTTCTAAA
7481 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
7546 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
* **
7611 AATATCTATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGT-AGAAAATTCATCGAAGG
131 CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAAAATTCATCGAAGG
7675 CCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAAAAGGCAAAAGGAAGCACCACAT
196 CCTTTTTAGTCACCCAAAAAGTGAGAAAAGAC---AAAAAAAAAAGGCAAAAGGAAGCACCACAT
7740 TAATTCTCAATTTGGCCTTTTAGGTAATTTCTAAA
258 TAATTCTCAATTTGGCCTTTTAGGTAATTTCTAAA
7775 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* *
7840 GAGGAGTTGAATCGGTAAATCCTAATATCCACACACAATTAATA-CATAATTAAAACACACTTAA
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATC-TAATTAAAACACACTTAA
* * * *
7904 TCATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGGATGAAAAGTAAGGGAGGAAATTTATC
130 TCATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAA--GA--AAATTCATC
* * * * *
7969 -AAGGGCCTTTTAAGTCACCCGAAAAGTGAGAAAAGAC--CAAAAAAAGCCAAAAGGAGGCACCA
191 GAA-GGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAGGCAAAAGGAAGCACCA
* * *
8031 TATTAATCCTCAATTTGGCC-TTTAAGTAATTTC
255 CATTAATTCTCAATTTGGCCTTTTAGGTAATTTC
8064 CATAGTCACT
Statistics
Matches: 545, Mismatches: 28, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
291 49 0.09
293 13 0.02
294 272 0.50
295 1 0.00
296 22 0.04
297 146 0.27
298 2 0.00
299 40 0.07
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (292 bp):
GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAAAATTCATCGAAGG
CCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAGGCAAAAGGAAGCACCACATTAA
TTCTCAATTTGGCCTTTTAGGTAATTTCTAAA
Done.