Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012129.1 Corchorus olitorius cultivar O-4 contig12162, 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: 24315
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:432 original size:16 final size:15
Alignment explanation
Indices: 394--435 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
384 ACAGAGGTTG
*
394 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
409 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
424 ACTAGAAAACAA
1 AC-AGAAAACAA
436 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4086 original size:13 final size:13
Alignment explanation
Indices: 4070--4095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4060 TTGTTCTATA
4070 CAATTTAATTTTT
1 CAATTTAATTTTT
4083 CAATTTAATTTTT
1 CAATTTAATTTTT
4096 TTTATCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
CAATTTAATTTTT
Found at i:5101 original size:444 final size:446
Alignment explanation
Indices: 4551--5421 Score: 1227
Period size: 444 Copynumber: 2.0 Consensus size: 446
4541 TTAACTTTTA
* ** *
4551 TTTTTGTATTTTTTGTTTTATTTTTCCGATTAAAGTGATTCAAGTTTCTATTAAAAGGTGATTTC
1 TTTTTGTATTTTTTGTTTTATTTGTCCGATTAAAGTGATTCAAGTGCCTATTAAAAGGTAATTTC
* *
4616 ATGATTTACAACTTTCATGAAGGGCTCAAAAGCCAATTTTTATGTTTCAATTCAAA-AAAATGC-
66 ATGATCTACAACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAATT-AAAGAAAATGCT
* * *
4679 TTCCGAAATTTGGTGGTTTTAATTGCCGGTCTATTTGATATCC-TATAATTTTTGATCCACATGT
130 TTCC-AAATTTGGTGGATTCAATTGCCGGTCTATTTAATA-CCATATAATTTTTGATCCACATGT
* *
4743 CCGATTAAAATTATTCAAGTGTCAGTTAAAAAGCTATTGCATGATCTACGACTTTCATGAAGGAT
193 CCGATTAAAATTATTCAAGTGTCAGTTAAAAAGCTATTCCATGATCTACGACTTTCATGAAGGAC
* * * * * * *
4808 CCGAAAGCTAAATTTGATATATGAGTTTCAT-CAGGGATT-AAAGGA-AATTTTTATGTTTCTAG
258 CCGAAAACTAAATTTAATATACGAGTTTCATGAAAGG-TTCAAAAGAGAATTTTTATGTTTCAAG
** * * *
4870 ATCT-CCATCAATGAACATTTTCTTAATTGGATTATTTATCAAATGACCCTCATATTTTTCTACT
322 ATCTCCCATCAACAAACATTTTCTTAATTGAATTATTTATCAAATGACCCTCATACTTTTATACT
* * *
4934 TTATACTACTTAATCCTTTACTAATTCTATTTTAATCGATTTAACACGATCATCTTTAAT
387 GTATACTACTTAATCCTTTACAAATTCTATCTTAATCGATTTAACACGATCATCTTTAAT
* *
4994 TTTTTGTTTGTTTTTGTTTTATTTGTCTGATT-AAGATGATTCAAGTGCCTATTAAAAGGTAATT
1 TTTTTGTAT-TTTTTGTTTTATTTGTCCGATTAAAG-TGATTCAAGTGCCTATTAAAAGGTAATT
* *
5058 TCATGATCTACAACTTTCATGAAGGATTCAAAAGTCAATTTTTATGTTTCAATTAAAGAAAATGC
64 TCATGATCTACAACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAATTAAAGAAAATGC
*
5123 TTTCCAAATTTGGTGGATTCGATTGCCGGTCTATTTAATACCATATAATTTTTGATCCACATGTC
129 TTTCCAAATTTGGTGGATTCAATTGCCGGTCTATTTAATACCATATAATTTTTGATCCACATGTC
* * * * * * *
5188 CGATTAAAGTTATTCAGGTGTCGGTTAAAAGGTTATTCCATGATTTACGACTTTGATGAAGGACC
194 CGATTAAAATTATTCAAGTGTCAGTTAAAAAGCTATTCCATGATCTACGACTTTCATGAAGGACC
* *
5253 CGAAAACTAAATTTAATATACGAGTTTGATGAAAGGTTCAAAAGAGAATTTTTATTTTTCAAGAT
259 CGAAAACTAAATTTAATATACGAGTTTCATGAAAGGTTCAAAAGAGAATTTTTATGTTTCAAGAT
* *
5318 CTCCCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATGACCCTCATACTTTTATACTG
324 CT-CCCATCAACAAACATTTTCTTAATTGAATTATTTATCAAATGACCCTCATACTTTTATACTG
* *
5383 TATACTACTTAGTCCTTTACAAATTCTATCTTACTCGAT
388 TATACTACTTAATCCTTTACAAATTCTATCTTAATCGAT
5422 GTTACGCTTA
Statistics
Matches: 374, Mismatches: 44, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
443 16 0.04
444 239 0.64
445 12 0.03
446 19 0.05
448 88 0.24
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (446 bp):
TTTTTGTATTTTTTGTTTTATTTGTCCGATTAAAGTGATTCAAGTGCCTATTAAAAGGTAATTTC
ATGATCTACAACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAATTAAAGAAAATGCTT
TCCAAATTTGGTGGATTCAATTGCCGGTCTATTTAATACCATATAATTTTTGATCCACATGTCCG
ATTAAAATTATTCAAGTGTCAGTTAAAAAGCTATTCCATGATCTACGACTTTCATGAAGGACCCG
AAAACTAAATTTAATATACGAGTTTCATGAAAGGTTCAAAAGAGAATTTTTATGTTTCAAGATCT
CCCATCAACAAACATTTTCTTAATTGAATTATTTATCAAATGACCCTCATACTTTTATACTGTAT
ACTACTTAATCCTTTACAAATTCTATCTTAATCGATTTAACACGATCATCTTTAAT
Found at i:5939 original size:6 final size:6
Alignment explanation
Indices: 5928--5957 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5918 GAGCTCGGCC
5928 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA
1 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA
5958 TTGCCCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
ATCCCA
Found at i:13410 original size:34 final size:34
Alignment explanation
Indices: 13372--13440 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
13362 ACTTCAAAAA
*
13372 CCTTGATCTGAAATATCTAAAATACTGTTTTTAG
1 CCTTGATCTGAAATATCTAAAATACTCTTTTTAG
13406 CCTTGATCTGAAATATCTAAAATACTCTTTTTAG
1 CCTTGATCTGAAATATCTAAAATACTCTTTTTAG
13440 C
1 C
13441 TTTAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (34 bp):
CCTTGATCTGAAATATCTAAAATACTCTTTTTAG
Found at i:15890 original size:72 final size:71
Alignment explanation
Indices: 15766--15969 Score: 205
Period size: 72 Copynumber: 2.8 Consensus size: 71
15756 AGGTAGCAGC
* * * *
15766 AAGGATTGTGCGAAGGATTGCCAATGTGGAAACT-ACTTCGGCTACAATCGCAATGAAGAAGATA
1 AAGGATTGTGCAAAGGACTGCCAATGTGGGAACTGCCTT-GGCTACAATCGCAATGAAGAAGATA
*
15830 ATTGCAT
65 ATTACAT
* * *
15837 AAGGATTGTGCAAAGGACTGTCAGATGTGGGAACTGCCTTGGCTACAACCGCAAT-ATGAAAGAT
1 AAGGATTGTGCAAAGGACTGCCA-ATGTGGGAACTGCCTTGGCTACAATCGCAATGAAG-AAGAT
* **
15901 GATTATGT
64 AATTACAT
** * * **
15909 AAGGATTGTGCAAAATACTGCCAAATATGGGACCTGCCTCCGCTACAATCGCAATGAAGAA
1 AAGGATTGTGCAAAGGACTGCC-AATGTGGGAACTGCCTTGGCTACAATCGCAATGAAGAA
15970 AAGGACCATG
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
71 22 0.20
72 80 0.74
73 6 0.06
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (71 bp):
AAGGATTGTGCAAAGGACTGCCAATGTGGGAACTGCCTTGGCTACAATCGCAATGAAGAAGATAA
TTACAT
Found at i:17912 original size:19 final size:20
Alignment explanation
Indices: 17881--17920 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
17871 TTCTCTTACT
17881 TTTTTGCGTTTAAAAAAAAA
1 TTTTTGCGTTTAAAAAAAAA
17901 TTTTTGCG-TTAAAAAAAAA
1 TTTTTGCGTTTAAAAAAAAA
17920 T
1 T
17921 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTTGCGTTTAAAAAAAAA
Done.