Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013800.1 Corchorus olitorius cultivar O-4 contig13833, 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: 46038
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--32 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 C
2 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 A
33 CCTTACTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8308 original size:68 final size:68
Alignment explanation
Indices: 8045--8475 Score: 511
Period size: 68 Copynumber: 6.4 Consensus size: 68
8035 CTGGCCATTT
*
8045 GACCAAAAGGGTA-TTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
8109 TTC
66 TTC
* * * * * * * * * *
8112 GACCGAAAGGGTGTTTTTGG-AAAA-CAAA-ACCAAACCTAGATGTGAAGAATATGAAACTGACC
1 GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATG-CAAAAAGACGAAAATGACC
*
8174 CTTT
65 CTTC
* * * * * ** *
8178 GTCCGAAAGGGTA-CTTCGGGAAAAG-AAA-ACT-AACTTAGGTATG-AAAAAGTTGAAATTGAC
1 GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTA--AATGCAAAAAGACGAAAATGAC
*
8238 CCTTT
64 CCTTC
* *
8243 GACCGAAAGGGTATTTTTGGAAAAAGAAAAGACTAAACTTAAATGCAAAAAGATGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
8308 TTC
66 TTC
* *
8311 GATCGAAAGGGTGTTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
8376 TTC
66 TTC
* *
8379 GACTGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
8444 TTC
66 TTC
* *
8447 GATCGAAAGGGTACTTTTGGAAAAAGAAA
1 GACCGAAAGGGTATTTTTGGAAAAAGAAA
8476 GGAACCGATG
Statistics
Matches: 310, Mismatches: 43, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
65 50 0.16
66 49 0.16
67 24 0.08
68 181 0.58
69 6 0.02
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (68 bp):
GACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC
TTC
Found at i:13150 original size:2 final size:2
Alignment explanation
Indices: 13143--13178 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13133 ATTCCAGCTT
*
13143 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13179 ATGGATTTGG
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14226 original size:21 final size:21
Alignment explanation
Indices: 14202--14241 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
14192 AGGATTTTGC
*
14202 ATTTCAATCTAAG-GAAAAAGG
1 ATTTAAAT-TAAGAGAAAAAGG
14223 ATTTAAATTAAGAGAAAAA
1 ATTTAAATTAAGAGAAAAA
14242 AATGACCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (21 bp):
ATTTAAATTAAGAGAAAAAGG
Found at i:14652 original size:110 final size:110
Alignment explanation
Indices: 14500--14720 Score: 361
Period size: 110 Copynumber: 2.0 Consensus size: 110
14490 GAAGGTGGTT
*
14500 TTGGATGTTGATTTTGGGATCTTGCAGCAAAGTATAGTTCAAGTTTCTTTTATTGGGTGAGTATT
1 TTGGATGGTGATTTTGGGATCTTGCAGCAAAGTATAGTTCAAGTTTCTTTTATTGGGTGAGTATT
* * * * *
14565 GTTGGTGGGGTAGACTTCATTTCCCAGTTATGGTATTATGTATTA
66 GTTGGTGGGGTAAACTTCATTTCACAATTATAGTATTACGTATTA
* * *
14610 TTGGATGGTGATTTTGGGATCTTGCAGTAGAGTATAGTTCAAGTTTCTTTTATTGGGTGATTATT
1 TTGGATGGTGATTTTGGGATCTTGCAGCAAAGTATAGTTCAAGTTTCTTTTATTGGGTGAGTATT
14675 GTTGGTGGGGTAAACTTCATTTCACAATTATAGTATTACGTATTA
66 GTTGGTGGGGTAAACTTCATTTCACAATTATAGTATTACGTATTA
14720 T
1 T
14721 ATTATTGGGC
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (110 bp):
TTGGATGGTGATTTTGGGATCTTGCAGCAAAGTATAGTTCAAGTTTCTTTTATTGGGTGAGTATT
GTTGGTGGGGTAAACTTCATTTCACAATTATAGTATTACGTATTA
Found at i:42635 original size:276 final size:277
Alignment explanation
Indices: 42138--42688 Score: 845
Period size: 276 Copynumber: 2.0 Consensus size: 277
42128 AAATTATCAT
* * * * *
42138 TTAATATATAGATTCTAAAAATATGAGATCTTTATTTTGAAGCTTAAGAAGATCATTTTATGAAC
1 TTAATATATAGATTCCAAAAATATCAAATCTCTATTTTGAAGCTTAACAAGATCATTTTATGAAC
42203 TCTAGGTTATAACAAAAGCAAGAAAAGGAAATGAAATTATCATCATCAATTTCAAATATAGATAC
66 TCTAGGTTATAACAAAAGCAAGAAAAGGAAATGAAATTATCATCATCAATTTCAAATATAGATAC
* * * * * * *
42268 ATGAAATCTTTATTTGAGAAGCAAAGATGAGGAATCATAATGAATGTCTTTTAATTTGAAGAGAG
131 ATAAAATATTTATTTCAAAAGAAAAGATGAGGAATCATAATGAATATCCTTTAATTTGAAGAGAG
* *
42333 CCTTTCGATTATAATAATCTATCCTCGACTAAA-CAACTGTCTACAACGTTTACAACACATCTTC
196 CCTTTCAATTATAATAATCCATCCTCGACTAAACCAACTGTCTACAACGTTTACAACACATCTTC
*
42397 ATAAGAACTGCTCCAAC
261 ATAAGAACTGATCCAAC
* * *
42414 TTAATATATAGATTCCAAAGATATCAAATCTCTGTTTTGAAGCTTAACAAGATCATTTTATTAAC
1 TTAATATATAGATTCCAAAAATATCAAATCTCTATTTTGAAGCTTAACAAGATCATTTTATGAAC
* * ** *
42479 TCTAGGTTATAATAAAAGCAAGAAGAGGAAATGAAATTATCATCATCGTTTTCAAATTTAGATAC
66 TCTAGGTTATAACAAAAGCAAGAAAAGGAAATGAAATTATCATCATCAATTTCAAATATAGATAC
42544 ATAAAATATTTATTTCAAAAGAAAAGATGAGGAATCATAATGAATATCCTTTAATTTGAAGAGAG
131 ATAAAATATTTATTTCAAAAGAAAAGATGAGGAATCATAATGAATATCCTTTAATTTGAAGAGAG
* * *
42609 -CTCTTCAATTATAATAATCCATCCTCGATTAAACCAACTGTCTGCAACGTTTACAACATATCTT
196 CCT-TTCAATTATAATAATCCATCCTCGACTAAACCAACTGTCTACAACGTTTACAACACATCTT
42673 CATAAGAACTGATCCA
260 CATAAGAACTGATCCA
42689 GCAAGACCTA
Statistics
Matches: 247, Mismatches: 26, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
275 2 0.01
276 202 0.82
277 43 0.17
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (277 bp):
TTAATATATAGATTCCAAAAATATCAAATCTCTATTTTGAAGCTTAACAAGATCATTTTATGAAC
TCTAGGTTATAACAAAAGCAAGAAAAGGAAATGAAATTATCATCATCAATTTCAAATATAGATAC
ATAAAATATTTATTTCAAAAGAAAAGATGAGGAATCATAATGAATATCCTTTAATTTGAAGAGAG
CCTTTCAATTATAATAATCCATCCTCGACTAAACCAACTGTCTACAACGTTTACAACACATCTTC
ATAAGAACTGATCCAAC
Found at i:43749 original size:22 final size:22
Alignment explanation
Indices: 43724--43771 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
43714 GTTAGATAGC
*
43724 ATTGCAAAAATTTGAAAATTAT
1 ATTGCAAAAATTTCAAAATTAT
* *
43746 ATTGGATAAATTTCAAAATTAT
1 ATTGCAAAAATTTCAAAATTAT
43768 ATTG
1 ATTG
43772 GATATTTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (22 bp):
ATTGCAAAAATTTCAAAATTAT
Found at i:43772 original size:22 final size:22
Alignment explanation
Indices: 43731--43775 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
43721 AGCATTGCAA
*
43731 AAATTTGAAAATTATATTGGAT
1 AAATTTCAAAATTATATTGGAT
43753 AAATTTCAAAATTATATTGGAT
1 AAATTTCAAAATTATATTGGAT
43775 A
1 A
43776 TTTCTATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (22 bp):
AAATTTCAAAATTATATTGGAT
Done.