Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005306.1 Kokia drynarioides strain JFW-HI SEQ_119235, 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: 14809
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Found at i:707 original size:15 final size:15
Alignment explanation
Indices: 683--722 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
673 ATATCATTAA
*
683 CAATATTAATGACAAT
1 CAATAATAATGAC-AT
699 -AATAATAATGACAT
1 CAATAATAATGACAT
713 CAATAATAAT
1 CAATAATAAT
723 ATTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (15 bp):
CAATAATAATGACAT
Found at i:1858 original size:30 final size:29
Alignment explanation
Indices: 1817--2033 Score: 167
Period size: 30 Copynumber: 7.4 Consensus size: 29
1807 TTTACCCCTG
1817 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTAA
* * **
1847 AACTTCTAAAAATTACCA-TTTTACCCTCG
1 AACTTCCAAAAA-TCCCATTTTTACCCTAA
* *
1876 AACTTCCAAAAATCCCATTTTTAACCTCGA
1 AACTTCCAAAAATCCCATTTTTACCCT-AA
* **
1906 AACTTCTAAAAA--CCA-TTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCTAA
*
1932 AACTTCCAAAAATCCCATTTTTGA-CCTCGA
1 AACTTCCAAAAATCCCATTTTT-ACCCT-AA
* * **
1962 AACTTCTAAAAATTACCA-TTTTACCCTTG
1 AACTTCCAAAAA-TCCCATTTTTACCCTAA
* * *
1991 AACTTTCAAAAATCTCATTTTTTGACCCCAA
1 AACTTCCAAAAATCCCA-TTTTT-ACCCTAA
2022 AACTTCCAAAAA
1 AACTTCCAAAAA
2034 ATTACTATTT
Statistics
Matches: 146, Mismatches: 28, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
26 12 0.08
27 7 0.05
28 13 0.09
29 41 0.28
30 50 0.34
31 23 0.16
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTAA
Found at i:1861 original size:59 final size:60
Alignment explanation
Indices: 1792--2046 Score: 337
Period size: 59 Copynumber: 4.3 Consensus size: 60
1782 CCCTAGGCTG
1792 TCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCT-AAAACT
1 TCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCTCAAAACT
* *
1851 TCTAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTT-AACCTCGAAACT
1 TCTAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGACCCTCAAAACT
** *
1910 TCT-AAAA--ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACT
1 TCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCTCAAAACT
* * *
1966 TCTAAAAATTACCATTTTACCCTTGAACTTTCAAAAATCTCATTTTTTGACCC-CAAAACT
1 TCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCA-TTTTTGACCCTCAAAACT
* *
2026 TCCAAAAAATTACTATTTTAC
1 T-CTAAAAATTACCATTTTAC
2047 TCCCGGATGT
Statistics
Matches: 174, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
56 44 0.25
57 8 0.05
58 12 0.07
59 77 0.44
60 14 0.08
61 19 0.11
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (60 bp):
TCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCTCAAAACT
Found at i:2004 original size:115 final size:115
Alignment explanation
Indices: 1802--2012 Score: 352
Period size: 115 Copynumber: 1.8 Consensus size: 115
1792 TCTAAAAATT
**
1802 ACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCTAAAAATTACCATT
1 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCTAAAAATTACCATT
1867 TTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCTAAAA
66 TTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCTAAAA
*
1917 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACTTCTAAAAATTACCAT
1 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCT-AAAACTTCTAAAAATTACCAT
* * *
1981 TTTACCCTTGAACTTTCAAAAATCTCATTTTT
65 TTTACCCTCGAACTTCCAAAAATCCCATTTTT
2013 TGACCCCAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 3 0.03
115 86 0.97
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (115 bp):
ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCTAAAAATTACCATT
TTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCTAAAA
Found at i:2130 original size:28 final size:29
Alignment explanation
Indices: 2099--2159 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
2089 AAAGTTACCC
2099 TTTT-ACCCTCGAATGTT-TAAAATT-CCAT
1 TTTTAACCC-CGAAT-TTCTAAAATTACCAT
2127 TTTTAACCCCGAATTTCCTAAAATTACCAT
1 TTTTAACCCCGAATTT-CTAAAATTACCAT
2157 TTT
1 TTT
2160 GCCCCGTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 2 0.07
28 9 0.31
29 11 0.38
30 7 0.24
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (29 bp):
TTTTAACCCCGAATTTCTAAAATTACCAT
Found at i:14050 original size:86 final size:86
Alignment explanation
Indices: 13946--14155 Score: 312
Period size: 86 Copynumber: 2.4 Consensus size: 86
13936 TGATAAAAAG
*
13946 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACTAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* *
14011 CGGATTGAAACAGACGACGCA
66 CGGATTGAAACAAACAACGCA
* *
14032 TTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAGG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
14097 CGGATTGAAACAAACAACGCA
66 CGGATTGAAACAAACAACGCA
* * ** * **
14118 GTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAAT
1 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAAT
14156 CAATCCCACG
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 111 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (86 bp):
GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGGATTGAAACAAACAACGCA
Done.