Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012371.1 Kokia drynarioides strain JFW-HI SEQ_127375, 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: 9610
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:148 original size:28 final size:28
Alignment explanation
Indices: 117--185 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
107 AAAATTTCAT
* **
117 TTTTTCCCTCGATTTTCCAAAATTACCA
1 TTTTACCCTCGACCTTCCAAAATTACCA
*
145 TTTTACCCCCGAACCTTCCAAAATTACCA
1 TTTTACCCTCG-ACCTTCCAAAATTACCA
174 TTTTACCCTCGA
1 TTTTACCCTCGA
186 ATGTCTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTTACCCTCGACCTTCCAAAATTACCA
Found at i:183 original size:57 final size:57
Alignment explanation
Indices: 83--329 Score: 200
Period size: 57 Copynumber: 4.3 Consensus size: 57
73 GGGTGTTACA
* * * * * * *
83 TACCATTTCACCTCCGAACTTTCAAAAATT-TCATTTTTTCCCTCGAT-TTTCCAAAAT
1 TACCATTTTACCCCCGAACTTTCCAAAATTACCA-TTTTCCCCTCGATGTCT-AAAAAT
* *
140 TACCATTTTACCCCCGAACCTTCCAAAATTACCATTTTACCCTCGAATGTCTAAAAAT
1 TACCATTTTACCCCCGAACTTTCCAAAATTACCATTTTCCCCTCG-ATGTCTAAAAAT
* * * * *
198 T-CCGTTCTTTAACCCCAAACTTTCCAAAAATTACCATTTTCCCCTAGATTTCTAAAAAT
1 TACC-AT-TTTACCCCCGAACTTTCC-AAAATTACCATTTTCCCCTCGATGTCTAAAAAT
* * * *
257 T-CCATTTTGA-CCCCAAACTTTCCAAAATTGCCATTTTGCCCCCCGAGTGTC-CAAAAT
1 TACCATTTT-ACCCCCGAACTTTCCAAAATTACCATTTT-CCCCTCGA-TGTCTAAAAAT
*
314 TACCATTCTACCCCCG
1 TACCATTTTACCCCCG
330 GGCATCCAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
56 13 0.08
57 67 0.43
58 26 0.17
59 31 0.20
60 19 0.12
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.34
Consensus pattern (57 bp):
TACCATTTTACCCCCGAACTTTCCAAAATTACCATTTTCCCCTCGATGTCTAAAAAT
Found at i:186 original size:29 final size:29
Alignment explanation
Indices: 131--329 Score: 103
Period size: 29 Copynumber: 6.9 Consensus size: 29
121 TCCCTCGATT
131 TTCCAAAATTACCATTTTACCCCCGAACC
1 TTCCAAAATTACCATTTTACCCCCGAACC
*
160 TTCCAAAATTACCATTTTACCCTCGAA--
1 TTCCAAAATTACCATTTTACCCCCGAACC
* * * * *
187 TGTCTAAAAATT-CCGTTCTTTAACCCCAAACT
1 T-TC-CAAAATTACC-AT-TTTACCCCCGAACC
* *
219 TTCCAAAAATTACCATTTT--CCCCTAGA-T
1 TTCC-AAAATTACCATTTTACCCCCGA-ACC
* * *
247 TTCTAAAAATT-CCATTTTGA-CCCCAAACT
1 TTC-CAAAATTACCATTTT-ACCCCCGAACC
* * *
276 TTCCAAAATTGCCATTTTGCCCCCCG-A-G
1 TTCCAAAATTACCATTTT-ACCCCCGAACC
*
304 TGTCCAAAATTACCATTCTACCCCCG
1 T-TCCAAAATTACCATTTTACCCCCG
330 GGCATCCAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 33
0.73 0.10 0.18
Matches are distributed among these distances:
27 8 0.06
28 33 0.24
29 67 0.49
30 16 0.12
31 9 0.07
32 3 0.02
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (29 bp):
TTCCAAAATTACCATTTTACCCCCGAACC
Found at i:258 original size:59 final size:57
Alignment explanation
Indices: 135--298 Score: 195
Period size: 59 Copynumber: 2.8 Consensus size: 57
125 TCGATTTTCC
* * * * *
135 AAAATTACCATTTTACCCCCGAACCTTCCAAAATTACCATTTTACCCTCGAATGTCTA
1 AAAATT-CCATTTTAACCCCAAACTTTCCAAAATTACCATTTTCCCCTAGAATGTCTA
* *
193 AAAATTCCGTTCTTTAACCCCAAACTTTCCAAAAATTACCATTTTCCCCTAG-ATTTCTA
1 AAAATTCC-AT-TTTAACCCCAAACTTTCC-AAAATTACCATTTTCCCCTAGAATGTCTA
* *
252 AAAATTCCATTTTGACCCCAAACTTTCCAAAATTGCCATTTTGCCCC
1 AAAATTCCATTTTAACCCCAAACTTTCCAAAATTACCATTTT-CCCC
299 CCGAGTGTCC
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
56 13 0.14
57 23 0.25
58 8 0.09
59 29 0.32
60 19 0.21
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (57 bp):
AAAATTCCATTTTAACCCCAAACTTTCCAAAATTACCATTTTCCCCTAGAATGTCTA
Found at i:1616 original size:3 final size:3
Alignment explanation
Indices: 1608--1646 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1598 TCTGCAATTC
1608 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1647 TACCAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5044 original size:29 final size:29
Alignment explanation
Indices: 5003--5078 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
4993 ATTTTGATAT
*
5003 ATTTTTA-AATTTTAAAAAATTAAATTAA
1 ATTTTTATCATTTTAAAAAATTAAATTAA
5031 ATTTTTATCATTTTAAAAAATTAAATTAA
1 ATTTTTATCATTTTAAAAAATTAAATTAA
5060 ATTTTTATCATTTTAAAAA
1 ATTTTTATCATTTTAAAAA
5079 CACTCTTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTTTATCATTTTAAAAAATTAAATTAA
Found at i:5558 original size:29 final size:31
Alignment explanation
Indices: 5486--5563 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
5476 TTAATTTTTT
*
5486 AAAATTTTAATTAAACTCACTTAAAATATTA
1 AAAATTTTAATTAAACTCACTAAAAATATTA
* *
5517 AAAATTCTT-ATTAATCTTAC-AAAAAT-TTA
1 AAAATT-TTAATTAAACTCACTAAAAATATTA
*
5546 AAAATTTTAATTAGACTC
1 AAAATTTTAATTAAACTC
5564 CCAATTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.05
29 15 0.38
30 5 0.13
31 15 0.38
32 2 0.05
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAATTTTAATTAAACTCACTAAAAATATTA
Done.