Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002286.1 Kokia drynarioides strain JFW-HI SEQ_114317, 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: 19325
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1316 original size:24 final size:23
Alignment explanation
Indices: 1273--1318 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1263 TTTTCTCTAA
*
1273 TAAAATTTATTTATCTCATCATC
1 TAAAATTTATTTATCACATCATC
1296 TAAATATTTA-TTACTCACATCAT
1 TAAA-ATTTATTTA-TCACATCAT
1319 TTATTCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAATTTATTTATCACATCATC
Found at i:2654 original size:43 final size:42
Alignment explanation
Indices: 2558--2808 Score: 304
Period size: 43 Copynumber: 5.9 Consensus size: 42
2548 TTATTAGGAA
* * * * ** * *
2558 AAACGCCGTTATAGAATATAGTCTTTAGCAACACTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
* *
2600 AAACGCCACTAAAGAACATGGTCTTTAGCGGCACTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCCCAC
**
2643 AAACGCTACTAAAGAACATGGTCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCAC
* *
2686 AAACGTCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCAC
* **
2729 AAACGCCGCTAAAGAACATGGTCTTTAGTGATGCTTTCTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTC-CCAC
*
2772 AAACGCCGCTAAATAACATGGTCTTTAGCGGCGCTTT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT
2809 TCTCCCACAA
Statistics
Matches: 183, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 31 0.17
43 152 0.83
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
Found at i:3138 original size:21 final size:21
Alignment explanation
Indices: 3112--3164 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3102 ACTTTCTTGT
* *
3112 TGCCTCTACTTCCCTCGCTGC
1 TGCCTCCACTTCCCTCGCTAC
*
3133 TGCCTCCGCTTCCCTCGCTAC
1 TGCCTCCACTTCCCTCGCTAC
3154 TGCCTCCACTT
1 TGCCTCCACTT
3165 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.49, G:0.13, T:0.32
Consensus pattern (21 bp):
TGCCTCCACTTCCCTCGCTAC
Found at i:4925 original size:19 final size:19
Alignment explanation
Indices: 4901--4943 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4891 AAACATAAAT
4901 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
4920 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
4939 TAAAT
1 TAAAT
4944 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:6772 original size:169 final size:169
Alignment explanation
Indices: 6493--6830 Score: 658
Period size: 169 Copynumber: 2.0 Consensus size: 169
6483 AAATCTTTTT
6493 CCATTAGATTTAGTGAATTACCTCTTGAATATTACATTGAAGCTAATGAATTATGTAATTTATAC
1 CCATTAGATTTAGTGAATTACCTCTTGAATATTACATTGAAGCTAATGAATTATGTAATTTATAC
6558 AATATTATACTAATATAATTCAAGATAATGAAAAGTTTCCCTTAATGTATCAATAATTAATTTAG
66 AATATTATACTAATATAATTCAAGATAATGAAAAGTTTCCCTTAATGTATCAATAATTAATTTAG
*
6623 CTTAACTGGATAAATGACTATTTTTTTTCGTTATTGTCC
131 CTTAACTGGATAAATGACTAATTTTTTTCGTTATTGTCC
6662 CCATTAGATTTAGTGAATTACCTCTTGAATATTACATTGAAGCTAATGAATTATGTAATTTATAC
1 CCATTAGATTTAGTGAATTACCTCTTGAATATTACATTGAAGCTAATGAATTATGTAATTTATAC
*
6727 AATATTATACTAATATAATTCAAGATAATGAAAATTTTCCCTTAATGTATCAATAATTAATTTAG
66 AATATTATACTAATATAATTCAAGATAATGAAAAGTTTCCCTTAATGTATCAATAATTAATTTAG
6792 CTTAACTGGATAAATGACTAATTTTTTTCGTTATTGTCC
131 CTTAACTGGATAAATGACTAATTTTTTTCGTTATTGTCC
6831 AGATTCGAAA
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 167 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (169 bp):
CCATTAGATTTAGTGAATTACCTCTTGAATATTACATTGAAGCTAATGAATTATGTAATTTATAC
AATATTATACTAATATAATTCAAGATAATGAAAAGTTTCCCTTAATGTATCAATAATTAATTTAG
CTTAACTGGATAAATGACTAATTTTTTTCGTTATTGTCC
Found at i:8092 original size:41 final size:41
Alignment explanation
Indices: 8009--8136 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
7999 CCATAAATGA
* **
8009 CGCTAATGCTCTGAGC-TTTAGTGGCACTTT-CTCATGAA-CGC
1 CGCTAATGCTCTGA-CTTTTAGTGACGTTTTCCT-AT-AAGCGC
*
8050 CGTTAATGCTCTGACTTTTAGCTG-CGTTTTCCTATAAGCGC
1 CGCTAATGCTCTGACTTTTAG-TGACGTTTTCCTATAAGCGC
* * * * *
8091 CGCTAATGCTTTGAGTTTTAGTGACGTTTTTCTATAAACGA
1 CGCTAATGCTCTGACTTTTAGTGACGTTTTCCTATAAGCGC
8132 CGCTA
1 CGCTA
8137 TTATTTTACC
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
40 5 0.07
41 64 0.88
42 4 0.05
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (41 bp):
CGCTAATGCTCTGACTTTTAGTGACGTTTTCCTATAAGCGC
Found at i:10312 original size:20 final size:19
Alignment explanation
Indices: 10280--10317 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
10270 ATTTTGTACC
10280 AATTTTTTATAATTTAATAT
1 AATTTTTTATAA-TTAATAT
10300 AATTTATTT-TAATTAATA
1 AATTT-TTTATAATTAATA
10318 CACATAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTTATAATTAATAT
Found at i:10619 original size:21 final size:22
Alignment explanation
Indices: 10582--10622 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
10572 TAAATATACC
10582 ATTTAAAAATGAAAAAAAATGT
1 ATTTAAAAATGAAAAAAAATGT
*
10604 ATTTGAAAAT-AAAAAAAAT
1 ATTTAAAAATGAAAAAAAAT
10623 AATTTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (22 bp):
ATTTAAAAATGAAAAAAAATGT
Done.