Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011357.1 Kokia drynarioides strain JFW-HI SEQ_126337, 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: 23382
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:1060 original size:56 final size:56
Alignment explanation
Indices: 992--1100 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 56
982 TCTGGTTTTT
* *
992 TTTTTTTAGCATTTTCTTTTGGGTTCA-AGTATG-TGAAAATAAAGATTTAATATGGG
1 TTTTTTTAGCATTTTCTTTTGGATTCAGA-TACGAT-AAAATAAAGATTTAATATGGG
*
1048 TTTTTTTGGCATTTTCTTTTGGATTCAGATACGATAAAATAAAGATTTAATAT
1 TTTTTTTAGCATTTTCTTTTGGATTCAGATACGATAAAATAAAGATTTAATAT
1101 CAATGGCTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
56 46 0.96
57 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (56 bp):
TTTTTTTAGCATTTTCTTTTGGATTCAGATACGATAAAATAAAGATTTAATATGGG
Found at i:2906 original size:24 final size:24
Alignment explanation
Indices: 2844--2911 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
2834 CCAAACAAAA
* *
2844 TTAGCTCATACGAGCCCAGATAGG
1 TTAGCTCATTCGAGCCCAGATAAG
* * *
2868 TTATCTC-TTATGAGCCTAGATAAG
1 TTAGCTCATT-CGAGCCCAGATAAG
2892 TTAGCTCATTCGAGCCCAGA
1 TTAGCTCATTCGAGCCCAGA
2912 CAGAGTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.03
24 31 0.91
25 2 0.06
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
TTAGCTCATTCGAGCCCAGATAAG
Found at i:6275 original size:22 final size:22
Alignment explanation
Indices: 6250--6291 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6240 CTTTTGAAGG
6250 GGAACGAG-GATGATGATGATAA
1 GGAACG-GTGATGATGATGATAA
*
6272 GGAATGGTGATGATGATGAT
1 GGAACGGTGATGATGATGAT
6292 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.24
Consensus pattern (22 bp):
GGAACGGTGATGATGATGATAA
Found at i:13683 original size:30 final size:29
Alignment explanation
Indices: 13647--13715 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
13637 TTAATGTTAT
*
13647 TTTATTTTTGTTTCTAATTT-GTACCTTTAA
1 TTTATTTTTGTTTCCAATTTAGT-CCTTT-A
*
13677 TTTATTTGTGTTTCCAATTTAGTCCTTTA
1 TTTATTTTTGTTTCCAATTTAGTCCTTTA
*
13706 TTTAATTTTG
1 TTTATTTTTG
13716 CCTCATTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.26
30 23 0.68
31 2 0.06
ACGTcount: A:0.19, C:0.10, G:0.09, T:0.62
Consensus pattern (29 bp):
TTTATTTTTGTTTCCAATTTAGTCCTTTA
Found at i:13788 original size:4 final size:4
Alignment explanation
Indices: 13781--13942 Score: 59
Period size: 4 Copynumber: 39.5 Consensus size: 4
13771 ATTTGGACCC
* * *
13781 ATTT ATTT -TTT ATATT AATT ATATT ATTTT ATTT A-GT ATTT AATT -TTT
1 ATTT ATTT ATTT AT-TT ATTT AT-TT A-TTT ATTT ATTT ATTT ATTT ATTT
* * * *
13829 ATTT AGTT ATTGT -TTT ATTT ATTT ATAT ATTT -GTT ATTC A-TT -TTT
1 ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * *
13874 ATGTT ATTT ATATT CTTGC CTTT ATTT AATCTT ATTG ATTT ATTGT ATTTT
1 AT-TT ATTT AT-TT ATT-T ATTT ATTT -AT-TT ATTT ATTT ATT-T A-TTT
* *
13925 ATTT ATTT GTTT TTTT AT
1 ATTT ATTT ATTT ATTT AT
13943 GCCATTTATA
Statistics
Matches: 117, Mismatches: 23, Indels: 36
0.66 0.13 0.20
Matches are distributed among these distances:
3 13 0.11
4 71 0.61
5 28 0.24
6 5 0.04
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:14991 original size:55 final size:55
Alignment explanation
Indices: 14903--15036 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 55
14893 ATTTGGATTG
* * * * * *
14903 AATCGATTGTTATGCTGGAATATTGCTTCTTTTGAATCGATTGTTTTTACATTTA
1 AATCGATTGTCATGTTGGAATACTGCTTATTTTGAATCGATTGTCTATACATTTA
**
14958 AATCGATTGTCATGTTGGAATACTGCTTATTTTGAATCGATTGTCTATGTATTTA
1 AATCGATTGTCATGTTGGAATACTGCTTATTTTGAATCGATTGTCTATACATTTA
* * *
15013 AATCAATTATCATGTTGAAATACT
1 AATCGATTGTCATGTTGGAATACT
15037 TTTATGATTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.46
Consensus pattern (55 bp):
AATCGATTGTCATGTTGGAATACTGCTTATTTTGAATCGATTGTCTATACATTTA
Found at i:16458 original size:55 final size:55
Alignment explanation
Indices: 16388--16493 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
16378 GTATTTCAAT
* * *
16388 ATGACAATTGGTTTAAATATATAAACAATCAATTCAAAACAAGCAATATTCAAAC
1 ATGACAATTGATTTAAACATAAAAACAATCAATTCAAAACAAGCAATATTCAAAC
* ** **
16443 ATGATAATTGATTTAAACATAAAAACAATTGATTCAAATGAAGCAATATTC
1 ATGACAATTGATTTAAACATAAAAACAATCAATTCAAAACAAGCAATATTC
16494 CAGCATAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.29
Consensus pattern (55 bp):
ATGACAATTGATTTAAACATAAAAACAATCAATTCAAAACAAGCAATATTCAAAC
Found at i:19446 original size:18 final size:19
Alignment explanation
Indices: 19412--19453 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
19402 AAAACATTTC
*
19412 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
19431 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
19449 AATAA
1 AATAA
19454 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:19557 original size:7 final size:7
Alignment explanation
Indices: 19524--19568 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
19514 AATGTTTTGG
19524 TAATAA-
1 TAATAAT
19530 TAATAA-
1 TAATAAT
19536 TAAT-AT
1 TAATAAT
*
19542 AAATAAT
1 TAATAAT
*
19549 TATTAAT
1 TAATAAT
19556 TAATAAT
1 TAATAAT
19563 TAATAA
1 TAATAA
19569 AAAAAAGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 1 0.03
6 13 0.39
7 19 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAATAAT
Found at i:21138 original size:29 final size:30
Alignment explanation
Indices: 20693--21152 Score: 293
Period size: 29 Copynumber: 15.6 Consensus size: 30
20683 GAAATTACCA
* *
20693 TTTTACCATTGAA-CTTCCAAAAATCCCATT
1 TTTTACCCTCGAACCTTCCAAAAATCCCA-T
* **
20723 TTTTGACCC-CGAACCTTCTAAAAATTAACA-
1 TTTT-ACCCTCGAACCTTCCAAAAA-TCCCAT
* * *
20753 TTTTACCC-CCAAACTTCCAAAAATCTCAT
1 TTTTACCCTCGAACCTTCCAAAAATCCCAT
* *
20782 TTTTGA-CCTCAAACCTTCTAAAAATCACCA-
1 TTTT-ACCCTCGAACCTTCCAAAAATC-CCAT
* * *
20812 TTTTACCC-CCAAACTTCTAAAAATCCCAT
1 TTTTACCCTCGAACCTTCCAAAAATCCCAT
** * *
20841 TTTTGA-CCTTAAACCTTCTAAAAATTACCA-
1 TTTT-ACCCTCGAACCTTCCAAAAA-TCCCAT
20871 TTTTATCCC-CGAA-CTTCCAAAAATCCCAT
1 TTTTA-CCCTCGAACCTTCCAAAAATCCCAT
* * *
20900 TTTTGACCC-CAAACCTTCTAAAAATTACCA-
1 TTTT-ACCCTCGAACCTTCCAAAAA-TCCCAT
20930 TTTTACCCTCGAA-CTTCCAAAAATCCCAT
1 TTTTACCCTCGAACCTTCCAAAAATCCCAT
* ** *
20959 TTTTAACCTTAAACCTTCTAAAAATCACCA-
1 TTTTACCCTCGAACCTTCCAAAAATC-CCAT
*
20989 TTTTACCCCCGAA-CTTCCAAAAATCCCAT
1 TTTTACCCTCGAACCTTCCAAAAATCCCAT
* * *
21018 TTTTGACCC-CAAACCTTCTAAAAATTACCA-
1 TTTT-ACCCTCGAACCTTCCAAAAA-TCCCAT
* *
21048 TTTTACCCT-TAAACTTCCAAAAATCCCAT
1 TTTTACCCTCGAACCTTCCAAAAATCCCAT
* * *
21077 TTTGACCCT-AAACC-TCCTAAAAATTACCA-
1 TTTTACCCTCGAACCTTCC-AAAAA-TCCCAT
* *
21106 TTTTACCCTCGAATC-TCCAAAAATCTCAT
1 TTTTACCCTCGAACCTTCCAAAAATCCCAT
21135 TTTTGACCC-CGAACCTTC
1 TTTT-ACCCTCGAACCTTC
21153 TGAAAATTAC
Statistics
Matches: 340, Mismatches: 56, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
28 27 0.08
29 158 0.46
30 121 0.36
31 31 0.09
32 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (30 bp):
TTTTACCCTCGAACCTTCCAAAAATCCCAT
Found at i:21188 original size:59 final size:59
Alignment explanation
Indices: 20673--21175 Score: 704
Period size: 59 Copynumber: 8.5 Consensus size: 59
20663 GGAGGTCCCT
* ***
20673 AAACCTTCTAGAAATTACCATTTTACCATTGAACTTCCAAAAATCCCATTTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCC
* * * * *
20733 GAACCTTCTAAAAATTAACATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTC
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * **
20792 AAACCTTCTAAAAATCACCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCTT
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*
20851 AAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * **
20910 AAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTT
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*
20969 AAACCTTCTAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*** *
21028 AAACCTTCTAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCCCA-TTTTGACCCT
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
21086 AAACCTCCTAAAAATTACCATTTTACCCTCGAA-TCTCCAAAAATCTCATTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATCCCATTTTTGACCCC
* * *
21145 GAACCTTCTGAAAATTACCATTTTGCCCCCG
1 AAACCTTCTAAAAATTACCATTTTACCCCCG
21176 TGCATTCGAA
Statistics
Matches: 395, Mismatches: 46, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
57 1 0.00
58 51 0.13
59 303 0.77
60 40 0.10
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
AAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Done.