Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000153.1 Kokia drynarioides strain JFW-HI SEQ_110815, 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: 2159
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:522 original size:82 final size:82
Alignment explanation
Indices: 318--702 Score: 296
Period size: 82 Copynumber: 4.7 Consensus size: 82
308 GCTTATGCCA
* * ** * * * *
318 AAACGCCGCTATTGCT-TAACCTTTAGCGGCACTTTCCAATAAATGTCGCTAATGCTCTGACCTT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCTCTAACCTT
382 TAGCGACGCTTTTCCAT
66 TAGCGACGCTTTTCCAT
* * **
399 AAACGCCGCTAATGATCTGACCTTTAGCGAC-ACTTCTCCATAAACGCCGCTAATGCTCTAACCT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTC-CCATAAACGCCGCTAATGCTCTAACCT
463 TTAGCGACGCTTTTCCAT
65 TTAGCGACGCTTTTCCAT
* * * * ** * * * * **
481 AAATGCCGCTAATGCTTTGACTTTTAGTGGCGTTTTCCCATAAACGCCGGAAAAGGT-AAAGCAA
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCTCTAACCTT
* **
545 TAGCGGCG-TTTATAGGA-
66 TAGCGACGCTTT-T-CCAT
* * * * * *
562 ATAACGCCGATAATGCTCTAACCTTTAGCGGCGCTTTCCCATAAATGCCGCTAATGCTTTGACCT
1 A-AACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCTCTAACCT
* **
627 TTAGCGGCATTTTTCCTAT
65 TTAGCGACGCTTTTCC-AT
* * * * * *
646 AAATGCCGCTATTGCT-TTACCTTTTGCGGCGTTTTTCCTATAAACGCCGCTATTGCT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCG-TTTTCCCATAAACGCCGCTAATGCT
703 TTATCTTTTA
Statistics
Matches: 235, Mismatches: 58, Indels: 20
0.75 0.19 0.06
Matches are distributed among these distances:
80 3 0.01
81 29 0.12
82 152 0.65
83 47 0.20
84 4 0.02
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (82 bp):
AAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCTCTAACCTT
TAGCGACGCTTTTCCAT
Found at i:522 original size:123 final size:122
Alignment explanation
Indices: 309--656 Score: 353
Period size: 123 Copynumber: 2.8 Consensus size: 122
299 ATTAGCGGTG
* * * *
309 CTTATGCCAAAACGCCGCTATTGCT-TAACCTTTAGCGGCAC-TTTCCAATAAATGTCGCTAATG
1 CTTATACCAAAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCC-ATAAATGCCGCTAATG
* * * ** **
372 CTCTGACCTTTAGCGACGCTTTT-CCATAAACGCCGCTAATGATCTGACCTTTAGCGACA
65 CTTTGACCTTTAGCGGCG-TTTTCCCATAAACGCCGCTAAAGAT-AAACCAATAGCGACA
* *
431 CTTCT-CCATAAACGCCGCTAATGCTCTAACCTTTAGCGACGCTTTTCCATAAATGCCGCTAATG
1 CTTATACCA-AAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCCATAAATGCCGCTAATG
* * ** * * * *
495 CTTTGACTTTTAGTGGCGTTTTCCCATAAACGCCGGAAAAGGTAAAGCAATAGCGGCG
65 CTTTGACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAAAGATAAACCAATAGCGACA
* ** * *
553 TTTATAGGAATAACGCCGATAATGCTCTAACCTTTAGCGGCGCTTTCCCATAAATGCCGCTAATG
1 CTTATACCAA-AACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCCATAAATGCCGCTAATG
* * *
618 CTTTGACCTTTAGCGGCATTTTTCCTATAAATGCCGCTA
65 CTTTGACCTTTAGCGGC-GTTTTCCCATAAACGCCGCTA
657 TTGCTTTACC
Statistics
Matches: 185, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
121 3 0.02
122 35 0.19
123 126 0.68
124 21 0.11
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (122 bp):
CTTATACCAAAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCCATAAATGCCGCTAATGC
TTTGACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAAAGATAAACCAATAGCGACA
Found at i:703 original size:41 final size:41
Alignment explanation
Indices: 318--710 Score: 251
Period size: 41 Copynumber: 9.6 Consensus size: 41
308 GCTTATGCCA
* * ** *
318 AAACGCCGCTATTGCTTAACCTTTAGCGGC-ACTTTCCAAT
1 AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTTTCCTAT
* * * * *
358 AAATGTCGCTAATGCTCTGACCTTTAGCGACGCTTTTCC-AT
1 AAACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCTAT
* * * ** *
399 AAACGCCGCTAATGATCTGACCTTTAGCGACACTTCTCC-AT
1 AAACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCTAT
* * *
440 AAACGCCGCTAATGCTCTAACCTTTAGCGACGCTTTTCC-AT
1 AAACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCTAT
* * * *
481 AAATGCCGCTAATGCTTTGACTTTTAGTGGCG-TTTTCCCAT
1 AAACGCCGCTAATGCTTT-ACCTTTAGCGGCGTTTTTCCTAT
** * * ** * ** * ***
522 AAACGCCGGAAAAGGTAAAGCAATAGCGGCGTTTATAGGA-
1 AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTTTCCTAT
* * * *
562 ATAACGCCGATAATGCTCTAACCTTTAGCGGCG-CTTTCCCAT
1 A-AACGCCGCTAATGCT-TTACCTTTAGCGGCGTTTTTCCTAT
* *
604 AAATGCCGCTAATGCTTTGACCTTTAGCGGCATTTTTCCTAT
1 AAACGCCGCTAATGCTTT-ACCTTTAGCGGCGTTTTTCCTAT
* * *
646 AAATGCCGCTATTGCTTTACCTTTTGCGGCGTTTTTCCTAT
1 AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTTTCCTAT
* *
687 AAACGCCGCTATTGCTTTATCTTT
1 AAACGCCGCTAATGCTTTACCTTT
711 TACGGTGTTT
Statistics
Matches: 282, Mismatches: 61, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
40 30 0.11
41 211 0.75
42 41 0.15
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAATGCTTTACCTTTAGCGGCGTTTTTCCTAT
Found at i:738 original size:41 final size:41
Alignment explanation
Indices: 604--722 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
594 GCTTTCCCAT
* * *
604 AAATGCCGCTAATGCTTTGACC-TTTAGCGGCATTTTTCCTAT
1 AAATGCCGCTATTGCTTT-ACCTTTTA-CGGCGTTTTTCCTAC
* *
646 AAATGCCGCTATTGCTTTACCTTTTGCGGCGTTTTTCCTAT
1 AAATGCCGCTATTGCTTTACCTTTTACGGCGTTTTTCCTAC
* * *
687 AAACGCCGCTATTGCTTTATCTTTTACGGTGTTTTT
1 AAATGCCGCTATTGCTTTACCTTTTACGGCGTTTTT
723 TGTCCAAATG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 49 0.71
42 20 0.29
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.43
Consensus pattern (41 bp):
AAATGCCGCTATTGCTTTACCTTTTACGGCGTTTTTCCTAC
Done.