Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000127.1 Kokia drynarioides strain JFW-HI SEQ_110773, 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: 3188
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Found at i:2460 original size:123 final size:122
Alignment explanation
Indices: 2255--2594 Score: 355
Period size: 123 Copynumber: 2.8 Consensus size: 122
2245 TGCTTATGCG
* * *
2255 AAAACGCCGCTATTGCT-TAACCTTTAGCGGCAC-TTTCCAATAAATGTCGCTAATGCTCTGACC
1 AAAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCC-ATAAATGCCGCTAATGCTCTGACC
* * ** ** *
2318 TTTAGCGACGCTTTT-CCATAAACGCCGCTAATGATCTGACCTTTAGCGACACTTCT-CC
65 TTTAGCGGCG-TTTTCCCATAAACGCCGCTAAAGAT-AAACCAATAGCGACACTTATACC
* *
2376 ATAAACGCCGCTAATGCTCTAACCTTTAGCGACGCTTTTCCATAAATGCCGCTAATGCTTTGACC
1 A-AAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCCATAAATGCCGCTAATGCTCTGACC
* ** * * * ** **
2441 TTTAGTGGCGTTTTCCCATAAACGCCGGAAAAGGTAAAGCAATAGCGGCGTTTATAGG
65 TTTAGCGGCGTTTTCCCATAAACGCCGCTAAAGATAAACCAATAGCGACACTTATACC
* *
2499 AATAACGCCGATAATGCTCTAACCTTTAGCGGCGCTTTCCCATAAATGCCGCTAATGCTCTGACC
1 AA-AACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCCATAAATGCCGCTAATGCTCTGACC
* * *
2564 TTTAGCGGCATTTTTCCTATAAATGCCGCTA
65 TTTAGCGGC-GTTTTCCCATAAACGCCGCTA
2595 TTGCTTTACC
Statistics
Matches: 180, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
121 1 0.01
122 31 0.17
123 127 0.71
124 21 0.12
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (122 bp):
AAAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTTCCATAAATGCCGCTAATGCTCTGACCT
TTAGCGGCGTTTTCCCATAAACGCCGCTAAAGATAAACCAATAGCGACACTTATACC
Found at i:2643 original size:41 final size:41
Alignment explanation
Indices: 2256--2640 Score: 303
Period size: 41 Copynumber: 9.4 Consensus size: 41
2246 GCTTATGCGA
* **
2256 AAACGCCGCTATTGCT-TAACCTTTAGCGGC-ACTTTCCAAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCC-AT
* * * * *
2296 AAATGTCGCTAATGCTCTGACCTTTAGCGACGCTTTTCCAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCAT
* * * ** *
2337 AAACGCCGCTAATGATCTGACCTTTAGCGACACTTCTCCAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCAT
* *
2378 AAACGCCGCTAATGCTCTAACCTTTAGCGACGCTTTTCCAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCAT
* * * * *
2419 AAATGCCGCTAATGCTTTGACCTTTAGTGGCGTTTTCCCAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCAT
** * * * * ** ***
2460 AAACGCCGGAAAAGGT-AAAGCAATAGCGGCGTTTATAGGA-
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTT-TTCCAT
* * *
2500 ATAACGCCGATAATGCTCTAACCTTTAGCGGCGCTTTCCCAT
1 A-AACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCAT
* * *
2542 AAATGCCGCTAATGCTCTGACCTTTAGCGGCATTTTTCCTAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCC-AT
* * * *
2584 AAATGCCGCTATTGCT-TTACCTTTTGCGGCGTTTTTCCTAT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCC-AT
*
2625 AAACGCCGCTATTGCT
1 AAACGCCGCTAATGCT
2641 TTATCTTTTA
Statistics
Matches: 278, Mismatches: 60, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
40 26 0.09
41 216 0.78
42 36 0.13
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCAT
Found at i:2649 original size:41 final size:41
Alignment explanation
Indices: 2520--2660 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
2510 TAATGCTCTA
* * * * *
2520 ACCTTTAGCGGCG-CTTTCCCATAAATGCCGCTAATGCTCTG
1 ACCTTTTGCGGCGTTTTTCCTATAAATGCCGCTATTGCT-TT
* *
2561 ACCTTTAGCGGCATTTTTCCTATAAATGCCGCTATTGCTTT
1 ACCTTTTGCGGCGTTTTTCCTATAAATGCCGCTATTGCTTT
*
2602 ACCTTTTGCGGCGTTTTTCCTATAAACGCCGCTATTGCTTT
1 ACCTTTTGCGGCGTTTTTCCTATAAATGCCGCTATTGCTTT
* * *
2643 ATCTTTTACGGTGTTTTT
1 ACCTTTTGCGGCGTTTTT
2661 TGTCCAAATG
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 66 0.75
42 22 0.25
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (41 bp):
ACCTTTTGCGGCGTTTTTCCTATAAATGCCGCTATTGCTTT
Done.