Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008912.1 Kokia drynarioides strain JFW-HI SEQ_123601, 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: 4313
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:484 original size:101 final size:101
Alignment explanation
Indices: 358--714 Score: 455
Period size: 101 Copynumber: 3.5 Consensus size: 101
348 ACAGTTGTGG
* * * * *
358 ATCTGAATCTCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATATCCTTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
*
423 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGG
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * *
459 ATTTCAATCTCCCTGAAGTTACAGTGGAGTGGAGTGAAGATACAACACCAAATCCTATATCCCTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
* * *
524 AAGTTGTTGTGGATCGAATTAAAATTACGATAACGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * * * * * *
560 ATCTCAATCTTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATATCCCTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
** * *
625 AAGTTGCGGTGGATCGGATTAAAACTATGATAGCGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * * *
661 ATCTCAATCTCCTTGAAGTTGTAGTGGAATGAAGTGAAGCTACAACGA-CAAATC
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAAC-ACCAAATC
715 TTATCTCATT
Statistics
Matches: 219, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
101 218 1.00
102 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (101 bp):
ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
Found at i:536 original size:50 final size:49
Alignment explanation
Indices: 367--630 Score: 145
Period size: 50 Copynumber: 5.2 Consensus size: 49
357 GATCTGAATC
* * * *
367 TCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATA
1 TCCCTGAAGTTGTAGTGG-ATGGAGTGAAGATACAACACCAAATCCTATA
* * * ** * * * *
417 TCCTTGAAGTTGTAGTGGATCGGA-TTAAAACTACGATA-ACGGATTTCAATC
1 TCCCTGAAGTTGTAGTGGAT-GGAGTGAAGA-TAC-A-ACACCAAATCCTATA
**
468 TCCCTGAAGTTACAGTGGAGTGGAGTGAAGATACAACACCAAATCCTATA
1 TCCCTGAAGTTGTAGTGGA-TGGAGTGAAGATACAACACCAAATCCTATA
* * * * * * * * * * *
518 TCCCTGAAGTTGTTGTGGATCGAATTAAAATTACGATAACGAATCTCAATC
1 TCCCTGAAGTTGTAGTGGATGGAGTGAAGA-TACAACACCAAATC-CTATA
* * * * * *
569 TTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATA
1 TCCCTGAAGTTGTAGTGG-ATGGAGTGAAGATACAACACCAAATCCTATA
619 TCCCTGAAGTTG
1 TCCCTGAAGTTG
631 CGGTGGATCG
Statistics
Matches: 153, Mismatches: 51, Indels: 20
0.68 0.23 0.09
Matches are distributed among these distances:
49 12 0.08
50 69 0.45
51 59 0.39
52 13 0.08
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (49 bp):
TCCCTGAAGTTGTAGTGGATGGAGTGAAGATACAACACCAAATCCTATA
Found at i:581 original size:51 final size:50
Alignment explanation
Indices: 421--688 Score: 157
Period size: 51 Copynumber: 5.3 Consensus size: 50
411 GCTATATCCT
* * * *
421 TGAAGTTGTAGTGGATCGGATTAAAACTACGATAACGGATTTCAATCTCCC
1 TGAAGTTGTAGTGGATC-GATTAAAATTACGATAACGAATCTCAATCTTCC
** * * * * * * * * * *
472 TGAAGTTACAGTGGAGTGGAGTGAAGA-TACAACACCAAATC-CTATATCCC
1 TGAAGTTGTAGTGGA-TCGA-TTAAAATTACGATAACGAATCTCAATCTTCC
*
522 TGAAGTTGTTGTGGATCGAATTAAAATTACGATAACGAATCTCAATCTTCC
1 TGAAGTTGTAGTGGATCG-ATTAAAATTACGATAACGAATCTCAATCTTCC
* * * * * * * * * *
573 TAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATC-CTATATCCC
1 TGAAGTTGTAGTGG-ATCGATTAAAATTACGATAACGAATCTCAATCTTCC
** * * *
623 TGAAGTTGCGGTGGATCGGATTAAAACTATGATAGCGAATCTCAATC-TCC
1 TGAAGTTGTAGTGGATC-GATTAAAATTACGATAACGAATCTCAATCTTCC
673 TTGAAGTTGTAGTGGA
1 -TGAAGTTGTAGTGGA
689 ATGAAGTGAA
Statistics
Matches: 155, Mismatches: 53, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
49 8 0.05
50 65 0.42
51 74 0.48
52 8 0.05
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (50 bp):
TGAAGTTGTAGTGGATCGATTAAAATTACGATAACGAATCTCAATCTTCC
Done.