Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003066.1 Kokia drynarioides strain JFW-HI SEQ_115605, 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: 2291
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Found at i:461 original size:30 final size:27
Alignment explanation
Indices: 431--835 Score: 246
Period size: 30 Copynumber: 13.8 Consensus size: 27
421 TTCGGAGTAA
*
431 AAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGAATTTTTGGAAGTTCG-GGGT
* *
459 AAAATGATAATTTTTGAAAAGTTCGGGGT
1 AAAATG-GAATTTTTG-GAAGTTCGGGGT
488 CAAAAAT-GAGATTTTTGGAAGTTCGAGGGT
1 --AAAATGGA-ATTTTTGGAAGTTCG-GGGT
* *
518 AAAATGGTAATTTTTAGAAGGTTCGGGAT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGT
*
547 CAAAAAT-GAGATTTTTGGAAGTTTGGGGGT
1 --AAAATGGA-ATTTTTGGAAG-TTCGGGGT
* *
577 AAAATGGTAATTTTTAGAAGGTTTGGGGT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGT
*
606 AAAAAATGGAATTTTTGGAGGTTCGAGGGT
1 --AAAATGGAATTTTTGGAAGTTCG-GGGT
*
636 AAAATGGTAA-TTTTGGAAGGTTTGGGGTT
1 AAAATGG-AATTTTTGGAA-GTTCGGGG-T
* *
665 GAAAAT-GAGATTTTTGGAAGTTTGGTTGT
1 -AAAATGGA-ATTTTTGGAAGTTCGG-GGT
* **
694 AAAATGGTAATTTTTAGAAGGTTTAGGGT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGT
* *
723 CAAAATGGTAATTTTTTAGAAGGTTTGGGGTT
1 -AAAATGG-AA-TTTTTGGAA-GTTCGGGG-T
*
755 AAAAAT-GAGATTTTTGGAAGTTTAGGGGT
1 -AAAATGGA-ATTTTTGGAAG-TTCGGGGT
*
784 AAAATGGTAA-TTTTAGAAGGTTCGGGGT
1 AAAATGG-AATTTTTGGAA-GTTCGGGGT
*
812 CAAAAATGGGATTTTTGGAAGTTC
1 --AAAATGGAATTTTTGGAAGTTC
836 AAGGACTTTC
Statistics
Matches: 308, Mismatches: 29, Indels: 79
0.74 0.07 0.19
Matches are distributed among these distances:
28 58 0.19
29 93 0.30
30 115 0.37
31 36 0.12
32 6 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:483 original size:59 final size:59
Alignment explanation
Indices: 401--716 Score: 390
Period size: 59 Copynumber: 5.4 Consensus size: 59
391 GCACGGGGGC
* * * * *
401 AAAATGGT-AGTTTTGGATGGTTCGGAGTAAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGGGT
* * *
459 AAAATGATAATTTTT-GAAAAGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAG-AAGGTTCGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGGGT
* * * *
518 AAAATGGTAATTTTTAGAAGGTTCGGGATCAAAAATGAGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGGGT
* *
577 AAAATGGTAATTTTTAGAAGGTTTGGGGTAAAAAATG-GAATTTTTGGAGGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAATGAG-ATTTTTGGAAGTTCGAGGGT
* * ** * *
636 AAAATGGTAA-TTTTGGAAGGTTTGGGGTTGAAAATGAGATTTTTGGAAGTTTG-GTTGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAATGAGATTTTTGGAAGTTCGAG-GGT
694 AAAATGGTAATTTTTAGAAGGTT
1 AAAATGGTAATTTTTAGAAGGTT
717 TAGGGTCAAA
Statistics
Matches: 226, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.00
58 57 0.25
59 167 0.74
60 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGGGT
Found at i:833 original size:58 final size:59
Alignment explanation
Indices: 694--834 Score: 187
Period size: 58 Copynumber: 2.4 Consensus size: 59
684 GTTTGGTTGT
* * * *
694 AAAATGGTAATTTTTAGAAGGTTTAGGGTCAAAATGGTAATTTTTTAGAAGGTTTGGGGTTA
1 AAAATGG-GATTTTTGGAA-GTTTAGGGTCAAAATGGTAA-TTTTTAGAAGGTTCGGGGTCA
*
756 AAAATGAGATTTTTGGAAGTTTAGGGGT-AAAATGGTAA-TTTTAGAAGGTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTA-GGGTCAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
814 AAAATGGGATTTTTGGAAGTT
1 AAAATGGGATTTTTGGAAGTT
835 CAAGGACTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
58 38 0.53
60 15 0.21
61 13 0.18
62 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTTAGGGTCAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
Done.