Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004313.1 Kokia drynarioides strain JFW-HI SEQ_117628, 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, 712
Length: 1188
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Found at i:559 original size:29 final size:28
Alignment explanation
Indices: 512--739 Score: 269
Period size: 29 Copynumber: 7.8 Consensus size: 28
502 AGGGTCCCTA
512 AACTGTCCAAAAATTCCATTTTTACGCCCG
1 AACT-TCCAAAAATTCCATTTTTAC-CCCG
*
542 AACTTCCAAAAATCCCATTTTTGACCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
* * *
571 TAACTTCCAAAAATTTCAATTTTACCCCTA
1 -AACTTCCAAAAATTCCATTTTTACCCC-G
* * *
601 AACTTCCAAAAATCCCATTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCC-G
630 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
**
659 AACTTCCAAAAATT-CATTTTTTGACTCCAA
1 AACTTCCAAAAATTCCA-TTTTT-AC-CCCG
689 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
718 AACTTCCAAAAATTCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
740 GACACATAAA
Statistics
Matches: 172, Mismatches: 17, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
28 2 0.01
29 118 0.69
30 48 0.28
31 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:609 original size:59 final size:59
Alignment explanation
Indices: 511--775 Score: 326
Period size: 59 Copynumber: 4.5 Consensus size: 59
501 GAGGGTCCCT
*
511 AAACTGTCCAAAAATTCCATTTTTACGCCC-GAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTAC-CCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
571 TAACTTCCAAAAATTTCAATTTTACCCCTAAACTTCCAAAAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
* *
629 AAACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAAT-TCATTTTTTGACTCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCCAAAAATCCCA-TTTTTGACCCCA
* * *
688 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA-CACA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
*
746 TAAACTTTCAAAAAATTACCA-TTTTACCCC
1 -AAAC-TTCCAAAAATT-CCATTTTTACCCC
776 CGGATGTCCA
Statistics
Matches: 180, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
57 6 0.03
58 49 0.27
59 94 0.52
60 28 0.16
61 3 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:692 original size:88 final size:87
Alignment explanation
Indices: 511--742 Score: 317
Period size: 88 Copynumber: 2.6 Consensus size: 87
501 GAGGGTCCCT
*
511 AAACTGTCCAAAAATTCCATTTTTACGCCCGAACTTCCAAAAATCCCATTTTTGACCCCGTAACT
1 AAACT-TCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATTCCATTTTTGACCCCGTAACT
*
576 TCCAAAAATTTCAATTTTACCCCT
64 TCCAAAAATTTCAATTTTACCCCA
* * *
600 AAACTTCCAAAAATCCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACT
1 AAACTTCCAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATTCCATTTTTGACCC-CGTAACT
* *
663 TCCAAAAA-TTCATTTTTTGACTCCA
64 TCCAAAAATTTCA-ATTTT-ACCCCA
688 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAC
1 AAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTGAC
743 ACATAAACTT
Statistics
Matches: 127, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
86 4 0.03
87 23 0.18
88 89 0.70
89 11 0.09
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (87 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCCCGTAACTTC
CAAAAATTTCAATTTTACCCCA
Done.