Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004460.1 Kokia drynarioides strain JFW-HI SEQ_117871, 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, 842
Length: 1404
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Found at i:687 original size:30 final size:29
Alignment explanation
Indices: 621--974 Score: 362
Period size: 30 Copynumber: 12.0 Consensus size: 29
611 GGAGGTCCCT
* * *
621 AAACTGTCCATAAATTTCATTTTTACCCCC
1 AAACT-TCCAAAAATCTCATTTTTACCCCG
*
651 AAACTTCCAAAAATCTCATTTTTGACCTCG
1 AAACTTCCAAAAATCTCATTTTT-ACCCCG
* *
681 AAACTTCCCAAAAT-TCTATTTTTACCCCT
1 AAACTTCCAAAAATCTC-ATTTTTACCCCG
* *
710 AAACGTCCAAAAATCTCATTTTTAACACCG
1 AAACTTCCAAAAATCTCATTTTT-ACCCCG
740 AAACTTCCAAAAAT-TCCATTTTTACCCTCG
1 AAACTTCCAAAAATCT-CATTTTTACCC-CG
*
770 -AACTTCCAAAAATCTCATTTTCGACCCCG
1 AAACTTCCAAAAATCTCATTTT-TACCCCG
* * **
799 AAACTTCCAAAAATCCCATTTTATTCCCTA
1 AAACTTCCAAAAATCTCATTTT-TACCCCG
*
829 AAACTTCCAAAAATTTCATTTTTACCCTC-
1 AAACTTCCAAAAATCTCATTTTTACCC-CG
858 AAACTTCCAAAAAT-TCTATTTTTGACCCCG
1 AAACTTCCAAAAATCTC-ATTTTT-ACCCCG
*
888 AAACTTCTAAAAAT-TCTATTTTTACCCCTG
1 AAACTTCCAAAAATCTC-ATTTTTACCCC-G
* *
918 -AACTTCCAAAAATCCCATTTTTTACCTCG
1 AAACTTCCAAAAATCTCA-TTTTTACCCCG
* *
947 AAACTTCTAAAAATCCCATTTTTACCCC
1 AAACTTCCAAAAATCTCATTTTTACCCC
975 TAATCCCATT
Statistics
Matches: 277, Mismatches: 30, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
28 2 0.01
29 118 0.43
30 157 0.57
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATCTCATTTTTACCCCG
Found at i:769 original size:89 final size:88
Alignment explanation
Indices: 617--977 Score: 380
Period size: 89 Copynumber: 4.1 Consensus size: 88
607 CCCCGGAGGT
* * *
617 CCCTAAACTGTCCATAAATTTCATTTTTACCCC-CAAACTTCCAAAAA-TCTCATTTTTGACCTC
1 CCCTAAAC-GTCCAAAAATCTCATTTTTACCCCTGAAACTTCCAAAAATTC-CATTTTT-ACCTC
*
680 GAAACTTCCCAAAATTCTATTTTTAC
63 GAAACTTCCAAAAATTCTATTTTTAC
*
706 CCCTAAACGTCCAAAAATCTCATTTTTAACACC-GAAACTTCCAAAAATTCCATTTTTACCCTCG
1 CCCTAAACGTCCAAAAATCTCATTTTT-ACCCCTGAAACTTCCAAAAATTCCATTTTTA-CCTCG
*
770 -AACTTCCAAAAA-TCTCATTTTCGAC
64 AAACTTCCAAAAATTCT-ATTTT-TAC
* * * * * *
795 CCCGAAACTTCCAAAAATCCCA-TTTTATTCCCTAAAACTTCCAAAAATTTCATTTTTACCCTC-
1 CCCTAAACGTCCAAAAATCTCATTTTTA-CCCCTGAAACTTCCAAAAATTCCATTTTTA-CCTCG
858 AAACTTCCAAAAATTCTATTTTTGAC
64 AAACTTCCAAAAATTCTATTTTT-AC
* * * *
884 CCCGAAACTTCTAAAAAT-TCTATTTTTACCCCTG-AACTTCCAAAAATCCCATTTTTTACCTCG
1 CCCTAAACGTCCAAAAATCTC-ATTTTTACCCCTGAAACTTCCAAAAATTCCA-TTTTTACCTCG
* * *
947 AAACTTCTAAAAATCCCATTTTTAC
64 AAACTTCCAAAAATTCTATTTTTAC
972 CCCTAA
1 CCCTAA
978 TCCCATTTTA
Statistics
Matches: 234, Mismatches: 24, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
87 4 0.02
88 67 0.29
89 153 0.65
90 10 0.04
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (88 bp):
CCCTAAACGTCCAAAAATCTCATTTTTACCCCTGAAACTTCCAAAAATTCCATTTTTACCTCGAA
ACTTCCAAAAATTCTATTTTTAC
Found at i:975 original size:59 final size:59
Alignment explanation
Indices: 621--974 Score: 382
Period size: 59 Copynumber: 6.0 Consensus size: 59
611 GGAGGTCCCT
* * * *
621 AAACTGTCCATAAATTTCA-TTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTTACCCCGAAACTTCCAAAAATCTCATTTTT-ACCCCG
* * * * *
681 AAACTTCCCAAAATTCTA-TTTTTACCCCTAAACGTCCAAAAATCTCATTTTTAACACCG
1 AAACTTCCAAAAATTCCATTTTTTACCCCGAAACTTCCAAAAATCTCATTTTT-ACCCCG
*
740 AAACTTCCAAAAATTCCA-TTTTTACCCTCG-AACTTCCAAAAATCTCATTTTCGACCCCG
1 AAACTTCCAAAAATTCCATTTTTTACCC-CGAAACTTCCAAAAATCTCATTTT-TACCCCG
* ** *
799 AAACTTCCAAAAATCCCATTTTATT-CCCTAAAACTTCCAAAAATTTCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTT-TTACCCCGAAACTTCCAAAAATCTCATTTTTACCC-CG
* * *
858 AAACTTCCAAAAATTCTATTTTTGACCCCGAAACTTCTAAAAAT-TCTATTTTTACCCCTG
1 AAACTTCCAAAAATTCCATTTTTTACCCCGAAACTTCCAAAAATCTC-ATTTTTACCCC-G
* * * *
918 -AACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCTAAAAATCCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTTACCCCGAAACTTCCAAAAATCTCATTTTTACCCC
975 TAATCCCATT
Statistics
Matches: 252, Mismatches: 31, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.02
59 212 0.84
60 34 0.13
61 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTTACCCCGAAACTTCCAAAAATCTCATTTTTACCCCG
Found at i:992 original size:17 final size:18
Alignment explanation
Indices: 958--992 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
948 AACTTCTAAA
*
958 AATCCCATTTTTACCCCT
1 AATCCCATTTTTAACCCT
976 AATCCCA-TTTTAACCCT
1 AATCCCATTTTTAACCCT
993 GAATTTTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (18 bp):
AATCCCATTTTTAACCCT
Found at i:1055 original size:29 final size:30
Alignment explanation
Indices: 1018--1074 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1008 TACTGTTTCA
*
1018 CCCCCGAGAATCC-AAAATTATCATTTTTT
1 CCCCCGAGAATCCGAAAAGTATCATTTTTT
*
1047 CCCCCGAGAATCCGAAAAGTCTCATTTT
1 CCCCCGAGAATCCGAAAAGTATCATTTT
1075 GAACTCCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (30 bp):
CCCCCGAGAATCCGAAAAGTATCATTTTTT
Done.