Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000053.1 Kokia drynarioides strain JFW-HI SEQ_109606, 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: 1906
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Found at i:617 original size:30 final size:30
Alignment explanation
Indices: 555--845 Score: 126
Period size: 29 Copynumber: 9.9 Consensus size: 30
545 AGAAATCATA
**
555 TTTTAACCTCGAACTTTTCCAAAATTTTAT
1 TTTTAACCTCGAACTTTTCCAAAATTACAT
* *
585 TTTTGACCTCGAGC-TTTCCGAAAATTACA-
1 TTTTAACCTCGAACTTTTCC-AAAATTACAT
* * *
614 TTTT-ACCCCTAAC-TTTCCAAAATTCCAT
1 TTTTAACCTCGAACTTTTCCAAAATTACAT
* * * **
642 TTTGACCCT-AAACTTTTTAAAAATTACAT
1 TTTTAACCTCGAACTTTTCCAAAATTACAT
* * *
671 TTTTACCCTCAAAC-TTTCCAAAATTCCAT
1 TTTTAACCTCGAACTTTTCCAAAATTACAT
* * *
700 TTTT-ACC-CCAATTTTTCCAAAAATTTCCA-
1 TTTTAACCTCGAACTTTTCC-AAAA-TTACAT
* *
729 TTTTACCCTCGAAC--TTCCAAAAATTTCCAT
1 TTTTAACCTCGAACTTTTCC-AAAA-TTACAT
* * * * *
759 TTTTGACCAC-TATTTTTCTAAAAATTACCA-
1 TTTTAACCTCGAACTTTTC-CAAAATTA-CAT
* * * * *
789 TTTTACCCTTGAAC-TTTCAAAAATTCCAA
1 TTTTAACCTCGAACTTTTCCAAAATTACAT
*
818 TTTTAACCCCGAAC-TTTCCAAAGATTAC
1 TTTTAACCTCGAACTTTTCCAAA-ATTAC
846 CATTGTACCC
Statistics
Matches: 199, Mismatches: 44, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
27 11 0.06
28 26 0.13
29 96 0.48
30 53 0.27
31 13 0.07
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTTAACCTCGAACTTTTCCAAAATTACAT
Found at i:855 original size:29 final size:29
Alignment explanation
Indices: 598--914 Score: 217
Period size: 29 Copynumber: 10.9 Consensus size: 29
588 TGACCTCGAG
* *
598 CTTTCCGAAAATTA-CATTTTACCCCTAA
1 CTTTCCAAAAATTACCATTTTACCCCGAA
**
626 CTTTCC-AAAATT-CCATTTTGACCCTAAA
1 CTTTCCAAAAATTACCATTTT-ACCCCGAA
** *
654 CTTTTTAAAAATTA-CATTTTTACCCTCAAA
1 CTTTCCAAAAATTACCA-TTTTACCC-CGAA
684 CTTTCC-AAAATT-CCATTTTTACCCC-AA
1 CTTTCCAAAAATTACCA-TTTTACCCCGAA
* *
711 TTTTTCCAAAAATTTCCATTTTACCCTCGAA
1 -CTTTCCAAAAATTACCATTTTACCC-CGAA
* * * *
742 C-TTCCAAAAATTTCCATTTTTGACCACTAT
1 CTTTCCAAAAATTACCA-TTTT-ACCCCGAA
* * *
772 TTTTCTAAAAATTACCATTTTACCCTTGAA
1 CTTTCCAAAAATTACCATTTTACCC-CGAA
802 CTTT-CAAAAATT-CCAATTTTAACCCCGAA
1 CTTTCCAAAAATTACC-ATTTT-ACCCCGAA
* * *
831 CTTTCCAAAGATTACCATTGTACCCCTATA
1 CTTTCCAAAAATTACCATTTTACCCCGA-A
* * *
861 -TATCTAAAAATT-CTATTTTTAACCCCGAA
1 CTTTCCAAAAATTACCA-TTTT-ACCCCGAA
*
890 CCTTCCAAAAATTACCATTTTACCC
1 CTTTCCAAAAATTACCATTTTACCC
915 TTGAATGTTT
Statistics
Matches: 229, Mismatches: 35, Indels: 49
0.73 0.11 0.16
Matches are distributed among these distances:
27 14 0.06
28 26 0.11
29 103 0.45
30 64 0.28
31 22 0.10
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.38
Consensus pattern (29 bp):
CTTTCCAAAAATTACCATTTTACCCCGAA
Found at i:855 original size:59 final size:59
Alignment explanation
Indices: 598--977 Score: 287
Period size: 58 Copynumber: 6.5 Consensus size: 59
588 TGACCTCGAG
* * * * **
598 CTTTCCGAAAATTA-CATTTTACCCCT-AACTTTCCAAAATTCC-ATTTTGACCCTAAA
1 CTTTCCAAAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCAATTTTAACCCCGAA
** ** * *
654 CTTTTTAAAAATTA-CATTTTTACCCTCAAACTTTCCAAAATTCC-ATTTTTACCCC-AA
1 CTTTCCAAAAATTACCA-TTTTACCCTTGAACTTTCAAAAATTCCAATTTTAACCCCGAA
* * * * * * * * *
711 TTTTTCCAAAAATTTCCATTTTACCCTCGAACTTCCAAAAATTTCCATTTTTGACCACTAT
1 -CTTTCCAAAAATTACCATTTTACCCTTGAACTTTCAAAAA-TTCCAATTTTAACCCCGAA
* *
772 TTTTCTAAAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCAATTTTAACCCCGAA
1 CTTTCCAAAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCAATTTTAACCCCGAA
* * * * * *
831 CTTTCCAAAGATTACCATTGTACCCCT-ATA-TATCTAAAAATTCTATTTTTAACCCCGAA
1 CTTTCCAAAAATTACCATTTTACCCTTGA-ACTTTC-AAAAATTCCAATTTTAACCCCGAA
* * * * *
890 CCTTCCAAAAATTACCATTTTACCCTTGAA-TGTT-TAAAATTACATTTTTAACCCTGAA
1 CTTTCCAAAAATTACCATTTTACCCTTGAACT-TTCAAAAATTCCAATTTTAACCCCGAA
* * *
948 CCTTCC-AAAATTATCATTTTGCCCCTTGAA
1 CTTTCCAAAAATTACCATTTT-ACCCTTGAA
978 TGTCCAAAAT
Statistics
Matches: 266, Mismatches: 46, Indels: 22
0.80 0.14 0.07
Matches are distributed among these distances:
56 13 0.05
57 23 0.09
58 93 0.35
59 90 0.34
60 46 0.17
61 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (59 bp):
CTTTCCAAAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCAATTTTAACCCCGAA
Found at i:932 original size:28 final size:29
Alignment explanation
Indices: 897--990 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
887 GAACCTTCCA
*
897 AAAATTACCATTTT-ACCCTTGAATGTTT
1 AAAATTACCATTTTAACCCTTGAATGTTC
**
925 AAAATTA-CATTTTTAACCC-TGAACCTTCC
1 AAAATTACCA-TTTTAACCCTTGAATGTT-C
* ** *
954 AAAATTATCATTTTGCCCCTTGAATGTCC
1 AAAATTACCATTTTAACCCTTGAATGTTC
983 AAAATTAC
1 AAAATTAC
991 TGTTCTACCC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.04
28 17 0.33
29 26 0.50
30 7 0.13
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCTTGAATGTTC
Found at i:953 original size:58 final size:58
Alignment explanation
Indices: 778--990 Score: 227
Period size: 59 Copynumber: 3.6 Consensus size: 58
768 CTATTTTTCT
* * *
778 AAAAATTACCATTTTACCCTTGAACT-TTCAAAAATTCCAATTTTAACCCCGAACTTTCC
1 AAAAATTACCATTTTACCCTTGAA-TGTT-AAAAATTACATTTTTAACCCCGAACCTTCC
* * * *
837 AAAGATTACCATTGTACCCCT-ATATATCTAAAAATT-CTATTTTTAACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCTTGA-ATGT-TAAAAATTAC-ATTTTTAACCCCGAACCTTCC
* *
896 AAAAATTACCATTTTACCCTTGAATGTTTAAAATTACATTTTTAACCCTGAACCTTCC
1 AAAAATTACCATTTTACCCTTGAATGTTAAAAATTACATTTTTAACCCCGAACCTTCC
* * **
954 -AAAATTATCATTTTGCCCCTTGAATGTCCAAAATTAC
1 AAAAATTACCATTTT-ACCCTTGAATGTTAAAAATTAC
991 TGTTCTACCC
Statistics
Matches: 132, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
57 13 0.10
58 49 0.37
59 68 0.52
60 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCTTGAATGTTAAAAATTACATTTTTAACCCCGAACCTTCC
Found at i:957 original size:29 final size:30
Alignment explanation
Indices: 600--967 Score: 113
Period size: 29 Copynumber: 12.6 Consensus size: 30
590 ACCTCGAGCT
* *
600 TTCCGAAAATTA-CA-TTTTACCCCT-AACT
1 TTCC-AAAATTACCATTTTTAACCCTGAACC
* * *
628 TTCCAAAATT-CCA-TTTTGACCCTAAACTT
1 TTCCAAAATTACCATTTTTAACCCTGAAC-C
** * *
657 TTTAAAAATTA-CATTTTT-ACCCTCAAACT
1 TTCCAAAATTACCATTTTTAACCCT-GAACC
* **
686 TTCCAAAATT-CCATTTTT-ACCC-CAATTT
1 TTCCAAAATTACCATTTTTAACCCTGAA-CC
*
714 TTCCAAAAATTTCCA-TTTT-ACCCTCGAA-C
1 TTCC-AAAATTACCATTTTTAACCCT-GAACC
* * ***
743 TTCCAAAAATTTCCATTTTTGACCACT-ATTT
1 TTCC-AAAATTACCATTTTTAACC-CTGAACC
* *
774 TTCTAAAAATTACCA-TTTT-ACCCTTGAACT
1 TTC-CAAAATTACCATTTTTAACCC-TGAACC
* * * *
804 TTCAAAAATT-CCAATTTTAACCCCGAACT
1 TTCCAAAATTACCATTTTTAACCCTGAACC
* *
833 TTCCAAAGATTACCA-TTGTACCCCT-ATA--
1 TTCCAAA-ATTACCATTTTTAACCCTGA-ACC
* * *
861 TATCTAAAAATT-CTATTTTTAACCCCGAACC
1 T-TC-CAAAATTACCATTTTTAACCCTGAACC
**
892 TTCCAAAAATTACCA-TTTT-ACCCTTGAATG
1 TTCC-AAAATTACCATTTTTAACCC-TGAACC
*
922 TT-TAAAATTA-CATTTTTAACCCTGAACC
1 TTCCAAAATTACCATTTTTAACCCTGAACC
*
950 TTCCAAAATTATCATTTT
1 TTCCAAAATTACCATTTT
968 GCCCCTTGAA
Statistics
Matches: 268, Mismatches: 35, Indels: 72
0.71 0.09 0.19
Matches are distributed among these distances:
27 20 0.07
28 36 0.13
29 120 0.45
30 67 0.25
31 23 0.09
32 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
TTCCAAAATTACCATTTTTAACCCTGAACC
Done.