Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011683.1 Kokia drynarioides strain JFW-HI SEQ_126676, 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: 3324
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Found at i:924 original size:29 final size:29
Alignment explanation
Indices: 871--1196 Score: 308
Period size: 29 Copynumber: 11.0 Consensus size: 29
861 GTCCCGAAAT
*
871 TTCCAAAAATCA-CATTTTTAACCCCGAACC
1 TTCCAAAAATTACCA-TTTT-ACCCCGAACC
*
901 TTTCAAAAATTACCATTTTACCCCCGAA-C
1 TTCCAAAAATTACCATTTTA-CCCCGAACC
* *
930 TTCCAAAAAATCCCATTTTTGACCCCGAACC
1 TTCCAAAAATTACCA-TTTT-ACCCCGAACC
*
961 TTCCAAAAATTACTATTTTACCCCGAA-C
1 TTCCAAAAATTACCATTTTACCCCGAACC
* * *
989 TTCCAAAAAATCCCATTTTTGACCTCGAACC
1 TTCCAAAAATTACCA-TTTT-ACCCCGAACC
*
1020 TTCCAAAATTTACCATTTTACCCCTGAA-C
1 TTCCAAAAATTACCATTTTACCCC-GAACC
1049 TTCCAAAAATTACCATTTTACCCCCGAA-C
1 TTCCAAAAATTACCATTTTA-CCCCGAACC
* * *
1078 TTCCAAAAAGTCCCATTTTTTTACCCCGAGCC
1 TTCCAAAAATTACCA---TTTTACCCCGAACC
*
1110 TTCCAAAAATGACCATTTTACCCCCGAA-C
1 TTCCAAAAATTACCATTTTA-CCCCGAACC
* *
1139 TTCC-AAAAGT-CTCATTTTTACCCCAAACC
1 TTCCAAAAATTAC-CA-TTTTACCCCGAACC
*
1168 TTCAAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATTACCATTTTA-CCCCGAAC
1197 GTTTGAAATT
Statistics
Matches: 245, Mismatches: 30, Indels: 42
0.77 0.09 0.13
Matches are distributed among these distances:
27 1 0.00
28 25 0.10
29 91 0.37
30 74 0.30
31 36 0.15
32 18 0.07
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCCGAACC
Found at i:947 original size:60 final size:60
Alignment explanation
Indices: 871--1146 Score: 307
Period size: 60 Copynumber: 4.7 Consensus size: 60
861 GTCCCGAAAT
* *
871 TTCC-AAAAATCACATTTTTAACCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAAC
* *
930 TTCCAAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACTATTTTA-CCCCGAAC
1 TTCCAAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAAC
* * * *
989 TTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAATTTACCATTTTACCCCTGAAC
1 TTCCAAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAAC
* * * * * *
1049 TTCCAAAAATTACCA-TTTTACCCCCGAA-CTTCCAAAAAGTCCCATTTTTTTA-CCCCGAGCC
1 TTCCAAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCA---TTTTACCCCCGA-AC
* *
1110 TTCC-AAAAATGACCA-TTTTACCCCCGAA-CTTCCAAAA
1 TTCCAAAAAAT-CCCATTTTTAACCCCGAACCTTCCAAAA
1147 GTCTCATTTT
Statistics
Matches: 191, Mismatches: 19, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
58 13 0.07
59 70 0.37
60 72 0.38
61 36 0.19
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (60 bp):
TTCCAAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAAC
Found at i:990 original size:59 final size:59
Alignment explanation
Indices: 871--1146 Score: 307
Period size: 59 Copynumber: 4.7 Consensus size: 59
861 GTCCCGAAAT
* * *
871 TTCC-AAAAATCACATTTTTAACCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTA-CCCCGAAC
*
930 TTCCAAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACTATTTTACCCCGAAC
1 TTCCAAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCGAAC
* *
989 TTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAATTTACCATTTTACCCCTGAAC
1 TTCCAAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCC-GAAC
* * * * *
1049 TTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAAGTCCCATTTTTTTACCCCGAGCC
1 TTCCAAAAAATCCCATTTTTGA-CCCCGAACCTTCCAAAAATTACCA---TTTTACCCCGA-AC
*
1110 TTCC-AAAAATGACCA-TTTT-ACCCCCGAA-CTTCCAAAA
1 TTCCAAAAAAT-CCCATTTTTGA-CCCCGAACCTTCCAAAA
1147 GTCTCATTTT
Statistics
Matches: 194, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
58 14 0.07
59 74 0.38
60 66 0.34
61 40 0.21
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (59 bp):
TTCCAAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCGAAC
Found at i:1117 original size:61 final size:57
Alignment explanation
Indices: 871--1196 Score: 250
Period size: 59 Copynumber: 5.5 Consensus size: 57
861 GTCCCGAAAT
* * * * * *
871 TTCCAAAAATCA-CATTTTTAACCCCGAACCTTTCAAAAATTACCA-TTTTACCCCCGAAC
1 TTCCAAAAATTACCA-TTTTACCCCCGAA-C-TTCCAAAAGTCCCATTTTTA-CCCCGACC
* * * ** *
930 TTCCAAAAAATCCCATTTTTGA-CCCCGAACCTTCCAAAAATTAC-TATTTTACCCCGAAC
1 TTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAGTCCCAT-TTTTACCCCGACC
* * * * * *
989 TTCCAAAAAATCCCATTTTTGA-CCTCGAACCTTCCAAAATTTACCA-TTTTACCCCTGAAC
1 TTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAA-GTCCCATTTTTACCCC-GACC
1049 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAGTCCCATTTTTTTACCCCGAGCC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAAGTCCCA--TTTTTACCCCGA-CC
* * *
1110 TTCCAAAAATGACCATTTTACCCCCGAACTTCCAAAAGTCTCATTTTTACCCCAAACC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTACCCC-GACC
*
1168 TTCAAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATTACCATTTTACCCCCGAAC
1197 GTTTGAAATT
Statistics
Matches: 231, Mismatches: 22, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
58 49 0.21
59 88 0.38
60 51 0.22
61 43 0.19
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (57 bp):
TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATTTTTACCCCGACC
Found at i:1142 original size:119 final size:113
Alignment explanation
Indices: 871--1196 Score: 329
Period size: 119 Copynumber: 2.8 Consensus size: 113
861 GTCCCGAAAT
*
871 TTCCAAAAAT-CACATTTTTAACCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCA
1 TTCCAAAAATAC-CATTTTT-ACCCCGAACC-TTCCAAAATTACCATTTTA-CCCCGAACTTCCA
* * *
935 AAAAATCCCATTTTTGA-CCCCGAACCTTCCAAAAATTACTATTTTACCCCGAAC
62 AAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAATCACTATTTTACCCCGAAC
* *
989 TTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAATTTACCATTTTACCCCTGAACTTCCA
1 TTCC-AAAAATACCATTTTT-ACCCCGAACCTTCCAAAA-TTACCATTTTACCCC-GAACTTCCA
* * *
1054 AAAATTACCATTTTACCCCCGAACTTCCAAAAAGTCCCATTTTTTTACCCCGAGCC
62 AAAATTACCATTTTACCCCCGAACTTCCAAAAA-T--CACTATTTTACCCCGA-AC
* * *
1110 TTCCAAAAATGACCA-TTTTACCCCCGAA-CTTCCAAAAGT-CTCATTTTTACCCCAAACCTTCA
1 TTCCAAAAAT-ACCATTTTTA-CCCCGAACCTTCCAAAATTAC-CA-TTTTACCCCGAA-CTTCC
1172 AAAAATTACCATTTTACCCCCGAAC
61 AAAAATTACCATTTTACCCCCGAAC
1197 GTTTGAAATT
Statistics
Matches: 180, Mismatches: 14, Indels: 27
0.81 0.06 0.12
Matches are distributed among these distances:
117 12 0.07
118 32 0.18
119 98 0.54
120 30 0.17
121 8 0.04
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (113 bp):
TTCCAAAAATACCATTTTTACCCCGAACCTTCCAAAATTACCATTTTACCCCGAACTTCCAAAAA
TTACCATTTTACCCCCGAACTTCCAAAAATCACTATTTTACCCCGAAC
Found at i:1176 original size:90 final size:87
Alignment explanation
Indices: 871--1186 Score: 288
Period size: 90 Copynumber: 3.5 Consensus size: 87
861 GTCCCGAAAT
* * *
871 TTCCAAAAATCACATTTTTAACCCCGAACCTTTCAAAAATTACCA--TTTT-ACCCCCGAA-CTT
1 TTCCAAAAATTACA-TTTT-ACCCCGAA-C-TTCAAAAAATCCCATTTTTTGA-CCCCGAACCTT
*
932 CCAAAAAAT-CCCATTTTTGA-CCCCGAACC
61 CC-AAAAATGACCA-TTTT-ACCCCCGAA-C
*
961 TTCCAAAAATTACTATTTTACCCCGAACTTCCAAAAAATCCCA-TTTTTGACCTCGAACCTTCCA
1 TTCCAAAAATTAC-ATTTTACCCCGAACTT-CAAAAAATCCCATTTTTTGACCCCGAACCTTCCA
* * *
1025 AAATTTACCATTTTACCCCTGAAC
64 AAAATGACCATTTTACCCCCGAAC
* * *
1049 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAGTCCCATTTTTTTACCCCGAGCCTTCC
1 TTCCAAAAATTA-CATTTTA-CCCCGAACTT-CAAAAAATCCCATTTTTTGACCCCGAACCTTCC
1114 AAAAATGACCATTTTACCCCCGAAC
63 AAAAATGACCATTTTACCCCCGAAC
* * *
1139 TTCCAAAAGTCT-CATTTTTACCCCAAACCTTCAAAAAATTACCATTTT
1 TTCCAAAAAT-TACA-TTTTACCCCGAA-CTTCAAAAAA-TCCCATTTT
1187 ACCCCCGAAC
Statistics
Matches: 194, Mismatches: 18, Indels: 28
0.81 0.08 0.12
Matches are distributed among these distances:
87 2 0.01
88 31 0.16
89 70 0.36
90 89 0.46
91 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (87 bp):
TTCCAAAAATTACATTTTACCCCGAACTTCAAAAAATCCCATTTTTTGACCCCGAACCTTCCAAA
AATGACCATTTTACCCCCGAAC
Done.