Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005515.1 Kokia drynarioides strain JFW-HI SEQ_119594, 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: 1770
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Found at i:699 original size:29 final size:29
Alignment explanation
Indices: 655--1023 Score: 289
Period size: 29 Copynumber: 12.6 Consensus size: 29
645 CCCTAAATTG
*
655 TCCAAAAATTATATTTTTACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCCAAAACT
* * **
684 TTCAAAAATTATATTTTTACCCCTGAACT
1 TCCAAAAATTACATTTTTACCCCAAAACT
* * *
713 TCCAAAAATTCCATTTTTGACCTCGAAACT
1 TCCAAAAATTACATTTTT-ACCCCAAAACT
* * * *
743 TCTAAAAATTATATTTTTATCCTC-GAACT
1 TCCAAAAATTACATTTTTA-CCCCAAAACT
* * *
772 TCCAAAACTTCCATTTTTAACCCAAAACT
1 TCCAAAAATTACATTTTTACCCCAAAACT
** * *
801 TCTGAAAATTGCATTTTTACCCTC-GAACT
1 TCCAAAAATTACATTTTTACCC-CAAAACT
* * * **
830 TCCCAAAATTCCATTTTTTATCCTGAAACT
1 TCCAAAAATTACA-TTTTTACCCCAAAACT
**
860 TCCAAAAATTACATTTTTACCCTTAAACT
1 TCCAAAAATTACATTTTTACCCCAAAACT
* * *
889 TCCGAAAATTTCATTTTGACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCCAAAACT
* ***
918 TCCAAAAATTACCA-TTTTGCCCCCGGA-T
1 TCCAAAAATTA-CATTTTTACCCCAAAACT
946 GTCCAAAAATTACATTTTTAACCCCAAAACT
1 -TCCAAAAATTACATTTTT-ACCCCAAAACT
* ** *
977 TTCAAAAATTACCCTTTTACCCCTAAA-T
1 TCCAAAAATTACATTTTTACCCCAAAACT
*
1005 GTCCAAAAATTCCATTTTT
1 -TCCAAAAATTACATTTTT
1024 GATCTCGATT
Statistics
Matches: 268, Mismatches: 60, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
28 6 0.02
29 188 0.70
30 73 0.27
31 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCCAAAACT
Found at i:755 original size:59 final size:59
Alignment explanation
Indices: 655--1025 Score: 339
Period size: 59 Copynumber: 6.3 Consensus size: 59
645 CCCTAAATTG
** *
655 TCCAAAAATTATATTTTT-ACCCCAAAACTT-TCAAAAATTATATTTTTACCCCTGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCT-AAAAATTACATTTTTACCCCTGAACT
* * * *
713 TCCAAAAATTCCATTTTTGACCTCGAAACTTCTAAAAATTATATTTTTA-TCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCT-GAACT
* * * *
772 TCCAAAACTTCCATTTTT-AACCCAAAACTTCTGAAAATTGCATTTTTA-CCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCT-GAACT
* * * ** * * *
830 TCCCAAAATTCCATTTTTTATCCTGAAACTTCCAAAAATTACATTTTTACCCTTAAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCTGAACT
* * * * * *
889 TCCGAAAATTTCA-TTTTGACCCCAAAACTTCCAAAAATTACCA-TTTTGCCCCCGGA-T
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTA-CATTTTTACCCCTGAACT
* * ** *
946 GTCCAAAAATTACATTTTTAACCCCAAAACTT-TCAAAAATTACCCTTTTACCCCT-AAAT
1 -TCCAAAAATTCCATTTTTGACCCCAAAACTTCT-AAAAATTACATTTTTACCCCTGAACT
1005 GTCCAAAAATTCCATTTTTGA
1 -TCCAAAAATTCCATTTTTGA
1026 TCTCGATTTT
Statistics
Matches: 258, Mismatches: 44, Indels: 21
0.80 0.14 0.07
Matches are distributed among these distances:
57 1 0.00
58 112 0.43
59 141 0.55
60 4 0.02
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCTGAACT
Found at i:809 original size:88 final size:88
Alignment explanation
Indices: 655--969 Score: 297
Period size: 88 Copynumber: 3.6 Consensus size: 88
645 CCCTAAATTG
* * * * * * *
655 TCCAAAAATTATATTTTTA-CCCCAAAACTTTCAAAAATTATATTTTTACCCCTGAACTTCCAAA
1 TCCAAAAATTATATTTTTATCCTC-GAACTTCCAAAAATTACATTTTTAACCCTAAACTTCCGAA
719 AATTCCATTTTTGACCTCGAAACT
65 AATTCCATTTTTGACCTCGAAACT
* * * * *
743 TCTAAAAATTATATTTTTATCCTCGAACTTCCAAAACTTCCATTTTTAACCCAAAACTTCTGAAA
1 TCCAAAAATTATATTTTTATCCTCGAACTTCCAAAAATTACATTTTTAACCCTAAACTTCCGAAA
*
808 ATTGCATTTTT-ACCCTCG-AACT
66 ATTCCATTTTTGA-CCTCGAAACT
*
830 TCCCAAAATTCCAT-TTTTTATCCT-GAAACTTCCAAAAATTACATTTTT-ACCCTTAAACTTCC
1 TCCAAAAATT--ATATTTTTATCCTCG-AACTTCCAAAAATTACATTTTTAACCC-TAAACTTCC
* * *
892 GAAAATTTCA-TTTTGACCCCAAAACT
62 GAAAATTCCATTTTTGACCTCGAAACT
* ** * *
918 TCCAAAAATTACCA-TTTTGCCCCCGGA-TGTCCAAAAATTACATTTTTAACCC
1 TCCAAAAATTA-TATTTTTATCCTCGAACT-TCCAAAAATTACATTTTTAACCC
970 CAAAACTTTC
Statistics
Matches: 186, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
86 2 0.01
87 50 0.27
88 129 0.69
89 5 0.03
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.36
Consensus pattern (88 bp):
TCCAAAAATTATATTTTTATCCTCGAACTTCCAAAAATTACATTTTTAACCCTAAACTTCCGAAA
ATTCCATTTTTGACCTCGAAACT
Found at i:1043 original size:59 final size:57
Alignment explanation
Indices: 921--1138 Score: 170
Period size: 59 Copynumber: 3.8 Consensus size: 57
911 CAAAACTTCC
* *** * * * * * * *
921 AAAAATTACCATTTTGCCCCCGGATGTCCAAAAATTACATTTTTAACCCCAAAACTTTC
1 AAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTGATCCC--GATTTTT
* * *
980 AAAAATTACCCTTTTACCCCTAAATGTCCAAAAATTCCATTTTTGATCTCGATTTTCCT
1 AAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTGATCCCGATTTT--T
* * * *
1039 AAAAAGTACCATTTTAGCCCC-GAATGTCTAAAAATTCCGTTTTTTATCCCGATTTTT
1 AAAAATTACCATTTTA-CCCCTAAATGTCTAAAAATTCCATTTTTGATCCCGATTTTT
* * * **
1096 TAAAGTTACCGTTTTA-CCCTAGGTGTCTAAAAATTCCATTTTT
1 AAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTT
1139 AACCCCAAAC
Statistics
Matches: 128, Mismatches: 27, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
55 3 0.02
56 19 0.15
57 17 0.13
59 85 0.66
60 4 0.03
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.37
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTGATCCCGATTTTT
Found at i:1210 original size:28 final size:28
Alignment explanation
Indices: 1153--1214 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1143 CCAAACTTTC
* * *
1153 CCAAAATTACTATTTTGCCCCTGAGAAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
**
1181 CCAAAATTACCATTTTACCCCCGATTAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
1209 CCAAAA
1 CCAAAA
1215 AGTCTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGAAT
Done.