Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011776.1 Kokia drynarioides strain JFW-HI SEQ_126771, 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: 6708
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:1480 original size:79 final size:78
Alignment explanation
Indices: 1349--1505 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 78
1339 TGAGTTTGAC
*
1349 CCAAGCTCTGACCTGACCCGATCCGACCCAGGCCAAGGATTCACGTGTTTTTATTAAATGGGATA
1 CCAAGCTCTGACCTGACCCGATCCGACCCAGGCCAAGGATTCACGTGTTTTTATTAAATGCGATA
1414 TTTATGCATTTGG
66 TTTATGCATTTGG
1427 NCCAAGCTCTGACCTGACCCGATCCGACCCAGGCCAAGGATTCACGTGTTTTTATTAAATGCGAT
1 -CCAAGCTCTGACCTGACCCGATCCGACCCAGGCCAAGGATTCACGTGTTTTTATTAAATGCGAT
1492 ATTTATGCATTTGG
65 ATTTATGCATTTGG
1506 TCCTTCCGCT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (78 bp):
CCAAGCTCTGACCTGACCCGATCCGACCCAGGCCAAGGATTCACGTGTTTTTATTAAATGCGATA
TTTATGCATTTGG
Found at i:1862 original size:29 final size:28
Alignment explanation
Indices: 1830--2105 Score: 116
Period size: 29 Copynumber: 9.5 Consensus size: 28
1820 TAAAACTTTT
1830 AAAATTCCATTTTTAACC-CAATTTTTCCA
1 AAAATTCCA-TTTTAACCTCAA-TTTTCCA
* * *
1859 AAAATTACCATTTTACCCCCTAA-CTTCCA
1 AAAATT-CCATTTTAACCTC-AATTTTCCA
* *
1888 AAAATTCCCTTTTAACCTCGATTTCTCCA
1 AAAATTCCATTTTAACCTCAATTT-TCCA
* * **
1917 AAAATTAACA-TTT-ACCCCTAAACTTCCA
1 AAAATT-CCATTTTAACCTC-AATTTTCCA
* * * *
1945 AAAATTCCATTTTTTATCCTGATTTTTCAA
1 AAAATTCCA--TTTTAACCTCAATTTTCCA
* *
1975 AAAATTACCA-TTTATCCTCGAA-CTTCCA
1 AAAATT-CCATTTTAACCTC-AATTTTCCA
* * *
2003 AAAATTTCATTTTTGACCTCGATTTTCCA
1 AAAATTCCA-TTTTAACCTCAATTTTCCA
* * * *
2032 AAACTTACCATTTTATCCACGAA-CTTCCA
1 AAAATT-CCATTTTAACCTC-AATTTTCCA
** *
2061 AAAATTCCATTTTTGGCCTCGATTTTTCCA
1 AAAATTCCA-TTTTAACCTC-AATTTTCCA
*
2091 AAAATTATCATTTTA
1 AAAATT-CCATTTTA
2106 TCCCTGGATG
Statistics
Matches: 181, Mismatches: 45, Indels: 41
0.68 0.17 0.15
Matches are distributed among these distances:
27 5 0.03
28 47 0.26
29 83 0.46
30 37 0.20
31 9 0.05
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAATTCCATTTTAACCTCAATTTTCCA
Found at i:1873 original size:58 final size:58
Alignment explanation
Indices: 1830--2110 Score: 299
Period size: 58 Copynumber: 4.8 Consensus size: 58
1820 TAAAACTTTT
*
1830 AAAATTCCATTTTTAACC-CAATTTTTCCAAAAATTACCATTTTACCCCCT-AACTTCCA
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTA--CCCTAAACTTCCA
* * *
1888 AAAATTCC-CTTTTAACCTCGATTTCTCCAAAAATTAACA-TTTACCCCTAAACTTCCA
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTA-CCCTAAACTTCCA
* * * *
1945 AAAATTCCATTTTTTATCCT-GATTTTTCAAAAAATTACCA-TTTATCCTCGAACTTCCA
1 AAAATTCCA-TTTTTAACCTCGATTTTTCCAAAAATTACCATTTTACCCT-AAACTTCCA
* * * *
2003 AAAATTTCATTTTTGACCTCGA-TTTTCCAAAACTTACCATTTTATCCAC-GAACTTCCA
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTA-CC-CTAAACTTCCA
** *
2061 AAAATTCCATTTTTGGCCTCGATTTTTCCAAAAATTATCATTTTATCCCT
1 AAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTA-CCCT
2111 GGATGTCTAA
Statistics
Matches: 191, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
56 5 0.03
57 54 0.28
58 99 0.52
59 32 0.17
60 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTACCCTAAACTTCCA
Found at i:2024 original size:116 final size:115
Alignment explanation
Indices: 1830--2109 Score: 341
Period size: 116 Copynumber: 2.4 Consensus size: 115
1820 TAAAACTTTT
** * *
1830 AAAATTCCATTTTTAACCCAATTTTTCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATTC
1 AAAATTCCATTTTTAACCTGATTTTTCCAAAAATTACCATTTTATCCCCGAACTTCCAAAAATTC
* *
1895 CCTTTTAACCTCGATTTCTCCAAAAATTAACA-TTTA-CCCCTAAACTTCCA
66 ACTTTTAACCTCGATTT-TCCAAAAATTAACATTTTATCCAC-AAACTTCCA
* * *
1945 AAAATTCCATTTTTTATCCTGATTTTTCAAAAAATTACCA-TTTATCCTCGAACTTCCAAAAATT
1 AAAATTCCA-TTTTTAACCTGATTTTTCCAAAAATTACCATTTTATCCCCGAACTTCCAAAAA-T
* * * * *
2009 TCATTTTTGACCTCGATTTTCCAAAACTTACCATTTTATCCACGAACTTCCA
64 TCACTTTTAACCTCGATTTTCCAAAAATTAACATTTTATCCACAAACTTCCA
** *
2061 AAAATTCCATTTTTGGCCTCGATTTTTCCAAAAATTATCATTTTATCCC
1 AAAATTCCATTTTTAACCT-GATTTTTCCAAAAATTACCATTTTATCCC
2110 TGGATGTCTA
Statistics
Matches: 140, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
115 48 0.34
116 82 0.59
117 10 0.07
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (115 bp):
AAAATTCCATTTTTAACCTGATTTTTCCAAAAATTACCATTTTATCCCCGAACTTCCAAAAATTC
ACTTTTAACCTCGATTTTCCAAAAATTAACATTTTATCCACAAACTTCCA
Found at i:2583 original size:97 final size:97
Alignment explanation
Indices: 2417--2605 Score: 265
Period size: 97 Copynumber: 1.9 Consensus size: 97
2407 CATGAAAACT
* *
2417 TTAAATCAAGGCAATATTTTTTTATTTCGAATATTGAAAATTTGTGCATTAACTTACTAGGCACG
1 TTAAATCAAGGCAATATTTCTTTATCTCGAATATTGAAAATTTGTGCATTAACTTACTAGGCACG
*
2482 ACTTTTCTTCAAATTG-GAATAATCGAATACCC
66 ACTTTTCTTCAAATCGAG-ATAATCGAATACCC
* * * * **
2514 TTAAATCGAGGCAATGTTTCTTTATCTCTAAT-TCTGAAAATTTGTGCCTTAACTTACTAGGTGC
1 TTAAATCAAGGCAATATTTCTTTATCTCGAATAT-TGAAAATTTGTGCATTAACTTACTAGGCAC
2578 GACTTTTCTTCAAATCGAGATAATCGAA
65 GACTTTTCTTCAAATCGAGATAATCGAA
2606 CATCCTTCTC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 1 0.01
97 79 0.98
98 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (97 bp):
TTAAATCAAGGCAATATTTCTTTATCTCGAATATTGAAAATTTGTGCATTAACTTACTAGGCACG
ACTTTTCTTCAAATCGAGATAATCGAATACCC
Done.