Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012667.1 Kokia drynarioides strain JFW-HI SEQ_127678, 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: 2112
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.21
Warning! 436 characters in sequence are not A, C, G, or T
Found at i:979 original size:39 final size:39
Alignment explanation
Indices: 936--1150 Score: 130
Period size: 39 Copynumber: 5.5 Consensus size: 39
926 GAAGATACCG
* * *
936 ATCTCTTACCCCGAGCTTGGGGCATATCATCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAAATCATCATCAACAA
* * ** *
975 ATCTCTTACCCCAAGCCTAGGGCAAAT--TGCATCCATTAG
1 ATCTCTTACCCCGAGCCTGGGGCAAATCAT-CAT-CAACAA
* * * * ** * *
1014 ATCTCTTACCTCGAGCTTGGGGTAGATCAAAACCGACAA
1 ATCTCTTACCCCGAGCCTGGGGCAAATCATCATCAACAA
* * * ** * * **
1053 ATCTCTTACCTCTAGCCGGGGGCAAATTGT-AGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAAATCATCA-TCAACAA
* *
1092 ATCTCTTACCCCGAGCCTGGGGTAGATCATCATCAACAA
1 ATCTCTTACCCCGAGCCTGGGGCAAATCATCATCAACAA
*
1131 ATCTCTTACCCCAAGCCTGG
1 ATCTCTTACCCCGAGCCTGG
1151 AGCANNNNNN
Statistics
Matches: 125, Mismatches: 45, Indels: 12
0.69 0.25 0.07
Matches are distributed among these distances:
37 1 0.01
38 4 0.03
39 118 0.94
40 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAAATCATCATCAACAA
Found at i:1076 original size:78 final size:78
Alignment explanation
Indices: 935--1147 Score: 273
Period size: 78 Copynumber: 2.7 Consensus size: 78
925 TGAAGATACC
* * * *
935 GATCTCTTACCCCGAGCTTGGGGCATATCATCATCAACCAATCTCTTACCCCAAGCCTAGGGCAA
1 GATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAACAAATCTCTTACCCCAAGCCGAGGGCAA
* *
1000 ATTGCATCCATTA
66 ATTGCAGCCATCA
* ** * * * * *
1013 GATCTCTTACCTCGAGCTTGGGGTAGATCAAAACCGACAAATCTCTTACCTCTAGCCGGGGGCAA
1 GATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAACAAATCTCTTACCCCAAGCCGAGGGCAA
* *
1078 ATTGTAGCCATCC
66 ATTGCAGCCATCA
*
1091 GATCTCTTACCCCGAGCCTGGGGTAGATCATCATCAACAAATCTCTTACCCCAAGCC
1 GATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAACAAATCTCTTACCCCAAGCC
1148 TGGAGCANNN
Statistics
Matches: 111, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 111 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (78 bp):
GATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAACAAATCTCTTACCCCAAGCCGAGGGCAA
ATTGCAGCCATCA
Found at i:1600 original size:39 final size:39
Alignment explanation
Indices: 1544--1795 Score: 269
Period size: 39 Copynumber: 6.5 Consensus size: 39
1534 NNNNNNTTTG
* *
1544 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * *
1583 ATCTCTTACCCCAAGCCTGGGGTAGATTGCAGCCAT---TCA
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGCCA
*
1622 ATCTCTTACCCCGAGCCTGAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * *
1661 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
** * * *
1700 ATCTCTTACCCCGAGCCTGGGGCAGAT-TGCAGCGGTTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-CCA
* * * *
1739 ATCTCTTACCTCGAGCCTAGGGTAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
*
1778 ATCTCTTACCCTGAGCCT
1 ATCTCTTACCCCGAGCCT
1796 NNNNNNNNNN
Statistics
Matches: 175, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
36 4 0.02
37 2 0.01
38 4 0.02
39 154 0.88
40 5 0.03
41 2 0.01
42 4 0.02
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:1754 original size:117 final size:117
Alignment explanation
Indices: 1544--1795 Score: 380
Period size: 117 Copynumber: 2.2 Consensus size: 117
1534 NNNNNNTTTG
* *
1544 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCAAGCCTGGGGTAGA
1 ATCTCTTACCCTGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCAAGCCTGGGGCAGA
1609 TTGCAGCCATTCAATCTCTTACCCCGAGCCT-GAGGCAGATCACCATCAGCCA
66 TTGCAGCCATTCAATCTCTTACCCCGAGCCTAG-GGCAGATCACCATCAGCCA
* * * * *
1661 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCATCCAATCTCTTACCCCGAGCCTGGGGCAGA
1 ATCTCTTACCCTGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCAAGCCTGGGGCAGA
** * * *
1726 TTGCAGCGGTTCAATCTCTTACCTCGAGCCTAGGGTAGATCATCATCAGCCA
66 TTGCAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCA
1778 ATCTCTTACCCTGAGCCT
1 ATCTCTTACCCTGAGCCT
1796 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
117 121 0.99
118 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (117 bp):
ATCTCTTACCCTGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCAAGCCTGGGGCAGA
TTGCAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCA
Found at i:1929 original size:78 final size:77
Alignment explanation
Indices: 1847--2102 Score: 316
Period size: 78 Copynumber: 3.3 Consensus size: 77
1837 NNNNNNNNNN
* * *
1847 CATCAACCAATCTCTTACCTCGAGCCTGGGGCAGATTGTAGTCATTCGATCTCTTACCCCAAGCT
1 CATCAGCCAATCTCTTACC-CGAGCCTGGGGCAGATTGCAGTCATTCGATCTCTTACCTCAAGCT
*
1912 TGTGGCAGATCAT
65 TGAGGCAGATCAT
* * ** * *
1925 CATCAGCAAATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCAATCTCGTACCTCAAGGC
1 CATCAGCCAATCTCTTA-CCCGAGCCTGGGGCAGATTGCAGTCATTCGATCTCTTACCTCAA-GC
* *
1990 -TAAGGCAGATCAC
64 TTGAGGCAGATCAT
* *
2003 CATCATCCAATCTCTTACCCGGAGCCTGGGGCAGATTGCAGTCATTCGATCTCTTACCTCGAGCT
1 CATCAGCCAATCTCTTACCC-GAGCCTGGGGCAGATTGCAGTCATTCGATCTCTTACCTCAAGCT
*
2068 TGAGACAGATCAT
65 TGAGGCAGATCAT
* *
2081 TATCAGCCAATCTCTCACCCGA
1 CATCAGCCAATCTCTTACCCGA
2103 TCATGGGATA
Statistics
Matches: 148, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
77 7 0.05
78 137 0.93
79 4 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (77 bp):
CATCAGCCAATCTCTTACCCGAGCCTGGGGCAGATTGCAGTCATTCGATCTCTTACCTCAAGCTT
GAGGCAGATCAT
Found at i:1976 original size:39 final size:39
Alignment explanation
Indices: 1854--2066 Score: 162
Period size: 39 Copynumber: 5.5 Consensus size: 39
1844 NNNCATCAAC
* * *
1854 CAATCTCTTACCTCGAGCCTGGGGCAGATTGTAGTCATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAATCATT
* * * * *
1893 CGATCTCTTACCCCAAGCTTGTGGCAGA-T-C-ATCATCAG
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAATCAT--T
* *
1931 CAAATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATT
1 C-AATCTCTTACCCCGAGCCTGGGGCAGATTGCAATCATT
* * * * ** ** * *
1971 CAATCTCGTACCTCAAGGCTAAGGCAGATCACCATCATC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAATCATT
* *
2010 CAATCTCTTACCCGGAGCCTGGGGCAGATTGCAGTCATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAATCATT
* *
2049 CGATCTCTTACCTCGAGC
1 CAATCTCTTACCCCGAGC
2067 TTGAGACAGA
Statistics
Matches: 126, Mismatches: 42, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
36 4 0.03
38 2 0.02
39 113 0.90
40 2 0.02
41 1 0.01
42 4 0.03
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAATCATT
Done.