Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010151.1 Kokia drynarioides strain JFW-HI SEQ_124954, 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: 7655
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.34
Warning! 274 characters in sequence are not A, C, G, or T
Found at i:999 original size:107 final size:106
Alignment explanation
Indices: 814--1247 Score: 805
Period size: 106 Copynumber: 4.1 Consensus size: 106
804 TCAAATGAAG
*
814 AATTGATGCAAAAAGATAATCAACCATGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCT
1 AATT-ATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCT
*
879 CTCCAAAACAATAAAATATCTTTTTGAAAAATCATATCAATC
65 CTCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
*
921 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAAATAGTTCAAGAAATTGAAATTCT
1 AATTATGCAAAAAGATAATCAACCACGCCAAGG-AAAAAAAAATAGTCCAAGAAATTGAAATTCT
986 CTCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
65 CTCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
1028 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
1 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
1093 TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
66 TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
1134 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
1 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
* *
1199 TCCAAAACAATAAAATATCTTATTGAAAAATCACATCAATC
66 TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
1240 AATTATGC
1 AATTATGC
1248 CTTTTGACTA
Statistics
Matches: 320, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
106 212 0.66
107 108 0.34
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (106 bp):
AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATC
Found at i:1124 original size:213 final size:212
Alignment explanation
Indices: 814--1247 Score: 805
Period size: 213 Copynumber: 2.0 Consensus size: 212
804 TCAAATGAAG
*
814 AATTGATGCAAAAAGATAATCAACCATGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCT
1 AATT-ATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCT
*
879 CTCCAAAACAATAAAATATCTTTTTGAAAAATCATATCAATCAATTATGCAAAAAGATAATCAAC
65 CTCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATCAATTATGCAAAAAGATAATCAAC
* *
944 CACGCCAAGGAAAAAAAAAATAGTTCAAGAAATTGAAATTCTCTCCAAAACAATAAAATATCTTC
130 CACGCCAAGG-AAAAAAAAATAGTCCAAGAAATTGAAATTCTCTCCAAAACAATAAAATATCTTA
*
1009 TTGAAAAATCATATCAATC
194 TTGAAAAATCACATCAATC
1028 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
1 AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
1093 TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATCAATTATGCAAAAAGATAATCAACC
66 TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATCAATTATGCAAAAAGATAATCAACC
1158 ACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTCTCCAAAACAATAAAATATCTTATT
131 ACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTCTCCAAAACAATAAAATATCTTATT
1223 GAAAAATCACATCAATC
196 GAAAAATCACATCAATC
1240 AATTATGC
1 AATTATGC
1248 CTTTTGACTA
Statistics
Matches: 215, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
212 78 0.36
213 133 0.62
214 4 0.02
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (212 bp):
AATTATGCAAAAAGATAATCAACCACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTC
TCCAAAACAATAAAATATCTTCTTGAAAAATCATATCAATCAATTATGCAAAAAGATAATCAACC
ACGCCAAGGAAAAAAAAATAGTCCAAGAAATTGAAATTCTCTCCAAAACAATAAAATATCTTATT
GAAAAATCACATCAATC
Found at i:1290 original size:76 final size:76
Alignment explanation
Indices: 1203--1354 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
1193 ATTCTCTCCA
*
1203 AAACAATAAAATATCTTATTGAAAAATCACATCAATCAATTATGCCTTTTGACTAA-TTAATTTC
1 AAACAATAAAATATCTTATTGAAAAATCACATCAATCAATTAAGCCTTTTGAC-AACTTAATTTC
*
1267 ATTGTTGGTTGT
65 ATTGTTGATTGT
*
1279 AAACAATAAAATATCTTCTTGAAAAATCACATCAATCAATTAAGCCTTTTGACAACTTAATTTCA
1 AAACAATAAAATATCTTATTGAAAAATCACATCAATCAATTAAGCCTTTTGACAACTTAATTTCA
1344 TTGTTGATTGT
66 TTGTTGATTGT
1355 TACTATAGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
75 2 0.03
76 70 0.97
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (76 bp):
AAACAATAAAATATCTTATTGAAAAATCACATCAATCAATTAAGCCTTTTGACAACTTAATTTCA
TTGTTGATTGT
Found at i:1988 original size:30 final size:32
Alignment explanation
Indices: 1938--2004 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
1928 TTTTAATGAT
1938 AAAATTATATTTTAAATTTTTTAAAAATGAAAA
1 AAAATTATATTTTAAA-TTTTTAAAAATGAAAA
* *
1971 AAAATTA-A-TTT-AATTTTTAAAAATTATAA
1 AAAATTATATTTTAAATTTTTAAAAATGAAAA
2000 AAAAT
1 AAAAT
2005 ATAAACTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 19 0.59
30 2 0.06
31 3 0.09
32 1 0.03
33 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
AAAATTATATTTTAAATTTTTAAAAATGAAAA
Found at i:4281 original size:32 final size:32
Alignment explanation
Indices: 4234--4301 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
4224 CTAGAATGCT
*
4234 TCCTAGTGCGCACGGGTAAATTTGTGATAAAC
1 TCCTAGTGCACACGGGTAAATTTGTGATAAAC
*
4266 TCCTAGTGCATACGGGTAAATTTGTGATAAAC
1 TCCTAGTGCACACGGGTAAATTTGTGATAAAC
4298 TCCT
1 TCCT
4302 TCCTTCACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (32 bp):
TCCTAGTGCACACGGGTAAATTTGTGATAAAC
Done.