Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010647.1 Kokia drynarioides strain JFW-HI SEQ_125590, 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: 1776
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.36
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:936 original size:29 final size:29
Alignment explanation
Indices: 886--1289 Score: 302
Period size: 29 Copynumber: 13.9 Consensus size: 29
876 GAGGTCCCTA
886 AACTGTCCAAAAATTCCATTTTT-CCCCAG
1 AACT-TCCAAAAATTCCATTTTTACCCCAG
915 AACTTCCAAAAATTCCATTTTTGACCCC-G
1 AACTTCCAAAAATTCCATTTTT-ACCCCAG
* *
944 AACTTCCAAAAATTCCATTATTAACCTC-G
1 AACTTCCAAAAATTCCATT-TTTACCCCAG
* * * *
973 AAACTTCCAAAAATTCCAATTATGCCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCCAG
*
1003 AACTTCCAAAACTTCCATTTTTACCCCTA-
1 AACTTCCAAAAATTCCATTTTTACCCC-AG
* * *
1032 AACTTTCAAAAATTTCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCAG
*
1062 AACTTCCAAAAACTCCATTTTTACCCTC-G
1 AACTTCCAAAAATTCCATTTTTACCC-CAG
** *
1091 AACTTCCAAAAATTCCATTTTTAAACCTG
1 AACTTCCAAAAATTCCATTTTTACCCCAG
* *
1120 AAACTTCTAAAAATTCCATTTTTATCCCA-
1 -AACTTCCAAAAATTCCATTTTTACCCCAG
* *
1149 AACTTCCAAAAATTTCATTTTAACCCTC-G
1 AACTTCCAAAAATTCCATTTTTACCC-CAG
* *
1178 AAAC-TCTC-AAAATTACC-CTTTTACCCCCG
1 -AACTTC-CAAAAATT-CCATTTTTACCCCAG
* * *
1207 AA-TATCTAAGAATTTCATTTTTAACCCC-G
1 AACT-TCCAAAAATTCCATTTTT-ACCCCAG
* *
1236 AATTTCCCAAAATTACCATTTTGT-CCCCGAG
1 AACTTCCAAAAATT-CCATTTT-TACCCC-AG
1267 AA--TCC-AAAATTACCA-TTTTACCC
1 AACTTCCAAAAATT-CCATTTTTACCC
1290 TCTGGGTATC
Statistics
Matches: 306, Mismatches: 41, Indels: 58
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.00
27 6 0.02
28 55 0.18
29 149 0.49
30 91 0.30
31 4 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCAG
Found at i:988 original size:59 final size:57
Alignment explanation
Indices: 886--1257 Score: 292
Period size: 59 Copynumber: 6.4 Consensus size: 57
876 GAGGTCCCTA
* * *
886 AACTGTCCAAAAATTCCATTTT-TCCCCAGAACTTCCAAAAATTCCATTTTTGACCCCG
1 AACT-TCCAAAAATTCCATTTTAACCCGA-AACTTCCAAAAATTCCATTTTTAACCCCG
* * **
944 AACTTCCAAAAATTCCATTATTAACCTCGAAACTTCCAAAAATTCCAATTATGCCCCCG
1 AACTTCCAAAAATTCCATT-TTAACC-CGAAACTTCCAAAAATTCCATTTTTAACCCCG
* * * * * *
1003 AACTTCCAAAACTTCCATTTTTACCCCTAAACTTTCAAAAATTTCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCA-TTTTAACCCGAAACTTCCAAAAATTCCATTTTTAACCCC-G
* * * *
1062 AACTTCCAAAAACTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTAAACCTG
1 AACTTCCAAAAATTCCA-TTTTAACC-CGAAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
1120 AAACTTCTAAAAATTCCATTTTTATCCC-AAACTTCCAAAAATTTCA-TTTTAACCCTCG
1 -AACTTCCAAAAATTCCA-TTTTAACCCGAAACTTCCAAAAATTCCATTTTTAACCC-CG
* * * * *
1178 AAAC-TCTC-AAAATTACCCTTTTACCCCCG-AA-TATCTAAGAATTTCATTTTTAACCCCG
1 -AACTTC-CAAAAATT-CCATTTTA-ACCCGAAACT-TCCAAAAATTCCATTTTTAACCCCG
* *
1236 AATTTCCCAAAATTACCATTTT
1 AACTTCCAAAAATT-CCATTTT
1258 GTCCCCGAGA
Statistics
Matches: 261, Mismatches: 36, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
57 40 0.15
58 87 0.33
59 129 0.49
60 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTAACCCGAAACTTCCAAAAATTCCATTTTTAACCCCG
Found at i:1036 original size:88 final size:86
Alignment explanation
Indices: 885--1179 Score: 335
Period size: 88 Copynumber: 3.4 Consensus size: 86
875 GGAGGTCCCT
* * *
885 AAACTGTCCAAAAATTCC-ATTTTTCCCCAGAACTTCCAAAAATTCCATTTTTGACCCC-GAACT
1 AAACT-TCCAAAAATTCCAATTTTACCCCCGAACTTCCAAAAATTCCATTTTT-ACCCCTAAACT
*
948 TCCAAAAATTCCATTATTAACCTC
64 TCCAAAAATTCCATTTTTAACC-C
* * *
972 GAAACTTCCAAAAATTCCAATTATGCCCCCGAACTTCCAAAACTTCCATTTTTACCCCTAAACTT
1 -AAACTTCCAAAAATTCCAATTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCTAAACTT
* *
1037 TCAAAAATTTCATTTTTAACCCC
65 CCAAAAATTCCATTTTTAA-CCC
* * * **
1060 AAAACTTCCAAAAACTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAAACCTGAAACT
1 -AAACTTCCAAAAATTCCAATTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCT-AAACT
* *
1125 TCTAAAAATTCCATTTTTATCCC
64 TCCAAAAATTCCATTTTTAACCC
* *
1148 AAACTTCCAAAAATTTC-ATTTTAACCCTCGAA
1 AAACTTCCAAAAATTCCAATTTT-ACCCCCGAA
1180 ACTCTCAAAA
Statistics
Matches: 178, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
86 4 0.02
87 41 0.23
88 110 0.62
89 23 0.13
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (86 bp):
AAACTTCCAAAAATTCCAATTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCTAAACTTC
CAAAAATTCCATTTTTAACCC
Done.