Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004754.1 Kokia drynarioides strain JFW-HI SEQ_118346, 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, 842
Length: 1404
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Found at i:899 original size:29 final size:30
Alignment explanation
Indices: 852--1252 Score: 309
Period size: 29 Copynumber: 13.6 Consensus size: 30
842 ACCTCGGAGG
*
852 TCCCCGAACCTTCTAAAAATTACCATTTTA
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
*
882 TCCCCGAA-CTTCCAAAAA-TCCCATTTTTA
1 TCCCCGAACCTTCCAAAAATTACCA-TTTTA
* * *
911 ACCCCGAACCTTCTAAAAAATACCATTTTA
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
* * * *
941 -CCCCCAAACTTCC-AAAAGTCCCATTTT-
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
*
968 TGACCCCGAACCTTCTAAAAATTACCATTTTA
1 T--CCCCGAACCTTCCAAAAATTACCATTTTA
* *
1000 TCCCCGAA-CTT-CAAAAAATCCCATTTT-
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
* *
1027 TGACCCCAAACCTTCTAAAAATTACCATTTTA
1 T--CCCCGAACCTTCCAAAAATTACCATTTTA
* *
1059 CCCCTCGAA-CTTCCAAAAA-TCCCATTTT-
1 TCCC-CGAACCTTCCAAAAATTACCATTTTA
* *
1087 TGACCCCGAACCTTTCGAAAATTACCATTTTA
1 T--CCCCGAACCTTCCAAAAATTACCATTTTA
* *
1119 -CCCCTAACCTTTCAAAAATTACCATTTTA
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
* * * *
1148 CCCCCGGA-CTCCCAAAAA-TCCCATTTT-
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
* *
1175 TGACCCCGAACCTTCTAAAAATAACCATTTTA
1 T--CCCCGAACCTTCCAAAAATTACCATTTTA
*
1207 CCCCCGAA-CTTCCAAAAA-T-CCATTTT-
1 TCCCCGAACCTTCCAAAAATTACCATTTTA
*
1233 TGACTCCGAACCTTCCAAAA
1 T--CCCCGAACCTTCCAAAA
1253 CTACCTATTT
Statistics
Matches: 295, Mismatches: 48, Indels: 57
0.74 0.12 0.14
Matches are distributed among these distances:
27 8 0.03
28 43 0.15
29 111 0.38
30 85 0.29
31 47 0.16
32 1 0.00
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (30 bp):
TCCCCGAACCTTCCAAAAATTACCATTTTA
Found at i:951 original size:59 final size:59
Alignment explanation
Indices: 853--1122 Score: 434
Period size: 59 Copynumber: 4.6 Consensus size: 59
843 CCTCGGAGGT
* *
853 CCCCGAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTAA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
912 CCCCGAACCTTCTAAAAAATACCATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
971 CCCCGAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCAAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
*
1030 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCC-CGAACTTCCAAAAATCCCATTTTTGA
*
1090 CCCCGAACCTT-TCGAAAATTACCATTTTACCCC
1 CCCCGAACCTTCT-AAAAATTACCATTTTACCCC
1123 TAACCTTTCA
Statistics
Matches: 194, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
59 140 0.72
60 54 0.28
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.29
Consensus pattern (59 bp):
CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:1187 original size:59 final size:57
Alignment explanation
Indices: 1114--1270 Score: 199
Period size: 59 Copynumber: 2.7 Consensus size: 57
1104 AAAATTACCA
* *
1114 TTTT-ACCCCTAACCTTTCAAAAATTACCATTTTACCCCCGGACTCCCAAAAATCCCAT
1 TTTTGACCCCGAACC-TTCAAAAATTACCATTTTACCCCCGAACTCCCAAAAAT-CCAT
* *
1172 TTTTGACCCCGAACCTTCTAAAAATAACCATTTTACCCCCGAACTTCCAAAAATCCAT
1 TTTTGACCCCGAACCTTC-AAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCAT
* * * *
1230 TTTTGACTCCGAACCTTCCAAAACTACCTATTTTGCCCCCG
1 TTTTGACCCCGAACCTTCAAAAATTACC-ATTTTACCCCCG
1271 TGCATCCAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 7 0.08
58 39 0.45
59 41 0.47
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.29
Consensus pattern (57 bp):
TTTTGACCCCGAACCTTCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCAT
Found at i:1263 original size:58 final size:58
Alignment explanation
Indices: 1114--1270 Score: 192
Period size: 58 Copynumber: 2.7 Consensus size: 58
1104 AAAATTACCA
* * *
1114 TTTT-ACCCCTAACCTTTCAAAAATTACCATTTTACCCCCGGACTCCCAAAAATCCCAT
1 TTTTGACCCCGAACC-TTCAAAAAATACCATTTTACCCCCGAACTCCCAAAAATCCCAT
* *
1172 TTTTGACCCCGAACCTTCTAAAAATAACCATTTTACCCCCGAACTTCCAAAAAT-CCAT
1 TTTTGACCCCGAACCTTCAAAAAAT-ACCATTTTACCCCCGAACTCCCAAAAATCCCAT
* * * *
1230 TTTTGACTCCGAACCTTCCAAAACTACCTATTTTGCCCCCG
1 TTTTGACCCCGAACCTTCAAAAAATACC-ATTTTACCCCCG
1271 TGCATCCAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 3 0.03
58 49 0.56
59 35 0.40
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.29
Consensus pattern (58 bp):
TTTTGACCCCGAACCTTCAAAAAATACCATTTTACCCCCGAACTCCCAAAAATCCCAT
Found at i:1270 original size:88 final size:88
Alignment explanation
Indices: 853--1232 Score: 406
Period size: 88 Copynumber: 4.3 Consensus size: 88
843 CCTCGGAGGT
* * * *
853 CCCCGAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGA
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
918 ACCTTCTAAAAA-ATACCATTTTA
66 ACCTTCTAAAAATA-ACCATTTTA
* * * *
941 CCCCCAAA-CTTCC-AAAAGTCCCATTTTTGA-CCCCGAACCTTCTAAAAATTACCA-TTTT-AT
1 -CCCCAAACCTTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGA-
* *
1001 CCCCGAA-CTTCAAAAAAT-CCCATTTTTGA
60 CCCCGAACCTTCTAAAAATAACCA-TTTT-A
*
1030 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCC-CGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
1095 AACCTT-TCGAAAATTACCATTTTA
65 AACCTTCT-AAAAATAACCATTTTA
* * * *
1119 CCCCTAACCTTTCAAAAATTACCATTTTACCCCCGGACTCCCAAAAATCCCATTTTTGACCCCGA
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
1184 ACCTTCTAAAAATAACCATTTTA
66 ACCTTCTAAAAATAACCATTTTA
*
1207 CCCCCGAA-CTTCCAAAAA-T-CCATTTT
1 -CCCCAAACCTTCCAAAAATTACCATTTT
1233 TGACTCCGAA
Statistics
Matches: 247, Mismatches: 25, Indels: 41
0.79 0.08 0.13
Matches are distributed among these distances:
86 7 0.03
87 12 0.05
88 99 0.40
89 97 0.39
90 29 0.12
91 3 0.01
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.29
Consensus pattern (88 bp):
CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
ACCTTCTAAAAATAACCATTTTA
Done.