Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000934.1 Kokia drynarioides strain JFW-HI SEQ_112090, 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: 3388
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:125 original size:19 final size:19
Alignment explanation
Indices: 94--142 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
84 TAAAATATAA
* *
94 ATTTTAGAATTTTTATAAAT
1 ATTTTA-AATTTTAAAAAAT
114 ATTTTAAATTTTAAAAAAT
1 ATTTTAAATTTTAAAAAAT
*
133 ATTTTGAATT
1 ATTTTAAATT
143 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAAAT
Found at i:1205 original size:17 final size:16
Alignment explanation
Indices: 1130--1195 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
1120 CCCAGTAAAC
**
1130 TTAAATTTATTTTTATT
1 TTAAATTTAAATTTA-T
*
1147 TTAAATTTAAATTTGGT
1 TTAAATTTAAATTT-AT
* *
1164 TGAAATTTAAGTTTAT
1 TTAAATTTAAATTTAT
1180 TATAAATTTAAATTTA
1 T-TAAATTTAAATTTA
1196 AAGTTTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 2 0.05
17 37 0.95
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:2977 original size:29 final size:29
Alignment explanation
Indices: 2944--3095 Score: 168
Period size: 29 Copynumber: 5.2 Consensus size: 29
2934 AAACTTTTCG
2944 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCA
* *
2973 AAAA-TCCCATTTTTGA-CCCCGAACCTTCAA
1 AAAATTACCA-TTTT-ACCCCCGAA-CTTCCA
*
3003 AAAATTACCATTTTACCCTCGAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCA
* * *
3032 AAAA-TCCCATTTTTGA-CCTCGAACCTTCTA
1 AAAATTACCA-TTTT-ACCCCCGAA-CTTCCA
3062 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCA
3091 AAAAT
1 AAAAT
3096 CCTGTACTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.08
29 47 0.46
30 40 0.39
31 8 0.08
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAACTTCCA
Found at i:3036 original size:59 final size:58
Alignment explanation
Indices: 2944--3246 Score: 353
Period size: 59 Copynumber: 5.4 Consensus size: 58
2934 AAACTTTTCG
2944 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC-A
* *
3003 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC-A
* *
3062 AAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CC-----T------GTACTTTCTA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC-A
* * * *
3109 AAAATTACCTTTTTA-CCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAACCTTTCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCA
* * *
3167 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACTCCGAACCTTCC
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACCTTCA
* *
3226 AAAACTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
3247 TGCATCCAAA
Statistics
Matches: 208, Mismatches: 21, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
46 17 0.08
47 23 0.11
52 1 0.00
53 1 0.00
58 20 0.10
59 132 0.63
60 14 0.07
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCA
Found at i:3150 original size:29 final size:29
Alignment explanation
Indices: 3118--3229 Score: 77
Period size: 29 Copynumber: 3.8 Consensus size: 29
3108 AAAAATTACC
3118 TTTTTACCCCAAACTTCCAAAAATCTCAT
1 TTTTTACCCCAAACTTCCAAAAATCTCAT
* * * *
3147 TTTTGACCTCGAACCTTTCAAAAAT-TACCA-
1 TTTTTACC-CCAAACTTCCAAAAATCT--CAT
* *
3177 -TTTTACCCTCGAACTTCCAAAAATCCCAT
1 TTTTTACCC-CAAACTTCCAAAAATCTCAT
* *
3206 TTTTTGACTCCGAACCTTCCAAAA
1 TTTTT-AC-CCCAAACTTCCAAAA
3230 CTACCATTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
28 3 0.05
29 25 0.41
30 17 0.28
31 14 0.23
32 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTTTACCCCAAACTTCCAAAAATCTCAT
Found at i:3150 original size:164 final size:165
Alignment explanation
Indices: 2944--3246 Score: 488
Period size: 164 Copynumber: 1.8 Consensus size: 165
2934 AAACTTTTCG
*
2944 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCAAAAAAT
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTC-AAAAAT
*
3008 TACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGAC-CTCGAACCTTCTAAAAATTACC
65 TACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACTC-CGAACCTTC-AAAAACTACC
3071 ATTTTACCCCCGAACTTCCAAAAATCCTGTACTTTCTA
128 ATTTTACCCCCGAACTTCCAAAAATCCTGTACTTTCTA
* * *
3109 AAAATTACCTTTTTA-CCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAACCTTTCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATT
*
3173 ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACTCCGAACCTTCCAAAACTACCATT
66 ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACTCCGAACCTTCAAAAACTACCATT
*
3238 TTGCCCCCG
131 TTACCCCCG
3247 TGCATCCAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
164 93 0.73
165 34 0.27
166 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (165 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATT
ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACTCCGAACCTTCAAAAACTACCATT
TTACCCCCGAACTTCCAAAAATCCTGTACTTTCTA
Found at i:3190 original size:105 final size:106
Alignment explanation
Indices: 3002--3202 Score: 343
Period size: 105 Copynumber: 1.9 Consensus size: 106
2992 CGAACCTTCA
*
3002 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAAT
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAAT
3067 TACCATTTTACCCCCGAACTTCCAAAAATCCTGTACTTTCT
66 TACCATTTTACCCCCGAACTTCCAAAAATCCTGTACTTTCT
* *
3108 AAAAATTACCTTTTTACCC-CAAACTTCCAAAAATCTCATTTTTGACCTCGAACCTT-TCAAAAA
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT-AAAAA
*
3171 TTACCATTTTACCCTCGAACTTCCAAAAATCC
65 TTACCATTTTACCCCCGAACTTCCAAAAATCC
3203 CATTTTTTGA
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
104 1 0.01
105 71 0.79
106 18 0.20
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (106 bp):
AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAAT
TACCATTTTACCCCCGAACTTCCAAAAATCCTGTACTTTCT
Found at i:3228 original size:31 final size:30
Alignment explanation
Indices: 3131--3239 Score: 111
Period size: 30 Copynumber: 3.6 Consensus size: 30
3121 TTACCCCAAA
3131 CTTCCAAAAAT-CTCATTTTTGACCTCGAAC
1 CTTCCAAAAATAC-CATTTTTGACCTCGAAC
*
3161 CTTTCAAAAATTACCA-TTTT-ACCCTCGAA-
1 CTTCCAAAAA-TACCATTTTTGA-CCTCGAAC
*
3190 CTTCCAAAAATCCCATTTTTTGA-CTCCGAAC
1 CTTCCAAAAATACCA-TTTTTGACCT-CGAAC
*
3221 CTTCCAAAACTACCATTTT
1 CTTCCAAAAATACCATTTT
3240 GCCCCCGTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
28 4 0.06
29 12 0.18
30 32 0.48
31 17 0.26
32 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (30 bp):
CTTCCAAAAATACCATTTTTGACCTCGAAC
Done.