Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011056.1 Kokia drynarioides strain JFW-HI SEQ_126027, 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: 3791
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Found at i:1055 original size:58 final size:57
Alignment explanation
Indices: 942--1346 Score: 326
Period size: 58 Copynumber: 7.0 Consensus size: 57
932 AAACTGTTCG
* * * * * *
942 AAAATTACA-TTTT-CCCTCTAACTT-CAAAAATTCCATTTTTGACCCCTAAATTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCTATTTTT-ACCTC-GAACTTCCA
* * *
998 AAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCTATTTTTA-CCTCGAACTTCCA
* * * * *
1056 AAAATTCCATTTTGACCCTCGAACTTTC-AAAATTTTAATTTTTGACCCCAAAACTTCC-
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCT-ATTTTT-ACCTC-GAACTTCCA
* * *
1114 AAAATTCCATTTTTACCCTCGATCTTCTAAAAATTCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCTATTTTT-ACCTCG-AACTTCCA
* * * * * * *
1173 AAAATTACATTTTTACCCTCAAACCTT-CAAAATTTCCAGTTTGACCTCGAAACTTTCA
1 AAAATTCCATTTTTACCCTCGAA-CTTCCAAAAATTCTATTTTTACCTCG-AACTTCCA
** * *
1231 AAAATTACCATTTTGCCCCTCG-A-TGTCCAAAAACTCTATTTTCGACCTCGAAACTT-CA
1 AAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCTATTTT-TACCTCG-AACTTCCA
*
1289 AAAATTCCATTTTTACCCTCGAA-TGTCTAAAAATTCTATCTTTTAACCTCGAACTTCC
1 AAAATTCCATTTTTACCCTCGAACT-TCCAAAAATTCTAT-TTTT-ACCTCGAACTTCC
1347 CCAAAATTAC
Statistics
Matches: 289, Mismatches: 41, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
56 9 0.03
57 25 0.09
58 153 0.53
59 99 0.34
60 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (57 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCTATTTTTACCTCGAACTTCCA
Found at i:1087 original size:87 final size:86
Alignment explanation
Indices: 942--1389 Score: 360
Period size: 87 Copynumber: 5.2 Consensus size: 86
932 AAACTGTTCG
* * * *
942 AAAATTACA-TTTT-CCCTCTAACTT-CAAAAATTCCATTTTTGACCC-CTAAATTTCCAAAAAT
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCCTC-GAACTTCCAAAAAT
1003 TCCATTTTTACCCCCAAACTTCCA
64 TCCATTTTTACCCCCAAACTT-CA
* * * * *
1027 AAAATTCTATTTTTACCCCCGAACTTCCAAAAATTCCATTTTGACCCTCGAACTTTCAAAATTTT
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTC
* * *
1092 AATTTTTGACCCCAAAACTTCC
66 CATTTTT-ACCCCCAAACTTCA
* *
1114 AAAATTCCATTTTTACCCTCGATCTTCTAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAAT
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCCTCG-AACTTCCAAAAAT
* *
1178 TACATTTTTACCCTCAAACCTTCA
64 TCCATTTTTACCCCCAAA-CTTCA
* * * * *
1202 AAATTTCCAGTTTGA-CCTCGAAACTTTCAAAAATTACCATTTTGCCCCTCG-A-TGTCCAAAAA
1 AAAATTCCATTTTTACCCTCG-AACTTCCAAAAATT-CCATTTTGACCCTCGAACT-TCCAAAAA
* * * * *
1264 CTCTATTTTCGACCTCGAAACTTCA
63 TTCCATTTT-TACCCCCAAACTTCA
* * * * *
1289 AAAATTCCATTTTTACCCTCGAA-TGTCTAAAAATTCTATCTTTTAACCTCGAACTTCCCCAAAA
1 AAAATTCCATTTTTACCCTCGAACT-TCCAAAAATTCCAT-TTTGACCCTCGAACTT-CCAAAAA
* * * *
1353 TTACCA-TCTTACCCCTAAA-GTCC
63 TT-CCATTTTTACCCCCAAACTTCA
1376 AAAATTACCATTTT
1 AAAATT-CCATTTT
1390 GCCCCCGGGT
Statistics
Matches: 287, Mismatches: 55, Indels: 39
0.75 0.14 0.10
Matches are distributed among these distances:
85 7 0.02
86 9 0.03
87 145 0.51
88 106 0.37
89 18 0.06
90 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (86 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTC
CATTTTTACCCCCAAACTTCA
Found at i:1320 original size:29 final size:28
Alignment explanation
Indices: 942--1345 Score: 293
Period size: 29 Copynumber: 14.0 Consensus size: 28
932 AAACTGTTCG
* *
942 AAAATTACA-TTTT-CCCTCTAACTTCA
1 AAAATTCCATTTTTACCCTCGAACTTCA
* *
968 AAAATTCCATTTTTGACCC-CTAAATTTCCA
1 AAAATTCCATTTTT-ACCCTC-GAACTT-CA
* *
998 AAAATTCCATTTTTACCCCCAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTT-CA
* *
1027 AAAATTCTATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTT-CA
*
1056 AAAATTCCATTTTGACCCTCGAACTTTCA
1 AAAATTCCATTTTTACCCTCGAAC-TTCA
* ** * *
1085 AAATTTTAATTTTTGACCC-CAAAACTTCC
1 AAAATTCCATTTTT-ACCCTC-GAACTTCA
*
1114 AAAATTCCATTTTTACCCTCGATCTTCTA
1 AAAATTCCATTTTTACCCTCGAACTTC-A
1143 AAAATTCCATTTTTGA-CCTCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCG-AACTT-CA
* *
1173 AAAATTACATTTTTACCCTCAAACCTTCA
1 AAAATTCCATTTTTACCCTCGAA-CTTCA
* * *
1202 AAATTTCCAGTTTGA-CCTCGAAACTTTCA
1 AAAATTCCATTTTTACCCTCG-AAC-TTCA
** ** *
1231 AAAATTACCATTTTGCCCCTCGATGTCCA
1 AAAATT-CCATTTTTACCCTCGAACTTCA
* * *
1260 AAAACTCTATTTTCGA-CCTCGAAACTTCA
1 AAAATTCCATTTT-TACCCTCG-AACTTCA
1289 AAAATTCCATTTTTACCCTCGAA-TGTCTA
1 AAAATTCCATTTTTACCCTCGAACT-TC-A
* *
1318 AAAATTCTATCTTTTAACCTCGAACTTC
1 AAAATTCCAT-TTTTACCCTCGAACTTC
1346 CCCAAAATTA
Statistics
Matches: 305, Mismatches: 46, Indels: 50
0.76 0.11 0.12
Matches are distributed among these distances:
26 8 0.03
27 5 0.02
28 31 0.10
29 180 0.59
30 74 0.24
31 7 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTCGAACTTCA
Found at i:3085 original size:340 final size:338
Alignment explanation
Indices: 2525--3279 Score: 976
Period size: 340 Copynumber: 2.2 Consensus size: 338
2515 GTACTTTGCA
* * * * * * * *
2525 ATTTTTTTTTCGTAAAATACGTCTAGCCGAGCATTATTTGGGTTTATTTACATTTGAATTTGAGT
1 ATTTTTTATTCGCAAAACACGTCTACCCAAGCATTATTTGGGTATATTTACATTTGAATTCGAGG
* * * ** **
2590 CTCAAATACGATGAAAGGTAGCCTTTATGTAAATAGATTGTGCAAAATCCTAACGGGTGCGTTCA
66 CTCAAATACGATAAAAGATAGCCTTTATGTAAATAGATTGCGCAAAATCCTAAAAGGTGCGACCA
* * * ** * * * *
2655 TACCAGCACTATTGCACCGAATCCTATCAGAACTCCGCACTTAGGTGTGCTTGGGTGAGAGTAGT
131 TACCAGCAATAATGCACCGAATCCCATCAGAACTCAACAATCAAGCGTGCTTGGGTGAGAGTAGT
* * * *
2720 ATTAGGATGGGTGACCTCTTGGGAAGTCTTCGTGTTGCACCCCTCTTTTTTTAATTATTTTATTT
196 ACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTC-CTTTTT-ATTATTTTATTT
*
2785 ATCGTAAGTTTGC-ATTTTGCGAAATAATAATGCTTATTGGGAAACATGAAAATTATTAGCGTAC
259 ATCGTAAGTTT-CAATTTTGCAAAATAATAATGCTTATTGGGAAACATGAAAATTATTAGCGTAC
2849 TTTAAATTTTTATTTT
323 TTTAAATTTTTATTTT
* * * *
2865 ATTTTATTATTTGCAAAACACGTCTTCCCAAGCTTTATTTGGGTATATTTACATTTAAATTCGAG
1 ATTTT-TTATTCGCAAAACACGTCTACCCAAGCATTATTTGGGTATATTTACATTTGAATTCGAG
* * * * *
2930 GCAT-GAATGCGATAAAAGATATCCTTTATGTCAATAGATTGCGCAAAA-CCTAAAAGGTTCGAC
65 GC-TCAAATACGATAAAAGATAGCCTTTATGTAAATAGATTGCGCAAAATCCTAAAAGGTGCGAC
*
2993 CATACCAGCAATAATGCATCGAATCCCATCAGAACTCAACAATCAAGCGTGCTTGGGTGAGAGTA
129 CATACCAGCAATAATGCACCGAATCCCATCAGAACTCAACAATCAAGCGTGCTTGGGTGAGAGTA
3058 GTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCTTTTTATTATTTTATTT
194 GTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCTTTTTATTATTTTATTT
* * *
3123 ATCGTAAGTTTCAATTTTGCAAAATAATGATGCTTATTGGGAAACATTAACATTATTAGCGTACT
259 ATCGTAAGTTTCAATTTTGCAAAATAATAATGCTTATTGGGAAACATGAAAATTATTAGCGTACT
**
3188 TTGTATTTTTATTTT
324 TTAAATTTTTATTTT
* * * *** *
3203 ATTTTTTATTCGTAAAATACGTCTACCCGAGCATTATTTAATTATATTTACATTCGAATTCGAGG
1 ATTTTTTATTCGCAAAACACGTCTACCCAAGCATTATTTGGGTATATTTACATTTGAATTCGAGG
*
3268 CGCAAATACGAT
66 CTCAAATACGAT
3280 GTGTAGATGC
Statistics
Matches: 353, Mismatches: 58, Indels: 11
0.84 0.14 0.03
Matches are distributed among these distances:
337 58 0.16
338 89 0.25
339 5 0.01
340 114 0.32
341 86 0.24
342 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (338 bp):
ATTTTTTATTCGCAAAACACGTCTACCCAAGCATTATTTGGGTATATTTACATTTGAATTCGAGG
CTCAAATACGATAAAAGATAGCCTTTATGTAAATAGATTGCGCAAAATCCTAAAAGGTGCGACCA
TACCAGCAATAATGCACCGAATCCCATCAGAACTCAACAATCAAGCGTGCTTGGGTGAGAGTAGT
ACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCTTTTTATTATTTTATTTAT
CGTAAGTTTCAATTTTGCAAAATAATAATGCTTATTGGGAAACATGAAAATTATTAGCGTACTTT
AAATTTTTATTTT
Done.