Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012252.1 Kokia drynarioides strain JFW-HI SEQ_127253, 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: 7395
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1239 original size:43 final size:42
Alignment explanation
Indices: 1144--1365 Score: 230
Period size: 43 Copynumber: 5.2 Consensus size: 42
1134 CCACTAAAGA
* * * *
1144 CCGCTAAAGAACATGGTCTTTAGCGGCTC-CTTCCTACAAACA
1 CCGCTAAAGAACATGATCTTTAGCGGCACTTTTCC-ACAAACG
* * * *
1186 CAGCTAAAGAACGTGATCTTTAACGACACTTTTCCAACAAACG
1 CCGCTAAAGAACATGATCTTTAGCGGCACTTTTCC-ACAAACG
* *
1229 CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCCACAAACG
1 CCGCTAAAGAACATGATCTTTAGCGGCACTTT-TCCACAAACG
* * *
1272 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGCCGCAAACG
1 CCGCTAAAGAACATGATCTTTAGCGGCACTTTT-CCACAAACG
* * * **
1315 CCGCTAAAGAACATGGTTTTTAGCAGTGCTTTTCACACAAACG
1 CCGCTAAAGAACATGATCTTTAGCGGCACTTTTC-CACAAACG
1358 CCGCTAAA
1 CCGCTAAA
1366 ATTAACAGAT
Statistics
Matches: 152, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
42 24 0.16
43 126 0.83
44 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
CCGCTAAAGAACATGATCTTTAGCGGCACTTTTCCACAAACG
Found at i:1304 original size:86 final size:85
Alignment explanation
Indices: 1144--1365 Score: 268
Period size: 86 Copynumber: 2.6 Consensus size: 85
1134 CCACTAAAGA
* * * * * *
1144 CCGCTAAAGAACATGGTCTTTAGCGGCTCCTTCCTACAAACACAGCTAAAGAACGTGATCTTTAA
1 CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCACAAACGCCGCTAAAGAACATGATCTTTAA
1209 CGACACTTTT-CCAACAAACG
66 CGACACTTTTGCC-ACAAACG
*
1229 CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGAACATGTTCTTTA
1 CCGCTAAAGAACATGGTCTTTAGCGGCACTTT-CCCACAAACGCCGCTAAAGAACATGATCTTTA
* * * *
1294 GCGGCGCTTTTGCCGCAAACG
65 ACGACACTTTTGCCACAAACG
* * *
1315 CCGCTAAAGAACATGGTTTTTAGCAGTGC-TTTTCACACAAACGCCGCTAAA
1 CCGCTAAAGAACATGGTCTTTAGC-G-GCACTTTCCCACAAACGCCGCTAAA
1366 ATTAACAGAT
Statistics
Matches: 119, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
85 30 0.25
86 81 0.68
87 6 0.05
88 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (85 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCACAAACGCCGCTAAAGAACATGATCTTTAA
CGACACTTTTGCCACAAACG
Found at i:5260 original size:168 final size:168
Alignment explanation
Indices: 4982--5317 Score: 548
Period size: 168 Copynumber: 2.0 Consensus size: 168
4972 AGCCCGACAA
* * *
4982 ATAGACATCTACGGGAATTAGCTTATCCATCCCCCAAACAGTACTATAAGAATCAGTACTGAACA
1 ATAGACATCCACGGGAATTAGCTTATCCACCCCCCAAACAGTACTATAAGAATCAGTACTGAAAA
* *
5047 TCCCTCCTGTAATTGTACACGCACCCATAACAATAACATATTTAGGTTCAGGCATTTGTTCATAT
66 ACCCTCCTGCAATTGTACACGCACCCATAACAATAACATATTTAGGTTCAGGCATTTGTTCATAT
* *
5112 AATCTCACTAAAGAGGGCGTCATTTTCATTGTTACTGT
131 AATCTCACTAAAGAGGACGCCATTTTCATTGTTACTGT
*
5150 ATAGACATCCACGGGAATTAGCTTATCGACCCCCCTAAA-AGTACTATAAGAATCAGTACTGAAA
1 ATAGACATCCACGGGAATTAGCTTATCCACCCCCC-AAACAGTACTATAAGAATCAGTACTGAAA
* * *
5214 AACCCTCCTGCAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATA
65 AACCCTCCTGCAATTGTACACGCACCCATAACAATAACATATTTAGGTTCAGGCATTTGTTCATA
*
5279 TAATCTCACTAAAGAGGATGCCATTTTCATTGTTACTGT
130 TAATCTCACTAAAGAGGACGCCATTTTCATTGTTACTGT
5318 TCCAACTGTT
Statistics
Matches: 155, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
168 152 0.98
169 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (168 bp):
ATAGACATCCACGGGAATTAGCTTATCCACCCCCCAAACAGTACTATAAGAATCAGTACTGAAAA
ACCCTCCTGCAATTGTACACGCACCCATAACAATAACATATTTAGGTTCAGGCATTTGTTCATAT
AATCTCACTAAAGAGGACGCCATTTTCATTGTTACTGT
Found at i:6035 original size:41 final size:41
Alignment explanation
Indices: 5998--6139 Score: 167
Period size: 41 Copynumber: 3.5 Consensus size: 41
5988 GTTAATGTCT
* *
5998 TGACCTTTAGCGGCGCTTGCGGGAAAGCGTCGCTAATGCCT
1 TGACCTTTAGCGGCGCTTGTGGGAAAGCGTCGCTAATGCCC
* * ** * * *
6039 TGACTTTTAACGGCATTTTTGGGAAAGCGTCGTTAATGACC
1 TGACCTTTAGCGGCGCTTGTGGGAAAGCGTCGCTAATGCCC
* * *
6080 TGACCTTTAGCGACGCTTGTGGAAAAGCGCCGCTAATGCCC
1 TGACCTTTAGCGGCGCTTGTGGGAAAGCGTCGCTAATGCCC
*
6121 TGACCTTTAGCAGCGCTTG
1 TGACCTTTAGCGGCGCTTG
6140 GACCTGACTT
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (41 bp):
TGACCTTTAGCGGCGCTTGTGGGAAAGCGTCGCTAATGCCC
Found at i:6177 original size:64 final size:64
Alignment explanation
Indices: 6076--6203 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 64
6066 CGTCGTTAAT
* *
6076 GACCTGACCTTTAGCGACGCTTGTGGAAAAGCGCCGCTAATGCCCTGACCTTT-AGCAGCGCTTG
1 GACCTGACCTTTAGCGACGCTTGTGGAAAAGCGCCGCTAATGACCTGA-CTTTCAGCAACGCTTG
* * * * * *
6140 GACCTGACTTTTAGTGGCGTTTTTGGTAAAGCGCCGCTAATGACCTGACTTTCAGCAACGCTTG
1 GACCTGACCTTTAGCGACGCTTGTGGAAAAGCGCCGCTAATGACCTGACTTTCAGCAACGCTTG
6204 TGGAAAAGCA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 4 0.07
64 51 0.93
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (64 bp):
GACCTGACCTTTAGCGACGCTTGTGGAAAAGCGCCGCTAATGACCTGACTTTCAGCAACGCTTG
Found at i:6221 original size:105 final size:105
Alignment explanation
Indices: 6039--6243 Score: 295
Period size: 105 Copynumber: 2.0 Consensus size: 105
6029 GCTAATGCCT
* * *
6039 TGACTTTTAACGGCATTTTTGGGAAAGCGTCGTTAATGACCTGACCTTTAGCGACGCTTGTGGAA
1 TGACTTTTAACGGCATTTTTGGGAAAGCGCCGCTAATGACCTGACCTTTAGCAACGCTTGTGGAA
* *
6104 AAGCGCCGCTAATGCCCTGACCTTTAGCAGCGCTTGGACC
66 AAGCACCGCTAATACCCTGACCTTTAGCAGCGCTTGGACC
** * *
6144 TGACTTTTAGTGGCGTTTTTGGTAAAGCGCCGCTAATGACCTGA-CTTTCAGCAACGCTTGTGGA
1 TGACTTTTAACGGCATTTTTGGGAAAGCGCCGCTAATGACCTGACCTTT-AGCAACGCTTGTGGA
* *
6208 AAAGCATCGCTAATACCCTGACCTTTAGCGGCGCTT
65 AAAGCACCGCTAATACCCTGACCTTTAGCAGCGCTT
6244 TTACCCTGAC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 4 0.05
105 84 0.95
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (105 bp):
TGACTTTTAACGGCATTTTTGGGAAAGCGCCGCTAATGACCTGACCTTTAGCAACGCTTGTGGAA
AAGCACCGCTAATACCCTGACCTTTAGCAGCGCTTGGACC
Found at i:6248 original size:24 final size:24
Alignment explanation
Indices: 6221--6285 Score: 130
Period size: 24 Copynumber: 2.7 Consensus size: 24
6211 GCATCGCTAA
6221 TACCCTGACCTTTAGCGGCGCTTT
1 TACCCTGACCTTTAGCGGCGCTTT
6245 TACCCTGACCTTTAGCGGCGCTTT
1 TACCCTGACCTTTAGCGGCGCTTT
6269 TACCCTGACCTTTAGCG
1 TACCCTGACCTTTAGCG
6286 TTTATTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.32
Consensus pattern (24 bp):
TACCCTGACCTTTAGCGGCGCTTT
Done.