Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010347.1 Kokia drynarioides strain JFW-HI SEQ_125215, 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: 32027
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:4237 original size:31 final size:31
Alignment explanation
Indices: 4202--4260 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4192 AATCATATTG
4202 ACACAATGTATAAATATTAAGGGTTAAATTA
1 ACACAATGTATAAATATTAAGGGTTAAATTA
* *
4233 ACACAATGTATAAATGTTGAGGGTTAAA
1 ACACAATGTATAAATATTAAGGGTTAAA
4261 GTTACAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (31 bp):
ACACAATGTATAAATATTAAGGGTTAAATTA
Found at i:9216 original size:49 final size:49
Alignment explanation
Indices: 9163--9545 Score: 300
Period size: 49 Copynumber: 7.8 Consensus size: 49
9153 CTTCGGCTTT
* * * *
9163 ATGGTA-TAAGATTTGTCGTTGCGGCTTCAATATTTCCTTTCATGTCTTC
1 ATGGTACT-AGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC
9212 ATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC
1 ATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC
* * *
9261 GTGGTACTAGATTCG-CTGTTGCGGCTTAAATCTTTCGCTTCGTG-CTTCC
1 ATGGTACTAGATTCGTC-GTTGCGGCTTAAATCTTTCCCTTCATGTCTT-C
* * ** * * *
9310 GA-GGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTT--TGTATTTC
1 -ATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGT-CTTC
* * *
9358 GTGGTACTAGATTCGTCATTGCGGTTTAAATCTTTTCCCTTCATG-CTTC
1 ATGGTACTAGATTCGTCGTTGCGGCTTAAATC-TTTCCCTTCATGTCTTC
* * * * ** ** *
9407 -TGAGGTACAAGGTCCGCCGTTGCGAATTAAA-CTTTTCCCTTTGTATCTTC
1 AT--GGTACTAGATTCGTCGTTGCGGCTTAAATC-TTTCCCTTCATGTCTTC
* * * *
9457 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTG
1 ATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTTC
* * * *
9507 A-GGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTT
1 ATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTT
9546 TAAACTTGTA
Statistics
Matches: 266, Mismatches: 51, Indels: 34
0.76 0.15 0.10
Matches are distributed among these distances:
47 2 0.01
48 28 0.11
49 202 0.76
50 31 0.12
51 3 0.01
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (49 bp):
ATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC
Found at i:9316 original size:98 final size:96
Alignment explanation
Indices: 9180--9546 Score: 443
Period size: 98 Copynumber: 3.8 Consensus size: 96
9170 AAGATTTGTC
* * * * * * * *
9180 GTTGCGGCTTCAATATTTCCTTTCATGTCTTC--ATGGTACTAGATTCGTCGTTGCGGCTTAAAT
1 GTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGA-GGTACAAGGTTCGCCGTTGCGACTTAAAC
9243 CTTTCCCTTCATGTCTTCGTGGTACTAGATTCGCT
64 CTTTCCCTT--TGTCTTCGTGGTACTAGATTCGCT
* * * *
9278 GTTGCGGCTTAAATCTTTCGCTTCGTGCTTCCGAGGTACAAGGTTCACCGTTGCGACTTAAACCT
1 GTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCT
*
9343 TTCCCTTTGTATTTCGTGGTACTAGATTCG-T
66 TTCCCTTTGT-CTTCGTGGTACTAGATTCGCT
* * * *
9374 CATTGCGGTTTAAATCTTTTCCCTTCATGCTTCTGAGGTACAAGGTCCGCCGTTGCGAATTAAAC
1 -GTTGCGGCTTAAATC-TTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
* *
9439 TTTTCCCTTTGTATCTTCGTGGTACTAGATTCGCC
64 CTTTCCCTTTG--TCTTCGTGGTACTAGATTCGCT
* *
9474 GTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCT
1 GTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCT
9539 TTCCCTTT
66 TTCCCTTT
9547 AAACTTGTAG
Statistics
Matches: 231, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
96 4 0.02
97 35 0.15
98 159 0.69
99 32 0.14
100 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (96 bp):
GTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCT
TTCCCTTTGTCTTCGTGGTACTAGATTCGCT
Found at i:19892 original size:57 final size:57
Alignment explanation
Indices: 19829--19938 Score: 202
Period size: 57 Copynumber: 1.9 Consensus size: 57
19819 ATAGATCTCA
19829 GAATTATTACAGCATAGTTGAGTACAAAGAAATTTGAATAAGTAAAATCAAATAATG
1 GAATTATTACAGCATAGTTGAGTACAAAGAAATTTGAATAAGTAAAATCAAATAATG
* *
19886 GAATTATTACAGCATAGTTGAGTACAAAGATATTTGAATAAGTAGAATCAAAT
1 GAATTATTACAGCATAGTTGAGTACAAAGAAATTTGAATAAGTAAAATCAAAT
19939 TGTTATTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (57 bp):
GAATTATTACAGCATAGTTGAGTACAAAGAAATTTGAATAAGTAAAATCAAATAATG
Found at i:24773 original size:34 final size:34
Alignment explanation
Indices: 24730--24796 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
24720 TGTGAAGTTA
24730 CTAATAATAACAACT-ATTTCTCATGGTAGATAGT
1 CTAATAATAACAACTAATTT-TCATGGTAGATAGT
24764 CTAATAATAACAACTAATTTTCATGGTAGATAG
1 CTAATAATAACAACTAATTTTCATGGTAGATAG
24797 ACTTCCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (34 bp):
CTAATAATAACAACTAATTTTCATGGTAGATAGT
Done.