Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010884.1 Kokia drynarioides strain JFW-HI SEQ_125852, 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: 5714
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:93 original size:4 final size:4
Alignment explanation
Indices: 86--147 Score: 72
Period size: 4 Copynumber: 15.2 Consensus size: 4
76 CATTACCTTC
* * *
86 CTTT CTTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT
134 CCTTT CTTT CTTT C
1 -CTTT CTTT CTTT C
148 CCGTTTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 7 0.14
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:127 original size:29 final size:28
Alignment explanation
Indices: 81--145 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
71 AAACACATTA
*
81 CCTTCCTTTCTTTCTTCTTTCTTTCCTCT
1 CCTT-CTTCCTTTCTTCTTTCTTTCCTCT
*
110 CCTTCTTCCTTTCTTTCTTTCTTTCCTTT
1 CCTTCTTCCTTTC-TTCTTTCTTTCCTCT
*
139 CTTTCTT
1 CCTTCTT
146 TCCCGTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (28 bp):
CCTTCTTCCTTTCTTCTTTCTTTCCTCT
Found at i:135 original size:17 final size:17
Alignment explanation
Indices: 83--147 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
73 ACACATTACC
83 TTCCTTTCTTTC-TTCT
1 TTCCTTTCTTTCTTTCT
* *
99 TT-CTTTCCTCTCCTTC-
1 TTCCTTT-CTTTCTTTCT
115 TTCCTTTCTTTCTTTCT
1 TTCCTTTCTTTCTTTCT
132 TTCCTTTCTTTCTTTC
1 TTCCTTTCTTTCTTTC
148 CCGTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.10
16 15 0.36
17 23 0.55
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCCTTTCTTTCTTTCT
Found at i:4059 original size:119 final size:119
Alignment explanation
Indices: 3838--4078 Score: 452
Period size: 119 Copynumber: 2.0 Consensus size: 119
3828 TAAATATCTG
3838 TTTTTTTTTT--TTTTACAAAAATATAATTACAAATAATATATATCCGAACCAACTAAAAAATCC
1 TTTTTTTTTTACTTTTACAAAAATATAATTACAAATAATATATATCCGAACCAACTAAAAAATCC
3901 TGAAAAAAAAAATCATAATTTAATCTTTGAAGTTCACTCATTTTCTCACTTCGA
66 TGAAAAAAAAAATCATAATTTAATCTTTGAAGTTCACTCATTTTCTCACTTCGA
3955 TTTTNTTTTTTACTTTTACAAAAATATAATTACAAATAATATATATCCGAACCAACTAAAAAATC
1 TTTT-TTTTTTACTTTTACAAAAATATAATTACAAATAATATATATCCGAACCAACTAAAAAATC
4020 CTG-AAAAAAAAATCATAATTTAATCTTTGAAGTTCACTCATTTTCTCACTTCGA
65 CTGAAAAAAAAAATCATAATTTAATCTTTGAAGTTCACTCATTTTCTCACTTCGA
4074 TTTTT
1 TTTTT
4079 GGTATCTAAA
Statistics
Matches: 121, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
117 4 0.03
118 7 0.06
119 55 0.45
120 55 0.45
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (119 bp):
TTTTTTTTTTACTTTTACAAAAATATAATTACAAATAATATATATCCGAACCAACTAAAAAATCC
TGAAAAAAAAAATCATAATTTAATCTTTGAAGTTCACTCATTTTCTCACTTCGA
Found at i:5587 original size:176 final size:178
Alignment explanation
Indices: 5383--5714 Score: 447
Period size: 176 Copynumber: 1.9 Consensus size: 178
5373 TAGGGTGGGA
* *** * * *
5383 TGGGAGGGGAGGAGAGTAAAAGTTTTAGGGGGGAAGTGAGAGGGAGTGAAAGTTTTGGGGAAAAA
1 TGGGAGGGGAGGAGAGTAAAAATTTTAGGGAAAAAGTGAGAGCGAGTAAAAGTTTTGGAGAAAAA
** *
5448 T-AAAAAGTTTTGAGGGTTTTCAGG-GAAAATAAATG-AGAGGAATAAAATTTTGGAAGG-AAAA
66 TAAAAAAAATTTGAGGGTTTT-AGGAGAAAATAAATGAAG-GGAATAAAAATTTGGAAGGAAAAA
* *
5509 TATTAAAATAAAATGGAGGGAAATGAGTTTGGGGTAGATAAGGAGTAGGG
129 TATTAAAAGAAAATGGAGAGAAATGAGTTTGGGGTAGATAAGGAGTAGGG
*
5559 TGGGATGGGAGGAGAGTAAAAATTTTAGGGAAAAAGTGAGAGCGAGTAAAAGTTTTGGAGAAAAA
1 TGGGAGGGGAGGAGAGTAAAAATTTTAGGGAAAAAGTGAGAGCGAGTAAAAGTTTTGGAGAAAAA
* * * *
5624 TAAAAAAAAAATTTGAGGGTTTTTGGAGAAAATAAATGAAGGGAGTAAAAATTTGTAGGGAAAAA
66 T--AAAAAAAATTTGAGGGTTTTAGGAGAAAATAAATGAAGGGAATAAAAATTTGGAAGGAAAAA
5689 TATTAAAAGAAAATGGAGAGAAATGA
129 TATTAAAAGAAAATGGAGAGAAATGA
Statistics
Matches: 133, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
176 58 0.44
178 2 0.02
179 43 0.32
180 30 0.23
ACGTcount: A:0.44, C:0.01, G:0.33, T:0.22
Consensus pattern (178 bp):
TGGGAGGGGAGGAGAGTAAAAATTTTAGGGAAAAAGTGAGAGCGAGTAAAAGTTTTGGAGAAAAA
TAAAAAAAATTTGAGGGTTTTAGGAGAAAATAAATGAAGGGAATAAAAATTTGGAAGGAAAAATA
TTAAAAGAAAATGGAGAGAAATGAGTTTGGGGTAGATAAGGAGTAGGG
Done.