Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011425.1 Kokia drynarioides strain JFW-HI SEQ_126409, 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: 20431
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:1678 original size:4 final size:4
Alignment explanation
Indices: 1648--1710 Score: 81
Period size: 4 Copynumber: 15.2 Consensus size: 4
1638 AACGGATTAC
* * *
1648 CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT CTTT CTTT CTTT CTTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT
1698 CTTT CTTT CTTT C
1 CTTT CTTT CTTT C
1711 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
4 44 0.86
5 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:1698 original size:25 final size:24
Alignment explanation
Indices: 1648--1711 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
1638 AACGGATTAC
*
1648 CTTTCTTTCCTCTCCTTCTTCCTTT
1 CTTTCTTT-CTTTCCTTCTTCCTTT
* *
1673 CTTTCTTTCTTTCTTTCTTTCTTTT
1 CTTTCTTTCTTTCCTTC-TTCCTTT
1698 CTTTCTTTCTTTCC
1 CTTTCTTTCTTTCC
1712 CGTTTATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
CTTTCTTTCTTTCCTTCTTCCTTT
Found at i:5836 original size:11 final size:12
Alignment explanation
Indices: 5821--5849 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5811 ATACTACAAG
5821 ATTTTTTTTTAT
1 ATTTTTTTTTAT
5833 -TTTTTTTTTAT
1 ATTTTTTTTTAT
5844 ATTTTT
1 ATTTTT
5850 ACATAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
ATTTTTTTTTAT
Found at i:9944 original size:195 final size:192
Alignment explanation
Indices: 9610--10239 Score: 692
Period size: 195 Copynumber: 3.2 Consensus size: 192
9600 ATAATTTATT
* *
9610 TCAATTTCGCATTAGTTTTTGTTATTTTTCTTTAGATTTCTATGATTGTTTATGTTATTTGATTG
1 TCAATTTCGCATTAGTTTTTGGT-TTTTTCTTTAGATTT-TATGATAGTTTATGTTATTTGATTG
*** * *
9675 AATGGGTTTTTGTTTACCATTGAATTATGCTTATTTTAGATCTTTAACTTGGTGGGATTACAAGA
64 AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTAAGATCTTTAACTTGGTGAGATTACAAGA
* * * *
9740 AACTTGTGATGGGTAATCTTAATATGTTGAAGCTTGCAAAGAGACTGAAATGAATGGTTTTTTGT
129 AAATTGTGATGGGTACTCTTAATATGTTGAGGCTTGCAAAGAGA-TGAAATTAATGG-TTTTTGT
9805 G
192 G
*
9806 TCAATTTTGCATTAGTTTTTGGTTTTTTCTTTAGATTTCTATGATAGTTTATGTTATTTGATTGA
1 TCAATTTCGCATTAGTTTTTGGTTTTTTCTTTAGATTT-TATGATAGTTTATGTTATTTGATTGA
* * * * *
9871 AGGGGGTTTTGTTTTTTATTGAATTATGCCTATTTAAGATCGTTAATTTGGTGAGATTACAAGAA
65 ATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTAAGATCTTTAACTTGGTGAGATTACAAGAA
* * *
9936 ATTTGTGATTGCTACTCTTAATATGTTGAGGCTTGCAAAGAGAGTGAAATTAATGGGTTTTTGTG
130 AATTGTGATGGGTACTCTTAATATGTTGAGGCTTGCAAAGAGA-TGAAATTAAT-GGTTTTTGTG
* * * ** * *** ** *
10001 TAAATTTTGCGTTAGTTTCTGTTTTTTTTTTCTTTAGATTTTATGTTTA-ACAATACTATTCGAG
1 TCAATTTCGCATTAG-TT-T-TTGGTTTTTTCTTTAGATTTTATG-ATAGTTTATGTTATTTGA-
* * * *
10065 TT-AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATATTTAACTTAGTGAGATTGCA
61 TTGAATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTAAGATCTTTAACTTGGTGAGATTACA
* * * *
10129 AGAAAAATGTGATGGGTACTATTGATATGTT-AGGGCTTGCAAAGAGTATGAATTTAATGGTTTT
126 AGAAAATTGTGATGGGTACTCTTAATATGTTGA-GGCTTGCAAAGAG-ATGAAATTAATGGTTTT
*
10193 TGTA
189 TGTG
* * *
10197 TCGGA-TTCGCATTAGTTTTGGGGGTTTTTCTTTAGATTTTATG
1 TC-AATTTCGCATTAGTTTT-TGGTTTTTTCTTTAGATTTTATG
10240 TTTAACAAAA
Statistics
Matches: 368, Mismatches: 56, Indels: 22
0.83 0.13 0.05
Matches are distributed among these distances:
193 1 0.00
194 20 0.05
195 166 0.45
196 44 0.12
197 114 0.31
198 23 0.06
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.48
Consensus pattern (192 bp):
TCAATTTCGCATTAGTTTTTGGTTTTTTCTTTAGATTTTATGATAGTTTATGTTATTTGATTGAA
TGGGTTTTTGTTTTTTATTGAATTATGCTTATTTAAGATCTTTAACTTGGTGAGATTACAAGAAA
ATTGTGATGGGTACTCTTAATATGTTGAGGCTTGCAAAGAGATGAAATTAATGGTTTTTGTG
Found at i:10308 original size:44 final size:44
Alignment explanation
Indices: 10257--10345 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
10247 AAACGATTCA
10257 AATGGATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAG
1 AATGGATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAG
10301 AATGGATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAG
1 AATGGATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAG
10345 A
1 A
10346 TCCTTAACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.49
Consensus pattern (44 bp):
AATGGATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAG
Found at i:10537 original size:239 final size:238
Alignment explanation
Indices: 10068--10540 Score: 711
Period size: 239 Copynumber: 2.0 Consensus size: 238
10058 ATTCGAGTTA
* * * *
10068 ATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATATTTAACTTAGTGAGATTGCAAGAA
1 ATGGGTTTTTGTTATTGATTGAATTATGCTTATTTGAGATACTTAACTTAGTGAGATTACAAGAA
* *
10133 AAATGTGATGGGTACTATTGATATGTTAGGGCTTGCAAAGAGTATGAATTTAATGGTTTTTGTAT
66 AAATGTGATGGGTACTATTAATATGTTAGGGCTTGCAAAGAGTATAAATTTAATGGTTTTTGTAT
*
10198 CGGATTCGCATTAGTTTTGGGGGTTTTTCTTTAGATTTTATGTTTAACAAAACGATTCAAATGGA
131 CGGATTCGCATTAGTTTTGGGGGTTTTTCTTTAGATTTTATGTTTAACAAAACGATTCAAATGAA
10263 TGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAGAATGG
196 TGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAGAATGG
* * * *
10306 ATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAGATCCTTAACTTGGTTAGATTACAAGA
1 ATGGGTTTTTGTTATTGATTGAATTA-TGCTTATTTGAGATACTTAACTTAGTGAGATTACAAGA
* * *
10371 AAAATGTGATGGGTACTATTAATATGTTGGGGCTTGTAAAGAGTATAAAATTT-TTGGTTTTTTG
65 AAAATGTGATGGGTACTATTAATATGTTAGGGCTTGCAAAGAGTAT-AAATTTAATGG-TTTTTG
* *
10435 TATC-GAGTTCGCATTAGGTTTT-GGTGTTTTTCTTTAGATTTTATGTTTAACAAAACGATTCGA
128 TATCGGA-TTCGCATTA-GTTTTGGGGGTTTTTCTTTAGATTTTATGTTTAACAAAACGATTCAA
* *
10498 ATTAATGGGTTTTTGTTATTGGTTGAATTA-TGTTTATTTGAGA
191 ATGAATGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAGA
10541 TCCTTAACTT
Statistics
Matches: 212, Mismatches: 18, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
238 23 0.11
239 93 0.44
240 91 0.43
241 5 0.02
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (238 bp):
ATGGGTTTTTGTTATTGATTGAATTATGCTTATTTGAGATACTTAACTTAGTGAGATTACAAGAA
AAATGTGATGGGTACTATTAATATGTTAGGGCTTGCAAAGAGTATAAATTTAATGGTTTTTGTAT
CGGATTCGCATTAGTTTTGGGGGTTTTTCTTTAGATTTTATGTTTAACAAAACGATTCAAATGAA
TGGGTTTTTGTTATTGGTTGAATTATTGCTTATTTGAGAATGG
Done.