Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013418.1 Kokia drynarioides strain JFW-HI SEQ_128443, 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: 1801
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Found at i:226 original size:17 final size:17
Alignment explanation
Indices: 206--245 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
196 AAATTAAATT
206 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
223 TAAATCTAAATTTAAAA
1 TAAATTTAAATTTAAAA
240 TAAATT
1 TAAATT
246 AAAAAAAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:240 original size:7 final size:6
Alignment explanation
Indices: 186--238 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
176 CTTTCGACTT
* * *
186 TTTAAC TTTGAAA -TTAAA TTTAAA TTTAAA TTTAAA -ATAAA TCTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
233 TTTAAA
1 TTTAAA
239 ATAAATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 7 0.17
6 31 0.77
7 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:1123 original size:201 final size:200
Alignment explanation
Indices: 488--1365 Score: 952
Period size: 201 Copynumber: 4.3 Consensus size: 200
478 ATTTGGTCTT
* * * ** *
488 CTTCTCAATATCTCATCTGGAAGCTAACCATTTTATTACTTCGACCTG-TGTCTCAGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTCATCGCTTCGACCTGCT-TCTCAGTGTCTCAT
* * * **
552 CAAGATA-CTGGGGTTCAAAGA-TTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCA
64 CAGGA-AGCTGGGGTTCGAAGATTTTGCTCAT-TTGAGC-CTCGTTTG----GGTCTTCTTCTCA
* * * * *** * *
615 GTATCTCATTAGGAAGCTAACCTTTTATCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGA
122 GTGTCTCATCAGGAAGATGACC--GCGTCGCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGA
* *
680 AGATGAATTTGG-TCTG
185 AGACGAATTTGGTTC-A
* * * * * * *
696 CTTCTTAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCAACCAGC--CTC----TC-AATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTCATCGCTTCGACCTGCTTCTCAGTGTCTCATC
* * * * *
754 AAGAAGCTGGGGTTCGAAGATTTTGCTCGTTTTGAGCCTCGTTTGGGCCTTCTTCTCCGTGCCTC
65 AGGAAGCTGGGGTTCGAAGATTTTGCTC-ATTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTC
* * * * * * * * *
819 GTCAGGAAGATGATCACATAGCTGTTTGTTTCAATTCGCTCCTCTGTATCTCATTAGGAAGACAA
129 ATCAGGAAGATGACCGCGT--C-GCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGA
884 ATTTGGTTCA
191 ATTTGGTTCA
* *
894 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTTTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTCATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
959 GGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
66 GGAAGCTGGGGTTCGAAGATTTTGCTCA-TTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
* *
1024 TCAAGAAGATGACCGCGTCGCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTT
130 TCAGGAAGATGACCGCGTCGCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
1089 GGTTCA
195 GGTTCA
* * * *
1095 CTTCTTAGTATCTCATCATGAAGCTAACCTTTCATTGCTTCGACCTG-TATCTCTGTGTCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTCATCGCTTCGACCTGCT-TCTCAGTGTCTCATC
* * *
1159 AGGAAACTAGGGTTCGAAGATTTTGCTCATATCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTC
65 AGGAAGCTGGGGTTCGAAGATTTTGCTCAT-TTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTC
* * **
1224 ATCAGGAAGATGACCGCGTCGATTGTTTCAACTCGCTTCTCTGTATCTCATCAAGAAGGTGAATT
129 ATCAGGAAGATGACCGCGTCGCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATT
1289 TGGTTCA
194 TGGTTCA
* *
1296 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTCATCGCTTCGACCTGCTTCTCAATGACTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTCATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
1361 GGAAG
66 GGAAG
1366 ATGGTCACAT
Statistics
Matches: 577, Mismatches: 74, Indels: 45
0.83 0.11 0.06
Matches are distributed among these distances:
195 2 0.00
197 43 0.07
198 69 0.12
199 5 0.01
200 3 0.01
201 317 0.55
202 16 0.03
203 2 0.00
204 76 0.13
206 3 0.01
208 41 0.07
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (200 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTCATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
GGAAGCTGGGGTTCGAAGATTTTGCTCATTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCAT
CAGGAAGATGACCGCGTCGCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
GTTCA
Found at i:1231 original size:405 final size:398
Alignment explanation
Indices: 488--1365 Score: 1036
Period size: 405 Copynumber: 2.2 Consensus size: 398
478 ATTTGGTCTT
* * ** *
488 CTTCTCAATATCTCATCTGGAAGCTAACCATTTTATTACTTCGACCTG-TGTCTCAGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATCGCTTCGACCTGCT-TCTCAGTGTCTCAT
* *
552 CAAGATA-CTGGGGTTCAAAGATTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAG
64 CAGGA-AGCTGGGGTTCAAAGATTTGCTCATATCGAGCGCGCGTTTG---TGGTCTTCTTCTCAG
* * * ** *
616 TATCTCATTAGGAAGCTAACCTTTTATCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAA
125 TATCTCATCAAGAAGATAACC-TGCATCACTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAA
* * *
681 GATGAATTTGGTCTGCTTCTTAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCAACCAGCC
189 GACGAATTTGGTCTACTTCTTAGTATCTCATCAAGAAGCTAACCATTTCATTGCTTCAACCAGCC
* * * * *
746 TCTCAATCAAGAAGCTGGGGTTCGAAGATTTTGCTCGTTTTGAGCCTCGTTTGGGCCTTCTTCTC
254 TCTCAATCAAGAAACTAGGGTTCGAAGATTTTGCTCATATCGAGCCTCGTTTGGGCCTTCTTCTC
* * * * * * *
811 CGTGCCTCGTCAGGAAGATGATCACATAGCTGTTTGTTTCAATTCGCTCCTCTGTATCTCATTAG
319 AGTGCCTCATCAGGAAGATGACCACAT--C-GATTGTTTCAACTCGCTCCTCTGTATCTCATCAA
876 GAAGACAAATTTGGTTCA
381 GAAGACAAATTTGGTTCA
*
894 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTTTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
* * * *
959 GGAAGCTGGGGTTCGAAGATTTTGCTCACT-TTGAGC-CTCGTTTG-GGTCTTCTTCTCAGTGTC
66 GGAAGCTGGGGTTCAAAGA-TTTGCTCA-TATCGAGCGCGCGTTTGTGGTCTTCTTCTCAGTATC
* * * *
1021 TCATCAAGAAGATGACC-GCGTCGCTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGA
129 TCATCAAGAAGATAACCTGCATCACTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGA
* * *
1085 ATTTGGT-TCACTTCTTAGTATCTCATCATGAAGCTAACC-TTTCATTGCTTCGACCTGTATCTC
194 ATTTGGTCT-ACTTCTTAGTATCTCATCAAGAAGCTAACCATTTCATTGCTTCAACC---AGC-C
* *
1148 TGTGTCTC-ATCAGGAAACTAGGGTTCGAAGATTTTGCTCATATCGAGCCTCGTTTGGGTCTTCT
254 ----TCTCAATCAAGAAACTAGGGTTCGAAGATTTTGCTCATATCGAGCCTCGTTTGGGCCTTCT
* * * *
1212 TCTCAGTGTCTCATCAGGAAGATGACCGCGTCGATTGTTTCAACTCGCTTCTCTGTATCTCATCA
315 TCTCAGTGCCTCATCAGGAAGATGACCACATCGATTGTTTCAACTCGCTCCTCTGTATCTCATCA
***
1277 AGAAGGTGAATTTGGTTCA
380 AGAAGACAAATTTGGTTCA
* * *
1296 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTCATCGCTTCGACCTGCTTCTCAATGACTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
1361 GGAAG
66 GGAAG
1366 ATGGTCACAT
Statistics
Matches: 406, Mismatches: 53, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
398 15 0.04
399 75 0.18
401 32 0.08
402 111 0.27
403 1 0.00
404 1 0.00
405 125 0.31
406 45 0.11
407 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (398 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
GGAAGCTGGGGTTCAAAGATTTGCTCATATCGAGCGCGCGTTTGTGGTCTTCTTCTCAGTATCTC
ATCAAGAAGATAACCTGCATCACTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAAT
TTGGTCTACTTCTTAGTATCTCATCAAGAAGCTAACCATTTCATTGCTTCAACCAGCCTCTCAAT
CAAGAAACTAGGGTTCGAAGATTTTGCTCATATCGAGCCTCGTTTGGGCCTTCTTCTCAGTGCCT
CATCAGGAAGATGACCACATCGATTGTTTCAACTCGCTCCTCTGTATCTCATCAAGAAGACAAAT
TTGGTTCA
Done.