Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000557.1 Kokia drynarioides strain JFW-HI SEQ_111465, 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: 1927
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Found at i:273 original size:17 final size:18
Alignment explanation
Indices: 231--305 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 18
221 TTTGGACATT
* *
231 AATTTAAATTTA-AATTT
1 AATTTAAATTTATAAGTA
* * *
248 AACTCAAATTTATAA-TC
1 AATTTAAATTTATAAGTA
265 AATTTAAATTT-TAAGTA
1 AATTTAAATTTATAAGTA
* *
282 AATTTAAACTTA-AAATA
1 AATTTAAATTTATAAGTA
299 AATTTAA
1 AATTTAA
306 TTTTTTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.06
17 42 0.89
18 2 0.04
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (18 bp):
AATTTAAATTTATAAGTA
Found at i:815 original size:47 final size:47
Alignment explanation
Indices: 746--865 Score: 186
Period size: 47 Copynumber: 2.6 Consensus size: 47
736 AATTCGGTTC
*
746 ACTTCTCAGTATTTCAACAGGAAGCTAACTATTTATTGCTTCAACCT
1 ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTCAACCT
* **
793 ACTTCTCAATATCTCAACAGGAAGCTAACTATTTATTGCTTTGACCT
1 ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTCAACCT
* *
840 GCTTCTCAGTATCTCATCAGGAAGCT
1 ACTTCTCAGTATCTCAACAGGAAGCT
866 GGGGTTTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (47 bp):
ACTTCTCAGTATCTCAACAGGAAGCTAACTATTTATTGCTTCAACCT
Found at i:1052 original size:201 final size:201
Alignment explanation
Indices: 793--1541 Score: 1094
Period size: 201 Copynumber: 3.7 Consensus size: 201
783 GCTTCAACCT
* * * * *
793 ACTTCTCAATATCTCAACAGGAAGCTAACTA-TTTATTGCTTTGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
* * *
857 CAGGAAGCTGGGGTTTGAAGATTTGCTCGTATTGAGCCTCGAGTTGGTATTCTTCTCTGTATCTC
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTC
* * * *
922 ATCAGGAAGATGACCGTCTTACTTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACAAATT
131 ATCAGGAAGATGACCGCCTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATT
987 TGGTCC
196 TGGTCC
*
993 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGCCCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
* * *
1058 CAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAACCTCGAGTTGGTATTCTTCTCTGTATCTC
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTC
*
1123 ATCAGGAAGATGACCGCCTTATTTGTTTCAATCCGCTTCTCTGTATCAT-ATCAGGAAGACGAAT
131 ATCAGGAAGATGACCGCCTTACTTGTTTCAATCCGCTTCTCTGTATC-TCATCAGGAAGACGAAT
1187 TTGGTCC
195 TTGGTCC
*
1194 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTCCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
* * * * ** * * *
1259 CAGGAAACT-AGGTTCAAAGATTTGCTCGC-GT-AGGTTTGATTTGGTCTTCTTCTCAGTATCTC
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTC
* * * * * *
1321 ATCAAGAGGATGACCACCTTACTTGTTTCAATCCGCTTCTTTATATCTCATTAGGAAGACGAATT
131 ATCAGGAAGATGACCGCCTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATT
1386 TGGTCC
196 TGGTCC
*
1392 ACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
*
1457 CAGGAAGCTGGGGTTCGAAGATTTGCTTGCATTGAGCCTCGAGTTGGTTTGATCTACTTCTCAGT
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGG--T-AT-T-CTTCTCAGT
1522 ATCTCATCAGGAAGATGACC
126 ATCTCATCAGGAAGATGACC
1542 ACATCACTTG
Statistics
Matches: 490, Mismatches: 48, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
197 1 0.00
198 157 0.32
199 18 0.04
200 47 0.10
201 236 0.48
202 1 0.00
203 1 0.00
204 1 0.00
205 1 0.00
206 27 0.06
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (201 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTC
ATCAGGAAGATGACCGCCTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATT
TGGTCC
Found at i:1448 original size:399 final size:405
Alignment explanation
Indices: 793--1541 Score: 1125
Period size: 399 Copynumber: 1.9 Consensus size: 405
783 GCTTCAACCT
* * *
793 ACTTCTCAATATCTCAACAGGAAGCTAACTATTTATTGCTTTGACCTGCTTCTCAGTATCTCATC
1 ACTTCTCAATATCTCAACAGGAAGCTAACCATTTATTGCTTCGACCTGCTCCTCAGTATCTCATC
* * ** * *
858 AGGAAGCTGGGGTTTGAAGATTTGCTCGTATTGAGCCTCGAGTTGGTATTCTTCTCTGTATCTCA
66 AGGAAACTGAGGTTCAAAGATTTGCTCGTAGTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTCA
* ** *
923 TCAGGAAGATGACCGTCTTACTTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACAAATTT
131 TCAAGAAGATGACCACCTTACTTGTTTCAATCCACTTCTCTATATCTCATCAAGAAGACAAATTT
* *
988 GGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGCCCTGCTTCTCAGTAT
196 GGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTAT
1053 CTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAACCTCGAGTTGG-T-AT-T-CTTCT
261 CTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAACCTCGAGTTGGTTGATCTACTTCT
*
1114 CTGTATCTCATCAGGAAGATGACCGCCTTATTTGTTTCAATCCGCTTCTCTGTATCATATCAGGA
326 CAGTATCTCATCAGGAAGATGACCGCCTTATTTGTTTCAATCCGCTTCTCTGTATCATATCAGGA
1179 AGACGAATTTGGTCC
391 AGACGAATTTGGTCC
* * *
1194 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTCCTCAGTATCTCAT
1 ACTTCTCAATATCTCAACAGGAAGCTAACCA-TTTATTGCTTCGACCTGCTCCTCAGTATCTCAT
* ** * * *
1259 CAGGAAACT-AGGTTCAAAGATTTGCTCG-CGT-AGGTTTGATTTGGTCTTCTTCTCAGTATCTC
65 CAGGAAACTGAGGTTCAAAGATTTGCTCGTAGTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTC
* * * * * *
1321 ATCAAGAGGATGACCACCTTACTTGTTTCAATCCGCTTCTTTATATCTCATTAGGAAGACGAATT
130 ATCAAGAAGATGACCACCTTACTTGTTTCAATCCACTTCTCTATATCTCATCAAGAAGACAAATT
1386 TGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTA
195 TGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTA
* * *
1451 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTGCATTGAGCCTCGAGTTGGTTTGATCTACTT
260 TCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAACCTCGAGTTGG-TTGATCTACTT
1516 CTCAGTATCTCATCAGGAAGATGACC
324 CTCAGTATCTCATCAGGAAGATGACC
1542 ACATCACTTG
Statistics
Matches: 308, Mismatches: 34, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
399 193 0.63
400 1 0.00
401 45 0.15
402 40 0.13
403 1 0.00
404 28 0.09
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (405 bp):
ACTTCTCAATATCTCAACAGGAAGCTAACCATTTATTGCTTCGACCTGCTCCTCAGTATCTCATC
AGGAAACTGAGGTTCAAAGATTTGCTCGTAGTGAGCCTCGAGTTGGTATTCTTCTCAGTATCTCA
TCAAGAAGATGACCACCTTACTTGTTTCAATCCACTTCTCTATATCTCATCAAGAAGACAAATTT
GGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTAT
CTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAACCTCGAGTTGGTTGATCTACTTCT
CAGTATCTCATCAGGAAGATGACCGCCTTATTTGTTTCAATCCGCTTCTCTGTATCATATCAGGA
AGACGAATTTGGTCC
Done.