Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002204.1 Kokia drynarioides strain JFW-HI SEQ_114188, 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: 8193
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Found at i:898 original size:144 final size:142
Alignment explanation
Indices: 685--974 Score: 426
Period size: 144 Copynumber: 2.0 Consensus size: 142
675 TCATCTCCAC
* * *
685 TTCTTTGAATACCCTTTTTGTTTCTTGTTATCATATTTACATGTTGAATGGTTTTTATTGAACTA
1 TTCTTTGAATACCCTTTTTGTTTCTTGTTATCATATTTACATGCTGAATGATTTTTACTGAACTA
750 TTTACAGCCTAGTTCTAGAGATTTTTTTAATGAATGCAG-AGACTTTTCCTGGTA-TTTTATGGT
66 TTTACAGCCTAGTTCTAGAGA-TTTTTTAATGAATGCAGAAG-CTTTTCCTGGTATTTTTATGGT
813 TTACC-GAGCTTAA
129 TTACCGGAGCTTAA
*
826 TTCTTTGAATACCCTTTTTGTTT-TTGTTTTTTATCATATTTACATGCTGTATGATTTTTACTGA
1 TTCTTTGAATACCCTTTTTGTTTCTTG----TTATCATATTTACATGCTGAATGATTTTTACTGA
* * *
890 ATTTTTTACAGCCTAGTTCTAGAGATTTTTTCATGAATGCAGAAGCTTTTCCTGGTATTTTTATG
62 ACTATTTACAGCCTAGTTCTAGAGATTTTTTAATGAATGCAGAAGCTTTTCCTGGTATTTTTATG
*
955 GTTTACCGGAGCTTAG
127 GTTTACCGGAGCTTAA
971 TTCT
1 TTCT
975 CTGTATTTTC
Statistics
Matches: 134, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
140 3 0.02
141 23 0.17
143 28 0.21
144 69 0.51
145 11 0.08
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (142 bp):
TTCTTTGAATACCCTTTTTGTTTCTTGTTATCATATTTACATGCTGAATGATTTTTACTGAACTA
TTTACAGCCTAGTTCTAGAGATTTTTTAATGAATGCAGAAGCTTTTCCTGGTATTTTTATGGTTT
ACCGGAGCTTAA
Found at i:1183 original size:179 final size:175
Alignment explanation
Indices: 819--1307 Score: 603
Period size: 179 Copynumber: 2.8 Consensus size: 175
809 TGGTTTACCG
* *
819 AGCTTAATTCTTTGAATACCCTTTT-TGTTTTTGTTTTTTATCATATTTACATG-CTGTAT-GAT
1 AGCTTAATTCTTTGAATACCCTTTTCTG-TTTTG--TTTTATCATATTTACATGTC-GAATGGCT
*
881 TTTTACTGAATTTTTTACAGCCTAGTTCTAGAGATTTTTTCATGAATGCAGAAGC-TTTTCCTGG
62 TTTTACTGAA-TTTTTACAGCCTAGTTCTAGAGATTTTTTTATGAATGCAGAAGCTTTTTCCTGG
* ** * *
945 TATTTTTATGGTTTACCGGAGCTTAGTTCTCTGTATTTTCATAAAAATTAA
126 TA-TTTTATGGTTTACCCGAGCTTAAATCTATGTATTTTCACAAAAATTAA
996 AGCTTAATTCTTTGAATACCCTTTTCTGTAGTTTGTTTTATCATATTTACATGTCGAATGGCTTT
1 AGCTTAATTCTTTGAATACCCTTTTCTGT--TTTGTTTTATCATATTTACATGTCGAATGGCTTT
* *
1061 TTACTGAATTTTTACAGCCTAAGTTCTATAGATTTTTTTTATGAATGCAGAACCTTTTTCCTGGT
64 TTACTGAATTTTTACAGCCT-AGTTCTAGAGA-TTTTTTTATGAATGCAGAAGCTTTTTCCTGGT
* * *
1126 CTTGTATGGTTTACCCGAGCTTAAATCTAT-TCGTTTTCGACAAAAA-TAA
127 ATTTTATGGTTTACCCGAGCTTAAATCTATGT-ATTTTC-ACAAAAATTAA
* *
1175 AGCTTAATTCTTTGAATACCC----C--TTTT-TTTTATCATATTTACATGTTGAATGAC-TTTT
1 AGCTTAATTCTTTGAATACCCTTTTCTGTTTTGTTTTATCATATTTACATGTCGAATGGCTTTTT
* *
1232 ACTGAATTTTTAAAGCCTACTTCTAGAGA-TTTTTTATGAATGCAGAAGCTTTTTCCTGGTATTT
66 ACTGAATTTTTACAGCCTAGTTCTAGAGATTTTTTTATGAATGCAGAAGCTTTTTCCTGGTATTT
*
1296 TATTGTTTACCC
131 TATGGTTTACCC
1308 TAGTTTTAAT
Statistics
Matches: 280, Mismatches: 22, Indels: 31
0.84 0.07 0.09
Matches are distributed among these distances:
166 43 0.15
168 9 0.03
169 21 0.08
170 25 0.09
171 3 0.01
173 1 0.00
175 1 0.00
177 59 0.21
178 26 0.09
179 76 0.27
180 16 0.06
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (175 bp):
AGCTTAATTCTTTGAATACCCTTTTCTGTTTTGTTTTATCATATTTACATGTCGAATGGCTTTTT
ACTGAATTTTTACAGCCTAGTTCTAGAGATTTTTTTATGAATGCAGAAGCTTTTTCCTGGTATTT
TATGGTTTACCCGAGCTTAAATCTATGTATTTTCACAAAAATTAA
Found at i:6713 original size:201 final size:198
Alignment explanation
Indices: 6469--7108 Score: 527
Period size: 211 Copynumber: 3.1 Consensus size: 198
6459 ATGTCGGACA
** * *
6469 CAAAAAGAATGAAGCCAACAATGGAAGAAAATAGTTTTTCTTTTTAGTTCTT-A-TCATAGG-TT
1 CAAAAAGAATGAAGCCAACAATGGGGGCAGATAGTTTTTCTTTTTAGTTCTTCATTCATAGGTTT
* * * *
6531 ACTTAGGCTCGGGTTTGAGTGTCCCCAACCTCAACACGGGTATGATTAGATTTTCCCAA-GTTTT
66 ACCTAGACTCGGGTTTGAGAGT---C--CC-CAACACGAGTATGATTAGATTTTCCCAAGGTTTT
* * * *
6595 CCCATATATT-GGAGTTCTTTGGAGGTCATGTCTCGATATCCGTGTATCAGACACTAATGTCGGA
125 -CCATATATTAGG-GATCTTTGGAGGTCATGTCTCCATATCCATGTATCAAACACTAATGTCGGA
*
6659 CTGGGGTACTT
188 CAGGGGTACTT
*
6670 CAAAAAGAATGAAGCCAACAATGGGGGCAGATAGTTTTTCTTTTAAGTTCTTGGTTACATCGGCA
1 CAAAAAGAATGAAGCCAACAATGGGGGCAGATAGTTTTTCTTTTTAGTTC-----T---T---CA
**
6735 TTGTCATAGGTTTACCTAGACTCGGGTTTGAGAGTCCCCGGCACGAGTATGATTAGATTTTCCCA
55 -T-TCATAGGTTTACCTAGACTCGGGTTTGAGAGTCCCCAACACGAGTATGATTAGATTTTCCCA
*
6800 AGGTTTTCCATATATTAAGGGATCTTTGGGGGTCATGTCTCCATATCCATGTATCAAACACTAAT
118 AGGTTTTCCATATATT-AGGGATCTTTGGAGGTCATGTCTCCATATCCATGTATCAAACACTAAT
6865 GTCGGACAGGGGTACTT
182 GTCGGACAGGGGTACTT
* * * * * *
6882 CAAGAAGAATGAAGCCAACAATTGGGGCAGATGGTTTTTCATTTTAGTTCTTCGTTGCACCAGCA
1 CAAAAAGAATGAAGCCAACAATGGGGGCAGATAGTTTTTCTTTTTAGTTCTTCATT-CA-TAG--
* * * * * * * * * *
6947 TTGTTCACATGTTACGCGACTCAGGTGTGA-ATATCCCCGACATGGGTATGATTAGACTTTCTCA
62 --GTTTAC---CTA---GACTCGGGTTTGAGA-GTCCCCAACACGAGTATGATTAGATTTTCCCA
* * * * **
7011 AGTTTTTCCTTATATTAAGGGATCTTTGAAGGTCGTGTCTCCATATCCACATATCAAACACTAAT
118 AGGTTTTCCATATATT-AGGGATCTTTGGAGGTCATGTCTCCATATCCATGTATCAAACACTAAT
* *
7076 GTCAGACAGGGGGGAACTT
182 GTCGGACA--GGGGTACTT
7095 CAAAAAGAATGAAG
1 CAAAAAGAATGAAG
7109 AATCCGAGCA
Statistics
Matches: 361, Mismatches: 44, Indels: 56
0.78 0.10 0.12
Matches are distributed among these distances:
199 1 0.00
200 3 0.01
201 48 0.13
204 1 0.00
205 5 0.01
206 1 0.00
207 1 0.00
208 2 0.01
209 1 0.00
210 1 0.00
211 136 0.38
212 108 0.30
213 24 0.07
214 1 0.00
216 7 0.02
217 21 0.06
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (198 bp):
CAAAAAGAATGAAGCCAACAATGGGGGCAGATAGTTTTTCTTTTTAGTTCTTCATTCATAGGTTT
ACCTAGACTCGGGTTTGAGAGTCCCCAACACGAGTATGATTAGATTTTCCCAAGGTTTTCCATAT
ATTAGGGATCTTTGGAGGTCATGTCTCCATATCCATGTATCAAACACTAATGTCGGACAGGGGTA
CTT
Found at i:7086 original size:211 final size:211
Alignment explanation
Indices: 6564--7108 Score: 688
Period size: 211 Copynumber: 2.6 Consensus size: 211
6554 CCCAACCTCA
* *
6564 ACACGGGTATGATTAGATTTTCCCAAGTTTTCCCATATATT--GGAGTTCTTTGGAGGTCATGTC
1 ACACGGGTATGATTAGATTTTCCCAAGTTTTTCCATATATTAAGG-GATCTTTGGAGGTCATGTC
* * * *
6627 TCGATATCCGTGTATCAGACACTAATGTCGGACTGGGGTACTTCAAAAAGAATGAAGCCAACAAT
65 TCCATATCCATGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAGCCAACAAT
* * * *
6692 GGGGGCAGATAGTTTTTCTTTTAAGTTCTTGGTTACATCGGCATTGTCATAGGTTTACCTAGACT
130 GGGGGCAGATAGTTTTTCTTTTAAGTTCTTCGTTACACCAGCATTGTCACAGGTTTACC-AGACT
* * *
6757 CGGGTTTGAGAGTCCCCG
194 CAGGTGTGAGAATCCCCG
* * * *
6775 GCACGAGTATGATTAGATTTTCCCAAGGTTTTCCATATATTAAGGGATCTTTGGGGGTCATGTCT
1 ACACGGGTATGATTAGATTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGGAGGTCATGTCT
* *
6840 CCATATCCATGTATCAAACACTAATGTCGGACAGGGGTACTTCAAGAAGAATGAAGCCAACAATT
66 CCATATCCATGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAGCCAACAATG
* * *
6905 GGGGCAGATGGTTTTTCATTTT-AGTTCTTCGTTGCACCAGCATTGTTCACATG-TTACGC-GAC
131 GGGGCAGATAGTTTTTC-TTTTAAGTTCTTCGTTACACCAGCATTG-TCACAGGTTTAC-CAGAC
6967 TCAGGTGTGA-ATATCCCCG
193 TCAGGTGTGAGA-ATCCCCG
* * * * * *
6986 ACATGGGTATGATTAGACTTTCTCAAGTTTTTCCTTATATTAAGGGATCTTTGAAGGTCGTGTCT
1 ACACGGGTATGATTAGATTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGGAGGTCATGTCT
** * *
7051 CCATATCCACATATCAAACACTAATGTCAGACAGGGGGGAACTTCAAAAAGAATGAAG
66 CCATATCCATGTATCAAACACTAATGTCGGACA--GGGGTACTTCAAAAAGAATGAAG
7109 AATCCGAGCA
Statistics
Matches: 289, Mismatches: 37, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
210 1 0.00
211 139 0.48
212 116 0.40
213 33 0.11
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (211 bp):
ACACGGGTATGATTAGATTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGGAGGTCATGTCT
CCATATCCATGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAGCCAACAATG
GGGGCAGATAGTTTTTCTTTTAAGTTCTTCGTTACACCAGCATTGTCACAGGTTTACCAGACTCA
GGTGTGAGAATCCCCG
Done.