Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004249.1 Kokia drynarioides strain JFW-HI SEQ_117528, 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, 751
Length: 1252
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Found at i:553 original size:193 final size:191
Alignment explanation
Indices: 197--588 Score: 445
Period size: 193 Copynumber: 2.0 Consensus size: 191
187 CAAAGACCAA
* * * *
197 AAGTTGTTTACAAAATGATAGATTATTTGTACCAAATGATGAGATTTCCCGAGAATGGAATGTTC
1 AAGTTTTTTACAAAAGGATAGACTATTTGGACCAAATGATGAGATTTCCCGAGAATGGAATGTTC
* * * *
262 GAAAAATTGTTCGAATGGATCGTCTTGAATACTTTAGCGAACCAAAGTTATAAAAAAAACTCGAA
66 GAAAAATTGCTCGAATCGATCGTCTTGAATACTTAAGCGAACCAAAGCTATAAAAAAAACTCGAA
* * * *
327 AAAGTTTGTAAAGTTCGGAAGTTTGGCCAAGAACGAAGAAAGAAATAATTCTCACATAAAT
131 AAAGTTTGTAAAGTTCGGAAGTTCGGCCAAGAACCAAGAAAGAAACAATTCCCACATAAAT
* *
388 AAGTTTTTTACAAAAGGACTA-ACTATTTGGACCAAGTGATGCGATTTCCCGAGAATGGAATG-T
1 AAGTTTTTTACAAAAGGA-TAGACTATTTGGACCAAATGATGAGATTTCCCGAGAATGGAATGTT
* * * *
451 C-ATAGAATTGCTCGAAGGAATCGATCGTCTTGAATACTCTAAG-GAACCGAAGCTAT-AAGAGA
65 CGA-AAAATTGCTC----GAATCGATCGTCTTGAATACT-TAAGCGAACCAAAGCTATAAAAAAA
* * * * **
513 ACTTGAAAAAGTTTG-ACTAGTTCGGAAGTTCGGTCAAGAACCAAGACAGAAACGTTTCCCACAT
124 ACTCGAAAAAGTTTGTA-AAGTTCGGAAGTTCGGCCAAGAACCAAGAAAGAAACAATTCCCACAT
577 AAAT
188 AAAT
*
581 AAATTTTT
1 AAGTTTTT
589 AATCCATAAA
Statistics
Matches: 168, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
189 1 0.01
190 10 0.06
191 53 0.32
192 3 0.02
193 67 0.40
194 31 0.18
195 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (191 bp):
AAGTTTTTTACAAAAGGATAGACTATTTGGACCAAATGATGAGATTTCCCGAGAATGGAATGTTC
GAAAAATTGCTCGAATCGATCGTCTTGAATACTTAAGCGAACCAAAGCTATAAAAAAAACTCGAA
AAAGTTTGTAAAGTTCGGAAGTTCGGCCAAGAACCAAGAAAGAAACAATTCCCACATAAAT
Found at i:798 original size:216 final size:211
Alignment explanation
Indices: 32--1252 Score: 1029
Period size: 216 Copynumber: 5.8 Consensus size: 211
22 CGATTTCCCG
* * * * **
32 AGAATGGAATGTCCGAAAAATTGCTCGAAGGAATCTATAATCTTGAATACTTTAAGGAACCAAAG
1 AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAG
* * * * *
97 ATATAAAAGTACTTGAAAAAGTTTG-ACAAGTTTAGAAGTTCAGCCAAGAACCAAGAGAGAA-AC
66 TTATAAAAGAACTCGAAAAAGTTTGCACAAGTTTGGAAGTTCGGCCAAGAACCAAGAGA-AATA-
* * *
160 GATTCTCACTTAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGATAGATTATTT
129 -ATTCTCACATAAATAAATTTTTAAT-CAAA-ACCAAAAGTTGTTTACAAAATAATAGATTATTT
* * * * *
225 GTACCAAATGATGAGATTTCCCG
191 GGACC-AATAATG-CATTTCTCA
* * *
248 AGAATGGAATGTTCGAAAAATTGTTC---G-AATGGATCGTCTTGAATACTTT-AGCGAACCAAA
1 AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAG-GAACCAAA
* * * * *
308 GTTATAAAAAAAACTCGAAAAAGTTTGTA-AAGTTCGGAAGTTTGGCCAAGAACGAAGAAAGAAA
65 GTTAT-AAAAGAACTCGAAAAAGTTTGCACAAGTTTGGAAGTTCGGCCAAGAACCAAG--AGAAA
* *
372 TAATTCTCACATAAATAAGTTTTT--T----A-CAAAAG--G---AC-------TA-ACTATTTG
127 TAATTCTCACATAAATAAATTTTTAATCAAAACCAAAAGTTGTTTACAAAATAATAGATTATTTG
* * *
417 GACCAAGTGATGCGATTTCCCG
192 GACCAA-TAATGC-ATTTCTCA
* * * * *
439 AGAATGGAATG-TCATAGAATTGCTCGAAGGAATCGATCGTCTTGAATACTCTAAGGAACCGAAG
1 AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAG
* * * * * * **
503 CTATAAGAGAACTTGAAAAAGTTTG-ACTAGTTCGGAAGTTCGGTCAAGAACCAAGACAGAAACG
66 TTATAAAAGAACTCGAAAAAGTTTGCACAAGTTTGGAAGTTCGGCCAAGAACCAAG--AGAAATA
* * * *
567 TTTCCCACATAAATAAATTTTTAATCCATAAAGCAAAAGTTGTTTACAAAATAACAGATTATTTG
129 ATTCTCACATAAATAAATTTTTAAT-CA-AAACCAAAAGTTGTTTACAAAATAATAGATTATTTG
*
632 GACCTAATAATGCAATTTCTTA
192 GACC-AATAATGC-ATTTCTCA
* * *
654 AGAATGGAATGTTCAAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAACCAAAG
1 AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAG
* * * * *
719 TTATAAAAGAACTCGAAAAAGTTTGCA-AAGTTTGGCAGTTCAGCCTAGAATCAAGGGTAAAGTA
66 TTATAAAAGAACTCGAAAAAGTTTGCACAAGTTTGGAAGTTCGGCCAAGAACCAAGAG-AAA-TA
** * *** * * *
783 ATTCTCATGTAAATAAGTTTTTAATTCAAAGATTGAAAGTTTTTTACAAAAGGATTAG-TTATTT
129 ATTCTCACATAAATAAATTTTTAA-TCAAA-ACCAAAAGTTGTTTACAAAA-TAATAGATTATTT
* *
847 GGACCAATGATGCGATTTCCCA
191 GGACCAATAATGC-ATTTCTCA
* * * * * *
869 AGAATGGAATGTTCGAAAAATTACGCGAAGGAATCAATCGTCTTGAATACTTTAAGGAACCGAAG
1 AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAG
* * * * * * *
934 TTATAAACGTATTCAAAAAAGTTT-AACAAGTTCT-GAAGTTCGTCCAAGAACCAAGAGAAACAA
66 TTATAAAAGAACTCGAAAAAGTTTGCACAAGTT-TGGAAGTTCGGCCAAGAACCAAGAGAAATAA
*
997 TTCTCACATAAATAAATTTTTAATCAAAGAACCAAAAGTTGTTTACAAAATGATAGATTATTTGG
130 TTCTCACATAAATAAATTTTTAATC-AA-AACCAAAAGTTGTTTACAAAATAATAGATTATTTGG
*
1062 ACCAAATGATATG-ATTTCTCG
193 ACC-AAT-A-ATGCATTTCTCA
* * *
1083 AGAATGGAATGTTCAAAAAATTGTTCGACGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAG
1 AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAG
* * *
1148 TTATAAAAGAACTTGAAAAAGTTTGCA-AAGTTTGGAAGTTTGGCCTAGAACCAAGAGTGAAATA
66 TTATAAAAGAACTCGAAAAAGTTTGCACAAGTTTGGAAGTTCGGCCAAGAACCAAGA--GAAATA
* * * *
1212 ATTATCACGTAAACAAGTTTTTAATTCAAAGACCAAAAGTT
129 ATTCTCACATAAATAAATTTTTAA-TCAAA-ACCAAAAGTT
Statistics
Matches: 804, Mismatches: 143, Indels: 116
0.76 0.13 0.11
Matches are distributed among these distances:
190 12 0.01
191 34 0.04
192 3 0.00
193 68 0.08
194 31 0.04
195 3 0.00
199 2 0.00
201 1 0.00
202 7 0.01
204 7 0.01
205 1 0.00
207 2 0.00
211 3 0.00
212 35 0.04
213 113 0.14
214 118 0.15
215 154 0.19
216 203 0.25
217 7 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (211 bp):
AGAATGGAATGTTCAAAAAATTGCTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAG
TTATAAAAGAACTCGAAAAAGTTTGCACAAGTTTGGAAGTTCGGCCAAGAACCAAGAGAAATAAT
TCTCACATAAATAAATTTTTAATCAAAACCAAAAGTTGTTTACAAAATAATAGATTATTTGGACC
AATAATGCATTTCTCA
Found at i:1196 original size:429 final size:429
Alignment explanation
Indices: 388--1243 Score: 1217
Period size: 429 Copynumber: 2.0 Consensus size: 429
378 TCACATAAAT
*
388 AAGTTTTTTACAAAAGGACTAACTATTTGGACCAAGTGATGCGATTTCCCGAGAATGGAATGTCA
1 AAGTTTTTTACAAAAGGACTAACTATTTGGACCAAGTGATGCGATTTCCCAAGAATGGAATGTCA
* * * * *
453 TAGAATTGCTCGAAGGAATCGATCGTCTTGAATACTCTAAGGAACCGAAGCTATAAGAGAACTTG
66 TAAAATTACGCGAAGGAATCAATCGTCTTGAATACTCTAAGGAACCGAAGCTATAAGAGAACTTA
* * **
518 AAAAAGTTTGACTAGTTCGGAAGTTCGGTCAAGAACCAAGACAGAAACGTTTCCCACATAAATAA
131 AAAAAGTTTAACAAGTTCGGAAGTTCGGTCAAGAACCAAGA-AGAAACAATTCCCACATAAATAA
* * *
583 ATTTTTAATCCATAAAGCAAAAGTTGTTTACAAAATAACAGATTATTTGGACCTAATAATGCAAT
195 ATTTTTAATCCAAAAACCAAAAGTTGTTTACAAAATAACAGATTATTTGGACCAAATAATG-AAT
* *
648 TTCTTAAGAATGGAATGTTCAAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAA
259 TTCTCAAGAATGGAATGTTCAAAAAATTGTTCGAAGAAATGGATCATCTTGAATACTTTAAGGAA
* * *
713 CCAAAGTTATAAAAGAACTCGAAAAAGTTTGCAAAGTTTGGCAGTTCAGCCTAGAATCAAGGGT-
324 CCAAAGTTATAAAAGAACTCGAAAAAGTTTGCAAAGTTTGGAAGTTCAGCCTAGAACCAAGAGTG
* * *
777 AAAGTAATTCTCATGTAAATAAGTTTTTAATTCAAAGATTGA
389 AAA-TAATTATCACGTAAACAAGTTTTTAATTCAAAGATTGA
* **
819 AAGTTTTTTACAAAAGGATTAGTTATTTGGACCAA-TGATGCGATTTCCCAAGAATGGAATGTTC
1 AAGTTTTTTACAAAAGGACTAACTATTTGGACCAAGTGATGCGATTTCCCAAGAATGGAATG-TC
* * *
883 GA-AAAATTACGCGAAGGAATCAATCGTCTTGAATACTTTAAGGAACCGAAGTTATAA-ACGTA-
65 -ATAAAATTACGCGAAGGAATCAATCGTCTTGAATACTCTAAGGAACCGAAGCTATAAGA-GAAC
* *
945 TTCAAAAAAGTTTAACAAGTTCTGAAGTTC-GTCCAAGAACCAAG-AGAAACAATTCTCACATAA
128 TT-AAAAAAGTTTAACAAGTTCGGAAGTTCGGT-CAAGAACCAAGAAGAAACAATTCCCACATAA
* *
1008 ATAAATTTTTAAT-CAAAGAACCAAAAGTTGTTTACAAAATGATAGATTATTTGGACCAAATGAT
191 ATAAATTTTTAATCCAAA-AACCAAAAGTTGTTTACAAAATAACAGATTATTTGGACCAAAT-A-
* * *
1072 ATG-ATTTCTCGAGAATGGAATGTTCAAAAAATTGTTCGACGAAATGGATCGTCTTGAATACTTT
253 ATGAATTTCTCAAGAATGGAATGTTCAAAAAATTGTTCGAAGAAATGGATCATCTTGAATACTTT
* **
1136 AAGGAACCAAAGTTATAAAAGAACTTGAAAAAGTTTGCAAAGTTTGGAAGTTTGGCCTAGAACCA
318 AAGGAACCAAAGTTATAAAAGAACTCGAAAAAGTTTGCAAAGTTTGGAAGTTCAGCCTAGAACCA
1201 AGAGTGAAATAATTATCACGTAAACAAGTTTTTAATTCAAAGA
383 AGAGTGAAATAATTATCACGTAAACAAGTTTTTAATTCAAAGA
1244 CCAAAAGTT
Statistics
Matches: 379, Mismatches: 37, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
428 3 0.01
429 219 0.58
430 34 0.09
431 122 0.32
432 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (429 bp):
AAGTTTTTTACAAAAGGACTAACTATTTGGACCAAGTGATGCGATTTCCCAAGAATGGAATGTCA
TAAAATTACGCGAAGGAATCAATCGTCTTGAATACTCTAAGGAACCGAAGCTATAAGAGAACTTA
AAAAAGTTTAACAAGTTCGGAAGTTCGGTCAAGAACCAAGAAGAAACAATTCCCACATAAATAAA
TTTTTAATCCAAAAACCAAAAGTTGTTTACAAAATAACAGATTATTTGGACCAAATAATGAATTT
CTCAAGAATGGAATGTTCAAAAAATTGTTCGAAGAAATGGATCATCTTGAATACTTTAAGGAACC
AAAGTTATAAAAGAACTCGAAAAAGTTTGCAAAGTTTGGAAGTTCAGCCTAGAACCAAGAGTGAA
ATAATTATCACGTAAACAAGTTTTTAATTCAAAGATTGA
Done.