Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010968.1 Kokia drynarioides strain JFW-HI SEQ_125936, 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, 739
Length: 1232
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Found at i:405 original size:215 final size:213
Alignment explanation
Indices: 49--1162 Score: 1049
Period size: 215 Copynumber: 5.2 Consensus size: 213
39 AAATTTCTGA
* * * * * *
49 AAGGAATGGTTCGTCTTGAATACCTTAAGGAACCGATGTTATAAAAGAACTCGTAAAAGTTTGTC
1 AAGGAATGGATCATCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTTTC
* * * * * *
114 AACTTCAGATGTTCGGCCTAGAACCAAGAGAGAAACT-ATTCTCACCTGAATAAGTTTTTAATTC
65 AAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAA-TAATTCTCACCTAAATAAGTTTTTAATTC
* * * * * *
178 ATAGATCAAAAGTTGTTTACATAATGGCAACTATTTAGACTAAATGATGTGATTTCTAGAGTATG
129 AAAGACCAAAAGTAGTTTACAAAATGACAACTATTTAGACT-AATGATGTGATTTCTAGAGCATG
* *
243 GAATGTTCTTTAAACAGCTTG
193 GAATGTTCTTAAAACAGCTCG
* * *
264 AAGGAATGGTTCATCTTGAATAGTTTAAGGAATCAAAGTTATAAAAAAACTCGTAAAAGTTTTTC
1 AAGGAATGGATCATCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTTTC
* *
329 AAGTTCGGAAGTTCGACCGAGAACCAAAAGAGAAATAATTCTCAGCTAAATAAGTTTTTAATTCA
65 AAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAATAATTCTCACCTAAATAAGTTTTTAATTCA
* *
394 AAGACCAAAAGTAGTTTA-AAAATGACAACTATTTAGGCCTAATGATGTGATCTTC-GGAGCATG
130 AAGACCAAAAGTAGTTTACAAAATGACAACTATTTA-GACTAATGATGTGAT-TTCTAGAGCATG
* *** **
457 GACTGTGT-GGGAAATTGCTCG
193 GAATGT-TCTTAAAACAGCTCG
* * * * * * *
478 AAAGAATGGATCATCCTGAATGCTTTAATGAACAAAAGTTATAAAAGAATTCGTTAAAGTTTGTC
1 AAGGAATGGATCATCTTGAATACTTTAAGGAAC-AAAGTTATAAAAGAACTCGTAAAAGTTTTTC
* * * * *
543 AACTTCGGAAGTTCGGCCTAGAAACAAGAGAGAAACT-ATTCTCACCTAAAAAAGTTTTTAATTC
65 AAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAA-TAATTCTCACCTAAATAAGTTTTTAATTC
* * * ** * * *
607 AAAGACCAAAAGTTGTTTGCATAATGGTTAATTATTCAGACTAAATGATGCGATTTCTAGAGCAT
129 AAAGACCAAAAGTAGTTTACAAAAT-GACAACTATTTAGACT-AATGATGTGATTTCTAGAGCAT
* * ** *
672 GCAATTTTCTTAAAATTGCTAG
192 GGAATGTTCTTAAAACAGCTCG
* * *
694 AAGGAATGGATCGTCTTGAATAATTTAGGGAATCAAAGTTAT-AAAGTAACTCGTAAAAGTTTTT
1 AAGGAATGGATCATCTTGAATACTTTAAGGAA-CAAAGTTATAAAAG-AACTCGTAAAAGTTTTT
* * * *
758 CAAGTTCGGAAGTTCGACCGAAAACCAAAAGAGAAACAATTCTCACCTAAATAAATTTTTAATTC
64 CAAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAATAATTCTCACCTAAATAAGTTTTTAATTC
* * *
823 GAAGACCAAAAGTAGTTTAAAAAATGACAACTATTTAGACCTAATGATGTGATTTTCCA-AGCAT
129 AAAGACCAAAAGTAGTTTACAAAATGACAACTATTTAGA-CTAATGATGTGA-TTTCTAGAGCAT
* * **
887 GGATTGTACAAAAAATCA-CTCG
192 GGAATGTTCTTAAAA-CAGCTCG
* * * * *
909 AAGGAATGAATAATCTTGAATACTTTAATGAACAAAAGTTATAAAAGTACTCGTAAAA--CTTT-
1 AAGGAATGGATCATCTTGAATACTTTAAGGAAC-AAAGTTATAAAAGAACTCGTAAAAGTTTTTC
* * * * * ** *
971 --G-TC--AAGTTCGGCTGAGAACGAATAGAGAAACAACTCTCACCTAAATACCTTTTTAATTGA
65 AAGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAATAATTCTCACCTAAATAAGTTTTTAATTCA
* * * *
1031 AAAACCAAAAGTAGTTTACAAAATGACAACTATTTATACCTAATGATGTGATTTCCCA-AGAATG
130 AAGACCAAAAGTAGTTTACAAAATGACAACTATTTAGA-CTAATGATGTGATTT-CTAGAGCATG
* * ** *
1095 GACTGTACAGAAAATTA-CTCG
193 GAATGTTCTTAAAA-CAGCTCG
* *
1116 AAGGAATGGATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAG
1 AAGGAATGGATCATCTTGAATACTTTAAGGAAC-AAAGTTATAAAAG
1163 TTTGTCAAGT
Statistics
Matches: 747, Mismatches: 132, Indels: 48
0.81 0.14 0.05
Matches are distributed among these distances:
206 3 0.00
207 165 0.22
209 2 0.00
210 1 0.00
213 4 0.01
214 171 0.23
215 230 0.31
216 170 0.23
217 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (213 bp):
AAGGAATGGATCATCTTGAATACTTTAAGGAACAAAGTTATAAAAGAACTCGTAAAAGTTTTTCA
AGTTCGGAAGTTCGGCCGAGAACCAAAAGAGAAATAATTCTCACCTAAATAAGTTTTTAATTCAA
AGACCAAAAGTAGTTTACAAAATGACAACTATTTAGACTAATGATGTGATTTCTAGAGCATGGAA
TGTTCTTAAAACAGCTCG
Found at i:1027 original size:207 final size:207
Alignment explanation
Indices: 787--1163 Score: 612
Period size: 207 Copynumber: 1.8 Consensus size: 207
777 GAAAACCAAA
* *
787 AGAGAAACAATTCTCACCTAAATAAATTTTTAATTCG-AAGACCAAAAGTAGTTTAAAAAATGAC
1 AGAGAAACAACTCTCACCTAAATAAATTTTTAATT-GAAAAACCAAAAGTAGTTTAAAAAATGAC
* * *
851 AACTATTTAGACCTAATGATGTGATTTTCCAAGCATGGATTGTACAAAAAATCACTCGAAGGAAT
65 AACTATTTAGACCTAATGATGTGATTTCCCAAGAATGGACTGTACAAAAAATCACTCGAAGGAAT
916 GAATAATCTTGAATACTTTAATGAACAAAAGTTATAAAAGTACTCGTAAAACTTTGTCAAGTTCG
130 GAATAATCTTGAATACTTTAATGAACAAAAGTTATAAAAGTACTCGTAAAACTTTGTCAAGTTCG
981 GCTGAGAACGAAT
195 GCTGAGAACGAAT
** *
994 AGAGAAACAACTCTCACCTAAATACCTTTTTAATTGAAAAACCAAAAGTAGTTTACAAAATGACA
1 AGAGAAACAACTCTCACCTAAATAAATTTTTAATTGAAAAACCAAAAGTAGTTTAAAAAATGACA
* * *
1059 ACTATTTATACCTAATGATGTGATTTCCCAAGAATGGACTGTACAGAAAATTACTCGAAGGAATG
66 ACTATTTAGACCTAATGATGTGATTTCCCAAGAATGGACTGTACAAAAAATCACTCGAAGGAATG
* **
1124 GATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGT
131 AATAATCTTGAATACTTTAATGAACAAAAGTTATAAAAGT
1164 TTGTCAAGTT
Statistics
Matches: 155, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
206 1 0.01
207 154 0.99
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (207 bp):
AGAGAAACAACTCTCACCTAAATAAATTTTTAATTGAAAAACCAAAAGTAGTTTAAAAAATGACA
ACTATTTAGACCTAATGATGTGATTTCCCAAGAATGGACTGTACAAAAAATCACTCGAAGGAATG
AATAATCTTGAATACTTTAATGAACAAAAGTTATAAAAGTACTCGTAAAACTTTGTCAAGTTCGG
CTGAGAACGAAT
Done.