Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009109.1 Kokia drynarioides strain JFW-HI SEQ_123810, 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: 7283
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:453 original size:216 final size:215
Alignment explanation
Indices: 58--1261 Score: 523
Period size: 216 Copynumber: 5.6 Consensus size: 215
48 ATAGAAATAA
* * * * *
58 TTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAATCTGTTTCCAAAATGAAAAACTATTAAG
1 TTCTCACATAAATAAGTTTTTAATTAAAAGACCAAAATCTGTTTACAAAATGAAAAACTATTAAC
* * *
123 ACCAAATGATTCGATTTCTCGAGCATGGAGATCGTAAAATTGCTCGAAGGAAGGGATCGCCTTGA
66 ACCAAATGATTCGATTTCCCGAGCATGGAGATCGAAAAATTGCTCGAAGGAAGGGATCACCTTGA
* *
188 ATACTTTATTAAACTAAAGTTATTAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACTTCGGTC
131 ATACTTTATTAAACTAAAGTGATAAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACTTCGGTC
253 AAGAACATGTAAAGAATTAG
196 AAGAACATGTAAAGAATTAG
* *
273 TTCTCACATAAATAAGTTTTTAATTAAAAGA-CAAAAGT-TGTTTACAATATGAAAAACTATTGA
1 TTCTCACATAAATAAGTTTTTAATTAAAAGACCAAAA-TCTGTTTACAAAATGAAAAACTATTAA
* * * * * * **
336 CACCATATTATGT-GATTTCCCGAGCATGGAATGTTCGAAAAATTTCTTGAAGGAATGGATCATT
65 CACCAAATGAT-TCGATTTCCCGAGCATGG-A-GATCGAAAAATTGCTCGAAGGAAGGGATCACC
* * * * *
400 TTGAATGC-TT-TTAGGAACTCAAGTGATAAAATAACTTGTAAAAGTTTGACAAG-TTTGGAAGT
127 TTGAATACTTTATTA--AACTAAAGTGATAAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACT
* * * ** *
462 TCAG-CAAGAACCAAG-AGAGAAACAA
190 TCGGTCAAGAA-CATGTAAAGAATTAG
* ** * * * ***
487 TTCTTATGTAAATAACTTTTTAATTCAAAGACCAAAA---G--T------TG--TAACTATTTTG
1 TTCTCACATAAATAAGTTTTTAATTAAAAGACCAAAATCTGTTTACAAAATGAAAAACTATTAAC
* * * * * * *
539 ACCAAATGATACAATTTCCCGAGCATCGA-ATGTCCAGAAAATTGCTCAAAGGAACGGATCACCA
66 ACCAAATGATTCGATTTCCCGAGCATGGAGA--TCGA-AAAATTGCTCGAAGGAAGGGATCACCT
*** * * *** * * *
603 TGAATACTTTAAGGAAC-AGAAGTTAGAAAAGAACCAATAAGAGTTTGACAAG-TTCGAAAGTTC
128 TGAATACTTTATTAAACTA-AAGTGATAAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACTTC
* * ** *
666 -GTCCAAGAACCAAG-AGAGAAACAA
192 GGT-CAAGAA-CATGTAAAGAATTAG
* * * * *
690 TTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGT-TGTTTACAAAATGACAAACAATTTA
1 TTCTCACATAAATAAGTTTTTAATTAAAAGACCAAAA-TCTGTTTACAAAATGAAAAACTA-TTA
* * * ** * *
754 A-ACCAAATGATACGATTTCCCGAGCAAGGAATGTTCTTAAAATTGCTCGAAGGAACGGATCAGC
64 ACACCAAATGATTCGATTTCCCGAGCATGG-A-GATCGAAAAATTGCTCGAAGGAAGGGATCACC
*** * * *** * *
818 TT-AAGTACTTTAAGGAA-TCGAAGTTATAAAAGAAC-CAAAAAGAGTTTGACAAG-TTTGGAAG
127 TTGAA-TACTTTATTAAACT-AAAGTGATAAAAGAACTTGTAAA-AGTTTGACAAGTTTTGAAAC
* * * ** *
879 TTC-ATCCCAA-AACCAAG-AGAGAAACAA
189 TTCGGT--CAAGAA-CATGTAAAGAATTAG
* * * ** * *
906 TTCTCACGTAAATAAGCTTTTAATTCAAAGATGGAAAGT-TGTTTACAAAATGAAAAACTATTTA
1 TTCTCACATAAATAAGTTTTTAATTAAAAGA-CCAAAATCTGTTTACAAAATGAAAAACTATTAA
* * * * * * ** *
970 GACCAAATGAAATT--ATTTCTCGAACATGGAATGTTCGAAAAATTTCTCAAAGGAACTGATCGC
65 CACCAAATG--ATTCGATTTCCCGAGCATGG-A-GATCGAAAAATTGCTCGAAGGAAGGGATCAC
* * * * *** * *
1033 CTTGAATACTTTA-AAGAACCAAAGTTATTAAAGAACCAATAAAAATTTGACAAGTTTT-AAAGT
126 CTTGAATACTTTATTA-AACTAAAGTGATAAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACT
* * * ** *
1096 TC-ATCCAAGAACCAAG-AGAGAAACAA
190 TCGGT-CAAGAA-CATGTAAAGAATTAG
* * * * * * * * *
1122 TTCTGACGTGAATAAATTTTTAATTCAAAGACCAATAGT-TGTTTACAGAATGACAAACTATTTA
1 TTCTCACATAAATAAGTTTTTAATTAAAAGACCAA-AATCTGTTTACAAAATGAAAAACTATTAA
* * * ** * * * * * *
1186 GACTAAATTATAAGATTTCCTGAGTATGGAATGTTCAAAAAATTGTTCGAAGGAATGGATCACCT
65 CACCAAATGATTCGATTTCCCGAGCATGG-A-GATCGAAAAATTGCTCGAAGGAAGGGATCACCT
1251 TGAATACTTTA
128 TGAATACTTTA
1262 AGGAACCGAA
Statistics
Matches: 794, Mismatches: 143, Indels: 103
0.76 0.14 0.10
Matches are distributed among these distances:
201 5 0.01
202 93 0.12
203 56 0.07
204 2 0.00
206 1 0.00
208 1 0.00
210 1 0.00
212 1 0.00
214 95 0.12
215 65 0.08
216 451 0.57
217 21 0.03
218 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (215 bp):
TTCTCACATAAATAAGTTTTTAATTAAAAGACCAAAATCTGTTTACAAAATGAAAAACTATTAAC
ACCAAATGATTCGATTTCCCGAGCATGGAGATCGAAAAATTGCTCGAAGGAAGGGATCACCTTGA
ATACTTTATTAAACTAAAGTGATAAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACTTCGGTC
AAGAACATGTAAAGAATTAG
Found at i:1097 original size:432 final size:430
Alignment explanation
Indices: 1--1752 Score: 1832
Period size: 432 Copynumber: 4.1 Consensus size: 430
* * *
1 GAACCAATAAGAGTTTGAAAAGTTTGGAAGTTCGTCCAAGAACCAAGATAGAAATAATTCTCACG
1 GAACCAATAAGAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACG
* * * * *
66 TGAATAAGTTTTTAATTCAAAGACCAAAATCTGTTTCCAAAATGAAAAACTATTAAGACCAAATG
66 TAAATAAGCTTTTAATTCAAAGA-CAAAGT-TGTTTACAAAAT-AAAAACTATTTAGACCAAATG
** * * * * * * *
131 ATTCGATTTCTCGAGCATGG-A-GATCG-TAAAATTGCTCGAAGGAAGGGATCGCCTTGAATACT
128 AAACTATTTCCCGAGCATGGAATGTTCGAGAAAATTGCTCAAAGGAACGGATCGCCATGAATACT
* * * *** * *
193 TTATTA-AACTAAAGTTATTAAAGAACTTGTAAAAGTTTGACAAGTTTTGAAACTTCGGT-CAAG
193 TTA-AAGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAG-TTCGAAAGTTC-GTCCAAG
* ** * * * *
256 AA-CATGTAAAGAATTAGTTCTCACATAAATAAGTTTTTAATTAAAAGA-CAAAAGTTGTTTACA
255 AACCAAG-AAAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACA
* * * * * ** * * *
319 ATATGAAAAACTATTGACACCATATTATGTGATTTCCCGAGCATGGAATGTTCGAAAAATTTCTT
319 AAATGACAAACTATTTAGACCAAATTATAAGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTC
* * * *
384 GAAGGAATGGATCATTTTGAATGCTTTTAGGAACTC-AAGTGATAAAA
384 GAAGGAATGGATCATCTTGAATACTTTAAGGAAC-CGAAGTTATAAAA
* *** * * *
431 TAACTTGTAAAAGTTTGACAAGTTTGGAAGTTCAG--CAAGAACCAAGAGAGAAACAATTCTTAT
1 GAACCAATAAGAGTTTGACAAGTTTGGAAGTTC-GTCCAAGAACCAAGAGAGAAACAATTCTCAC
*
494 GTAAATAA-CTTTTTAATTCAAAGACCAAAAGTTG---------T---AACTATTTTGACCAAAT
65 GTAAATAAGC-TTTTAATTCAAAGA-C-AAAGTTGTTTACAAAATAAAAACTATTTAGACCAAAT
* * * * *
546 GATACAATTTCCCGAGCATCGAATG-TCCAGAAAATTGCTCAAAGGAACGGATCACCATGAATAC
127 GAAACTATTTCCCGAGCATGGAATGTTCGAGAAAATTGCTCAAAGGAACGGATCGCCATGAATAC
* * *
610 TTTAAGGAA-CAGAAGTTAGAAAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGA
192 TTTAAAGAACCA-AAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGA
*
674 ACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
256 ACCAAGAAAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* * * * * **
739 ATGACAAACAATTTAAACCAAATGATACGATTTCCCGAGCAAGGAATGTTCTTAAAATTGCTCGA
321 ATGACAAACTATTTAGACCAAATTATAAGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCGA
* * *
804 AGGAACGGATCAGCTT-AAGTACTTTAAGGAATCGAAGTTATAAAA
386 AGGAATGGATCATCTTGAA-TACTTTAAGGAACCGAAGTTATAAAA
* *
849 GAACCAAAAAGAGTTTGACAAGTTTGGAAGTTCATCCCAA-AACCAAGAGAGAAACAATTCTCAC
1 GAACCAATAAGAGTTTGACAAGTTTGGAAGTTCGT-CCAAGAACCAAGAGAGAAACAATTCTCAC
*
913 GTAAATAAGCTTTTAATTCAAAGATGGAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAAT
65 GTAAATAAGCTTTTAATTCAAAGA--CAAAGTTGTTTACAAAAT-AAAAACTATTTAGACCAAAT
* * * * * *
978 GAAATTATTTCTCGAACATGGAATGTTCGA-AAAATTTCTCAAAGGAACTGATCGCCTTGAATAC
127 GAAACTATTTCCCGAGCATGGAATGTTCGAGAAAATTGCTCAAAGGAACGGATCGCCATGAATAC
* * ** *
1042 TTTAAAGAACCAAAGTTATTAAAGAACCAATAAAAATTTGACAAGTTTTAAAGTTCATCCAAGAA
192 TTTAAAGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA
* * * * *
1107 CCAAGAGAGAAACAATTCTGACGTGAATAAATTTTTAATTCAAAGACCAATAGTTGTTTACAGAA
257 CCAAGAAAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA
* * * *
1172 TGACAAACTATTTAGACTAAATTATAAGATTTCCTGAGTATGGAATGTTCAAAAAATTGTTCGAA
322 TGACAAACTATTTAGACCAAATTATAAGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCGAA
*
1237 GGAATGGATCACCTTGAATACTTTAAGGAACCGAAGTTATAAAA
387 GGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAA
* * * * *
1281 TAACCAATAAGAGTTTGACAAGTTTGGAAGTTTGTCTAAGAACCAAGAGAGAAA-ACATTATCCC
1 GAACCAATAAGAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACA-ATTCTCAC
* * * * *
1345 GTGAATAAGTTTTTAA-T-ACA-A-AAAGTTGTTTACAAAATAACAAATTATTTAGACCGAAT-A
65 GTAAATAAGCTTTTAATTCAAAGACAAAGTTGTTTACAAAATAA-AAACTATTTAGACCAAATGA
** * * * *
1405 ATACTATTTCCCGAGCATGGTGTGTT-TAGGAAATTACTCAAAGGAATGGATCGCCATGAATACT
129 A-ACTATTTCCCGAGCATGGAATGTTCGAGAAAATTGCTCAAAGGAACGGATCGCCATGAATACT
* * * *
1469 TTAAGGAACCGAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCGGAAGTTCGTCAAAGAAC
193 TTAAAGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAAC
* * * * *
1534 CATGAAAGAAACAATTCTCACGTGACTAGGTTTTTAATTCAAACACCAAAAGTTGTTTACAAATT
258 CAAGAAAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
* ** * * * *
1599 GACAACCTATTTAGATTACA-TATAAGATTTCTCGAGCAGGGAATGTTCAGAAAATTGCTCGAAG
323 GACAAACTATTTAGACCAAATTATAAGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCGAAG
* * *
1663 GAATGGATCATCATGAATACTTCAAGGAACCAAAGTTATAAAA
388 GAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAA
* * *
1706 GAACCAATAAGAGTTTGACATGTTCGAAAGTTCGTCCGAA-AACCAAG
1 GAACCAATAAGAGTTTGACAAGTTTGGAAGTTCGTCC-AAGAACCAAG
1753 TACTAATTAC
Statistics
Matches: 1107, Mismatches: 175, Indels: 85
0.81 0.13 0.06
Matches are distributed among these distances:
416 34 0.03
417 56 0.05
418 195 0.18
419 51 0.05
420 5 0.00
425 120 0.11
426 212 0.19
428 1 0.00
429 50 0.05
430 33 0.03
431 6 0.01
432 337 0.30
433 7 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (430 bp):
GAACCAATAAGAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACG
TAAATAAGCTTTTAATTCAAAGACAAAGTTGTTTACAAAATAAAAACTATTTAGACCAAATGAAA
CTATTTCCCGAGCATGGAATGTTCGAGAAAATTGCTCAAAGGAACGGATCGCCATGAATACTTTA
AAGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAA
GAAAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
AAACTATTTAGACCAAATTATAAGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCGAAGGAA
TGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAA
Found at i:1262 original size:216 final size:215
Alignment explanation
Indices: 529--1752 Score: 1391
Period size: 216 Copynumber: 5.7 Consensus size: 215
519 CAAAAGTTGT
* * *
529 AACTATTTTGACCAAATGATACA-ATTTCCCGAGCATCGAATGTCCAGAAAATTGCTCAAAGGAA
1 AACTATTTAGACCAAATGATA-AGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAA
* * *
593 CGGATCACCATGAATACTTTAAGGAA-CAGAAGTTAGAAAAGAACCAATAAGAGTTTGACAAGTT
65 TGGATCACCATGAATACTTTAAGGAACCA-AAGTTATAAAAGAACCAATAAAAGTTTGACAAGTT
657 CGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGAC
129 CGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGAC
722 CAAAAGTTGTTTACAAAATGACA
194 C-AAAGTTGTTTACAAAATGACA
* * * * ** * *
745 AACAATTTAAACCAAATGATACGATTTCCCGAGCAAGGAATGTTCTTAAAATTGCTCGAAGGAAC
1 AACTATTTAGACCAAATGATAAGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAAT
* * * *
810 GGATCAGC-TTAAGTACTTTAAGGAATCGAAGTTATAAAAGAACCAA-AAAGAGTTTGACAAGTT
66 GGATCACCATGAA-TACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAA-AGTTTGACAAGTT
* * * * *
873 TGGAAGTTCATCCCAA-AACCAAGAGAGAAACAATTCTCACGTAAATAAGCTTTTAATTCAAAGA
129 CGAAAGTTCGT-CCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGA
** *
937 TGGAAAGTTGTTTACAAAATGAAA
193 -CCAAAGTTGTTTACAAAATGACA
* * * *
961 AACTATTTAGACCAAATGA-AATTATTTCTCGAACATGGAATGTTC-GAAAAATTTCTCAAAGGA
1 AACTATTTAGACCAAATGATAA-GATTTCCCGAGCATGGAATGTTCAG-AAAATTGCTCAAAGGA
* * * * *
1024 ACT-GATCGCCTTGAATACTTTAAAGAACCAAAGTTATTAAAGAACCAATAAAAATTTGACAAGT
64 A-TGGATCACCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGT
** * * *
1088 TTTAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTGACGTGAATAAATTTTTAATTCAAAGA
128 TCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGA
*
1153 CCAATAGTTGTTTACAGAATGACA
193 CCAA-AGTTGTTTACAAAATGACA
* * * * * * *
1177 AACTATTTAGACTAAATTATAAGATTTCCTGAGTATGGAATGTTCAAAAAATTGTTCGAAGGAAT
1 AACTATTTAGACCAAATGATAAGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAAT
* * * * *
1242 GGATCACCTTGAATACTTTAAGGAACCGAAGTTATAAAATAACCAATAAGAGTTTGACAAGTTTG
66 GGATCACCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCG
* * * * * *
1307 GAAGTTTGTCTAAGAACCAAGAGAGAAA-ACATTATCCCGTGAATAAGTTTTTAA-T-ACA-A--
131 AAAGTTCGTCCAAGAACCAAGAGAGAAACA-ATTCTCACGTGAATAAGTTTTTAATTCAAAGACC
*
1366 AAAGTTGTTTACAAAATAACA
195 AAAGTTGTTTACAAAATGACA
* * * ** ** * * *
1387 AATTATTTAGACCGAATAATACTATTTCCCGAGCATGGTGTGTTTAGGAAATTACTCAAAGGAAT
1 AACTATTTAGACCAAATGATAAGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAAT
* *
1452 GGATCGCCATGAATACTTTAAGGAACCGAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCG
66 GGATCACCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCG
* * * * * * *
1517 GAAGTTCGTCAAAGAACCATGAAAGAAACAATTCTCACGTGACTAGGTTTTTAATTCAAACACCA
131 AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACC-
*
1582 AAAGTTGTTTACAAATTGACA
195 AAAGTTGTTTACAAAATGACA
* ** * * * *
1603 ACCTATTTAGATTACAT-ATAAGATTTCTCGAGCAGGGAATGTTCAGAAAATTGCTCGAAGGAAT
1 AACTATTTAGACCAAATGATAAGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAAT
* * * *
1667 GGATCATCATGAATACTTCAAGGAACCAAAGTTATAAAAGAACCAATAAGAGTTTGACATGTTCG
66 GGATCACCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCG
1732 AAAGTTCGTCCGAA-AACCAAG
131 AAAGTTCGTCC-AAGAACCAAG
1753 TACTAATTAC
Statistics
Matches: 844, Mismatches: 139, Indels: 51
0.82 0.13 0.05
Matches are distributed among these distances:
210 170 0.20
211 4 0.00
212 2 0.00
213 2 0.00
214 2 0.00
215 126 0.15
216 525 0.62
217 13 0.02
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (215 bp):
AACTATTTAGACCAAATGATAAGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCAAAGGAAT
GGATCACCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAAAGTTTGACAAGTTCG
AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCA
AAGTTGTTTACAAAATGACA
Found at i:4409 original size:20 final size:20
Alignment explanation
Indices: 4384--4422 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4374 TATAGTTAGA
4384 ATGAAATTAT-TTGTGTATTG
1 ATGAAA-TATGTTGTGTATTG
4404 ATGAAATATGTTGTGTATT
1 ATGAAATATGTTGTGTATT
4423 CAATTCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (20 bp):
ATGAAATATGTTGTGTATTG
Found at i:5566 original size:21 final size:21
Alignment explanation
Indices: 5536--5611 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
5526 GATTATTTTT
*
5536 AGTATTGGTAGAACCCATCAG
1 AGTATCGGTAGAACCCATCAG
*
5557 AGTATCGGTAAAACCCATCAG
1 AGTATCGGTAGAACCCATCAG
*
5578 AGTATCGATAGAACCCTAT-AG
1 AGTATCGGTAGAACCC-ATCAG
5599 AGTATCGGTAGAA
1 AGTATCGGTAGAA
5612 ATATAGGGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
21 47 0.96
22 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
AGTATCGGTAGAACCCATCAG
Found at i:5997 original size:3 final size:3
Alignment explanation
Indices: 5989--6020 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5979 TTTTGTTTTG
5989 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6021 GGATTAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.