Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003918.1 Kokia drynarioides strain JFW-HI SEQ_116988, 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: 2359
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Found at i:497 original size:216 final size:216
Alignment explanation
Indices: 40--2359 Score: 2428
Period size: 216 Copynumber: 10.8 Consensus size: 216
30 TTTCCAAGGT
* * *
40 TGGAATGTTTGGAAAATTGCTCGAAGGAATCGATCGTCTTGAATATTTTAAGGAACCAAAGTTAT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * * *
105 AAAAGAACTTGAAAAAGTTTGACAAGCTCGGAAGTTCGGCCAAGAACCAA-A-AGAAACAATTCT
66 AAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT
* * *
168 CACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCTTTACAAAATGACAGATTATTTTGTACC
131 CACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTA-TTTGGACC
*
233 AAATGATGCGA-TTTTCGAGAG
195 AAATGATGCGATTTTTCGAGAA
* * *
254 TGGAATGTTTGAAAAATTGCTCGAAGGAATGGATTGTCTTGAATACTTTAAGGAAACGAAGTTAT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * * * * * *
319 AAATGAACTCGAAAAAGTTGGAAAAGTTTGAAAGTTTGACCAAGAACCAAGAGAGAAACCACTCT
66 AAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT
** * * * **
384 CATGTAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTTTACAAAAAGACAAACAATTTGGACCA
131 CACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGACCA
* *
449 AACGATGCGATTTTTCGAGCA
196 AATGATGCGATTTTTCGAGAA
* * * ** *
470 TGGAATG-TTCAGAAAATTACTCGAAGGAATTGATCGTCTTGAATACTTTAAGGAACATAAGTTT
1 TGGAATGTTTGA-AAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTA
* * * * * *
534 TAAAAGAACTCAAAAAATTTTGCAAAGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATTC
65 TAAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* * * * *
599 TCACATAAATAGGTTTTTAATCCAAAGACTAAAAGTTATTTACAAAAAT-ACAGATTATTTTGAC
130 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTAC-AAAATGACAAATTATTTGGAC
663 CAAATGATGCGATTTTTCGAGAA
194 CAAATGATGCGATTTTTCGAGAA
* * * * * * ** *
686 T-GAATGTTCGAAAAATTACTCGAAGGAATAGATTGTCTTGATTATTTTAAGGAATTGAAGTTGT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * * * * *
750 AAAAGAACTTGAAAAATTTTGGAAATTTC-AGAAGTTCGGCCAAAAACCAAGAGAGAAACAAATC
66 AAAAGAACTCGAAAAAGTTTGAAAAGTTCGA-AAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* ** * *
814 TCACAT-AATAAAGTTTTTAATCCAAAGATCAAAAGTTGCTTACAAAATGACATATTATTTAGAC
130 TCACATAAAT-AAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGAC
** * **
878 TGAATAATGCGATTTCCCGAGAA
194 CAAATGATGCGATTTTTCGAGAA
* * * *
901 TGGAATTTTTGAAAAACTGTTCGAAGAAAT-GAATCGTCTTGAATACTTTAAGGAACCGAAGTTA
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCG-ATCGTCTTGAATACTTTAAGGAACCGAAGTTA
* * * * * *
965 CAAAATAACTCGAAAAACTTCGAAAAGTTTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
65 TAAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* * * * * * *
1030 TCACATAAATAAGTTTTTAATTCAAAGATCGAAAGTTTTTTTAGAAAAGGACAAACTATTTTGAC
130 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAG-TTTTTTACAAAATGACAAATTATTTGGAC
* * * **
1095 CAAATGGTGCAATTTCTCGAGGC
194 CAAATGATGCGATTTTTCGAGAA
* * *
1118 TGGAATGTTTGGAAAATTGCTCGAAGGAATCGATCGTCTTGAATATTTTAAGGAACCTAAGTTAT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* ** *
1183 AAAAGAACTCGAAAAAGTTTTGACAAGTTCGAAAGTTCAACCAAGAACCAAGAGAGAAAAAATTC
66 AAAAGAACTCGAAAAAG-TTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* * *
1248 TCGCATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCTTTACAAAAT---AGATTATTTGGACC
130 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGACC
* **
1310 AAAAGATGCGATTTCCCGAGAA
195 AAATGATGCGATTTTTCGAGAA
* * *
1332 TGTAATGTTTGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATA-TTGTAAGGAACTGAAGTTA
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTT-TAAGGAACCGAAGTTA
* * ** * * * *
1396 TAAAGGGACTTAAAAAAGCTTT-AAAACTTC-AGAAGTTTGGCCAAGAACCAAGAGGGAAACCAT
65 TAAAAGAACTCGAAAAAG-TTTGAAAAGTTCGA-AAGTTCGGCCAAGAACCAAGAGAGAAACAAT
* * * * * *
1459 TCTCACGTAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTTTTCAAAAGGACAAACTATTTGGA
128 TCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGA
*
1524 CCAAATGATGCGATTTCTT-GAGCA
193 CCAAATGATGCGATTT-TTCGAGAA
* * * *
1548 TGGAATGTTTGAAAAATTGCTCGAAGGATTCGATCCTCTTGAATGCTTTAAGGAATCGAAGTT-T
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * * *
1612 CAAAAGAACTCGAAAAAGTTTCACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTC
66 -AAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* * * * * *
1677 TCACATAAATAAGTTTCTAGTCCAAATACTAAAAGATGTTTACAAAATGA-AAGATTATTTGGAC
130 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAA-ATTATTTGGAC
* * *
1741 CAAATGATACGA-TATCCTGAGAA
194 CAAATGATGCGATTTTTC-GAGAA
* * * * * *
1764 TTGAATGTTTGAAAAATTGCTTGCAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTGT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * * * * * * *
1829 AAAAGAACTCAAAAAATTTTGAAAATTTTGGAAGTTCGGCCAATAACCAAGAGAGAAAGATTTCT
66 AAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT
* * * *
1894 CATATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGACAAATTATTTAGATCA
131 CACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGACCA
**
1959 AATGATGCGATTTCCCGAGAA
196 AATGATGCGATTTTTCGAGAA
* * * * ** * *
1980 TGAAATGTTAGAGAAATTGTTCGAA-GAA--GATTATCTTGGATGCTTTAAGGAACCGAAGTTAT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * ** * * * *
2042 AAAAGAACTCAAAAAAGTTTGAAAAGTTCGGAAGTTTAGCTAAGAACCAAGACATAAATAATTCT
66 AAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT
** * * * * *
2107 CATGTAAATAAGTTTTTAATTCAAAGACTAAAAGTTTTTTAGAAAAGGACAAACTATTTGGACCA
131 CACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGACCA
*
2172 AATGATGCGATTTCTT-GAGCA
196 AATGATGCGATTT-TTCGAGAA
** * * * * * * *
2193 TTAAATGTTTGGATAATTGCTCGAAGGAATCGATTGTCATAAATAGTTTAA-GAATCGAAGTTAT
1 TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
* * * * * * * * *
2257 AAGAGAACCCAAAAAAATATGACAAGTTC-AGAAGTTTGGCCAAGAAGC-A-AGAGAAATAATTC
66 AAAAGAACTCGAAAAAGTTTGAAAAGTTCGA-AAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* * *
2319 TCACATAAATAAATTTTT-ATCCAAAGACCAAGAGTTGTTTA
130 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTA
Statistics
Matches: 1742, Mismatches: 327, Indels: 76
0.81 0.15 0.04
Matches are distributed among these distances:
212 20 0.01
213 276 0.16
214 214 0.12
215 251 0.14
216 776 0.45
217 133 0.08
218 72 0.04
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (216 bp):
TGGAATGTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
AAAAGAACTCGAAAAAGTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT
CACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAATGACAAATTATTTGGACCA
AATGATGCGATTTTTCGAGAA
Found at i:830 original size:431 final size:433
Alignment explanation
Indices: 40--2359 Score: 2339
Period size: 431 Copynumber: 5.4 Consensus size: 433
30 TTTCCAAGGT
* * * *
40 TGGAATG-TTTGGAAAATTGCTCGAAGGAATCGATCGTCTTGAATATTTTAAGGAACCAAAGTTA
1 TGGAATGTTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAATCGAAGTTA
** * * * *
104 TAAAAGAACTTGAAAAAGTTTGACAAGCTCGGAAGTTCGGCCAAGAACCAA-A-AGAAACAATTC
66 TAAAAGAACTCAAAAAACTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* *
167 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCTTTAC-AAAATGACAGATTATTTTGTA
131 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAAAT-ACAAATTATTTTG-A
* *
231 CCAAATGATGCGA-TTTTCGAGAGTGGAATGTTTGAAAAATTGCTCGAAGGAATGGATTGTCTTG
194 CCAAATGATGCGATTTTTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATAGATTGTCTTG
* * * *
295 AATACTTTAAGGAAACGAAGTTATAAATGAACTCGAAAAAG-TTGGAAAAGTT-TGAAAGTTTGA
259 AATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGG-AAAGTTCAG-AAGTTCGA
* * ** * * *
358 CCAAGAACCAAGAGAGAAACCACTCTCATGTAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTT
322 CCAAGAACCAAGAGAGAAACAAATCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTT
** * * *
423 TACAAAAAGACAAACAATTTGGACCAAACGATGCGATTTTTCGAGCA
387 TACAAAAAGACAAATTATTTGGACCAAATGATGCGATTTTCCGAGAA
** * * *
470 TGGAATGTTCAG-AAAATTACTCGAAGGAATTGATCGTCTTGAATACTTTAAGGAA-CATAAGTT
1 TGGAATGTTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAATC-GAAGTT
* * * * * *
533 TTAAAAGAACTCAAAAAATTTTGCAAAGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATT
65 ATAAAAGAACTCAAAAAACTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATT
* * * *
598 CTCACATAAATAGGTTTTTAATCCAAAGACTAAAAGTTATTTACAAAAATACAGATTATTTTGAC
130 CTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAAATACAAATTATTTTGAC
* *
663 CAAATGATGCGATTTTTCGAGAAT-GAATGTTCGAAAAATTACTCGAAGGAATAGATTGTCTTGA
195 CAAATGATGCGATTTTTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATAGATTGTCTTGA
* * ** * * * * *
727 TTATTTTAAGGAATTGAAGTTGTAAAAGAACTTGAAAAATTTTGGAAATTTCAGAAGTTCGGCCA
260 ATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGGAAAGTTCAGAAGTTCGACCA
* * *
792 AAAACCAAGAGAGAAACAAATCTCACAT-AATAAAGTTTTTAATCCAAAGATCAAAAGTTGCTTA
325 AGAACCAAGAGAGAAACAAATCTCACATAAAT-AAGTTTTTAATCCAAAGACCAAAAGTTGTTTA
* * * ** * *
856 CAAAATGACATATTATTTAGACTGAATAATGCGATTTCCCGAGAA
389 CAAAAAGACAAATTATTTGGACCAAATGATGCGATTTTCCGAGAA
* * * *
901 TGGAAT-TTTTGAAAAACTGTTCGAAGAAAT-GAATCGTCTTGAATACTTTAAGGAACCGAAGTT
1 TGGAATGTTTTGAAAAATTGCTCGAAGGAATCG-ATCGTCTTGAATACTTTAAGGAATCGAAGTT
* * * * * *
964 ACAAAATAACTCGAAAAACTTCGAAAAGTTTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATT
65 ATAAAAGAACTCAAAAAACTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATT
* * * * ** *
1029 CTCACATAAATAAGTTTTTAATTCAAAGATCGAAAGTTTTTTTAGAAAAGGACAAACTATTTTGA
130 CTCACATAAATAAGTTTTTAATCCAAAGACCAAAAG-TTTTTTACAAAAATACAAATTATTTTGA
* * * ** * * *
1094 CCAAATGGTGCAATTTCTCGAGGCTGGAATGTTTGGAAAATTGCTCGAAGGAATCGATCGTCTTG
194 CCAAATGATGCGATTTTTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATAGATTGTCTTG
* * * *
1159 AATATTTTAAGGAACCTAAGTTATAAAAGAACTCGAAAAAGTTTTGACAAGTTC-GAAAGTTCAA
259 AATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGGA-AAGTTCAG-AAGTTCGA
* *
1223 CCAAGAACCAAGAGAGAAA-AAATTCTCGCATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCT
322 CCAAGAACCAAGAGAGAAACAAA-TCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGT
* *
1287 TTACAAAATAG----ATTATTTGGACCAAAAGATGCGATTTCCCGAGAA
386 TTACAAAA-AGACAAATTATTTGGACCAAATGATGCGATTTTCCGAGAA
* *
1332 TGTAATG-TTTGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATA-TTGTAAGGAA-CTGAAGT
1 TGGAATGTTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTT-TAAGGAATC-GAAGT
* * * * * * *
1394 TATAAAGGGACTTAAAAAAGCTTT-AAAACTTC-AGAAGTTTGGCCAAGAACCAAGAGGGAAACC
64 TATAAAAGAACTCAAAAAA-CTTTGAAAAGTTCGA-AAGTTCGGCCAAGAACCAAGAGAGAAACA
* * * * ** * *
1457 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTTTTCAAAAGGACAAACTATTTG
127 ATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAAATACAAATTATTTT
* * * **
1522 GACCAAATGATGCGATTTCTT-GAGCATGGAATGTTTGAAAAATTGCTCGAAGGATTCGATCCTC
192 GACCAAATGATGCGATTT-TTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATAGATTGTC
* * * *
1586 TTGAATGCTTTAAGGAATCGAAGTT-TCAAAAGAACTCGAAAAAGTTT-CACAAGTTCAAAAGTT
256 TTGAATACTTTAAGGAACCGAAGTTAT-AAAAGAACTCGAAAAAGTTTGGA-AAGTTCAGAAGTT
* * * * * * *
1649 CGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTCTAGTCCAAATACTAAAAGAT
319 CGACCAAGAACCAAGAGAGAAACAAATCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTT
* * *
1714 GTTTACAAAATGA-AAGATTATTTGGACCAAATGATACGA-TATCCTGAGAA
384 GTTTACAAAAAGACAA-ATTATTTGGACCAAATGATGCGATTTTCC-GAGAA
* * * * *
1764 TTGAATG-TTTGAAAAATTGCTTGCAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTG
1 TGGAATGTTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAATCGAAGTTA
* * * * * * *
1828 TAAAAGAACTCAAAAAATTTTGAAAATTTTGGAAGTTCGGCCAATAACCAAGAGAGAAAGATTTC
66 TAAAAGAACTCAAAAAACTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
* * * *
1893 TCATATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTAC-AAAATGACAAATTATTTAGAT
131 TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAAAT-ACAAATTATTTTGAC
** * * * * * *
1957 CAAATGATGCGATTTCCCGAGAATGAAATGTTAGAGAAATTGTTCGAA-G-A-AGATTATCTTGG
195 CAAATGATGCGATTTTTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATAGATTGTCTTGA
* * * * * *
2019 ATGCTTTAAGGAACCGAAGTTATAAAAGAACTCAAAAAAGTTTGAAAAGTTCGGAAGTT-TAGCT
260 ATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGGAAAGTTCAGAAGTTCGA-CC
* * * * ** * * *
2083 AAGAACCAAGACATAAATAATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAAAAGTTTTTTA
324 AAGAACCAAGAGAGAAACAAATCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTA
* * * * *
2148 GAAAAGGACAAACTATTTGGACCAAATGATGCGA-TTTCTTGAGCA
389 CAAAAAGACAAATTATTTGGACCAAATGATGCGATTTTC-CGAGAA
** * * * * * *
2193 TTAAATG-TTTGGATAATTGCTCGAAGGAATCGATTGTCATAAATAGTTTAA-GAATCGAAGTTA
1 TGGAATGTTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAATCGAAGTTA
* * * * * * * *
2256 TAAGAGAACCCAAAAAAATATGACAAGTTC-AGAAGTTTGGCCAAGAAGC-A-AGAGAAATAATT
66 TAAAAGAACTCAAAAAACTTTGAAAAGTTCGA-AAGTTCGGCCAAGAACCAAGAGAGAAACAATT
* * *
2318 CTCACATAAATAAATTTTT-ATCCAAAGACCAAGAGTTGTTTA
130 CTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTA
Statistics
Matches: 1579, Mismatches: 265, Indels: 97
0.81 0.14 0.05
Matches are distributed among these distances:
425 22 0.01
426 27 0.02
427 1 0.00
428 49 0.03
429 265 0.17
430 227 0.14
431 487 0.31
432 342 0.22
433 85 0.05
434 70 0.04
435 4 0.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (433 bp):
TGGAATGTTTTGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAATCGAAGTTA
TAAAAGAACTCAAAAAACTTTGAAAAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
TCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTTTTTACAAAAATACAAATTATTTTGACC
AAATGATGCGATTTTTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATAGATTGTCTTGAA
TACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTGGAAAGTTCAGAAGTTCGACCAA
GAACCAAGAGAGAAACAAATCTCACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTGTTTACA
AAAAGACAAATTATTTGGACCAAATGATGCGATTTTCCGAGAA
Found at i:1394 original size:647 final size:641
Alignment explanation
Indices: 42--2346 Score: 2465
Period size: 647 Copynumber: 3.6 Consensus size: 641
32 TCCAAGGTTG
* * **
42 GAATGTTTGGAAAATTGCTCGAAGGAATCGATCGTCTTGAATATTTTAAGGAACCAAAGTTATAA
1 GAATGTTTGAAAAATTGCTCGAAGGAATAGATCGTCTTGAATATTTTAAGGAACTGAAGTTATAA
* *
107 AAGAACTTGAAAAAGTTTGACAAGC-TCGGAAGTTCGGCCAAGAACCAA-A-AGAAACAATTCTC
66 AAGAACTTGAAAAACTTTGA-AA-CTTCAGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTC
* *
169 ACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCTTTACAAAATGACAGATTATTTTGTACCA
129 ACATAAATAAGTTTTTAATCCAAAGACCAAAAGTTC-TTACAAAATGACAAATTATTTAG-ACCA
* *
234 AATGATGCGATTT-TCGAGAGTGGAATGTTTGAAAAATTGCTCGAAGGAATGGATTGTCTTGAAT
192 AATGATGCGATTTCTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAAT-GATCGTCTTGAAT
* * * *
298 ACTTTAAGGAAACGAAGTTA-TAAATGAACTCGAAAAAGTTGGAAAAGTTTGAAAGTTTGACCAA
256 ACTTTAAGGAAACGAAGTTACAAAAT-AACTCGAAAAACTTCGAAAAGTTTGAAAGTTCGACCAA
* * **
362 GAACCAAGAGAGAAACCACTCTCATGTAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTTTACA
320 GAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGA-CGAAAGTTTTTTACA
* * * ** *
427 AAAAGACAAACAATTTGGACCAAACGATGCGATTTTTCGA-GCATGGAATGTTCAGAAAATTACT
384 AAAAGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGGC-TGGAATGTTTGGAAAATTGCT
* * *
491 CGAAGGAATTGATCGTCTTGAATACTTTAAGGAACATAAGTTTTAAAAGAACTCAAAAAATTTTG
448 CGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCAAAAAATTTTG
* * * * *
556 -CAAAGTTCGAAAGTTTGTCCAAGAACCAGGAGAGAAACAATTCTCACATAAATAGGTTTTTAAT
513 AC-AAGTTCGAAAGTTCGACCAAGAACCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAAT
* * **
620 CCAAAGACTAAAAGTTATTTACAAAAATACAGATTATTTTGACCAAATGATGCGATTTTTCGAGA
577 CCAAAGACCAAAAGTTATTTAC-AAAATA-AGATTATTTAGACCAAATGATGCGATTTCCCGAGA
685 AT
640 AT
* * * * * *
687 GAATGTTCGAAAAATTACTCGAAGGAATAGATTGTCTTGATTATTTTAAGGAATTGAAGTTGTAA
1 GAATGTTTGAAAAATTGCTCGAAGGAATAGATCGTCTTGAATATTTTAAGGAACTGAAGTTATAA
* * * *
752 AAGAACTTGAAAAATTTTGGAAATTTCAGAAGTTCGGCCAAAAACCAAGAGAGAAACAAATCTCA
66 AAGAACTTGAAAAACTTT-GAAACTTCAGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCA
* * **
817 CAT-AATAAAGTTTTTAATCCAAAGATCAAAAGTTGCTTACAAAATGACATATTATTTAGACTGA
130 CATAAAT-AAGTTTTTAATCCAAAGACCAAAAGTT-CTTACAAAATGACAAATTATTTAGACCAA
* * * * * *
881 ATAATGCGATTTCCCGAGAATGGAATTTTTGAAAAACTGTTCGAAGAAATGAATCGTCTTGAATA
193 ATGATGCGATTTCTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATG-ATCGTCTTGAATA
* * *
946 CTTTAAGGAACCGAAGTTACAAAATAACTCGAAAAACTTCGAAAAGTTTGGAAGTTCGGCCAAGA
257 CTTTAAGGAAACGAAGTTACAAAATAACTCGAAAAACTTCGAAAAGTTTGAAAGTTCGACCAAGA
*
1011 ACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGATCGAAAGTTTTTTTAGAA
322 ACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGA-CGAAAG-TTTTTTACAA
* * * *
1076 AAGGACAAACTATTTTGACCAAATGGTGCAATTTCTCGAGGCTGGAATGTTTGGAAAATTGCTCG
385 AAAGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGGCTGGAATGTTTGGAAAATTGCTCG
* *
1141 AAGGAATCGATCGTCTTGAATATTTTAAGGAACCTAAGTTATAAAAGAACTCGAAAAAGTTTTGA
450 AAGGAATCGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTC-AAAAAATTTTGA
* *
1206 CAAGTTCGAAAGTTCAACCAAGAACCAAGAGAGAAAAAATTCTCGCATAAATAAGTTTTTAATCC
514 CAAGTTCGAAAGTTCGACCAAGAACCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAATCC
* * *
1271 AAAGACCAAAAGTTCTTTACAAAAT-AGATTATTTGGACCAAAAGATGCGATTTCCCGAGAAT
579 AAAGACCAAAAGTTATTTACAAAATAAGATTATTTAGACCAAATGATGCGATTTCCCGAGAAT
* *
1333 GTAATGTTTGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATATTGTAAGGAACTGAAGTTATA
1 G-AATGTTTGAAAAATTGCTCGAAGGAATAGATCGTCTTGAATATTTTAAGGAACTGAAGTTATA
* * * * * * *
1398 AAGGGACTTAAAAAAGCTTTAAAACTTCAGAAGTTTGGCCAAGAACCAAGAGGGAAACCATTCTC
65 AAAGAACTTGAAAAA-CTTTGAAACTTCAGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTC
* * * * * * * *
1463 ACGTAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTTTTCAAAAGGACAAACTATTTGGACCAA
129 ACATAAATAAGTTTTTAATCCAAAGACCAAAAG-TTCTTACAAAATGACAAATTATTTAGACCAA
* * * * *
1528 ATGATGCGATTTCTTGAGCATGGAATGTTTGAAAAATTGCTCGAAGGATTCGATCCTCTTGAATG
193 ATGATGCGATTTCTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAAT-GATCGTCTTGAATA
* * * * * ** *
1593 CTTTAAGGAATCGAAGTTTCAAAAGAACTCGAAAAAGTTTC-ACAAGTTCAAAAGTTCGTCCAAG
257 CTTTAAGGAAACGAAGTTACAAAATAACTCGAAAAA-CTTCGAAAAGTTTGAAAGTTCGACCAAG
* * * * * * *
1657 AACCAAGAGAGAAACAATTCTCACATAAATAAGTTTCTAGTCCAAATACTAAAAGATGTTTACAA
321 AACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGAC-GAAAGTTTTTTACAA
* * * * ** * *
1722 AATGA-AAGATTATTTGGACCAAATGATACGATATC-CTGAGAATTGAATGTTTGAAAAATTGCT
385 AAAGACAA-ACTATTTGGACCAAATGATGCGATTTCTC-GAGGCTGGAATGTTTGGAAAATTGCT
* * * * * *
1785 TGCAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTGTAAAAGAACTCAAAAAATTTTG
448 CGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCAAAAAATTTTG
* * * * * * * * *
1850 AAAATTTTGGAAGTTCGGCCAATAACCAAGAGAGAAAGATTTCTCATATAAATAAGTTTTTAATC
513 ACAAGTTCGAAAGTTCGACCAAGAACCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAATC
* * *
1915 CAAAGACCAAAAGTTGTTTACAAAATGACAAATTATTTAGATCAAATGATGCGATTTCCCGAGAA
578 CAAAGACCAAAAGTTATTTACAAAAT-A-AGATTATTTAGACCAAATGATGCGATTTCCCGAGAA
1980 T
641 T
* * * ** * ** *
1981 GAAATGTTAGAGAAATTGTTCGAA-G-A-AGATTATCTTGGATGCTTTAAGGAACCGAAGTTATA
1 G-AATGTTTGAAAAATTGCTCGAAGGAATAGATCGTCTTGAATATTTTAAGGAACTGAAGTTATA
** * * * ** * * * *
2043 AAAGAACTCAAAAAAGTTTGAAAAGTTCGGAAGTTTAGCTAAGAACCAAGACATAAATAATTCTC
65 AAAGAACTTGAAAAACTTTG-AAACTTCAGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTC
** * * * * * * *
2108 ATGTAAATAAGTTTTTAATTCAAAGACTAAAAGTTTTTTAGAAAAGGACAAACTATTTGGACCAA
129 ACATAAATAAGTTTTTAATCCAAAGACCAAAAG-TTCTTACAAAATGACAAATTATTTAGACCAA
* * ** * * * * *
2173 ATGATGCGATTTCTTGAGCATTAAATGTTTGGATAATTGCTCGAAGGAATCGATTGTCATAAATA
193 ATGATGCGATTTCTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAAT-GATCGTCTTGAATA
* * * * * * * * * * * *
2238 GTTTAA-GAATCGAAGTTATAAGAGAACCCAAAAAAATAT-GACAAG-TTCAGAAGTTTGGCCAA
257 CTTTAAGGAAACGAAGTTACAAAATAACTCGAAAAACT-TCGAAAAGTTTGA-AAGTTCGACCAA
* * * *
2300 GAAGC-A-AGAGAAATAATTCTCACATAAATAAATTTTT-ATCCAAAGAC
320 GAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGAC
2347 CAAGAGTTGT
Statistics
Matches: 1410, Mismatches: 221, Indels: 62
0.83 0.13 0.04
Matches are distributed among these distances:
641 8 0.01
642 28 0.02
643 4 0.00
644 47 0.03
645 382 0.27
646 158 0.11
647 511 0.36
648 184 0.13
649 87 0.06
650 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (641 bp):
GAATGTTTGAAAAATTGCTCGAAGGAATAGATCGTCTTGAATATTTTAAGGAACTGAAGTTATAA
AAGAACTTGAAAAACTTTGAAACTTCAGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCAC
ATAAATAAGTTTTTAATCCAAAGACCAAAAGTTCTTACAAAATGACAAATTATTTAGACCAAATG
ATGCGATTTCTCGAGAATGGAATGTTTGAAAAATTGCTCGAAGGAATGATCGTCTTGAATACTTT
AAGGAAACGAAGTTACAAAATAACTCGAAAAACTTCGAAAAGTTTGAAAGTTCGACCAAGAACCA
AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACGAAAGTTTTTTACAAAAAGAC
AAACTATTTGGACCAAATGATGCGATTTCTCGAGGCTGGAATGTTTGGAAAATTGCTCGAAGGAA
TCGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCAAAAAATTTTGACAAGTTC
GAAAGTTCGACCAAGAACCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAATCCAAAGACC
AAAAGTTATTTACAAAATAAGATTATTTAGACCAAATGATGCGATTTCCCGAGAAT
Done.