Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013417.1 Kokia drynarioides strain JFW-HI SEQ_128442, 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: 5752
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:378 original size:216 final size:216
Alignment explanation
Indices: 1--2994 Score: 3044
Period size: 216 Copynumber: 13.8 Consensus size: 216
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
** * * * * * * * *
66 TTGGATACAAAATGACAAATTATTTAGACCAAATGAAGTGATTTACCAAGGATGGAATATTCGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
* * * *
131 AAATTTCTCAAAGGAATGGATCTTGTTGAATACTTCAGGGAACTGAAGTTAAAAAATAACTCTTA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
* *
196 AAAGTTTGAAAAGTTCAAAAG
196 AAAGTTTGACAAGTTCGAAAG
* * *
217 TTCGTCCAAGAACAAAGAGATAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGAGCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* * * * *
282 TTGTTTGCAAAATAACAAATTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTTTGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
* * *
347 AGATTGCTCAAAGGAATGGATCTTATTGAATACTTTAGGGAACCGAAGTTAAAAAGTAACTCGTA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
*
412 GAAGTTTGACAAGTTCGAAAG
196 AAAGTTTGACAAGTTCGAAAG
* * * * *
433 TTCGTACAA-AGAGAAAGAAAGAAACAATTCTCATGTAAATAAGTGTTTAATTCAAAGACCAAAA
1 TTCGTCCAAGA-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * * *
497 CTTGTTTGCAAAATGACAAACTAATTAGGCCAAATGATGCGATCTCCCGAGCATGAAATGTTTGA
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGA
* * * * * * * * * *
562 AAAATTGGTCGAAA-GAATGGATCGTCTTGAATTCTTTAAGGATCCAAAGTTATAAAAGAACTAG
130 AAAATTGCTC-AAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCG
*
626 TAAAAGTTTGAAAAGTTCGAAAG
194 TAAAAGTTTGACAAGTTCGAAAG
649 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
** * ** * * * * *
714 TTGGATACAAAATGAGAAACTATTTAGACCAAATGAAACGATTTCCCAAGGATGGAATATTCGGA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
* * * *
779 AAATTGCTCAAAGGAATGGATCTTGTTGAACAGTTTAGGGAACTGAAGTTAAAGAATAACTCG-A
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
*
843 GAATGTTTGACAAGTTCGAAAG
196 -AAAGTTTGACAAGTTCGAAAG
* * * **
865 TTCGTCCAATAGCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAGAGTGCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* ** * * * *
930 TTATTTGGAAACTGACAAATTATTTAAACCAAATGATACGATTTCCCGAGCATGGAATGTTT-AG
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGA-
* * * *
994 AAAATTGCTCTAAGGAATGGATCTTGATGAATACTTTAGGGAACCAAAGTTAAAAAATAACTTGT
130 AAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGT
1059 AAAAGTTTGACAAGTTCGAAAG
195 AAAAGTTTGACAAGTTCGAAAG
* * * * *
1081 TTCGTACAA-AGATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTGAATTCATAGACAAAAA
1 TTCGTCCAAGA-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * *
1145 CTTGGTTACAAAATGACAAACTATTTAAACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGG
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGA
1210 AAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGT
130 AAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGT
*
1275 AAAAGTTTGACAAGTTCGAATG
195 AAAAGTTTGACAAGTTCGAAAG
* * *
1297 TTCGTACAA-AGACAAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATGCAAAGACCAAAA
1 TTCGTCCAAGA-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * * *
1361 CTTGTTTGCAAAATGACAAACTAATTAGGCCAAATGATGCGATCTCCCGAGCATGAAATGTTTGA
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGA
* * * * * * * *
1426 AAAATTTCTCGAAA-GAATGGATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAG
130 AAAATTGCTC-AAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCG
1490 TAAAAGTTTGACAAGTTCGAAAG
194 TAAAAGTTTGACAAGTTCGAAAG
*
1513 TTCGTCCAAGAAGAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
** ** * * * *
1578 TTGGATACAAAATGACAAACTATTTAGACCAAATGAAACGATTTCCCAAGGATGGAATATTCGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
* * *
1643 AAATTGCTCAAAGAAATGGATCTTGTTGAATACTTTAGGAAACTGAAGTTAAAAAATAACTCGTA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
1708 AAAGTTTGACAAGTTCGAAAG
196 AAAGTTTGACAAGTTCGAAAG
* **********
1729 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCATGTAANNNNNNNNNNNNNNNNNNNNNNNNNNN
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAA-----------------ATAAGTTTTT
*********************** *** * * **
1794 NNNNNNNNNNNNNNNNNNNNNNNACTTGGAT-ACAAAATGACAAACTATTTAGACCAAATGAAAC
49 AATTCAAAGACCAAAACTTGTTTAC-AAAATGACAAACT-----A-T-TTA-GACCAAATGATGC
* * * * * *
1858 GATTTCCCAAGGATGGAATATTCGAAAAATTGCTCAAAGAAATAGATCTTGTTGAATACTTTAGG
105 GATTTCCCGAGCATGGAATGTTTGAAAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGG
* * *
1923 AAACTGAAGTTAAAAAATAACTCGTAAAAGTTTAACAAGTTCGAAAG
170 GAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAG
* **
1970 TTCATCCAAGAAC-AA-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGTGCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* *
2033 TTGTTTACAAAATGACAAATTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCG--
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
* * * *
2096 --ATTGCTCTACGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCATA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
2159 AAAGTTTGACAAGTTCGAAAG
196 AAAGTTTGACAAGTTCGAAAG
* * *
2180 TTTGTACAA-AGACAAAGAGAGAAACAATTCTCACGTATATAAGTTTTTAATTCAAAGACCAAAA
1 TTCGTCCAAGA-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * ** * * *
2244 CCTGTTTGCAAAATGACAAACTACTTT-GACCAAATGATGCGATCTGTCGAGCATGAAATATTCG
65 CTTGTTTACAAAATGACAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTG
* ** *
2308 AAAAATTGCTCGAAA-GAATGGATCGTT-TTGAATACTTT-GAGGATCCGAAGTTATCAAAGAAC
129 AAAAATTGCTC-AAAGGAATGGATC-TTGTTGAATACTTTAG-GGAACCGAAGTTAAAAAATAAC
* *
2370 TAGTAAAAGTTTGACAAGCTC-AGAAG
191 TCGTAAAAGTTTGACAAGTTCGA-AAG
* * * * **
2396 TTCGTCCAAGAACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAAAGTTCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* * * * * *
2461 TTGTTTACAAAATGAC--A-TATTTTGATCGATTGATGCGCTTTCCCGAGCATGGAATGTTCGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
* * * * * *
2523 AAATTGCTCTAAGGAATGGATTTTGTTGAATGCTTTAGGGATCCAAAGTTAAAAAATAACTTGTA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
* * * * *
2588 GAAGTTTGACCAGTTTGGATG
196 AAAGTTTGACAAGTTCGAAAG
* * *
2609 TTCGTCC-AGAAATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAACGACCAAAA
1 TTCGTCCAAG-AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * ** *
2673 CTCGTTTACAAAACGA-AAGTA-TATTCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTTT
65 CTTGTTTACAAAATGACAA--ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTT
* * * * *** * * * * *
2736 GGAAAATTACTCGAAGGAATGAATCGCCTTGAATGCTTTAAGGAA-CGAAAGTTATAAAAGAAGT
128 GAAAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCG-AAGTTAAAAAATAACT
*
2800 CGTAAAAGTTTGACACGTTCGAAAG
192 CGTAAAAGTTTGACAAGTTCGAAAG
* * * *
2825 TTCGTCCAAGAAGAAAGAGAGAAACAATCCTCACGT-AA-AAGTTTTTAACTGC-ATGACCAAAA
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TTCAAAGACCAAAA
* * * * * * * *** *
2887 CTTGATTACGAAATGACAAACTCTTTACACCCAATGTTGCAATTTCTTAAGCATTGAATGTTTAG
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTT-G
* * * *
2952 AAAAATT-CTCAAAGGAATGGGTCGTCTTGAATACTTTAAGGAA
129 AAAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAA
2995 GTTAAGTTAT
Statistics
Matches: 2302, Mismatches: 408, Indels: 138
0.81 0.14 0.05
Matches are distributed among these distances:
209 1 0.00
210 85 0.04
211 2 0.00
212 105 0.05
213 165 0.07
214 129 0.06
215 27 0.01
216 1591 0.69
217 16 0.01
221 2 0.00
222 8 0.00
233 8 0.00
234 2 0.00
238 1 0.00
239 21 0.01
240 4 0.00
241 135 0.06
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (216 bp):
TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAA
AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTA
AAAGTTTGACAAGTTCGAAAG
Found at i:1279 original size:648 final size:641
Alignment explanation
Indices: 1--5351 Score: 4107
Period size: 648 Copynumber: 8.3 Consensus size: 641
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
** * * * * * * * *
66 TTGGATACAAAATGACAAATTATTTAGACCAAATGAAGTGATTTACCAAGGATGGAATATTCGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
* * * *
131 AAATTTCTCAAAGGAATGGATCTTGTTGAATACTTCAGGGAACTGAAGTTAAAAAATAACTCTTA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTT-AAAAATAACTC-GA
* * * *
196 AAAGTTTGAAAAGTTCAAAAGTTCGTCCAAGAA-CAAAGAGATAAACAATTCTCACGTAAAAAAG
194 AAAGTTTGACAAGTTCGAAAGTTCGTCCAA-AAGCAAAGAGAGAAACAATTCTCACGTAAATAAG
* * * **
260 TTTTTAATTCAAAGAGCAAAACTTGTTTGCAAAATAACAAATTATTTAGACCAAATGATGTGATT
258 TTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATACGATT
* * *
325 TCCCAAGCATGGAATGTTTGAAAGATTGCTCAAAGGAATGGATCTTATTGAATACTTTAGGGAAC
323 TCCCAAGCATGGAATATTCGAAAAATTGCTCAAAGGAATGGATCTTA-TGAATACTTTAGGGAAC
* * *
390 CGAAGTTAAAAAGTAACTCGTAGAAGTTTGACAAGTTCGAAAGTTCGTACAAAGAGAAAGAAAGA
387 CGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGT-CAAAGA-AAAGAGAGA
* * *
455 AACAATTCTCATGTAAATAAGTGTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTA
450 AACAATTCTCACGTAAATAAGT-TTTAATTCAAAGA-CAAAACTTGGTTACAAAATGACAAACTA
* * * * * *
520 ATTAGGCCAAATGATGCGATCTCCCGAGCATGAAATGTTTGAAAAATTGGTCGAAA-GAATGGAT
513 TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTC-AAAGGAATGGAT
* * * * * * * *
584 CGTCTTGAATTCTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGAAAAGTTCGAAAG
577 CTTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGAAAAGTTCGAAAG
649 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
** * ** * * *
714 TTGGATACAAAATGAGAAACTATTTAGACCAAATGAAACGATTTCCCAAGGATGGAATATTCGGA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
* * *
779 AAATTGCTCAAAGGAATGGATCTTGTTGAACAGTTTAGGGAACTGAAGTTAAAGAATAACTCGAG
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAA-AATAACTCGA-
* *
844 AATGTTTGACAAGTTCGAAAGTTCGTCCAATAGCAAAGAGAGAAACAATTCTCACGTAAATAAGT
194 AAAGTTTGACAAGTTCGAAAGTTCGTCCAAAAGCAAAGAGAGAAACAATTCTCACGTAAATAAGT
* ** * * * * *
909 TTTTAATTCAGAGTGCAAAACTTATTTGGAAACTGACAAATTATTTAAACCAAATGATACGATTT
259 TTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATACGATTT
* * * *
974 CCCGAGCATGGAATGTT-TAGAAAATTGCTCTAAGGAATGGATCTTGATGAATACTTTAGGGAAC
324 CCCAAGCATGGAATATTCGA-AAAATTGCTCAAAGGAATGGATCTT-ATGAATACTTTAGGGAAC
* *
1038 CAAAGTTAAAAAATAACTTGTAAAAGTTTGACAAGTTCGAAAGTTCGTACAAAGATAAAGAGAGA
387 CGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGT-CAAAGA-AAAGAGAGA
*
1103 AACAATTCTCACGTAAATAAGTTTTGAATTCATAGACAAAAACTTGGTTACAAAATGACAAACTA
450 AACAATTCTCACGTAAATAAGTTTT-AATTCAAAGAC-AAAACTTGGTTACAAAATGACAAACTA
* *
1168 TTTAAACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATC
513 TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATC
* * *
1233 TTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAATG
578 TTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGAAAAGTTCGAAAG
* * *
1297 TTCGTACAA-AGACAAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATGCAAAGACCAAAA
1 TTCGTCCAAGA-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * * * * *
1361 CTTGTTTGCAAAATGACAAACTAATTAGGCCAAATGATGCGATCTCCCGAGCATGAAATGTTTGA
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGG
* * * * * * *
1426 AAAATTTCTCGAAA-GAATGGATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAG
130 AAAATTGCTC-AAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTA-AAAATAACTCG
1490 TAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAAG-AAAGAGAGAAACAATTCTCACGTAAATA
193 -AAAAGTTTGACAAGTTCGAAAGTTCGTCCAA-AAGCAAAGAGAGAAACAATTCTCACGTAAATA
** * *
1554 AGTTTTTAATTCAAAGACCAAAACTTGGATACAAAATGACAAACTATTTAGACCAAATGAAACGA
256 AGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATACGA
* * * *
1619 TTTCCCAAGGATGGAATATTCGAAAAATTGCTCAAAGAAATGGATCTTGTTGAATACTTTAGGAA
321 TTTCCCAAGCATGGAATATTCGAAAAATTGCTCAAAGGAATGGATCTT-ATGAATACTTTAGGGA
* *
1684 ACTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGA
385 ACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCAAAG-A-AAAGAGA
* ********************
1749 GAAACAATTCTCATGTAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
448 GAAACAATTCTCACGTAA---------------------------ATAAGTTTTAATTCAAAGAC
*** * ** * * *
1814 NNNACTTGGATACAAAATGACAAACTATTTAGACCAAATGAAACGATTTCCCAAGGATGGAATAT
486 AAAACTTGGTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
* * * **
1879 TCGAAAAATTGCTCAAAGAAATAGATCTTGTTGAATACTTTAGGAAACTGAAGTTAAAAAATAAC
551 TCGAAAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAAC
1944 TCGTAAAAGTTT-AACAAGTTCGAAAG
616 TCGTAAAAGTTTGAA-AAGTTCGAAAG
* **
1970 TTCATCCAAGAAC-AA-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGTGCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
*
2033 TTGTTTACAAAATGACAAATTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC-G-
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
* * * *
2096 --ATTGCTCTACGAAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCATA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTT-AAAAATAACTC-GA
* * *
2159 AAAGTTTGACAAGTTCGAAAGTTTGTAC-AAAGACAAAGAGAGAAACAATTCTCACGTATATAAG
194 AAAGTTTGACAAGTTCGAAAGTTCGTCCAAAAG-CAAAGAGAGAAACAATTCTCACGTAAATAAG
* *
2223 TTTTTAATTCAAAGACCAAAACCTGTTTGCAAAATGACAAACTACTTT-GACCAAATGATGCGAT
258 TTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTA-TTTAGACCAAATGATACGAT
* ** * * *
2287 CTGTCGAGCATGAAATATTCGAAAAATTGCTCGAAA-GAATGGATCGTTTTGAATACTTT-GAGG
322 TTCCCAAGCATGGAATATTCGAAAAATTGCTC-AAAGGAATGGATC-TTATGAATACTTTAG-GG
* ** * * * * *
2350 ATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGACAAGCTC-AGAAGTTCGTCCAAGAACAGAGG
384 AACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGA-AAGTTCGTCAAAGAA-A-AGA
* * *
2414 GAGAAACAATTCTCACATAAATAAGTTCTTAATTCAAAGTTCAAAACTTGTTTACAAAATGAC--
446 GAGAAACAATTCTCACGTAAATAAGTT-TTAATTCAAAG-ACAAAACTTGGTTACAAAATGACAA
* * * * * *
2477 A-TATTTTGATCGATTGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATG
509 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATG
* * * * * ** * *
2541 GATTTTGTTGAATGCTTTAGGGATCCAAAGTTAAAAAATAACTTGTAGAAGTTTGACCAGTTTGG
574 GATCTTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGAAAAGTTCGA
*
2606 ATG
639 AAG
* * *
2609 TTCGTCC-AGAAATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAACGACCAAAA
1 TTCGTCCAAG-AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * ** * *
2673 CTCGTTTACAAAACGA-AAGTA-TATTCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTTT
65 CTTGTTTACAAAATGACAA--ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* * * *** * * * *
2736 GGAAAATTACTCGAAGGAATGAATCGCCTTGAATGCTTTAAGGAA-CGAAAGTTATAAAAGAAGT
128 GGAAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCG-AAGTTA-AAAATAACT
* *
2800 CGTAAAAGTTTGACACGTTCGAAAGTTCGTCCAAGAAG-AAAGAGAGAAACAATCCTCACGT-AA
191 CG-AAAAGTTTGACAAGTTCGAAAGTTCGTCCAA-AAGCAAAGAGAGAAACAATTCTCACGTAAA
* * * * * * * * * *
2863 -AAGTTTTTAACTGC-ATGACCAAAACTTGATTACGAAATGACAAACTCTTTACACCCAATGTTG
254 TAAGTTTTTAA-TTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATA
* ** * * * *
2926 CAATTTCTTAAGCATTGAATGTTTAGAAAAATT-CTCAAAGGAATGGGTCGTCT-TGAATACTTT
318 CGATTTCCCAAGCATGGAAT-ATTCGAAAAATTGCTCAAAGGAATGGATC-T-TATGAATACTTT
* *** * * * * *
2989 AAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTG-C-----C--AAG-T--TC---G----G
380 AGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCAAAGAAAAG
***********************************************
3036 -GAG-------T-T--CGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
445 AGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAAAGACAAAACTTGGTTACAAAATGACAAA
*** * * * * * *
3090 NNNTTTTGATCGATTGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGG
510 CTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGG
* * * * ** * *
3155 ATTTTGTTGAATGCTTTAGGGAACCAAAGTTAAAAAATAACTTGTAGAAGTTTGACCAGTTTGGA
575 ATCTTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGAAAAGTTCGAA
*
3220 TG
640 AG
* * * *
3222 TTCGT-CTAGAAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTACAACGACCAAAA
1 TTCGTCCAAG-AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * ** * *
3286 CTCGTTTACAAAACGA-AAGTA-TATTCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTTT
65 CTTGTTTACAAAATGACAA--ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* * * *** * * * *
3349 GGAAAATTACTCGAAGGAATGAATCGCCTTGAATGCTTTAAGGAA-CGAAAGTTATAAAAGAAGT
128 GGAAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCG-AAGTTA-AAAATAACT
* * *
3413 CGTAAAAGTTTGACACGTTCGAAAGTTCGTCCAAGAAG-AAAGAGAGAAACAATCCTCATGT-AA
191 CG-AAAAGTTTGACAAGTTCGAAAGTTCGTCCAA-AAGCAAAGAGAGAAACAATTCTCACGTAAA
* * * * *
3476 -AAGTTTTTAACTGC-ATGACCAAAACTTGATTATG--AAATGACAAACTCTTTAGACCCAATGT
254 TAAGTTTTTAA-TTCAAAGACCAAAACTTG-TT-TGCAAAATGACAAACTATTTAGACCAAATGA
* * ** * * * *
3537 TGCAATTTCTTAAGCATTGAATGTTTAGAAAAA-TGCTCAAAGGAATGGGTCGTCT-TGAATACT
316 TACGATTTCCCAAGCATGGAAT-ATTCGAAAAATTGCTCAAAGGAATGGATC-T-TATGAATACT
* *** * * * * * * ** * *
3600 TTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCCAAGTTCGGGAGTTCGTCCATGAAC
378 TTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCAAAGAA-
* * * * * *
3665 CAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCAAAAAACAAAACTTGTTTACAAAAT
442 -AAGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTC-AAAGACAAAACTTGGTTACAAAAT
* * * * * *
3730 GGCAAACTATTTAGACCAAATGATGCGATTTCCCGAGCGTGGAATGTT-TAGAAATTTTCTCTAA
504 GACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTCAAA
* *
3794 GGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAA
568 GGAATGGATCTTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGAAAA
* *
3859 GTTTGGAAG
633 GTTCGAAAG
* * * * * *
3868 TTCGTCAAAGATCAAAGATAGAAATAGTTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* * * * *
3933 TTGTTTACAAAATGGCAAACTATTTAGACTAAATGATGAGATTTGCCGAGCATGGAATGTTCGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
** * * * ** * * * ** *
3998 AAATTGCTTGAAGGAATGGATCATGTTGAAGACTTTAAGGATTCAAATTTATAAAAGATTTAGTA
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTA-AAAATAACTCG-A
* * * * * *
4063 AAAGTTTGATATGTTCGGAAGTTCGT-CAAAGAACAAAGAGAGAAACTATTCTCACGTGAATAAG
194 AAAGTTTGACAAGTTCGAAAGTTCGTCCAAA-AGCAAAGAGAGAAACAATTCTCACGTAAATAAG
* *
4127 TTTTTAATTCAAAGACCAAAACTAGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATT
258 TTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATACGATT
* * * * * * * *
4192 TCTCGAGCGTGGAATGTTC-AGAAAATTGCTCGAAA-GAATAGATCGTCTGGAATACTTTAGATC
323 TCCCAAGCATGGAATATTCGA-AAAATTGCTC-AAAGGAATGGATCTTAT-GAATACTTTAG--G
* ** ** * * * * * *
4255 GAA-TGATGAGATTTGCTGAGCATGGAATGTTTGATAAATTGCTCGAAGGAATGGATCGTCTTGA
383 GAACCGA--AG--TT--AAAAAAT--AA--CTCG-TAAA-AGTTTG-A-CAA--G-T--TC--GA
* * * *
4319 ATACTTTAAGGATCCGAGAAG-AAAGATAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAA
427 A-A-GTT--CG-T-C-A-AAGAAAAGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCAAA
** * * *
4383 GACCAAAACTTATTTACAAAATGACAAGCTATTTAGACCAAATGATGTGATTTCTCGAGCATGGA
483 GA-CAAAACTTGGTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGA
* * *
4448 ATGTTCGAAAAATTCCT-ATAAGGAATGGATCTTGTTGAATACTTTAGGGAATCGAAGTTAAAAA
547 ATGTTCGAAAAATTGCTCA-AAGGAATGGATCTTGTTGAATACTTTAGGGAACCAAAGTTAAAAA
**
4512 ATAACTCGTAAAAGTTTGGCAAGTTCGAAAG
611 ATAACTCGTAAAAGTTTGAAAAGTTCGAAAG
* *
4543 TTCGTCCAAGAACAAAGAGAGAAACAATTTTCACGTAAATAAGTTTTTAATTTAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* * * * *
4608 TTG-TTAGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGGGAATGGAATGTTTGA
66 TTGTTTA-CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGG
* * * * * * * * * **
4672 AAAATTGCTCGAAGGAATGGATCGTCTTCAACACTTTAAGGATCTGACGTTATAAAATAACAAGT
130 AAAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTA-AAAATAACTCG-
* * * * * * * * *
4737 AAAATTTTGACAAGCTTAG-ACGTTCATCTATGATG-AAAGACA-AATACCATTCTCACGTAAAT
193 AAAAGTTTGACAAG-TTCGAAAGTTCGTCCA-AAAGCAAAGAGAGAA-ACAATTCTCACGTAAAT
* * * * * *
4799 AAGTTCTGAATTCAAAGAACAAAAC-TGTTTTCGAAATGACAAACTATTTAGACCAAATGATGCG
255 AAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATACG
* * * * *
4863 ATTTCCCAAGGATGGAATGTTC-AGAAAATTGCTCTAAA--AATTGGATCTTGTTTAATACTTAA
320 ATTTCCCAAGCATGGAATATTCGA-AAAATTGCTC-AAAGGAA-TGGATCTT-ATGAATACTTTA
* * *
4925 GGGAACCGAAGTTAAAATATAACTTGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCATGAACAAA
381 GGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGT-CA--AAGAAA
* * * * * *
4990 AGAGAGAAACAATTCTCAAGT-AATAAGTTTTTAACTCAAAGACTGAAACTTGTTTGCAAAAGGA
443 AGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCAAAGAC-AAAACTTGGTTACAAAATGA
* ** * * *
5054 CAAACTATTTAGACCAAATGATGTGATTTGTCGAGTATGGAATGTTCGAAATATTGCTCAGAGGA
506 CAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGA
* ** * * * * *
5119 ATGGATC-AGTTGAATACTTTAATGAACCGAA-TTAATAAAA-GATTCAGTGAAAGTTTGACAAG
571 ATGGATCTTGTTGAATACTTTAGGGAACCAAAGTTAA-AAAATAACTC-GTAAAAGTTTGAAAAG
* *
5181 TTCGGATG
634 TTCGAAAG
* * * * *
5189 TTCGTCCAACAACAGAGAGAGAAATAATTCTCACATATATAAGTTTTTAATTCAAAGACCAAAAC
1 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
* *** * * *
5254 TTGTTTGCAAAATGACAAACTATTTAGACCAAATGATATAATTTGCCGAGCATAGAATGTTCAGA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
** * *
5319 AAATTGCTTGAAGAAATGGATCGTGTTGAATAC
131 AAATTGCTCAAAGGAATGGATCTTGTTGAATAC
5352 ATTAAGGATT
Statistics
Matches: 3855, Mismatches: 663, Indels: 372
0.79 0.14 0.08
Matches are distributed among these distances:
612 3 0.00
613 531 0.14
614 3 0.00
615 2 0.00
619 1 0.00
621 2 0.00
622 4 0.00
623 1 0.00
624 2 0.00
627 1 0.00
629 1 0.00
632 2 0.00
633 1 0.00
634 3 0.00
635 3 0.00
637 1 0.00
638 2 0.00
639 111 0.03
640 6 0.00
641 95 0.02
642 26 0.01
643 108 0.03
644 19 0.00
645 104 0.03
646 491 0.13
647 147 0.04
648 1067 0.28
649 15 0.00
650 5 0.00
651 3 0.00
652 3 0.00
653 2 0.00
654 2 0.00
655 2 0.00
656 1 0.00
657 2 0.00
659 3 0.00
660 4 0.00
661 6 0.00
662 4 0.00
663 5 0.00
665 7 0.00
666 7 0.00
667 272 0.07
668 11 0.00
669 2 0.00
670 1 0.00
671 102 0.03
672 8 0.00
673 150 0.04
674 95 0.02
675 396 0.10
676 6 0.00
677 2 0.00
678 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.27
Consensus pattern (641 bp):
TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGA
AAATTGCTCAAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGAAGTTAAAAATAACTCGAAA
AGTTTGACAAGTTCGAAAGTTCGTCCAAAAGCAAAGAGAGAAACAATTCTCACGTAAATAAGTTT
TTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATACGATTTCC
CAAGCATGGAATATTCGAAAAATTGCTCAAAGGAATGGATCTTATGAATACTTTAGGGAACCGAA
GTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCAAAGAAAAGAGAGAAACAAT
TCTCACGTAAATAAGTTTTAATTCAAAGACAAAACTTGGTTACAAAATGACAAACTATTTAGACC
AAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCTTGTTGAA
TACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGAAAAGTTCGAAAG
Found at i:3799 original size:216 final size:216
Alignment explanation
Indices: 3104--5359 Score: 1598
Period size: 216 Copynumber: 10.3 Consensus size: 216
3094 TTTGATCGAT
* * * ** *
3104 TGATGCGCTTTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATTTTGTTGAATG
1 TGATGCGATTTCTCGAGCATGGAATGTTTAG-AAAATTGCTCTAAGGAATGGATCGTGTTGAATA
* ** * * * * * * * * *
3168 CTTTAGGGAACCAAAGTTAAAAAATAACTTGTAGAAGTTTGACCAGTTTGGATGTTCGT-CTAGA
65 CTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAG-
* * * *
3232 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTACAACGACCAAAACTCGTTTACAA
129 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* *
3297 AACGA-AAGTA-TATTCAGACCAAA
194 AATGACAA--ACTATTTAGACCAAA
* * * * * * ** *
3320 TGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGAATCGCCTTGAATGC
1 TGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCTAAGGAATGGATCGTGTTGAATAC
* *
3385 TTTAAGGAAC-GAAAGTTATAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAGTTCGTCCAAGA
66 TTTAAGGAACTG-AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGA
* * * * * * **
3449 AGAAAGAGAGAAACAATCCTCATGT-AA-AAGTTTTTAACTGC-ATGACCAAAACTTGATTATGA
130 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TTCAAAGACCAAAACTTGTTTACAA
* *
3511 AATGACAAACTCTTTAGACCCAA
194 AATGACAAACTATTTAGACCAAA
* * ** * * * * *
3534 TGTTGCAATTTCTTAAGCATTGAATGTTTAGAAAAATGCTCAAAGGAATGGGTCGTCTTGAATAC
1 TGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCTAAGGAATGGATCGTGTTGAATAC
* * * * * * ** *
3599 TTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCCAAGTTCGGGAGTTCGTCCATGAA
66 TTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA
* * * * * * *
3664 CCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCAAAAAACAAAACTTGTTTACAAAA
131 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
*
3729 TGGCAAACTATTTAGACCAAA
196 TGACAAACTATTTAGACCAAA
* * * * *
3750 TGATGCGATTTCCCGAGCGTGGAATGTTTAGAAATTTTCTCTAAGGAATGGATCTTGTTGAATAC
1 TGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCTAAGGAATGGATCGTGTTGAATAC
* * * * * * * *
3815 TTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCAAAGAT
66 TTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA
* * * *
3880 CAAAGATAGAAATAGTTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAACTTGTTTACAAAA
131 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
* *
3945 TGGCAAACTATTTAGACTAAA
196 TGACAAACTATTTAGACCAAA
* * *
3966 TGATGAGATTTGC-CGAGCATGGAATG-TTCGAAAAATTGCT-TGAAGGAATGGATCATGTTGAA
1 TGATGCGATTT-CTCGAGCATGGAATGTTTAG-AAAATTGCTCT-AAGGAATGGATCGTGTTGAA
* * * * ** * * * * *
4028 GACTTTAAGG-ATTCAAATTTATAAAAGATTTAGTAAAAGTTTGATATGTTCGGAAGTTCGTCAA
63 TACTTTAAGGAACT-GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCA
* * * *
4092 AGAACAAAGAGAGAAACTATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAACTAGTTTGC
127 AGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
4157 AAAATGACAAACTATTTAGACCAAA
192 AAAATGACAAACTATTTAGACCAAA
* * * * * * *
4182 TGATGCGATTTCTCGAGCGTGGAATGTTCAGAAAATTGCTCGAAAGAATAGATCGTCTGGAATAC
1 TGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCTAAGGAATGGATCGTGTTGAATAC
* *** * * * * *
4247 TTTAGATCGAA-TGATGAGATT-T-GCTGAGCAT-G-GAATGTTTGATAAATTGCTCGAAGGAAT
66 TTTA-A-GGAACTGA--AG-TTATAAAAGAAC-TCGTAAAAGTTTGA-CAA--GTTCG-A--AA-
* * * * ** *
4307 GGATCGTCTTGAA-TACTTTAAGGATCCGAGAAGA-AA-GAT-A-G-AAACAA-TTCTCACCTAA
118 -GTTCGTC--CAAGAAC---AAAGA---GAGAA-ACAATTCTCACGTAAATAAGTT-T----T--
** ** * * * ** *
4365 ATAAGTTTTTAA-TTCAAAGACCAAAACT-TATTTACAAAATGA-CAA-GCTATTTAGACCAAA
166 -TAA--TTCAAAGACCAAA-A-C--T--TGT-TTA-CAAAATGACAAACTAT-TTA-GACCAAA
* * * * *
4425 TGATGTGATTTCTCGAGCATGGAATG-TTCGAAAAATTCCTATAAGGAATGGATCTTGTTGAATA
1 TGATGCGATTTCTCGAGCATGGAATGTTTAG-AAAATTGCTCTAAGGAATGGATCGTGTTGAATA
* * * *
4489 CTTTAGGGAA-TCGAAGTTAAAAAATAACTCGTAAAAGTTTGGCAAGTTCGAAAGTTCGTCCAAG
65 CTTTAAGGAACT-GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAG
* *
4553 AACAAAGAGAGAAACAATTTTCACGTAAATAAGTTTTTAATTTAAAGACCAAAACTTG-TTAGCA
129 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA-CA
4617 AAATGACAAACTATTTAGACCAAA
193 AAATGACAAACTATTTAGACCAAA
* * * * * *
4641 TGATGCGATTTCTCGGGAATGGAATGTTT-GAAAAATTGCTCGAAGGAATGGATCGTCTTCAACA
1 TGATGCGATTTCTCGAGCATGGAATGTTTAG-AAAATTGCTCTAAGGAATGGATCGTGTTGAATA
* * * ** * * * * * *
4705 CTTTAAGGATCTGACGTTATAAAATAACAAGTAAAATTTTGACAAGCTTAG-ACGTTCATCTATG
65 CTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-TTCGAAAGTTCGTCCAAG
** * * * * * * *
4769 ATGAAAGACA-AATACCATTCTCACGTAAATAAGTTCTGAATTCAAAGAACAAAAC-TGTTTTCG
129 AACAAAGAGAGAA-ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
4832 AAATGACAAACTATTTAGACCAAA
193 AAATGACAAACTATTTAGACCAAA
* * * * * * *
4856 TGATGCGATTTCCCAAGGATGGAATGTTCAGAAAATTGCTCTAA-AAATTGGATCTTGTTTAATA
1 TGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCTAAGGAA-TGGATCGTGTTGAATA
* * * *
4920 C-TTAAGGGAACCGAAGTTA-AAATATAACTTGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAT
65 CTTTAA-GGAACTGAAGTTATAAA-AGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAA
* * ** *
4983 GAACAAAAGAGAGAAACAATTCTCAAGT-AATAAGTTTTTAACTCAAAGACTGAAACTTGTTTGC
128 GAAC-AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
*
5047 AAAAGGACAAACTATTTAGACCAAA
192 AAAATGACAAACTATTTAGACCAAA
* * * * *
5072 TGATGTGATTTGTCGAGTATGGAATG-TTCGAAATATTGCTC-AGAGGAATGGATC-AGTTGAAT
1 TGATGCGATTTCTCGAGCATGGAATGTTTAGAAA-ATTGCTCTA-AGGAATGGATCGTGTTGAAT
* * * * * *
5134 ACTTTAATGAACCGAA-TTAATAAAAG-ATTCAGTGAAAGTTTGACAAGTTCGGATGTTCGTCCA
64 ACTTTAAGGAACTGAAGTT-ATAAAAGAACTC-GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCA
* * * * * *
5197 ACAACAGAGAGAGAAATAATTCTCACATATATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGC
127 AGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
5262 AAAATGACAAACTATTTAGACCAAA
192 AAAATGACAAACTATTTAGACCAAA
*** * * *
5287 TGATATAATTTGC-CGAGCATAGAATGTTCAGAAAATTGCT-TGAAGAAATGGATCGTGTTGAAT
1 TGATGCGATTT-CTCGAGCATGGAATGTTTAGAAAATTGCTCT-AAGGAATGGATCGTGTTGAAT
*
5350 ACATTAAGGA
64 ACTTTAAGGA
5360 TTCGAATGTA
Statistics
Matches: 1588, Mismatches: 348, Indels: 208
0.74 0.16 0.10
Matches are distributed among these distances:
213 1 0.00
214 195 0.12
215 305 0.19
216 832 0.52
217 34 0.02
218 7 0.00
219 4 0.00
220 6 0.00
221 1 0.00
222 6 0.00
223 6 0.00
224 3 0.00
225 6 0.00
226 3 0.00
227 12 0.01
228 6 0.00
229 6 0.00
230 6 0.00
231 7 0.00
232 11 0.01
233 3 0.00
234 6 0.00
235 3 0.00
236 6 0.00
237 5 0.00
238 2 0.00
239 6 0.00
240 3 0.00
241 11 0.01
242 17 0.01
243 69 0.04
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (216 bp):
TGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCTAAGGAATGGATCGTGTTGAATAC
TTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA
CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
TGACAAACTATTTAGACCAAA
Found at i:4297 original size:76 final size:76
Alignment explanation
Indices: 4171--4326 Score: 208
Period size: 76 Copynumber: 2.1 Consensus size: 76
4161 TGACAAACTA
* *
4171 TTTAGACCAAATGATGCGATTTCTCGAGCGTGGAATGTTCAGAAAATTGCTCGAAAGAATAGATC
1 TTTAGACCAAATGATGAGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGATC
4236 GTCTGGAATAC
66 GTCTGGAATAC
* * * * *
4247 TTTAGATCGAATGATGAGATTTGCT-GAGCATGGAATGTT-TGATAAATTGCTCGAAGGAATGGA
1 TTTAGACCAAATGATGAGATTT-CTCGAGCATGGAATGTTCAGA-AAATTGCTCGAAAGAATAGA
*
4310 TCGTCTTGAATAC
64 TCGTCTGGAATAC
4323 TTTA
1 TTTA
4327 AGGATCCGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
75 2 0.03
76 66 0.94
77 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (76 bp):
TTTAGACCAAATGATGAGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGATC
GTCTGGAATAC
Found at i:5269 original size:431 final size:428
Alignment explanation
Indices: 4337--5358 Score: 1243
Period size: 431 Copynumber: 2.4 Consensus size: 428
4327 AGGATCCGAG
* * *
4337 AAGAAAGATAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAACTTATTTACAA
1 AAGAAAG--AGAAATAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* * *
4402 AATGACAAGCTATTTAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTC-GAAAAATTCCTA
64 AATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCAG-AAAATTGCT-
* * * *
4466 TAAGGAATGGATCTTGTTGAATACTTTAGGGAATCGAAGTTAAAAAATAACTCGTAAAAGTTTGG
127 TAAGAAATGGATCTTGTTGAATACTTAAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGA
* * * *
4531 CAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTTTCACGTAAATAAGTTTTTAATTT
192 CAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAACTC
* *
4596 AAAGACCAAAACTTGTTAGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGGGAAT
257 AAAGACCAAAACTTGTTAGCAAAAGGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGAAT
* * * *
4661 GGAATGTTTGAAAAATTGCTCGAAGGAATGGATCGTCTTCAACACTTTAAGGATCTGACGTTATA
322 GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCG-CTTCAACACTTTAAGGAACCGACATTATA
* * * **
4726 AAATAACAAGTAAAATTTTGACAAGCTTAGACGTTCATCTATG
386 AAAGAACAAGTAAAAGTTTGACAAGCTTAGACGTTCATCAACA
* * * * * * * *
4769 ATGAAAGACAAATACCATTCTCACGTAAATAAGTTCTGAATTCAAAGAACAAAAC-TGTTTTCGA
1 AAGAAAGAGAAATA--ATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* * *
4833 AATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGAATGTTCAGAAAATTGCTCT
64 AATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCAGAAAATTGCT-T
* * *
4898 AA-AAATTGGATCTTGTTTAATACTTAAGGGAACCGAAGTTAAAATATAACTTGTAAAAGTTTGA
128 AAGAAA-TGGATCTTGTTGAATACTTAAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGA
*
4962 CAAGTTCGAAAGTTCGTCCATGAACAAAAGAGAGAAACAATTCTCAAGT-AATAAGTTTTTAACT
192 CAAGTTCGAAAGTTCGTCCAAGAAC-AAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAACT
** * * * *
5026 CAAAGACTGAAACTTGTTTGCAAAAGGACAAACTATTTAGACCAAATGATGTGATTTGTCGAGTA
256 CAAAGACCAAAACTTGTTAGCAAAAGGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGAA
* * * *
5091 TGGAATGTTCGAAATATTGCTC-AGAGGAATGGATCAG-TTGAATACTTTAATGAACCGA-ATTA
321 TGGAATGTTCGAAAAATTGCTCGA-AGGAATGGATC-GCTTCAACACTTTAAGGAACCGACATT-
* * * * *
5153 ATAAAAGATTC-AGTGAAAGTTTGACAAG-TTCGGATGTTCGTCCAACA
383 ATAAAAGA-ACAAGTAAAAGTTTGACAAGCTT-AGACGTTCAT-CAACA
* * *
5200 ACAGAGAGAGAAATAATTCTCACATATATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAA
1 A-AGAAAGAGAAATAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
* * * *
5265 ATGACAAACTATTTAGACCAAATGATATAATTTGCCGAGCATAGAATGTTCAGAAAATTGCTTGA
65 ATGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTT-A
*
5330 AGAAATGGATCGTGTTGAATACATTAAGG
129 AGAAATGGATCTTGTTGAATAC-TTAAGG
5359 ATTCGAATGT
Statistics
Matches: 500, Mismatches: 74, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
429 4 0.01
430 88 0.18
431 325 0.65
432 83 0.17
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (428 bp):
AAGAAAGAGAAATAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
TGACAAACTATTTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTAAG
AAATGGATCTTGTTGAATACTTAAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAG
TTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAACTCAAAG
ACCAAAACTTGTTAGCAAAAGGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGAATGGAA
TGTTCGAAAAATTGCTCGAAGGAATGGATCGCTTCAACACTTTAAGGAACCGACATTATAAAAGA
ACAAGTAAAAGTTTGACAAGCTTAGACGTTCATCAACA
Done.