Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000586.1 Kokia drynarioides strain JFW-HI SEQ_111516, 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: 2304
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:835 original size:216 final size:215
Alignment explanation
Indices: 1--2304 Score: 2043
Period size: 216 Copynumber: 10.7 Consensus size: 215
* ** * *
1 TAAGTAACCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCATGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-TTCGGAAGTTCGTCCAAGAACC
* * * * * * *
66 AAAAGAGAGACAATTCTCAGGTAAATAAGATTTTAATTCAAAGACTAAAACTTGTTTACCAACTG
65 AAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
* * * *
131 ACAAACTATTTAAACCAAATGATGCGATTTACT-GAATAAGGAATGTTC-GAAAATTTTCTCGAA
130 ACAAACTATTTAGACCAAATGATGCGATTT-CTCGAGTATGGAATGTTCAGAAAA-TTTCTCAAA
* *
194 GGAATTGATCGTCTTGAAAACTT
193 GGAATGGATCGTCTTGAATACTT
* * * * * * * * * * *
217 TAAGGAACTGAAGTTTTAAAACATCTCGTAAAAGTTTCACAAATGCAGAAGTACATCTAAGAATC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC-AATTCGGAAGTTCGTCCAAGAACC
* * * **
282 AAGAGAGAGACAATT-ATCATGTAAATAAGTTTTTAATTCAAA-ATTAAAACTTG-TTACAAAAT
65 AAAAGAGAAACAATTCA-CACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
* * * * * * * *
344 GACATACTATTTAAACTAAATGATGCTATTTCTAGAGCAAGGTATGTTCAGAAAATTTCTCAAAG
129 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGTATGGAATGTTCAGAAAATTTCTCAAAG
409 GAATGGATCGTCTTGAATACTT
194 GAATGGATCGTCTTGAATACTT
* * * * ** * *
431 T-AGAAAACCGAAGTTATAAAAGAACTCATAATAGTTTGACATGTTTTGAAGTTTGTGC-AGAAC
1 TAAG-GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA-ATTCGGAAGTTCGTCCAAGAAC
* * * * *
494 CAAGAGAGAAACAATTCTCATGTAAGTAAGTTTTTATTTCAAAGACCAAAACTTGTTTACAAAAT
64 CAAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
* * * * *
559 CG-TAAACTATTTAGACCAAATGATGCGATTTCTCGAGCT-CGAAATGTCCAGAAAATTGCTCAA
129 -GACAAACTATTTAGACCAAATGATGCGATTTCTCGAG-TATGGAATGTTCAGAAAATTTCTCAA
*
622 AGGAATGGATTGTCTTGAATACTT
192 AGGAATGGATCGTCTTGAATACTT
* * * * * * *
646 TAAGGGACCGAAGTTGTGAAGGCACTCGTAAAAGTTTGACTAATTTGGAAGTTCGTGCAAGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC-AATTCGGAAGTTCGTCCAAGAACC
* * * * *
711 AAAAGAGAAACAATTCAAACATAATTAAGCTTTTAATTCAAAGACCAAAACTTGTTTACAAAATA
65 AAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
* * ** * * *
776 ACAAAATATTTAGACCAAATTATAAGATTTC-CTAAGTATGGAATGTTCAGAATATTGCTCGAAA
130 ACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGTATGGAATGTTCAGAAAATTTCTC-AAA
840 -GAATGGATCAG-CTTGAATACTT
193 GGAATGGATC-GTCTTGAATACTT
* *
862 TAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA-C
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-TTCGGAAGTTCGTCCAAGAACC
* * * * ** * * * * *
926 -TAAGAGAAA-AATTGTA-ATGCAAATAAGTTTAAAATTCAAAAACAAAAAGTTTTTGTAAAAAA
65 AAAAGAGAAACAATT-CACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTT-TACAAAA
* * * * *
988 TGACAAA-TTTTTAGACCAAATGATGCGATTTCTCGAGCATGAAATGTTTAGAAAATTTTTCAAA
128 TGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGTATGGAATGTTCAGAAAATTTCTCAAA
* * ** * *
1052 GGTACGGATTATCCTGAAAACTT
193 GGAATGGATCGTCTTGAATACTT
* * ** * * *
1075 TAAGTACCCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCATCCATGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-TTCGGAAGTTCGTCCAAGAACC
* * * * * *
1140 AAAAGAGAGACAATTCTCAGGTAAATAAGTTTTTAATTCAAAGACTAAAACTTATTTACAAATTG
65 AAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
* * * * * *
1205 ACAAACTATTTAAACCAAATGATGCGATTTACT-GATTAAGGAATGTTCGGAGAATTTCTCGAAG
130 ACAAACTATTTAGACCAAATGATGCGATTT-CTCGAGTATGGAATGTTCAGAAAATTTCTCAAAG
* * *
1269 GAATGGATCGTCTTAAACACAT
194 GAATGGATCGTCTTGAATACTT
* * * * * * * * *
1291 TAAGGAACCGAAGTTTTAAAACATCTCGTCAAAGTTTCACCAATGCGGAAGTACATCTAAGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-CAATTCGGAAGTTCGTCCAAGAACC
* * * **
1356 AAGAGAGAAACAATTCACATGTAAATAAGTTTTTAATT-AAAAATTAAAACTTG-TTACAAAATG
65 AAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
* * * * *
1419 TCAAACTATTTAAACTAAATGATGCGATTTC-CTGA-TCATGGTATGTTCAGAAAATTTCTCGAA
130 ACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGT-ATGGAATGTTCAGAAAATTTCTCAAA
*
1482 GGAATGGATCGTCTAGAATACTT
193 GGAATGGATCGTCTTGAATACTT
* * * ** *
1505 TACA-AAACCGAGGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTTGAAGTTCGTGCAA-AAC
1 TA-AGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA-ATTCGGAAGTTCGTCCAAGAAC
* * * * * *
1568 CAAGAGGGAAACAATTCTCATGTAAGTAAGTTTTTATTTCAAAGACCAAAACTTGTTTACAAAAT
64 CAAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
* * * * *
1633 CG-TAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAATGTTC-GAAGAATTGCTCAG
129 -GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGTATGGAATGTTCAGAA-AATTTCTCAA
*
1696 AGGAATGGATTGTCTTGAATACTT
192 AGGAATGGATCGTCTTGAATACTT
* * * * * * * * * * *
1720 TAAGGGACAGAAATTGTGAAGGCACTCGTAAAAGCTTGACTAATTTGGAAGTTCATGCAAGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC-AATTCGGAAGTTCGTCCAAGAACC
* * * * *
1785 AAAAGAGAAACAATTCAAACGTAATTAAGCTTTTAATTCGAAGACCAAAACTTGTTTACAAAATA
65 AAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
* * ** * * * *
1850 ACAAAATATTTAGACCAAATTATAAGATTTC-CTGAGTGTGGAATGTTTAGAATATTGCTCGAAA
130 ACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGTATGGAATGTTCAGAAAATTTCTC-AAA
1914 -GAATGGATCAG-CTTGAATACTT
193 GGAATGGATC-GTCTTGAATACTT
* *
1936 TAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA-C
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-TTCGGAAGTTCGTCCAAGAACC
* * * * * ** * * *
2000 -TAAGAGAAA-AATTGTA-ATGCAAATAAGCTTAAAATTCAAAAACCAAAAGTTTTTTA-AAAAT
65 AAAAGAGAAACAATT-CACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA-
* * * * * *
2061 TGACAAAAT-TTTAGACGAAATGAAT-CGATTTCTCGAGCATGAAATGTTCAAAAAATTTCTCGA
128 TGACAAACTATTTAGACCAAATG-ATGCGATTTCTCGAGTATGGAATGTTCAGAAAATTTCTCAA
* * *
2124 AGGAACGGATCGTCTTGAAAACAT
192 AGGAATGGATCGTCTTGAATACTT
* * ** * * * *
2148 TAAGTACCCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAGTGCGAAAGTTAGTCCATGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-TTCGGAAGTTCGTCCAAGAACC
* * * * *
2213 AAAAGAGAGACAATTCTCAGGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAACTG
65 AAAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
*
2278 ACAAACTATTTAAACCAAATGATGCGA
130 ACAAACTATTTAGACCAAATGATGCGA
Statistics
Matches: 1680, Mismatches: 343, Indels: 130
0.78 0.16 0.06
Matches are distributed among these distances:
211 3 0.00
212 114 0.07
213 277 0.16
214 296 0.18
215 342 0.20
216 631 0.38
217 17 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (215 bp):
TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAATTCGGAAGTTCGTCCAAGAACCA
AAAGAGAAACAATTCACACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA
CAAACTATTTAGACCAAATGATGCGATTTCTCGAGTATGGAATGTTCAGAAAATTTCTCAAAGGA
ATGGATCGTCTTGAATACTT
Found at i:955 original size:429 final size:428
Alignment explanation
Indices: 1--2304 Score: 2021
Period size: 429 Copynumber: 5.4 Consensus size: 428
* ** *
1 TAAGTAACCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCATGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACC
* * * * * *
66 AAAAGAGAGACAATTCTCAGGTAAATAAGATTTTAATTCAAAGACTAAAACTTGTTTACCAACTG
66 AAAAGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATG
* *
131 ACAAACTATTTAAACCAAATGATGCGATTTACT-GA-ATAAGGAATGTTC-GAAAATTTTCTCGA
131 -CAAACTATTTAAACCAAATGATGCGATTT-CTCGAGCT--GGAATGTTCAGAAAA-TTTCTCAA
* * * * * * *
193 AGGAATTGATCGTCTTGAAAACTTTAAGGAACTGAAGTTTTAAAACATCTCGTAAAAGTTTCACA
191 AGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC-
* * * * * * * * *
258 AATGCAGAAGTACATCTAAGAATCAAGAGAGAGACAATT--ATCATGTAAATAAGTTTTTAATTC
255 AATTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCAAACA--TAAATAAGTTTTTAATTC
** * * * * *
321 AAA-ATTAAAACTTG-TTACAAAATGACATACTATTTAAACTAAATGATGCTATTTCTAGAGCAA
318 AAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCT-GAGCAT
* * *
384 GGTATGTTCAGAAAATTTCTCAAAGGAATGGATCGTCTTGAATACTT
382 GGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* * * * *** * *
431 T-AGAAAACCGAAGTTATAAAAGAACTCATAATAGTTTGACATGTTTTGAAGTTTGTGC-AGAAC
1 TAAG-GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAAC
* * * * *
494 CAAGAGAGAAACAATTCTCATGTAAGTAAGTTTTTATTTCAAAGACCAAAACTTGTTTACAAAAT
65 CAAAAGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAAT
* * * * *
559 CGTAAACTATTTAGACCAAATGATGCGATTTCTCGAGCTCGAAATGTCCAGAAAATTGCTCAAAG
130 -GCAAACTATTTAAACCAAATGATGCGATTTCTCGAGCT-GGAATGTTCAGAAAATTTCTCAAAG
* * * * * *
624 GAATGGATTGTCTTGAATACTTTAAGGGACCGAAGTTGTGAAGGCACTCGTAAAAGTTTGACTAA
193 GAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC-AA
* * * *
689 TTTGGAAGTTCGTGCAAGAACCAAAAGAGAAACAATTCAAACATAATTAAGCTTTTAATTCAAAG
257 TTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCAAACATAAATAAGTTTTTAATTCAAAG
* * * ** * *
754 ACCAAAACTTGTTTACAAAATAACAAAATATTTAGACCAAATTATAAGATTTCCTAAGTATGGAA
322 ACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-CTGAGCATGGAA
* *
819 TGTTCAGAATATTGCTCGAAAGAATGGATCAG-CTTGAATACTT
386 TGTTCAGAAAATTGCTCGAAGGAATGGATC-GTCTTGAATACTT
* * *
862 TAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA-C
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACC
* * * ** * * * * *
926 -TAAGAGAAA-AATTGTAATGCAAATAAGTTTAAAATTCAAAAACAAAAAGTTTTTGTAAAAAAT
66 AAAAGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTT-TACAAAAT
* * * * *
989 GACAAA-TTTTTAGACCAAATGATGCGATTTCTCGAGCATGAAATGTTTAGAAAATTTTTCAAAG
130 G-CAAACTATTTAAACCAAATGATGCGATTTCTCGAGC-TGGAATGTTCAGAAAATTTCTCAAAG
* * ** * * * * **
1053 GTACGGATTATCCTGAAAACTTTAAGTACCCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAG
193 GAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-
* * * * ** **
1118 TGCGGAAGTTCATCCATGAACCAAAAGAGAGACAATTCTCAGGTAAATAAGTTTTTAATTCAAAG
257 TTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCAAACATAAATAAGTTTTTAATTCAAAG
* * * * ** *
1183 ACTAAAACTTATTTACAAATTGACAAACTATTTAAACCAAATGATGCGATTTACTGATTAAGGAA
322 ACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-CTGAGCATGGAA
* * * * * *
1248 TGTTCGGAGAATTTCTCGAAGGAATGGATCGTCTTAAACACAT
386 TGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* * * * * * * *
1291 TAAGGAACCGAAGTTTTAAAACATCTCGTCAAAGTTTCACCAA-TGCGGAAGTACATCTAAGAAC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-CAAGTGCGGAAGTTCGTCCAAGAAC
* * *
1355 CAAGAGAGAAACAATTC-ACATGTAAATAAGTTTTTAATT-AAAAATTAAAACTTG-TTACAAAA
65 CAAAAGAGAAACAATTCTA-ATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAA
* * * *
1417 TGTCAAACTATTTAAACTAAATGATGCGATTTC-CTGATCATGGTATGTTCAGAAAATTTCTCGA
129 TG-CAAACTATTTAAACCAAATGATGCGATTTCTC-GAGC-TGGAATGTTCAGAAAATTTCTCAA
* * *
1481 AGGAATGGATCGTCTAGAATACTTTACA-AAACCGAGGTTATAAAAGAACTCGTAAAAGTTTGAC
191 AGGAATGGATCGTCTTGAATACTTTA-AGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC
* ** * * * ** ** * *
1545 ATGTTTTGAAGTTCGTGCAA-AACCAAGAGGGAAACAATTCTCATGTAAGTAAGTTTTTATTTCA
255 A-ATTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCAAACATAAATAAGTTTTTAATTCA
*
1609 AAGACCAAAACTTGTTTACAAAATCG-TAAACTATTTAGACCAAATGATGCGATTTCTCGAGCAT
319 AAGACCAAAACTTGTTTACAAAAT-GACAAACTATTTAGACCAAATGATGCGATTTCT-GAGCAT
* *
1673 GAAATGTTC-GAAGAATTGCTC-AGAGGAATGGATTGTCTTGAATACTT
382 GGAATGTTCAGAA-AATTGCTCGA-AGGAATGGATCGTCTTGAATACTT
* * * * * * * * ** * *
1720 TAAGGGACAGAAATTGTGAAGGCACTCGTAAAAGCTTGACTAA-TTTGGAAGTTCATGCAAGAAC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC-AAGTGCGGAAGTTCGTCCAAGAAC
* * * * * *
1784 CAAAAGAGAAACAATTCAAACGTAATTAAGCTTTTAATTCGAAGACCAAAACTTGTTTACAAAAT
65 CAAAAGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAAT
* * * * ** * * * *
1849 AACAAAATATTTAGACCAAATTATAAGATTTC-CTGAGTGTGGAATGTTTAGAATATTGCTCGAA
130 -GCAAACTATTTAAACCAAATGATGCGATTTCTC-GAG-CTGGAATGTTCAGAAAATTTCTC-AA
* *
1913 A-GAATGGATCAG-CTTGAATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTTGAC
191 AGGAATGGATC-GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC
* ** *** * **
1976 AAGTTCGGAAGTTCGTCCAAGAA-C-TAAGAGAAA-AATTGTAATGCAAATAAGCTTAAAATTCA
255 AA-TTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCAAACATAAATAAGTTTTTAATTCA
* * * * *
2038 AAAACCAAAAGTTTTTTA-AAAATTGACAAAAT-TTTAGACGAAATGAAT-CGATTTCTCGAGCA
319 AAGACCAAAACTTGTTTACAAAA-TGACAAACTATTTAGACCAAATG-ATGCGATTTCT-GAGCA
* * * * * *
2100 TGAAATGTTCAAAAAATTTCTCGAAGGAACGGATCGTCTTGAAAACAT
381 TGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* * ** * * *
2148 TAAGTACCCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAGTGCGAAAGTTAGTCCATGAACC
1 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACC
* * * *
2213 AAAAGAGAGACAATTCTCAGGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAACTG
66 AAAAGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATG
2278 ACAAACTATTTAAACCAAATGATGCGA
131 -CAAACTATTTAAACCAAATGATGCGA
Statistics
Matches: 1501, Mismatches: 324, Indels: 100
0.78 0.17 0.05
Matches are distributed among these distances:
427 2 0.00
428 200 0.13
429 787 0.52
430 210 0.14
431 267 0.18
432 35 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (428 bp):
TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACC
AAAAGAGAAACAATTCTAATGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATG
CAAACTATTTAAACCAAATGATGCGATTTCTCGAGCTGGAATGTTCAGAAAATTTCTCAAAGGAA
TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAATTCG
GAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCAAACATAAATAAGTTTTTAATTCAAAGACCA
AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTGAGCATGGAATGTTC
AGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTT
Found at i:1272 original size:645 final size:638
Alignment explanation
Indices: 1--2304 Score: 2097
Period size: 645 Copynumber: 3.6 Consensus size: 638
* * * *
1 TAAGTAACCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCATGAACC
1 TAAGGAACCGAAGT-TTAAAAGCACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACC
* ** ** * * * * *
66 AAAAGAGAGACAATTCTCAGGTAAATAAGATTTTAATTCAAAGACTAAAACTTGTTTACCAACTG
65 AAAAGAGAAACAATTCAAACATAAATAAGCTTTTAATTCAAAAACCAAAACTTGTTTACAAAATG
* * * * *
131 ACAAACTATTTAAACCAAATGATGCGATTTACTGAATAAGGAATGTTC-GAAAATTTTCTCGAAG
130 ACAAAATATTTAAACCAAATGATACGATTTCCTCAATATGGAATGTTCAGAAAA-TTTCTCGAAG
* * * * * * *
195 GAATTGATCGTCTTGAAAACTTTAAGGAACTGAAGTTTTAAAACATCTCGTAAAAGTTTCACAAA
194 GAATGGATCGTCTTGAAAACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
* * * *
260 TGCAGAAGTACATCTAAGAA-TCAAGAGAGAGACAATTATCATGTAAATAAGTTTTTAATTC-AA
259 TGCGGAAGTTCGTCCAAGAACT-AAGAGA-A-ACAATTATCATGTAAATAAGTTTTTAATTCAAA
** * * * * * * * **
323 AATTAAAACTTGTTACAAAATGACATACTATTTAAACTAAATGATGCTATTTCTAGAGCAAGGTA
321 AACAAAAATTTTTTACAAAATGACA-ACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAA
* * * *
388 TGTTCAGAAAATTTCTCAAAGGAATGGATCGTCTTGAATACTTTAGAAAACCGAAGTTATAAAAG
385 TGTTTAGAAAATTTCTCAAAGGAATGGATTGTCTTGAATACTTTA-AGAACCGAAGTTGTAAAAG
* * * * ** * *
453 AACTCATAATAGTTTGACATGTTTTGAAGTTTGTGCAGAACCAAGAGAGAAACAATTCTCATGTA
449 AACTCGTAAAAGTTTGACAAGTTTGGAAGTTCATGCAGAACCAAAAGAGAAACAATTCTCACGTA
* * * *
518 AGTAAGTTTTTATTTCAAAGACCAAAACTTGTTTACAAAATCG-TAAACTATTTAGACCAAATGA
514 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC-AAATTGACAAACTATTTAGACCAAATGA
* * * * * * *
582 TGCGATTTCTCGAGCTCGAAATGTCCAGAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTT
578 TGCGATTTCT-GA-CTAGGAATGTTC-GAGAATTTCTCGAAGGAATGGATAGTCTTGAATACTT
* * * ** *
646 TAAGGGACCGAAGTTGTGAAGGCACTCGTAAAAGTTTGACTAA-TTTGGAAGTTCGTGCAAGAAC
1 TAAGGAACCGAAGTT-TAAAAGCACTCGTAAAAGTTTGAC-AAGTGCGGAAGTTCGTCCAAGAAC
* *
710 CAAAAGAGAAACAATTCAAACATAATTAAGCTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
64 CAAAAGAGAAACAATTCAAACATAAATAAGCTTTTAATTCAAAAACCAAAACTTGTTTACAAAAT
* * * * * *
775 AACAAAATATTTAGACCAAATTATAAGATTTCCT-AAGTATGGAATGTTCAGAATATTGCTCGAA
129 GACAAAATATTTAAACCAAATGATACGATTTCCTCAA-TATGGAATGTTCAGAAAATTTCTCGAA
* * * *
839 AGAATGGATCAG-CTTGAATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTTGACA
193 GGAATGGATC-GTCTTGAAAACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA
* * * * **
903 AGTTCGGAAGTTCGTCCAAGAACTAAGAGAAA-AATTGTAATGCAAATAAGTTTAAAATTCAAAA
257 AGTGCGGAAGTTCGTCCAAGAACTAAGAGAAACAATTATCATGTAAATAAGTTTTTAATTCAAAA
* * *
967 ACAAAAAGTTTTTGTAAAAAATGACAAATTTTTAGACCAAATGATGCGATTTCTCGAGCATGAAA
322 ACAAAAA-TTTTT-TACAAAATGACAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAA
* * * * * * * *
1032 TGTTTAGAAAATTTTTCAAAGGTACGGATTATCCTGAAAACTTTAAGTACCCGAAGTCGTAAAAG
385 TGTTTAGAAAATTTCTCAAAGGAATGGATTGTCTTGAATACTTTAAG-AACCGAAGTTGTAAAAG
** * * *
1097 AACTCGTAAAAGTTTGACAAGTGCGGAAGTTCATCCATGAACCAAAAGAGAGACAATTCTCAGGT
449 AACTCGTAAAAGTTTGACAAGTTTGGAAGTTCATGCA-GAACCAAAAGAGAAACAATTCTCACGT
* * *
1162 AAATAAGTTTTTAATTCAAAGACTAAAACTTATTTACAAATTGACAAACTATTTAAACCAAATGA
513 AAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAATTGACAAACTATTTAGACCAAATGA
* * * * *
1227 TGCGATTTACTGATTAAGGAATGTTCGGAGAATTTCTCGAAGGAATGGATCGTCTTAAACACAT
578 TGCGATTT-CTGACT-AGGAATGTTC-GAGAATTTCTCGAAGGAATGGATAGTCTTGAATACTT
* * * * *
1291 TAAGGAACCGAAGTTTTAAAA-CATCTCGTCAAAGTTTCACCAA-TGCGGAAGTACATCTAAGAA
1 TAAGGAACCGAAG-TTTAAAAGCA-CTCGTAAAAGTTTGA-CAAGTGCGGAAGTTCGTCCAAGAA
* * ** * **
1354 CCAAGAGAGAAACAATTCACATGTAAATAAGTTTTTAATT-AAAAATTAAAACTTG-TTACAAAA
63 CCAAAAGAGAAACAATTCAAACATAAATAAGCTTTTAATTCAAAAACCAAAACTTGTTTACAAAA
* * * * * *
1417 TGTCAAACTATTTAAACTAAATGATGCGATTTCCT-GATCATGGTATGTTCAGAAAATTTCTCGA
128 TGACAAAATATTTAAACCAAATGATACGATTTCCTCAAT-ATGGAATGTTCAGAAAATTTCTCGA
* * * *
1481 AGGAATGGATCGTCTAGAATACTTTACA-AAACCGAGGTTATAAAAGAACTCGTAAAAGTTTGAC
192 AGGAATGGATCGTCTTGAAAACTTTA-AGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC
* *** * * * * *
1545 ATGTTTTGAAGTTCGTGCAA-AACCAAGAGGGAAACAATTCTCATGTAAGTAAGTTTTTATTTCA
256 AAGTGCGGAAGTTCGTCCAAGAACTAAGA--GAAACAATTATCATGTAAATAAGTTTTTAATTCA
* * *
1609 AAGACCAAAACTTGTTTACAAAATCGTA-AACTATTTAGACCAAATGATGCGATTTCTCGAGCAT
319 AA-AACAAAAATTTTTTACAAAAT-G-ACAACTATTTAGACCAAATGATGCGATTTCTCGAGCAT
* * * * * *
1673 GAAATG-TTCGAAGAATTGCTCAGAGGAATGGATTGTCTTGAATACTTTAAGGGACAGAAATTGT
381 GAAATGTTTAGAA-AATTTCTCAAAGGAATGGATTGTCTTGAATACTTTAA-GAACCGAAGTTGT
* * * *
1737 GAAGGCACTCGTAAAAGCTTGACTAA-TTTGGAAGTTCATGCAAGAACCAAAAGAGAAACAATTC
444 AAAAGAACTCGTAAAAGTTTGAC-AAGTTTGGAAGTTCATGC-AGAACCAAAAGAGAAACAATTC
** * * * * * *
1801 AAACGTAATTAAGCTTTTAATTCGAAGACCAAAACTTGTTTACAAAATAACAAAATATTTAGACC
507 TCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAATTGACAAACTATTTAGACC
* ** * * * *
1866 AAATTATAAGATTTCCTGAGTGTGGAATGTT-TAGAATATTGCTCGAAAGAATGGATCAG-CTTG
572 AAATGATGCGATTT-CTGACT-AGGAATGTTCGAGAAT-TT-CTCGAAGGAATGGAT-AGTCTTG
1929 AATACTT
632 AATACTT
* * * *
1936 TAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA-C
1 TAAGGAACCGAAG-TTTAAAAGCACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACC
* ** *** ** * *
2000 -TAAGAGAAA-AATTGTAATGCAAATAAGCTTAAAATTCAAAAACCAAAAGTTTTTTA-AAAATT
65 AAAAGAGAAACAATTCAAACATAAATAAGCTTTTAATTCAAAAACCAAAACTTGTTTACAAAA-T
* * ** * *
2062 GACAAAAT-TTTAGACGAAATGA-ATCGATTT-CTCGAGCATGAAATGTTCAAAAAATTTCTCGA
129 GACAAAATATTTAAACCAAATGATA-CGATTTCCTC-AATATGGAATGTTCAGAAAATTTCTCGA
* * * * **
2124 AGGAACGGATCGTCTTGAAAACATTAAGTACCCGAAGTCGTAAAAGAACTCGTAAAAGTTTGACA
192 AGGAATGGATCGTCTTGAAAACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA
* * * * * * *
2189 AGTGCGAAAGTTAGTCCATGAACCAAAAGAGAGACAATTCTCAGGTAAATAAGTTTTTAATTCAA
257 AGTGCGGAAGTTCGTCCAAGAA-C-TAAGAGAAACAATTATCATGTAAATAAGTTTTTAATTCAA
* * * * *
2254 AGACTAAAACTTGTTTACAAACTGACAAACTATTTAAACCAAATGATGCGA
320 AAAC-AAAAATTTTTTACAAAATGAC-AACTATTTAGACCAAATGATGCGA
Statistics
Matches: 1340, Mismatches: 271, Indels: 97
0.78 0.16 0.06
Matches are distributed among these distances:
642 56 0.04
643 272 0.20
644 242 0.18
645 740 0.55
646 30 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (638 bp):
TAAGGAACCGAAGTTTAAAAGCACTCGTAAAAGTTTGACAAGTGCGGAAGTTCGTCCAAGAACCA
AAAGAGAAACAATTCAAACATAAATAAGCTTTTAATTCAAAAACCAAAACTTGTTTACAAAATGA
CAAAATATTTAAACCAAATGATACGATTTCCTCAATATGGAATGTTCAGAAAATTTCTCGAAGGA
ATGGATCGTCTTGAAAACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTG
CGGAAGTTCGTCCAAGAACTAAGAGAAACAATTATCATGTAAATAAGTTTTTAATTCAAAAACAA
AAATTTTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAATGTTTA
GAAAATTTCTCAAAGGAATGGATTGTCTTGAATACTTTAAGAACCGAAGTTGTAAAAGAACTCGT
AAAAGTTTGACAAGTTTGGAAGTTCATGCAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAAAGACCAAAACTTGTTTACAAATTGACAAACTATTTAGACCAAATGATGCGATTT
CTGACTAGGAATGTTCGAGAATTTCTCGAAGGAATGGATAGTCTTGAATACTT
Done.