Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011755.1 Kokia drynarioides strain JFW-HI SEQ_126749, 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: 4249
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Found at i:841 original size:216 final size:216
Alignment explanation
Indices: 136--2209 Score: 2081
Period size: 216 Copynumber: 9.6 Consensus size: 216
126 GCTTGGGATA
** * * *
136 TTCGAAAAACAGCTCGAAGGAAAGGATTATCTTGAATACTTTAAGGAATCGAAGTTATAAAGGAA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
* * * * * * * * **
201 CGCATAGAAGTTTGACAAGTTTGGAAGTTCGTCCAAAAACCAAGATAGAAACAATTTTTGCGTAA
66 CTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTAA
* *** * * *
266 ACAAGTTTTT-ATTCAAAGATGTAATCTAGTTTACAAAATGGA-AAACTATTTAG-CCTAAATAA
131 ATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-GACAAACTATTTAGACC-AAATGA
* ** *
328 TGCGTTTTCCCAAGTAGGGAATG
194 TGCGATTTCCTGAGTATGGAATG
* * ** *
351 TTCAAAAAATTGCTCGAAGGAATGAATTGTCTTGAATACTTTAAGGAA-CTGAAGTTATAAATGA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATC-GAAGTTATAAAAGA
* * * * * * * *
415 ACTCATAAATGTTTGACAAGTTCAAAAGTTCATCCAAGAACCAACAGAGAAATAACTGTCACGTA
65 ACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGT-
* * * *
480 AAATAAGTTTTTAATTCAAATACCAAAA---GTTAACAAAATAACAAACTGTTTAGACCAAATGA
129 AAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
* *
542 TGCGATTT-CTCAAGCATGGAATG
194 TGCGATTTCCT-GAGTATGGAATG
* * ** * * *
565 TTCGAAAAATTGCTCGAAGGAATGAATCATCTTGAATACTATAACAAACCAAAATTATAAAAGAA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
* * ** *
630 CTCGTAAAAGTTTGACAAGTTTGGAAGTTCAT-CAAAAAATAATGAGAGAAAAAATTCTCACGTA
66 CTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAA-GAGAGAAACAATTCTCACGTA
* * * * *
694 AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACTATTTAGACTAGATGAA
130 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAT
* *
759 GTGATTTCCTGAGTATGAAATG
195 GCGATTTCCTGAGTATGGAATG
* * ** * *
781 CTT-GGAAAACTGCTCGAAGGAGA-GGATTGTCTTGAATGCTTTAAGGAATCGAAGTTATAAAGG
1 -TTCGAAAAATTGCTCGAAGGA-ATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAG
* * * * * * * * *
844 AACTCGTAGAAGTTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGATAAAAATAATTCACGCGT
64 AACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGT
* * * * * * *
909 AAACAAGTTTTAAATTCAAAGACCTAATCTAGTTTACAAAATGACACACTATTTTGACCAAATGA
129 AAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
* * *
974 TGCGTTTTCCCGAGCATGGAATG
194 TGCGATTTCCTGAGTATGGAATG
* * * * *
997 TTCGAAAAATTCCTCGAAGGAATGGATCGTCTTGAATACTTTCAGGAACCAAAGTTATAAAAGAA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
* * * * * *
1062 CTCATAAATGTTTGACAAGTTCGAAAGTTCGTCC-AAGACCGAA-AGAGAATCAACTCTCACGTA
66 CTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACC-AAGAGAGAAACAATTCTCACGTA
* * * * *
1125 AACAAGTTTTTAAGTCAAAGACCAAAA---GTTTAAAAAATGACAAACTGTTCAGACCAAATGAT
130 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAT
*
1187 GCGATTTCCCT-AGAATGGAATG
195 GCGATTT-CCTGAGTATGGAATG
* * * * * *
1209 TCCGAAAAGTTCCTCGAAGGAATGGATCATCTTGAATACTGTAATGAAACGAAGTTATAAAAGAA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
* *
1274 CTCGTAAAAGTTTGACAAGTTC-AGAAGTTCATCCAAAAACCAAGAGAGGAACAATTCCCACGTA
66 CTCGTAAAAGTTTGACAAGTTCGA-AAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTA
* * *
1338 AATAAG-TTTTAATTTAAAGACCAAAAGC-GGTTTACAAAATGACAAACTATTTAGACCAAAAGA
130 AATAAGTTTTTAATTCAAAGACCAAAA-CTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
**
1401 TGCGATTT-CTCGAGCGTGGAATG
194 TGCGATTTCCT-GAGTATGGAATG
*
1424 TTCGAAAAATTGCTCGATA-GAATGGATCATCTTGAATAGTTTAAGGAATCGAAGTTATAAAAGA
1 TTCGAAAAATTGCTCGA-AGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGA
** * * * * * * * *
1488 ACTCGTAAAAGTTTTTCAAGTTTGAAAGTTCATCCAAGATCTATGAGATAAACAATTCCCATGTA
65 ACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTA
* * * * *
1553 AATAAGTTTTTAATTCAAAGACCAAAACATGTATACAAAATAACAAACTATTTAGAACAATTGAT
130 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAT
* * *
1618 GAGATTT-CTCAAGTATGGACTG
195 GCGATTTCCT-GAGTATGGAATG
* * *
1640 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTGAGGAA-C-TA-TAATAAAAGAA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
* * * *
1702 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCTAAACACCAAGAGAGAAACAATTTTCACGTAA
66 CTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTAA
* * * * * *
1767 ATAAATTTTTAATTCAAAGACCAAATCCTGTTTACAAATTGACAAACAATTTTGACCAAATGATG
131 ATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
*
1832 TGATTT-CTCGAGTATGGAAATG
196 CGATTTCCT-GAGTATGG-AATG
* * * *
1854 TTTGAAAAAAATT--TCGACGGAATGGATCATCTTGAATACTTTAAAGAATGGAAGTTATAAAAG
1 TTCG--AAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAG
* * ** * *
1917 AACTCGTAGAAGTTTGACAACTTC-AGAAGTTTGT-CAAAGAACCAAGAGAGAAATAGTTCTCAC
64 AACTCGTAAAAGTTTGACAAGTTCGA-AAGTTCATCCAAA-AACCAAGAGAGAAACAATTCTCAC
* * * * * *
1980 GTAAATAATTTTTTAATTCAAAAACAAAAATTTGTTTACAAAATAACAAACTATTTAGTCCAAAT
127 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAAT
* *
2045 GATGCGGTTTCCT-AGTCATTGAATG
192 GATGCGATTTCCTGAGT-ATGGAATG
* * * * *
2070 TTAGGAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTTTAAGGAA-CTGAAGTTATAAAAGA
1 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATC-GAAGTTATAAAAGA
* * * * * *
2134 ACTCGTAAAAGTTTTACAAGTTCGAAAGCTCGTCCAAGAACCAAAAGAGAAATAATTCTCACGTA
65 ACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTA
2199 AATAAGTTTTT
130 AATAAGTTTTT
2210 GACAAGTTCA
Statistics
Matches: 1537, Mismatches: 275, Indels: 93
0.81 0.14 0.05
Matches are distributed among these distances:
211 1 0.00
212 152 0.10
213 197 0.13
214 185 0.12
215 314 0.20
216 539 0.35
217 147 0.10
218 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
CTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTAA
ATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
CGATTTCCTGAGTATGGAATG
Found at i:2023 original size:430 final size:426
Alignment explanation
Indices: 148--2209 Score: 2148
Period size: 430 Copynumber: 4.8 Consensus size: 426
138 CGAAAAACAG
* * * * * *
148 CTCGAAGGAAAGGATTATCTTGAATACTTTAAGGAATCGAAGTTATAAAGGAACGCATAGAAGTT
1 CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTT
* * * ** *
213 TGACAAGTTTGGAAGTTCGTCCAAA-AACCAAGATAGAAACAATTTTTGCGTAAACAAGTTTTT-
66 TGACAAGTTCGGAAGTTCGT-CAAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
*** * * * *
276 ATTCAAAGA-TGTAATCTAGTTTACAAAATGGA-AAACTATTTAGCCTAAATAATGCGTTTTCCC
130 ATTCAAAGACCAAAAT-TTGTTTACAAAAT-AACAAACTATTTAGCC-AAATGATGCGATTT-CC
* * * *
339 AAGTAGGGAATGTTCAAAAAATTGCTCGAAGGAATGAATTGTCTTGAATACTTTAAGGAACTGAA
191 AAGTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACT--A
* * * * *
404 GTTATAAATGAACTCATAAATGTTTGACAAGTTCAAAAGTTCATCCAAGAACCAACAGAGAAATA
254 GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAATA
* * * * * * *
469 ACTGTCACGTAAAATAAGTTTTTAATTCAAATACCAAA--AGTTAACAAAATAACAAACTGTTTA
319 ATTCTCACGT-AAATAAGTTTTTAATTCAAAGACCAAATCTGTTTACAAAATGACAAACTATTTA
*
532 GACCAAATGATGCGATTTCTCAAGCATGGAATGTTCGAAAAATT
383 GACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATT
* * ** * * *
576 GCTCGAAGGAATGAATCATCTTGAATACTATAACAAACCAAAATTATAAAAGAACTCGTAAAAGT
1 -CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGT
* * ** *
641 TTGACAAGTTTGGAAGTTCATCAAA-AAATAATGAGAGAAAAAATTCTCACGTAAATAAGTTTTT
65 TTGACAAGTTCGGAAGTTCGTCAAAGAACCAA-GAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * *
705 AATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACTATTTAGACTAGATGAAGTGATTTCCTG
129 AATTCAAAGACCAAAATTTGTTTACAAAATAACAAACTATTTAG-CCAAATGATGCGATTTCC-A
* * * * * *
770 AGTATGAAATGCTT-GGAAAACTGCTCGAAGGAGA-GGATTGTCTTGAATGCTTTAAGGAATCGA
192 AGTATGGAATG-TTCGAAAAATTGCTCGAAGGA-ATGGATCGTCTTGAATACTTTAAGGAA-C-T
* * * * * *
833 AGTTATAAAGGAACTCGTAGAAGTTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGATAAAAAT
253 AGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAAT
* * * * * *
898 AATTCACGCGTAAACAAGTTTTAAATTCAAAGACCTAATCTAGTTTACAAAATGACACACTATTT
318 AATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAATCT-GTTTACAAAATGACAAACTATTT
* * *
963 TGACCAAATGATGCGTTTTCCCGAGCATGGAATGTTCGAAAAATT
382 AGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATT
* * * * * *
1008 CCTCGAAGGAATGGATCGTCTTGAATACTTTCAGGAACCAAAGTTATAAAAGAACTCATAAATGT
1 -CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGT
* * * * *
1073 TTGACAAGTTCGAAAGTTCGTCCAAG-ACCGAA-AGAGAATCAACTCTCACGTAAACAAGTTTTT
65 TTGACAAGTTCGGAAGTTCGTCAAAGAACC-AAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * *
1136 AAGTCAAAGACCAAAA---GTTTAAAAAATGACAAACTGTTCAGACCAAATGATGCGATTTCCCT
129 AATTCAAAGACCAAAATTTGTTTACAAAATAACAAACTATTTAG-CCAAATGATGCGATTT-CCA
* * * * * * * *
1198 AGAATGGAATGTCCGAAAAGTTCCTCGAAGGAATGGATCATCTTGAATACTGTAATGAAACGAAG
192 AGTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAA-GGAAC-TAG
* * *
1263 TTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-AGAAGTTCATCCAAAAACCAAGAGAGGAACA
255 TTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA-AAGTTCATCCAAGAACCAAGAGAGAAATA
* * * *
1327 ATTCCCACGTAAATAAG-TTTTAATTTAAAGACCAAAAGCGGTTTACAAAATGACAAACTATTTA
319 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACC-AAATCTGTTTACAAAATGACAAACTATTTA
* *
1391 GACCAAAAGATGCGATTTCTCGAGCGTGGAATGTTCGAAAAATT
383 GACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATT
*
1435 GCTCGATA-GAATGGATCATCTTGAATAGTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAG
1 -CTCGA-AGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAG
** * * * * * * * * * *
1499 TTTTTCAAGTTTGAAAGTTCATCCAAGATCTATGAGATAAACAATTCCCATGTAAATAAGTTTTT
64 TTTGACAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
** * * * *
1564 AATTCAAAGACCAAAACATGTATACAAAATAACAAACTATTTAGAACAATTGATGAGATTTCTCA
129 AATTCAAAGACCAAAATTTGTTTACAAAATAACAAACTATTTAG-CCAAATGATGCGATTTC-CA
* * * *
1629 AGTATGGACTGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTGAGGAACTA-TA
192 AGTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACTAGTT
* * *
1693 ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCTAA-ACACCAAGAGAGAAACAAT
257 ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGA-ACCAAGAGAGAAATAAT
* * * * *
1757 TTTCACGTAAATAAATTTTTAATTCAAAGACCAAATCCTGTTTACAAATTGACAAACAATTTTGA
321 TCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAT-CTGTTTACAAAATGACAAACTATTTAGA
* * *
1822 CCAAATGATGTGATTTCTCGAGTATGGAAATGTTTGAAAAAAATT
385 CCAAATGATGCGATTTCTCGAGCATGG-AATGTTCG--AAAAATT
* * * *
1867 -TCGACGGAATGGATCATCTTGAATACTTTAAAGAATGGAAGTTATAAAAGAACTCGTAGAAGTT
1 CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTT
* * * * * *
1931 TGACAACTTCAGAAGTTTGTCAAAGAACCAAGAGAGAAATAGTTCTCACGTAAATAATTTTTTAA
66 TGACAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
* * * *
1996 TTCAAAAACAAAAATTTGTTTACAAAATAACAAACTATTTAGTCCAAATGATGCGGTTTCCTAGT
131 TTCAAAGACCAAAATTTGTTTACAAAATAACAAACTATTTAG-CCAAATGATGCGATTTCCAAGT
* * * * *
2061 CATTGAATGTTAGGAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTT
195 -ATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACT--AGTT
* * * *
2126 ATAAAAGAACTCGTAAAAGTTTTACAAGTTCGAAAGCTCGTCCAAGAACCAAAAGAGAAATAATT
257 ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAATAATT
2191 CTCACGTAAATAAGTTTTT
322 CTCACGTAAATAAGTTTTT
2210 GACAAGTTCA
Statistics
Matches: 1347, Mismatches: 245, Indels: 78
0.81 0.15 0.05
Matches are distributed among these distances:
427 158 0.12
428 273 0.20
429 195 0.14
430 367 0.27
431 132 0.10
432 145 0.11
433 76 0.06
434 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (426 bp):
CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTT
TGACAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
TTCAAAGACCAAAATTTGTTTACAAAATAACAAACTATTTAGCCAAATGATGCGATTTCCAAGTA
TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACTAGTTATAA
AAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAATAATTCTCA
CGTAAATAAGTTTTTAATTCAAAGACCAAATCTGTTTACAAAATGACAAACTATTTAGACCAAAT
GATGCGATTTCTCGAGCATGGAATGTTCGAAAAATT
Found at i:2143 original size:646 final size:639
Alignment explanation
Indices: 147--2209 Score: 2297
Period size: 646 Copynumber: 3.2 Consensus size: 639
137 TCGAAAAACA
** * * * *
147 GCTCGAAGGAAA-GGATTATCTTGAATACTTTAAGGAATCGAAGTTATAAAGGAACGCATAGAAG
1 GCTCGAA-GAAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAG
* * * * * * **** *
211 TTTGACAAGTTTGGAAGTTCGTCCAAAAACCAAGATAGAAACAATTTTTGCGTAAACAAGTTTTT
65 TTTTACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAAAAATAATTCACACGTAAATAAGTTTTT
*** * * * * * * *
276 -ATTCAAAGATGTAATCTAGTTTACAAAATGGA-AAACTATTTAG-CCTAAATAATGCGTTTTCC
130 AATTCAAAGACCAAAACTAGTATACAAAAT-AACAAACTATTTAGAAC-AAATGATGAGATTTCC
* * * *
338 CAAGTAGGGAATGTTCAAAAAATTGCTCGAAGGAATGAATTGTCTTGAATACTTTAAGGAACTGA
193 CAAGTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACT--
* *
403 AGTTATAAATGAACTCATAAATGTTTGACAAGTTCAAAAGTTCATCCAAGA-ACCAACAGAGAAA
256 AGTTATAAAAGAACTCATAAATGTTTGACAAGTTCGAAAGTTCATCCAAGACACCAA-AGAGAAA
* * * * *
467 TAACTGTCACGTAAAATAAGTTTTTAATTCAAATACCAAAAGTTAACAAAATAACAAACTGTTTA
320 CAACTCTCACGT-AAATAAGTTTTTAATTCAAAGACCAAAAGTTTACAAAATGACAAACTGTTTA
* *
532 GACCAAATGATGCGATTTCTCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGAATCATCT
384 GACCAAATGATGCGATTTCTCAAGAATGGAATGTTCGAAAAATT-CTCGAAGGAATGGATCATCT
* * * **
597 TGAATACTATAACA-AACCAAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCA
448 TGAATACTATAA-AGAAACGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCA
**
661 TCAAAAAATAATGAGAGAAAAAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
512 TCAAAAACCAA-GAGAGAAAAAATTCTCACGTAAATAA-TTTTTAATTCAAAGACCAAAAGTTGT
* * * *
726 TTACAAAATAACAAACTATTTAGACTAGATGAAGTGATTTCCTGAGT-A-TGAAATGCTTGGAAA
575 TTACAAAATAACAAACTATTTAGACCAAATGATGCGATTTCCT-AGTCATTG-AATG-TTGGAAA
*
789 ACT
637 ATT
* * * * *
792 GCTCGAAGGAGA-GGATTGTCTTGAATGCTTTAAGGAATCGAAGTTATAAAGGAACTCGTAGAAG
1 GCTCGAA-GAAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAG
* * * * *
856 TTTGACAAGTTTGAAAGTTCGTCCAAGAACCAAGATAAAAATAATTCACGCGTAAACAAGTTTTA
65 TTTTACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAAAAATAATTCACACGTAAATAAGTTTTT
* * * * * * * * * *
921 AATTCAAAGACCTAATCTAGTTTACAAAATGACACACTATTTTGACCAAATGATGCGTTTTCCCG
130 AATTCAAAGACCAAAACTAGTATACAAAATAACAAACTATTTAGAACAAATGATGAGATTTCCCA
* * * *
986 AGCATGGAATGTTCGAAAAATTCCTCGAAGGAATGGATCGTCTTGAATACTTTCAGGAACCAAAG
195 AGTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C-TAG
* * *
1051 TTATAAAAGAACTCATAAATGTTTGACAAGTTCGAAAGTTCGTCCAAGAC-CGAAAGAGAATCAA
258 TTATAAAAGAACTCATAAATGTTTGACAAGTTCGAAAGTTCATCCAAGACACCAAAGAGAAACAA
* * * *
1115 CTCTCACGTAAACAAGTTTTTAAGTCAAAGACCAAAAGTTTAAAAAATGACAAACTGTTCAGACC
323 CTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTTACAAAATGACAAACTGTTTAGACC
* * * *
1180 AAATGATGCGATTTCCCTAGAATGGAATGTCCGAAAAGTTCCTCGAAGGAATGGATCATCTTGAA
388 AAATGATGCGATTTCTCAAGAATGGAATGTTCGAAAAATT-CTCGAAGGAATGGATCATCTTGAA
* *
1245 TACTGTAATGAAACGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAA
452 TACTATAAAGAAACGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCAT-CAA
* * * * * **
1310 AAACCAAGAGAGGAACAATTCCCACGTAAATAAGTTTTAATTTAAAGACCAAAAGCGGTTTACAA
516 AAACCAAGAGAGAAAAAATTCTCACGTAAATAATTTTTAATTCAAAGACCAAAAGTTGTTTACAA
* * * * * *
1375 AATGACAAACTATTTAGACCAAAAGATGCGATTTCTCGAG-CGTGGAATGTTCGAAAAATT
581 AATAACAAACTATTTAGACCAAATGATGCGATTTC-CTAGTCATTGAATGTT-GGAAAATT
* *
1435 GCTCGATAG-AATGGATCATCTTGAATAGTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAG
1 GCTCGA-AGAAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAG
* * * * * * * * *
1499 TTTTTCAAGTTTGAAAGTTCATCCAAGATCTATGAGATAAACAATTCCCATGTAAATAAGTTTTT
65 TTTTACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAAAAATAATTCACACGTAAATAAGTTTTT
* *
1564 AATTCAAAGACCAAAAC-ATGTATACAAAATAACAAACTATTTAGAACAATTGATGAGATTTCTC
130 AATTCAAAGACCAAAACTA-GTATACAAAATAACAAACTATTTAGAACAAATGATGAGATTTCCC
* * *
1628 AAGTATGGACTGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTGAGGAACTA-T
194 AAGTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACTAGT
* * * * *
1692 AATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCTAA-ACACCAAGAGAGAAACAA
259 TATAAAAGAACTCATAAATGTTTGACAAGTTCGAAAGTTCATCCAAGACACCAA-AGAGAAACAA
* * * * * ** *
1756 TTTTCACGTAAATAAATTTTTAATTCAAAGACCAAATCCTGTTTACAAATTGACAAACAATTTTG
323 CTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA---AGTTTACAAAATGACAAACTGTTTAG
* * * * *
1821 ACCAAATGATGTGATTTCTCGAGTATGGAAATGTTTGAAAAAAATT-TCGACGGAATGGATCATC
385 ACCAAATGATGCGATTTCTCAAGAATGG-AATGTTCG--AAAAATTCTCGAAGGAATGGATCATC
* ** * * **
1885 TTGAATACTTTAAAGAATGGAAGTTATAAAAGAACTCGTAGAAGTTTGACAACTTCAGAAGTTTG
447 TTGAATACTATAAAGAAACGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCA
* * * * *
1950 TCAAAGAACCAAGAGAGAAATAGTTCTCACGTAAATAATTTTTTAATTCAAAAACAAAAATTTGT
512 TCAAA-AACCAAGAGAGAAAAAATTCTCACGTAAATAA-TTTTTAATTCAAAGACCAAAAGTTGT
* *
2015 TTACAAAATAACAAACTATTTAGTCCAAATGATGCGGTTTCCTAGTCATTGAATGTTAGGAAAAT
575 TTACAAAATAACAAACTATTTAGACCAAATGATGCGATTTCCTAGTCATTGAATGTT-GGAAAAT
2080 T
639 T
*
2081 GCTAGAAGAAATGGATCGTCTTGAATACTTTAAGGAA-CTGAAGTTATAAAAGAACTCGTAAAAG
1 GCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAATC-GAAGTTATAAAAGAACTCGTAAAAG
* * * * *
2145 TTTTACAAGTTCGAAAGCTCGTCCAAGAACCAAAAGAGAAATAATTCTCACGTAAATAAGTTTTT
65 TTTTACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAAAAATAATTCACACGTAAATAAGTTTTT
2210 GACAAGTTCA
Statistics
Matches: 1205, Mismatches: 185, Indels: 55
0.83 0.13 0.04
Matches are distributed among these distances:
639 2 0.00
640 44 0.04
641 41 0.03
642 5 0.00
643 278 0.23
644 233 0.19
645 257 0.21
646 336 0.28
647 9 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (639 bp):
GCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGT
TTTACAAGTTTGAAAGTTCGTCCAAGAACCAAGAGAAAAATAATTCACACGTAAATAAGTTTTTA
ATTCAAAGACCAAAACTAGTATACAAAATAACAAACTATTTAGAACAAATGATGAGATTTCCCAA
GTATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACTAGTTA
TAAAAGAACTCATAAATGTTTGACAAGTTCGAAAGTTCATCCAAGACACCAAAGAGAAACAACTC
TCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTTACAAAATGACAAACTGTTTAGACCAAA
TGATGCGATTTCTCAAGAATGGAATGTTCGAAAAATTCTCGAAGGAATGGATCATCTTGAATACT
ATAAAGAAACGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCAAAAACC
AAGAGAGAAAAAATTCTCACGTAAATAATTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAA
CAAACTATTTAGACCAAATGATGCGATTTCCTAGTCATTGAATGTTGGAAAATT
Found at i:2235 original size:62 final size:61
Alignment explanation
Indices: 2145--2272 Score: 193
Period size: 62 Copynumber: 2.1 Consensus size: 61
2135 CTCGTAAAAG
* * *
2145 TTTTACAAGTTCGAAAGCTCGTCCAAGAACCAAAAGAGAAATAATTCTCACGTAAATAAGT
1 TTTTACAAGTTCAAAAGCTCGTCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGT
* * *
2206 TTTTGACAAGTTCAAAAGTTCGTCGAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGT
1 TTTT-ACAAGTTCAAAAGCTCGTCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGT
2268 TTTTA
1 TTTTA
2273 ATTCAAAGAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 5 0.08
62 55 0.92
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (61 bp):
TTTTACAAGTTCAAAAGCTCGTCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGT
Done.