Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023550.1 Corchorus olitorius cultivar O-4 contig23583, 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: 3345
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Found at i:745 original size:154 final size:153
Alignment explanation
Indices: 4--1814 Score: 2510
Period size: 154 Copynumber: 11.7 Consensus size: 153
1 ATC
* * * *
4 GAGGATTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGACCCCCAAAGGCACAAAATAACA
1 GAGGTTTGCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGAAAGGCACAAAATAACA
* * * *
69 AGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTATGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCC
* *
134 ATAAACAGTGGAAACAAAAGCATT
130 ATAAACAATGGAAAGAAAAGCATT
* * * *
158 GAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGTC-CAAAAATAAC
1 GAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGGCAC-AAAATAAC
* * * * *
222 AGGTGTTCCAAATGAGCTAAAACCTTCACAGTGGACT--TCTCTCTAAAATAAATATAGTTAGGC
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGC
* *
285 CAAAAATAATGGAAAGAAAAGCATT
129 CATAAACAATGGAAAGAAAAGCATT
* * * * * *
310 GAGGGATTTTTTCCATATCGAAGACGATTCAAAACGTCACTAATGGACCCTGATAGGCACAAAAT
1 GA-GG---TTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGGCACAAAAT
*
375 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGTAAAATGATTATAGTTA
61 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTA
* * * *
440 TGCCTTAAACAATGGAAAGAAAGGCATC
126 GGCCATAAACAATGGAAAGAAAAGCATT
468 GAGGGTTT-CCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAA-GCACAAAATAAC
1 GA-GGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATAAC
*
531 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGTACTAATCTCACTAAAATGATTATAGTTAGGC
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGC
*
596 CATAAACAATGGAAAGAAAAGCTTT
129 CATAAACAATGGAAAGAAAAGCATT
* * * * * *
621 GAAGTTTGTCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCACAAAACAACA
1 GAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGGCACAAAATAACA
* ** * * *
686 GGTGTTCCAAATGAGCTAAAATTTTTACAGTGGACTAAACTCACTATAATGATTATAGTTAGGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCC
*
751 ATAAACAATGGAAAGAAAAAGCATC
130 ATAAACAATGGAAAG-AAAAGCATT
*
776 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACA
1 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATAACA
* * *
841 AGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCC
* *
906 ATAAACAATGGAAAGAAAGGCATC
130 ATAAACAATGGAAAGAAAAGCATT
*
930 GAGGGTTT-CCAAATCGAAGACGATTCAAAAAGAACTAATGGGCCCCGAAAGGCACAAAATAACA
1 GA-GGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCACAAAATAACA
994 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAAC-AAAATGATTATAGTTAGGC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC-ACTAAAATGATTATAGTTAGGC
* * *
1058 CTTTAACAATGGAAAGAAATGCATCT
129 CATAAACAATGGAAAGAAAAGCAT-T
* *
1084 -AGGGTTT-CCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCAAAAAGCACAAAATAAC
1 GA-GGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATAAC
* * * *
1147 AAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCAGTAAAATGATTATATTTAGGG
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGC
*
1212 CATAAACAATGGAAAGAAAAGCATC
129 CATAAACAATGGAAAGAAAAGCATT
* *
1237 GAGGGTTGCCAAATCGAAGACGAATCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACA
1 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATAACA
* * * *
1302 AGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTATGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCC
*
1367 ATAAACAATAGAAAGAAAAGCATT
130 ATAAACAATGGAAAGAAAAGCATT
*
1391 GAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAAGGCACAAAATAAC
1 GAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCG-AAAGGCACAAAATAAC
*
1456 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGTAAAATGATTATAGTTAGGC
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGC
* *
1521 CATAAACAATGGAAAGAAAGGCATC
129 CATAAACAATGGAAAGAAAAGCATT
* *
1546 GAGGGTTT-CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATTAC
1 GA-GGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATAAC
* * *
1610 AAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTC
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGC
* *
1675 AATAAACAATGGAAAGAAAAGCTTT
129 CATAAACAATGGAAAGAAAAGCATT
* * * * * *
1700 GAGGTTTGCCAAATCGAGGTCGATTCAAAACGGATCTAATGGGCCTCGAATGGCCCAAAATAACA
1 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATAACA
* *
1765 AGTTTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAAT
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACTAAAAT
1815 TGTAGACACT
Statistics
Matches: 1487, Mismatches: 142, Indels: 56
0.88 0.08 0.03
Matches are distributed among these distances:
152 49 0.03
153 292 0.20
154 723 0.49
155 280 0.19
156 96 0.06
157 1 0.00
158 46 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (153 bp):
GAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCACAAAATAACAA
GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCA
TAAACAATGGAAAGAAAAGCATT
Found at i:1584 original size:309 final size:307
Alignment explanation
Indices: 1--1814 Score: 2579
Period size: 309 Copynumber: 5.9 Consensus size: 307
* * * * *
1 ATCGAGGATTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGACCCCCAAAGGCACAAAATA
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATA
* *
66 ACAAGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAT
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAT
* * *
131 GCCATAAACAGTGGAAACAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
131 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTA
* * * * *
196 ATGGGCCCTGATAGTC-CAAAAATAACAGGTGTTCCAAATGAGCTAAAACCTTCACAGTGGACT-
195 ATGGGCCCCGAAAGGCAC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * * * *
259 -TCTCTCTAAAATAAATATAGTTAGGCCAAAAATAATGGAAAGAAAAGC
259 ATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * ** * * *
307 ATTGAGGGATTTTTTCCATATCGAAGACGATTCAAAACGTCACTAATGGACCCTGATAGGCACAA
1 ATCGAGGG----TTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAA
**
372 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGTAAAATGATTATAG
62 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* * *
437 TTATGCCTTAAACAATGGAAAGAAAGGCATCGAGGGTTT-CCAAATCGAAGACGATTCAAAACAG
127 TTATGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTGCCAAATCGAAGACGATTCAAAAC-G
*
501 AACTAATGGGCCCCGAAA-GCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGT
190 AACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
565 ACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
255 ACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * * ** * * *
618 TTTGA-AGTTTGTCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCACAAAAC
1 ATCGAGGGTTT-CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAAT
* ** * * * *
682 AACAGGTGTTCCAAATGAGCTAAAATTTTTACAGTGGACTAAACTCACTATAATGATTATAGTTA
65 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
* * *
747 GGCCATAAACAATGGAAAGAAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAC
130 TGCCATAAACAATGGAAAG-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAAC
* *
812 TAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACT
193 TAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
877 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGC
258 AATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
927 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAA-AGAACTAATGGGCCCCGAAAGGCACAAAATA
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATA
* *
991 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAACAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAT
* * *
1056 GCCTTTAACAATGGAAAGAAATGCATCT-AGGGTTT-CCAAATCGAAGACGATTCAAAACAGAAC
131 GCCATAAACAATGGAAAGAAAAGCAT-TGA-GGTTTGCCAAATCGAAGACGATTCAAAAC-GAAC
* * *
1119 TAATGGGCCCCAAAAAGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACT
193 TAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* * *
1184 AATCTCAGTAAAATGATTATATTTAGGGCATAAACAATGGAAAGAAAAGC
258 AATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* *
1234 ATCGAGGGTTGCCAAATCGAAGACGAATCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATA
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATA
* *
1299 ACAAGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAT
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAT
* *
1364 GCCATAAACAATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
131 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTA
1429 ATGGGCCCCGAAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
195 ATGGGCCCCG-AAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* *
1494 ATCTCAGTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGC
259 ATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* *
1543 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATT
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATA
*
1608 ACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAT
* * * * *
1672 GTCAATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAGGTCGATTCAAAACGGATCT
131 G-CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACT
* * * *
1737 AATGGGCCTCGAATGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGAC-A
194 AATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
1801 TATCTCACCAAAAT
259 -ATCTCACTAAAAT
1815 TGTAGACACT
Statistics
Matches: 1358, Mismatches: 126, Indels: 46
0.89 0.08 0.03
Matches are distributed among these distances:
306 9 0.01
307 307 0.23
308 365 0.27
309 445 0.33
310 179 0.13
311 53 0.04
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (307 bp):
ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATA
ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAT
GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAA
TGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
CTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
Found at i:1622 original size:463 final size:461
Alignment explanation
Indices: 1--1814 Score: 2609
Period size: 463 Copynumber: 3.9 Consensus size: 461
* * * * *
1 ATCGAGGATTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGACCCCCAAAGGCACAAAATA
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGAAAGGCACAAAATA
* * *
66 ACAAGTGTTCCAAATGAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAT
65 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* * * **
131 GCCATAAACAGTGGAAACAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
130 GCCATAAACAATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* * * * *
196 ATGGGCCCTGATAGTC-CAAAAATAACAGGTGTTCCAAATGAGCTAAAACCTTCACAGTGGACT-
195 ATGGGCCCCGAAAGGCAC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * * * * * *
259 -TCTCTCTAAAATAAATATAGTTAGGCCAAAAATAATGGAAAGAAAAGCATTGAGGGATTTTTTC
259 ATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGG----TTGC
* ** * * *
323 CATATCGAAGACGATTCAAAACGTCACTAATGGACCCTGATAGGCACAAAATAACAAGTGTTCCA
320 CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCA
** *
388 AATGAGCTAAAAACTTCACAGTGGACTAATCTCAGTAAAATGATTATAGTTATGCCTTAAACAAT
385 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAAT
453 GGAAAGAAAGGC
450 GGAAAGAAAGGC
465 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAA-GCACAAAATA
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCACAAAATA
* *
529 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGTACTAATCTCACTAAAATGATTATAGTTAG
65 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* * * * **
594 GCCATAAACAATGGAAAGAAAAGCTTTGAAGTTTGTCAAATCGAAGACGATTCAAAACGTCACTA
130 GCCATAAACAATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* * * * ** *
659 ATGGGCCCTGATAGGCACAAAACAACAGGTGTTCCAAATGAGCTAAAATTTTTACAGTGGACTAA
195 ATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* *
724 ACTCACTATAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATCGAGGGTTGCCAAA
260 TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATCGAGGGTTGCCAAA
789 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATG
324 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATG
* * *
854 AGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
389 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAA
919 AGAAAGGC
454 AGAAAGGC
*
927 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAAAGAACTAATGGGCCCCGAAAGGCACAAAATAA
1 ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCACAAAATAA
*
992 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAACAAAATGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * *
1057 CCTTTAACAATGGAAAGAAATGCATCTAGGGTTT-CCAAATCGAAGACGATTCAAAACAGAACTA
131 CCATAAACAATGGAAAGAAAAGCATCGA-GGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* * *
1121 ATGGGCCCCAAAAAGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAA
195 ATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* * *
1186 TCTCAGTAAAATGATTATATTTAGGGCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAAT
260 TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAAT
*
1251 CGAAGACGAATCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGA
325 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGA
* * *
1316 GCTAAAACCTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATAGAAA
390 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAA
*
1381 GAAAAGC
455 GAAAGGC
* *
1388 ATTGA-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAAGGCACAAAA
1 ATCGAGGGTTT-CCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCG-AAAGGCACAAAA
**
1452 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGTAAAATGATTATAGTT
63 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
1517 AGGCCATAAACAATGGAAAGAAAGGCATCGAGGGTTT-CCAAATCGAAGACGATTCAAAACGGAA
128 AGGCCATAAACAATGGAAAGAAAAGCATCGA-GGTTTGCCAAATCGAAGACGATTCAAAACGGAA
* * *
1581 CTAATGGGCCCCGAAAGGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAC
192 CTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* * * * * *
1646 TAATCTCACCAAAATGATTATAGTTAGTCAATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
257 TAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCA
* * * * * * *
1711 AATCGAGGTCGATTCAAAACGGATCTAATGGGCCTCGAATGGCCCAAAATAACAAGTTTTCCAAA
322 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAA
1776 TGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAAT
387 TGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAAT
1815 TGTAGACACT
Statistics
Matches: 1231, Mismatches: 108, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
460 5 0.00
461 202 0.16
462 396 0.32
463 531 0.43
464 49 0.04
465 35 0.03
466 13 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (461 bp):
ATCGAGGGTTTCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCACAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
TGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
CTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATC
GAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAG
CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTATGCCATAAACAATGGAAAG
AAAGGC
Found at i:1919 original size:28 final size:28
Alignment explanation
Indices: 1887--1962 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 28
1877 AGGGTCATTT
** *
1887 AGGGGCATTTTGGGTCATTTGCATGTTC-
1 AGGGGCATTTT-GGTCATTTGCACATCCA
*
1915 AGGGGCATTTTAGTCATTTGCACATCCA
1 AGGGGCATTTTGGTCATTTGCACATCCA
1943 AGGGGGCATTTTGGTCATTT
1 A-GGGGCATTTTGGTCATTT
1963 TTAAGTTCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.29
28 12 0.29
29 17 0.41
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTGCACATCCA
Done.