Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024740.1 Corchorus olitorius cultivar O-4 contig24773, 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: 37258
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:388 original size:154 final size:154
Alignment explanation
Indices: 108--2035 Score: 3007
Period size: 154 Copynumber: 12.6 Consensus size: 154
98 TGAGGTTTGC
*
108 CAAAACGGAACTAATGGG-CCCGAAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
1 CAAAACGGAACTAATGGGCCCCG-AAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
* *
172 TCACAGTGGACTAATCTCACCAAAAGGATTATTGTTAGGCCATAAACATTGGAAAGAAAAGCATT
65 TCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
237 GGGGTTTGCCAAATCGAAGACGATT
130 GGGGTTTGCCAAATCGAAGACGATT
* * * * *
262 CAAAACGTCAA-TAATTGGCCCCGAAATGCTCAATATAACAAGTGTTCCAAATGAGATAAAAACT
1 CAAAACG-GAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
*
326 TCACAGTGGACTAATCTCACCAAAAGGATTATAGTTATGCCATAAACAATGGAAAGAAAAGCATT
65 TCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
* *
391 GAGGTTTGCCAAATCGAAAACGATT
130 GGGGTTTGCCAAATCGAAGACGATT
416 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * * *
481 CACAGTAGACTAATCTCACCAAAAGGATTATAGTTATGCCATAAACAATGAAAAGGAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
*
546 GGGTTTGCCAAATCGAAAACGATT
131 GGGTTTGCCAAATCGAAGACGATT
570 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
635 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
* * * *
700 AGGTTTCCCAAATAGAATACGATT
131 GGGTTTGCCAAATCGAAGACGATT
** *
724 CAAAAC-GACACTAATGGGCCCCGTTAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
1 CAAAACGGA-ACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
* * *
788 TCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATC
65 TCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
*
853 GAGGG-TTGCCAAATCGAATACGATT
130 G-GGGTTTGCCAAATCGAAGACGATT
* * *
878 CAAAACGGAACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGATAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
*
942 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGGAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
*
1007 GGGTTTGCCAAATCGAAAACGATT
131 GGGTTTGCCAAATCGAAGACGATT
1031 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
1096 CGCAATGGACTAATCTCACAAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
*
1161 GGATTTGCCAAA---AA-ACG--T
131 GGGTTTGCCAAATCGAAGACGATT
* * * * * *
1179 -----C--AA-TAATTGGCCCCAAAATGCTCAATATAACAAGTGTTCGAAATGAGATAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
1236 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGTCATAAACAATTGAAAGAAATGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
*
1301 GGGTTTGTCAAATCGAAGACGATT
131 GGGTTTGCCAAATCGAAGACGATT
* * * * *
1325 CAAAACGGAACTAACGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
1390 CACAGTGGACGAATCTCATCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
*
1455 AGGTTTGCCAAATCGAAGACGATT
131 GGGTTTGCCAAATCGAAGACGATT
* *
1479 CAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
1544 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAATGAAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
1609 GGGTTTGCCAAATCGAAGACGATT
131 GGGTTTGCCAAATCGAAGACGATT
*
1633 CAAAACCGAACTAATGGGCCCCGAAATGCCCAAAAT-ACAAGTGTTCCAAATGAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
1697 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGAAAAGAAAACCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
* *
1762 AGGTTTCCCAAATCGAAGACGATT
131 GGGTTTGCCAAATCGAAGACGATT
*
1786 CAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
1 CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
1851 CACAGTAGACTAATCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
66 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
* *
1916 AGGTTTCCCAAATCGAAGACGATT
131 GGGTTTGCCAAATCGAAGACGATT
1940 CAAAACGGAACTAATGGGCCCCG-AATGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
1 CAAAACGGAACTAATGGGCCCCGAAATG-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
*
2004 TCACAGTGGACTAATCTCACCAAAATGATTAT
65 TCACAGTGGACTAATCTCACCAAAAGGATTAT
2036 TGTAGACGCT
Statistics
Matches: 1637, Mismatches: 113, Indels: 48
0.91 0.06 0.03
Matches are distributed among these distances:
140 117 0.07
141 2 0.00
143 3 0.00
144 3 0.00
146 1 0.00
148 1 0.00
150 3 0.00
151 3 0.00
152 3 0.00
153 294 0.18
154 1197 0.73
155 10 0.01
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
GGGTTTGCCAAATCGAAGACGATT
Found at i:1882 original size:909 final size:912
Alignment explanation
Indices: 1--2035 Score: 3207
Period size: 909 Copynumber: 2.2 Consensus size: 912
* * *
1 AAAATAAAAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATTTCACCAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
66 AGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGG-TT-----T-G---C----CAAAACGGA
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAACGATTCAAAACGGA
*
117 ACTAATGGG-CCCGAAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
131 ACTAATGGGCCCCG-AAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* * *
181 ACTAATCTCACCAAAAGGATTATTGTTAGGCCATAAACATTGGAAAGAAAAGCATTGGGGTTTGC
195 ACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGATTTGC
*
246 CAAATCGAAGACGATTCAAAACGTCAATAATTGGCCCCGAAATGCTCAATATAACAAGTGTTCCA
260 C--A-C--A-AC-A-T-AAAACGTCAATAATTGGCCCCAAAATGCTCAATATAACAAGTGTTCCA
*
311 AATGAGATAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTATGCCATAAACAAT
316 AATGAGATAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAAT
*
376 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCCGAA
381 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAACGGGCCCCGAA
* * *
441 ATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAAG
446 AGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTAGACGAATCTCACCAAAAG
* * *
506 GATTATAGTTATGCCATAAACAATGAAAAGGAAAGCATTGGGGTTTGCCAAATCGAAAACGATTC
511 GATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTC
*
571 AAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
576 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
636 ACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
641 ACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
* **
701 GGTTTCCCAAATAGAATACGATTCAAAACGACACTAATGGGCCCCGTTAGGCCCAAAATAACAAG
706 GGTTTCCCAAATAGAAGACGATTCAAAACGACACTAATGGGCCCCGAAAGGCCCAAAATAACAAG
*
766 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCAT
771 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * *
831 AAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAATGGC
836 AAACAATGAAAAGAAAACCATCGAGGGTTCCCAAATCGAAGACGATTCAAAACGGAACTAATGGC
*
896 CCCGAAAGGCCT
901 CCCGAAAGGCCC
* *
908 AAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
973 AGTTAGGCCATAAACAATGGAAAGGAAAGCATTGGGGTTTGCCAAATCGAAAACGATTCAAAACG
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CCAAATCG-AAACGATTCAAAACG
* *
1038 GAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCGCAATG
129 GAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
1103 GACTAATCTCACAAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGATTTG
194 GACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGATTTG
*
1168 -C-C-A-A-AAAACGTCAATAATTGGCCCCAAAATGCTCAATATAACAAGTGTTCGAAATGAGAT
259 CCACAACATAAAACGTCAATAATTGGCCCCAAAATGCTCAATATAACAAGTGTTCCAAATGAGAT
* *
1228 AAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGTCATAAACAATTGAAAGAA
324 AAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * * *
1293 ATGCATTGGGGTTTGTCAAATCGAAGACGATTCAAAACGGAACTAACGGGCCCCGATAGGCTCAA
389 AAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAACGGGCCCCGAAAGGCCCAA
* * *
1358 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACGAATCTCATCAAAATGATTATAG
454 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTAGACGAATCTCACCAAAAGGATTATAG
* * *
1423 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGA
519 TTAGGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGA
1488 ACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
584 ACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * * * *
1553 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAATGAAAAGCATTGGGGTTTGCC
649 CTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCC
* *
1618 AAATCGAAGACGATTCAAAACCGA-ACTAATGGGCCCCGAAATGCCCAAAAT-ACAAGTGTTCCA
714 AAATAGAAGACGATTCAAAA-CGACACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
1681 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
778 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
1746 GAAAAGAAAACCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
843 GAAAAGAAAACCATCGAGGGTTCCCAAATCGAAGACGATTCAAAACGGAACTAAT-GGCCCCGAA
1811 AGGCCC
907 AGGCCC
* *
1817 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACAAAAATGATTAT
1 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
1882 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACG
66 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CCAAATCGAA-ACGATTCAAAACG
1947 GAACTAATGGGCCCCG-AATGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
129 GAACTAATGGGCCCCGAAATG-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
2011 GGACTAATCTCACCAAAATGATTAT
193 GGACTAATCTCACCAAAAGGATTAT
2036 TGTAGACGCT
Statistics
Matches: 1038, Mismatches: 69, Indels: 40
0.90 0.06 0.03
Matches are distributed among these distances:
907 94 0.09
908 133 0.13
909 672 0.65
910 3 0.00
912 1 0.00
914 2 0.00
915 1 0.00
918 1 0.00
919 1 0.00
922 1 0.00
923 125 0.12
924 4 0.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (912 bp):
AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAACGATTCAAAACGGA
ACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGATTTGCC
ACAACATAAAACGTCAATAATTGGCCCCAAAATGCTCAATATAACAAGTGTTCCAAATGAGATAA
AAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
GCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAACGGGCCCCGAAAGGCCCAAAA
TAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTAGACGAATCTCACCAAAAGGATTATAGTT
AGGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAAC
TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
AATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAA
ATAGAAGACGATTCAAAACGACACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGAA
AAGAAAACCATCGAGGGTTCCCAAATCGAAGACGATTCAAAACGGAACTAATGGCCCCGAAAGGC
CC
Found at i:1929 original size:307 final size:308
Alignment explanation
Indices: 1182--2035 Score: 1424
Period size: 307 Copynumber: 2.8 Consensus size: 308
1172 AAAACGTCAA
* * * * * * *
1182 TAATTGGCCCCAAAATGCTCAATATAACAAGTGTTCGAAATGAGATAAAAACTTCACAGTGGACT
1 TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* * * *
1247 AATCTCACCAAAAGGATTATAGTTAGGTCATAAACAATTGAAAGAAATGCATTGGGGTTTGTCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGGGGTTTGCCAA
* * * *
1312 ATCGAAGACGATTCAAAACGGAACTAACGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAAT
131 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAAT
* * * *
1377 AAGCTAAAAACTTCACAGTGGACGAATCTCATCAAAATGATTATAGTTAGGCCATAAACAATGGA
196 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGAA
* * *
1442 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAAC
261 AAGAAAACCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAAC
1490 TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
1 TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
1555 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAATGAAAAGCATTGGGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGGGGTTTGCCAA
*
1620 ATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAATGCCCAAAAT-ACAAGTGTTCCAAAT
131 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAAT
1684 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGAA
196 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGAA
1749 AAGAAAACCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAAC
261 AAGAAAACCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAAC
*
1797 TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACT
1 TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* * * *
1862 AATCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGGGGTTTGCCAA
1927 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG-AATGACCCAAAATAACAAGTGTTCCAAA
131 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAATG-CCCAAAATAACAAGTGTTCCAAA
1991 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
195 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
2036 TGTAGACGCT
Statistics
Matches: 513, Mismatches: 31, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
306 4 0.01
307 288 0.56
308 221 0.43
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (308 bp):
TAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGGGGTTTGCCAA
ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAAT
GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGAA
AAGAAAACCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAAC
Found at i:9675 original size:10 final size:10
Alignment explanation
Indices: 9660--9688 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
9650 TACGTTCCAT
9660 GCATTCATGG
1 GCATTCATGG
9670 GCATTCATGG
1 GCATTCATGG
9680 GCATTCATG
1 GCATTCATG
9689 TACACATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (10 bp):
GCATTCATGG
Found at i:9899 original size:25 final size:25
Alignment explanation
Indices: 9871--9919 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9861 GTAAGACCTC
9871 CGGGCATA-ATTTCTGATAAATCCTT
1 CGGGCATATA-TTCTGATAAATCCTT
* *
9896 CGGGTATTTATTCTGATAAATCCT
1 CGGGCATATATTCTGATAAATCCT
9920 CCAGGTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (25 bp):
CGGGCATATATTCTGATAAATCCTT
Found at i:10193 original size:141 final size:143
Alignment explanation
Indices: 9818--10356 Score: 696
Period size: 146 Copynumber: 3.7 Consensus size: 143
9808 CAAAGTTGTG
* *
9818 TTTAAATTT-TAAT-AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCATAAT
1 TTTAAATTTAAAATAAAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACAAT
* * * *
9881 TTCTGATAAATCCTTCGGGTATTTATTCTGATAAATCCTCCAGGTATCATTTCATTTCATCAAAT
66 TTC--AGAAA-CCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAA-
*
9946 TTTTAATCAAAGCTGCA
127 TTTTAAGCAAAGCTGCA
* * *
9963 TTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTCAAG-TTTGCATTTCTAAGACCTCCGGGCACA
1 TTTAAATTT-AAAAT-AAAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACA
* *
10027 ATTCCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCGTTTCATCAAATT
64 ATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAATT
* * **
10092 TTCAGCAAAGTTGTG
129 TTAAGCAAAGCTGCA
* * *
10107 TTTAAATTT-TAAT-AAACCTTGCTCAAGG-CTGATTTTTGCATTTGTAAGACCTCCGAGCACAA
1 TTTAAATTTAAAATAAAACCTTGCTCAAGGTC-GAGTTTTGCATTTGTAAGACCTCCGGGCACAA
* * *
10169 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTTCGAGTATCATTTCATTTCATCAAGTTT
65 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAA-ATT
*
10234 TTAATCAAAGCTGCA
129 TTAAGCAAAGCTGCA
* * *
10249 TTTTAGTTTCAAAATCAAAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTTCGGGCACA
1 TTTAAATTT-AAAAT-AAAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACA
10314 ATTTCAGAAACCTCCGGGTATTAATTCTGA-AAAGTCCTCCGGG
64 ATTTCAGAAACCTCCGGGTATTAATTCTGATAAA-TCCTCCGGG
10357 CATTCTATAT
Statistics
Matches: 341, Mismatches: 40, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
139 1 0.00
140 16 0.05
141 83 0.24
142 22 0.06
144 23 0.07
145 60 0.18
146 84 0.25
147 4 0.01
148 29 0.09
149 19 0.06
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (143 bp):
TTTAAATTTAAAATAAAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACAAT
TTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAATTTT
AAGCAAAGCTGCA
Found at i:10320 original size:146 final size:145
Alignment explanation
Indices: 9831--10351 Score: 707
Period size: 141 Copynumber: 3.6 Consensus size: 145
9821 AAATTTTAAT
* * *
9831 AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCATAATTTCTGATAAATCCTT
1 AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACAATTTC--AGAAA-CCTC
* *
9896 CGGGTATTTATTCTGATAAATCC-TCCAGGTATCATTTCATTTCATCAAATTTTTAATCAAAGCT
63 CGGGTATTAATTCTGATAAATCCTTCGA-GTATCATTTCATTTCATC-AATTTTTAATCAAAGCT
9960 GCATTTAAGTTTCAAAATCA
126 GCATTTAAGTTTCAAAATCA
* * *
9980 AAACCTTGCTCAAGGTCAAG-TTTGCATTTCTAAGACCTCCGGGCACAATTCCAGAAACCTCCGG
1 AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGG
* * * * * * * **
10044 GTATTAATTCTGATAAATCCTCCGGGTATCATTTCGTTTCATCAAATTTTCAGCAAAGTTGTGTT
66 GTATTAATTCTGATAAATCCTTCGAGTATCATTTCATTTCATCAATTTTTAATCAAAGCTGCATT
* *
10109 TAAATTT--TAAT--
131 TAAGTTTCAAAATCA
* *
10120 AAACCTTGCTCAAGG-CTGATTTTTGCATTTGTAAGACCTCCGAGCACAATTTCAGAAACCTCCG
1 AAACCTTGCTCAAGGTC-GAGTTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCG
10184 GGTATTAATTCTGATAAATCCTTCGAGTATCATTTCATTTCATCAAGTTTTTAATCAAAGCTGCA
65 GGTATTAATTCTGATAAATCCTTCGAGTATCATTTCATTTCATCAA-TTTTTAATCAAAGCTGCA
*
10249 TTTTAGTTTCAAAATCA
129 TTTAAGTTTCAAAATCA
*
10266 AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTTCGGGCACAATTTCAGAAACCTCCGG
1 AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGG
10331 GTATTAATTCTGA-AAAGTCCT
66 GTATTAATTCTGATAAA-TCCT
10352 CCGGGCATTC
Statistics
Matches: 323, Mismatches: 39, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
139 1 0.00
140 16 0.05
141 83 0.26
142 22 0.07
144 25 0.08
145 45 0.14
146 82 0.25
147 1 0.00
148 29 0.09
149 19 0.06
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (145 bp):
AAACCTTGCTCAAGGTCGAGTTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGG
GTATTAATTCTGATAAATCCTTCGAGTATCATTTCATTTCATCAATTTTTAATCAAAGCTGCATT
TAAGTTTCAAAATCA
Found at i:10492 original size:40 final size:40
Alignment explanation
Indices: 10406--10650 Score: 309
Period size: 40 Copynumber: 6.2 Consensus size: 40
10396 TATGGGTTTT
* * * *
10406 AATCCTGCTCAGGATCATTTCTTTA-CCAGTTAA--TCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
10443 AATCCTGCTCAGGGTCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
10483 AATCCTGCTCAGGATCATCTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
*
10524 AACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * * *
10564 AATCCTACTCGGGATCATTGCTTTATCAAGTGAATTTCAG
1 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
10604 AATCCTGTTCAGGATCATTTGCTTTATC-AGTCAATTTCAAA
1 AATCCTGCTCAGGATCA-TTGCTTTATCAAATTAATTTC-AA
10645 AATCCT
1 AATCCT
10651 ATTCAGGACC
Statistics
Matches: 184, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
37 23 0.12
38 6 0.03
40 99 0.54
41 56 0.30
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (40 bp):
AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
Found at i:10545 original size:81 final size:80
Alignment explanation
Indices: 10406--10699 Score: 330
Period size: 81 Copynumber: 3.7 Consensus size: 80
10396 TATGGGTTTT
* * *
10406 AATCCTGCTCAGGATCATTTCTTTA-CCAGTTAA--TCAGAATCCTGCTCAGGGTCATTGCTTTA
1 AATCCTGCTCAGGATCATTGCTTTATCAAGTTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
10468 TCAAATTAATTTCAA
66 TCAAATTAATTTCAA
* * *
10483 AATCCTGCTCAGGATCATCTGCTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTT
1 AATCCTGCTCAGGATCAT-TGCTTTATCAAGTTAATTTCAGAATCCTGCTCAGGATCATTGCTTT
10548 ATCAAATTAATTTCAA
65 ATCAAATTAATTTCAA
* * * *
10564 AATCCTACTCGGGATCATTGCTTTATCAAGTGAATTTCAGAATCCTGTTCAGGATCATTTGCTTT
1 AATCCTGCTCAGGATCATTGCTTTATCAAGTTAATTTCAGAATCCTGCTCAGGATCA-TTGCTTT
* *
10629 ATC-AGTCAATTTCAAA
65 ATCAAATTAATTTC-AA
** * * * * **
10645 AATCCTATTCAGGACCAGTGGC-TTATC-AGTTGATTTCAGCATCCAACTCAGGATC
1 AATCCTGCTCAGGATCA-TTGCTTTATCAAGTTAATTTCAGAATCCTGCTCAGGATC
10700 CTGATTTAGG
Statistics
Matches: 185, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
77 18 0.10
78 6 0.03
79 6 0.03
80 64 0.35
81 88 0.48
82 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (80 bp):
AATCCTGCTCAGGATCATTGCTTTATCAAGTTAATTTCAGAATCCTGCTCAGGATCATTGCTTTA
TCAAATTAATTTCAA
Found at i:10600 original size:121 final size:117
Alignment explanation
Indices: 10409--10645 Score: 314
Period size: 121 Copynumber: 2.0 Consensus size: 117
10399 GGGTTTTAAT
* * * * *
10409 CCTGCTCAGGATCATTTCTTTACCAGTTAATCAGAATCCTGCTCAGGGTCATTGCTTTATCAAAT
1 CCTGCTCAGGATCATTGCTTTACAAATTAATCAAAATCCTACTCAGGGTCATTGCTTTATCAAAT
* *
10474 TAATTTCAAAATCCTGCTCAGGATCATCTGCTTTATCAAATTAATTTCAAAAC
66 GAATTTCAAAATCCTGCTCAGGATCATCTGCTTTATC-AATCAATTTCAAAAC
10527 CCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAAAATCCTACTC-GGGATCATTGCTTTATC
1 CCTGCTCAGGATCATTGCTTTA-CAAATTAA--TCAAAATCCTACTCAGGG-TCATTGCTTTATC
* * * * *
10591 AAGTGAATTTCAGAATCCTGTTCAGGATCATTTGCTTTATCAGTCAATTTCAAAA
62 AAATGAATTTCAAAATCCTGCTCAGGATCATCTGCTTTATCAATCAATTTCAAAA
10646 ATCCTATTCA
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
118 21 0.20
119 6 0.06
120 15 0.15
121 61 0.59
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.36
Consensus pattern (117 bp):
CCTGCTCAGGATCATTGCTTTACAAATTAATCAAAATCCTACTCAGGGTCATTGCTTTATCAAAT
GAATTTCAAAATCCTGCTCAGGATCATCTGCTTTATCAATCAATTTCAAAAC
Found at i:10671 original size:121 final size:121
Alignment explanation
Indices: 10443--10672 Score: 295
Period size: 121 Copynumber: 1.9 Consensus size: 121
10433 AGTTAATCAG
* *
10443 AATCCTGCTCAGGGTCATTGCTTTATCAAATTAATTTCAAAATCCTGCTCAGGATCATCTGCTTT
1 AATCCTACTCAGGGTCATTGCTTTATCAAATGAATTTCAAAATCCTGCTCAGGATCATCTGCTTT
* * * *
10508 ATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
66 ATCAAATCAATTTCAAAACCCTACTCAGGACCATGGCTTTATCAAATTAATTTCAA
* * * *
10564 AATCCTACTC-GGGATCATTGCTTTATCAAGTGAATTTCAGAATCCTGTTCAGGATCATTTGCTT
1 AATCCTACTCAGGG-TCATTGCTTTATCAAATGAATTTCAAAATCCTGCTCAGGATCATCTGCTT
* * *
10628 TATC-AGTCAATTTCAAAAATCCTATTCAGGACCAGTGGC-TTATCA
65 TATCAAATCAATTTC-AAAACCCTACTCAGGACCA-TGGCTTTATCA
10673 GTTGATTTCA
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
120 11 0.12
121 79 0.85
122 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (121 bp):
AATCCTACTCAGGGTCATTGCTTTATCAAATGAATTTCAAAATCCTGCTCAGGATCATCTGCTTT
ATCAAATCAATTTCAAAACCCTACTCAGGACCATGGCTTTATCAAATTAATTTCAA
Found at i:10682 original size:40 final size:41
Alignment explanation
Indices: 10556--10674 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 41
10546 TTATCAAATT
* * * * *
10556 AATTTC-AAAATCCTACTCGGGATCA-TTGCTTTATCAAGTG
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATC-AGTC
* * * * *
10596 AATTTC-AGAATCCTGTTCAGGATCATTTGCTTTATCAGTC
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATCAGTC
10636 AATTTCAAAAATCCTATTCAGGACCAGTGGC-TTATCAGT
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATCAGT
10675 TGATTTCAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 38 0.57
41 29 0.43
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATCAGTC
Found at i:18674 original size:33 final size:34
Alignment explanation
Indices: 18633--18700 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
18623 GGGACAAAAT
18633 TTTTTTTTATGACGCAGAAACTTTT-TTTTATTA
1 TTTTTTTTATGACGCAGAAACTTTTATTTTATTA
*
18666 TTTTTTTTATGACGCAGAAACTTTTATTTTTTTA
1 TTTTTTTTATGACGCAGAAACTTTTATTTTATTA
18700 T
1 T
18701 CGACACAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (34 bp):
TTTTTTTTATGACGCAGAAACTTTTATTTTATTA
Found at i:18826 original size:39 final size:40
Alignment explanation
Indices: 18757--18834 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
18747 ACACAAAATT
18757 AAAAACGCAAATTTTTTTTTCAGATCAAAAACGCAGAAAAG
1 AAAAACG-AAATTTTTTTTTCAGATCAAAAACGCAGAAAAG
* * *
18798 AAAAACG-AATTTTTTTTTTAGGTTAAAAACGCAGAAA
1 AAAAACGAAATTTTTTTTTCAGATCAAAAACGCAGAAA
18835 CGCAGAGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 27 0.79
41 7 0.21
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (40 bp):
AAAAACGAAATTTTTTTTTCAGATCAAAAACGCAGAAAAG
Found at i:28297 original size:30 final size:30
Alignment explanation
Indices: 28252--28763 Score: 774
Period size: 30 Copynumber: 16.9 Consensus size: 30
28242 ATTTTATCAG
* * *
28252 TTTATTTTCAATCCTGGTTCAGGATCGTCGC
1 TTTATTTT-AATCCTGGTTGAGGATCATTGC
* *
28283 TTTATTTTAATCCTGGTTTAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
28313 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
28343 TTTATTTTTAATCCTGGTTGAGGATCATTGC
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGC
*
28374 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
28404 TTTATTTTTAATCTTGGTTGAGGATCATTGG
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGC
*
28435 TTTGTTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
28465 TTTATTTTAATCGTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
28495 TTCATTTTAATCCTAGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
28525 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
28555 TTTATTTTTAATCCTGGTTGAGGATCATTGC
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGC
*
28586 TTTATTTTTATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
28616 TTCATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
28646 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
28676 TTTATTTTAATCCTGGCTT-AGGATCATTGC
1 TTTATTTTAATCCTGG-TTGAGGATCATTGC
* * *
28706 TTTATTTTAATCTTGGTTTAGGACCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
28736 TTTATTTTAATTCTGGTTTAGGATCATT
1 TTTATTTTAATCCTGGTTGAGGATCATT
28764 ACTTCATCAG
Statistics
Matches: 446, Mismatches: 30, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
29 2 0.00
30 349 0.78
31 95 0.21
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:28407 original size:91 final size:90
Alignment explanation
Indices: 28252--28763 Score: 792
Period size: 91 Copynumber: 5.6 Consensus size: 90
28242 ATTTTATCAG
* * * *
28252 TTTATTTTCAATCCTGGTTCAGGATCGTCGCTTTATTTTAATCCTGGTTTAGGATCGTTGCTTTA
1 TTTATTTT-AATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTA
*
28317 TTTTAATCCTGGTTTAGGATCATTGC
65 TTTTAATCCTGGTTGAGGATCATTGC
28343 TTTATTTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTA
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTA
* *
28408 TTTTTAATCTTGGTTGAGGATCATTGG
65 -TTTTAATCCTGGTTGAGGATCATTGC
* * * *
28435 TTTGTTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCGTGGTTGAGGATCATTGCTTCAT
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
*
28500 TTTAATCCTAGTTGAGGATCATTGC
66 TTTAATCCTGGTTGAGGATCATTGC
*
28525 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTTAATCCTGGTTGAGGATCATTGCTTTA
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTA-TTTTAATCCTGGTTTAGGATCATTGCTTTA
*
28590 TTTTTATCCTGGTTGAGGATCATTGC
65 TTTTAATCCTGGTTGAGGATCATTGC
* *
28616 TTCATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
28681 TTTAATCCTGGCTT-AGGATCATTGC
66 TTTAATCCTGG-TTGAGGATCATTGC
* * * *
28706 TTTATTTTAATCTTGGTTTAGGACCATTGCTTTATTTTAATTCTGGTTTAGGATCATT
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATT
28764 ACTTCATCAG
Statistics
Matches: 388, Mismatches: 29, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
90 159 0.41
91 199 0.51
92 30 0.08
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (90 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
TTTAATCCTGGTTGAGGATCATTGC
Found at i:29277 original size:27 final size:27
Alignment explanation
Indices: 29247--29318 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
29237 GATCACCTAG
* *
29247 GGGGCATTTTAGTCATTTGCACGTCCA
1 GGGGCATTTTGGTCATTTGCACATCCA
*
29274 GGGGCATTTTGGTCATTTGCACATTCA
1 GGGGCATTTTGGTCATTTGCACATCCA
29301 GGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
29319 CAAGTTCACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.38
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACATCCA
Found at i:32300 original size:41 final size:41
Alignment explanation
Indices: 32116--32292 Score: 284
Period size: 41 Copynumber: 4.3 Consensus size: 41
32106 CTTTTTTGTG
32116 CAATTT-GCTCCCTGATTGAGGGTAATATTTATTAATTGGTT
1 CAATTTCG-TCCCTGATTGAGGGTAATATTTATTAATTGGTT
*
32157 CAATTTCGTCCCTGATTGAGGGTAATATTTATTAACTGGTT
1 CAATTTCGTCCCTGATTGAGGGTAATATTTATTAATTGGTT
*
32198 CAATTTCGTCCCTGATTGAGTGTAATATTTATTAATTGGTT
1 CAATTTCGTCCCTGATTGAGGGTAATATTTATTAATTGGTT
* * *
32239 CAATTTTGTCCCTGATTTAGGTTAATATTTATTAATTGGTT
1 CAATTTCGTCCCTGATTGAGGGTAATATTTATTAATTGGTT
*
32280 CAATTTCATCCCT
1 CAATTTCGTCCCT
32293 AATTTAGGAT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 125 0.99
42 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (41 bp):
CAATTTCGTCCCTGATTGAGGGTAATATTTATTAATTGGTT
Found at i:32984 original size:15 final size:15
Alignment explanation
Indices: 32966--33010 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
32956 AAAATTTAAA
32966 AAAAAATGAAGAAA-G
1 AAAAAATGAA-AAATG
32981 AAAAAATGAAAAATG
1 AAAAAATGAAAAATG
*
32996 AAAAACTGGAAAAAT
1 AAAAAAT-GAAAAAT
33011 CAGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 3 0.11
15 17 0.63
16 7 0.26
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.11
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:34164 original size:154 final size:154
Alignment explanation
Indices: 33731--36143 Score: 3572
Period size: 154 Copynumber: 15.7 Consensus size: 154
33721 CGTTTCGACA
*
33731 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAACTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* * *
33796 TATCCATTGTTTATGGCCTAAC-AGTAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAC
66 TTTCCATTGTTTATGGACTAACTA-TAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAG
33860 CTCATTTGGAACACTTGTTATTTTG
130 CTCATTTGGAACACTTGTTATTTTG
* ** * * * *
33885 GGCCTTTCGAGGCCCATTAAATCCGTTTTGAATCGACATCGATTTCG-ACAATCT-AAAGCTTTG
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCA-AACCTCAAAGCTTTT
* *
33948 CTTTCCATTGTTTATGGATTAACTATAATCATTTTGGTGAGAT-TAGTCCACTGTGAAATTTTTA
65 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTA
34012 GCTCATTTGGAACACTTGTTATTTTG
129 GCTCATTTGGAACACTTGTTATTTTG
* * * *
34038 GACCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* *
34103 TTTCCATTATTTATGGACTAACTGTAATCATTTTGGTGAGAT-TAGTCCACTGTGAAGTTTTTAG
66 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAG
* *
34167 CTCATTTGGAACACTTCTTATTTTA
130 CTCATTTGGAACACTTGTTATTTTG
* *
34192 GGCCTTTAGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* *
34257 TTT-AAGTTGTTTAT-GACCTAACAATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
66 TTTCCA-TTGTTTATGGA-CTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
**
34320 GCTCATTTGGAACACTTGTTATTTCC
129 GCTCATTTGGAACACTTGTTATTTTG
* * * * * *
34346 GGCCATTCGAGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTCGAAAACCTTAAAACTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* ** *
34411 TTTCCATCGTTTACT-CCCTAACTATAATCATTTTGGTGCGATATGTCCACTGTGAAGTTTTTAG
66 TTTCCATTGTTTA-TGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAG
34475 CTCATTTGGAACACTTGTTATTTTG
130 CTCATTTGGAACACTTGTTATTTTG
* * *
34500 GGCCTTTCTGGGCCCATTAGATCCGTTTTGAATCGA-TATCGATTTGGCAAAACTCAAAGCTTTT
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACT-TCGATTTGGCAAACCTCAAAGCTTTT
* *
34564 CTTTCCAATGTTTAT-GAGCTAACTATAATCATTTTGGTGAGATATGTCCATTGTGAAGTTTTTA
65 CTTTCCATTGTTTATGGA-CTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
* *
34628 GCTCAATTGGAACACTTTTTATTTTG
129 GCTCATTTGGAACACTTGTTATTTTG
* *
34654 GGCCTTTCGGGGCCCATTAGTTCCGTTTTTAATCGACATCGATTTGGCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* * * * *
34719 TTTCCAGTGTTTATGGCCAAACTATAATCATTTTCGTGAGATATGTCGACTGTGAAGTTTTTAGC
66 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGC
34784 TCATTTGGAACACTTGTTATTTTG
131 TCATTTGGAACACTTGTTATTTTG
* * *
34808 GGCCTTTTGGAGCCCATTAGATT-CGTTTTGAATCGATTTCGATTTGGCAAACCTCAAAGCTATT
1 GGCCTTTCGGGGCCCATTAG-TTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCT-TT
* * *
34872 T-TTTCCATTATTTATGGCCTAACTATAATCATTTTGATGAGATATGTCCACTGTGAAGTTTTTA
64 TCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
* *
34936 ACTCATTTGGAACACTTCTTATTTTG
129 GCTCATTTGGAACACTTGTTATTTTG
* * * * * *
34962 GGCCTTTCAGGGCCCACTAGATCAGTTTTAAATCGACATT-GATTTGGCAAACCTCAAACCTTTT
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGAC-TTCGATTTGGCAAACCTCAAAGCTTTT
* *
35026 CTTTCCATTGTTTATGGACTTACTATAATCATTTTGGTGAGAT-TAGTCCATTGTGAAGTTTTTA
65 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTA
* * *
35090 GATCATATGGAACACTTCTTATTTTG
129 GCTCATTTGGAACACTTGTTATTTTG
* *
35116 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAAACGTCTTCGATTTGGCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* * * *
35181 TTT-AAGTTGTTTATGGCCTAACAATAATCATTTTCGTGAGATATGTCCACTGTGAAG-TTTTAG
66 TTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAG
*
35244 TTCATTTGGAACACTTGTTATTTTG
130 CTCATTTGGAACACTTGTTATTTTG
* *
35269 GGTCTTTC-GGGCCCATTAGTTCCGTTTTGAATCAACTTCGATTTGGCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* *
35333 TTTCCATTCTTTATGGACTAACTATAATCATTTTGGTGAGATATGTGCACTGTGAATGTTTTTAG
66 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAA-GTTTTTAG
35398 CTCATTTGGAACACTTGTTATTTTG
130 CTCATTTGGAACACTTGTTATTTTG
* * * *
35423 GACCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGTCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* * * *
35488 TTT-AAGTTGTTTATGGCCTAACAATAATCATTTTCGTGAGATATGTCCACTGTGAAG-TTTTAG
66 TTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAG
35551 CTCATTTGGAACACTTGTTATTTTG
130 CTCATTTGGAACACTTGTTATTTTG
*
35576 GGTCTTTC-GGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
*
35640 TTTCCATTCTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGC
66 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGC
*
35705 TTATTTGGAACACTTGTTATTTTG
131 TCATTTGGAACACTTGTTATTTTG
* * *
35729 GGCCTTTCGGGGCCAATTAGTTCCGTTTTGAATCGATTTCGATTTGGCAAACCTCAAAGCTATTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* *
35794 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATATGTCAACTGTGAAGTTTTTAGC
66 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGC
35859 TCATTTGGAACACTTGTTATTTTG
131 TCATTTGGAACACTTGTTATTTTG
* * *
35883 GGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGATTTCGATTTGGCAAATCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
*
35948 TTTCCAATTGTTTAT-GAGCTAACTATAATCATTTTGGTGAGATATGTCCATTGTGAAGTTTTTA
66 TTTCC-ATTGTTTATGGA-CTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTA
*
36012 GCTCAATTGGAACACTTGTTATTTTG
129 GCTCATTTGGAACACTTGTTATTTTG
* * *
36038 GGCCTTTCGGGGCCCATTAGATCCGTTTTGATTCGACATCGATTTGGCAAACCTCAAAGCTTTTC
1 GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
36103 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGA
66 TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGA
36144 GCTTCGTGAT
Statistics
Matches: 2037, Mismatches: 188, Indels: 68
0.89 0.08 0.03
Matches are distributed among these distances:
152 206 0.10
153 256 0.13
154 1316 0.65
155 259 0.13
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (154 bp):
GGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGC
TCATTTGGAACACTTGTTATTTTG
Done.