Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_pilon, 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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1564324 original size:414 final size:414
Alignment explanation
Indices: 1563679--1564908 Score: 1950
Period size: 414 Copynumber: 3.0 Consensus size: 414
1563669 GCTATCTGCC
** * * * * *
1563679 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATAGCTTAAGTCG
* ** * * * *
1563744 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
65 AGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * * * ** *
1563808 TTGCAGTATAGCTTAAGTCGAGAAGGGCTATCT----TCCAAAGACCCCCGAGTTCGATTACACT
126 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACT
* * * *
1563869 CAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
191 CAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
1563934 CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGG
255 CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGG
* *
1563999 GTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATA
320 GTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATA
1564064 ACTCAAGGCTAGAAGGGTTATCTGTGACCA
385 ACTCAAGGCTAGAAGGGTTATCTGTGACCA
1564094 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1564159 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
66 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
* * *
1564224 GCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACATTCGAGTTCGACTACGCTCAGCT
131 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT
1564289 CCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTG
196 CCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTG
1564354 AGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATC
261 AGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATC
1564419 TGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAA
326 TGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAA
1564484 GGCTAGAAGGGTTATCTGTGACCA
391 GGCTAGAAGGGTTATCTGTGACCA
1564508 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
*
1564573 GAAGGGCTATCTGCCAAAGACTCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
66 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
*
1564638 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTAAGCT
131 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT
* * * *
1564703 CCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTG
196 CCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTG
* * *
1564768 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
261 AGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTAT
* * * * *
1564832 CTGCCAAAGACCCTCGAGTTCGATTACACTCAACCTCGAGGTCATATCATTTACAACATAGCTCA
325 CTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCA
*
1564897 AGGCAAGAAGGG
390 AGGCTAGAAGGG
1564909 CTATTTGTCA
Statistics
Matches: 761, Mismatches: 48, Indels: 13
0.93 0.06 0.02
Matches are distributed among these distances:
410 27 0.04
411 42 0.06
414 638 0.84
415 54 0.07
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (414 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT
CCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTG
AGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATC
TGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAA
GGCTAGAAGGGTTATCTGTGACCA
Found at i:1564908 original size:249 final size:245
Alignment explanation
Indices: 1563635--1564908 Score: 1524
Period size: 249 Copynumber: 5.1 Consensus size: 245
1563625 AGCTCAACGA
* * *
1563635 CACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
1 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTA
* *
1563700 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
66 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAA
*
1563765 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
131 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * * *
1563830 AAGGGCTATCTTCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
196 AAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACCTCGA-GG
* * ***
1563881 CACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCCCCGAGTTCG
* * * * * * * *
1563946 ACTACGCTCAGC-TCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATCTG-C-
62 ATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCA
** * * * * * * *
1564008 -C-AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
127 ACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * * * * * * *
1564071 GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTC-AGCTCTAAGG
191 TCGAGAAGGGCTATC--TG-CC-AAAGACCCTCGAGTTCGATTACACTCAACCTC-GAGG
*
1564130 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
1 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTA
*
1564195 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT-TGAGAAGGGTTATCTGCCAACC
66 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCT-AGAAGGGTTATCTGCCAACA
* * *
1564259 AAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
130 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * * * * *
1564324 GAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTC-AGCTCAACGG
195 GAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAACCTCGA-GG
* *
1564379 CACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTA
1 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTA
* * * * * ** *
1564444 CACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
66 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAA
*
1564509 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
131 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* *
1564574 AAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATTACACTCAGCTTCGAGGG
196 AAGGGCTATCTGCCAAAGAC-CCTCGAGTTCGATTACACTCAACCTCGA-GG
* **
1564625 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
1 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCCCCGAGTTCG
* * * * * * *
1564690 ACTACACTAAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCA
62 ATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCA
*
1564754 ACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
127 ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1564819 CGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACCTCGAGG
192 CGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACCTCGAGG
* * * * * *
1564873 TCATATCATTTACAACATAGCTCAAGGCAAGAAGGG
1 -CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
1564909 CTATTTGTCA
Statistics
Matches: 878, Mismatches: 121, Indels: 55
0.83 0.11 0.05
Matches are distributed among these distances:
245 73 0.08
246 163 0.19
247 3 0.00
248 8 0.01
249 528 0.60
250 103 0.12
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (245 bp):
CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAA
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACCTCGAGG
Found at i:1565451 original size:2 final size:2
Alignment explanation
Indices: 1565444--1565482 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1565434 TCGTCTCATT
*
1565444 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1565483 GTTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1565594 original size:36 final size:36
Alignment explanation
Indices: 1565465--1565913 Score: 276
Period size: 36 Copynumber: 12.6 Consensus size: 36
1565455 ATATATATAT
* *
1565465 ATATATATATATATTATAG-TTTAAAAATATTTTTAAA
1 ATATATATA-ATA-TATAGTTTTTAAAATATTTTGAAA
* *
1565502 ACCTATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 A--TATATATAATATATAGTTTTTAAAATAT-TTTGAAA
*
1565541 ATATTTATATATTATATAGTTTTTAAAATATTTTGAAA
1 ATA--TATATAATATATAGTTTTTAAAATATTTTGAAA
* *
1565579 ATAAATATAATATATAGTTTTT-ACATATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATA-TTTTGAAA
* * *
1565615 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* * * * *
1565651 ATAAATATACTATATAAGTTTTAAAACATTTTTTTAAA
1 ATATATATAATATAT-AGTTTTTAAA-ATATTTTGAAA
1565689 ATATATAT--TATATAGTTTTT-AAATATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* ***
1565722 ATATATATAGT-T-T--TTAAAAAAATATTTTGAAGAA
1 ATATATATAATATATAGTTTTTAAAATATTTTG-A-AA
* *
1565756 CATATATATATTATATAGTTTTT-AAATCA-TTTCAAA
1 -ATATATATAATATATAGTTTTTAAAAT-ATTTTGAAA
* * * *
1565792 A-ACT-TATAATATATAATTTTAAAAAACATTTT-TAA
1 ATA-TATATAATATATAGTTTT-TAAAATATTTTGAAA
* * ** *
1565827 A-A-A-CT-ATATA-A-TTTTGAAAACGTTTTAAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* * * *
1565857 AAACATATAATATATA-ATTTTAAAATATTTTTAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
*
1565892 A-ATATATATTATATAGATTTTT
1 ATATATATAATATATAG-TTTTT
1565914 GGAAAATGTT
Statistics
Matches: 327, Mismatches: 51, Indels: 69
0.73 0.11 0.15
Matches are distributed among these distances:
29 9 0.03
30 7 0.02
31 4 0.01
32 16 0.05
33 21 0.06
34 37 0.11
35 44 0.13
36 82 0.25
37 22 0.07
38 44 0.13
39 41 0.13
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAATATTTTGAAA
Found at i:1565647 original size:72 final size:71
Alignment explanation
Indices: 1565465--1565913 Score: 305
Period size: 72 Copynumber: 6.3 Consensus size: 71
1565455 ATATATATAT
** * *
1565465 ATATATATATATATTATAGTTTAAAAATATTTTTAAAACCTATATATAATATATAGTTTTGAAA-
1 ATATAT-TAT-TA-TATAGTTTTTAAATATTTTGAAAA--TAAATATAATATATAGTTTT-AAAC
* *
1565529 ACATGTTTGAAA
60 ATATTTTTGAAA
*
1565541 ATATTTATATATTATATAGTTTTTAAAATATTTTGAAAATAAATATAATATATAGTTTT-TACAT
1 ATA--TAT-TATTATATAGTTTTT-AAATATTTTGAAAATAAATATAATATATAGTTTTAAACAT
1565605 ATTTTTGAAA
62 ATTTTTGAAA
*
1565615 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAAATAAATATACTATATAAGTTTTAAAACAT
1 ATATAT-TATTATATAGTTTTTAAA-TATTTTGAAAATAAATATAATATAT-AGTTTT-AAACAT
*
1565680 -TTTTTTAAA
62 ATTTTTGAAA
* * *
1565689 ATATA-TATTATATAGTTTTTAAATATTTTGAAAAT--ATAT-ATA-GT--TTTTAAAAAAATAT
1 ATATATTATTATATAGTTTTTAAATATTTTGAAAATAAATATAATATATAGTTTTAAACATAT-T
1565747 TTTGAAGAA
65 TTTG-A-AA
* ** * * *
1565756 CATATATATATTATATAGTTTTTAAATCA-TTTCAAAA-ACTTATAATATATAATTTTAAAAAAC
1 -ATATAT-TATTATATAGTTTTTAAAT-ATTTTGAAAATAAATATAATATATAGTTTT-AAACAT
1565819 ATTTTT--AA
62 ATTTTTGAAA
* * * *
1565827 A-A-ACTA-TATA-A-TTTTGAAA-ACGTTTT-AAAAAAACATATAATATATAATTTTAAA-ATA
1 ATATATTATTATATAGTTTTTAAATA--TTTTGAAAATAA-ATATAATATATAGTTTTAAACATA
*
1565884 TTTTTAAAA
63 TTTTTGAAA
1565893 ATATA-TATTATATAGATTTTT
1 ATATATTATTATATAG-TTTTT
1565914 GGAAAATGTT
Statistics
Matches: 311, Mismatches: 26, Indels: 77
0.75 0.06 0.19
Matches are distributed among these distances:
62 1 0.00
63 4 0.01
64 23 0.07
65 12 0.04
66 24 0.08
67 8 0.03
68 13 0.04
69 6 0.02
70 27 0.09
71 25 0.08
72 63 0.20
73 8 0.03
74 26 0.08
75 31 0.10
76 18 0.06
77 15 0.05
78 7 0.02
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (71 bp):
ATATATTATTATATAGTTTTTAAATATTTTGAAAATAAATATAATATATAGTTTTAAACATATTT
TTGAAA
Found at i:1565857 original size:29 final size:31
Alignment explanation
Indices: 1565801--1565867 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
1565791 AAACTTATAA
*
1565801 TATATAATTTTAAAAAACATTTT-TAAAAAC
1 TATATAATTTTAAAAAACATTTTAAAAAAAC
* *
1565831 TATATAATTTT-GAAAACGTTTTAAAAAAAC
1 TATATAATTTTAAAAAACATTTTAAAAAAAC
1565861 -ATATAAT
1 TATATAAT
1565868 ATATAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (31 bp):
TATATAATTTTAAAAAACATTTTAAAAAAAC
Found at i:1565982 original size:29 final size:28
Alignment explanation
Indices: 1565932--1565997 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1565922 TTTTTTTAGT
1565932 TTATTTA-TTTACCTTTTGTTATGTATTTA
1 TTATTTATTTTACCTTTTGTTAT-T-TTTA
1565961 TTATTTATTTTA-CTTATT-TTATTTTTA
1 TTATTTATTTTACCTT-TTGTTATTTTTA
1565988 TT-TTTATTTT
1 TTATTTATTTT
1565998 GTTGCAGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.23
27 6 0.17
28 1 0.03
29 14 0.40
30 6 0.17
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.73
Consensus pattern (28 bp):
TTATTTATTTTACCTTTTGTTATTTTTA
Found at i:1567890 original size:14 final size:14
Alignment explanation
Indices: 1567871--1567914 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 14
1567861 CGTTCGATAA
1567871 TATGTTCGTTCATT
1 TATGTTCGTTCATT
1567885 TATGTTCGTT--TT
1 TATGTTCGTTCATT
1567897 TATG--CGTTCATT
1 TATGTTCGTTCATT
1567909 TATGTT
1 TATGTT
1567915 TAGTCTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.15
12 12 0.46
14 10 0.38
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:1568131 original size:23 final size:23
Alignment explanation
Indices: 1568100--1568211 Score: 127
Period size: 23 Copynumber: 4.8 Consensus size: 23
1568090 GTTTGTTTAC
* *
1568100 GTTCATTTATGTTCATCTATTGT
1 GTTCGTTTATGTTCATTTATTGT
1568123 GTTCGTTTACT-TTCATTTATTGT
1 GTTCGTTTA-TGTTCATTTATTGT
** *
1568146 GTTCGTTTATGTTTGTTCATTTGT
1 GTTCGTTTATGTTCATTTA-TTGT
* *
1568170 GTTCGTTTACGTTCGTTTATTGT
1 GTTCGTTTATGTTCATTTATTGT
*
1568193 GTTCGTTTATGTTCGTTTA
1 GTTCGTTTATGTTCATTTA
1568212 CATCCGTTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
22 1 0.01
23 55 0.71
24 21 0.27
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (23 bp):
GTTCGTTTATGTTCATTTATTGT
Found at i:1568158 original size:10 final size:10
Alignment explanation
Indices: 1568159--1568236 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 10
1568149 CGTTTATGTT
* *
1568159 TGTTCATTTG
1 TGTTCGTTTA
1568169 TGTTCGTTTA
1 TGTTCGTTTA
*
1568179 CGTTCGTTTA
1 TGTTCGTTTA
1568189 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
1568202 TGTTCGTTTACA
1 TGTTCGTTT--A
*
1568214 TCCGTTCATTTA
1 T--GTTCGTTTA
1568226 TGTTCGTTTA
1 TGTTCGTTTA
1568236 T
1 T
1568237 CATTTAAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 35 0.64
12 4 0.07
13 9 0.16
14 7 0.13
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.56
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1568231 original size:47 final size:47
Alignment explanation
Indices: 1568123--1568236 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 47
1568113 CATCTATTGT
* * * * ** **
1568123 GTTCGTTTACTTTCATTTATTGTGTTCGTTTATGTTTGTTCATTTGT
1 GTTCATTTACGTTCGTTTATTGTGTTCGTTTATGTTCGTTCACATCC
* *
1568170 GTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCGTTTACATCC
1 GTTCATTTACGTTCGTTTATTGTGTTCGTTTATGTTCGTTCACATCC
*
1568217 GTTCATTTATGTTCGTTTAT
1 GTTCATTTACGTTCGTTTAT
1568237 CATTTAAATG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.11, C:0.13, G:0.18, T:0.58
Consensus pattern (47 bp):
GTTCATTTACGTTCGTTTATTGTGTTCGTTTATGTTCGTTCACATCC
Found at i:1568506 original size:45 final size:45
Alignment explanation
Indices: 1568442--1568532 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1568432 AAACCTGCAA
*
1568442 TAACATGACAATAAAATTATAAATTATAATATTATTTATGTAATG
1 TAACATGACAAGAAAATTATAAATTATAATATTATTTATGTAATG
1568487 TAACATGACAAGAAAATTATAAATTATAATATTATTTATGTAATG
1 TAACATGACAAGAAAATTATAAATTATAATATTATTTATGTAATG
1568532 T
1 T
1568533 GAACCTTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (45 bp):
TAACATGACAAGAAAATTATAAATTATAATATTATTTATGTAATG
Found at i:1568919 original size:30 final size:31
Alignment explanation
Indices: 1568854--1568924 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
1568844 TTAATTAAAA
*
1568854 ATTTCATAATAATTTGATAAATATAATGATC
1 ATTTTATAATAATTTGATAAATATAATGATC
* * *
1568885 ATTTTATAATAATTT-ATAAATTTAATTATT
1 ATTTTATAATAATTTGATAAATATAATGATC
1568915 ATTTTATAAT
1 ATTTTATAAT
1568925 TTTTAACAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTTATAATAATTTGATAAATATAATGATC
Found at i:1576847 original size:17 final size:17
Alignment explanation
Indices: 1576811--1576862 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1576801 TCGAATATAA
*
1576811 TAAATAATATTATT-TAT
1 TAAA-AATATTATTATTT
1576828 TAAAAATATTATTATTT
1 TAAAAATATTATTATTT
*
1576845 TAAAAATATTATAATTT
1 TAAAAATATTATTATTT
1576862 T
1 T
1576863 TTATTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAAATATTATTATTT
Found at i:1576876 original size:13 final size:13
Alignment explanation
Indices: 1576851--1576888 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1576841 ATTTTAAAAA
1576851 TATTATAAT-TTTT
1 TATT-TAATATTTT
1576864 TATTTAATATTTT
1 TATTTAATATTTT
1576877 TATTTTAATATT
1 TA-TTTAATATT
1576889 AGTTTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTAATATTTT
Found at i:1577058 original size:29 final size:28
Alignment explanation
Indices: 1577021--1577091 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1577011 GTATAAATTG
*
1577021 ATAATTAATATTTTTATTAAAATGATATTAA
1 ATAA-TAATATTTTTATT-AAAT-ATATAAA
**
1577052 A-AATAATATTAATATTAAATATATAAA
1 ATAATAATATTTTTATTAAATATATAAA
1577079 ATAATAATATTTT
1 ATAATAATATTTT
1577092 GAGTATTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 7 0.21
28 13 0.38
29 11 0.32
30 2 0.06
31 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
ATAATAATATTTTTATTAAATATATAAA
Found at i:1577478 original size:13 final size:13
Alignment explanation
Indices: 1577460--1577493 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1577450 TTATTTATTT
1577460 ATAAATAATTAAA
1 ATAAATAATTAAA
*
1577473 ATAAATTATTAAA
1 ATAAATAATTAAA
*
1577486 ATTAATAA
1 ATAAATAA
1577494 ATTATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATAATTAAA
Found at i:1578045 original size:15 final size:15
Alignment explanation
Indices: 1578025--1578054 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1578015 ATATTTTTAT
1578025 GCATGAAATAAAGGA
1 GCATGAAATAAAGGA
*
1578040 GCATGAATTAAAGGA
1 GCATGAAATAAAGGA
1578055 TCAAAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.27, T:0.17
Consensus pattern (15 bp):
GCATGAAATAAAGGA
Found at i:1590467 original size:17 final size:15
Alignment explanation
Indices: 1590445--1590484 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
1590435 TTTAAGAAAA
1590445 AATATTATATTCTTATT
1 AATATTATA-T-TTATT
1590462 AATATT-TATTTATT
1 AATATTATATTTATT
1590476 AATATTATA
1 AATATTATA
1590485 GAAAGTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.50
15 3 0.14
16 2 0.09
17 6 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATTATATTTATT
Found at i:1591964 original size:36 final size:36
Alignment explanation
Indices: 1591914--1591984 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1591904 AGTTATGCAT
* *
1591914 ACAAAGATCATGTTATATTAATACCAAAAGTATTAC
1 ACAAAGATCATGTTAGATTAATACCAAAAGCATTAC
*
1591950 ACAAAGATCCTGTTAGATTAATACCAAAAGCATTA
1 ACAAAGATCATGTTAGATTAATACCAAAAGCATTA
1591985 TACGGTAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (36 bp):
ACAAAGATCATGTTAGATTAATACCAAAAGCATTAC
Found at i:1592743 original size:34 final size:33
Alignment explanation
Indices: 1592676--1592779 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 33
1592666 TTGAATTTTT
*
1592676 ATTTTTGCATTTCTACATCTTTGTATTTGCATTTGC
1 ATTTTTGCATTTCT--A-CTTTGTATTTACATTTGC
* *
1592712 ATTTTTGCATTTTTACGTTTGTATTTACATTTTC
1 ATTTTTGCATTTCTAC-TTTGTATTTACATTTGC
*
1592746 ATTTTTGCATTTGTATCTTTGTATAATTACATTT
1 ATTTTTGCATTTCTA-CTTTGTAT--TTACATTT
1592780 TGTTTCAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
33 1 0.02
34 37 0.62
35 1 0.02
36 21 0.35
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (33 bp):
ATTTTTGCATTTCTACTTTGTATTTACATTTGC
Found at i:1597060 original size:72 final size:73
Alignment explanation
Indices: 1596943--1597090 Score: 217
Period size: 72 Copynumber: 2.0 Consensus size: 73
1596933 GGGGCATGCT
* * * *
1596943 GAAGGCCCACAACATCATGTGTTAAAGATCATTGACTTGAGCAAATATTTCCAATGAGACAGAAA
1 GAAGGCCCACAACATCATATGTTAAAGATCATTGACTTGACCAAATATTTCCAATAAGACAAAAA
*
1597008 GGTATGAA
66 GGAATGAA
* * *
1597016 GAAGGCCTACATCATCATATGTT-AAGATCATTGACTTGACCAAATATTTTCAATAAGACAAAAA
1 GAAGGCCCACAACATCATATGTTAAAGATCATTGACTTGACCAAATATTTCCAATAAGACAAAAA
1597080 GGAATGAA
66 GGAATGAA
1597088 GAA
1 GAA
1597091 TGAAAATGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 47 0.70
73 20 0.30
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (73 bp):
GAAGGCCCACAACATCATATGTTAAAGATCATTGACTTGACCAAATATTTCCAATAAGACAAAAA
GGAATGAA
Found at i:1597906 original size:54 final size:54
Alignment explanation
Indices: 1597841--1597944 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
1597831 CTGACCAGAA
* *
1597841 ATCTGGGCAGAAACCACATGAAATGATGAATGTATTGTCAAATATTTTACGAAT
1 ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTATCAAATATTTTACGAAT
* *
1597895 ATCTGTGCAGAAACCACAGGAAATGATGAATGTATTATCAAATGTTTTAC
1 ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTATCAAATATTTTAC
1597945 AAACCAGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (54 bp):
ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTATCAAATATTTTACGAAT
Found at i:1599177 original size:36 final size:36
Alignment explanation
Indices: 1599080--1599184 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 36
1599070 ACTACATTTT
* *
1599080 GCTTGAGACATTTTCACTCGAAACAATAATTTATCTC
1 GCTTGAGACAGTTTCACTAGAAACAA-AATTTATCTC
* ** ** *
1599117 ACTTGAGATTGTTTTTCTTA-AAACAAAATTTGTCTC
1 GCTTGAGACAGTTTCAC-TAGAAACAAAATTTATCTC
1599153 GCTTGAGACAGTTTCACTAGAAACAGAAATTT
1 GCTTGAGACAGTTTCACTAGAAACA-AAATTT
1599185 CCATCACTCG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
35 2 0.04
36 26 0.50
37 23 0.44
38 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (36 bp):
GCTTGAGACAGTTTCACTAGAAACAAAATTTATCTC
Found at i:1599184 original size:73 final size:73
Alignment explanation
Indices: 1599032--1599177 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
1599022 GTTTTCAAAT
* * * *
1599032 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTACATTTTGCTTGAGACATTTTCAC
1 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATACATCTCGCTTGAGACAGTTTCAC
*
1599097 TCGAAACA
66 TAGAAACA
***
1599105 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCAC
1 ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATACATCTCGCTTGAGACAGTTTCAC
1599170 TAGAAACA
66 TAGAAACA
1599178 GAAATTTCCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (73 bp):
ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATACATCTCGCTTGAGACAGTTTCAC
TAGAAACA
Found at i:1599476 original size:15 final size:15
Alignment explanation
Indices: 1599456--1599494 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
1599446 TTGGGCCAGG
1599456 TATATATATTTAAAT
1 TATATATATTTAAAT
*
1599471 TATATATA--TATAT
1 TATATATATTTAAAT
1599484 TATATATATTT
1 TATATATATTT
1599495 TTTAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 12 0.57
15 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATATATTTAAAT
Found at i:1600251 original size:134 final size:134
Alignment explanation
Indices: 1599916--1600275 Score: 429
Period size: 139 Copynumber: 2.6 Consensus size: 134
1599906 ATAGATCAAC
*
1599916 ATCAACATTTCCAGAAGG-GTTCATAATGAGAAAAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * ** *
1599980 ATGAGAATAACTTGTTCGACCTTAGCTTGATTCATCATTTATGGAGTTGAATGAAAGAAAAACCT
65 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAAT---A-AAAAACCT
1600045 CACTTGAGG
126 CACTTGAGG
* * *
1600054 ATCAATATTTTCAAAGGAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAAAGG-AGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * **
1600119 ATGAGAAGAACTTATTCAATCTT-GCCTTAATTCATCACATATGAAGTTGAAT-CAACACCTCTT
65 ATGAGAAGAACTTGTTCAACCTTAG-CTTAATTCATCACATATGAAGTTGAATAAAAAACCTCAC
1600182 TTGAGG
129 TTGAGG
* * * * *
1600188 ATCAGCATTTCCACAAGGAGTTCATAATGAGAAGAACTCATCTGAGGAAGAAGAAGAAATTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1600253 CTGAGAAGAACTTGTTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
1600276 TTGCTATATT
Statistics
Matches: 191, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
134 85 0.45
135 4 0.02
137 4 0.02
138 12 0.06
139 86 0.45
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (134 bp):
ATCAACATTTCCAAAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAATAAAAAACCTCACTT
GAGG
Found at i:1600260 original size:23 final size:22
Alignment explanation
Indices: 1600217--1600262 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1600207 GTTCATAATG
1600217 AGAAGAACTCATCTGAGGAAGA
1 AGAAGAACTCATCTGAGGAAGA
*
1600239 AGAAGAAATTCATACTGA-GAAGA
1 AGAAG-AACTCAT-CTGAGGAAGA
1600262 A
1 A
1600263 CTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.15
Consensus pattern (22 bp):
AGAAGAACTCATCTGAGGAAGA
Found at i:1600293 original size:134 final size:132
Alignment explanation
Indices: 1599916--1600293 Score: 388
Period size: 134 Copynumber: 2.8 Consensus size: 132
1599906 ATAGATCAAC
*
1599916 ATCAACATTTCCAGAAGG-GTTCATAATGAGAAAAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
1599980 ATGAGAATAACTTGTTCGACC-TTAGCTTGATTCATCATTTATGGAGTTGAATGAAAGAAAAACC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTT-ATTCAACA--TATGAAGTTGAAT---A-AAAAACC
1600044 TCACTTGAGG
123 TCACTTGAGG
* * *
1600054 ATCAATATTTTCAAAGGAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAAAGG-AGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
1600119 ATGAGAAGAACTTATTCAA--TCTTGCCTTAATTCATCACATATGAAGTTGAAT-CAACACCTCT
65 ATGAGAAGAACTTGTTCAACCTTTTG-CTT-ATTCA--ACATATGAAGTTGAATAAAAAACCTCA
*
1600181 TTTGAGG
126 CTTGAGG
* * * * *
1600188 ATCAGCATTTCCACAAGGAGTTCATAATGAGAAGAACTCATCTGAGGAAGAAGAAGAAATTCATA
1 ATCAACATTTCCA-AAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1600253 CTGAGAAGAACTTGTTCAACCTTTTGCTATATTTCAACATA
65 ATGAGAAGAACTTGTTCAACCTTTTGCT-TA-TTCAACATA
1600294 GAATGAGATA
Statistics
Matches: 202, Mismatches: 27, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
134 87 0.43
135 7 0.03
136 9 0.04
137 4 0.02
138 13 0.06
139 80 0.40
141 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (132 bp):
ATCAACATTTCCAAAGGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTTATTCAACATATGAAGTTGAATAAAAAACCTCACTTGA
GG
Found at i:1601718 original size:23 final size:23
Alignment explanation
Indices: 1601692--1601735 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1601682 TCTATTCCGA
*
1601692 TATTTTTAAATAAATAAATATTG
1 TATTTATAAATAAATAAATATTG
* *
1601715 TATTTATAAATATATATATAT
1 TATTTATAAATAAATAAATAT
1601736 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATTG
Found at i:1601731 original size:2 final size:2
Alignment explanation
Indices: 1601719--1601756 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1601709 ATATTGTATT
*
1601719 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1601757 GTTATTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1601994 original size:2 final size:2
Alignment explanation
Indices: 1601987--1602042 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1601977 CTGCTCATAA
*
1601987 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1602029 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1602043 TACTTCGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604346 original size:2 final size:2
Alignment explanation
Indices: 1604339--1604375 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1604329 CATTTACCAT
1604339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1604376 GCCAAACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1605586 original size:25 final size:26
Alignment explanation
Indices: 1605540--1605600 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
1605530 TACATACATA
1605540 TATACATGTATATGTAATTATGTATG
1 TATACATGTATATGTAATTATGTATG
*
1605566 TATACATGTGT-TGT-ATGTATGTATG
1 TATACATGTATATGTAAT-TATGTATG
*
1605591 TATGCATGTA
1 TATACATGTA
1605601 AATGAGAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 19 0.61
26 10 0.32
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.46
Consensus pattern (26 bp):
TATACATGTATATGTAATTATGTATG
Found at i:1608051 original size:21 final size:23
Alignment explanation
Indices: 1608022--1608077 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
1608012 AATTTTCATG
* *
1608022 ATAATATTAATT-A-TATTTTTT
1 ATAAAATTAATTAATTATTTTTA
1608043 ATAAAATTAATTTAATTATTTTTA
1 ATAAAATTAA-TTAATTATTTTTA
*
1608067 ATTAAATTAAT
1 ATAAAATTAAT
1608078 ACTTGATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 2 0.07
24 16 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATAAAATTAATTAATTATTTTTA
Found at i:1614003 original size:23 final size:23
Alignment explanation
Indices: 1613959--1614007 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1613949 ATAAAGAACC
*
1613959 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
1613982 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
1614005 AAA
1 AAA
1614008 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:1617859 original size:22 final size:22
Alignment explanation
Indices: 1617834--1617877 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1617824 GCTGTTCTTT
1617834 CTATAGAATGATTCCCATTTCA
1 CTATAGAATGATTCCCATTTCA
1617856 CTATAGAATGATTCCCATTTCA
1 CTATAGAATGATTCCCATTTCA
1617878 GCCGATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATAGAATGATTCCCATTTCA
Found at i:1619169 original size:20 final size:20
Alignment explanation
Indices: 1619144--1619183 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1619134 AAGAGAAACC
1619144 TTTTTTATTATTTATGTTTA
1 TTTTTTATTATTTATGTTTA
1619164 TTTTTTATTATTTATGTTTA
1 TTTTTTATTATTTATGTTTA
1619184 AAGGAGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTTATTATTTATGTTTA
Found at i:1619335 original size:7 final size:7
Alignment explanation
Indices: 1619323--1619371 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
1619313 TGAAAATTGA
1619323 TAATAAT
1 TAATAAT
1619330 TAATAATT
1 TAATAA-T
1619338 TAATAAT
1 TAATAAT
*
1619345 AAAT-AT
1 TAATAAT
1619351 TAATAA-
1 TAATAAT
1619357 TAAT-AT
1 TAATAAT
1619363 TAAATAAT
1 T-AATAAT
1619371 T
1 T
1619372 GATTATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
5 1 0.03
6 10 0.29
7 14 0.40
8 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATAAT
Found at i:1619366 original size:19 final size:20
Alignment explanation
Indices: 1619328--1619368 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1619318 ATTGATAATA
1619328 ATTAATAATTTAATAATAAAT
1 ATTAATAA-TTAATAATAAAT
*
1619349 ATTAATAA-TAATATTAAAT
1 ATTAATAATTAATAATAAAT
1619368 A
1 A
1619369 ATTGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTAATAATTAATAATAAAT
Found at i:1619514 original size:23 final size:23
Alignment explanation
Indices: 1619484--1619529 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1619474 GAGTTCTTTT
1619484 TTTAGTCTATCTAAAATAAAATA
1 TTTAGTCTATCTAAAATAAAATA
1619507 TTTAGTCTATCTAAAATAAAATA
1 TTTAGTCTATCTAAAATAAAATA
1619530 GGAGATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (23 bp):
TTTAGTCTATCTAAAATAAAATA
Found at i:1621155 original size:69 final size:69
Alignment explanation
Indices: 1621026--1621161 Score: 173
Period size: 69 Copynumber: 2.0 Consensus size: 69
1621016 CTAATATATA
** * * *
1621026 TTCTAAATAATATCAACCATTTGACAACGAACGTTCAATCACCTTGCTGTAGCCGCTGGTGCTCA
1 TTCTAAATAATATCAACCATTTGACAACGAACACTCAATCACCCTACTGCAGCCGCTGGTGCTCA
1621091 AATG
66 AATG
* * * * * *
1621095 TTCTAAATACTCTCAACTATTTGACAACGAACACTCAATTACCCTACTGCATCCGTTGGTGCTCA
1 TTCTAAATAATATCAACCATTTGACAACGAACACTCAATCACCCTACTGCAGCCGCTGGTGCTCA
1621160 AA
66 AA
1621162 CCCGTGACCT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (69 bp):
TTCTAAATAATATCAACCATTTGACAACGAACACTCAATCACCCTACTGCAGCCGCTGGTGCTCA
AATG
Found at i:1622605 original size:13 final size:13
Alignment explanation
Indices: 1622589--1622614 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1622579 AAATATTAAT
1622589 TATATTATTATTA
1 TATATTATTATTA
1622602 TATATTATTATTA
1 TATATTATTATTA
1622615 ATACAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATTATTATTA
Found at i:1634706 original size:25 final size:25
Alignment explanation
Indices: 1634671--1634735 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
1634661 CTTTTCAAAT
1634671 CACC-TTTCGGTGGATTTGTTTTTC
1 CACCTTTTCGGTGGATTTGTTTTTC
1634695 CACCTTTTCGGTGGATTTGTTTTTC
1 CACCTTTTCGGTGGATTTGTTTTTC
1634720 CACCTTTTCGGTGGAT
1 CACCTTTTCGGTGGAT
1634736 AGTCAACAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 4 0.10
25 36 0.90
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.48
Consensus pattern (25 bp):
CACCTTTTCGGTGGATTTGTTTTTC
Found at i:1642083 original size:2 final size:2
Alignment explanation
Indices: 1642076--1642104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1642066 TATCAAATTT
1642076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1642105 CTTTTATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1645917 original size:24 final size:23
Alignment explanation
Indices: 1645870--1645919 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1645860 GATTCTCTTC
1645870 TTTTTTTTAAATTCTGCACTAAT
1 TTTTTTTTAAATTCTGCACTAAT
* * *
1645893 TTTTTTTTACATTTTGCACTAAA
1 TTTTTTTTAAATTCTGCACTAAT
1645916 TTTT
1 TTTT
1645920 CCAAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTTTTAAATTCTGCACTAAT
Found at i:1648105 original size:12 final size:12
Alignment explanation
Indices: 1648084--1648138 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
1648074 GTCTTGTACA
*
1648084 TAATAATAATAT
1 TAATATTAATAT
*
1648096 TAATATTAATAA
1 TAATATTAATAT
*
1648108 TATTATTAATAT
1 TAATATTAATAT
1648120 T-ATATATAATAT
1 TAATAT-TAATAT
1648132 ATAATAT
1 -TAATAT
1648139 ATATAAACGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 3 0.09
12 27 0.77
13 1 0.03
14 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATATTAATAT
Found at i:1648107 original size:18 final size:18
Alignment explanation
Indices: 1648084--1648138 Score: 76
Period size: 18 Copynumber: 3.0 Consensus size: 18
1648074 GTCTTGTACA
1648084 TAATAATAATATTAATAT
1 TAATAATAATATTAATAT
*
1648102 TAATAATATTATTAATAT
1 TAATAATAATATTAATAT
1648120 T-ATATATAATATATAATAT
1 TAATA-ATAATAT-TAATAT
1648139 ATATAAACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 3 0.09
18 24 0.73
19 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATAATATTAATAT
Found at i:1648122 original size:9 final size:9
Alignment explanation
Indices: 1648087--1648122 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1648077 TTGTACATAA
*
1648087 TAATAATAT
1 TAATATTAT
*
1648096 TAATATTAA
1 TAATATTAT
1648105 TAATATTAT
1 TAATATTAT
1648114 TAATATTAT
1 TAATATTAT
1648123 ATATAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATATTAT
Found at i:1648634 original size:20 final size:20
Alignment explanation
Indices: 1648611--1648858 Score: 325
Period size: 20 Copynumber: 12.4 Consensus size: 20
1648601 CATAACCCGT
1648611 AGGCTTTACAAATGACCCAG
1 AGGCTTTACAAATGACCCAG
*
1648631 AGGCTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCAG
* *
1648651 AGGCTTTACAAATAACCCAA
1 AGGCTTTACAAATGACCCAG
*
1648671 AGGCTTTACAAATGACCCAA
1 AGGCTTTACAAATGACCCAG
*
1648691 AGGCTTTACAAATGACCCAA
1 AGGCTTTACAAATGACCCAG
* *
1648711 AGGCTTTACAAATGACTCGG
1 AGGCTTTACAAATGACCCAG
* **
1648731 AGGCTTTACAAATAACCTGG
1 AGGCTTTACAAATGACCCAG
* * *
1648751 AGGCTTTACAAATTATCTAG
1 AGGCTTTACAAATGACCCAG
1648771 AGGCTTTACAAATGACCCAG
1 AGGCTTTACAAATGACCCAG
* *
1648791 AGGCTTTACAAATAACCCGG
1 AGGCTTTACAAATGACCCAG
* * *
1648811 AGGCTTTATAAATAACCCGG
1 AGGCTTTACAAATGACCCAG
*
1648831 AGGCTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCAG
1648851 AGGCTTTA
1 AGGCTTTA
1648859 ATTTTCTAGA
Statistics
Matches: 206, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 206 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
AGGCTTTACAAATGACCCAG
Found at i:1653250 original size:24 final size:23
Alignment explanation
Indices: 1653203--1653252 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1653193 GATTCTCTTC
1653203 TTTTTTTTAAATTCTGCACTAAT
1 TTTTTTTTAAATTCTGCACTAAT
* * *
1653226 TTTTTTTTACATTTTGCACTAAA
1 TTTTTTTTAAATTCTGCACTAAT
1653249 TTTT
1 TTTT
1653253 CCAACAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTTTTAAATTCTGCACTAAT
Found at i:1655468 original size:16 final size:16
Alignment explanation
Indices: 1655417--1655468 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1655407 CTTGTACATA
1655417 ATAATA-ATATAATAT
1 ATAATATATATAATAT
1655432 AATAATAT-TAT--TA-
1 -ATAATATATATAATAT
*
1655445 ATATTATATATAATAT
1 ATAATATATATAATAT
1655461 ATAATATA
1 ATAATATA
1655469 AACGTTACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 2 0.07
15 2 0.07
16 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATATATAATAT
Found at i:1655959 original size:20 final size:20
Alignment explanation
Indices: 1655936--1656183 Score: 325
Period size: 20 Copynumber: 12.4 Consensus size: 20
1655926 CATAACCCGT
1655936 AGGCTTTACAAATGACCCAG
1 AGGCTTTACAAATGACCCAG
*
1655956 AGGCTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCAG
* *
1655976 AGGCTTTACAAATAACCCAA
1 AGGCTTTACAAATGACCCAG
*
1655996 AGGCTTTACAAATGACCCAA
1 AGGCTTTACAAATGACCCAG
*
1656016 AGGCTTTACAAATGACCCAA
1 AGGCTTTACAAATGACCCAG
* *
1656036 AGGCTTTACAAATGACTCGG
1 AGGCTTTACAAATGACCCAG
* **
1656056 AGGCTTTACAAATAACCTGG
1 AGGCTTTACAAATGACCCAG
* * *
1656076 AGGCTTTACAAATTATCTAG
1 AGGCTTTACAAATGACCCAG
1656096 AGGCTTTACAAATGACCCAG
1 AGGCTTTACAAATGACCCAG
* *
1656116 AGGCTTTACAAATAACCCGG
1 AGGCTTTACAAATGACCCAG
* * *
1656136 AGGCTTTATAAATAACCCGG
1 AGGCTTTACAAATGACCCAG
*
1656156 AGGCTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCAG
1656176 AGGCTTTA
1 AGGCTTTA
1656184 ATTTTCTAGA
Statistics
Matches: 206, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 206 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
AGGCTTTACAAATGACCCAG
Found at i:1660567 original size:24 final size:23
Alignment explanation
Indices: 1660520--1660569 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1660510 GATTCTCTTC
1660520 TTTTTTTTAAATTCTGCACTAAT
1 TTTTTTTTAAATTCTGCACTAAT
* * *
1660543 TTTTTTTTACATTTTGCACTAAA
1 TTTTTTTTAAATTCTGCACTAAT
1660566 TTTT
1 TTTT
1660570 CCAAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTTTTAAATTCTGCACTAAT
Found at i:1663245 original size:20 final size:20
Alignment explanation
Indices: 1663217--1663450 Score: 324
Period size: 20 Copynumber: 11.7 Consensus size: 20
1663207 ATAACACATA
1663217 ACCCGGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
* *
1663237 ACCCAGAGGCTTTAAAAATG
1 ACCCGGAGGCTTTACAAATG
*
1663257 ACCCGGAGGCTTTACAAATA
1 ACCCGGAGGCTTTACAAATG
*
1663277 ACCCAGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
**
1663297 ACCCAAAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
*
1663317 ACCCAGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
* *
1663337 ACTCGGAGGCTTTACAAATA
1 ACCCGGAGGCTTTACAAATG
* *
1663357 ACCTGGAGGCTTTACAAATT
1 ACCCGGAGGCTTTACAAATG
* **
1663377 ATCTAGAGGCTTTACAAATG
1 ACCCGGAGGCTTTACAAATG
*
1663397 ACCCGGAGGCTTTACAAATA
1 ACCCGGAGGCTTTACAAATG
*
1663417 ACCCGGAGGCTTTACAAATA
1 ACCCGGAGGCTTTACAAATG
1663437 ACCCGGAGGCTTTA
1 ACCCGGAGGCTTTA
1663451 ATTTTCTAGA
Statistics
Matches: 192, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 192 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (20 bp):
ACCCGGAGGCTTTACAAATG
Found at i:1674477 original size:2 final size:2
Alignment explanation
Indices: 1674472--1674501 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1674462 TTCTTTTTTA
1674472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1674502 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1674647 original size:9 final size:10
Alignment explanation
Indices: 1674623--1674648 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1674613 CATACTCGCA
1674623 TCCCCCTCGT
1 TCCCCCTCGT
1674633 TCCCCCTCGT
1 TCCCCCTCGT
1674643 TCCCCC
1 TCCCCC
1674649 ACTGTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.65, G:0.08, T:0.27
Consensus pattern (10 bp):
TCCCCCTCGT
Found at i:1676454 original size:59 final size:60
Alignment explanation
Indices: 1676380--1676493 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 60
1676370 TTGCTGTCAT
*
1676380 AAACAATTAACACATTCCATGTAAGCAAA-TCAACCACAAATTCGAAACAAGATATAAAC
1 AAACAATTAACACATTCCATGTAAGCAAACACAACCACAAATTCGAAACAAGATATAAAC
* * *
1676439 AAACAATTAATACATTCCATGTAAGTAAACACAACCAGAAATTCGAAACAAGATA
1 AAACAATTAACACATTCCATGTAAGCAAACACAACCACAAATTCGAAACAAGATA
1676494 CAAATAACCA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 27 0.54
60 23 0.46
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (60 bp):
AAACAATTAACACATTCCATGTAAGCAAACACAACCACAAATTCGAAACAAGATATAAAC
Found at i:1681145 original size:22 final size:21
Alignment explanation
Indices: 1681101--1681156 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
1681091 CTCTAACCTA
*
1681101 AAACCCTAAATTATAATCCTT
1 AAACCCTAACTTATAATCCTT
* *
1681122 AAACCCTAACTCTATTATCTTT
1 AAACCCTAACT-TATAATCCTT
*
1681144 AAACACTAACTTA
1 AAACCCTAACTTA
1681157 GGATTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (21 bp):
AAACCCTAACTTATAATCCTT
Found at i:1692712 original size:3 final size:3
Alignment explanation
Indices: 1692704--1692730 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1692694 AAGACGTAAG
1692704 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1692731 AAACAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1702478 original size:23 final size:22
Alignment explanation
Indices: 1702448--1702496 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1702438 TTAATATTTA
*
1702448 ATTTATATT-TTGTTTATAATAT
1 ATTTATATTATTGTTTA-AATAC
*
1702470 ATTTAATATTATTTTTTAAATAC
1 ATTT-ATATTATTGTTTAAATAC
1702493 ATTT
1 ATTT
1702497 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTATATTATTGTTTAAATAC
Found at i:1709545 original size:21 final size:21
Alignment explanation
Indices: 1709516--1709568 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1709506 ATTCTGACTA
1709516 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1709537 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1709558 TCGCAATGCGA
1 TCGCATTGCGA
1709569 GCCTAATTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1709575 original size:18 final size:18
Alignment explanation
Indices: 1709552--1709586 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1709542 TTGCGATTTT
1709552 CCTAATTCGCAATGCGAG
1 CCTAATTCGCAATGCGAG
1709570 CCTAATTCGCAATGCGA
1 CCTAATTCGCAATGCGA
1709587 TTACGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (18 bp):
CCTAATTCGCAATGCGAG
Found at i:1709613 original size:13 final size:13
Alignment explanation
Indices: 1709595--1709619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1709585 GATTACGTAA
1709595 ATCGCAATGCGAT
1 ATCGCAATGCGAT
1709608 ATCGCAATGCGA
1 ATCGCAATGCGA
1709620 ATTAGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (13 bp):
ATCGCAATGCGAT
Found at i:1709634 original size:21 final size:21
Alignment explanation
Indices: 1709608--1709681 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
1709598 GCAATGCGAT
1709608 ATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGAATTAGGAAA
1709629 ATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGAATTAGGAAA
* *
1709650 ATCGCAATGCGAA-TACGTAA
1 ATCGCAATGCGAATTAGGAAA
1709670 ATCGCAATGCGA
1 ATCGCAATGCGA
1709682 TTACGTATTC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 17 0.33
21 34 0.67
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (21 bp):
ATCGCAATGCGAATTAGGAAA
Found at i:1709636 original size:34 final size:33
Alignment explanation
Indices: 1709576--1709640 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
1709566 CGAGCCTAAT
*
1709576 TCGCAATGCGATTACGTAAATCGCAATGCGATA
1 TCGCAATGCGATTACGAAAATCGCAATGCGATA
*
1709609 TCGCAATGCGAATTAGGAAAATCGCAATGCGA
1 TCGCAATGCG-ATTACGAAAATCGCAATGCGA
1709641 ATTAGGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 10 0.34
34 19 0.66
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (33 bp):
TCGCAATGCGATTACGAAAATCGCAATGCGATA
Found at i:1709782 original size:61 final size:61
Alignment explanation
Indices: 1709671--1709785 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
1709661 AATACGTAAA
*
1709671 TCGCAATGCGATTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCTTAAT
1 TCGCAATGCGATTACGTATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCTTAAT
* * * * * *
1709732 TCGCATTGCGATTTACGTATTTGCGTTGCGATTTACGT-ATTTGCGTTGCGATTT
1 TCGCAATGCGA-TTACGTATTCGCATTGCGATTTACCTAATTCGCATTGCGATTT
1709786 ACGTATTTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
61 24 0.52
62 22 0.48
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (61 bp):
TCGCAATGCGATTACGTATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCTTAAT
Found at i:1709874 original size:21 final size:21
Alignment explanation
Indices: 1709608--1709927 Score: 208
Period size: 20 Copynumber: 15.7 Consensus size: 21
1709598 GCAATGCGAT
* *
1709608 ATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGAATTACGTAA
* *
1709629 ATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGAATTACGTAA
1709650 ATCGCAATGCGAA-TACGTAA
1 ATCGCAATGCGAATTACGTAA
1709670 ATCGCAATGCG-ATTACGT-A
1 ATCGCAATGCGAATTACGTAA
* * * * *
1709689 TTCGCATTGCGATTTTCCTAA
1 ATCGCAATGCGAATTACGTAA
* * * * *
1709710 TTCGCATTGCGATTTTCTTAA
1 ATCGCAATGCGAATTACGTAA
* * *
1709731 TTCGCATTGCGATTTACGT-A
1 ATCGCAATGCGAATTACGTAA
* * ** *
1709751 TTTGCGTTGCGATTTACGT-A
1 ATCGCAATGCGAATTACGTAA
* * ** *
1709771 TTTGCGTTGCGATTTACGT-A
1 ATCGCAATGCGAATTACGTAA
* * ** * * *
1709791 TTTGCGTTGCGATTTTCATAA
1 ATCGCAATGCGAATTACGTAA
*
1709812 TTCGCAATGCGAA-TACGTAA
1 ATCGCAATGCGAATTACGTAA
* *
1709832 ATCGCAACGCG-ATTAAGTAA
1 ATCGCAATGCGAATTACGTAA
* *
1709852 ATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGAATTACGTAA
* *
1709873 ATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGAATTACGTAA
1709894 ATCGCAATGCGAA-TACGTAA
1 ATCGCAATGCGAATTACGTAA
1709914 ATCGCAATGCGAAT
1 ATCGCAATGCGAAT
1709928 CTGACTATCG
Statistics
Matches: 264, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.05
20 129 0.49
21 123 0.47
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (21 bp):
ATCGCAATGCGAATTACGTAA
Found at i:1710534 original size:19 final size:19
Alignment explanation
Indices: 1710512--1710556 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1710502 GCGACGAGAG
**
1710512 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
1710531 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1710550 AATCGCA
1 AATCGCA
1710557 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1710574 original size:19 final size:19
Alignment explanation
Indices: 1710552--1710611 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
1710542 GAAACCAAAA
*
1710552 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1710571 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1710590 CTCTCGTTACGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1710610 TC
1 TC
1710612 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1710602 original size:20 final size:19
Alignment explanation
Indices: 1710560--1710611 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
1710550 AATCGCATTG
*
1710560 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTA
*
1710579 CGATTTTCATTCTCTCGTTA
1 CGATTTTCATT-TCGCGTTA
1710599 CGATTTTCATTTC
1 CGATTTTCATTTC
1710612 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTA
Found at i:1712485 original size:94 final size:93
Alignment explanation
Indices: 1712298--1712673 Score: 573
Period size: 94 Copynumber: 4.1 Consensus size: 93
1712288 TAGATTGCTT
* * *
1712298 AGTAAATTTATTCGGTTGTTGCCAA-TACTGCCAAAC--TGT-TT-ATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTA-TGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1712358 TATTTGTCTTTTGTTTTGTCTTTTGGTTGA
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
1712388 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1712453 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
1712482 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1712547 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
1712576 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1712641 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1712669 AGTAA
1 AGTAA
1712674 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 12, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
90 31 0.12
91 2 0.01
92 3 0.01
93 28 0.10
94 204 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1712808 original size:19 final size:19
Alignment explanation
Indices: 1712762--1712819 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
1712752 TCTTTTGGTT
1712762 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1712781 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
1712801 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
1712820 CAAAATCGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.50, C:0.17, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1712905 original size:19 final size:21
Alignment explanation
Indices: 1712881--1712932 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
1712871 GCGATTCTCT
*
1712881 CGTTGCGATTTTCA-TTTT-G
1 CGTTGCGATTTTCATTTTTCA
**
1712900 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCATTTTTCA
1712921 CGTTGCGATTTT
1 CGTTGCGATTTT
1712933 AAGTTCCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.46
20 4 0.15
21 10 0.38
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.48
Consensus pattern (21 bp):
CGTTGCGATTTTCATTTTTCA
Found at i:1713409 original size:42 final size:42
Alignment explanation
Indices: 1713333--1713421 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1713323 GACTCGCCTG
* * *
1713333 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1713375 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
1713417 TCATC
1 TCATC
1713422 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1714769 original size:14 final size:14
Alignment explanation
Indices: 1714750--1714785 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1714740 ATTGTTTAAT
1714750 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1714764 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1714778 TGATTTGT
1 TGATTTGT
1714786 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1714953 original size:19 final size:19
Alignment explanation
Indices: 1714892--1714943 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1714882 AAAAATGACC
*
1714892 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1714911 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1714930 ATCGCAACGTGAAA
1 ATCGCAACGCGAAA
1714944 CTAAATTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1714971 original size:19 final size:19
Alignment explanation
Indices: 1714949--1715099 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
1714939 TGAAACTAAA
1714949 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1714968 TTCGCTTTGCGA--TTCCC
1 TTCGCGTTGCGATTTTCAT
1714985 TT---GTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1715001 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1715016 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1715034 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1715049 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1715067 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
1715087 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1715100 AGACATTAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 24 0.24
16 11 0.11
17 11 0.11
19 39 0.40
20 13 0.13
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1714996 original size:33 final size:33
Alignment explanation
Indices: 1714953--1715079 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
1714943 ACTAAATTCG
* *
1714953 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1714986 TGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1715019 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1715052 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1715080 AGTCATTTTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1715026 original size:14 final size:14
Alignment explanation
Indices: 1715007--1715061 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1714997 TCATTTCGCA
1715007 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1715021 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1715038 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1715054 TTGCGATT
1 TTGCGATT
1715062 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1715091 original size:20 final size:20
Alignment explanation
Indices: 1715066--1715106 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1715056 GCGATTTTCA
*
1715066 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGACAT
*
1715086 TTTCGCGTTGCGATAGACAT
1 TTTCGCATTGCGATAGACAT
1715106 T
1 T
1715107 AAGATGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTCGCATTGCGATAGACAT
Found at i:1715145 original size:20 final size:20
Alignment explanation
Indices: 1715073--1715145 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1715063 TCATTTCGCA
* *
1715073 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTAGTG
* *
1715093 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTTAG-TG
*
1715113 ATTGCGA-ACGTCATTTTTGTG
1 -TTGCGATA-GTCATTTTAGTG
1715134 TTGCGATAGTCA
1 TTGCGATAGTCA
1715146 AATGATTGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTAGTG
Found at i:1717653 original size:24 final size:24
Alignment explanation
Indices: 1717619--1717672 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1717609 CTGAAAAATC
1717619 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1717643 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1717667 ATCAAA
1 ATCAAA
1717673 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1717686 original size:24 final size:24
Alignment explanation
Indices: 1717619--1717686 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1717609 CTGAAAAATC
* * *
1717619 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1717643 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1717667 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1717687 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1718558 original size:20 final size:20
Alignment explanation
Indices: 1718535--1718672 Score: 158
Period size: 20 Copynumber: 7.0 Consensus size: 20
1718525 AGAATCTCGT
1718535 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
* *
1718555 TGCGATTACGTAAATCGGAG
1 TGCGATTACGTAAATCGCAA
* * *
1718575 TACGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
1718596 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
1718616 TGCGATTACATAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
1718636 TGCGAATACGT--ATCGCAA
1 TGCGATTACGTAAATCGCAA
1718654 TGCGATTTACGT-AATCGCA
1 TGCGA-TTACGTAAATCGCA
1718673 TTTACGTAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
18 12 0.12
19 9 0.09
20 64 0.64
21 15 0.15
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:1718592 original size:41 final size:40
Alignment explanation
Indices: 1718541--1718660 Score: 140
Period size: 41 Copynumber: 3.0 Consensus size: 40
1718531 TCGTTGCGAT
* *
1718541 TTAC-TAAATCGCAATGCGATTACGTAAATCGGAGTACGAA
1 TTACATAAATCGCAATGCGATTACGTAAATCGCAATACG-A
* *
1718581 TTAGGA-AAATCGCAATGCGATTACGTAAATCGCAATGCGA
1 TTA-CATAAATCGCAATGCGATTACGTAAATCGCAATACGA
* *
1718621 TTACATAAATCGCAATGCGAATACGT--ATCGCAATGCGA
1 TTACATAAATCGCAATGCGATTACGTAAATCGCAATACGA
1718659 TT
1 TT
1718661 TACGTAATCG
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
38 14 0.20
39 1 0.01
40 26 0.37
41 30 0.42
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (40 bp):
TTACATAAATCGCAATGCGATTACGTAAATCGCAATACGA
Found at i:1718642 original size:61 final size:59
Alignment explanation
Indices: 1718535--1718672 Score: 174
Period size: 61 Copynumber: 2.3 Consensus size: 59
1718525 AGAATCTCGT
* * * *
1718535 TGCGATTTAC-TAAATCGCAATGCGATTACGTAAATCGGAGTACGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGATTACATAAATCGCAATACGAA-TACG--AATCGCAA
* *
1718596 TGCGA-TTACGTAAATCGCAATGCGATTACATAAATCGCAATGCGAATACGTATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGATTACATAAATCGCAATACGAATACGAATCGCAA
1718654 TGCGATTTACGT-AATCGCA
1 TGCGATTTACGTAAATCGCA
1718673 TTTACGTAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
58 19 0.28
59 6 0.09
60 7 0.10
61 37 0.54
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (59 bp):
TGCGATTTACGTAAATCGCAATGCGATTACATAAATCGCAATACGAATACGAATCGCAA
Found at i:1718677 original size:14 final size:14
Alignment explanation
Indices: 1718658--1718688 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1718648 TCGCAATGCG
1718658 ATTTACGTAATCGC
1 ATTTACGTAATCGC
*
1718672 ATTTACGTAATTGC
1 ATTTACGTAATCGC
1718686 ATT
1 ATT
1718689 GCGATTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (14 bp):
ATTTACGTAATCGC
Found at i:1718707 original size:20 final size:20
Alignment explanation
Indices: 1718679--1718773 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
1718669 CGCATTTACG
*
1718679 TAATTGCATTGCGATTTTCC
1 TAATCGCATTGCGATTTTCC
* * *
1718699 TAAGCGCATTGCGATTTACG
1 TAATCGCATTGCGATTTTCC
*
1718719 TAATCGCATTACGATTTTCC
1 TAATCGCATTGCGATTTTCC
* * *
1718739 TAATTCGTATTGCGATTTACG
1 TAA-TCGCATTGCGATTTTCC
*
1718760 TATTCGCATTGCGA
1 TAATCGCATTGCGA
1718774 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 45 0.75
21 15 0.25
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
TAATCGCATTGCGATTTTCC
Found at i:1718728 original size:40 final size:41
Alignment explanation
Indices: 1718672--1718773 Score: 152
Period size: 40 Copynumber: 2.5 Consensus size: 41
1718662 ACGTAATCGC
*
1718672 ATTTACGTAATTGCATTGCGATTTTCCTAA-GCGCATTGCG
1 ATTTACGTAATCGCATTGCGATTTTCCTAATGCGCATTGCG
* * *
1718712 ATTTACGTAATCGCATTACGATTTTCCTAATTCGTATTGCG
1 ATTTACGTAATCGCATTGCGATTTTCCTAATGCGCATTGCG
*
1718753 ATTTACGTATTCGCATTGCGA
1 ATTTACGTAATCGCATTGCGA
1718774 ATTAGGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 28 0.51
41 27 0.49
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (41 bp):
ATTTACGTAATCGCATTGCGATTTTCCTAATGCGCATTGCG
Found at i:1718794 original size:21 final size:21
Alignment explanation
Indices: 1718770--1718815 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1718760 TATTCGCATT
1718770 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1718791 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1718812 GCGA
1 GCGA
1718816 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1719774 original size:18 final size:20
Alignment explanation
Indices: 1719744--1719800 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 20
1719734 AGAATGCTCG
1719744 AATGGTA-CTGATACCCCCAT
1 AATGGTATC-GATACCCCCAT
1719764 -A-GGTATCGATACCCCCAT
1 AATGGTATCGATACCCCCAT
1719782 GCAATGGTATCGATACCCC
1 --AATGGTATCGATACCCC
1719801 TAAGGTGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 15 0.47
19 2 0.06
21 1 0.03
22 14 0.44
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (20 bp):
AATGGTATCGATACCCCCAT
Found at i:1719822 original size:19 final size:20
Alignment explanation
Indices: 1719786--1719824 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1719776 CCCCATGCAA
*
1719786 TGGTATCGATACCCCTAAGG
1 TGGTACCGATACCCCTAAGG
1719806 TGGTACCGATA-CCCTAAGG
1 TGGTACCGATACCCCTAAGG
1719825 CATATAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (20 bp):
TGGTACCGATACCCCTAAGG
Found at i:1725636 original size:23 final size:23
Alignment explanation
Indices: 1725581--1725687 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 23
1725571 ATTTTTGTGC
**
1725581 ATAGAGTATCGATACC-CCTAAGA
1 ATAG-GTATCGATACCTCCTTTGA
*
1725604 CT-GGTATCGATACCTCCTTTGA
1 ATAGGTATCGATACCTCCTTTGA
*
1725626 ATAGGTATCGATA-C-CC-TCGCA
1 ATAGGTATCGATACCTCCTTTG-A
* *
1725647 ATAAGTATCAATACCAT-CTTTGA
1 ATAGGTATCGATACC-TCCTTTGA
*
1725670 ATGGGTATCGATACCTCC
1 ATAGGTATCGATACCTCC
1725688 CTGATGGTAC
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.03
21 25 0.38
22 10 0.15
23 26 0.40
24 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (23 bp):
ATAGGTATCGATACCTCCTTTGA
Found at i:1728459 original size:19 final size:20
Alignment explanation
Indices: 1728423--1728461 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1728413 CCCCATGCAA
1728423 TGGTACCGATACCCCTAAGG
1 TGGTACCGATACCCCTAAGG
1728443 TGGTACCGATA-CCCTAAGG
1 TGGTACCGATACCCCTAAGG
1728462 CATATAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.21
Consensus pattern (20 bp):
TGGTACCGATACCCCTAAGG
Found at i:1729336 original size:368 final size:368
Alignment explanation
Indices: 1728659--1729396 Score: 1476
Period size: 368 Copynumber: 2.0 Consensus size: 368
1728649 ATTGATCAAC
1728659 AAGAAATCATTGAGAAACAAGAGAGAAAGCATCAAACACCAACTTTGTGCAATTCAAGCCAATTT
1 AAGAAATCATTGAGAAACAAGAGAGAAAGCATCAAACACCAACTTTGTGCAATTCAAGCCAATTT
1728724 TCCTTTCAATATTCATTTTGCTTTCAAGAACACACATTGTGCTCATTTGTAATCATTTTTTAGTG
66 TCCTTTCAATATTCATTTTGCTTTCAAGAACACACATTGTGCTCATTTGTAATCATTTTTTAGTG
1728789 TTCTTTTCTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAGGTTTTCTTATAAGTTTGCAAA
131 TTCTTTTCTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAGGTTTTCTTATAAGTTTGCAAA
1728854 ATTTGTGTATTTCTCTTTGGGAGAGAGTGTGCTCAAGAATTGGGGCATAATTCTTGAGGGAGTTG
196 ATTTGTGTATTTCTCTTTGGGAGAGAGTGTGCTCAAGAATTGGGGCATAATTCTTGAGGGAGTTG
1728919 TAAGGTTACTCTTTGTCCTCAAAAGAAATAACAAATTAGTGAATTTATTGGAAAATCCTTAGTGT
261 TAAGGTTACTCTTTGTCCTCAAAAGAAATAACAAATTAGTGAATTTATTGGAAAATCCTTAGTGT
1728984 GGATAGCTAAGGTAGTGGACGTAGACTTTGAATGAGAAAGTCG
326 GGATAGCTAAGGTAGTGGACGTAGACTTTGAATGAGAAAGTCG
1729027 AAGAAATCATTGAGAAACAAGAGAGAAAGCATCAAACACCAACTTTGTGCAATTCAAGCCAATTT
1 AAGAAATCATTGAGAAACAAGAGAGAAAGCATCAAACACCAACTTTGTGCAATTCAAGCCAATTT
1729092 TCCTTTCAATATTCATTTTGCTTTCAAGAACACACATTGTGCTCATTTGTAATCATTTTTTAGTG
66 TCCTTTCAATATTCATTTTGCTTTCAAGAACACACATTGTGCTCATTTGTAATCATTTTTTAGTG
1729157 TTCTTTTCTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAGGTTTTCTTATAAGTTTGCAAA
131 TTCTTTTCTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAGGTTTTCTTATAAGTTTGCAAA
1729222 ATTTGTGTATTTCTCTTTGGGAGAGAGTGTGCTCAAGAATTGGGGCATAATTCTTGAGGGAGTTG
196 ATTTGTGTATTTCTCTTTGGGAGAGAGTGTGCTCAAGAATTGGGGCATAATTCTTGAGGGAGTTG
1729287 TAAGGTTACTCTTTGTCCTCAAAAGAAATAACAAATTAGTGAATTTATTGGAAAATCCTTAGTGT
261 TAAGGTTACTCTTTGTCCTCAAAAGAAATAACAAATTAGTGAATTTATTGGAAAATCCTTAGTGT
1729352 GGATAGCTAAGGTAGTGGACGTAGACTTTGAATGAGAAAGTCG
326 GGATAGCTAAGGTAGTGGACGTAGACTTTGAATGAGAAAGTCG
1729395 AA
1 AA
1729397 CCACTATAAA
Statistics
Matches: 370, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
368 370 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (368 bp):
AAGAAATCATTGAGAAACAAGAGAGAAAGCATCAAACACCAACTTTGTGCAATTCAAGCCAATTT
TCCTTTCAATATTCATTTTGCTTTCAAGAACACACATTGTGCTCATTTGTAATCATTTTTTAGTG
TTCTTTTCTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAGGTTTTCTTATAAGTTTGCAAA
ATTTGTGTATTTCTCTTTGGGAGAGAGTGTGCTCAAGAATTGGGGCATAATTCTTGAGGGAGTTG
TAAGGTTACTCTTTGTCCTCAAAAGAAATAACAAATTAGTGAATTTATTGGAAAATCCTTAGTGT
GGATAGCTAAGGTAGTGGACGTAGACTTTGAATGAGAAAGTCG
Found at i:1729903 original size:16 final size:16
Alignment explanation
Indices: 1729882--1729915 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1729872 AAATAATAAT
1729882 AAAATAAGTA-AAAATA
1 AAAATAAG-ACAAAATA
1729898 AAAATAAGACAAAATA
1 AAAATAAGACAAAATA
1729914 AA
1 AA
1729916 TAAAATGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATAAGACAAAATA
Found at i:1729911 original size:26 final size:25
Alignment explanation
Indices: 1729856--1729920 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
1729846 TGTAAATATG
*
1729856 AAAATAATAAACAAAAAAATAATAAT
1 AAAATAATAAA-AAAAAAATAATAAC
*
1729882 AAAATAAGTAAAAATAAAAATAA-GAC
1 AAAATAA-TAAAAA-AAAAATAATAAC
1729908 AAAATAAATAAAA
1 AAAAT-AATAAAA
1729921 TGGGAACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (25 bp):
AAAATAATAAAAAAAAAATAATAAC
Found at i:1729918 original size:20 final size:20
Alignment explanation
Indices: 1729893--1729983 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1729883 AAATAAGTAA
1729893 AAATAAAAATAAGACAAAAT
1 AAATAAAAATAAGACAAAAT
** *
1729913 AAAT-AAAAT--GGGAACAT
1 AAATAAAAATAAGACAAAAT
* *
1729930 AAATAAAAATAAAACAAAAC
1 AAATAAAAATAAGACAAAAT
*
1729950 AAAAAAAAATAAGA-AAAAT
1 AAATAAAAATAAGACAAAAT
*
1729969 AAAACAAAAATAAGA
1 -AAATAAAAATAAGA
1729984 AAAGAGAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
17 9 0.16
18 5 0.09
19 9 0.16
20 32 0.58
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (20 bp):
AAATAAAAATAAGACAAAAT
Found at i:1729948 original size:10 final size:10
Alignment explanation
Indices: 1729935--1729977 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1729925 AACATAAATA
1729935 AAAATAAAAC
1 AAAATAAAAC
* *
1729945 AAAACAAAAA
1 AAAATAAAAC
*
1729955 AAAATAAGA-
1 AAAATAAAAC
1729964 AAAATAAAAC
1 AAAATAAAAC
1729974 AAAA
1 AAAA
1729978 ATAAGAAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.84, C:0.07, G:0.02, T:0.07
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:1730054 original size:29 final size:28
Alignment explanation
Indices: 1729934--1730054 Score: 82
Period size: 29 Copynumber: 4.1 Consensus size: 28
1729924 GAACATAAAT
* * *
1729934 AAAAATAAAACAAAACAAAAAAAAATAAG
1 AAAAATAAAACAAAA-AAAATAAAAGAAA
* *
1729963 AAAAATAAAACAAAAATAAGAAAAGAGAA
1 AAAAATAAAACAAAAAAAATAAAAGA-AA
** * * *
1729992 AAATAATGAAATTAAATAAAATACATA-AAC
1 AAA-AAT-AAAACAAAAAAAATA-AAAGAAA
*
1730022 AAAAATGAAACAAAAAAAAGTAAAAGAAA
1 AAAAATAAAACAAAAAAAA-TAAAAGAAA
1730051 AAAA
1 AAAA
1730055 GAAAAAAATA
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
28 19 0.28
29 30 0.43
30 7 0.10
31 11 0.16
32 2 0.03
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.11
Consensus pattern (28 bp):
AAAAATAAAACAAAAAAAATAAAAGAAA
Found at i:1730076 original size:2 final size:2
Alignment explanation
Indices: 1730071--1730095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1730061 AATACAAATA
1730071 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1730096 GTGTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1730183 original size:2 final size:2
Alignment explanation
Indices: 1730178--1730214 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1730168 AAATAAATTA
*
1730178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1730215 AATAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1736873 original size:21 final size:21
Alignment explanation
Indices: 1736849--1736913 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1736839 GTTCCATCTA
* *
1736849 AAATGGCTGTGATGCCATTTG
1 AAATGGCTGTGGTGCCATATG
* **
1736870 AAATGACTACGGTGCCATATG
1 AAATGGCTGTGGTGCCATATG
*
1736891 AAATGGTTGTGGTGCCATATG
1 AAATGGCTGTGGTGCCATATG
1736912 AA
1 AA
1736914 CCTACAGGGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (21 bp):
AAATGGCTGTGGTGCCATATG
Found at i:1738359 original size:12 final size:12
Alignment explanation
Indices: 1738294--1738359 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
1738284 ATCATTCCCC
1738294 TAATTAAATAAA
1 TAATTAAATAAA
*
1738306 TAGTATATAAATTAA
1 TA--AT-TAAATAAA
*
1738321 -AATCTAAACAAA
1 TAAT-TAAATAAA
1738333 T-ATTAAAATAAA
1 TAATT-AAATAAA
1738345 TAATTAAATAAA
1 TAATTAAATAAA
1738357 TAA
1 TAA
1738360 AATATTCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
11 1 0.02
12 29 0.67
13 3 0.07
14 3 0.07
15 7 0.16
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
TAATTAAATAAA
Found at i:1745844 original size:2 final size:2
Alignment explanation
Indices: 1745839--1745873 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1745829 AATGCATGTA
1745839 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1745874 ACTCACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1763436 original size:19 final size:20
Alignment explanation
Indices: 1763367--1763437 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
1763357 ATATTTCGAT
1763367 CTTTATATATTTATTCTCAC
1 CTTTATATATTTATTCTCAC
*
1763387 CTTTA-ATA-TTATTGCCTCGC
1 CTTTATATATTTATT--CTCAC
1763407 ACTTTATATATTTATTCTCAC
1 -CTTTATATATTTATTCTCAC
1763428 CTTTA-ATATT
1 CTTTATATATT
1763438 ACTACCTTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
18 5 0.11
19 8 0.18
20 14 0.32
21 9 0.20
22 3 0.07
23 5 0.11
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.52
Consensus pattern (20 bp):
CTTTATATATTTATTCTCAC
Found at i:1769584 original size:18 final size:18
Alignment explanation
Indices: 1769563--1769624 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1769553 TTTGTCTCGT
1769563 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
* * *
1769581 AGGACCATTGTGTTCCGA
1 AGGACCACTATGTCCCGA
*
1769599 AGGACCACTATGTCCTGA
1 AGGACCACTATGTCCCGA
1769617 AGGACCAC
1 AGGACCAC
1769625 GTAGACCCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.19
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:1769828 original size:23 final size:23
Alignment explanation
Indices: 1769798--1769843 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1769788 TTTACTTGTA
1769798 TTCCTTTTCACATAGTTCATAGC
1 TTCCTTTTCACATAGTTCATAGC
1769821 TTCCTTTTCACATAGTTCATAGC
1 TTCCTTTTCACATAGTTCATAGC
1769844 CATGATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.43
Consensus pattern (23 bp):
TTCCTTTTCACATAGTTCATAGC
Found at i:1770643 original size:21 final size:21
Alignment explanation
Indices: 1770614--1770654 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1770604 TTTATTTATT
1770614 TGAGAGTGCATCGATACACAA
1 TGAGAGTGCATCGATACACAA
* *
1770635 TGAGTGTGCATCGATGCACA
1 TGAGAGTGCATCGATACACA
1770655 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGAGAGTGCATCGATACACAA
Found at i:1771549 original size:20 final size:20
Alignment explanation
Indices: 1771524--1771578 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1771514 TTTACACCTA
1771524 GGGAACCGATTCCCCATTAG
1 GGGAACCGATTCCCCATTAG
1771544 GGGAACCGATTCCCCATTAG
1 GGGAACCGATTCCCCATTAG
*
1771564 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
1771579 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (20 bp):
GGGAACCGATTCCCCATTAG
Found at i:1777347 original size:21 final size:22
Alignment explanation
Indices: 1777300--1777359 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
1777290 ACCCTCATGA
**
1777300 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCCT-AAG
1777323 GGGAACCGATTCCCCCCCT-AG
1 GGGAACCGATTCCCCCCCTAAG
* *
1777344 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
1777360 TTGGGGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.48
23 17 0.52
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCCTAAG
Found at i:1784717 original size:7 final size:7
Alignment explanation
Indices: 1784705--1784740 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
1784695 TTTGGTATGC
1784705 ATATAAT
1 ATATAAT
1784712 ATATAAT
1 ATATAAT
1784719 ATATAAT
1 ATATAAT
1784726 ATATAA-
1 ATATAAT
1784732 ATATAAT
1 ATATAAT
1784739 AT
1 AT
1784741 TATGTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:1786678 original size:22 final size:23
Alignment explanation
Indices: 1786635--1786678 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1786625 CGTTAGACAT
1786635 GGGGGAACCGGTACCCCATGGGG
1 GGGGGAACCGGTACCCCATGGGG
* *
1786658 GGGGGAATCTGTACCCC-TGGG
1 GGGGGAACCGGTACCCCATGGG
1786679 CAATCTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.16, C:0.25, G:0.45, T:0.14
Consensus pattern (23 bp):
GGGGGAACCGGTACCCCATGGGG
Found at i:1788858 original size:18 final size:18
Alignment explanation
Indices: 1788837--1788883 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1788827 TTTGTCTCGT
1788837 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
* * *
1788855 AGGACCATTGTGTTCCGA
1 AGGACCACTATGTCCCGA
1788873 AGGACCACTAT
1 AGGACCACTAT
1788884 AATGAAGGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:1790286 original size:30 final size:30
Alignment explanation
Indices: 1790228--1790290 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1790218 AAATTTTGTC
** **
1790228 TAGTGACTAAAATGTAAGTTTTTGAAAGTT
1 TAGTGACTAAAATGTAAACTTTAAAAAGTT
*
1790258 TAGTGACTAAATTGTAAACTTTAAAAAGTT
1 TAGTGACTAAAATGTAAACTTTAAAAAGTT
1790288 TAG
1 TAG
1790291 GGACCATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (30 bp):
TAGTGACTAAAATGTAAACTTTAAAAAGTT
Found at i:1803655 original size:24 final size:25
Alignment explanation
Indices: 1803623--1803678 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
1803613 TATTTTTATA
*
1803623 TATTTTTTGTTGTTTT-ACTATTTT
1 TATTATTTGTTGTTTTAACTATTTT
*
1803647 TATTATTTGTTGTTTTAATTATTTT
1 TATTATTTGTTGTTTTAACTATTTT
*
1803672 AATTATT
1 TATTATT
1803679 ATTAAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (25 bp):
TATTATTTGTTGTTTTAACTATTTT
Found at i:1803676 original size:25 final size:24
Alignment explanation
Indices: 1803628--1803678 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
1803618 TTATATATTT
*
1803628 TTTGTTGTTTTACTATTTTTATTA
1 TTTGTTGTTTTACTATTTTAATTA
*
1803652 TTTGTTGTTTTAATTATTTTAATTA
1 TTTGTTGTTTT-ACTATTTTAATTA
1803677 TT
1 TT
1803679 ATTAAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (24 bp):
TTTGTTGTTTTACTATTTTAATTA
Found at i:1814485 original size:22 final size:21
Alignment explanation
Indices: 1814447--1814487 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1814437 TGCAAAAATT
1814447 AAAATAACAGTAGCTAAATCA
1 AAAATAACAGTAGCTAAATCA
1814468 AAAACTAACAG-AGACTAAAT
1 AAAA-TAACAGTAG-CTAAAT
1814488 TGAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATAACAGTAGCTAAATCA
Found at i:1815680 original size:75 final size:75
Alignment explanation
Indices: 1815522--1815730 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 75
1815512 CAAAGCCAAA
* * * **
1815522 AATTCCAGATTGCTC-AGAGGGAACCGATTCCCCCCCATCGGAGGAACCGATTCCCCCCTGAATG
1 AATTCCAGAATGCTCGA-AGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACA
1815586 GTTTGGCTCCGAG
63 GTTTGGCTCCGAG
*
1815599 ATTTCCAGAATGCTCGAAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGAAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* * *
1815664 TTGTTCTGAG
66 TGGCTCCGAG
* * * * *
1815674 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGAAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
1815731 TGTACAACGG
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
75 83 0.72
76 6 0.05
77 25 0.22
78 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGAAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Done.