Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 55
Found at i:6322457 original size:43 final size:43
Alignment explanation
Indices: 6322331--6322574 Score: 266
Period size: 43 Copynumber: 5.8 Consensus size: 43
6322321 CATTTGTATT
* *
6322331 AAAAATGCCGCTATAGATCT-GACCTTTTGCGGTGTTTGTTCC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGGCGTTTGTTCC
* ** * *
6322373 AAAAATGTTGGTATAGATCTTA-A-CTTTTGTGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATC-TAGACCTTTTGCGGCGTTTGTTCC
*
6322415 AAAAACGCCGCTATAGATCTAGACCTTTTGCAGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGGCGTTTGTTCC
* * *
6322458 AAAAACACCGCTATAGATCTTGACCTTTTGCGGCATTTGTTCC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGGCGTTTGTTCC
* * * *
6322501 AAAAACACTGCTATAGATCTCGACCTTTT---GCGATTGTTCC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGGCGTTTGTTCC
* * * *
6322541 AAAAAAGCCGCTATATATCTTGACCTATTGCGGC
1 AAAAACGCCGCTATAGATCTAGACCTTTTGCGGC
6322575 ATTTTTATTC
Statistics
Matches: 170, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
40 32 0.19
41 2 0.01
42 49 0.29
43 87 0.51
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTAGACCTTTTGCGGCGTTTGTTCC
Found at i:6322526 original size:86 final size:83
Alignment explanation
Indices: 6322338--6322578 Score: 281
Period size: 83 Copynumber: 2.9 Consensus size: 83
6322328 ATTAAAAATG
* *** * *
6322338 CCGCTATAGATCTGACCTTTTGCGGTGTTTGTTCCAAAAATGTTGGTATAGATCTT-AACTTTTG
1 CCGCTATAGATCTGACCTTTTGC-GCGTTTGTTCCAAAAA-ACCGCTATAGATCTTGACCTTTTG
* * *
6322402 TGGCGTTTGTTCCAAAAACG
64 CGGCATTTGTTCCAAAAACA
6322422 CCGCTATAGATCTAGACCTTTTGCAGCGTTTGTTCCAAAAACACCGCTATAGATCTTGACCTTTT
1 CCGCTATAGATCT-GACCTTTTGC-GCGTTTGTTCCAAAAA-ACCGCTATAGATCTTGACCTTTT
6322487 GCGGCATTTGTTCCAAAAACA
63 GCGGCATTTGTTCCAAAAACA
* * * *
6322508 CTGCTATAGATCTCGACCTTTT--GCGATTGTTCCAAAAAAGCCGCTATATATCTTGACCTATTG
1 CCGCTATAGATCT-GACCTTTTGCGCGTTTGTTCCAAAAAA-CCGCTATAGATCTTGACCTTTTG
6322571 CGGCATTT
64 CGGCATTT
6322579 TTATTCTCAA
Statistics
Matches: 138, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 44 0.32
84 13 0.09
85 36 0.26
86 44 0.32
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (83 bp):
CCGCTATAGATCTGACCTTTTGCGCGTTTGTTCCAAAAAACCGCTATAGATCTTGACCTTTTGCG
GCATTTGTTCCAAAAACA
Found at i:6322968 original size:61 final size:62
Alignment explanation
Indices: 6322873--6322997 Score: 164
Period size: 61 Copynumber: 2.0 Consensus size: 62
6322863 ACCTAGGTGC
* *
6322873 AAATATAAGCAGATACAGAGTCAGAACTAAATATTGA-AAGGGTC-GAAATATTAGAATATTT
1 AAATATAAGCAGAGACAGAGTCAGAACTAAATATTGACAAGAG-CAGAAATATTAGAATATTT
* * * * *
6322934 AAATATAAGCAGGGACGGAGTCATAACTAAATATTGACATGAGCATAAATATTAGAATATTT
1 AAATATAAGCAGAGACAGAGTCAGAACTAAATATTGACAAGAGCAGAAATATTAGAATATTT
6322996 AA
1 AA
6322998 GAAAAATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
61 34 0.62
62 21 0.38
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (62 bp):
AAATATAAGCAGAGACAGAGTCAGAACTAAATATTGACAAGAGCAGAAATATTAGAATATTT
Found at i:6326008 original size:36 final size:36
Alignment explanation
Indices: 6325957--6326066 Score: 202
Period size: 36 Copynumber: 3.1 Consensus size: 36
6325947 AATTATTGCG
6325957 GCCATGGTCGGTTTGTTTGTCTTTCTCTTATGGGAT
1 GCCATGGTCGGTTTGTTTGTCTTTCTCTTATGGGAT
*
6325993 GCCGTGGTCGGTTTGTTTGTCTTTCTCTTATGGGAT
1 GCCATGGTCGGTTTGTTTGTCTTTCTCTTATGGGAT
*
6326029 GCCATGGTCGGTTTGTTTGTCTCTCTCTTATGGGAT
1 GCCATGGTCGGTTTGTTTGTCTTTCTCTTATGGGAT
6326065 GC
1 GC
6326067 GCACTGAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.07, C:0.18, G:0.29, T:0.45
Consensus pattern (36 bp):
GCCATGGTCGGTTTGTTTGTCTTTCTCTTATGGGAT
Found at i:6330912 original size:5 final size:5
Alignment explanation
Indices: 6330902--6330928 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6330892 ATCTATAAAA
6330902 ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT AT
6330929 TGCTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:6330953 original size:18 final size:18
Alignment explanation
Indices: 6330932--6330981 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
6330922 ATATTATTGC
* *
6330932 TATTATTATTATTTTTTT
1 TATTATTATTATTTTATA
* *
6330950 TATTTTTATTAATTTATA
1 TATTATTATTATTTTATA
*
6330968 TATTATAATTATTT
1 TATTATTATTATTT
6330982 CACTGACCCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTATTATTTTATA
Found at i:6332349 original size:8 final size:8
Alignment explanation
Indices: 6332336--6332374 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
6332326 TAATTTCTAT
6332336 TTTTTTTA
1 TTTTTTTA
6332344 TTTTTTTA
1 TTTTTTTA
6332352 TTTTGTTTA
1 TTTT-TTTA
* *
6332361 TTATTTTC
1 TTTTTTTA
6332369 TTTTTT
1 TTTTTT
6332375 AACTCTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:6332355 original size:17 final size:17
Alignment explanation
Indices: 6332328--6332374 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
6332318 TACGCTTCTA
6332328 ATTTCTATTTTTTTTATT
1 ATTT-TATTTTTTTTATT
* *
6332346 TTTTTATTTTGTTTATT
1 ATTTTATTTTTTTTATT
*
6332363 ATTTTCTTTTTT
1 ATTTTATTTTTT
6332375 AACTCTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (17 bp):
ATTTTATTTTTTTTATT
Found at i:6335308 original size:23 final size:23
Alignment explanation
Indices: 6335282--6335334 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
6335272 AAAAAACACA
6335282 AAAAAAACAAAGAGAAAAA-AAAG
1 AAAAAAACAAAG-GAAAAATAAAG
*
6335305 AAAAAAACAAAGGAAAAATGAAG
1 AAAAAAACAAAGGAAAAATAAAG
6335328 AAAAAAA
1 AAAAAAA
6335335 GGCAAGACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAAAAACAAAGGAAAAATAAAG
Found at i:6335321 original size:11 final size:11
Alignment explanation
Indices: 6335260--6335333 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
6335250 AAAAGAGAAG
6335260 AAGAAAAAAC-
1 AAGAAAAAACA
6335270 AA-AAAAAACA
1 AAGAAAAAACA
6335280 CAA-AAAAAACA
1 -AAGAAAAAACA
6335291 AAGAGAAAAA-A
1 AAGA-AAAAACA
6335302 AAGAAAAAAACA
1 AAG-AAAAAACA
* **
6335314 AAGGAAAAATG
1 AAGAAAAAACA
6335325 AAGAAAAAA
1 AAGAAAAAA
6335334 AGGCAAGACA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
9 7 0.13
10 4 0.07
11 33 0.61
12 10 0.19
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.01
Consensus pattern (11 bp):
AAGAAAAAACA
Found at i:6335321 original size:19 final size:19
Alignment explanation
Indices: 6335298--6335336 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
6335288 ACAAAGAGAA
*
6335298 AAAAAAGAAAAAAACAAAGG
1 AAAAATGAAAAAAA-AAAGG
*
6335318 AAAAATGAAGAAAAAAAGG
1 AAAAATGAAAAAAAAAAGG
6335337 CAAGACACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAATGAAAAAAAAAAGG
Found at i:6336294 original size:21 final size:21
Alignment explanation
Indices: 6336268--6336312 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6336258 GATTTCTGGG
* *
6336268 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
6336289 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
6336310 CAA
1 CAA
6336313 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:6337324 original size:149 final size:149
Alignment explanation
Indices: 6337137--6337589 Score: 879
Period size: 149 Copynumber: 3.0 Consensus size: 149
6337127 GAGTCGAGGG
* *
6337137 TCTACGCGTTTCTTATGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
6337202 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
6337267 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
6337286 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
6337351 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
6337416 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
6337435 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
*
6337500 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
6337565 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
6337584 TCTACG
1 TCTACG
6337590 GGGCACTTCG
Statistics
Matches: 301, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 301 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:6337612 original size:23 final size:23
Alignment explanation
Indices: 6337568--6337612 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6337558 ATCATTATAT
*
6337568 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
6337591 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
6337613 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:6340755 original size:21 final size:21
Alignment explanation
Indices: 6340729--6340773 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6340719 GATTTCTGGG
* *
6340729 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
6340750 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
6340771 CAA
1 CAA
6340774 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:6340846 original size:23 final size:22
Alignment explanation
Indices: 6340802--6340846 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6340792 TATGTCACGG
*
6340802 GGGAACCGATACCCCCATAGGA
1 GGGAACCGATACCCCCAAAGGA
*
6340824 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
6340847 AAATTGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:6341783 original size:149 final size:149
Alignment explanation
Indices: 6341598--6342050 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
6341588 GAGTCGAGGG
6341598 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
6341663 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
6341728 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
6341747 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
6341812 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
*
6341877 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTGCAAT
6341896 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
*
6341961 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
6342026 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
6342045 TCTACG
1 TCTACG
6342051 GGGCACTTCG
Statistics
Matches: 301, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 301 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:6342073 original size:23 final size:23
Alignment explanation
Indices: 6342029--6342073 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6342019 ATCATTATAT
*
6342029 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
6342052 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
6342074 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:6343607 original size:32 final size:31
Alignment explanation
Indices: 6343557--6343643 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 31
6343547 GGAACAATGG
*
6343557 GGGCATCTTT-GAAGATTCAACATC-ACATGTT
1 GGGCATCTTTGGAA-ATTCAACATCGA-ATATT
*
6343588 AGGGCATTTTTGGAAATTCAACATCGAATATT
1 -GGGCATCTTTGGAAATTCAACATCGAATATT
*
6343620 GGGCCATCTTTGGGAATTCAACAT
1 GGG-CATCTTTGGAAATTCAACAT
6343644 ACTGATACGA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 3 0.06
32 41 0.85
33 4 0.08
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (31 bp):
GGGCATCTTTGGAAATTCAACATCGAATATT
Found at i:6344716 original size:85 final size:85
Alignment explanation
Indices: 6344471--6344927 Score: 573
Period size: 85 Copynumber: 5.4 Consensus size: 85
6344461 TCCCAACCTA
* * * * * * *
6344471 TTACAGTATAGCTCAAGGCGAGAAAGGCTATCTGTCAGCAAAAACCTTCAAGTTCGATTTCATTC
1 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
* ** *
6344536 AGCTCAAGGGCA-GCCGAAT
66 AGCTCAAGGACATATCAAAT
* *
6344555 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGT-AA-AAAAACCTTCGAGTTCGATTACACTC
1 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
6344618 AGCTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* *
6344638 TTACAGCATAACTCAAGGCGAGAAGGGCAATCTGTCAACCAAAACCTTTGAGTTCGATTACATTC
1 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
6344703 AGCTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* * * *
6344723 TTACAGCATAGCTCGAGACGAGAAGGACTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
1 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
*
6344788 AGCTCAAAGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* * * * *
6344808 TTACAGCATAACTCAAGGAGAGAAGAGTTATGTGTCAA-CAAATACCTTCTAGTTCGATT-CAAT
1 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAA-ACCTTCGAGTTCGATTAC-AT
* * **
6344871 TCAACTCAAGGGCAGGTCAAAT
64 TCAGCTCAAGGACATATCAAAT
* * *
6344893 TTATAGCATAACTCAAGGCGAGAAAGACTATCTGT
1 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGT
6344928 TAATAAAAAA
Statistics
Matches: 325, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
82 34 0.10
83 39 0.12
84 39 0.12
85 213 0.66
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (85 bp):
TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
AGCTCAAGGACATATCAAAT
Found at i:6346416 original size:18 final size:17
Alignment explanation
Indices: 6346391--6346429 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
6346381 ATTTTTGCTA
*
6346391 TTATTATTATTATTAAT
1 TTATTATTATAATTAAT
*
6346408 TTATATATTATAATTATT
1 TTAT-TATTATAATTAAT
6346426 TTAT
1 TTAT
6346430 GGGCCCCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTATAATTAAT
Found at i:6348432 original size:17 final size:17
Alignment explanation
Indices: 6348412--6348445 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6348402 ATAATTTACA
6348412 TAAAAAAATTATTTATT
1 TAAAAAAATTATTTATT
6348429 TAAAAAAATTATTTATT
1 TAAAAAAATTATTTATT
6348446 CATAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAAAATTATTTATT
Found at i:6349360 original size:26 final size:26
Alignment explanation
Indices: 6349324--6349380 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
6349314 TGTTAAGAAC
* *
6349324 TCGAGTCGAGCTCAAGTCGAATCTAT
1 TCGAGGCGAGCTCAAGTCGAATCCAT
*
6349350 TCGAGGCGAGCTCGAGTCGAATCCAT
1 TCGAGGCGAGCTCAAGTCGAATCCAT
6349376 TCGAG
1 TCGAG
6349381 TAGAGTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (26 bp):
TCGAGGCGAGCTCAAGTCGAATCCAT
Found at i:6350241 original size:2 final size:2
Alignment explanation
Indices: 6350234--6350271 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6350224 TGTTTGTCTT
6350234 TA TA TA 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
6350272 CCTGAGTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6353046 original size:20 final size:20
Alignment explanation
Indices: 6353023--6353079 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
6353013 ATTAATTTTT
*
6353023 AAATTTTAAATTTATTTTAA
1 AAATATTAAATTTATTTTAA
*
6353043 AAATATTAAATTTATTTTTAT
1 AAATATTAAATTTA-TTTTAA
*
6353064 ACATATTAAATTTATT
1 AAATATTAAATTTATT
6353080 ATCATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATATTAAATTTATTTTAA
Found at i:6353069 original size:21 final size:19
Alignment explanation
Indices: 6353011--6353079 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
6353001 AGTTTTGATA
* *
6353011 AAATTAATTTTTAAATTTT
1 AAATTTATTTTTAAATATT
*
6353030 AAATTTATTTTAAAAATATT
1 AAATTTATTTT-TAAATATT
6353050 AAATTTATTTTTATACATATT
1 AAATTTATTTTTA-A-ATATT
6353071 AAATTTATT
1 AAATTTATT
6353080 ATCATTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.26
20 18 0.42
21 14 0.33
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTTATTTTTAAATATT
Found at i:6353089 original size:17 final size:17
Alignment explanation
Indices: 6353056--6353097 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
6353046 TATTAAATTT
6353056 ATTTTTATACATATTAA
1 ATTTTTATACATATTAA
*
6353073 ATTTATTAT-CATTTTAA
1 ATTT-TTATACATATTAA
6353090 ATATTTTA
1 AT-TTTTA
6353098 AATATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTATACATATTAA
Found at i:6353111 original size:24 final size:23
Alignment explanation
Indices: 6353032--6353112 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 23
6353022 TAAATTTTAA
*
6353032 ATTTATTTTAAAAATATTAAATTT
1 ATTTATTTTAAATAT-TTAAATTT
* *
6353056 ATTT-TTATACATA-TTAAATTT
1 ATTTATTTTAAATATTTAAATTT
6353077 ATTATCATTTTAAATATTTTAAATATT
1 ATT-T-ATTTTAAATA-TTTAAAT-TT
*
6353104 ATTTTTTTT
1 ATTTATTTT
6353113 TATAAAAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
21 11 0.24
22 1 0.02
23 6 0.13
24 11 0.24
25 4 0.09
26 7 0.16
27 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTATTTTAAATATTTAAATTT
Found at i:6356585 original size:2 final size:2
Alignment explanation
Indices: 6356578--6356641 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
6356568 TATAGCAGTA
6356578 AT AT AT AT AT 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
6356620 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
6356642 GTACATGAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6365100 original size:2 final size:2
Alignment explanation
Indices: 6365093--6365142 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
6365083 TTGATTTTGG
6365093 AT AT AT AT AT 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
6365135 AT AT AT AT
1 AT AT AT AT
6365143 CTTTTAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6375638 original size:2 final size:2
Alignment explanation
Indices: 6375631--6375676 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6375621 AGTAAAATTA
6375631 AT AT AT AT AT 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
6375673 AT AT
1 AT AT
6375677 CTTTAGTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6377692 original size:12 final size:12
Alignment explanation
Indices: 6377654--6377706 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
6377644 ATTAGTTTGA
*
6377654 TTATAAACTCAT
1 TTATAAATTCAT
6377666 TTATAAATTCAT
1 TTATAAATTCAT
* *
6377678 TTATAAGTTCGT
1 TTATAAATTCAT
* *
6377690 TTATTAATTAAT
1 TTATAAATTCAT
6377702 TTATA
1 TTATA
6377707 CACATGTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (12 bp):
TTATAAATTCAT
Found at i:6377793 original size:20 final size:22
Alignment explanation
Indices: 6377759--6377801 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
6377749 TAAAATATTT
6377759 TTTATAATTTAATTATTA-ATA
1 TTTATAATTTAATTATTAGATA
*
6377780 TTTAT-ATTTGATTATTAGATA
1 TTTATAATTTAATTATTAGATA
6377801 T
1 T
6377802 AAGAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTATAATTTAATTATTAGATA
Found at i:6382688 original size:21 final size:21
Alignment explanation
Indices: 6382646--6382689 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
6382636 ACCCCGGGAG
* *
6382646 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
6382667 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
6382688 CT
1 CT
6382690 CCTCCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:6383897 original size:19 final size:19
Alignment explanation
Indices: 6383873--6383924 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
6383863 AATGCATTTG
*
6383873 ATGCATCAATGCACCAGCC
1 ATGCATCGATGCACCAGCC
6383892 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
6383911 ATGCATCGATGCAC
1 ATGCATCGATGCAC
6383925 TCTGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:6383915 original size:84 final size:83
Alignment explanation
Indices: 6383807--6383969 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 83
6383797 GAATGCATTT
*
6383807 CATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCAT
1 CATGCATCGATGCACATACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCAT
*
6383870 TTGATGCATCAATGCACCAGC
63 TTCATGCATCAATGCACCAGC
* *
6383891 CATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTT
1 CATGCATCGATGCA-CATACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTT
*
6383955 CATGCATCGATGCAC
65 CATGCATCAATGCAC
6383970 TCTTAGTGCA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
83 31 0.44
84 35 0.49
85 5 0.07
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (83 bp):
CATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
ATGCATCAATGCACCAGC
Found at i:6383988 original size:83 final size:82
Alignment explanation
Indices: 6383827--6383988 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 82
6383817 TGCACATACT
*
6383827 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCATCAATGCACCAGCC
1 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTCATGCATCAATGCACCAG-C
* *
6383892 ATGCATCGATGCACCAGCC
65 -TGCACCAATGCACCAGCC
* *
6383911 ATGCATCGATGCACTCTG-GCTATTT-TG-AAACATCGAATGCATTTCATGCATCGATGCACTCT
1 ATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATTTCATGCATCAATGCAC-C-
6383973 TAG-TGCACCAATGCAC
62 -AGCTGCACCAATGCAC
6383989 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
83 42 0.62
84 21 0.31
85 3 0.04
86 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (82 bp):
ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTCATGCATCAATGCACCAGCT
GCACCAATGCACCAGCC
Found at i:6384005 original size:19 final size:19
Alignment explanation
Indices: 6383957--6384008 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
6383947 ATGCATTTCA
*
6383957 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
*
6383976 TGCACCAATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
*
6383995 TGCACTGATGCACT
1 TGCACCGATGCACT
6384009 AAGGGTCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:6390632 original size:65 final size:62
Alignment explanation
Indices: 6390516--6390705 Score: 188
Period size: 65 Copynumber: 3.0 Consensus size: 62
6390506 ATCCACGAAT
* ** *
6390516 CCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGTATTCTATGCATCGATGCACAT
1 CCATGCATCGATGCACTCA--GACTATTTTGAAACATCGAATGCATT-TATGCATCGATGCACA-
6390579 A
62 A
* *
6390580 CTATGCATCGATGCACTCAGAGT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCA
1 CCATGCATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCATTT-ATGCATCGATGCA-CA
*
6390644 G
62 A
* * *
6390645 CCATGTATCGATGCACTCTGACTATTTTGAAACATCGAATGCATTTCATGCATCGGTGCAC
1 CCATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTT-ATGCATCGATGCAC
6390706 TCTTAGTGAA
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 6 0.06
64 45 0.42
65 50 0.47
66 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (62 bp):
CCATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTATGCATCGATGCACAA
Found at i:6390721 original size:64 final size:64
Alignment explanation
Indices: 6390546--6390725 Score: 174
Period size: 65 Copynumber: 2.8 Consensus size: 64
6390536 GAATAAATTG
* * *
6390546 AACATCGAATGTA-TTCTATGCATCGATGCACATACTA-TGCATCGATGCACTCAGAGTTTTATG
1 AACATCGAATGCATTTC-ATGCATCGATGCAC-T-CTAGTGAATCGATGCACTCAGACTTTTATG
6390609 AA
63 AA
* * *
6390611 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGTATCGATGCACTCTGACTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACTCTAG---TGAATCGATGCACTCAGACT-TTTAT
6390673 G-A
62 GAA
* *
6390675 AACATCGAATGCATTTCATGCATCGGTGCACTCTTAGTGAACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TAGTGAATCGATGCACT
6390726 AAAGGTCCAA
Statistics
Matches: 97, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 42 0.43
65 46 0.47
66 5 0.05
67 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTAGTGAATCGATGCACTCAGACTTTTATGAA
Found at i:6401054 original size:30 final size:30
Alignment explanation
Indices: 6401020--6401078 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
6401010 ATTAAAGGTT
*
6401020 CAATTTTTTCAATACTTATTACTAGGGGCC
1 CAATTTTTTCAACACTTATTACTAGGGGCC
* *
6401050 CAATTTTTTCAACATTTATTATTAGGGGC
1 CAATTTTTTCAACACTTATTACTAGGGGC
6401079 ATACTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (30 bp):
CAATTTTTTCAACACTTATTACTAGGGGCC
Found at i:6402379 original size:2 final size:2
Alignment explanation
Indices: 6402374--6402414 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6402364 GAGAATTGCT
6402374 TA TA 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 TA TA T
6402415 GTATGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6402419 original size:4 final size:4
Alignment explanation
Indices: 6402412--6402470 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
6402402 TATATATATA
6402412 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
6402460 TATG TATG TAT
1 TATG TATG TAT
6402471 TAAGCATCCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:6402966 original size:23 final size:23
Alignment explanation
Indices: 6402940--6402984 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6402930 CAATTAAAGC
*
6402940 CACTTGATTAATTTAAATTCATT
1 CACTTGATAAATTTAAATTCATT
*
6402963 CACTTGATAAATTTAATTTCAT
1 CACTTGATAAATTTAAATTCAT
6402985 CATTTTCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
CACTTGATAAATTTAAATTCATT
Found at i:6403071 original size:21 final size:21
Alignment explanation
Indices: 6403045--6403086 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6403035 AACTCTTTGC
6403045 TTCATTTTATTTCCTTGAACT
1 TTCATTTTATTTCCTTGAACT
*
6403066 TTCATTTTATTTCCTTTAACT
1 TTCATTTTATTTCCTTGAACT
6403087 CTCGATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (21 bp):
TTCATTTTATTTCCTTGAACT
Found at i:6403095 original size:21 final size:21
Alignment explanation
Indices: 6403046--6403094 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6403036 ACTCTTTGCT
*
6403046 TCATTTTATTTCCTTGAACTT
1 TCATTTTATTTCCTTGAACTC
*
6403067 TCATTTTATTTCCTTTAACTC
1 TCATTTTATTTCCTTGAACTC
6403088 TCGATTT
1 TC-ATTT
6403095 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.18, C:0.20, G:0.04, T:0.57
Consensus pattern (21 bp):
TCATTTTATTTCCTTGAACTC
Found at i:6404760 original size:19 final size:19
Alignment explanation
Indices: 6404736--6404788 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
6404726 AGAATTTTTA
6404736 AAAGTATCGATACTTATAT
1 AAAGTATCGATACTTATAT
* *
6404755 AAAGTATCAATATTTATAT
1 AAAGTATCGATACTTATAT
*
6404774 AAAGTATCGAAACTT
1 AAAGTATCGATACTT
6404789 TTACAGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (19 bp):
AAAGTATCGATACTTATAT
Found at i:6408664 original size:21 final size:21
Alignment explanation
Indices: 6408639--6408700 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
6408629 AACAGCCTGT
*
6408639 AACAACTTCATCTCAGTCTAC
1 AACAAATTCATCTCAGTCTAC
*
6408660 AACAAATTCATCTCAGT-TAAT
1 AACAAATTCATCTCAGTCT-AC
*
6408681 AACAATTTCATCTCA-TCTAC
1 AACAAATTCATCTCAGTCTAC
6408701 TAAAAATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.32
Consensus pattern (21 bp):
AACAAATTCATCTCAGTCTAC
Found at i:6409231 original size:89 final size:90
Alignment explanation
Indices: 6409119--6409303 Score: 246
Period size: 90 Copynumber: 2.1 Consensus size: 90
6409109 TCTTTTATGC
* * ** **** * *
6409119 ATGGTACATTGCACTTGCAATCTATAAGTAAACCTAAC-ATTTTTTTTGTTCAATAGAATTCATA
1 ATGGAACATTACACTTGCAATCTATAAGTAAACCTAACAATAGTAACAGATAAATAGAATTCATA
6409183 TCAAACAACACTAATTCATAGATTA
66 TCAAACAACACTAATTCATAGATTA
* *
6409208 ATGGAACATTACACTTGCAATCTATATGTAAACCTAACAATAGTAACAGATAAATGGAATTCATA
1 ATGGAACATTACACTTGCAATCTATAAGTAAACCTAACAATAGTAACAGATAAATAGAATTCATA
*
6409273 TCAAACAACATTAATTCATAGATTA
66 TCAAACAACACTAATTCATAGATTA
6409298 ATGGAA
1 ATGGAA
6409304 TTCATAAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 35 0.43
90 47 0.57
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (90 bp):
ATGGAACATTACACTTGCAATCTATAAGTAAACCTAACAATAGTAACAGATAAATAGAATTCATA
TCAAACAACACTAATTCATAGATTA
Found at i:6410777 original size:22 final size:21
Alignment explanation
Indices: 6410738--6410781 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
6410728 CTCTTCCTCA
*
6410738 TCCTCCACTGCTCGCCTTTCCC
1 TCCTCCACTCCTCGCC-TTCCC
* *
6410760 TCCTCCGCTCCTCTCCTTCCC
1 TCCTCCACTCCTCGCCTTCCC
6410781 T
1 T
6410782 TTCTTTCTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.02, C:0.57, G:0.07, T:0.34
Consensus pattern (21 bp):
TCCTCCACTCCTCGCCTTCCC
Found at i:6417192 original size:31 final size:31
Alignment explanation
Indices: 6417148--6417224 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
6417138 ATTAACCTTC
*
6417148 AGTGACCACATCTTAATTAAAACGAAACAAA
1 AGTGACCAAATCTTAATTAAAACGAAACAAA
* * *
6417179 AGTGATCAAATCTTAATTAAAATGAAACGAA
1 AGTGACCAAATCTTAATTAAAACGAAACAAA
6417210 AGTGACCAAATCTTA
1 AGTGACCAAATCTTA
6417225 TGTTTTCTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (31 bp):
AGTGACCAAATCTTAATTAAAACGAAACAAA
Found at i:6418839 original size:17 final size:17
Alignment explanation
Indices: 6418819--6418857 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6418809 CATATACATT
6418819 TAAT-TTATAATAATAAA
1 TAATATTATAAT-ATAAA
*
6418836 TAATATTATAATGTAAA
1 TAATATTATAATATAAA
6418853 TAATA
1 TAATA
6418858 AACAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATATTATAATATAAA
Found at i:6419347 original size:20 final size:20
Alignment explanation
Indices: 6419322--6419364 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
6419312 AATATGTTAT
6419322 TTATTATTTA-TATTATAATA
1 TTATTATTTATTATTATAA-A
6419342 TTATTATTTATTATTATAAA
1 TTATTATTTATTATTATAAA
6419362 TTA
1 TTA
6419365 AATGTATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTATTTATTATTATAAA
Found at i:6423633 original size:29 final size:29
Alignment explanation
Indices: 6423587--6423646 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
6423577 ATTTTAGTTT
6423587 ATGTCTTAATTTTATAATTAAATTTTAAA
1 ATGTCTTAATTTTATAATTAAATTTTAAA
* * * *
6423616 ATGTTTTATTTTTTTAATTGAATTTTAAA
1 ATGTCTTAATTTTATAATTAAATTTTAAA
6423645 AT
1 AT
6423647 TATTTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (29 bp):
ATGTCTTAATTTTATAATTAAATTTTAAA
Found at i:6428275 original size:60 final size:59
Alignment explanation
Indices: 6428210--6428383 Score: 239
Period size: 60 Copynumber: 2.9 Consensus size: 59
6428200 AAATGTCACC
* *
6428210 TTTTCAAAATAATTCCCAGAATGTCACATTTTTCTAAATATTTCCTAGATTGTCACTTTT
1 TTTTCAAAATAATTCCCAAAATGTCACATTTTT-TAAATATTTCCTAGAATGTCACTTTT
*
6428270 TTTTCAAAATAATTCCCAAAATGTCACTTTTTTTTAAATATTT-CTCAGAATGTCA-TTTT
1 TTTTCAAAATAATTCCCAAAATGTCAC-ATTTTTTAAATATTTCCT-AGAATGTCACTTTT
*
6428329 TTTT-AAAATAATTCTCAAAATGTCACATTTTTTAAAATATTTTCC-AGAATGTCAC
1 TTTTCAAAATAATTCCCAAAATGTCACATTTTTT-AAATA-TTTCCTAGAATGTCAC
6428384 CGGGTCGGGT
Statistics
Matches: 103, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
57 6 0.06
58 35 0.34
59 13 0.13
60 44 0.43
61 5 0.05
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (59 bp):
TTTTCAAAATAATTCCCAAAATGTCACATTTTTTAAATATTTCCTAGAATGTCACTTTT
Found at i:6428280 original size:31 final size:31
Alignment explanation
Indices: 6428210--6428383 Score: 175
Period size: 29 Copynumber: 5.9 Consensus size: 31
6428200 AAATGTCACC
*
6428210 TTTTCAAAATAATTCCCAGAATGTCAC--AT
1 TTTTCAAAATAATTCCCAGAATGTCACTTTT
* * * *
6428239 TTTTCTAAATATTTCCTAGATTGTCACTTTT
1 TTTTCAAAATAATTCCCAGAATGTCACTTTT
*
6428270 TTTTCAAAATAATTCCCAAAATGTCACTTTT
1 TTTTCAAAATAATTCCCAGAATGTCACTTTT
* *
6428301 TTTT--AAATATTTCTCAGAATGTCA-TTTT
1 TTTTCAAAATAATTCCCAGAATGTCACTTTT
* * *
6428329 TTTT-AAAATAATTCTCAAAATGTCAC-ATT
1 TTTTCAAAATAATTCCCAGAATGTCACTTTT
* *
6428358 TTTT-AAAATATTTTCCAGAATGTCAC
1 TTTTCAAAATAATTCCCAGAATGTCAC
6428384 CGGGTCGGGT
Statistics
Matches: 121, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
28 8 0.07
29 82 0.68
31 31 0.26
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (31 bp):
TTTTCAAAATAATTCCCAGAATGTCACTTTT
Found at i:6428360 original size:58 final size:59
Alignment explanation
Indices: 6428210--6428383 Score: 237
Period size: 58 Copynumber: 2.9 Consensus size: 59
6428200 AAATGTCACC
* * * *
6428210 TTTTCAAAATAATTCCCAGAATGTCACATTTTTCTAAATATTTC-CTAGATTGTCACTTT
1 TTTTTAAAATAATTCCCAAAATGTCACATTTTTTTAAATATTTCTC-AGAATGTCACTTT
*
6428269 TTTTTCAAAATAATTCCCAAAATGTCACTTTTTTTTAAATATTTCTCAGAATGTCA-TTT
1 TTTTT-AAAATAATTCCCAAAATGTCACATTTTTTTAAATATTTCTCAGAATGTCACTTT
* *
6428328 TTTTTAAAATAATTCTCAAAATGTCACATTTTTTAAAATATTT-TCCAGAATGTCAC
1 TTTTTAAAATAATTCCCAAAATGTCACATTTTTTTAAATATTTCT-CAGAATGTCAC
6428384 CGGGTCGGGT
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
57 1 0.01
58 45 0.44
59 12 0.12
60 44 0.43
61 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (59 bp):
TTTTTAAAATAATTCCCAAAATGTCACATTTTTTTAAATATTTCTCAGAATGTCACTTT
Found at i:6428435 original size:19 final size:19
Alignment explanation
Indices: 6428411--6428456 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
6428401 ATGGGTCGAG
*
6428411 TCAGACCGGTCAACCCGGT
1 TCAGACCGGTCAAACCGGT
6428430 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
6428449 TCAGACCG
1 TCAGACCG
6428457 ATTTGGACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:6428456 original size:10 final size:9
Alignment explanation
Indices: 6428410--6428456 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
6428400 AATGGGTCGA
6428410 GTCAGACCG
1 GTCAGACCG
6428419 GTCA-ACCCG
1 GTCAGA-CCG
6428428 GTTCAGACCG
1 G-TCAGACCG
*
6428438 GTCAAACCG
1 GTCAGACCG
6428447 GTTCAGACCG
1 G-TCAGACCG
6428457 ATTTGGACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 1 0.03
9 16 0.50
10 14 0.44
11 1 0.03
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.15
Consensus pattern (9 bp):
GTCAGACCG
Found at i:6435039 original size:19 final size:19
Alignment explanation
Indices: 6435015--6435072 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
6435005 GTCGGGTCAA
*
6435015 ACCGATCAATCAGGTTCAG
1 ACCGATCAATCCGGTTCAG
6435034 ACCGATCAATCCGGTTCAG
1 ACCGATCAATCCGGTTCAG
*
6435053 ACCGATCAAACCGGTTCAG
1 ACCGATCAATCCGGTTCAG
6435072 A
1 A
6435073 TCGGTCACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (19 bp):
ACCGATCAATCCGGTTCAG
Found at i:6437418 original size:33 final size:33
Alignment explanation
Indices: 6437379--6437445 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
6437369 TAAAACAGTC
6437379 AAGGAAGATTGGCTCTATCTGCTTCACACGAGG
1 AAGGAAGATTGGCTCTATCTGCTTCACACGAGG
* *
6437412 AAGGAAGATTGGCTCTATCTGTTTCGCACGAGG
1 AAGGAAGATTGGCTCTATCTGCTTCACACGAGG
6437445 A
1 A
6437446 CATAATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (33 bp):
AAGGAAGATTGGCTCTATCTGCTTCACACGAGG
Found at i:6444569 original size:264 final size:261
Alignment explanation
Indices: 6444093--6444862 Score: 897
Period size: 264 Copynumber: 2.9 Consensus size: 261
6444083 TTCAACTTCG
** * *
6444093 GTTTCTAATGAATCGATCTTCGCAGACGTCATCCGAGCCTCTTCTTTGATGCTAATGAGTTGAGA
1 GTTTCTAACAAATCGATCTTTGCAGACATCATCC-AGCCTC-TCTTTGATGCTAATGAGTTGAGA
* * * * * *
6444158 CTCGAGAAGTTTCTTTGATTTGTTTGCGGTTACTAAAACCTGCTCTGACAAGGTCCTTTCCTTTT
64 CTCAAGAAGTTGCTTTGA-TTGATTGC-GTGACTGAAACTTGCTCTGACAAGGTCCTTTCCTTTT
*
6444223 CAATTTCTGCTTCTAATGAGTCTATCTTTGTGGACATTGTCTCTGCATCTGTTTCCAATGTACTG
127 CAATTTCTGCTTCTAATGAGTCAATCTTTGTGGACATTGTCTCTGCATCTGTTTCCAATGTACTG
*
6444288 AGTTGAGACTT-GAGATGTTGCTTAGTTTCATTTGATGTACAAAGCTCCT-CTCGCAACTCCACC
192 AGTTGAGA-TTCGAGATGTTGCTTAGCTTCATTTGATGTACAAAGCTCCTACTCGCAACTCCACC
*
6444351 AATTCT
256 AATTCC
* *
6444357 GTTTCTAACAAATCAATCTTTGCAGACATCATCCAAGCGTCTGCTTTGATGCTAATGAGTTGAGA
1 GTTTCTAACAAATCGATCTTTGCAGACATCATCC-AGCCTCT-CTTTGATGCTAATGAGTTGAGA
* * *
6444422 CTCAAGAAGTTGCTTTGACTCGGTTGCGTGAGCTGAAACTTGCTGTGACAAGGTCCTTTCCTTTT
64 CTCAAGAAGTTGCTTTGA-TTGATTGCGTGA-CTGAAACTTGCTCTGACAAGGTCCTTTCCTTTT
* * * **
6444487 CGATTTCTGCTTCTAAAGAGTCGATCTTTGCAGACATTGTCTCTGCATCTGTTTCCAATGTACTG
127 CAATTTCTGCTTCTAATGAGTCAATCTTTGTGGACATTGTCTCTGCATCTGTTTCCAATGTACTG
* * * * *
6444552 AGTTGAGATTCGAGATGTAGCTTAGCTTCATCTTTCATG--CAAAGCT-CTATTCGCATCTCCGC
192 AGTTGAGATTCGAGATGTTGCTTAGCTTCA--TTTGATGTACAAAGCTCCTACTCGCAACTCCAC
6444614 CAATTCC
255 CAATTCC
* * * * * * * *
6444621 ATTTCTAACAAATGGATCTTTGAAGACATCATCTCTGCCTCCTCTTTGCTGTTGATGAATTGAGA
1 GTTTCTAACAAATCGATCTTTGCAGACATCATC-CAGCCT-CTCTTTGATGCTAATGAGTTGAGA
* * * ** *
6444686 CTCAAGAAGCTGCTTTGATTTATTG-GTGTTAACAGAAACTTGCTCCAACAAGGTACTTTCCTTT
64 CTCAAGAAGTTGCTTTGATTGATTGCGTG---ACTGAAACTTGCTCTGACAAGGTCCTTTCCTTT
* * *
6444750 TCAATTTCTGCTTCTACTGAGTCAATCTTTGTGGACATCGACTCTGCATCTGTTTCCAATGTACT
126 TCAATTTCTGCTTCTAATGAGTCAATCTTTGTGGACATTGTCTCTGCATCTGTTTCCAATGTACT
* * * *
6444815 AAGTTGAGACTCGAGATGGTGCTTAGCTTCATTTG-TCATACAAAGCTC
191 GAGTTGAGATTCGAGATGTTGCTTAGCTTCATTTGAT-GTACAAAGCTC
6444863 TGTTCTCAAC
Statistics
Matches: 430, Mismatches: 61, Indels: 29
0.83 0.12 0.06
Matches are distributed among these distances:
261 1 0.00
262 6 0.01
263 12 0.03
264 401 0.93
265 4 0.01
266 6 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (261 bp):
GTTTCTAACAAATCGATCTTTGCAGACATCATCCAGCCTCTCTTTGATGCTAATGAGTTGAGACT
CAAGAAGTTGCTTTGATTGATTGCGTGACTGAAACTTGCTCTGACAAGGTCCTTTCCTTTTCAAT
TTCTGCTTCTAATGAGTCAATCTTTGTGGACATTGTCTCTGCATCTGTTTCCAATGTACTGAGTT
GAGATTCGAGATGTTGCTTAGCTTCATTTGATGTACAAAGCTCCTACTCGCAACTCCACCAATTC
C
Found at i:6449001 original size:7 final size:7
Alignment explanation
Indices: 6448989--6449022 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
6448979 CTTTAATTGC
6448989 AAAAATT
1 AAAAATT
6448996 AAAAATT
1 AAAAATT
*
6449003 -TAAATT
1 AAAAATT
6449009 AAAAATT
1 AAAAATT
6449016 AAAAATT
1 AAAAATT
6449023 CGACCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAAATT
Found at i:6449007 original size:13 final size:13
Alignment explanation
Indices: 6448991--6449015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6448981 TTAATTGCAA
6448991 AAATTAAAAATTT
1 AAATTAAAAATTT
6449004 AAATTAAAAATT
1 AAATTAAAAATT
6449016 AAAAATTCGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:6451398 original size:165 final size:162
Alignment explanation
Indices: 6451126--6451765 Score: 597
Period size: 165 Copynumber: 3.9 Consensus size: 162
6451116 GAATATAATT
* * * * **
6451126 GAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGC
1 GAACTCGAAGGTCTTTGG-T-ACAGATAACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGC
* * *
6451191 CCTCCAAGCTGAGAGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
64 CCTCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
6451256 ACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTC
129 ACTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTC
* * *
6451291 GAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
1 GAACTCGAAGGTC-TTTGGT-ACAGATAACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGC
* *
6451356 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
64 CCTCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
6451421 ACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
129 ACTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTC
* * * * * * *
6451456 GAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAG-ATTCAAGTTGTGCTGCAAATGATATG
1 GAACTCGAAGGTCTTTGG-T-ACAGATAACCCTTCTAGCCTT-AAGTTATACTGCAAATGATGTG
* * * * * * * * *
6451520 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
63 CCCTCGAAGCTGAGCGTAATCGAACTCGAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAA
* * * * * *
6451584 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
124 GCTATACTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTC
** * * * * *
6451625 GAACTCGGGGGTCTTTGG--CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCG
1 GAACTCGAAGGTCTTTGGTACAGATAACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGCCC
* * * * * * * *
6451688 TTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
66 TCGAAGCTGAGCGTAATCGAACTCGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
6451752 GTGCTGCAAATGAT
127 ATACTGCAAATGAT
6451766 TTGTTTTAAA
Statistics
Matches: 405, Mismatches: 55, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
164 33 0.08
165 288 0.71
166 12 0.03
167 2 0.00
168 41 0.10
169 29 0.07
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (162 bp):
GAACTCGAAGGTCTTTGGTACAGATAACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGCCC
TCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
TGCAAATGATGTGCCTTGAGCTGAGCGTAGTC
Found at i:6451480 original size:249 final size:249
Alignment explanation
Indices: 6451225--6451765 Score: 976
Period size: 249 Copynumber: 2.2 Consensus size: 249
6451215 TCGAGGGTCT
* * * * * * *
6451225 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
*
6451290 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
6451355 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
6451420 TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
196 TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
*
6451474 TTGGCAGACAACCCTTCTAGA-TTCAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
1 TTGGCAGACAACCCTTCTAGACTT-AAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAG
6451538 TCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
65 TCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
6451603 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
6451668 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
195 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
6451723 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGAT
1 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGAT
6451766 TTGTTTTAAA
Statistics
Matches: 280, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
248 2 0.01
249 276 0.99
250 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (249 bp):
TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
CGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
TACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
Found at i:6454868 original size:18 final size:19
Alignment explanation
Indices: 6454827--6454871 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
6454817 AGTTAATGTG
6454827 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
6454846 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
6454864 AATGCAAA
1 AATGCAAA
6454872 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:6456474 original size:7 final size:7
Alignment explanation
Indices: 6456462--6456495 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
6456452 CTTTAATTGC
6456462 AAAAATT
1 AAAAATT
6456469 AAAAATT
1 AAAAATT
*
6456476 -TAAATT
1 AAAAATT
6456482 AAAAATT
1 AAAAATT
6456489 AAAAATT
1 AAAAATT
6456496 CGACCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAAATT
Found at i:6456480 original size:13 final size:13
Alignment explanation
Indices: 6456464--6456488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6456454 TTAATTGCAA
6456464 AAATTAAAAATTT
1 AAATTAAAAATTT
6456477 AAATTAAAAATT
1 AAATTAAAAATT
6456489 AAAAATTCGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:6461395 original size:23 final size:24
Alignment explanation
Indices: 6461342--6461412 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
6461332 TTTATGAATT
**
6461342 TAATATTAA-TAAAATATTTTAATA
1 TAAT-TTAATTAAAATATTAAAATA
6461366 TCAATTTAATTAAAATATTAAAATA
1 T-AATTTAATTAAAATATTAAAATA
6461391 T-ATTT-ATT--AATATTAATAATA
1 TAATTTAATTAAAATATTAA-AATA
6461412 T
1 T
6461413 TATATTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 8 0.19
21 5 0.12
22 3 0.07
23 4 0.10
24 5 0.12
25 17 0.40
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATTTAATTAAAATATTAAAATA
Found at i:6461418 original size:20 final size:20
Alignment explanation
Indices: 6461379--6461423 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
6461369 ATTTAATTAA
*
6461379 AATATTAAAATATATTTATT
1 AATATTAAAATATATATATT
6461399 AATATTAATAATAT-TATATT
1 AATATTAA-AATATATATATT
6461419 -ATATT
1 AATATT
6461424 TTTCATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTAAAATATATATATT
Found at i:6462958 original size:23 final size:23
Alignment explanation
Indices: 6462932--6463000 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
6462922 CACCACAGCT
*
6462932 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
6462955 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
6462978 CGTAGAGATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
6463001 TATAAGATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:6463315 original size:24 final size:25
Alignment explanation
Indices: 6463287--6463334 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6463277 TAGATCTTTA
6463287 TCATATAATGCAT-ATAATATGAAT
1 TCATATAATGCATCATAATATGAAT
* * *
6463311 TCATATCATGTATCATATTATGAA
1 TCATATAATGCATCATAATATGAA
6463335 ATGTGAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (25 bp):
TCATATAATGCATCATAATATGAAT
Found at i:6463803 original size:21 final size:21
Alignment explanation
Indices: 6463777--6463834 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
6463767 AAATTGGTCT
*
6463777 TAGGGTATCGGTACCCATTCA
1 TAGGGTATCGATACCCATTCA
6463798 TAGGGTATCGATACCCATTCA
1 TAGGGTATCGATACCCATTCA
*
6463819 TAGGGTATCGAAACCC
1 TAGGGTATCGATACCC
6463835 CTTGCCCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (21 bp):
TAGGGTATCGATACCCATTCA
Found at i:6465134 original size:23 final size:23
Alignment explanation
Indices: 6465104--6465148 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
6465094 TGTAGTATCG
6465104 ATTGATACCATTGAGCTGAAAGT
1 ATTGATACCATTGAGCTGAAAGT
6465127 ATTGATACCATTGAGCTGAAAG
1 ATTGATACCATTGAGCTGAAAG
6465149 GCAATGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (23 bp):
ATTGATACCATTGAGCTGAAAGT
Found at i:6466340 original size:70 final size:69
Alignment explanation
Indices: 6466227--6466390 Score: 204
Period size: 70 Copynumber: 2.3 Consensus size: 69
6466217 GTCAAATATG
* *
6466227 CACTGAAGTGCTAAACCGAATATGACACATAAGGTCGTGCCCACCA-TACACACTAAGTGTCTTA
1 CACTGTAGTGCTAAACCAAATATGACACATAAGGTCGTGCCCACCACT-CA-ACTAAGTGTCTTA
6466291 GGTATA
64 GGTATA
* * * *
6466297 CACTGTAGTGCTAAACCAAATATGGCATATAAGGTCGTGCCCACCACCTGAACTAAGTGTCTTGG
1 CACTGTAGTGCTAAACCAAATATGACACATAAGGTCGTGCCCACCA-CTCAACTAAGTGTCTTAG
6466362 GTATA
65 GTATA
* * * *
6466367 CACTCTAGTTCTAAATCAGATATG
1 CACTGTAGTGCTAAACCAAATATG
6466391 CAGCATGTTG
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
70 80 0.98
71 1 0.01
72 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (69 bp):
CACTGTAGTGCTAAACCAAATATGACACATAAGGTCGTGCCCACCACTCAACTAAGTGTCTTAGG
TATA
Found at i:6467790 original size:19 final size:20
Alignment explanation
Indices: 6467766--6467811 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
6467756 CAAAATAATC
*
6467766 CAATTTC-ACATTCTAAAAT
1 CAATTTCAACACTCTAAAAT
*
6467785 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAAAAT
*
6467805 TAATTTC
1 CAATTTC
6467812 CAGCATAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAAAAT
Found at i:6469442 original size:69 final size:69
Alignment explanation
Indices: 6469348--6469504 Score: 188
Period size: 69 Copynumber: 2.3 Consensus size: 69
6469338 CGCACTATAG
* * * * * *
6469348 CACCTAATCACATGTATTCTAGGTGTCTCGCATAGGATCCCCGAAGGATTAGAGCAACTCACACG
1 CACCTAATCATATGTATTTTAGGTGTCTCACACAGGAGCCCCGAAAGATTAGAGCAACTCACACG
6469413 GGAA
66 GGAA
* * * ** * *
6469417 CACCTAGTCATATGTATTTTGGGTGTCTCACACGGGAGCCCCGAAAGATTAGAGTGACTCGCATG
1 CACCTAATCATATGTATTTTAGGTGTCTCACACAGGAGCCCCGAAAGATTAGAGCAACTCACACG
*
6469482 GGAG
66 GGAA
6469486 CACCTAATCATATGTATTT
1 CACCTAATCATATGTATTT
6469505 CGAGTATCTG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (69 bp):
CACCTAATCATATGTATTTTAGGTGTCTCACACAGGAGCCCCGAAAGATTAGAGCAACTCACACG
GGAA
Found at i:6469656 original size:38 final size:38
Alignment explanation
Indices: 6469552--6469659 Score: 128
Period size: 38 Copynumber: 2.8 Consensus size: 38
6469542 ACTCACATGG
* * * * *
6469552 GAGCGCCTAATCATATGTATTTTGTGTGCCTCGCACGA
1 GAGCACCTAATCATATATATTTTGGGTGTCTCGCAAGA
* *
6469590 GAGCACCTAATCATATTTATTTTGGGTGTCTCGCAAGG
1 GAGCACCTAATCATATATATTTTGGGTGTCTCGCAAGA
*
6469628 GAG-ACCCTAATCATATATATTATGGGTGTCTC
1 GAGCA-CCTAATCATATATATTTTGGGTGTCTC
6469660 ACACGGATGC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 1 0.02
38 60 0.98
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (38 bp):
GAGCACCTAATCATATATATTTTGGGTGTCTCGCAAGA
Found at i:6473048 original size:11 final size:11
Alignment explanation
Indices: 6473032--6473060 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
6473022 TAACATATAA
6473032 GTTGTTATTTG
1 GTTGTTATTTG
6473043 GTTGTTATTTG
1 GTTGTTATTTG
6473054 GTTGTTA
1 GTTGTTA
6473061 GGGATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (11 bp):
GTTGTTATTTG
Found at i:6474818 original size:34 final size:36
Alignment explanation
Indices: 6474755--6474824 Score: 108
Period size: 34 Copynumber: 2.0 Consensus size: 36
6474745 ATACAATGAT
* *
6474755 ATCACATTGGAAATCACCATATGCACACAAAGTGCA
1 ATCACATCGGAAATCAACATATGCACACAAAGTGCA
6474791 ATCACATCGGAAAT-AACA-ATGCACACAAAGTGCA
1 ATCACATCGGAAATCAACATATGCACACAAAGTGCA
6474825 TTTGGATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 16 0.50
35 3 0.09
36 13 0.41
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.17
Consensus pattern (36 bp):
ATCACATCGGAAATCAACATATGCACACAAAGTGCA
Found at i:6474843 original size:2 final size:2
Alignment explanation
Indices: 6474836--6474876 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6474826 TTGGATCAGA
6474836 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
6474877 CACTAGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6480879 original size:16 final size:16
Alignment explanation
Indices: 6480858--6480888 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6480848 TTTTGTTTCT
6480858 AAAATAAAAGAAATTA
1 AAAATAAAAGAAATTA
*
6480874 AAAATAAAGGAAATT
1 AAAATAAAAGAAATT
6480889 TTGTTTCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAATAAAAGAAATTA
Found at i:6480933 original size:44 final size:39
Alignment explanation
Indices: 6480833--6480917 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
6480823 TTATTACAAG
* *
6480833 TAAAAATAAAGGAAGTTTTGTTTCTAAAATAAAAGAAAT
1 TAAAAATAAAGGAAATTTTGTTTCTAAAATAAAAGAAAA
6480872 TAAAAATAAAGGAAATTTTGTTTCTAAAATAAAAGAAAA
1 TAAAAATAAAGGAAATTTTGTTTCTAAAATAAAAGAAAA
6480911 TAAAAAT
1 TAAAAAT
6480918 TAAACGAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (39 bp):
TAAAAATAAAGGAAATTTTGTTTCTAAAATAAAAGAAAA
Found at i:6485555 original size:14 final size:15
Alignment explanation
Indices: 6485529--6485560 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
6485519 AAATAATTAA
6485529 AATAATATAATTTAT
1 AATAATATAATTTAT
6485544 AATAATAT-ATTTAT
1 AATAATATAATTTAT
6485558 AAT
1 AAT
6485561 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAATATAATTTAT
Found at i:6485604 original size:12 final size:12
Alignment explanation
Indices: 6485587--6485612 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6485577 ACAGTTTAAT
6485587 TAATATTTTTTA
1 TAATATTTTTTA
6485599 TAATATTTTTTA
1 TAATATTTTTTA
6485611 TA
1 TA
6485613 CTTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TAATATTTTTTA
Found at i:6485654 original size:21 final size:21
Alignment explanation
Indices: 6485615--6485654 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6485605 TTTTTATACT
*
6485615 TTTTAATAAGTAAATAATATA
1 TTTTAATAAGTAAAAAATATA
6485636 TTTTAATAA-TATAAAAATA
1 TTTTAATAAGTA-AAAAATA
6485655 AAAAAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TTTTAATAAGTAAAAAATATA
Found at i:6488309 original size:30 final size:30
Alignment explanation
Indices: 6488270--6488327 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
6488260 ACTTTTAAAA
6488270 AGTTGAATGAT-TAAAAAATCATTTTATTAT
1 AGTTGAATGATATAAAAAAT-ATTTTATTAT
* *
6488300 AGTTTAATGATCATAAAATATATTTTAT
1 AGTTGAATGAT-ATAAAAAATATTTTAT
6488328 ATTATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.42
31 7 0.29
32 7 0.29
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (30 bp):
AGTTGAATGATATAAAAAATATTTTATTAT
Found at i:6491473 original size:27 final size:27
Alignment explanation
Indices: 6491444--6491543 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
6491434 ATTTTAACAT
*
6491444 AAAATATATATATTTTTAAATCAAAATA
1 AAAATA-AAATATTTTTAAATCAAAATA
6491472 AAAATAAAATATTTTTAAATCAAAATA
1 AAAATAAAATATTTTTAAATCAAAATA
* *
6491499 AAAATAAAATATTTTTAAATTAAATTA
1 AAAATAAAATATTTTTAAATCAAAATA
** *
6491526 GTAATAAAATATATTTAA
1 AAAATAAAATATTTTTAA
6491544 TAAGTTAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
27 60 0.91
28 6 0.09
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (27 bp):
AAAATAAAATATTTTTAAATCAAAATA
Found at i:6491569 original size:27 final size:27
Alignment explanation
Indices: 6491453--6491574 Score: 81
Period size: 27 Copynumber: 4.6 Consensus size: 27
6491443 TAAAATATAT
* * *
6491453 ATATTTTTAAATCAAAATAA-AAATAAA
1 ATATTTTTTAATTAAATTAATAAA-AAA
* * *
6491480 ATATTTTTAAATCAAAATAA-AAATAAA
1 ATATTTTTTAATTAAATTAATAAA-AAA
* * *
6491507 ATATTTTTAAATTAAATTAGTAATAAA
1 ATATTTTTTAATTAAATTAATAAAAAA
* *
6491534 ATA-TATTTAA-TAAGTTAATATAAAAA
1 ATATTTTTTAATTAAATTAATA-AAAAA
*
6491560 ATATTTTTTAGTTAA
1 ATATTTTTTAATTAA
6491575 TATATATAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.10
26 12 0.15
27 55 0.69
28 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATTTTTTAATTAAATTAATAAAAAA
Found at i:6493248 original size:14 final size:14
Alignment explanation
Indices: 6493216--6493248 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6493206 AAAATATTCA
6493216 CAAAATAAAAATTT
1 CAAAATAAAAATTT
*
6493230 -TAAATAAAAATTT
1 CAAAATAAAAATTT
6493243 CAAAAT
1 CAAAAT
6493249 TATAAACTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 2
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (14 bp):
CAAAATAAAAATTT
Found at i:6498077 original size:2 final size:2
Alignment explanation
Indices: 6498070--6498099 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6498060 TGATCTAGTT
6498070 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
6498100 ATTCCTCATA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:6500102 original size:18 final size:17
Alignment explanation
Indices: 6500068--6500106 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
6500058 CCCAGCAGCT
* *
6500068 CACCAGAACTCCTCGGA
1 CACCAGAACACCCCGGA
6500085 CACCACGAACACCCCGGA
1 CACCA-GAACACCCCGGA
6500103 CACC
1 CACC
6500107 GAGGAACAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.31, C:0.49, G:0.15, T:0.05
Consensus pattern (17 bp):
CACCAGAACACCCCGGA
Found at i:6506371 original size:20 final size:22
Alignment explanation
Indices: 6506348--6506390 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6506338 TAATTAAGCC
*
6506348 TTATTTA-AA-TATATTATTTT
1 TTATTTATAATTATAATATTTT
6506368 TTATTTATAATTATAATATTTT
1 TTATTTATAATTATAATATTTT
6506390 T
1 T
6506391 AAATAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTATAATTATAATATTTT
Found at i:6511335 original size:21 final size:20
Alignment explanation
Indices: 6511307--6511345 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6511297 GATGCTGGTA
6511307 TCAATTCTAT-CACTGCATTT
1 TCAATTCT-TGCACTGCATTT
6511327 TCAACTTCTTGCACTGCAT
1 TCAA-TTCTTGCACTGCAT
6511346 CACCATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (20 bp):
TCAATTCTTGCACTGCATTT
Found at i:6516235 original size:34 final size:34
Alignment explanation
Indices: 6516187--6516260 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
6516177 TCTCACTAGG
* * *
6516187 CTTTGAGGGTGAAGGTTACTTGTCATTCTGACTA
1 CTTTCAGGGTGAAGGTTACTTATCATTCCGACTA
6516221 CTTTCAGGGTGAAGGTTACTTATCATTCCGACTA
1 CTTTCAGGGTGAAGGTTACTTATCATTCCGACTA
6516255 CTTTCA
1 CTTTCA
6516261 AGAGTAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (34 bp):
CTTTCAGGGTGAAGGTTACTTATCATTCCGACTA
Found at i:6518497 original size:15 final size:15
Alignment explanation
Indices: 6518477--6518508 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6518467 GAGATTTTGA
6518477 AATAACTTACGGTTT
1 AATAACTTACGGTTT
6518492 AATAACTTACGGTTT
1 AATAACTTACGGTTT
6518507 AA
1 AA
6518509 AGATAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (15 bp):
AATAACTTACGGTTT
Found at i:6519168 original size:16 final size:17
Alignment explanation
Indices: 6519133--6519176 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
6519123 TTATGAGGCA
6519133 AAAAATAATATTATTGT
1 AAAAATAATATTATTGT
6519150 AAAAAT-ATAGTTATT-T
1 AAAAATAATA-TTATTGT
6519166 -AAAATAATATT
1 AAAAATAATATT
6519177 TAGCTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAAATAATATTATTGT
Found at i:6522027 original size:19 final size:19
Alignment explanation
Indices: 6522003--6522044 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
6521993 TCTTTTTTTT
6522003 TTATTAAAATATATTATTA
1 TTATTAAAATATATTATTA
6522022 TTATTAAAATATATTATTA
1 TTATTAAAATATATTATTA
6522041 TTAT
1 TTAT
6522045 AGGCCCGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTAAAATATATTATTA
Found at i:6524176 original size:27 final size:27
Alignment explanation
Indices: 6524123--6524177 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
6524113 CATCGGCGCC
*
6524123 ATTGGCCCCATCAATAGCAGCAGTGGT
1 ATTGGCCCCATCAATAGCAGCAATGGT
* ** *
6524150 ATTGGCCCCTTCGGTAGCAGTAATGGT
1 ATTGGCCCCATCAATAGCAGCAATGGT
6524177 A
1 A
6524178 GCATCGGTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (27 bp):
ATTGGCCCCATCAATAGCAGCAATGGT
Found at i:6524939 original size:23 final size:23
Alignment explanation
Indices: 6524892--6524940 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6524882 AATAACATAT
* **
6524892 TAGGTAGCTCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
6524915 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
6524938 TAG
1 TAG
6524941 ACATTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:6525003 original size:87 final size:87
Alignment explanation
Indices: 6524856--6525017 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 87
6524846 ATGTTATATT
* * * * * *
6524856 ATTTAACCGAAAATATTATTAAGCACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATAAAACACAATAACAAATTAGATAGCGCTTATATAATATAATAGGTA
6524921 GCGCTTATATAATAAAATAGAC
66 GCGCTTATATAATAAAATAGAC
* *
6524943 ATTTAACCGAAAATATTATAAAATACAATAACAAATTAGATAGCGCTTATATACTATAATAGGTA
1 ATTTAACCGAAAATATTATAAAACACAATAACAAATTAGATAGCGCTTATATAATATAATAGGTA
6525008 GCGCTTATAT
66 GCGCTTATAT
6525018 TGACCTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (87 bp):
ATTTAACCGAAAATATTATAAAACACAATAACAAATTAGATAGCGCTTATATAATATAATAGGTA
GCGCTTATATAATAAAATAGAC
Found at i:6525205 original size:21 final size:21
Alignment explanation
Indices: 6525181--6525232 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
6525171 GAAAAAAGTA
*
6525181 TCGACACATATTTAAAGAGTG
1 TCGATACATATTTAAAGAGTG
6525202 TCGATACATATTTAAAGAGTG
1 TCGATACATATTTAAAGAGTG
6525223 TCGATACATA
1 TCGATACATA
6525233 ATGTAGACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (21 bp):
TCGATACATATTTAAAGAGTG
Found at i:6529146 original size:178 final size:180
Alignment explanation
Indices: 6528939--6529297 Score: 650
Period size: 178 Copynumber: 2.0 Consensus size: 180
6528929 TTGTTATGTT
*
6528939 ACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTACGGATTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
*
6529004 CACTTTTTCGTGAACTTGTTTTGAAAATTTATTATGGACATAAAGTGTCGACACAAATGTATAAA
66 CACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGTATAAA
*
6529069 GTATCGATACATTATGTATAC-CTT-TTTTTTAATAACTGGTATATTTAG
131 GTATCGATACATTATGTATACACTTCTTTTTTAATAACCGGTATATTTAG
* *
6529117 ACCTATTACATTATAATTATGTATTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTACGGATTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
6529182 CACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGTATAAA
66 CACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGTATAAA
*
6529247 GTATCGATACATTATGTATACATTTCTTTTTTAATAACCGGTATATTTAG
131 GTATCGATACATTATGTATACACTTCTTTTTTAATAACCGGTATATTTAG
6529297 A
1 A
6529298 TCGGTTACAT
Statistics
Matches: 173, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
178 147 0.85
179 2 0.01
180 24 0.14
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (180 bp):
ACCTATTACATTATAATTACGGATTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
CACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGTATAAA
GTATCGATACATTATGTATACACTTCTTTTTTAATAACCGGTATATTTAG
Found at i:6529351 original size:200 final size:200
Alignment explanation
Indices: 6529117--6529546 Score: 806
Period size: 200 Copynumber: 2.1 Consensus size: 200
6529107 GTATATTTAG
*
6529117 ACCTATTACATTATAATTATGTATTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
* *
6529182 CACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGTATAAA
66 CACTATTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTAGACACAAATGTATAAA
*
6529247 GTATCGATACATTATGTATACATTTCTTTTTTAATAACCGGTATATTTAGATCGGTTACATTGTT
131 GTATCGATACATTATGTATACATTTCTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGTT
6529312 ATGTT
196 ATGTT
*
6529317 ACCTATTACATTATAATTATGTGTTTCGATGTTTTTGTGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
6529382 CACTATTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTAGACACAAATGTATAAA
66 CACTATTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTAGACACAAATGTATAAA
*
6529447 GTATCGATACATTATGTATACCTTTCTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGTT
131 GTATCGATACATTATGTATACATTTCTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGTT
6529512 ATGTT
196 ATGTT
6529517 ACCTATTACATTATAATTATGTGTTTCGAT
1 ACCTATTACATTATAATTATGTGTTTCGAT
6529547 ATTTAGTCTG
Statistics
Matches: 224, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 224 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (200 bp):
ACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
CACTATTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTAGACACAAATGTATAAA
GTATCGATACATTATGTATACATTTCTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGTT
ATGTT
Found at i:6529872 original size:182 final size:181
Alignment explanation
Indices: 6529556--6530039 Score: 720
Period size: 182 Copynumber: 2.7 Consensus size: 181
6529546 TATTTAGTCT
* * * *
6529556 GGTTTTGTCATTTCGATACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACA
1 GGTTTTATCATTTCGAGACCGGTTTTGTCATA-TTTTACATGTTATATTGTTATGGATCGATACA
* *
6529621 TTTTCATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-ACGAAAGTAT
65 TTTT-ATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCACAAAAGTAT
** *
6529685 CGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACC
129 CGATACTTATATTAACGTATCGACACTTTCAATATATCCGGTAGCTCTTTACC
* * *
6529738 GGTTTTATCATTTCGAGACCTGTTTTGTCATATTCTTACTTGTTATATTGCTATGGATCGATACA
1 GGTTTTATCATTTCGAGACCGGTTTTGTCATATT-TTACATGTTATATTGTTATGGATCGATACA
*
6529803 TTTGTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCA-AAAAGTGT
65 TTT-TATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCACAAAAGTAT
6529867 CGATACTTATATTAACGTATCGACACTTTCAATATATCCGGTAGCTCTTTACC
129 CGATACTTATATTAACGTATCGACACTTTCAATATATCCGGTAGCTCTTTACC
* * * *
6529920 AGTTTTATCATTTCGTGACCGGTTTTGTCATACTTATACATGTTATATTGTTATGGATCGAAACG
1 GGTTTTATCATTTCGAGACCGGTTTTGTCATA-TTTTACATGTTATATTGTTATGGATCGATAC-
* * *
6529985 TTTTTATAAAGTATCGACACCTTATAGGCGCTATTACTTCTTCTCTTTTAAATTC
64 ATTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTC
6530040 CAGTAGCGGT
Statistics
Matches: 275, Mismatches: 22, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
181 2 0.01
182 266 0.97
183 7 0.03
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (181 bp):
GGTTTTATCATTTCGAGACCGGTTTTGTCATATTTTACATGTTATATTGTTATGGATCGATACAT
TTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCACAAAAGTATCG
ATACTTATATTAACGTATCGACACTTTCAATATATCCGGTAGCTCTTTACC
Found at i:6530881 original size:29 final size:29
Alignment explanation
Indices: 6530844--6530920 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
6530834 CCCCAACACA
* **
6530844 TAGGTCGCCATGCCCTCCGGGCAACCTTG
1 TAGGTCGCCATGCACTCCCAGCAACCTTG
* *
6530873 TAGGGCGCCATGCACTCCCAGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCAACCTTG
*
6530902 TAGGTCGCCATGTACTCCC
1 TAGGTCGCCATGCACTCCC
6530921 GACGACCAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.16, C:0.38, G:0.26, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCAACCTTG
Found at i:6531382 original size:21 final size:22
Alignment explanation
Indices: 6531361--6531409 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
6531351 ACAAAATTTT
6531361 AGTTAATTAGT-TTGTTAGTTTA
1 AGTT-ATTAGTATTGTTAGTTTA
*
6531383 AGTT-TTATTATTGTTAGTTTA
1 AGTTATTAGTATTGTTAGTTTA
6531404 AGTTAT
1 AGTTAT
6531410 ATCATACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (22 bp):
AGTTATTAGTATTGTTAGTTTA
Found at i:6531506 original size:28 final size:27
Alignment explanation
Indices: 6531467--6531519 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
6531457 ATATTAAAAA
6531467 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
6531495 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
6531520 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:6531525 original size:27 final size:29
Alignment explanation
Indices: 6531466--6531530 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
6531456 TATATTAAAA
6531466 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
6531495 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
6531521 AAATAGTTAA
1 AAATAATTAA
6531531 GTTATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:6531683 original size:18 final size:18
Alignment explanation
Indices: 6531660--6531714 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
6531650 AATAATTATT
6531660 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
6531678 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
6531690 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
6531707 TAAATTAG
1 TAAATTAG
6531715 AGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:6531768 original size:21 final size:21
Alignment explanation
Indices: 6531742--6531781 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6531732 GATAATGAGT
6531742 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
6531763 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
6531782 CATATAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:6532000 original size:370 final size:357
Alignment explanation
Indices: 6531288--6532023 Score: 880
Period size: 370 Copynumber: 2.0 Consensus size: 357
6531278 GTAAGTTTTT
* ** *
6531288 TAATTATTTAAATTAGTTTATTATTTTAAATTATTAGTTTGTTAGTTTATGGTTTAAGGTAAAAC
1 TAATTATTTAAATTAGTTTATTATTATAAATTATTAGTTAATTAGTTTATGATTTAAGGTAAAAC
** * * * *
6531353 AAAATTTTAGTTAATTAGTTTGTTAGTTTAAGTTTTATTATTGTTAGTTTAAGTTATATCATACA
66 AAAAAATTAGATAATGAGTTTGTTAGTTTAAATTATATTATTGTTAGTTTAAGTTATATCATACA
* * *
6531418 TAAATATAAAATTATTTAATTAGTTTGTTTGATGGTTATATATTAAAAAAATAATTAATTAGTGT
131 TAAATATAAAATTATTTAATTAGTATGTTTGATAGTTACATATTAAAAAAATAATTAATTAGTGT
*
6531483 GTTAGTTAGTCTAATATTTAATTAGTTTGTAGTTAGTTAAATAGTTAAGTTATATATATTTTGGT
196 GTTAGTTAGTATAATATTTAATTAGTTTGTAGTTAGTTAAATAGTTAA--TATATATATTTTGGT
*
6531548 TGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATTAGTAGTTTAAGTTTTATTATA
259 TGTTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATTAGTAG-TTAA----TATAATA
* *
6531613 ATAAAAAAATAGTTTATTAGTTTAAGTTATATAAAAGAA
319 ATAAAAAAATAGTTTATTAGTTAAAGTTACATAAAAGAA
* *
6531652 TAATTATTTAAATTAGTTTATTGTTATAAATTATTAGTTAATTAGTTTATTATTATAAATTAGAG
1 TAATTATTTAAATTAGTTTATTATTATAAATTATTAGTTAATTAGTTTATGATT-T--A--AG-G
6531717 TAAAACAAAAAATTAGATAATGAGTTTGTTAGTTTAAATTATATTATTGTTAGTTTAAGTTATAT
60 TAAAACAAAAAATTAGATAATGAGTTTGTTAGTTTAAATTATATTATTGTTAGTTTAAGTTATAT
*
6531782 CATATAGT-AATA-AAAATTTATTTAATTAGTATGTTTGATAGTTACATATTAATAAAAATAATT
125 CATACA-TAAATATAAAA-TTATTTAATTAGTATGTTTGATAGTTACATATTAA-AAAAATAATT
* * *
6531845 AGTTAGTTTGTTAGTCGTTAGTTATATATAAAAAAATATGTAATTAGTTT-TTGTTAGTTAAATA
187 AATTAGTGTGTTA---GTTAG-TATA-AT------AT-T-TAATTAGTTTGTAGTTAGTTAAATA
* *
6531909 GTTAA-AT-TATA-TTTGTTTGTTGAATTTATATTATATAAAAAATTTAGTTAATTAGGTTT-TT
239 GTTAATATATATATTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAATTA-GTTTATT
* * *
6531970 AGTAG-TAA-ATAATAAT-TAAAAATCGTTTATTAGTTAAAGTTACATTAAAGAA
303 AGTAGTTAATATAATAATAAAAAAATAGTTTATTAGTTAAAGTTACATAAAAGAA
6532022 TA
1 TA
6532024 GTTTATTAGT
Statistics
Matches: 321, Mismatches: 28, Indels: 40
0.83 0.07 0.10
Matches are distributed among these distances:
364 48 0.15
365 1 0.00
367 1 0.00
369 6 0.02
370 134 0.42
371 29 0.09
374 5 0.02
375 3 0.01
376 5 0.02
378 48 0.15
379 8 0.02
380 2 0.01
382 2 0.01
383 19 0.06
384 10 0.03
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (357 bp):
TAATTATTTAAATTAGTTTATTATTATAAATTATTAGTTAATTAGTTTATGATTTAAGGTAAAAC
AAAAAATTAGATAATGAGTTTGTTAGTTTAAATTATATTATTGTTAGTTTAAGTTATATCATACA
TAAATATAAAATTATTTAATTAGTATGTTTGATAGTTACATATTAAAAAAATAATTAATTAGTGT
GTTAGTTAGTATAATATTTAATTAGTTTGTAGTTAGTTAAATAGTTAATATATATATTTTGGTTG
TTGAATTTATATTATATAAAAAAATTAGTTAATTAGTTTATTAGTAGTTAATATAATAATAAAAA
AATAGTTTATTAGTTAAAGTTACATAAAAGAA
Found at i:6532030 original size:30 final size:30
Alignment explanation
Indices: 6531984--6532064 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
6531974 GTAAATAATA
*
6531984 ATTAAA-AATCGTTTATTAGTTAAAGTTAC
1 ATTAAAGAATAGTTTATTAGTTAAAGTTAC
*
6532013 ATTAAAGAATAGTTTATTAGTTAAAGTTAT
1 ATTAAAGAATAGTTTATTAGTTAAAGTTAC
6532043 ATTAAAGAATAGTTTATTAGTT
1 ATTAAAGAATAGTTTATTAGTT
6532065 GTTTAAGGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 6 0.12
30 43 0.88
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.43
Consensus pattern (30 bp):
ATTAAAGAATAGTTTATTAGTTAAAGTTAC
Found at i:6532031 original size:15 final size:15
Alignment explanation
Indices: 6532013--6532061 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
6532003 TTAAAGTTAC
6532013 ATTAAAGAATAGTTT
1 ATTAAAGAATAGTTT
***
6532028 ATTAGTTAA-AGTTAT
1 ATTAAAGAATAGTT-T
6532043 ATTAAAGAATAGTTT
1 ATTAAAGAATAGTTT
6532058 ATTA
1 ATTA
6532062 GTTGTTTAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (15 bp):
ATTAAAGAATAGTTT
Found at i:6534265 original size:5 final size:5
Alignment explanation
Indices: 6534255--6534677 Score: 687
Period size: 5 Copynumber: 86.4 Consensus size: 5
6534245 TTCATAAATC
6534255 ATAAT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT
6534307 AT-AT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6534354 ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6534401 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6534450 AT-AT ATAAT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT
6534500 ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT AT-AT A-ATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
6534547 AATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT
1 -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6534596 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6534646 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
6534678 TAACATTAAA
Statistics
Matches: 397, Mismatches: 0, Indels: 42
0.90 0.00 0.10
Matches are distributed among these distances:
3 6 0.02
4 37 0.09
5 338 0.85
6 7 0.02
7 9 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:6534942 original size:21 final size:20
Alignment explanation
Indices: 6534912--6534982 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
6534902 TTTATTTTTT
6534912 TTAAATATCAAATAAATTTG
1 TTAAATATCAAATAAATTTG
*
6534932 TTAATTAATC-AATCAAATTTG
1 TTAAAT-ATCAAAT-AAATTTG
*
6534953 TTAAATATAAAATAAA--T-
1 TTAAATATCAAATAAATTTG
6534970 TTAAATATCAAAT
1 TTAAATATCAAAT
6534983 TTATTAATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 12 0.27
18 1 0.02
20 13 0.30
21 18 0.41
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (20 bp):
TTAAATATCAAATAAATTTG
Found at i:6535075 original size:21 final size:19
Alignment explanation
Indices: 6535041--6535091 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
6535031 AATTAAACAA
6535041 AATATTTTTAAACAACAATT
1 AATATTTTTAAAC-ACAATT
*
6535061 AATATTTTTTTAACACAA-T
1 AATA-TTTTTAAACACAATT
*
6535080 -ATTTTTTTAAAC
1 AATATTTTTAAAC
6535092 GGGAATAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.30
18 2 0.07
19 1 0.04
20 8 0.30
21 8 0.30
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTTTTAAACACAATT
Found at i:6535590 original size:28 final size:30
Alignment explanation
Indices: 6535541--6535604 Score: 96
Period size: 28 Copynumber: 2.2 Consensus size: 30
6535531 TTTATATAAT
6535541 ATAATATAATATATAACTTAAACTAACAAA
1 ATAATATAATATATAACTTAAACTAACAAA
* *
6535571 CTAATAT-A-ATATAACTTAAACTAAGAAA
1 ATAATATAATATATAACTTAAACTAACAAA
6535599 ATAATA
1 ATAATA
6535605 ATTTATACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 24 0.77
29 1 0.03
30 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (30 bp):
ATAATATAATATATAACTTAAACTAACAAA
Found at i:6535611 original size:28 final size:28
Alignment explanation
Indices: 6535546--6535611 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
6535536 ATAATATAAT
*
6535546 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAAATA
*
6535574 AT-ATAATATAACTTAAACTAAGAAAATA
1 ATAAT-ATATAACTTAAACTAACAAAATA
*
6535602 ATAATTTATA
1 ATAATATATA
6535612 CTAACAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAAATA
Done.