Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 159 of 190
Found at i:46340538 original size:20 final size:20
Alignment explanation
Indices: 46340513--46340550 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46340503 TCCATATTTA
*
46340513 TTAATATCATTTTCTAAATT
1 TTAATACCATTTTCTAAATT
*
46340533 TTAATACCATTTTTTAAA
1 TTAATACCATTTTCTAAA
46340551 CATTTTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATACCATTTTCTAAATT
Found at i:46347542 original size:8 final size:8
Alignment explanation
Indices: 46347529--46347557 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
46347519 CACTAGAGAT
46347529 CAGTGTTA
1 CAGTGTTA
46347537 CAGTGTTA
1 CAGTGTTA
46347545 CAGTGTTA
1 CAGTGTTA
46347553 CAGTG
1 CAGTG
46347558 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:46347696 original size:22 final size:23
Alignment explanation
Indices: 46347644--46347718 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
46347634 AGTGTTATTG
46347644 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
46347667 CTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
46347690 -TCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
46347712 ATCAGTG
1 ATCAGTG
46347719 TGGCACTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 22 0.44
23 28 0.56
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:46350526 original size:107 final size:108
Alignment explanation
Indices: 46350397--46350662 Score: 399
Period size: 107 Copynumber: 2.5 Consensus size: 108
46350387 GGTAGAACAG
* * *
46350397 TCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCC
1 TCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTAACC
* *
46350462 TATAGAGGTATTTCGGTTATTTTACCCTATA-GGGTATTTTGA
66 TATAGAGGTATTTCAGTTATTTTACCCTATAGGGGTATTTCGA
* * * *
46350504 TCATTTTACCCTATGGGGGTATTTCAGTTATTTTACCCTATGAGGGTATTTCAGTCATTTTAACC
1 TCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTAACC
*
46350569 TATAGGGGTATTTCAGTTATTTTACCCTATAGGGGTATTTCGA
66 TATAGAGGTATTTCAGTTATTTTACCCTATAGGGGTATTTCGA
* * * *
46350612 TTATTTAACCCTATAGGGGTATATCAGACATTTTACCCTATGGGGGTATTT
1 TCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTT
46350663 TGGTTATTTA
Statistics
Matches: 141, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
107 87 0.62
108 54 0.38
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (108 bp):
TCATTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTAACC
TATAGAGGTATTTCAGTTATTTTACCCTATAGGGGTATTTCGA
Found at i:46350671 original size:27 final size:27
Alignment explanation
Indices: 46350394--46350662 Score: 330
Period size: 27 Copynumber: 10.0 Consensus size: 27
46350384 AGGGGTAGAA
*
46350394 CAGTCATTTTACCCTTTAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* *
46350421 CGGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* *
46350448 CAGTCATTCTACCCTATAGAGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* *
46350475 CGGTTATTTTACCCTATA-GGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* *
46350501 -TGATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATAGGGGTATTT
*
46350528 CAGTTATTTTACCCTAT-GAGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTT
*
46350555 CAGTCATTTTAACCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
*
46350582 CAGTTATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* * *
46350609 C-GATTATTTAACCCTATAGGGGTATAT
1 CAG-TCATTTTACCCTATAGGGGTATTT
* *
46350636 CAGACATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
46350663 TGGTTATTTA
Statistics
Matches: 208, Mismatches: 27, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
25 1 0.00
26 22 0.11
27 182 0.88
28 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTATAGGGGTATTT
Found at i:46353766 original size:23 final size:23
Alignment explanation
Indices: 46353722--46353780 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
46353712 CAATCTTGGG
46353722 ATGATTTGT-AATCTTAGAAGAT
1 ATGATTTGTAAATCTTAGAAGAT
46353744 ATGATTCTGTAAATCTTAG-AGAT
1 ATGATT-TGTAAATCTTAGAAGAT
*
46353767 TTGATTTTGTAAAT
1 ATGA-TTTGTAAAT
46353781 AGTTAATCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 6 0.18
23 17 0.52
24 10 0.30
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (23 bp):
ATGATTTGTAAATCTTAGAAGAT
Found at i:46364730 original size:43 final size:43
Alignment explanation
Indices: 46364669--46364767 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
46364659 CAGTGTTTAT
**
46364669 GTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATTTC
1 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTTC
* *
46364712 GTGTAGGACCATAGCTGGGCTATTGGCATTGATACGAGATTTCC
1 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTT-C
*
46364756 ATGTAAGACCAT
1 GTGTAAGACCAT
46364768 GTCTGGGACA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 38 0.78
44 11 0.22
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTTC
Found at i:46372305 original size:25 final size:25
Alignment explanation
Indices: 46372275--46372376 Score: 64
Period size: 25 Copynumber: 3.8 Consensus size: 25
46372265 AGCTCTTATT
46372275 AGCTTCCCGATTATGGCTCTTTGTG
1 AGCTTCCCGATTATGGCTCTTTGTG
* * * *
46372300 AGCTTCCTGA-TAAGGCTCACTTGAACTTCA
1 AGCTTCCCGATTATGGCTC-TTTG----T-G
*
46372330 AGCTATCCCGATTATGGCCCTTTGTG
1 AGCT-TCCCGATTATGGCTCTTTGTG
*
46372356 AGCTTCCTG-TTAATGGCTCTT
1 AGCTTCCCGATT-ATGGCTCTT
46372377 CGGAGCTACC
Statistics
Matches: 57, Mismatches: 11, Indels: 18
0.66 0.13 0.21
Matches are distributed among these distances:
24 9 0.16
25 24 0.42
26 4 0.07
27 1 0.02
29 1 0.02
30 4 0.07
31 8 0.14
32 6 0.11
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (25 bp):
AGCTTCCCGATTATGGCTCTTTGTG
Found at i:46377001 original size:26 final size:26
Alignment explanation
Indices: 46376941--46377006 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
46376931 ACACCTTAGT
* *
46376941 TCTT-ATGAGCATCCCGATATATGGC
1 TCTTCATGAGCTTCCCGATAAATGGC
*
46376966 TCTTCATGAGCTTCCCGTTAAATGGC
1 TCTTCATGAGCTTCCCGATAAATGGC
**
46376992 TCTTTGTGAGCTTCC
1 TCTTCATGAGCTTCC
46377007 TAATATAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (26 bp):
TCTTCATGAGCTTCCCGATAAATGGC
Found at i:46378293 original size:117 final size:115
Alignment explanation
Indices: 46378059--46378303 Score: 364
Period size: 117 Copynumber: 2.1 Consensus size: 115
46378049 ACGGGCAGAG
* *
46378059 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACAGCCATGCGTACGAACATGTGGTTGGATGTG
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACAGCCATGCGCACGAACATGTGGTTGGACGTG
*
46378124 TGTACCCTGCACCTAATTTTTTAAAAATTTAATTGTTCACACGGCCTAGC
66 TGTACCCTGCACCTAATTTTTTAAAAATTTAATTGTTCACACAGCCTAGC
* * * * *
46378174 ACACGGGCGTGTGTCTCAGTCGTGTGTGACACATAGCCATGCGCACGAGCGTGTGGTTTGGCCGT
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACAGCCATGCGCACGAACATGTGG-TTGGACGT
* * *
46378239 GTGTCCCCCTGCACCTAATTTTTTGAAAATTTAATTGTTTACACAGCCTAGC
65 GTGT-ACCCTGCACCTAATTTTTTAAAAATTTAATTGTTCACACAGCCTAGC
*
46378291 ACACGGGCTTGTG
1 ACACGGGCGTGTG
46378304 GCTGGCCGTG
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 51 0.44
116 10 0.09
117 55 0.47
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (115 bp):
ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACAGCCATGCGCACGAACATGTGGTTGGACGTG
TGTACCCTGCACCTAATTTTTTAAAAATTTAATTGTTCACACAGCCTAGC
Found at i:46380289 original size:24 final size:25
Alignment explanation
Indices: 46380260--46380325 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 25
46380250 GAAGTTCACA
* *
46380260 AAGAGCCTA-TAACGGGTAACTCTG
1 AAGAGCCAATTAACGGGTAACTCCG
*
46380284 AAGAG-CAATTAACGGGTAGCTCCG
1 AAGAGCCAATTAACGGGTAACTCCG
46380308 AAGAG-CAATTAACGGGTA
1 AAGAGCCAATTAACGGGTA
46380326 GCACCAGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 2 0.05
24 36 0.95
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (25 bp):
AAGAGCCAATTAACGGGTAACTCCG
Found at i:46380326 original size:24 final size:24
Alignment explanation
Indices: 46380269--46380327 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
46380259 AAAGAGCCTA
* *
46380269 TAACGGGTAACTCTGAAGAGCAAT
1 TAACGGGTAGCTCCGAAGAGCAAT
46380293 TAACGGGTAGCTCCGAAGAGCAAT
1 TAACGGGTAGCTCCGAAGAGCAAT
46380317 TAACGGGTAGC
1 TAACGGGTAGC
46380328 ACCAGATAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (24 bp):
TAACGGGTAGCTCCGAAGAGCAAT
Found at i:46380433 original size:26 final size:25
Alignment explanation
Indices: 46380400--46380459 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
46380390 AAGGGAAGCT
*
46380400 CTCA-AAGAGCC-TTTAATCGGGAAG
1 CTCATAAGAGCCATATAAT-GGGAAG
*
46380424 CTCATGAAGAGCCATATAATGGGATG
1 CTCAT-AAGAGCCATATAATGGGAAG
46380450 CTCATAAGAG
1 CTCATAAGAG
46380460 TTGTGGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.13
25 5 0.16
26 17 0.55
27 5 0.16
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (25 bp):
CTCATAAGAGCCATATAATGGGAAG
Found at i:46400435 original size:7 final size:7
Alignment explanation
Indices: 46400425--46400456 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
46400415 ATTTTTATTT
46400425 TTTTGAA
1 TTTTGAA
46400432 TTTTGAA
1 TTTTGAA
46400439 TTTTGAA
1 TTTTGAA
46400446 TTTTGAA
1 TTTTGAA
46400453 TTTT
1 TTTT
46400457 TAAGAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTTGAA
Found at i:46400753 original size:20 final size:19
Alignment explanation
Indices: 46400728--46400785 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
46400718 AATTAATAAA
46400728 AAACTATTAATATAAGTATT
1 AAACTATTAATATAA-TATT
*
46400748 AAACTA--AATTTAATATT
1 AAACTATTAATATAATATT
*
46400765 AAATCTATTAAAATAATATT
1 AAA-CTATTAATATAATATT
46400785 A
1 A
46400786 TTTTTGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 7 0.22
18 9 0.28
20 16 0.50
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AAACTATTAATATAATATT
Found at i:46402655 original size:19 final size:19
Alignment explanation
Indices: 46402626--46402677 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
46402616 CACATTGTAG
*
46402626 AAATAAATTAAAAAATAAA
1 AAATAATTTAAAAAATAAA
* *
46402645 AAAT-ATTTTAAAAATATA
1 AAATAATTTAAAAAATAAA
*
46402663 AATTAATTTAAAAAA
1 AAATAATTTAAAAAA
46402678 GTATAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAATTTAAAAAATAAA
Found at i:46402685 original size:19 final size:19
Alignment explanation
Indices: 46402633--46402683 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
46402623 TAGAAATAAA
* *
46402633 TTAAAAAATAAAAAAT-AT
1 TTAAAAAATATAAATTAAT
*
46402651 TTTAAAAATATAAATTAAT
1 TTAAAAAATATAAATTAAT
46402670 TTAAAAAAGTATAA
1 TTAAAAAA-TATAA
46402684 TTTTTTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.48
19 9 0.33
20 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAAAAATATAAATTAAT
Found at i:46403986 original size:2 final size:2
Alignment explanation
Indices: 46403941--46403974 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46403931 GATTGAATGA
46403941 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
46403975 GAAGAGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46405535 original size:6 final size:5
Alignment explanation
Indices: 46405523--46405602 Score: 97
Period size: 6 Copynumber: 14.6 Consensus size: 5
46405513 CATTTTATTG
46405523 TTTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TTTAT TTTAT
1 TTTAT T-TTAT T-TTAT T-TTAT T-TTAT T-TTAT T-TTAT TTTAT TTTAT
46405574 TTTAT TTTAT TTTAT TTTAT TTTGAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTT-AT TTT
46405603 TCTCTTTTCG
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
5 33 0.45
6 40 0.55
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:46405538 original size:9 final size:9
Alignment explanation
Indices: 46405524--46405594 Score: 100
Period size: 9 Copynumber: 8.6 Consensus size: 9
46405514 ATTTTATTGT
46405524 TTATTATTA
1 TTATTATTA
46405533 TTATTATTA
1 TTATTATTA
46405542 TTATTATTA
1 TTATTATTA
46405551 TTATTATTA
1 TTATTATTA
46405560 TTATT-TTA
1 TTATTATTA
46405568 TT-TTATT-
1 TTATTATTA
46405575 TTATT-TTA
1 TTATTATTA
46405583 TT-TTATT-
1 TTATTATTA
46405590 TTATT
1 TTATT
46405595 TTGATTTTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
7 10 0.18
8 15 0.26
9 32 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTATTA
Found at i:46405544 original size:15 final size:15
Alignment explanation
Indices: 46405524--46405594 Score: 100
Period size: 15 Copynumber: 5.1 Consensus size: 15
46405514 ATTTTATTGT
46405524 TTATTATTATTATTA
1 TTATTATTATTATTA
46405539 TTATTATTATTATTA
1 TTATTATTATTATTA
46405554 TTATTATTATT-TTA
1 TTATTATTATTATTA
46405568 TT-TTATT-TTATT-
1 TTATTATTATTATTA
46405580 TTATT-TTATT-TTA
1 TTATTATTATTATTA
46405593 TT
1 TT
46405595 TTGATTTTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.15
13 13 0.25
14 5 0.10
15 26 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:46413676 original size:21 final size:21
Alignment explanation
Indices: 46413638--46413766 Score: 91
Period size: 21 Copynumber: 6.1 Consensus size: 21
46413628 ACATTAGTGC
* * *
46413638 TAAACAGAAACTCGTAAGGGT
1 TAAACGGAAACTCATAAGAGT
* *
46413659 TAAACGGAAGCTCATAAGAGC
1 TAAACGGAAACTCATAAGAGT
*
46413680 TAAACGGAAACCCATAA-AGGT
1 TAAACGGAAACTCATAAGA-GT
* * * *
46413701 TAAACTGAAGCTCAAAAGAGC
1 TAAACGGAAACTCATAAGAGT
* * * *
46413722 TAAACTGAAACCCAAAAGGGT
1 TAAACGGAAACTCATAAGAGT
*
46413743 TAAACTGG-AACTCATATGAGT
1 TAAAC-GGAAACTCATAAGAGT
46413764 TAA
1 TAA
46413767 CTGAAGCTCA
Statistics
Matches: 83, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.01
21 80 0.96
22 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (21 bp):
TAAACGGAAACTCATAAGAGT
Found at i:46413702 original size:42 final size:42
Alignment explanation
Indices: 46413636--46413758 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
46413626 TCACATTAGT
* * *
46413636 GCTAAACAGAAACTCGTAAGGGTTAAACGGAAGCTCATAAGA
1 GCTAAACAGAAACCCATAAAGGTTAAACGGAAGCTCATAAGA
* * *
46413678 GCTAAACGGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACAGAAACCCATAAAGGTTAAACGGAAGCTCATAAGA
*
46413720 GCTAAACTGAAACCCA-AAAGGGTTAAACTGGAA-CTCATA
1 GCTAAACAGAAACCCATAAA-GGTTAAAC-GGAAGCTCATA
46413759 TGAGTTAACT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 3 0.04
42 64 0.91
43 3 0.04
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (42 bp):
GCTAAACAGAAACCCATAAAGGTTAAACGGAAGCTCATAAGA
Found at i:46416557 original size:106 final size:106
Alignment explanation
Indices: 46416372--46416584 Score: 363
Period size: 106 Copynumber: 2.0 Consensus size: 106
46416362 AAAATAAGCA
46416372 TTCTTATTTTCGAGAATTCGAGACATCGTGCCCTAACTTACGAGACATGATTTTCTTCCCGATTA
1 TTCTTATTTTCGAGAATTCGAGACATCGTGCCCTAACTTACGAGACATGATTTTCTTCCCGATTA
*
46416437 ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
66 ACTCAAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
* * * *
46416478 TTCTTATTTTTGGGAATTCGAGACATCGTGTCCTAACTTACGAGATATGATTTTCTTCCCGATTA
1 TTCTTATTTTCGAGAATTCGAGACATCGTGCCCTAACTTACGAGACATGATTTTCTTCCCGATTA
* *
46416543 ACTCAAAATACGAAGGCATTTTTCATAAAATTTGATTTAAT
66 ACTCAAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
46416584 T
1 T
46416585 AGTGCTATTT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (106 bp):
TTCTTATTTTCGAGAATTCGAGACATCGTGCCCTAACTTACGAGACATGATTTTCTTCCCGATTA
ACTCAAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
Found at i:46424202 original size:27 final size:27
Alignment explanation
Indices: 46424167--46424218 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
46424157 ATAGAGTATT
* *
46424167 TATTCATTTATCGATAAATTAATAAAA
1 TATTAATTTATCGATAAACTAATAAAA
46424194 TATTAATTTATCGATAAACTAATAA
1 TATTAATTTATCGATAAACTAATAA
46424219 CCTCGATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (27 bp):
TATTAATTTATCGATAAACTAATAAAA
Found at i:46427006 original size:26 final size:26
Alignment explanation
Indices: 46426951--46427022 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
46426941 TGAAGGAAGT
* * *
46426951 ATACTGTTACTGGCAGCGTTGCTACG
1 ATACTGTTACTGGCAGCTTTGATACA
* *
46426977 ATACTGTTACTGGTAGCTTTGATGCA
1 ATACTGTTACTGGCAGCTTTGATACA
* *
46427003 ATACTATTACTAGCAGCTTT
1 ATACTGTTACTGGCAGCTTT
46427023 CCTGTGATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGATACA
Found at i:46427202 original size:27 final size:28
Alignment explanation
Indices: 46427142--46427203 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
46427132 ATACTGATAT
* * *
46427142 TGTATTGGGCTAAGGCCCACATTATTAT
1 TGTACTGGGCTAAGGCCCACACTATTAC
46427170 TGTACTGGGCTAAGG-CCACACTA-TAC
1 TGTACTGGGCTAAGGCCCACACTATTAC
46427196 TGTTACTG
1 TG-TACTG
46427204 AATAGGGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 12 0.40
28 14 0.47
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
TGTACTGGGCTAAGGCCCACACTATTAC
Found at i:46431573 original size:2 final size:2
Alignment explanation
Indices: 46431522--46431556 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46431512 AATATAATGC
46431522 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 A
46431557 AATGAGGTAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46437407 original size:26 final size:26
Alignment explanation
Indices: 46437377--46437457 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
46437367 TGGAGGAAGT
*
46437377 ATACTGTTACTGGCAGCGTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
46437403 ATACTGTTGCTGGCAACTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
46437429 ATACTATTATTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
46437455 ATA
1 ATA
46437458 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:46437413 original size:14 final size:14
Alignment explanation
Indices: 46437394--46437433 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
46437384 TACTGGCAGC
46437394 GTTGCTGCGATACT
1 GTTGCTGCGATACT
46437408 GTTGCTG-GCA-ACT
1 GTTGCTGCG-ATACT
46437421 -TTGCTGCGATACT
1 GTTGCTGCGATACT
46437434 ATTATTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.30
13 8 0.35
14 8 0.35
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.35
Consensus pattern (14 bp):
GTTGCTGCGATACT
Found at i:46439682 original size:24 final size:23
Alignment explanation
Indices: 46439629--46439684 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
46439619 ATTTTTTTTC
46439629 AAATTATTTACATAATGAAAAAT
1 AAATTATTTACATAATGAAAAAT
46439652 AAGATTATTT-CAATTAAT-AAATAAT
1 AA-ATTATTTAC-A-TAATGAAA-AAT
46439677 AAATTATT
1 AAATTATT
46439685 AATTTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 3 0.10
24 17 0.59
25 9 0.31
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATTATTTACATAATGAAAAAT
Found at i:46441538 original size:19 final size:21
Alignment explanation
Indices: 46441504--46441551 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
46441494 TAATACATTT
46441504 TTTTAAATTATTATCAATATG
1 TTTTAAATTATTATCAATATG
46441525 TTTTAAA-T-TTATCAATATTG
1 TTTTAAATTATTATCAATA-TG
*
46441545 TTATAAA
1 TTTTAAA
46441552 AATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
TTTTAAATTATTATCAATATG
Found at i:46443446 original size:34 final size:35
Alignment explanation
Indices: 46443402--46443468 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
46443392 CAGTAAAATA
*
46443402 TTTTCCGTAAAATGATTT-CAGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
* *
46443436 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTT
46443469 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
Found at i:46444092 original size:17 final size:17
Alignment explanation
Indices: 46444038--46444096 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
46444028 TTATGTCTAC
46444038 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
* *
46444055 TAAATTTCACATT-TTGTAT
1 T--ATTT-ATATTATTGAAT
46444074 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
46444091 TATTTA
1 TATTTA
46444097 ATCATGCTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.12
17 16 0.47
19 10 0.29
20 4 0.12
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:46444264 original size:18 final size:18
Alignment explanation
Indices: 46444227--46444264 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
46444217 TAAAAATCAC
*
46444227 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAAAAT
46444245 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTACATTT-AAAAT
46444263 AT
1 AT
46444265 ATGGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:46444393 original size:19 final size:19
Alignment explanation
Indices: 46444369--46444406 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
46444359 AAAGTTAATA
46444369 ACAAATTTAATTACGGTGG
1 ACAAATTTAATTACGGTGG
*
46444388 ACAAATTTTATTACGGTGG
1 ACAAATTTAATTACGGTGG
46444407 GTGGTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (19 bp):
ACAAATTTAATTACGGTGG
Found at i:46452133 original size:20 final size:21
Alignment explanation
Indices: 46452108--46452163 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
46452098 CGAAAATTTT
*
46452108 GAAACACGAGATTTT-TTTAG
1 GAAACACGAAATTTTCTTTAG
**
46452128 GAAACAC-AAATTTTCTTTTT
1 GAAACACGAAATTTTCTTTAG
46452148 GAAACACGAAAATTTT
1 GAAACACG-AAATTTT
46452164 TAAAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.20
20 17 0.57
22 7 0.23
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
GAAACACGAAATTTTCTTTAG
Found at i:46452180 original size:16 final size:17
Alignment explanation
Indices: 46452143--46452179 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
46452133 ACAAATTTTC
*
46452143 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
46452160 TTTTTAAAACAC--AAA
1 TTTTTAAAACACGAAAA
46452175 TTTTT
1 TTTTT
46452180 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:46452184 original size:37 final size:39
Alignment explanation
Indices: 46452104--46452188 Score: 120
Period size: 37 Copynumber: 2.2 Consensus size: 39
46452094 AAAACGAAAA
**
46452104 TTTTGAAACACGAGATTTTTTTAGGAAACACAAATTTTCT
1 TTTTGAAACACGAGAAATTTTTA-GAAACACAAATTTTCT
*
46452144 TTTTGAAACACGA-AAATTTTTA-AAACACAAATTTTTT
1 TTTTGAAACACGAGAAATTTTTAGAAACACAAATTTTCT
46452181 TTTTGAAA
1 TTTTGAAA
46452189 ACATAATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 22 0.52
39 7 0.17
40 13 0.31
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (39 bp):
TTTTGAAACACGAGAAATTTTTAGAAACACAAATTTTCT
Found at i:46452255 original size:17 final size:17
Alignment explanation
Indices: 46452229--46452466 Score: 129
Period size: 17 Copynumber: 13.3 Consensus size: 17
46452219 GAGGATTTTT
46452229 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* **
46452246 TTTATGAAACACGGTCAATT
1 TTTTTGAAACAC-G--AAAA
*
46452266 TTTTTGAAAATACGAAAA
1 TTTTTG-AAACACGAAAA
* * * **
46452284 TTTTTGAAAGATGGGATT
1 TTTTTGAAACA-CGAAAA
*
46452302 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* *
46452320 TTTATGAAACACGGAAATT
1 TTTTTGAAACAC-GAAA-A
*
46452339 TTTTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* * *
46452357 TTTTCGAAATACG-AGA
1 TTTTTGAAACACGAAAA
* *
46452373 CTTTTGAAAACAAGGAAAA
1 TTTTTG-AAAC-ACGAAAA
*
46452392 TTTTTTGAAAACACGACAA
1 -TTTTTG-AAACACGAAAA
*
46452411 TTTTTGAAACACCG-GAA
1 TTTTTGAAACA-CGAAAA
** *
46452428 TTTTAAAAACACGAAGA
1 TTTTTGAAACACGAAAA
46452445 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
46452462 TTTTT
1 TTTTT
46452467 TTAAAACACG
Statistics
Matches: 164, Mismatches: 42, Indels: 30
0.69 0.18 0.13
Matches are distributed among these distances:
16 8 0.05
17 65 0.40
18 43 0.26
19 20 0.12
20 23 0.14
21 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:46452289 original size:18 final size:18
Alignment explanation
Indices: 46452229--46452476 Score: 129
Period size: 18 Copynumber: 13.8 Consensus size: 18
46452219 GAGGATTTTT
46452229 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
46452246 TTTATG-AAACACGGTCAATT
1 TTTTTGAAAACAC-G--AAAA
*
46452266 TTTTTGAAAATACGAAAA
1 TTTTTGAAAACACGAAAA
** * **
46452284 TTTTTGAAAGA-TGGGATT
1 TTTTTGAAA-ACACGAAAA
*
46452302 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
* *
46452320 TTTATG-AAACACGGAAATT
1 TTTTTGAAAACAC-GAAA-A
*
46452339 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * *
46452357 TTTTCG-AAATACG-AGA
1 TTTTTGAAAACACGAAAA
* *
46452373 CTTTTGAAAACAAGGAAAA
1 TTTTTGAAAAC-ACGAAAA
*
46452392 TTTTTTGAAAACACGACAA
1 -TTTTTGAAAACACGAAAA
*
46452411 TTTTTG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
* *
46452428 -TTTTAAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
46452445 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
46452462 TTTTTTTAAAACACG
1 -TTTTTGAAAACACG
46452477 GAAACACGAA
Statistics
Matches: 171, Mismatches: 41, Indels: 36
0.69 0.17 0.15
Matches are distributed among these distances:
16 12 0.07
17 49 0.29
18 58 0.34
19 24 0.14
20 23 0.13
21 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:46452303 original size:36 final size:37
Alignment explanation
Indices: 46452227--46452359 Score: 171
Period size: 36 Copynumber: 3.6 Consensus size: 37
46452217 ACGAGGATTT
*
46452227 TTTTTTTG-AAACACGAAAATTTATGAAACACGGTCAA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGG-AAA
* * * * *
46452264 TTTTTTTGAAAATACGAAAATTTTTGAAAGATGG-GA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGGAAA
*
46452300 TTTTTTTGAAAACACGGAAATTTATGAAACACGGAAA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGGAAA
*
46452337 TTTTTTTGAAAACAAGAAAATTT
1 TTTTTTTGAAAACACGAAAATTT
46452360 TCGAAATACG
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
36 30 0.37
37 30 0.37
38 21 0.26
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.35
Consensus pattern (37 bp):
TTTTTTTGAAAACACGAAAATTTATGAAACACGGAAA
Found at i:46452313 original size:74 final size:72
Alignment explanation
Indices: 46452227--46452365 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 72
46452217 ACGAGGATTT
* * * *
46452227 TTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAATACGAAAATTTTTGAA
1 TTTTTTTGAAACACGAAAATTTATGAAACACGG-AAATTTTTTTGAAAACAAGAAAATTTTCGAA
46452292 AGATGGGA
65 AGATGGGA
*
46452300 TTTTTTTGAAAACACGGAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAATTTTCGAA
1 TTTTTTTG-AAACACGAAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAATTTTCGAA
46452365 A
65 A
46452366 TACGAGACTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 36 0.60
74 24 0.40
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (72 bp):
TTTTTTTGAAACACGAAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAATTTTCGAAA
GATGGGA
Found at i:46452437 original size:54 final size:53
Alignment explanation
Indices: 46452302--46452466 Score: 158
Period size: 54 Copynumber: 3.1 Consensus size: 53
46452292 AGATGGGATT
* * * * *
46452302 TTTTTGAAAACACGGAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAA
1 TTTTTGAAAAC-CGGAATTTTA-AAAACAAGGAAAATTTTTTGAAAACACGAAAA
* * * *
46452357 TTTTCGAAATA-CGAGACTTTTGAAAACAAGGAAAATTTTTTGAAAACACGACAA
1 TTTTTGAAA-ACCG-GAATTTTAAAAACAAGGAAAATTTTTTGAAAACACGAAAA
* *
46452411 TTTTTGAAACACCGGAATTTTAAAAAC-ACGAAGA-TTTTTG-AAACACGAAAA
1 TTTTTGAAA-ACCGGAATTTTAAAAACAAGGAAAATTTTTTGAAAACACGAAAA
46452462 TTTTT
1 TTTTT
46452467 TTAAAACACG
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
51 15 0.16
52 6 0.07
53 5 0.05
54 49 0.54
55 15 0.16
56 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (53 bp):
TTTTTGAAAACCGGAATTTTAAAAACAAGGAAAATTTTTTGAAAACACGAAAA
Found at i:46452576 original size:20 final size:19
Alignment explanation
Indices: 46452551--46452704 Score: 99
Period size: 20 Copynumber: 8.3 Consensus size: 19
46452541 TTCACGAGAG
46452551 TTTTTTTGAAACACGAAAAA
1 TTTTTTTGAAACACG-AAAA
46452571 TTTTTTTGAAACACGAAAA
1 TTTTTTTGAAACACGAAAA
* **
46452590 --TTTATGAAACACGGTCAA
1 TTTTTTTGAAACAC-GAAAA
46452608 TTTTTTTGAAAACACGAAAA
1 TTTTTTTG-AAACACGAAAA
* **
46452628 --TTTTTGAAAGACG-GGA
1 TTTTTTTGAAACACGAAAA
* *
46452644 TATTTTTGAAAACACGGAAA
1 TTTTTTTG-AAACACGAAAA
* *
46452664 --TTTATGAAACACG-GAA
1 TTTTTTTGAAACACGAAAA
* *
46452680 TTTTGTTGTAAACAAGAAAA
1 TTTTTTTG-AAACACGAAAA
46452700 TTTTT
1 TTTTT
46452705 GAAATACGAG
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
16 3 0.03
17 24 0.23
18 24 0.23
19 16 0.16
20 30 0.29
21 6 0.06
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (19 bp):
TTTTTTTGAAACACGAAAA
Found at i:46452598 original size:37 final size:36
Alignment explanation
Indices: 46452569--46452708 Score: 174
Period size: 36 Copynumber: 3.9 Consensus size: 36
46452559 AAACACGAAA
46452569 AATTTTTTTG-AAACACGAAAATTTATGAAACACGG
1 AATTTTTTTGAAAACACGAAAATTTATGAAACACGG
* *
46452604 TCAATTTTTTTGAAAACACGAAAATTTTTGAAAGACGG
1 --AATTTTTTTGAAAACACGAAAATTTATGAAACACGG
* * *
46452642 GATATTTTTGAAAACACGGAAATTTATGAAACACGG
1 AATTTTTTTGAAAACACGAAAATTTATGAAACACGG
* * * *
46452678 AATTTTGTTGTAAACAAGAAAATTTTTGAAA
1 AATTTTTTTGAAAACACGAAAATTTATGAAA
46452709 TACGAGACTT
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
36 55 0.62
37 10 0.11
38 23 0.26
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (36 bp):
AATTTTTTTGAAAACACGAAAATTTATGAAACACGG
Found at i:46452633 original size:18 final size:17
Alignment explanation
Indices: 46452553--46452795 Score: 139
Period size: 17 Copynumber: 13.5 Consensus size: 17
46452543 CACGAGAGTT
46452553 TTTTTGAAACACGAAAAA
1 TTTTTGAAACACG-AAAA
46452571 TTTTTTTGAAACACGAAAA
1 --TTTTTGAAACACGAAAA
* **
46452590 TTTATGAAACACGGTCAATT
1 TTTTTGAAACAC-G--AAAA
46452610 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* * *
46452628 TTTTTGAAAGACGGGATA
1 TTTTTGAAACAC-GAAAA
*
46452646 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* * *
46452664 TTTATGAAACACGGAAT
1 TTTTTGAAACACGAAAA
*
46452681 TTTGTTGTAAACAAGAAAA
1 TTT-TTG-AAACACGAAAA
* *
46452700 TTTTTGAAATACG-AGA
1 TTTTTGAAACACGAAAA
* * *
46452716 CTTTTGAAAAGAAGGAAAA
1 TTTTTG-AAA-CACGAAAA
* ** *
46452735 TTTTTTATTCACGAGAA
1 TTTTTGAAACACGAAAA
*
46452752 TTTTTGAAACACGAAGAT
1 TTTTTGAAACACGAA-AA
*
46452770 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
46452788 -TTTTGAAA
1 TTTTTGAAA
46452796 ACATGAATTT
Statistics
Matches: 172, Mismatches: 38, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
16 10 0.06
17 58 0.34
18 43 0.25
19 34 0.20
20 21 0.12
21 6 0.03
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:46452657 original size:36 final size:35
Alignment explanation
Indices: 46452572--46452798 Score: 160
Period size: 36 Copynumber: 6.4 Consensus size: 35
46452562 CACGAAAAAT
46452572 TTTTTTG-AAACACGAAAATTTATGAAACACGGTCAA
1 TTTTTTGAAAACACGAAAATTTATGAAACACGG--AA
* * *
46452608 TTTTTTTGAAAACACGAAAATTTTTGAAAGACGGGA
1 -TTTTTTGAAAACACGAAAATTTATGAAACACGGAA
*
46452644 TATTTTTGAAAACACGGAAATTTATGAAACACGGAA
1 T-TTTTTGAAAACACGAAAATTTATGAAACACGGAA
* * * *
46452680 TTTTGTTGTAAACAAGAAAATTTTTGAAATAC-GAGA
1 TTTT-TTGAAAACACGAAAATTTATGAAACACGGA-A
* * * * * **
46452716 -CTTTTGAAAAGAAGGAAAATTTTTTATTCACGAGAA
1 TTTTTTGAAAA-CACGAAAATTTATGAAACACG-GAA
* *
46452752 -TTTTTG-AAACACGAAGATTTTTTGAAAACACGGAA
1 TTTTTTGAAAACACGAA-AATTTATG-AAACACGGAA
*
46452787 -ATTTTGAAAACA
1 TTTTTTGAAAACA
46452799 TGAATTTTTT
Statistics
Matches: 152, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
34 10 0.07
35 39 0.26
36 71 0.47
37 9 0.06
38 23 0.15
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (35 bp):
TTTTTTGAAAACACGAAAATTTATGAAACACGGAA
Found at i:46452755 original size:72 final size:71
Alignment explanation
Indices: 46452574--46452733 Score: 189
Period size: 72 Copynumber: 2.2 Consensus size: 71
46452564 CGAAAAATTT
* * * *
46452574 TTTTG-AAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAATTTTTGAAAG
1 TTTTGAAAACAAGGAAATTTATGAAACACGG--AATTTTGTTGAAAACAAGAAAATTTTTGAAAG
* *
46452638 ACGGGATAT
64 AC-GGAGAC
* * *
46452647 TTTTGAAAACACGGAAATTTATGAAACACGGAATTTTGTTGTAAACAAGAAAATTTTTGAAATAC
1 TTTTGAAAACAAGGAAATTTATGAAACACGGAATTTTGTTGAAAACAAGAAAATTTTTGAAAGAC
46452712 -GAGAC
66 GGAGAC
*
46452717 TTTTGAAAAGAAGGAAA
1 TTTTGAAAACAAGGAAA
46452734 ATTTTTTATT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
70 18 0.23
72 30 0.39
73 5 0.06
74 24 0.31
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (71 bp):
TTTTGAAAACAAGGAAATTTATGAAACACGGAATTTTGTTGAAAACAAGAAAATTTTTGAAAGAC
GGAGAC
Found at i:46453402 original size:14 final size:14
Alignment explanation
Indices: 46453380--46453416 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
46453370 ACTAGGCCGA
*
46453380 AGCTGCTGGGCTGG
1 AGCTGCTGGGCTGC
*
46453394 AGCTACTGGGCTGC
1 AGCTGCTGGGCTGC
46453408 AGCTGCTGG
1 AGCTGCTGG
46453417 ACTACTGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (14 bp):
AGCTGCTGGGCTGC
Found at i:46453482 original size:12 final size:12
Alignment explanation
Indices: 46453465--46453507 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
46453455 GCTGCGCTGG
46453465 GCCTGGCCTGCT
1 GCCTGGCCTGCT
46453477 GCCTGG-CTGCT
1 GCCTGGCCTGCT
**
46453488 GGAGTGGCCTGCT
1 -GCCTGGCCTGCT
46453501 GCCTGGC
1 GCCTGGC
46453508 TGTTGGGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.20
12 15 0.60
13 5 0.20
ACGTcount: A:0.02, C:0.35, G:0.40, T:0.23
Consensus pattern (12 bp):
GCCTGGCCTGCT
Found at i:46453637 original size:19 final size:20
Alignment explanation
Indices: 46453603--46453652 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
46453593 TTTACTTTTA
*
46453603 TTCTTTCTTATTCTCTCTTT
1 TTCTTTCTTATTCTCTCTTC
*
46453623 TTCTTT-TTTTTCTCTCTTC
1 TTCTTTCTTATTCTCTCTTC
46453642 TTCTTCTCTTA
1 TTCTT-TCTTA
46453653 ACTTTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 16 0.64
20 7 0.28
21 2 0.08
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTTTCTTATTCTCTCTTC
Found at i:46454260 original size:30 final size:28
Alignment explanation
Indices: 46454212--46454296 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 28
46454202 GTAAAGTTTC
*
46454212 TGGGGTAAAAGTGGAATTTTAGCAAAAATA
1 TGGGGTAAAA-TGTAATTTTAG-AAAAATA
* *
46454242 TGGGGTTAAAATGTAATTTTTGAAAAATT
1 TGGGG-TAAAATGTAATTTTAGAAAAATA
46454271 TAGGGGCTAAAATGTAA-TTTAGAAAA
1 T-GGGG-TAAAATGTAATTTTAGAAAA
46454297 GTTTAGGGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.31
30 28 0.58
31 5 0.10
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.32
Consensus pattern (28 bp):
TGGGGTAAAATGTAATTTTAGAAAAATA
Found at i:46454295 original size:29 final size:29
Alignment explanation
Indices: 46454243--46454381 Score: 147
Period size: 29 Copynumber: 4.7 Consensus size: 29
46454233 GCAAAAATAT
* * *
46454243 GGGGTTAAAATGTAATTTTTGAAAAATTTA
1 GGGGCTAAAATGTAA-TTTAGAAAAGTTTA
46454273 GGGGCTAAAATGTAATTTAGAAAAGTTTA
1 GGGGCTAAAATGTAATTTAGAAAAGTTTA
*
46454302 GGGG-TAGATATGTAAATTT-GAGAAAGTTTA
1 GGGGCTA-AAATGT-AATTTAGA-AAAGTTTA
* *
46454332 GGGGTTGAAATGTAATTTAGAAAAGTTTA
1 GGGGCTAAAATGTAATTTAGAAAAGTTTA
*
46454361 GGGGCCCAAAAATGTAATTTA
1 GGGG--CTAAAATGTAATTTA
46454382 TATTTTTTGT
Statistics
Matches: 93, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.02
29 40 0.43
30 38 0.41
31 13 0.14
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (29 bp):
GGGGCTAAAATGTAATTTAGAAAAGTTTA
Found at i:46455356 original size:80 final size:82
Alignment explanation
Indices: 46455172--46455396 Score: 232
Period size: 84 Copynumber: 2.8 Consensus size: 82
46455162 NNNNNCACGA
* * *
46455172 CATGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGAGTGATTTTTTGAAAAACAGAAA
1 CATGTGACCCGAGGCTCAACTCACCTCTCGC-ATATAAGTTGAATGATTTTTTGAAAAACAGAAA
*
46455237 TTTAAAAGAAATACCTTGG
65 TTT-AAAGAAATACCTCGG
* ** ** *
46455256 CATGTGACCTGAGGCTCAACTCACCTCTCGCATATAAGTTGAAATTTTTTTTTGAAAAGTAGTAA
1 CATGTGACCCGAGGCTCAACTCACCTCTCGCATATAAGTTG-AATGATTTTTTGAAAAACAGAAA
*
46455321 -TT-GA-AAATACCTCGG
65 TTTAAAGAAATACCTCGG
* * *
46455336 CGTGTGACCCGGGGCTCAACTCACCTCTCGCA-AT-A--TGAGCTGA-TTTTTGAAAAACAGAAA
1 CATGTGACCCGAGGCTCAACTCACCTCTCGCATATAAGTTGA-ATGATTTTTTGAAAAACAGAAA
46455396 T
65 T
46455397 CGAAAATAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
75 15 0.13
76 3 0.03
78 1 0.01
79 2 0.02
80 39 0.33
81 1 0.01
83 11 0.09
84 46 0.39
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (82 bp):
CATGTGACCCGAGGCTCAACTCACCTCTCGCATATAAGTTGAATGATTTTTTGAAAAACAGAAAT
TTAAAGAAATACCTCGG
Found at i:46456314 original size:21 final size:20
Alignment explanation
Indices: 46456254--46456337 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 20
46456244 TTCATCTTGA
*
46456254 TTTTTCTTTTTCTTTTTTCTT-
1 TTTTT-TTTTTATTTTTT-TTG
46456275 TTTTCTTTTTTATTTTTTTTG
1 TTTT-TTTTTTATTTTTTTTG
*
46456296 TTTTTTTTGTTGTTTTTTTTG
1 TTTTTTTT-TTATTTTTTTTG
*
46456317 TTTTTTTGTCTACTTTTTTTT
1 TTTTTTT-TTTA-TTTTTTTT
46456338 AAGCATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.11
21 38 0.70
22 10 0.19
ACGTcount: A:0.02, C:0.07, G:0.06, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTATTTTTTTTG
Found at i:46456337 original size:1 final size:1
Alignment explanation
Indices: 46456254--46456323 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
46456244 TTCATCTTGA
* * * * * * * * *
46456254 TTTTTCTTTTTCTTTTTTCTTTTTTCTTTTTTATTTTTTTTGTTTTTTTTGTTGTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46456319 TTTTT
1 TTTTT
46456324 GTCTACTTTT
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.01, C:0.06, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:46467517 original size:20 final size:21
Alignment explanation
Indices: 46467492--46467547 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
46467482 CGAAAATTTT
*
46467492 GAAACACGAGATTTT-TTTAG
1 GAAACACGAAATTTTCTTTAG
**
46467512 GAAACAC-AAATTTTCTTTTT
1 GAAACACGAAATTTTCTTTAG
46467532 GAAACACGAAAATTTT
1 GAAACACG-AAATTTT
46467548 TAAAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.20
20 17 0.57
22 7 0.23
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
GAAACACGAAATTTTCTTTAG
Found at i:46467583 original size:35 final size:37
Alignment explanation
Indices: 46467488--46467570 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 37
46467478 AAAACGAAAA
**
46467488 TTTTGAAACACGAGATTTTTTTAGGAAACACAAATTTTCT
1 TTTTGAAACACGA-AAATTTTTA--AAACACAAATTTTCT
46467528 TTTTGAAACACGAAAATTTTTAAAACAC-AATTTT-T
1 TTTTGAAACACGAAAATTTTTAAAACACAAATTTTCT
46467563 TTTTGAAA
1 TTTTGAAA
46467571 ATATAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
35 9 0.22
36 6 0.15
37 6 0.15
39 7 0.17
40 13 0.32
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTGAAACACGAAAATTTTTAAAACACAAATTTTCT
Found at i:46467636 original size:17 final size:17
Alignment explanation
Indices: 46467610--46467857 Score: 135
Period size: 17 Copynumber: 13.8 Consensus size: 17
46467600 CGAGGATTTT
46467610 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* **
46467627 TTTATGAAACACGGTCAATT
1 TTTTTGAAACAC-G--AAAA
46467647 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
46467665 TTTTTGAAAGAC-AAGATT
1 TTTTTGAAACACGAA-A-A
*
46467683 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* **
46467701 TTTATGAAACACGGAATTT
1 TTTTTGAAACAC-GAA-AA
*
46467720 TTTTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* * *
46467738 TTTTCGAAATACG-AGA
1 TTTTTGAAACACGAAAA
* *
46467754 CTTTTGAAAACAAGGAAAA
1 TTTTTG-AAAC-ACGAAAA
*
46467773 TTTTTTGAAAACACGACAA
1 -TTTTTG-AAACACGAAAA
*
46467792 TTTTTGAAACACCG-GAA
1 TTTTTGAAACA-CGAAAA
*
46467809 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
*
46467826 TTTTTGAAACACTAAAA
1 TTTTTGAAACACGAAAA
46467843 TTTTTTGAAAACACG
1 -TTTTTG-AAACACG
46467858 GAAACACGAA
Statistics
Matches: 173, Mismatches: 37, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
16 15 0.09
17 53 0.31
18 48 0.28
19 27 0.16
20 24 0.14
21 6 0.03
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:46467649 original size:36 final size:36
Alignment explanation
Indices: 46467608--46467740 Score: 171
Period size: 36 Copynumber: 3.6 Consensus size: 36
46467598 CACGAGGATT
46467608 TTTTTTTG-AAACACGAAAATTTATGAAACACGGTCAA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGG--AA
* * *
46467645 TTTTTTTGAAAACACGAAAATTTTTGAAAGAC-AAGA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGGA-A
*
46467681 TTTTTTTGAAAACACGGAAATTTATGAAACACGGAA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGGAA
*
46467717 TTTTTTTTGAAAACAAGAAAATTT
1 -TTTTTTTGAAAACACGAAAATTT
46467741 TCGAAATACG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.01
36 31 0.37
37 30 0.36
38 21 0.25
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (36 bp):
TTTTTTTGAAAACACGAAAATTTATGAAACACGGAA
Found at i:46467731 original size:73 final size:73
Alignment explanation
Indices: 46467608--46467796 Score: 224
Period size: 73 Copynumber: 2.6 Consensus size: 73
46467598 CACGAGGATT
* * *
46467608 TTTTTTTG-AAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAATTTTTGA
1 TTTTTTTGAAAACACGGAAATTTATGAAACACGG-CAATTTTTTTGAAAACAAGAAAATTTTCGA
46467672 AAGACAAGA
65 AAGACAAGA
46467681 TTTTTTTGAAAACACGGAAATTTATGAAACACGG-AATTTTTTTTGAAAACAAGAAAATTTTCGA
1 TTTTTTTGAAAACACGGAAATTTATGAAACACGGCAA-TTTTTTTGAAAACAAGAAAATTTTCGA
* *
46467745 AATACGAGA
65 AAGACAAGA
* * * *
46467754 --CTTTTGAAAACAAGGAAAATTTTTTGAAAACACGACAATTTTT
1 TTTTTTTGAAAACACGG-AAA-TTTATG-AAACACGGCAATTTTT
46467797 GAAACACCGG
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
71 13 0.13
72 5 0.05
73 45 0.45
74 36 0.36
75 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (73 bp):
TTTTTTTGAAAACACGGAAATTTATGAAACACGGCAATTTTTTTGAAAACAAGAAAATTTTCGAA
AGACAAGA
Found at i:46467765 original size:54 final size:54
Alignment explanation
Indices: 46467648--46467830 Score: 144
Period size: 54 Copynumber: 3.4 Consensus size: 54
46467638 CGGTCAATTT
** ** *
46467648 TTTTGAAAACAC-GAA-AATTTTTGAAAGACAAG-ATTTTTTTGAAA-ACACGGAAA
1 TTTTGAAAACACGGAATTTTTTTTGAAA-ACAAGAAAATTTTCGAAACAC-CGG-AA
* *
46467701 TTTATG-AAACACGGAATTTTTTTTGAAAACAAGAAAATTTTCGAAATA-CGAGAC
1 TTT-TGAAAACACGGAATTTTTTTTGAAAACAAGAAAATTTTCGAAACACCG-GAA
* ** * * *
46467755 TTTTGAAAACAAGGAAAATTTTTTGAAAACACGACAATTTTTGAAACACCGGAA
1 TTTTGAAAACACGGAATTTTTTTTGAAAACAAGAAAATTTTCGAAACACCGGAA
*
46467809 TTTTGAAAACACGAAGATTTTT
1 TTTTGAAAACACGGA-ATTTTT
46467831 GAAACACTAA
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
53 11 0.11
54 66 0.64
55 25 0.24
56 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (54 bp):
TTTTGAAAACACGGAATTTTTTTTGAAAACAAGAAAATTTTCGAAACACCGGAA
Found at i:46467956 original size:20 final size:20
Alignment explanation
Indices: 46467931--46467972 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
46467921 TTCACGAGAG
46467931 TTTTTTTGAAACACGAAAAT
1 TTTTTTTGAAACACGAAAAT
*
46467951 TTTTTTTGAAACATGAAAAT
1 TTTTTTTGAAACACGAAAAT
46467971 TT
1 TT
46467973 ATGAAACACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTTTTTGAAACACGAAAAT
Found at i:46467999 original size:36 final size:37
Alignment explanation
Indices: 46467937--46468019 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
46467927 AGAGTTTTTT
* *
46467937 TGAAACACGAAAATTTTTTTTGAAACATGAAAATTTA
1 TGAAACACGAAAATTTTTTGTGAAACAAGAAAATTTA
* *
46467974 TGAAACACG-GAATTTTGTTGT-AAACAAGAAAATTTT
1 TGAAACACGAAAATTTT-TTGTGAAACAAGAAAATTTA
*
46468010 TGAAATACGA
1 TGAAACACGA
46468020 GACTTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
36 27 0.69
37 12 0.31
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (37 bp):
TGAAACACGAAAATTTTTTGTGAAACAAGAAAATTTA
Found at i:46468086 original size:19 final size:17
Alignment explanation
Indices: 46467932--46468124 Score: 90
Period size: 17 Copynumber: 10.8 Consensus size: 17
46467922 TCACGAGAGT
46467932 TTTTTTGAAACACGAAAA
1 TTTTTTGAAACACG-AAA
*
46467950 TTTTTTTTGAAACATGAAA
1 --TTTTTTGAAACACGAAA
* * *
46467969 ATTTATGAAACACGGAA
1 TTTTTTGAAACACGAAA
*
46467986 TTTTGTTGTAAACAAGAAA
1 TTTT-TTG-AAACACGAAA
* * *
46468005 ATTTTTGAAATACGAGA
1 TTTTTTGAAACACGAAA
* * *
46468022 -CTTTTGAAAATAAGGAAAA
1 TTTTTTG-AAA-CACG-AAA
**
46468041 TTTTTT-ATTCACGAGAA
1 TTTTTTGAAACACGA-AA
46468058 -TTTTTGAAACACGAAGA
1 TTTTTTGAAACACGAA-A
46468075 TTTTTTGAAAACACGGAAA
1 TTTTTTG-AAACAC-GAAA
* *
46468094 --TTTTGAAAACATGAATT
1 TTTTTTG-AAACACGAA-A
46468111 TTTTTTGAAACACG
1 TTTTTTGAAACACG
46468125 GGAGATTTTA
Statistics
Matches: 131, Mismatches: 27, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
16 15 0.11
17 48 0.37
18 20 0.15
19 28 0.21
20 20 0.15
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (17 bp):
TTTTTTGAAACACGAAA
Found at i:46468098 original size:35 final size:35
Alignment explanation
Indices: 46468050--46468125 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
46468040 ATTTTTTATT
*
46468050 CACGAGAATTTTTG-AAACACGAAGATTTTTTGAAAA
1 CACG-GAAATTTTGAAAACACGAAGATTTTTTG-AAA
* **
46468086 CACGGAAATTTTGAAAACATGAATTTTTTTTGAAA
1 CACGGAAATTTTGAAAACACGAAGATTTTTTGAAA
46468121 CACGG
1 CACGG
46468126 GAGATTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 16 0.46
36 19 0.54
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (35 bp):
CACGGAAATTTTGAAAACACGAAGATTTTTTGAAA
Found at i:46468564 original size:14 final size:14
Alignment explanation
Indices: 46468547--46468578 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
46468537 GCCGAACCTG
46468547 CTGGGCTGGAGCTA
1 CTGGGCTGGAGCTA
*
46468561 CTGGGCTGGAGCTG
1 CTGGGCTGGAGCTA
46468575 CTGG
1 CTGG
46468579 ACTACTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.22, G:0.47, T:0.22
Consensus pattern (14 bp):
CTGGGCTGGAGCTA
Found at i:46468644 original size:12 final size:12
Alignment explanation
Indices: 46468627--46468669 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
46468617 GCTGCTCTGG
46468627 GCCTGGCCTGCT
1 GCCTGGCCTGCT
46468639 GCCTGG-CTGCT
1 GCCTGGCCTGCT
**
46468650 GGAGTGGCCTGCT
1 -GCCTGGCCTGCT
46468663 GCCTGGC
1 GCCTGGC
46468670 TGTTGGGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.20
12 15 0.60
13 5 0.20
ACGTcount: A:0.02, C:0.35, G:0.40, T:0.23
Consensus pattern (12 bp):
GCCTGGCCTGCT
Found at i:46468793 original size:28 final size:30
Alignment explanation
Indices: 46468750--46468827 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 30
46468740 CCTGCTGTTT
* *
46468750 TTATTTTTATTTTTTCTTTCTTATTC-TCTC
1 TTATTTCT-TTTTTTCTCTCTTATTCTTCTC
*
46468780 TT-TTTCTTTTTTTCTCTCTTCTTCTTCTC
1 TTATTTCTTTTTTTCTCTCTTATTCTTCTC
46468809 TTAACTTTCTTTTTTTCTC
1 TT-A-TTTCTTTTTTTCTC
46468828 CTTCGGCAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 15 0.37
29 10 0.24
30 2 0.05
32 14 0.34
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (30 bp):
TTATTTCTTTTTTTCTCTCTTATTCTTCTC
Found at i:46468796 original size:18 final size:20
Alignment explanation
Indices: 46468760--46468811 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 20
46468750 TTATTTTTAT
46468760 TTTTTCTTTCTTATTCTCTC
1 TTTTTCTTTCTTATTCTCTC
46468780 TTTTTCTTT-TT-TTCTCTC
1 TTTTTCTTTCTTATTCTCTC
*
46468798 TTCTTCTTCTCTTA
1 TTTTTCTT-TCTTA
46468812 ACTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 14 0.50
19 3 0.11
20 11 0.39
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTCTTTCTTATTCTCTC
Found at i:46468970 original size:21 final size:21
Alignment explanation
Indices: 46468930--46469000 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
46468920 CCCTTTTTCC
* *
46468930 CTTTTCCTTTTTCTTC-TTTG
1 CTTTTCTTTTTTTTTCTTTTG
46468950 CTTTTCTTTTTTTTTCTTTTG
1 CTTTTCTTTTTTTTTCTTTTG
* *
46468971 C-TTGCTGTTTTCTTTT-TGTTG
1 CTTTTCT-TTTT-TTTTCTTTTG
46468992 CTTTTCTTT
1 CTTTTCTTT
46469001 GTAGGCGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 18 0.43
21 16 0.38
22 8 0.19
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.73
Consensus pattern (21 bp):
CTTTTCTTTTTTTTTCTTTTG
Found at i:46469388 original size:30 final size:30
Alignment explanation
Indices: 46469354--46469424 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
46469344 GTAAAAGTAC
* *
46469354 AATTTTGGCAAAAA-TACGGGGTTAAAATGT
1 AATTTTGG-AAAAATTACGGGGCTAAAACGT
* *
46469384 AATTTTTGAAAAATTAGGGGGCTAAAACGT
1 AATTTTGGAAAAATTACGGGGCTAAAACGT
* *
46469414 AAATTAGGAAA
1 AATTTTGGAAA
46469425 GTTTAGGGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.28
Consensus pattern (30 bp):
AATTTTGGAAAAATTACGGGGCTAAAACGT
Found at i:46469431 original size:30 final size:28
Alignment explanation
Indices: 46469401--46469492 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
46469391 GAAAAATTAG
*
46469401 GGGGCTAAAACGTAAATTAGGAAAGTTTA
1 GGGG-TAAAATGTAAATTAGGAAAGTTTA
* *
46469430 GGGGTAGATATGTAAATTTGAGAAAGTTTA
1 GGGGTA-AAATGTAAATTAG-GAAAGTTTA
* * *
46469460 GGGGTTGAAATGTAATTTAGAAAAGTTTA
1 GGGG-TAAAATGTAAATTAGGAAAGTTTA
46469489 GGGG
1 GGGG
46469493 CCCAAAAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.04
29 26 0.50
30 23 0.44
31 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.32, T:0.29
Consensus pattern (28 bp):
GGGGTAAAATGTAAATTAGGAAAGTTTA
Found at i:46469444 original size:29 final size:29
Alignment explanation
Indices: 46469412--46469492 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 29
46469402 GGGCTAAAAC
*
46469412 GTAAATTAGGAAAGTTTAGGGGTAGATAT
1 GTAAATTAGGAAAGTTTAGGGGTAGAAAT
* *
46469441 GTAAATTTGAGAAAGTTTAGGGGTTGAAAT
1 GTAAATTAG-GAAAGTTTAGGGGTAGAAAT
* *
46469471 GTAATTTAGAAAAGTTTAGGGG
1 GTAAATTAGGAAAGTTTAGGGG
46469493 CCCAAAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 20 0.44
30 25 0.56
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.32
Consensus pattern (29 bp):
GTAAATTAGGAAAGTTTAGGGGTAGAAAT
Found at i:46470078 original size:16 final size:18
Alignment explanation
Indices: 46470032--46470083 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
46470022 TTTTTTCCTC
46470032 AAAATTATAGATAATTTTTT
1 AAAATTAT--ATAATTTTTT
46470052 AAAATTATATAATTTTTT
1 AAAATTATATAATTTTTT
46470070 AAAATTATATAATT
1 AAAATTATATAATT
46470084 ATATAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 24 0.75
20 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AAAATTATATAATTTTTT
Found at i:46473025 original size:29 final size:32
Alignment explanation
Indices: 46472982--46473049 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 32
46472972 TTTTTATTTT
* *
46472982 TTAAAATATTATTT-ATTTAATT-T-ATTCAA
1 TTAAATTATTATTTAATCTAATTATAATTCAA
* *
46473011 TTAAATTATTTTTTAATCTAATTATAATTCTA
1 TTAAATTATTATTTAATCTAATTATAATTCAA
46473043 TTAAATT
1 TTAAATT
46473050 TATAACAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.38
30 7 0.22
31 1 0.03
32 12 0.38
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (32 bp):
TTAAATTATTATTTAATCTAATTATAATTCAA
Found at i:46475862 original size:24 final size:24
Alignment explanation
Indices: 46475835--46475909 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
46475825 TAACGAGAAA
46475835 CTCATAAGAGCC-ATAATTGGGAAG
1 CTCATAAGAGCCAATAA-TGGGAAG
* *
46475859 CTCATACGAGCCAATAATGGGTAG
1 CTCATAAGAGCCAATAATGGGAAG
** * * *
46475883 CTCCGAAGAGCTATTAACGGGAAG
1 CTCATAAGAGCCAATAATGGGAAG
46475907 CTC
1 CTC
46475910 TATATAGCCA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 37 0.90
25 4 0.10
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.20
Consensus pattern (24 bp):
CTCATAAGAGCCAATAATGGGAAG
Found at i:46476018 original size:26 final size:26
Alignment explanation
Indices: 46475976--46476035 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
46475966 CATTAATCAA
*
46475976 GAAGCTCACAAAGAGCC-TTTAATCGG
1 GAAGCTCACAAAGAGCCATATAA-CGG
* *
46476002 GAAGCTCACGAATAGCCATATAACGG
1 GAAGCTCACAAAGAGCCATATAACGG
*
46476028 GACGCTCA
1 GAAGCTCA
46476036 TAAGAGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCATATAACGG
Found at i:46477542 original size:2 final size:2
Alignment explanation
Indices: 46477537--46477563 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46477527 ATCAAAAAAT
46477537 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 T
46477564 CAATTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46479042 original size:6 final size:7
Alignment explanation
Indices: 46479023--46479053 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
46479013 ATTTTTCTAA
46479023 TATTTTT
1 TATTTTT
46479030 TATTTTT
1 TATTTTT
46479037 TATTTTTT
1 TA-TTTTT
46479045 TATTTTT
1 TATTTTT
46479052 TA
1 TA
46479054 CTTTACCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:46479045 original size:15 final size:15
Alignment explanation
Indices: 46479025--46479053 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46479015 TTTTCTAATA
46479025 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
46479040 TTTTTTATTTTTTA
1 TTTTTTATTTTTTA
46479054 CTTTACCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:46484338 original size:3 final size:3
Alignment explanation
Indices: 46484330--46484354 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46484320 CCAAGTCTAC
46484330 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
46484355 TAAAGAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:46511933 original size:6 final size:6
Alignment explanation
Indices: 46511924--46511950 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46511914 TAATTCATGA
46511924 GGGCTG GGGCTG GGGCTG GGGCTG GGG
1 GGGCTG GGGCTG GGGCTG GGGCTG GGG
46511951 GCTCATTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.70, T:0.15
Consensus pattern (6 bp):
GGGCTG
Found at i:46520397 original size:42 final size:43
Alignment explanation
Indices: 46520311--46520454 Score: 120
Period size: 42 Copynumber: 3.4 Consensus size: 43
46520301 TCGTGTTTGC
* * * * *
46520311 TTTCCATTTAGCTCTCATGAGCTTGAG-TTAACTCATATGAGG
1 TTTCCATTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGAGG
* * *
46520353 TTT-TAGTTCAGCTCTTTTGAGCTTTAGTTTAACCCTTATG-GG
1 TTTCCA-TTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGAGG
*
46520395 TTTCCATTCAGCTCTTATAAGCTTCCA-TTTAACCCTTA--AGG
1 TTTCCATTCAGCTCTTATGAGCTT-CAGTTTAACCCTTATGAGG
* * *
46520436 TTTCCGTTTAGCACTTATG
1 TTTCCATTCAGCTCTTATG
46520455 TGTTTCTGTG
Statistics
Matches: 82, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
41 18 0.22
42 52 0.63
43 12 0.15
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (43 bp):
TTTCCATTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGAGG
Found at i:46520432 original size:21 final size:21
Alignment explanation
Indices: 46520380--46520432 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
46520370 TGAGCTTTAG
** *
46520380 TTTAACCCTTATGGGTTTCCA
1 TTTAACCCTTATAAGCTTCCA
* * *
46520401 TTCAGCTCTTATAAGCTTCCA
1 TTTAACCCTTATAAGCTTCCA
46520422 TTTAACCCTTA
1 TTTAACCCTTA
46520433 AGGTTTCCGT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (21 bp):
TTTAACCCTTATAAGCTTCCA
Found at i:46522539 original size:24 final size:24
Alignment explanation
Indices: 46522417--46522584 Score: 101
Period size: 24 Copynumber: 6.9 Consensus size: 24
46522407 CTGTTTGTAG
46522417 GCTCTTTGTGAGCTTCCCGTTAAAG-
1 GCTCTTTG-GAGCTTCCCGTT-AAGT
* *
46522442 GCTCCTCGGAGCTTCCCGTT-AGT
1 GCTCTTTGGAGCTTCCCGTTAAGT
* *
46522465 GCTCTCTT-GAACTTCTCGTTATA-T
1 GCTCT-TTGGAGCTTCCCGTTA-AGT
* * * * * *
46522489 GACTATCTGGTGCTTTCTGATTGAGT
1 G-CTCTTTGGAGCTTCCCG-TTAAGT
46522515 GCTCTTTGGAGCTTCCCGTTAAGT
1 GCTCTTTGGAGCTTCCCGTTAAGT
* * * * * *
46522539 GCTCTTCGGAGCTACCTGATATGG
1 GCTCTTTGGAGCTTCCCGTTAAGT
46522563 GCTCTTTGTGAGCTTCCCGTTA
1 GCTCTTTG-GAGCTTCCCGTTA
46522585 TTAAGCCTAG
Statistics
Matches: 104, Mismatches: 30, Indels: 18
0.68 0.20 0.12
Matches are distributed among these distances:
22 2 0.02
23 14 0.13
24 46 0.44
25 38 0.37
26 4 0.04
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.38
Consensus pattern (24 bp):
GCTCTTTGGAGCTTCCCGTTAAGT
Found at i:46525116 original size:16 final size:16
Alignment explanation
Indices: 46525095--46525126 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46525085 CGAAATTCAC
46525095 TTAACAAAATAGTCCT
1 TTAACAAAATAGTCCT
46525111 TTAACAAAATAGTCCT
1 TTAACAAAATAGTCCT
46525127 AAAATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
TTAACAAAATAGTCCT
Found at i:46529763 original size:45 final size:45
Alignment explanation
Indices: 46529707--46529945 Score: 374
Period size: 45 Copynumber: 5.3 Consensus size: 45
46529697 CCAGTATACA
* * * *
46529707 GTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAACCT
1 GTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
*
46529753 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
* *
46529798 ATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCG
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
*
46529843 GTAACAGTAACAGTAACAGTATTCG--ACACAAAGTGCCGAGTCG
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
*
46529886 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCA
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
46529931 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
46529946 GTCGGCACAT
Statistics
Matches: 180, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
43 43 0.24
45 133 0.74
46 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
Found at i:46529900 original size:88 final size:89
Alignment explanation
Indices: 46529707--46529945 Score: 372
Period size: 88 Copynumber: 2.7 Consensus size: 89
46529697 CCAGTATACA
* * * * *
46529707 GTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAACCTGTAACAGTAACGGTAACAG
1 GTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAG
46529772 TATTCGACACACAAAGTGCCGAATCG
65 TATTCGA-ACACAAAGTGCCGAATCG
* * *
46529798 ATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACAGTAACAGTAACAGT
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAGT
*
46529863 ATTCG-ACACAAAGTGCCGAGTCG
66 ATTCGAACACAAAGTGCCGAATCG
46529886 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTA
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTA
46529946 GTCGGCACAT
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
88 74 0.54
90 60 0.44
91 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (89 bp):
GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAGT
ATTCGAACACAAAGTGCCGAATCG
Found at i:46529969 original size:38 final size:39
Alignment explanation
Indices: 46529709--46529972 Score: 181
Period size: 45 Copynumber: 6.2 Consensus size: 39
46529699 AGTATACAGT
* * *
46529709 AATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* *
46529748 AACCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AA----T--CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
*
46529793 AATCGATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 -A---AT--CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* * *
46529838 AGTCGGTAACAGTAACAGTA-ACAGTATTCGACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAGTC-G-A--C-ACACAAAGTGCCG
* *
46529881 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 A------ATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* * *
46529926 AATCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCT
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
46529964 AATCAGTAA
1 AATCAGTAA
46529973 GCCGGCAAAT
Statistics
Matches: 187, Mismatches: 16, Indels: 45
0.75 0.06 0.18
Matches are distributed among these distances:
38 17 0.09
39 44 0.24
40 1 0.01
41 1 0.01
42 1 0.01
43 15 0.08
44 1 0.01
45 85 0.45
46 2 0.01
48 1 0.01
49 18 0.10
50 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
Found at i:46536405 original size:23 final size:23
Alignment explanation
Indices: 46536345--46536419 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
46536335 TCTACTCACT
46536345 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
*
46536368 CAGAC-TATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
*
46536391 AACAAATCAAGAACAATAT-CAG
1 AACAAATCAAGAACAATTTCCAG
46536413 AACAAAT
1 AACAAAT
46536420 GCAACAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
21 2 0.04
22 16 0.36
23 19 0.42
24 6 0.13
25 2 0.04
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.17
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:46539089 original size:14 final size:15
Alignment explanation
Indices: 46539070--46539108 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
46539060 TTGTTTCATT
46539070 AAAAATGACTTT-TA
1 AAAAATGACTTTCTA
*
46539084 AAAAATGA-TTTCTG
1 AAAAATGACTTTCTA
46539098 AAAAATGACTT
1 AAAAATGACTT
46539109 ACTTTTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 17 0.77
15 2 0.09
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (15 bp):
AAAAATGACTTTCTA
Found at i:46541002 original size:18 final size:19
Alignment explanation
Indices: 46540963--46541005 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
46540953 AAAATTACAA
*
46540963 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
*
46540982 AAAATTCATAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
46541000 AAAATT
1 AAAATT
46541006 TTCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:46541007 original size:27 final size:26
Alignment explanation
Indices: 46540975--46541031 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
46540965 AATTCAAAAT
*
46540975 AATTTTTAAAATTCATAATATTTATAA
1 AATTTTCAAAATTCATAATATTTA-AA
* * *
46541002 AATTTTCAAAATTTATATTTTTTAAA
1 AATTTTCAAAATTCATAATATTTAAA
46541028 AATT
1 AATT
46541032 ATCTAAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTTTCAAAATTCATAATATTTAAA
Found at i:46553891 original size:2 final size:2
Alignment explanation
Indices: 46553884--46553910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46553874 AACAATAACA
46553884 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 A
46553911 AGCTACTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46559742 original size:2 final size:2
Alignment explanation
Indices: 46559735--46559767 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
46559725 AAAATCTGAT
46559735 TA TA TA 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
46559768 ACGTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46560069 original size:10 final size:11
Alignment explanation
Indices: 46560054--46560086 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
46560044 CATGTAATAT
46560054 GAAAAAATAAA
1 GAAAAAATAAA
46560065 GAAAAAAATAAA
1 G-AAAAAATAAA
46560077 G-AAAAATAAA
1 GAAAAAATAAA
46560087 CCCCAGGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
12 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
GAAAAAATAAA
Found at i:46560072 original size:12 final size:12
Alignment explanation
Indices: 46560055--46560082 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
46560045 ATGTAATATG
46560055 AAAAAATAAAGA
1 AAAAAATAAAGA
46560067 AAAAAATAAAGA
1 AAAAAATAAAGA
46560079 AAAA
1 AAAA
46560083 TAAACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAATAAAGA
Found at i:46565383 original size:25 final size:24
Alignment explanation
Indices: 46565355--46565419 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
46565345 AATGAAAGTT
*
46565355 TTTATTTAAATTTGAA-TTTTTATAA
1 TTTATTT-AATTT-AATTTTTTAAAA
46565380 TTTAATTTAATTTAATTTTTTAAAA
1 TTT-ATTTAATTTAATTTTTTAAAA
*
46565405 TTAATTTTAATTTAA
1 TTTA-TTTAATTTAA
46565420 AAATGTCACG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.09
25 28 0.80
26 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTATTTAATTTAATTTTTTAAAA
Found at i:46566704 original size:22 final size:23
Alignment explanation
Indices: 46566676--46566719 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
46566666 TAACAATATA
46566676 ATAAATATATAAATTT-ATTATC
1 ATAAATATATAAATTTAATTATC
*
46566698 ATAAATATATAAGTTTAATTAT
1 ATAAATATATAAATTTAATTAT
46566720 TATTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAATATATAAATTTAATTATC
Found at i:46568957 original size:64 final size:63
Alignment explanation
Indices: 46568868--46568992 Score: 137
Period size: 64 Copynumber: 2.0 Consensus size: 63
46568858 ATTATAAAAA
* * *
46568868 ATATATATGTATATATGTACGTATAT-TACAATTATAAAGTATAAAAAAATATATGTATGTAGAT
1 ATATATATATATATATGTAC-TATATGTA-AATTATAAAATATAAAAAAATATATATATGTAGAT
* * **
46568932 ATATATATATATATATAGATA-TATATGTAAGTTGTAAAATATAGGAAAATATATATATGTA
1 ATATATATATATATAT-G-TACTATATGTAAATTATAAAATATAAAAAAATATATATATGTA
46568993 TATGTGAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
64 46 0.90
65 3 0.06
66 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (63 bp):
ATATATATATATATATGTACTATATGTAAATTATAAAATATAAAAAAATATATATATGTAGAT
Found at i:46571522 original size:17 final size:17
Alignment explanation
Indices: 46571500--46571533 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46571490 GGGCTGTGCA
46571500 TTGTAATTGGGCTCGGG
1 TTGTAATTGGGCTCGGG
*
46571517 TTGTAATTGGGTTCGGG
1 TTGTAATTGGGCTCGGG
46571534 GTATTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (17 bp):
TTGTAATTGGGCTCGGG
Found at i:46575201 original size:25 final size:25
Alignment explanation
Indices: 46575167--46575322 Score: 67
Period size: 25 Copynumber: 6.2 Consensus size: 25
46575157 GCAACTCTTA
46575167 TGAGCGTTCCGATATATGGCTCTTCG
1 TGAGC-TTCCGATATATGGCTCTTCG
* **
46575193 TGAGCTTCCCGAT-TAAAGGCTCTTTA
1 TGAGCTT-CCGATAT-ATGGCTCTTCG
* * *
46575219 TGACCTTCTCGTTA-ATGGCTC-TCC
1 TGAGCTTC-CGATATATGGCTCTTCG
* * *
46575243 AGAGCTTCCTGATAT-TGGCTC-GCT
1 TGAGCTTCC-GATATATGGCTCTTCG
* * * *
46575267 TGAACTTTCTGATATATGGCTATCCG
1 TGAGC-TTCCGATATATGGCTCTTCG
46575293 -GAGCTTCCCGAT-TAATGGCTCTTCG
1 TGAGCTT-CCGATAT-ATGGCTCTTCG
46575318 -GAGCT
1 TGAGCT
46575323 ACCCGTTATT
Statistics
Matches: 96, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
23 1 0.01
24 28 0.29
25 39 0.41
26 28 0.29
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCGATATATGGCTCTTCG
Found at i:46576092 original size:2 final size:2
Alignment explanation
Indices: 46576085--46576126 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
46576075 NNNNNATTGT
46576085 TA TA 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 TA TA
46576127 AGTATATGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46577806 original size:25 final size:24
Alignment explanation
Indices: 46577778--46577824 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
46577768 AAGCTATTTC
46577778 GAGCCATATAACAGGAAGCTCATAA
1 GAGCCATA-AACAGGAAGCTCATAA
* * *
46577803 GAGCCGTAATCGGGAAGCTCAT
1 GAGCCATAAACAGGAAGCTCAT
46577825 GCGAGCCAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
GAGCCATAAACAGGAAGCTCATAA
Found at i:46577822 original size:24 final size:24
Alignment explanation
Indices: 46577791--46577843 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
46577781 CCATATAACA
46577791 GGAAGCTCATAAGAGCC-GTAATCG
1 GGAAGCTCATAAGAGCCAGT-ATCG
**
46577815 GGAAGCTCATGCGAGCCAGTATCG
1 GGAAGCTCATAAGAGCCAGTATCG
46577839 GGAAG
1 GGAAG
46577844 GTTCAAGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.30, C:0.21, G:0.34, T:0.15
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCAGTATCG
Found at i:46577897 original size:26 final size:25
Alignment explanation
Indices: 46577859--46577907 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
46577849 AGCAAGTCAT
* *
46577859 TATCGGGAAGCTCGCAAAGAGCTATA
1 TATCGAGAAGCTC-AAAAGAGCTATA
*
46577885 TATCGAGACGCTCAAAAGAGCTA
1 TATCGAGAAGCTCAAAAGAGCTA
46577908 CGGTGTGTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.18
Consensus pattern (25 bp):
TATCGAGAAGCTCAAAAGAGCTATA
Found at i:46578361 original size:21 final size:21
Alignment explanation
Indices: 46578335--46578380 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
46578325 TATATGAATG
*
46578335 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTCAATAC
*
46578356 AATTTACATTCAATTCAATCC
1 AATTTACATTCAATTCAATAC
46578377 AATT
1 AATT
46578381 CATATCTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTACATTCAATTCAATAC
Found at i:46586421 original size:18 final size:16
Alignment explanation
Indices: 46586395--46586436 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
46586385 TTATTTTATT
*
46586395 ATATTATTTTTAATATAA
1 ATATAATTTTTAA-AT-A
46586413 ATATAA-TTTTAAATA
1 ATATAATTTTTAAATA
46586428 ATATAATTT
1 ATATAATTT
46586437 GTGTAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 6 0.27
18 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATTTTTAAATA
Found at i:46586432 original size:15 final size:17
Alignment explanation
Indices: 46586402--46586436 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
46586392 ATTATATTAT
46586402 TTTTAATATAAATATAA
1 TTTTAATATAAATATAA
46586419 TTTTAA-AT-AATATAA
1 TTTTAATATAAATATAA
46586434 TTT
1 TTT
46586437 GTGTAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATATAAATATAA
Found at i:46592369 original size:13 final size:13
Alignment explanation
Indices: 46592351--46592388 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
46592341 CAAAAACAAC
46592351 AAAAGAAGGGAAA
1 AAAAGAAGGGAAA
**
46592364 AAAAGAACAGAAA
1 AAAAGAAGGGAAA
46592377 AAAAG-AGGGAAA
1 AAAAGAAGGGAAA
46592389 TTAATTAGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAAGAAGGGAAA
Found at i:46598358 original size:51 final size:50
Alignment explanation
Indices: 46598229--46598364 Score: 184
Period size: 50 Copynumber: 2.7 Consensus size: 50
46598219 AAAGTGATGG
* * *
46598229 TCACGTGTGTAGTACTGTGTGCAGGCTACTACGTGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
* * * *
46598279 TCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-ATAGA
46598330 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTG
46598365 AACCAAACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
49 2 0.03
50 38 0.51
51 35 0.47
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
Found at i:46599198 original size:35 final size:33
Alignment explanation
Indices: 46599139--46599232 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 33
46599129 TGAATTGACG
* *
46599139 GATAAGACCATGGTTGGACCATGGCAATGTTTAAAT
1 GATAAGACCATAGTTGG-CTATGGCAAT-TTT-AAT
46599175 G-TAAGACCATAGTTAGGCTATGGC-ATTTTAAT
1 GATAAGACCATAGTT-GGCTATGGCAATTTTAAT
* * *
46599207 GAAAAGACCATAATTGGGTTATGGCA
1 GATAAGACCATAGTT-GGCTATGGCA
46599233 CCTTGAACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
32 4 0.08
33 22 0.45
34 2 0.04
35 18 0.37
36 3 0.06
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (33 bp):
GATAAGACCATAGTTGGCTATGGCAATTTTAAT
Found at i:46599351 original size:33 final size:32
Alignment explanation
Indices: 46599279--46599355 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
46599269 TAGATACATG
** * * **
46599279 TGTAAGACCATAGTTGGGTTATGGCATTCTGA
1 TGTAAGACCATAACTGGGTTATGACATACAAA
46599311 TGATAAGACCATAACTGGGTTATGACACTACAAA
1 TG-TAAGACCATAACTGGGTTATGACA-TACAAA
46599345 TGTAAGACCAT
1 TGTAAGACCAT
46599356 GGCAGGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGTTATGACATACAAA
Found at i:46613381 original size:42 final size:42
Alignment explanation
Indices: 46613329--46613408 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
46613319 AAAAAAGAAG
* *
46613329 AAGAAGTAATAATCATTGCTTATATGCACTTAACATGGTATT
1 AAGAAATAATAATCATTGCTTATATGCACTTAAAATGGTATT
*
46613371 AAGAAATAATAATCATTGCTTATCTGCACTTAAAATGG
1 AAGAAATAATAATCATTGCTTATATGCACTTAAAATGG
46613409 AGAATCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (42 bp):
AAGAAATAATAATCATTGCTTATATGCACTTAAAATGGTATT
Found at i:46613944 original size:34 final size:35
Alignment explanation
Indices: 46613900--46613966 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
46613890 CAATAAAATA
* *
46613900 TTTTCCGTAAAATGA-TTTCTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
* *
46613934 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTT
46613967 CTACTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
Found at i:46613953 original size:20 final size:20
Alignment explanation
Indices: 46613915--46613954 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46613905 CGTAAAATGA
**
46613915 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGACTTACT
*
46613935 TTTCTGTAAAATGACTTACT
1 TTTCTGAAAAATGACTTACT
46613955 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTCTGAAAAATGACTTACT
Found at i:46618897 original size:23 final size:23
Alignment explanation
Indices: 46618863--46618921 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
46618853 CCGAGCTGAT
* * *
46618863 AAACAGTAAGCTCTATTGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
* *
46618886 AGACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
46618909 AAACGGTAAGCTC
1 AAACGGTAAGCTC
46618922 ATACAAGCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:46618930 original size:23 final size:23
Alignment explanation
Indices: 46618863--46618931 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
46618853 CCGAGCTGAT
* * **
46618863 AAACAGTAAGCTCTATTGAGCTG
1 AAACGGTAAGCTCCATAAAGCTG
* * *
46618886 AGACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAAAGCTG
46618909 AAACGGTAAGCT-CATACAAGCTG
1 AAACGGTAAGCTCCATA-AAGCTG
46618932 TGGTGAGTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 3 0.08
23 34 0.92
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAAAGCTG
Done.