Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 12 of 82
Found at i:3811444 original size:111 final size:110
Alignment explanation
Indices: 3811284--3811494 Score: 273
Period size: 111 Copynumber: 1.9 Consensus size: 110
3811274 AATGTTAAAG
* * *
3811284 TTTTTAAAAATAATTAATAAGATTAATGTTTTTAGATTCGGATATCTTATCAAATAATAAAATTG
1 TTTTTAAAAATAATTAACAAAATTAATGTTTTTAGATTCGGATATCTTATCAAATAATAAAATTC
* * *
3811349 AAATTAAAATATTTTAAAAATAACGGATACTCTATTTGATTATAT
66 AAATTAAAATACTTAAAAAATAACAGATACTCTATTTGATTATAT
* * * *
3811394 TTTTGTAAAAA-AATTAACAAAATTAATATTTTTTA-AGTTTGGATATCTTATTAAATAATAGAA
1 TTTT-TAAAAATAATTAACAAAATTAAT-GTTTTTAGA-TTCGGATATCTTATCAAATAATAAAA
* *
3811457 TTCAAATTAAAATGCTTAAAAAATGACAGATACTCTAT
63 TTCAAATTAAAATACTTAAAAAATAACAGATACTCTAT
3811495 CTATCTATTG
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
110 19 0.22
111 67 0.78
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (110 bp):
TTTTTAAAAATAATTAACAAAATTAATGTTTTTAGATTCGGATATCTTATCAAATAATAAAATTC
AAATTAAAATACTTAAAAAATAACAGATACTCTATTTGATTATAT
Found at i:3817765 original size:3 final size:3
Alignment explanation
Indices: 3817757--3817785 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3817747 AATGAAAGGC
3817757 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3817786 GAGTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3821954 original size:32 final size:32
Alignment explanation
Indices: 3821918--3821981 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3821908 ATATCTGTAA
* * *
3821918 TCAATTTTACCATAAAATTCAGTTATTCGAAC
1 TCAATTTGACCATAAAATTCAGTAATCCGAAC
*
3821950 TCAATTTGATCATAAAATTCAGTAATCCGAAC
1 TCAATTTGACCATAAAATTCAGTAATCCGAAC
3821982 GAGCCCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (32 bp):
TCAATTTGACCATAAAATTCAGTAATCCGAAC
Found at i:3823155 original size:60 final size:60
Alignment explanation
Indices: 3823038--3823156 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
3823028 ATTAACTTTA
* * * * *
3823038 ATGTGAATTTGCTACTATGTAGTATGTATTATATTTAGTCTCTTGATTTCTTGAATTGGG
1 ATGTGAATTTGCTACTATGTAGCATGTATCATATTTAGTCTCTTAATTTATTAAATTGGG
* *
3823098 ATGTGAATTTGCTATTATGTAGCATGTATCATATTTTATTC-CTTAATTTATTAAATTGG
1 ATGTGAATTTGCTACTATGTAGCATGTATCATA-TTTAGTCTCTTAATTTATTAAATTGG
3823157 ATTGGGCATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 45 0.88
61 6 0.12
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (60 bp):
ATGTGAATTTGCTACTATGTAGCATGTATCATATTTAGTCTCTTAATTTATTAAATTGGG
Found at i:3823591 original size:3 final size:3
Alignment explanation
Indices: 3823583--3823633 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
3823573 AATCACTATT
* *
3823583 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3823631 ATA
1 ATA
3823634 CATTTAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3824404 original size:20 final size:20
Alignment explanation
Indices: 3824371--3824413 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3824361 ATTATTTTCA
3824371 ATTAAGTCTCAAAG-TAATTT
1 ATTAAGTCTCAAAGAT-ATTT
* *
3824391 ATTAAGTTTTAAAGATATTT
1 ATTAAGTCTCAAAGATATTT
3824411 ATT
1 ATT
3824414 TGAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
ATTAAGTCTCAAAGATATTT
Found at i:3830720 original size:18 final size:17
Alignment explanation
Indices: 3830697--3830730 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3830687 AGGTTTTCCT
*
3830697 CCCCTTAAGTGTGTGCTC
1 CCCCTT-AGTATGTGCTC
3830715 CCCCTTAGTATGTGCT
1 CCCCTTAGTATGTGCT
3830731 TATTTTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.32, G:0.21, T:0.35
Consensus pattern (17 bp):
CCCCTTAGTATGTGCTC
Found at i:3839362 original size:35 final size:34
Alignment explanation
Indices: 3839294--3839363 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
3839284 TTTCACCAAG
* *
3839294 CTTTACAATAGTTTTTACTAGGCTTAACCAAAAC
1 CTTTACAATAGTTTTTACTAGGATCAACCAAAAC
* * *
3839328 CTTTCACAATAGTTTTTATTGGGATCAACTAAAAC
1 CTTT-ACAATAGTTTTTACTAGGATCAACCAAAAC
3839363 C
1 C
3839364 CAACACTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (34 bp):
CTTTACAATAGTTTTTACTAGGATCAACCAAAAC
Found at i:3850276 original size:39 final size:39
Alignment explanation
Indices: 3850215--3850333 Score: 148
Period size: 39 Copynumber: 3.0 Consensus size: 39
3850205 TGAGTTCTTT
* * *
3850215 ATAGGCATTACGTGACTAAATATTTGTTAGCGTTGTGTG
1 ATAGGCGTTACGTGATTGAATATTTGTTAGCGTTGTGTG
* **
3850254 ATAGGCGTTACATGATTGAATATTTGTTAGCGTTGCATG
1 ATAGGCGTTACGTGATTGAATATTTGTTAGCGTTGTGTG
* * *
3850293 ACAGGCGTTATGTGATTGAATATTTGTTGAGCATTGTGTG
1 ATAGGCGTTACGTGATTGAATATTTGTT-AGCGTTGTGTG
3850333 A
1 A
3850334 CCTGTTTGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 58 0.87
40 9 0.13
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (39 bp):
ATAGGCGTTACGTGATTGAATATTTGTTAGCGTTGTGTG
Found at i:3851800 original size:111 final size:111
Alignment explanation
Indices: 3851583--3852002 Score: 581
Period size: 111 Copynumber: 3.7 Consensus size: 111
3851573 GGTGCGTGAC
* * * * *
3851583 TGACTTGTGCAATTCATGTGTTATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGACAGTACGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGAC
* *
3851648 TGGTTTTTATATATTGCATTACCTGTTGTAGCGAGAGTGGTGGCGCG
65 TAGTTTTTATATATTGCATTACCTGTTATAGCGAGAGTGGTGGCGCG
* *
3851695 TGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTATTCAGTAGTTTCTTAGGCTTGCGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
*
3851760 AGTTTTTATATATTGCATTACCTGTTATAGCGTGAGTGGTGGCGCG
66 AGTTTTTATATATTGCATTACCTGTTATAGCGAGAGTGGTGGCGCG
* * * *
3851806 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAAGCTTGCATGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * * **
3851871 GGTTTTTATATATTACGTTACCTATTGTTATGTATTGCGAGAGTGGTGGCATG
66 AGTTTTTATATATTGCATTACC---TGTTA--TA--GCGAGAGTGGTGGCGCG
3851924 TGACTTGTGCAATTCATGTGTTGTTTTG-AGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTTGAAG-CTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGAC
3851988 TAGTTTTTATATATT
65 TAGTTTTTATATATT
3852003 AAGTGACCTG
Statistics
Matches: 273, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
111 129 0.47
112 50 0.18
114 5 0.02
116 2 0.01
117 1 0.00
118 86 0.32
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.45
Consensus pattern (111 bp):
TGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
AGTTTTTATATATTGCATTACCTGTTATAGCGAGAGTGGTGGCGCG
Found at i:3852067 original size:118 final size:114
Alignment explanation
Indices: 3851583--3852055 Score: 559
Period size: 118 Copynumber: 4.1 Consensus size: 114
3851573 GGTGCGTGAC
* * * * *
3851583 TGACTTGTGCAATTCATGTGTTATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGACAGTACGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGAC
* *
3851648 TGGTTTTTATATATTGCATTACCTGTTG---TAGCGAGAGTGGTGGCGCG
65 TAGTTTTTATATATTGAATTACCTGTTGTTATAGCGAGAGTGGTGGCGCG
* *
3851695 TGACTTGTGCAATTCATGTGTTGTTTTGA-AGCTTTTATTCAGTAGTTTCTTAGGCTTGCGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGA-CTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGAC
* *
3851759 TAGTTTTTATATATTGCATTACC---TGTTATAGCGTGAGTGGTGGCGCG
65 TAGTTTTTATATATTGAATTACCTGTTGTTATAGCGAGAGTGGTGGCGCG
* * * *
3851806 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAAGCTTGCATGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * * **
3851871 GGTTTTTATATATT-ACGTTACCTATTGTTATGTATTGCGAGAGTGGTGGCATG
66 AGTTTTTATATATTGA-ATTACCTGTTGTTA--TA--GCGAGAGTGGTGGCGCG
3851924 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
3851989 AGTTTTTATATATT-AAGTGACCTGTTGTTATATATTGCGAGAGCGGTGGCGCA
66 AGTTTTTATATATTGAA-TTACCTGTTG-T-TATA--GCGAGAGTGGTGGCGCG
*
3852042 TAACTTGTGCAATT
1 TGACTTGTGCAATT
3852056 TACCTCTTGT
Statistics
Matches: 311, Mismatches: 34, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
108 2 0.01
111 123 0.40
112 49 0.16
114 5 0.02
116 2 0.01
118 127 0.41
119 1 0.00
120 2 0.01
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (114 bp):
TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
AGTTTTTATATATTGAATTACCTGTTGTTATAGCGAGAGTGGTGGCGCG
Found at i:3856488 original size:159 final size:159
Alignment explanation
Indices: 3856199--3856613 Score: 688
Period size: 159 Copynumber: 2.6 Consensus size: 159
3856189 AAGAATTGCA
* *
3856199 TGAATATTTGTTATGCATTGAGTCACTGGATATTAGGGTGTGTGACTGGATATTAAGAATCGTTA
1 TGAATATTTGTTATGCATTGAGTCACTGAATATTAGGGTGTGTGACTGGATATTAGGAATCGTTA
**
3856264 CCTGTTTATTTGGCATTAGGTGCCTGAATATTATGTGACTGGAAACTTAAATCTGGATGGGGGTA
66 CCTGTTTATTTGGCATTAGGTGCCTGAATATTACATGACTGGAAACTTAAATCTGGATGGGGGTA
3856329 GCGAAAGCAATCAATTTATAGGCGATGCG
131 GCGAAAGCAATCAATTTATAGGCGATGCG
*
3856358 TGAATATTTGTTATGCATTGAGTCACTGAATATTAGGGTGTGTGATTGGATATTAGGAATCGTTA
1 TGAATATTTGTTATGCATTGAGTCACTGAATATTAGGGTGTGTGACTGGATATTAGGAATCGTTA
* * * *
3856423 CCTGTTTATTTGGTATTAGGTGCTTGAATATTACATGATTGGAAACTTAAATCTGGGTGGGGGTA
66 CCTGTTTATTTGGCATTAGGTGCCTGAATATTACATGACTGGAAACTTAAATCTGGATGGGGGTA
* *
3856488 GTGAAAGCAATCAGTTTATAGGCGATGCG
131 GCGAAAGCAATCAATTTATAGGCGATGCG
* *
3856517 TGAATATTTGTTATGCATTGAGTCACTGAA-ATCAGGGTGTGTGACTGGGTATTAGGAATTCGTT
1 TGAATATTTGTTATGCATTGAGTCACTGAATATTAGGGTGTGTGACTGGATATTAGGAA-TCGTT
*
3856581 ACTTGTTTATTTGGCATTAGGTGCCTGAATATT
65 ACCTGTTTATTTGGCATTAGGTGCCTGAATATT
3856614 TGTTGAGCAT
Statistics
Matches: 238, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
158 25 0.11
159 213 0.89
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.36
Consensus pattern (159 bp):
TGAATATTTGTTATGCATTGAGTCACTGAATATTAGGGTGTGTGACTGGATATTAGGAATCGTTA
CCTGTTTATTTGGCATTAGGTGCCTGAATATTACATGACTGGAAACTTAAATCTGGATGGGGGTA
GCGAAAGCAATCAATTTATAGGCGATGCG
Found at i:3856783 original size:103 final size:103
Alignment explanation
Indices: 3856605--3856902 Score: 499
Period size: 103 Copynumber: 2.9 Consensus size: 103
3856595 CATTAGGTGC
*
3856605 CTGAATATTTGTTGAGCATTGCGTGAGTT-TTTATAGGCATTACGTGACTGAATATATGTTGAGC
1 CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATTTGTTGAGC
*
3856669 GTTGCGTGACAGGTAATACGTGATTGAATATTACCTGA
66 GTTGCGTGACAGGTATTACGTGATTGAATATTACCTGA
* *
3856707 CTGAATATTTGTTGAGCATTGTGTGAGTTCTTTATAGGCATTACGTGATTGAATATTTGTTGAGC
1 CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATTTGTTGAGC
* * *
3856772 ATTGGGTGACAGGTATTACGTAATTGAATATTACCTGA
66 GTTGCGTGACAGGTATTACGTGATTGAATATTACCTGA
* *
3856810 CTGAATATTTGTTGAGCATTACGTGAGTTCTTTATAGGCATTACGTGACTGAATATTTGTTGAGG
1 CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATTTGTTGAGC
*
3856875 GTTGCGTGACAGGTATTACATGATTGAA
66 GTTGCGTGACAGGTATTACGTGATTGAA
3856903 AATTCTTTTT
Statistics
Matches: 180, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
102 28 0.16
103 152 0.84
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (103 bp):
CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATTTGTTGAGC
GTTGCGTGACAGGTATTACGTGATTGAATATTACCTGA
Found at i:3856830 original size:26 final size:26
Alignment explanation
Indices: 3856801--3856873 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 26
3856791 GTAATTGAAT
*
3856801 ATTACCTGACTGAATATTTGTTGAGC
1 ATTACGTGACTGAATATTTGTTGAGC
* * * *
3856827 ATTACGTGA--G-TTCTTTATAG-GC
1 ATTACGTGACTGAATATTTGTTGAGC
3856849 ATTACGTGACTGAATATTTGTTGAG
1 ATTACGTGACTGAATATTTGTTGAG
3856874 GGTTGCGTGA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
22 11 0.32
23 6 0.18
24 2 0.06
25 6 0.18
26 9 0.26
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (26 bp):
ATTACGTGACTGAATATTTGTTGAGC
Found at i:3858906 original size:23 final size:23
Alignment explanation
Indices: 3858874--3858931 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
3858864 GTATCACATG
*
3858874 AATGAATACAAAGAATAACATGTA
1 AATG-ATACAAAGAATAACATGGA
*
3858898 AATGATACAACAAAGAATAATATGGA
1 AATGAT---ACAAAGAATAACATGGA
3858924 AATGATAC
1 AATGATAC
3858932 CGAATAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
26 21 0.72
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.21
Consensus pattern (23 bp):
AATGATACAAAGAATAACATGGA
Found at i:3858912 original size:26 final size:26
Alignment explanation
Indices: 3858881--3858931 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3858871 ATGAATGAAT
*
3858881 ACAAAGAATAACATGTAAATGATACA
1 ACAAAGAATAACATGGAAATGATACA
*
3858907 ACAAAGAATAATATGGAAATGATAC
1 ACAAAGAATAACATGGAAATGATAC
3858932 CGAATAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.20
Consensus pattern (26 bp):
ACAAAGAATAACATGGAAATGATACA
Found at i:3860558 original size:69 final size:69
Alignment explanation
Indices: 3860471--3860629 Score: 198
Period size: 69 Copynumber: 2.3 Consensus size: 69
3860461 GCTTATTCAG
* * *
3860471 TGACTGCGTCTGCATCTGCATCG-CTCGCTGGATCTCCAATTGCATTGACTG-TTGAATCT-TCA
1 TGACTGCATCTGCATCTGCATCGCCT-GCTGGATCTCCAACTGCATTGACTGCTAG-ATCTCT-A
3860533 ACTGCAT
63 ACTGCAT
* * *
3860540 TGACTGCATCTGCATCTGCGTCGCCTGCTGGATCTCTAACTGCATTGATTGCTAGATCTCTAACT
1 TGACTGCATCTGCATCTGCATCGCCTGCTGGATCTCCAACTGCATTGACTGCTAGATCTCTAACT
*
3860605 GTAT
66 GCAT
*
3860609 TGACTGCATCTACATCTGCAT
1 TGACTGCATCTGCATCTGCAT
3860630 ATTCGTCTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 73 0.94
70 5 0.06
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.34
Consensus pattern (69 bp):
TGACTGCATCTGCATCTGCATCGCCTGCTGGATCTCCAACTGCATTGACTGCTAGATCTCTAACT
GCAT
Found at i:3860582 original size:24 final size:24
Alignment explanation
Indices: 3860555--3860615 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
3860545 GCATCTGCAT
* * *
3860555 CTGCGTCGCCTGCTGGATCTCTAA
1 CTGCATCGACTGCTAGATCTCTAA
* *
3860579 CTGCATTGATTGCTAGATCTCTAA
1 CTGCATCGACTGCTAGATCTCTAA
* *
3860603 CTGTATTGACTGC
1 CTGCATCGACTGC
3860616 ATCTACATCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (24 bp):
CTGCATCGACTGCTAGATCTCTAA
Found at i:3862533 original size:23 final size:21
Alignment explanation
Indices: 3862488--3862551 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
3862478 AATTTCCTAC
* * *
3862488 AACAATAGTCACGTAATGCCT
1 AACATTAGTCACGCAATGACT
*
3862509 AATCAATTAGTCACGCAATTACT
1 AA-C-ATTAGTCACGCAATGACT
*
3862532 AACATTAAATCACGCAATGA
1 AACATT-AGTCACGCAATGA
3862552 TTTATAAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 5 0.15
22 13 0.38
23 16 0.47
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (21 bp):
AACATTAGTCACGCAATGACT
Found at i:3863659 original size:26 final size:28
Alignment explanation
Indices: 3863597--3863660 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
3863587 TTATTGAAAA
* *
3863597 AATTTAAA-CATATTTTTATCTTTTATT
1 AATTTAAATTATATTTTTATCATTTATT
*
3863624 AATTTTAATTATATTTTTAT-ATTT-TT
1 AATTTAAATTATATTTTTATCATTTATT
3863650 AATTTAAATTA
1 AATTTAAATTA
3863661 AATAAATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 12 0.38
27 10 0.31
28 10 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (28 bp):
AATTTAAATTATATTTTTATCATTTATT
Found at i:3865528 original size:17 final size:17
Alignment explanation
Indices: 3865503--3865546 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3865493 TTATCATTCC
* * *
3865503 TATACATTTTATTACTA
1 TATATATTTTATAAATA
*
3865520 TGTATATTTTATAAATA
1 TATATATTTTATAAATA
3865537 TATATATTTT
1 TATATATTTT
3865547 TTCGTTGGCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATATTTTATAAATA
Found at i:3867872 original size:12 final size:12
Alignment explanation
Indices: 3867823--3867875 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
3867813 TGCTAATGCA
3867823 ATTATATATTTT
1 ATTATATATTTT
3867835 ATT-TATTATTATT
1 ATTATA-TATT-TT
* *
3867848 ATT-TTTGTTTT
1 ATTATATATTTT
3867859 ATTATATATTTT
1 ATTATATATTTT
3867871 ATTAT
1 ATTAT
3867876 CCTATTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 7 0.21
12 21 0.62
13 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
ATTATATATTTT
Found at i:3867881 original size:20 final size:18
Alignment explanation
Indices: 3867823--3867875 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3867813 TGCTAATGCA
3867823 ATTATATATTTTATTTATT
1 ATTATATATTTTA-TTATT
*
3867842 ATTAT-TATTTT-TGTTTT
1 ATTATATATTTTAT-TATT
3867859 ATTATATATTTTATTAT
1 ATTATATATTTTATTAT
3867876 CCTATTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 8 0.28
18 14 0.48
19 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTATATATTTTATTATT
Found at i:3868113 original size:13 final size:13
Alignment explanation
Indices: 3868097--3868123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3868087 TATTATTTAT
3868097 TTTTATCAAGTAA
1 TTTTATCAAGTAA
3868110 TTTTATCAAGTAA
1 TTTTATCAAGTAA
3868123 T
1 T
3868124 AATTTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTATCAAGTAA
Found at i:3868443 original size:10 final size:10
Alignment explanation
Indices: 3868428--3868457 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3868418 CTTAACATAA
3868428 TATATTTATT
1 TATATTTATT
3868438 TATATTTATT
1 TATATTTATT
*
3868448 TACATTTATT
1 TATATTTATT
3868458 CATCTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (10 bp):
TATATTTATT
Found at i:3869253 original size:34 final size:34
Alignment explanation
Indices: 3869210--3869471 Score: 150
Period size: 34 Copynumber: 7.6 Consensus size: 34
3869200 AATCATTACC
* * *
3869210 CACCGGCGGCTAACACTCC-AGCTACTACTCCTCT
1 CACCGGCAGCAAACACTCCAAGCT-TTACTCCTCT
* *
3869244 CACCGGCGGCAAACCCTCCCAAGCTGTTACTCCTCT
1 CACCGGCAGCAAACACT-CCAAGCT-TTACTCCTCT
*
3869280 CTCCGGCAGCAAAC-CTCCAAGCTTTCACTCCTC-
1 CACCGGCAGCAAACACTCCAAGCTTT-ACTCCTCT
* * *
3869313 CTACCGGCAGCAAACACTCC-AGATTTCAGTCTTC-
1 C-ACCGGCAGCAAACACTCCAAGCTTT-ACTCCTCT
* * *
3869347 CTACCGGCGGCCAAC-CTCCAAGCTGTTGCTCCTCT
1 C-ACCGGCAGCAAACACTCCAAGCT-TTACTCCTCT
* * *
3869382 CTAAACGGCGGCAAAC-CTCCAAGCTGTTGCTCCTC-
1 C--ACCGGCAGCAAACACTCCAAGCT-TTACTCCTCT
* *
3869417 CTACCGGCGGCAAACCAAC-CC-AGATTTCACTCCTC-
1 C-ACCGGCAGCAAA-C-ACTCCAAGCTTT-ACTCCTCT
3869452 CTACCGGCAGCAAACACTCC
1 C-ACCGGCAGCAAACACTCC
3869472 TCCCCTCTTT
Statistics
Matches: 190, Mismatches: 24, Indels: 28
0.79 0.10 0.12
Matches are distributed among these distances:
33 9 0.05
34 88 0.46
35 35 0.18
36 57 0.30
37 1 0.01
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (34 bp):
CACCGGCAGCAAACACTCCAAGCTTTACTCCTCT
Found at i:3869326 original size:70 final size:70
Alignment explanation
Indices: 3869211--3869471 Score: 227
Period size: 70 Copynumber: 3.8 Consensus size: 70
3869201 ATCATTACCC
* * * * *
3869211 ACCGGCGGCTAACACTCC-AGC-TACTACTCCT-CTCACCGGCGGCAAACCCTCCCAAGCTGTTA
1 ACCGGCGGCAAAC-CTCCAAGCTTTC-ACTCCTCCTAACCGGCAGCAAACACT-CCAAGCTGTTA
3869273 CTCCTCTCT
63 CTCCTC-CT
* * *
3869282 -CCGGCAGCAAACCTCCAAGCTTTCACTCCTCCT-ACCGGCAGCAAACACTCC-AGAT-TTCAGT
1 ACCGGCGGCAAACCTCCAAGCTTTCACTCCTCCTAACCGGCAGCAAACACTCCAAGCTGTT-ACT
*
3869343 CTTCCT
65 CCTCCT
* * * * *
3869349 ACCGGCGGCCAACCTCCAAGCTGTT-GCTCCTCTCTAAACGGCGGCAAAC-CTCCAAGCTGTTGC
1 ACCGGCGGCAAACCTCCAAGCT-TTCACTCCTC-CTAACCGGCAGCAAACACTCCAAGCTGTTAC
3869412 TCCTCCT
64 TCCTCCT
* * *
3869419 ACCGGCGGCAAACCAACCCAGATTTCACTCCTCCT-ACCGGCAGCAAACACTCC
1 ACCGGCGGCAAACC-TCCAAGCTTTCACTCCTCCTAACCGGCAGCAAACACTCC
3869472 TCCCCTCTTT
Statistics
Matches: 153, Mismatches: 24, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
67 4 0.03
68 33 0.22
69 25 0.16
70 74 0.48
71 17 0.11
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (70 bp):
ACCGGCGGCAAACCTCCAAGCTTTCACTCCTCCTAACCGGCAGCAAACACTCCAAGCTGTTACTC
CTCCT
Found at i:3869396 original size:104 final size:105
Alignment explanation
Indices: 3869236--3869471 Score: 295
Period size: 104 Copynumber: 2.3 Consensus size: 105
3869226 TCCAGCTACT
*
3869236 ACTCCT-CTCACCGGCGGCAAACCCTCCCAAGCTGTTACTCCTCTCTCCGGCAGCAAACCTCCAA
1 ACTCCTCCT-ACCGGCGGCAAACCCTCCCAAGCTGTTACTCCTCTCTACGGCAGCAAACCTCCAA
3869300 GCT-TTCACTCCTCCTACCGGCAGCAAA-C-ACTCCAGATTTC
65 GCTGTT-ACTCCTCCTACCGGCAGCAAACCAAC-CCAGATTTC
* * * * *
3869340 AGTCTTCCTACCGGCGGCCAA-CCT-CCAAGCTGTTGCTCCTCTCTAAACGGCGGCAAACCTCCA
1 ACTCCTCCTACCGGCGGCAAACCCTCCCAAGCTGTTACTCCTCTCT--ACGGCAGCAAACCTCCA
* *
3869403 AGCTGTTGCTCCTCCTACCGGCGGCAAACCAACCCAGATTTC
64 AGCTGTTACTCCTCCTACCGGCAGCAAACCAACCCAGATTTC
* *
3869445 ACTCCTCCTACCGGCAGCAAACACTCC
1 ACTCCTCCTACCGGCGGCAAACCCTCC
3869472 TCCCCTCTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
102 19 0.17
103 3 0.03
104 53 0.48
105 31 0.28
106 4 0.04
107 1 0.01
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (105 bp):
ACTCCTCCTACCGGCGGCAAACCCTCCCAAGCTGTTACTCCTCTCTACGGCAGCAAACCTCCAAG
CTGTTACTCCTCCTACCGGCAGCAAACCAACCCAGATTTC
Found at i:3869777 original size:16 final size:17
Alignment explanation
Indices: 3869747--3869780 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3869737 ACCTCTCTCA
*
3869747 TTTTTTCCTTCTTTCAT
1 TTTTTTCATTCTTTCAT
3869764 TTTTTTCATT-TTTCAT
1 TTTTTTCATTCTTTCAT
3869780 T
1 T
3869781 ATATTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTCATTCTTTCAT
Found at i:3875042 original size:19 final size:22
Alignment explanation
Indices: 3874998--3875045 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3874988 TCCTAATCTT
*
3874998 AATCTAATTTAACCTATATCCA
1 AATCTAATTTAACATATATCCA
3875020 AATCTAATTT-ACATA-AT-CA
1 AATCTAATTTAACATATATCCA
3875039 AATCTAA
1 AATCTAA
3875046 GAATTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 4 0.16
22 10 0.40
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (22 bp):
AATCTAATTTAACATATATCCA
Found at i:3878047 original size:2 final size:2
Alignment explanation
Indices: 3878042--3878085 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3878032 AGAAAATTAG
3878042 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3878084 GA
1 GA
3878086 AACCGACCCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3878985 original size:22 final size:22
Alignment explanation
Indices: 3878957--3879003 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3878947 AGCCATGGCG
3878957 GACAGCCATAGCAAAACAACAA
1 GACAGCCATAGCAAAACAACAA
3878979 GACAGCCATAGCAAAACAACAA
1 GACAGCCATAGCAAAACAACAA
3879001 GAC
1 GAC
3879004 TATTGGTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.28, G:0.15, T:0.04
Consensus pattern (22 bp):
GACAGCCATAGCAAAACAACAA
Found at i:3890249 original size:27 final size:27
Alignment explanation
Indices: 3890198--3890249 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3890188 NNNNNNNNNT
*
3890198 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTGACCCTGA
*
3890225 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
3890250 TATACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGA
Found at i:3890320 original size:20 final size:20
Alignment explanation
Indices: 3890295--3890340 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3890285 CTTCTAAACC
3890295 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
3890315 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
3890335 TCAAAT
1 TCAAAT
3890341 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:3890722 original size:42 final size:42
Alignment explanation
Indices: 3890663--3890786 Score: 185
Period size: 42 Copynumber: 3.0 Consensus size: 42
3890653 GGGCTTTACA
*
3890663 CAACGGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAG
* * **
3890705 CAACGGCTTATGTGCACTCCCATTCACACATAGTTGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAG
* *
3890747 CAACGGCTTATGTGCATTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
3890787 CACATCAACA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.23
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAG
Found at i:3894741 original size:7 final size:7
Alignment explanation
Indices: 3894708--3894770 Score: 74
Period size: 7 Copynumber: 8.7 Consensus size: 7
3894698 AACCAAGCTT
3894708 TTTCTTCC
1 TTTC-TCC
3894716 TTTCTCTC
1 TTTCTC-C
*
3894724 TTT-TTC
1 TTTCTCC
3894730 TTTCTCC
1 TTTCTCC
*
3894737 TTTCTTTC
1 TTTC-TCC
3894745 TTTCTCC
1 TTTCTCC
3894752 TTTCTCC
1 TTTCTCC
3894759 TTTCTCC
1 TTTCTCC
3894766 TTTCT
1 TTTCT
3894771 TCCAACTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
6 4 0.08
7 30 0.62
8 14 0.29
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTCTCC
Found at i:3894750 original size:29 final size:29
Alignment explanation
Indices: 3894708--3894773 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
3894698 AACCAAGCTT
*
3894708 TTTCTTCCTTTCTCTCTTT-TTCTTTCTCC
1 TTTCTTCCTTTCTC-CTTTCTCCTTTCTCC
*
3894737 TTTCTTTCTTTCTCCTTTCTCCTTTCTCC
1 TTTCTTCCTTTCTCCTTTCTCCTTTCTCC
3894766 TTTCTTCC
1 TTTCTTCC
3894774 AACTGATTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTCTTCCTTTCTCCTTTCTCCTTTCTCC
Found at i:3901431 original size:35 final size:35
Alignment explanation
Indices: 3901405--3901653 Score: 229
Period size: 35 Copynumber: 7.2 Consensus size: 35
3901395 CTTAATTGTT
*
3901405 TAATTTAATTAATTAGGCTCAATAACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* * *
3901440 TAATTTAATTAATTAAGCCCAACAATTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* * *
3901475 CAATTTTAATCAATTAGG-CCAATGACTTAATTAGACA
1 TAA-TTTAATTAATTAGGCCCAATAACTTAATTA-A-A
* * ***
3901512 -AATTTAATCAATTAGGCCCAATGACTTAATTGTT
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* *
3901546 TAATTTAATTAATTAAGCCCAATTACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* * ** *
3901581 CAATTTAATTAATTAGGCCAAAGGATTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* * *
3901616 CAATTCAATTAATTAGG--C-ACAACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
*
3901648 CAATTT
1 TAATTT
3901654 TAATCAAGTG
Statistics
Matches: 178, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
32 16 0.09
35 132 0.74
36 29 0.16
37 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (35 bp):
TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
Found at i:3901528 original size:106 final size:104
Alignment explanation
Indices: 3901406--3901653 Score: 304
Period size: 106 Copynumber: 2.4 Consensus size: 104
3901396 TTAATTGTTT
*
3901406 AATTTAATTAATTAGGCTCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATTAATTAGGC-CAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
* *
3901471 TAAACAATTTTAATCAATTAGGCC-AATGACTTAATTAGAC
65 TAAACAA-TTTAATCAATTAGGCCAAAGGACTTAATTAAAC
* * *** **
3901511 AAATTTAATCAATTAGGCCCAATGACTTAATTGTTTAATTTAATTAATTAAGCCCAATTACTTAA
1 -AATTTAATTAATTAGG-CCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAA
* *
3901576 TTAAACAATTTAATTAATTAGGCCAAAGGATTTAATTAAAC
64 TTAAACAATTTAATCAATTAGGCCAAAGGACTTAATTAAAC
* * *
3901617 AATTCAATTAATTAGG-C-ACAACTTAATTAAACAATTT
1 AATTTAATTAATTAGGCCAATAACTTAATTAAATAATTT
3901654 TAATCAAGTG
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
102 14 0.12
103 1 0.01
105 29 0.24
106 75 0.62
107 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (104 bp):
AATTTAATTAATTAGGCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAATT
AAACAATTTAATCAATTAGGCCAAAGGACTTAATTAAAC
Found at i:3901545 original size:141 final size:138
Alignment explanation
Indices: 3901394--3901660 Score: 383
Period size: 141 Copynumber: 1.9 Consensus size: 138
3901384 AGCCCAGTTA
* * *
3901394 ACTTAATTGTTTAATTTAATTAATTAGGCTCAATAACTTAATTAAATAATTTAATTAATTAAGCC
1 ACTTAATTGTTTAATTTAATTAATTAAGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCC
* * *
3901459 CAACAATTTAATTAAACAATTTTAATCAATTAGGC-CAATGACTTAATTAGACAAATTTAATCAA
66 AAACAATTTAATTAAACAA-TTCAATCAATTAGGCAC-A--ACTTAATTAAACAAATTTAATCAA
3901523 TTAGGCCCAATG
127 TTAGGCCCAATG
* *
3901535 ACTTAATTGTTTAATTTAATTAATTAAGCCCAATTACTTAATTAAACAATTTAATTAATTAGGCC
1 ACTTAATTGTTTAATTTAATTAATTAAGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCC
** * *
3901600 AAAGGATTTAATTAAACAATTCAATTAATTAGGCACAACTTAATTAAACAATTTTAATCAA
66 AAACAATTTAATTAAACAATTCAATCAATTAGGCACAACTTAATTAAACAAATTTAATCAA
3901661 GTGCTAGAGA
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
138 22 0.19
140 14 0.12
141 77 0.68
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.37
Consensus pattern (138 bp):
ACTTAATTGTTTAATTTAATTAATTAAGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCC
AAACAATTTAATTAAACAATTCAATCAATTAGGCACAACTTAATTAAACAAATTTAATCAATTAG
GCCCAATG
Found at i:3918504 original size:2 final size:2
Alignment explanation
Indices: 3918497--3918526 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3918487 TTTTAGGATT
3918497 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
3918527 ATAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3920397 original size:17 final size:18
Alignment explanation
Indices: 3920375--3920431 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
3920365 TAATTTTTAA
3920375 TTATAATTTA-GTTATTT
1 TTATAATTTATGTTATTT
*
3920392 TTATAA-TTATTTTATTT
1 TTATAATTTATGTTATTT
* *
3920409 TTATTAATTTATTTTAATT
1 TTA-TAATTTATGTTATTT
3920428 TTAT
1 TTAT
3920432 GTTTATTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 3 0.09
17 15 0.43
18 4 0.11
19 13 0.37
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATAATTTATGTTATTT
Found at i:3920419 original size:25 final size:25
Alignment explanation
Indices: 3920391--3920438 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3920381 TTTAGTTATT
*
3920391 TTTATAATT-ATTTTATTTTTATTAA
1 TTTAT-ATTAATTTTATGTTTATTAA
*
3920416 TTTATTTTAATTTTATGTTTATT
1 TTTATATTAATTTTATGTTTATT
3920439 TACTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATATTAATTTTATGTTTATTAA
Found at i:3920422 original size:19 final size:18
Alignment explanation
Indices: 3920386--3920431 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
3920376 TATAATTTAG
3920386 TTATTTTTA-TAATTATT
1 TTATTTTTATTAATTATT
3920403 TTATTTTTATTAATTTATT
1 TTATTTTTATTAA-TTATT
*
3920422 TTAATTTTAT
1 TTATTTTTAT
3920432 GTTTATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
18 3 0.12
19 14 0.54
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTTATTAATTATT
Found at i:3924384 original size:12 final size:12
Alignment explanation
Indices: 3924367--3924392 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3924357 CAATTTATTC
3924367 TTTGTTAATTAA
1 TTTGTTAATTAA
3924379 TTTGTTAATTAA
1 TTTGTTAATTAA
3924391 TT
1 TT
3924393 ATTTTTAGTT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTGTTAATTAA
Found at i:3931798 original size:21 final size:20
Alignment explanation
Indices: 3931774--3931864 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
3931764 ATACTCTTTA
* *
3931774 TTATGTATATTATTATATATT
1 TTATTTATAATATTA-ATATT
*
3931795 TTATTTTTAAATATTAATATT
1 TTATTTAT-AATATTAATATT
3931816 TTATTTATAAT-TTAATCATT
1 TTATTTATAATATTAAT-ATT
* * * *
3931836 GATATTATAAAATATAAATATA
1 -TTATT-TATAATATTAATATT
3931858 TTATTTA
1 TTATTTA
3931865 CAATTTATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.09
20 8 0.14
21 26 0.46
22 13 0.23
23 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATTTATAATATTAATATT
Found at i:3933559 original size:80 final size:78
Alignment explanation
Indices: 3933464--3933622 Score: 273
Period size: 80 Copynumber: 2.0 Consensus size: 78
3933454 AAGTTATTCA
3933464 TTTTACTATTATTATCATTATTTACAAAAGTTTTTATCAAATGACCAATCATTAATAATATATAT
1 TTTTACTATTATTATCATTATTTACAAAAGTTTTTATCAAATGACCAATCATTAATAATAT-TAT
3933529 TTTAAAATATATTT
65 TTTAAAATATATTT
** *
3933543 TTTTAACTATTATTATCATTATTTACAAATTTTTTTATCAAATGACCAATCATTAATAATATTTT
1 TTTT-ACTATTATTATCATTATTTACAAAAGTTTTTATCAAATGACCAATCATTAATAATATTAT
3933608 TTTAAAATATATTT
65 TTTAAAATATATTT
3933622 T
1 T
3933623 ATATATAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
79 21 0.28
80 55 0.72
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (78 bp):
TTTTACTATTATTATCATTATTTACAAAAGTTTTTATCAAATGACCAATCATTAATAATATTATT
TTAAAATATATTT
Found at i:3939824 original size:17 final size:17
Alignment explanation
Indices: 3939802--3939838 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3939792 ATGAACACTC
3939802 ATAATTTCAAGTATCAT
1 ATAATTTCAAGTATCAT
3939819 ATAATTTCAAGTATCAT
1 ATAATTTCAAGTATCAT
3939836 ATA
1 ATA
3939839 CCTAAGAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (17 bp):
ATAATTTCAAGTATCAT
Found at i:3942846 original size:37 final size:36
Alignment explanation
Indices: 3942796--3942865 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
3942786 AAATTCTAAT
*
3942796 TAGTGGAGTCCTAATAAAATGGGAGTTGTTAGTAGCA
1 TAGTGGAGTCCTAATAAAATGGG-GTGGTTAGTAGCA
*
3942833 TAGTGGAGTCCTAATAAAGTGGGGTGGTTAGTA
1 TAGTGGAGTCCTAATAAAATGGGGTGGTTAGTA
3942866 ACAGAGTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (36 bp):
TAGTGGAGTCCTAATAAAATGGGGTGGTTAGTAGCA
Found at i:3959296 original size:42 final size:42
Alignment explanation
Indices: 3959248--3959380 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 42
3959238 TAGTTTATAA
3959248 TTTATTTAAAATGTTAA-TAAT-TCGTATTTT-AAATATTAATAT
1 TTTATTTAAAAT-TTAATTAATATC--ATTTTAAAATATTAATAT
* *
3959290 TTTATTTATAAATTTAATTAGTATCATTTTAAAATATTATTAT
1 TTTATTTA-AAATTTAATTAATATCATTTTAAAATATTAATAT
* ** * * *
3959333 TTTATTTATAATTTAAACATTATTATGATTAAAATATTAATCAT
1 TTTATTTAAAATTTAATTAATATCAT-TTTAAAATATTAAT-AT
3959377 TTTA
1 TTTA
3959381 ATCATTTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
42 30 0.39
43 38 0.50
44 8 0.11
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (42 bp):
TTTATTTAAAATTTAATTAATATCATTTTAAAATATTAATAT
Found at i:3961038 original size:28 final size:28
Alignment explanation
Indices: 3960996--3961127 Score: 167
Period size: 28 Copynumber: 4.6 Consensus size: 28
3960986 CTTTTTCACG
* *
3960996 AGTTCACCACGAACCCATGGCTTTAACA
1 AGTTCACCACAAACCCATGGTTTTAACA
*
3961024 AGTTCACCATAAACCCATGGTTTTAACA
1 AGTTCACCACAAACCCATGGTTTTAACA
* *
3961052 GGTTCACTACAAAACCCATGGTTTTTAACGA
1 AGTTCACCAC-AAACCCATGG-TTTTAAC-A
*
3961083 A-TTCACCACAAAACCATGGTTTTAACA
1 AGTTCACCACAAACCCATGGTTTTAACA
*
3961110 AGATCACCACAAACCCAT
1 AGTTCACCACAAACCCAT
3961128 ACACAATTCA
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
27 2 0.02
28 53 0.60
29 19 0.21
30 14 0.16
31 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.24
Consensus pattern (28 bp):
AGTTCACCACAAACCCATGGTTTTAACA
Found at i:3961088 original size:58 final size:56
Alignment explanation
Indices: 3960999--3961127 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 56
3960989 TTTCACGAGT
* * * * *
3960999 TCACCACGAACCCATGGCTTTAACAAGTTCACCATAAACCCATGGTTTTAACAGGT
1 TCACCACAAACCCATGGCTTTAACAAGTTCACCACAAAACCATGGTTTTAACAAGA
* *
3961055 TCACTACAAAACCCATGGTTTTTAACGAA-TTCACCACAAAACCATGGTTTTAACAAGA
1 TCACCAC-AAACCCATGG-CTTTAAC-AAGTTCACCACAAAACCATGGTTTTAACAAGA
3961113 TCACCACAAACCCAT
1 TCACCACAAACCCAT
3961128 ACACAATTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
56 6 0.10
57 17 0.27
58 37 0.60
59 2 0.03
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (56 bp):
TCACCACAAACCCATGGCTTTAACAAGTTCACCACAAAACCATGGTTTTAACAAGA
Found at i:3961241 original size:42 final size:42
Alignment explanation
Indices: 3961182--3961264 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
3961172 ACTTTTACAA
*
3961182 AATAACTTTTCAAAGCTAAGCTA-AGACCTTTACAATAATAGT
1 AATAACTTTTCAAAGCTAAGCTATA-ACCTTTACAAGAATAGT
*
3961224 AATAACTTTTCAAAGCTAAGTTATAACCTTTACAAGAATAG
1 AATAACTTTTCAAAGCTAAGCTATAACCTTTACAAGAATAG
3961265 CAAGAGTGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (42 bp):
AATAACTTTTCAAAGCTAAGCTATAACCTTTACAAGAATAGT
Found at i:3961249 original size:21 final size:21
Alignment explanation
Indices: 3961183--3961250 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
3961173 CTTTTACAAA
*
3961183 ATAACTTTTCAAAGCTAAGCT
1 ATAACTTTTCAAAGCTAAGTT
* * *
3961204 A-AGACCTTTACAATA-AT-AGTA
1 ATA-A-CTTTTCAA-AGCTAAGTT
3961225 ATAACTTTTCAAAGCTAAGTT
1 ATAACTTTTCAAAGCTAAGTT
3961246 ATAAC
1 ATAAC
3961251 CTTTACAAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 14 0.41
22 9 0.26
23 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (21 bp):
ATAACTTTTCAAAGCTAAGTT
Found at i:3967156 original size:20 final size:19
Alignment explanation
Indices: 3967120--3967162 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
3967110 AAGTACTTTA
3967120 AAACAAAATAACATAAAATT
1 AAACAAAATAACAT-AAATT
*
3967140 AAACAAAA-ATACTTAAATT
1 AAACAAAATA-ACATAAATT
3967159 AAAC
1 AAAC
3967163 TAATCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (19 bp):
AAACAAAATAACATAAATT
Found at i:3968923 original size:4 final size:4
Alignment explanation
Indices: 3968888--3968981 Score: 66
Period size: 4 Copynumber: 23.2 Consensus size: 4
3968878 TATAAATATG
* * * * *
3968888 TAAT TAA- T-AT TAAT TGAT TAAC TATTT TAAT TAAT TAAAT TGAT TGAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TA-AT TAAT TAAT T-AAT TAAT TAAT
* * * *
3968936 TAAC TAAT TAAT TAAT TATT TAAAT TAAC TAAT TAAC TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT T-AAT TAAT TAAT TAAT TAAT TAAT T
3968982 TATAAAAAAA
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
2 1 0.01
3 2 0.03
4 57 0.83
5 9 0.13
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:3968943 original size:25 final size:25
Alignment explanation
Indices: 3968934--3968983 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3968924 AAATTGATTG
3968934 ATTAACTAATTAATTAATTATTTAA
1 ATTAACTAATTAATTAATTATTTAA
*
3968959 ATTAACTAATTAACTAATTAATTTA
1 ATTAACTAATTAATTAATT-ATTTA
3968984 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTAACTAATTAATTAATTATTTAA
Found at i:3973460 original size:22 final size:23
Alignment explanation
Indices: 3973417--3973462 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3973407 TAGGCGAGCT
* *
3973417 AGCCCGCACAGCCCCAAGCAGAC
1 AGCCCGCACAGACCCAAACAGAC
3973440 AGCCCGCACA-ACCCAAACAGAC
1 AGCCCGCACAGACCCAAACAGAC
3973462 A
1 A
3973463 ATCTGTGCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.37, C:0.46, G:0.17, T:0.00
Consensus pattern (23 bp):
AGCCCGCACAGACCCAAACAGAC
Found at i:3973919 original size:20 final size:21
Alignment explanation
Indices: 3973881--3973929 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
3973871 AACCGATTAC
3973881 CCTGTGCTGGGGGGCGTGCTG
1 CCTGTGCTGGGGGGCGTGCTG
* *
3973902 TCTGTGCT-GGGTGCGTGCTG
1 CCTGTGCTGGGGGGCGTGCTG
3973922 CCTGTGCT
1 CCTGTGCT
3973930 ATGTGCGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.00, C:0.24, G:0.45, T:0.31
Consensus pattern (21 bp):
CCTGTGCTGGGGGGCGTGCTG
Found at i:3973935 original size:20 final size:20
Alignment explanation
Indices: 3973894--3973936 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3973884 GTGCTGGGGG
* *
3973894 GCGTGCTGTCTGTGCTGGGT
1 GCGTGCTGCCTGTGCTAGGT
*
3973914 GCGTGCTGCCTGTGCTATGT
1 GCGTGCTGCCTGTGCTAGGT
3973934 GCG
1 GCG
3973937 GGTGAGGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.23, G:0.42, T:0.33
Consensus pattern (20 bp):
GCGTGCTGCCTGTGCTAGGT
Found at i:3975432 original size:2 final size:2
Alignment explanation
Indices: 3975425--3975485 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
3975415 ATTTAAGCTC
*
3975425 AT AT AT AT AT AC 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
3975467 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
3975486 ATCTTTGATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3976277 original size:18 final size:18
Alignment explanation
Indices: 3976250--3976313 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
3976240 CGTTTAATTA
3976250 ATCGTG-TTAATCATATT
1 ATCGTGTTTAATCATATT
3976267 ATCGTGTTTAA--ATATAT
1 ATCGTGTTTAATCATAT-T
* * *
3976284 ACACGTGTTTAATCGTGTT
1 A-TCGTGTTTAATCATATT
3976303 ATCGTGTTTAA
1 ATCGTGTTTAA
3976314 ACGTGTATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 4 0.11
17 8 0.21
18 22 0.58
19 2 0.05
20 2 0.05
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (18 bp):
ATCGTGTTTAATCATATT
Found at i:3976515 original size:16 final size:16
Alignment explanation
Indices: 3976470--3976515 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3976460 ATAATTTTAA
3976470 ATTTTGTTTTGTTA-T
1 ATTTTGTTTTGTTATT
* *
3976485 A-TTTGATGTTCTTATT
1 ATTTTG-TTTTGTTATT
3976501 ATTTTGTTTTGTTAT
1 ATTTTGTTTTGTTAT
3976516 AATTGTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 9 0.38
17 4 0.17
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.70
Consensus pattern (16 bp):
ATTTTGTTTTGTTATT
Found at i:3979217 original size:68 final size:70
Alignment explanation
Indices: 3979093--3979303 Score: 329
Period size: 68 Copynumber: 3.0 Consensus size: 70
3979083 GATGGCATTA
3979093 GTATATTATAAAGGTGTAATATCCAGCTTTCATTGTTCTCTATCATTGGAA-ATGAAATCAGAAA
1 GTATATTATAAAGGTGTAATATCCAGC-TTCATTGTTCTCTATCATTGGAATATGAAATCAGAAA
3979157 TTTACT
65 TTTACT
* * *
3979163 GTATGTTGTAAAGGTGTAATGTCCAG-TTCATTGTTCTCTATC-TTGGAATATGAAATCAGAAAT
1 GTATATTATAAAGGTGTAATATCCAGCTTCATTGTTCTCTATCATTGGAATATGAAATCAGAAAT
*
3979226 TTAAT
66 TTACT
*
3979231 GTATATTATAAAGGTGTAATATCCAGCTTTTATTGTTCTCTATCATTGGAATATGAAATCAGAAA
1 GTATATTATAAAGGTGTAATATCCAGC-TTCATTGTTCTCTATCATTGGAATATGAAATCAGAAA
*
3979296 TTCACT
65 TTTACT
3979302 GT
1 GT
3979304 TCTTTATCAT
Statistics
Matches: 127, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
67 6 0.05
68 57 0.45
70 38 0.30
71 26 0.20
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (70 bp):
GTATATTATAAAGGTGTAATATCCAGCTTCATTGTTCTCTATCATTGGAATATGAAATCAGAAAT
TTACT
Found at i:3981589 original size:13 final size:13
Alignment explanation
Indices: 3981571--3981605 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3981561 CTTCTGGAGC
3981571 TTTTTTTAAAGTT
1 TTTTTTTAAAGTT
*
3981584 TTTTTTT-AATTT
1 TTTTTTTAAAGTT
3981596 TTTTTTTAAA
1 TTTTTTTAAA
3981606 ATTATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTTAAAGTT
Found at i:3981613 original size:10 final size:10
Alignment explanation
Indices: 3981597--3981640 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
3981587 TTTTAATTTT
3981597 TTTTTTAAAA
1 TTTTTTAAAA
*
3981607 TTATTT--AA
1 TTTTTTAAAA
3981615 TTTTTTAAAA
1 TTTTTTAAAA
3981625 TTTTTTTAAAA
1 -TTTTTTAAAA
3981636 TTTTT
1 TTTTT
3981641 GTTTGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 7 0.24
10 12 0.41
11 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:3987009 original size:66 final size:66
Alignment explanation
Indices: 3986903--3987034 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 66
3986893 CTTGATTTGT
* * *
3986903 TTACACCTAAGTTTAGCGTGTATGTCATGTATAATAACATATATTGGTGGGTCAAGGTTTTCCTG
1 TTACACCTAAGTTTAGCGTCTACGTCATGTATAATAACATATATTGGTGGCTCAAGGTTTTCCTG
3986968 G
66 G
* *
3986969 TTACACCTAAGTTT-GATGTCTACGTCATGTATGATAACATATATTGGTGGCTCAAGGTTTTCCT
1 TTACACCTAAGTTTAG-CGTCTACGTCATGTATAATAACATATATTGGTGGCTCAAGGTTTTCCT
3987033 GG
65 GG
3987035 GGAGACTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.02
66 59 0.98
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (66 bp):
TTACACCTAAGTTTAGCGTCTACGTCATGTATAATAACATATATTGGTGGCTCAAGGTTTTCCTG
G
Found at i:4004628 original size:137 final size:139
Alignment explanation
Indices: 4004471--4004747 Score: 508
Period size: 137 Copynumber: 2.0 Consensus size: 139
4004461 TAGAAAATAC
4004471 TCTTTTTTATGCTTATAATTTTTAAAATTATAAAAATGATTTCCTCTAT-AATTTTAATAAACTT
1 TCTTTTTTATGCTTATAATTTTTAAAATTATAAAAATGATTTCCTCTATAAATTTTAATAAACTT
4004535 TTAAAAATAAAAATAATTTTTTTTCAAAAAATCTCCTTTTGAG-TTTTTTTTTTC-AAAAAA-AA
66 TTAAAAATAAAAATAA-TTTTTTTCAAAAAATCTCCTTTTGAGTTTTTTTTTTTCAAAAAAAGAA
4004597 TTCTTTCCAT
130 TTCTTTCCAT
4004607 TNCTTTTTTATGCTTATAATTTTTAAAATTATAAAAATGATTTCCTCTATAAATTTTAATAAACT
1 T-CTTTTTTATGCTTATAATTTTTAAAATTATAAAAATGATTTCCTCTATAAATTTTAATAAACT
4004672 TTTAAAAATAAAAATAATTTTTTTCAAAAAATCTCCTTTTGAGTTTTTTTTTTTCAAAAAAAGAA
65 TTTAAAAATAAAAATAATTTTTTTCAAAAAATCTCCTTTTGAGTTTTTTTTTTTCAAAAAAAGAA
4004737 TTCTTTCCAT
130 TTCTTTCCAT
4004747 T
1 T
4004748 TTTAATTTTT
Statistics
Matches: 136, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
136 1 0.01
137 74 0.54
138 42 0.31
139 6 0.04
140 13 0.10
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (139 bp):
TCTTTTTTATGCTTATAATTTTTAAAATTATAAAAATGATTTCCTCTATAAATTTTAATAAACTT
TTAAAAATAAAAATAATTTTTTTCAAAAAATCTCCTTTTGAGTTTTTTTTTTTCAAAAAAAGAAT
TCTTTCCAT
Found at i:4005063 original size:33 final size:34
Alignment explanation
Indices: 4005026--4005105 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 34
4005016 ATGAGATTAT
*
4005026 AATATTTTGAGATTATAATAAGAAATGAAAA-AA
1 AATATTTTGAGATTATAATAAAAAATGAAAATAA
* *
4005059 AATATATT-AGATTGTAATAAAAAATGAAAATAA
1 AATATTTTGAGATTATAATAAAAAATGAAAATAA
*
4005092 AATA-TATGAGATTA
1 AATATTTTGAGATTA
4005106 AAATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.54
33 18 0.46
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (34 bp):
AATATTTTGAGATTATAATAAAAAATGAAAATAA
Found at i:4005071 original size:32 final size:33
Alignment explanation
Indices: 4005026--4005105 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
4005016 ATGAGATTAT
* *
4005026 AATATTTTGAGATTATAATAAGAAATGAAAA-AA
1 AATATATT-AGATTATAATAAAAAATGAAAATAA
*
4005059 AATATATTAGATTGTAATAAAAAATGAAAATAA
1 AATATATTAGATTATAATAAAAAATGAAAATAA
*
4005092 AATATATGAGATTA
1 AATATATTAGATTA
4005106 AAATTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 20 0.49
33 21 0.51
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (33 bp):
AATATATTAGATTATAATAAAAAATGAAAATAA
Found at i:4011150 original size:19 final size:20
Alignment explanation
Indices: 4011123--4011168 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
4011113 AAGAGACAAG
*
4011123 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
4011142 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
4011161 ATAATATT
1 ATAATATT
4011169 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:4011595 original size:20 final size:20
Alignment explanation
Indices: 4011570--4011615 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
4011560 TTTTGACCCC
4011570 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
4011590 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
4011610 ATTTGA
1 ATTTGA
4011616 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:4011691 original size:28 final size:27
Alignment explanation
Indices: 4011660--4011712 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
4011650 TTTGGAGTAT
*
4011660 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
4011688 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
4011713 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:4011718 original size:28 final size:28
Alignment explanation
Indices: 4011660--4011718 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
4011650 TTTGGAGTAT
* *
4011660 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
4011688 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
4011716 AGG
1 AGG
4011719 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:4012871 original size:13 final size:13
Alignment explanation
Indices: 4012853--4012877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4012843 AGGGAAATTG
4012853 TGATTTTATAAAA
1 TGATTTTATAAAA
4012866 TGATTTTATAAA
1 TGATTTTATAAA
4012878 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:4017210 original size:28 final size:28
Alignment explanation
Indices: 4017163--4017365 Score: 217
Period size: 28 Copynumber: 7.0 Consensus size: 28
4017153 TGACAGTTTT
4017163 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
4017192 AACATGTTTGTCTTAATTTAGAAAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
4017220 ACCATGTTTTGTCTTAATTTAGACAAGAA
1 AACATG-TTTGTCTTAATTTAGACAAGAA
* *
4017249 AATATATTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * *
4017279 AATATGTTTTATCTTAATCTAGACAAGAA
1 AACATG-TTTGTCTTAATTTAGACAAGAA
* * *
4017308 AACATATTTGCCTCAATTTAGACAAGATA
1 AACATGTTTGTCTTAATTTAGACAAGA-A
* * *
4017337 ATATATTTTTGTCTTAATTAAAGACAAGA
1 A-ACATGTTTGTCTTAATT-TAGACAAGA
4017366 GTTATCTTAA
Statistics
Matches: 147, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
28 53 0.36
29 48 0.33
30 27 0.18
31 19 0.13
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:4017235 original size:57 final size:56
Alignment explanation
Indices: 4017163--4017365 Score: 235
Period size: 57 Copynumber: 3.5 Consensus size: 56
4017153 TGACAGTTTT
* * *
4017163 AACATGTTTGGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGAAAAGA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGA
*
4017219 AACCATGTTTTGTCTTAATTTAGACAAGAAAATATATTTGTCTTAATTTAAGACAAGAAA
1 AA-CATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTT-AGACAAG--A
* * * * *
4017279 AATATGTTTTATCTTAATCTAGACAAGAAAACATATTTGCCTCAATTTAGACAAGA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGA
* * *
4017335 TAATATATTTTTGTCTTAATTAAAGACAAGA
1 -AACAT-GTTTTGTCTTAATT-TAGACAAGA
4017366 GTTATCTTAA
Statistics
Matches: 126, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
56 3 0.02
57 48 0.38
58 24 0.19
59 48 0.38
60 3 0.02
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (56 bp):
AACATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGA
Found at i:4017307 original size:59 final size:58
Alignment explanation
Indices: 4017166--4017365 Score: 251
Period size: 59 Copynumber: 3.4 Consensus size: 58
4017156 CAGTTTTAAC
* * * **
4017166 ATGTTTGGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGAAAAG-AAACC
1 ATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGAAAAAT
*
4017223 ATGTTTTGTCTTAATTTAGACAAGAAAATATATTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTT-AGACAAGAAAAAT
* * * * *
4017282 ATGTTTTATCTTAATCTAGACAAGAAAACATATTTGCCTCAATTTAGACAAGATAATAT
1 ATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGA-AAAAT
*
4017341 AT-TTTTGTCTTAATTAAAGACAAGA
1 ATGTTTTGTCTTAATT-TAGACAAGA
4017366 GTTATCTTAA
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
57 42 0.34
58 25 0.20
59 57 0.46
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (58 bp):
ATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGAAAAAT
Found at i:4019217 original size:6 final size:6
Alignment explanation
Indices: 4019206--4019238 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
4019196 TCAAATTAGG
4019206 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTA
4019239 GGGATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:4027475 original size:27 final size:29
Alignment explanation
Indices: 4027429--4027483 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
4027419 GACAAGTGCT
4027429 GGGGTAAAAAATTTATCGA-TTTGCCCCC
1 GGGGTAAAAAATTTATCGATTTTGCCCCC
4027457 GGGGTGAAAAAA-TTA-CGATTTTGCCCC
1 GGGGT-AAAAAATTTATCGATTTTGCCCC
4027484 TATACTCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 16 0.64
29 6 0.24
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (29 bp):
GGGGTAAAAAATTTATCGATTTTGCCCCC
Found at i:4028320 original size:88 final size:87
Alignment explanation
Indices: 4028123--4028350 Score: 305
Period size: 88 Copynumber: 2.6 Consensus size: 87
4028113 TGGCAGCTTT
* *
4028123 AACATGATTTGTCTTAATTTAGACAAGAAAACATATTATGTCGTAATTT-AGAAAAGAAAACATG
1 AACAT-ATTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTAAGAAAAGAAAACATG
* *
4028187 TTTTGTCTTAATTTAGATAAGAA
65 TTTTGTCTTAATCTAGACAAGAA
* ** * *
4028210 AATATGCTTGTCTTAATTTAGACAAGAAAACATATTTTGGCTTAATTTAAGAAAAGAAAAATATG
1 AACATATTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTAAGAAAAG-AAAACATG
*
4028275 TTTTGTTTTAATCTAGACAAGAA
65 TTTTGTCTTAATCTAGACAAGAA
* * *
4028298 AACATATTTGTCTCAATTTAGACAAGATAACATATTTTAGTCTTAATTAAAGA
1 AACATATTTGTCTTAATTTAGACAAGAAAACATATTTT-GTCTTAATTTAAGA
4028351 TAAAAGTTGT
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
86 38 0.31
87 11 0.09
88 60 0.50
89 12 0.10
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (87 bp):
AACATATTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTAAGAAAAGAAAACATGT
TTTGTCTTAATCTAGACAAGAA
Found at i:4028329 original size:28 final size:28
Alignment explanation
Indices: 4028123--4028345 Score: 232
Period size: 29 Copynumber: 7.6 Consensus size: 28
4028113 TGGCAGCTTT
4028123 AACATGATTTGTCTTAATTTAGACAAGAA
1 AACAT-ATTTGTCTTAATTTAGACAAGAA
* *
4028152 AACATATTATGTCGTAATTTAGAAAAGAA
1 AACATATT-TGTCTTAATTTAGACAAGAA
* *
4028181 AACATGTTTTGTCTTAATTTAGATAAGAA
1 AACAT-ATTTGTCTTAATTTAGACAAGAA
* **
4028210 AATATGCTTGTCTTAATTTAGACAAGAA
1 AACATATTTGTCTTAATTTAGACAAGAA
* *
4028238 AACATATTTTGGCTTAATTTAAGAAAAGAA
1 AACATA-TTTGTCTTAATTT-AGACAAGAA
* *
4028268 AA-ATATGTTTTGTTTTAATCTAGACAAGAA
1 AACATA---TTTGTCTTAATTTAGACAAGAA
* *
4028298 AACATATTTGTCTCAATTTAGACAAGAT
1 AACATATTTGTCTTAATTTAGACAAGAA
4028326 AACATATTTTAGTCTTAATT
1 AACATA-TTT-GTCTTAATT
4028346 AAAGATAAAA
Statistics
Matches: 162, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
28 51 0.31
29 67 0.41
30 30 0.19
31 14 0.09
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:4032359 original size:38 final size:38
Alignment explanation
Indices: 4032290--4032440 Score: 191
Period size: 38 Copynumber: 4.1 Consensus size: 38
4032280 CACACTCAGC
* ***
4032290 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
* *
4032328 TCATGTGCACTCCTTACTCACACATTTCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
4032366 TCATGTGCACTCCCTACTCGCACATTTC-A-AT-ATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
* * * *
4032401 TCGTGTGCACTCTCTACTCGTACACTTCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
4032439 TC
1 TC
4032441 CACACTTCCG
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
35 28 0.29
36 3 0.03
37 3 0.03
38 64 0.65
ACGTcount: A:0.27, C:0.33, G:0.09, T:0.30
Consensus pattern (38 bp):
TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
Found at i:4032438 original size:73 final size:76
Alignment explanation
Indices: 4032290--4032440 Score: 193
Period size: 73 Copynumber: 2.0 Consensus size: 76
4032280 CACACTCAGC
*
4032290 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCATCATGTGCACTCCTTACTCACACATTT
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCATCATGTGCACTCCTTACTCACACACTT
4032355 CAATATCATCA
66 CAATATCATCA
* *** * **
4032366 TCATGTGCACTCCCTACTCGCACATTTC-A-AT-ATCATCGTGTGCACT-CTCTACTCGTACACT
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCATCATGTGCACTCCT-TACTCACACACT
4032427 TCAATATCATCA
65 TCAATATCATCA
4032439 TC
1 TC
4032441 CACACTTCCG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 2 0.03
73 37 0.56
74 2 0.03
75 1 0.02
76 24 0.36
ACGTcount: A:0.27, C:0.33, G:0.09, T:0.30
Consensus pattern (76 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCATCATCATGTGCACTCCTTACTCACACACTT
CAATATCATCA
Found at i:4038186 original size:28 final size:28
Alignment explanation
Indices: 4038121--4038188 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
4038111 TAGAATTACC
*
4038121 ATTTTGCCCCTACGGTGGCAAAATGACT
1 ATTTTGCCCTTACGGTGGCAAAATGACT
*
4038149 ATTTTGCCCTTAGGGTGGCAAAATGACT
1 ATTTTGCCCTTACGGTGGCAAAATGACT
4038177 ATTTTGCCCTTA
1 ATTTTGCCCTTA
4038189 TCATCGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (28 bp):
ATTTTGCCCTTACGGTGGCAAAATGACT
Found at i:4038199 original size:28 final size:28
Alignment explanation
Indices: 4038140--4038199 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
4038130 CTACGGTGGC
** * *
4038140 AAAATGACTATTTTGCCCTTAGGGTGGC
1 AAAATGACTATTTTGCCCTTAGCATCGA
*
4038168 AAAATGACTATTTTGCCCTTATCATCGA
1 AAAATGACTATTTTGCCCTTAGCATCGA
4038196 AAAA
1 AAAA
4038200 ACACCAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (28 bp):
AAAATGACTATTTTGCCCTTAGCATCGA
Found at i:4043510 original size:42 final size:42
Alignment explanation
Indices: 4043464--4043586 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
4043454 TGTGGACTCT
* * **
4043464 GCTATGTGCGAGTAGGAGTGTACATAAGCTGATGATGACCTG
1 GCTATGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCA
4043506 GCTATGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCA
1 GCTATGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCA
* * * *
4043548 GCCATGTGCTAGTGGGGAGTACACATGAGCTGATGATGA
1 GCTATGTGCGAGT-GGGAGTGCACATAAGCTGATGATGA
4043587 TGGGAGAGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 49 0.68
43 23 0.32
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (42 bp):
GCTATGTGCGAGTGGGAGTGCACATAAGCTGATGATGACCCA
Found at i:4043615 original size:2 final size:2
Alignment explanation
Indices: 4043610--4043634 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4043600 TTGATGATGA
4043610 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4043635 CATGTATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4048571 original size:15 final size:16
Alignment explanation
Indices: 4048551--4048582 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4048541 TGTTATTATG
4048551 ATTA-TTTATTTTTAA
1 ATTATTTTATTTTTAA
4048566 ATTATTTTATTTTTAA
1 ATTATTTTATTTTTAA
4048582 A
1 A
4048583 CATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTTTATTTTTAA
Found at i:4048914 original size:27 final size:26
Alignment explanation
Indices: 4048834--4048925 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 26
4048824 ATTTTTATCT
* * *
4048834 TTTAAATATTAATAATTTATATATATT
1 TTTAAATATTAATATTTTATTTATA-A
* *
4048861 TTTAAATATTAATA----ATTGATTA
1 TTTAAATATTAATATTTTATTTATAA
4048883 TTTAAATATTAATATTTTTATTTATAA
1 TTTAAATATTAATA-TTTTATTTATAA
4048910 TTT-AATCATTAATATT
1 TTTAAAT-ATTAATATT
4048926 ATAAAATACT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
22 14 0.26
23 4 0.08
26 5 0.09
27 30 0.57
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTAAATATTAATATTTTATTTATAA
Found at i:4049047 original size:28 final size:27
Alignment explanation
Indices: 4048975--4049061 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 27
4048965 ATGATTATTT
* * *
4048975 TATTTTTATTTTATTTTAAAATATTAA
1 TATTTATAATTTAATTTAAAATATTAA
*
4049002 TTAATTTATAA-TTGATTTAAAATATTAA
1 -T-ATTTATAATTTAATTTAAAATATTAA
* *
4049030 TATTTGGTAATTTAATTTATAAT-TTAAA
1 TATTT-ATAATTTAATTTAAAATATT-AA
4049058 TATT
1 TATT
4049062 ATTATGATCA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.08
27 6 0.12
28 32 0.67
29 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (27 bp):
TATTTATAATTTAATTTAAAATATTAA
Found at i:4049244 original size:15 final size:15
Alignment explanation
Indices: 4049205--4049246 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4049195 TAAATTTCAC
*
4049205 TTAATAATTTAAAAA
1 TTAATATTTTAAAAA
4049220 TTAATATTTTAAAATA
1 TTAATATTTTAAAA-A
*
4049236 TTAATTTTTTA
1 TTAATATTTTA
4049247 TTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATATTTTAAAAA
Found at i:4059250 original size:30 final size:31
Alignment explanation
Indices: 4059209--4059277 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
4059199 TTTTTTCATG
*
4059209 GGATTAAGGGTTATACATATGC-TTTTAACA
1 GGATCAAGGGTTATACATATGCTTTTTAACA
*
4059239 GGATCAAGGGTTATACATATGCTTTTTAACG
1 GGATCAAGGGTTATACATATGCTTTTTAACA
4059270 GGATCAAG
1 GGATCAAG
4059278 CGATAACCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 21 0.58
31 15 0.42
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (31 bp):
GGATCAAGGGTTATACATATGCTTTTTAACA
Found at i:4059383 original size:35 final size:36
Alignment explanation
Indices: 4059249--4059394 Score: 170
Period size: 36 Copynumber: 4.0 Consensus size: 36
4059239 GGATCAAGGG
* * * *
4059249 TTATACATATGCTTTTTAACGGGATCAAGCGATAACCC
1 TTATAC-T-TGCTTTTTCATGGAATCAAGTGATAACCC
* *
4059287 TTATACTTGCTTTTTCATGGAATCAAGCGATAACTC
1 TTATACTTGCTTTTTCATGGAATCAAGTGATAACCC
*
4059323 TTATACTTGCTTTTTCATGGAATCAAATGATAACCC
1 TTATACTTGCTTTTTCATGGAATCAAGTGATAACCC
* *
4059359 TTATACTGGC-TTTTCA-CGAGATCAAGTGATAACCC
1 TTATACTTGCTTTTTCATGGA-ATCAAGTGATAACCC
4059394 T
1 T
4059395 CACATTAACA
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
34 2 0.02
35 21 0.22
36 67 0.69
37 1 0.01
38 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
TTATACTTGCTTTTTCATGGAATCAAGTGATAACCC
Found at i:4067899 original size:43 final size:43
Alignment explanation
Indices: 4067851--4067973 Score: 151
Period size: 43 Copynumber: 2.9 Consensus size: 43
4067841 TTGTGTGATA
* *
4067851 ATGATGACCCGACTATGTGTGAGTAGGGAGTGCACATAAGCTG
1 ATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATAAGCAG
* *
4067894 ATGATGA-CCAAGCTATGTGCGAGTAGGGAGTGCGCATAAGCAG
1 ATGATGACCCGA-CTATGTGCGAGTAGGGAGTGCACATAAGCAG
** *
4067937 ATGATGACCCGGTTATGAGCG-GATAGGGAGTGCACAT
1 ATGATGACCCGACTATGTGCGAG-TAGGGAGTGCACAT
4067974 GATGATGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 4 0.06
43 62 0.91
44 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.34, T:0.21
Consensus pattern (43 bp):
ATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATAAGCAG
Found at i:4071666 original size:22 final size:22
Alignment explanation
Indices: 4071638--4071681 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4071628 GGTCGGGATG
4071638 GTTTTTCTTCATTATTTTATCA
1 GTTTTTCTTCATTATTTTATCA
*
4071660 GTTTTTCTTCGTTATTTTATCA
1 GTTTTTCTTCATTATTTTATCA
4071682 ACATTGCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.64
Consensus pattern (22 bp):
GTTTTTCTTCATTATTTTATCA
Found at i:4076359 original size:21 final size:23
Alignment explanation
Indices: 4076316--4076360 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
4076306 CACCTTAATC
* *
4076316 TTATTCAAACAACTAAATTTAAA
1 TTATTCAAAAAACTAAAATTAAA
4076339 TTATT-AAAAAAC-AAAATTAAA
1 TTATTCAAAAAACTAAAATTAAA
4076360 T
1 T
4076361 CTTATAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
TTATTCAAAAAACTAAAATTAAA
Found at i:4076365 original size:23 final size:25
Alignment explanation
Indices: 4076312--4076365 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
4076302 AACACACCTT
* *
4076312 AATCTTATTCAAACAACTAAATTTA
1 AATCTTATTCAAAAAACTAAAATTA
4076337 AA--TTATT-AAAAAAC-AAAATTA
1 AATCTTATTCAAAAAACTAAAATTA
4076358 AATCTTAT
1 AATCTTAT
4076366 AAACTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 8 0.32
22 6 0.24
23 9 0.36
25 2 0.08
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (25 bp):
AATCTTATTCAAAAAACTAAAATTA
Found at i:4090316 original size:17 final size:17
Alignment explanation
Indices: 4090300--4090342 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
4090290 CACACATTTA
4090300 AGGGG-AGCACATGTTT
1 AGGGGCAGCACATGTTT
** *
4090316 AGGGGCAGCACATACTC
1 AGGGGCAGCACATGTTT
4090333 AGGGGCAGCA
1 AGGGGCAGCA
4090343 ATCCCAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.28, C:0.21, G:0.37, T:0.14
Consensus pattern (17 bp):
AGGGGCAGCACATGTTT
Found at i:4093968 original size:30 final size:31
Alignment explanation
Indices: 4093922--4093979 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
4093912 GTCCTTGTAC
4093922 TTTATTCTGAGCCAAATAAG-CTTTTATAGT
1 TTTATTCTGAGCCAAATAAGCCTTTTATAGT
* *
4093952 TTTATTTTGAGTCAAATAAGCCTTTTAT
1 TTTATTCTGAGCCAAATAAGCCTTTTAT
4093980 GACTAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
TTTATTCTGAGCCAAATAAGCCTTTTATAGT
Found at i:4094080 original size:33 final size:33
Alignment explanation
Indices: 4094036--4094112 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
4094026 TAAGGCACTA
*
4094036 ACATAGCATGCTAACATATCATACTTGATGATG
1 ACATAGCATGCTAACATATCATAATTGATGATG
* * * *
4094069 ATATAGCATGCTGACGTATCTTAATTGATGATG
1 ACATAGCATGCTAACATATCATAATTGATGATG
*
4094102 ACATGGCATGC
1 ACATAGCATGC
4094113 CAATTTGGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (33 bp):
ACATAGCATGCTAACATATCATAATTGATGATG
Found at i:4094529 original size:19 final size:21
Alignment explanation
Indices: 4094505--4094551 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4094495 AATTGTAATG
*
4094505 AATTTGAT-ACTTTA-TGTAA
1 AATTTGATAAATTTAGTGTAA
*
4094524 AATTTGCTAAATTTAGTGTAA
1 AATTTGATAAATTTAGTGTAA
4094545 AATTTGA
1 AATTTGA
4094552 GATTGAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 5 0.22
21 11 0.48
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (21 bp):
AATTTGATAAATTTAGTGTAA
Found at i:4096655 original size:2 final size:2
Alignment explanation
Indices: 4096648--4096692 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4096638 CCAAAACCTC
4096648 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
4096690 TA T
1 TA T
4096693 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4096730 original size:2 final size:2
Alignment explanation
Indices: 4096723--4096762 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4096713 NNNNNNNNNN
4096723 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
4096763 AACATACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4096856 original size:42 final size:42
Alignment explanation
Indices: 4096803--4096967 Score: 190
Period size: 42 Copynumber: 3.9 Consensus size: 42
4096793 AACTCTATCT
* * *
4096803 CAGCTTATGTGCACT-ACCACACGGCACATAGCTGGGTCAGCA
1 CAGCTCATGTGCACTCA-CACACCGCACATGGCTGGGTCAGCA
* ** * *
4096845 CAACTCATGTGCACTCTTACACCGCACATGGCTGAGTCAACA
1 CAGCTCATGTGCACTCACACACCGCACATGGCTGGGTCAGCA
* * *
4096887 CAGCTCAAGTGCACTCATACACCGCACATGGTTGGGTCAGCA
1 CAGCTCATGTGCACTCACACACCGCACATGGCTGGGTCAGCA
*
4096929 CAGCTCATGTGCACTC-CTACACCACACATGGCTGGGTCA
1 CAGCTCATGTGCACTCAC-ACACCGCACATGGCTGGGTCA
4096968 TAATTATCAC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (42 bp):
CAGCTCATGTGCACTCACACACCGCACATGGCTGGGTCAGCA
Found at i:4098223 original size:21 final size:22
Alignment explanation
Indices: 4098199--4098240 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4098189 CTTATTTCAC
4098199 CCTC-AAAATC-GACAGCCAAAA
1 CCTCAAAAATCAG-CAGCCAAAA
4098220 CCTCAAAAATCAGCAGCCAAA
1 CCTCAAAAATCAGCAGCCAAA
4098241 GTTGCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 14 0.74
23 1 0.05
ACGTcount: A:0.48, C:0.33, G:0.10, T:0.10
Consensus pattern (22 bp):
CCTCAAAAATCAGCAGCCAAAA
Found at i:4098269 original size:36 final size:35
Alignment explanation
Indices: 4098220--4098310 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 35
4098210 ACAGCCAAAA
* *
4098220 CCTCAAAAATCAGCAGCCAAAGTTGCTCATTTCAGC
1 CCTCAAAAATCAGCAGCCAAAGCTGCTCATCTCA-C
* *
4098256 CTTCAAAAATCAGCAGCTAAAGCTGCTCATCTCAC
1 CCTCAAAAATCAGCAGCCAAAGCTGCTCATCTCAC
4098291 CCTC-AAAAT-AGACAGCCAAA
1 CCTCAAAAATCAG-CAGCCAAA
4098311 ACCTCAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 2 0.04
34 12 0.25
35 4 0.08
36 30 0.62
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (35 bp):
CCTCAAAAATCAGCAGCCAAAGCTGCTCATCTCAC
Found at i:4098324 original size:92 final size:92
Alignment explanation
Indices: 4098161--4098358 Score: 299
Period size: 92 Copynumber: 2.2 Consensus size: 92
4098151 TTGCCCCTTA
* * * *
4098161 CAACC-TCAAAAATCAGTAGCCAAAGCTGCTTATTTCACCCTCAAAATCGACAGCCAAAACCTCA
1 CAACCTTCAAAAATCAGCAGCCAAAGCTGCTCATCTCACCCTCAAAATAGACAGCCAAAACCTCA
*
4098225 AAAATCAGCAGCCAAAGTTGCTCATTT
66 AAAATCAGCAGCCAAAGCTGCTCATTT
* *
4098252 CAGCCTTCAAAAATCAGCAGCTAAAGCTGCTCATCTCACCCTCAAAATAGACAGCCAAAACCTCA
1 CAACCTTCAAAAATCAGCAGCCAAAGCTGCTCATCTCACCCTCAAAATAGACAGCCAAAACCTCA
* * *
4098317 AACATCAGTAGCCAAAGCTGCTCCTTT
66 AAAATCAGCAGCCAAAGCTGCTCATTT
4098344 CAACCTTCAAAAATC
1 CAACCTTCAAAAATC
4098359 GACCCTTTAT
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 4 0.04
92 91 0.96
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (92 bp):
CAACCTTCAAAAATCAGCAGCCAAAGCTGCTCATCTCACCCTCAAAATAGACAGCCAAAACCTCA
AAAATCAGCAGCCAAAGCTGCTCATTT
Found at i:4098519 original size:12 final size:13
Alignment explanation
Indices: 4098504--4098533 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4098494 CTCTTTTTTT
4098504 TTTCTTCTTTC-C
1 TTTCTTCTTTCTC
4098516 TTTCTTCTTTCTC
1 TTTCTTCTTTCTC
4098529 TTTCT
1 TTTCT
4098534 CTCCCTCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTCTTTCTC
Found at i:4101547 original size:19 final size:20
Alignment explanation
Indices: 4101518--4101557 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
4101508 TCACTTCTAA
4101518 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
4101538 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
4101557 A
1 A
4101558 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:4106408 original size:19 final size:20
Alignment explanation
Indices: 4106379--4106418 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4106369 TCACTTCTAA
*
4106379 ACTTCAAATCATACTTCAAT
1 ACTTCAAATCATACTCCAAT
4106399 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
4106418 A
1 A
4106419 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:4121812 original size:62 final size:62
Alignment explanation
Indices: 4121728--4121908 Score: 317
Period size: 62 Copynumber: 2.9 Consensus size: 62
4121718 GAGCCGCGAT
*
4121728 CTGCCGGCGCAAGAGGAAGGAGAGCTGGGCAGAAAAATAGAGAATGAGGGAGAGGCGTTCTG
1 CTGCCGGCGCAAGAGGAAGGAGAGCTGGGCAGAAAAATAGAGAAGGAGGGAGAGGCGTTCTG
* *
4121790 CTGCCGGCGCAAGAGGATGGAGAGCTGGGCAGAAAAATAGAGAAGGAGGGAGAGGTGTTCTG
1 CTGCCGGCGCAAGAGGAAGGAGAGCTGGGCAGAAAAATAGAGAAGGAGGGAGAGGCGTTCTG
**
4121852 CTGCCGGCGCAAGAGGAAGGAGAGCTGGGCAGAGGAATAGAGAAGGAGGGAGAGGCG
1 CTGCCGGCGCAAGAGGAAGGAGAGCTGGGCAGAAAAATAGAGAAGGAGGGAGAGGCG
4121909 GAGCAGCGAT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 112 1.00
ACGTcount: A:0.31, C:0.14, G:0.45, T:0.10
Consensus pattern (62 bp):
CTGCCGGCGCAAGAGGAAGGAGAGCTGGGCAGAAAAATAGAGAAGGAGGGAGAGGCGTTCTG
Found at i:4123716 original size:22 final size:23
Alignment explanation
Indices: 4123673--4123717 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4123663 CAATTTATCT
4123673 AATTAGAAAAGAAAAATATAAAA
1 AATTAGAAAAGAAAAATATAAAA
* *
4123696 AATTAGAATA-AAAAATGTAAAA
1 AATTAGAAAAGAAAAATATAAAA
4123718 TATGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (23 bp):
AATTAGAAAAGAAAAATATAAAA
Found at i:4123728 original size:30 final size:29
Alignment explanation
Indices: 4123685--4123820 Score: 95
Period size: 30 Copynumber: 4.7 Consensus size: 29
4123675 TTAGAAAAGA
* *
4123685 AAAATAT-AAAAAATTAGAATAAAAAATG
1 AAAATATGAAAAAATAATAATAAAAAATG
*
4123713 TAAAATATGAAAAAATAATAATAAGAAATG
1 -AAAATATGAAAAAATAATAATAAAAAATG
* *
4123743 -AAATA-GAAAACATGATAATAAAAAAT-
1 AAAATATGAAAAAATAATAATAAAAAATG
* ** *
4123769 ATAATAAAATAAAAATAATAATTAAATAAT-
1 AAAATATGA-AAAAATAATAA-TAAAAAATG
*
4123799 AATAA-ATAAAAAAATAGATAAT
1 AA-AATATGAAAAAATA-ATAAT
4123821 TGTATTAGTA
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
27 22 0.25
28 6 0.07
29 24 0.28
30 33 0.38
31 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.24
Consensus pattern (29 bp):
AAAATATGAAAAAATAATAATAAAAAATG
Found at i:4123751 original size:27 final size:27
Alignment explanation
Indices: 4123686--4123789 Score: 88
Period size: 27 Copynumber: 3.8 Consensus size: 27
4123676 TAGAAAAGAA
* * *
4123686 AAATATAAAAAATTAGAATAAAAAATG
1 AAATAGAAAAAATAATAATAAAAAATG
*
4123713 TAAAATATGAAAAAATAATAATAAGAAATG
1 --AAATA-GAAAAAATAATAATAAAAAATG
* *
4123743 AAATAGAAAACATGATAATAAAAAAT-
1 AAATAGAAAAAATAATAATAAAAAATG
4123769 ATAATA-AAATAAA-AATAATAA
1 A-AATAGAAA-AAATAATAATAA
4123790 TTAAATAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
26 11 0.17
27 24 0.38
28 5 0.08
29 5 0.08
30 18 0.29
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.22
Consensus pattern (27 bp):
AAATAGAAAAAATAATAATAAAAAATG
Found at i:4123774 original size:12 final size:13
Alignment explanation
Indices: 4123690--4123777 Score: 63
Period size: 13 Copynumber: 6.5 Consensus size: 13
4123680 AAAGAAAAAT
* *
4123690 ATAAAAAATTAGA
1 ATAAAAAATGATA
*
4123703 ATAAAAAATGTAAAA
1 ATAAAAAATG--ATA
*
4123718 TATGAAAAAATAATA
1 -AT-AAAAAATGATA
*
4123733 ATAAGAAATGA-A
1 ATAAAAAATGATA
4123745 ATAGAAAACATGATA
1 ATA-AAAA-ATGATA
4123760 ATAAAAAAT-ATA
1 ATAAAAAATGATA
4123772 ATAAAA
1 ATAAAA
4123778 TAAAAATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
12 13 0.21
13 21 0.34
14 10 0.16
15 8 0.13
16 2 0.03
17 7 0.11
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (13 bp):
ATAAAAAATGATA
Found at i:4123781 original size:17 final size:16
Alignment explanation
Indices: 4123763--4123809 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
4123753 CATGATAATA
4123763 AAAAATATAATAAAAT
1 AAAAATATAATAAAAT
*
4123779 AAAAATAATAATTAAAT
1 AAAAAT-ATAATAAAAT
*
4123796 AATAATA-AATAAAA
1 AAAAATATAATAAAA
4123810 AAATAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 14 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATATAATAAAAT
Found at i:4123788 original size:14 final size:13
Alignment explanation
Indices: 4123757--4123819 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
4123747 AGAAAACATG
*
4123757 ATAATAAA-AAAT
1 ATAATAAATAAAA
4123769 ATAATAAAATAAAA
1 ATAAT-AAATAAAA
*
4123783 ATAATAATTAAATA
1 ATAATAAATAAA-A
4123797 ATAATAAATAAAA
1 ATAATAAATAAAA
*
4123810 A-AATAGATAA
1 ATAATAAATAA
4123820 TTGTATTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
12 13 0.30
13 11 0.25
14 20 0.45
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
ATAATAAATAAAA
Found at i:4127132 original size:15 final size:16
Alignment explanation
Indices: 4127097--4127129 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4127087 CAATTATGTG
*
4127097 AATTAAAATTATTTTT
1 AATTAAAACTATTTTT
4127113 AATTAAAACTATTTTT
1 AATTAAAACTATTTTT
4127129 A
1 A
4127130 TTAGCCAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAAAACTATTTTT
Found at i:4128839 original size:96 final size:96
Alignment explanation
Indices: 4128716--4129009 Score: 416
Period size: 96 Copynumber: 3.1 Consensus size: 96
4128706 AAGTTAACGA
** *
4128716 AAAC-CTCATACTCCCGTTGCTACTCTTTTTCTTTCAGCTTTTGATTATTTTTTTCATACTCCAA
1 AAACTCTCATACTCTTGTTGCTTCTCTTTTTCTTTCAGCTTTTGATTATTTTTTTCATACTCCAA
4128780 TAATTCCTTCAACTTTTTC-ATTTCACACTTC
66 TAATTCCTTCAAC-TTTTCAATTTCACACTTC
* * *
4128811 AAACTCTCATACTCTTGTTGCTTCTCTTTTTTTTTCAACTGTTGATTATTTTTTTCATACTCCAA
1 AAACTCTCATACTCTTGTTGCTTCTCTTTTTCTTTCAGCTTTTGATTATTTTTTTCATACTCCAA
*
4128876 TAATTCCTTCAACTTTTCAATTTCACACTCC
66 TAATTCCTTCAACTTTTCAATTTCACACTTC
* * *
4128907 AAACTCTCATACTCTTGTTACTTCTCTTTTTCTTTCAG-TTGTTGATTGTTTTTATCATACTCCA
1 AAACTCTCATACTCTTGTTGCTTCTCTTTTTCTTTCAGCTT-TTGATTATTTTTTTCATACTCCA
* * *
4128971 ACAA-TCCTTTCAACTTTTCAATTTCATACTTT
65 ATAATTCC-TTCAACTTTTCAATTTCACACTTC
4129003 AAACTCT
1 AAACTCT
4129010 TAATTTCACT
Statistics
Matches: 178, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
95 13 0.07
96 165 0.93
ACGTcount: A:0.22, C:0.25, G:0.04, T:0.48
Consensus pattern (96 bp):
AAACTCTCATACTCTTGTTGCTTCTCTTTTTCTTTCAGCTTTTGATTATTTTTTTCATACTCCAA
TAATTCCTTCAACTTTTCAATTTCACACTTC
Done.