Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 73 of 120
Found at i:8877166 original size:3 final size:3
Alignment explanation
Indices: 8877160--8877204 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
8877150 GTAGTAGTAG
8877160 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8877205 AATTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:8892683 original size:4 final size:4
Alignment explanation
Indices: 8892674--8892699 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
8892664 AAAACACCAC
8892674 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
8892700 AGATGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:8893795 original size:49 final size:49
Alignment explanation
Indices: 8893642--8893850 Score: 212
Period size: 49 Copynumber: 4.3 Consensus size: 49
8893632 AAACCAAATT
* * * * * *
8893642 TTTTAAAAAAAGATTTTAAAATTTTAAAGCCTTTGTTTATGAGGAGCCA
1 TTTTCAAACAAGATTTTAAAATTTCAAAGCCTCTATTTAGGAGGAGCCA
* * * * *
8893691 TTTTCAAATAAGATTTATTTTAAGTTTCAAAGCCTCTATTTAGGGGGAGCTA
1 TTTTCAAACAAGA--T-TTTAAAATTTCAAAGCCTCTATTTAGGAGGAGCCA
* *
8893743 TTTTCAAACAAGATTTTAAAATTTCAAAGCCTCTATATAGGATGAGCCA
1 TTTTCAAACAAGATTTTAAAATTTCAAAGCCTCTATTTAGGAGGAGCCA
* * *
8893792 TTTTCAAAGAAGA-TTT----TTTCAAAGCCCCTATTTAGGGGGAGCCA
1 TTTTCAAACAAGATTTTAAAATTTCAAAGCCTCTATTTAGGAGGAGCCA
8893836 TTTTCAAACAAGATT
1 TTTTCAAACAAGATT
8893851 AAAAAAAAAA
Statistics
Matches: 133, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
44 36 0.27
45 1 0.01
48 3 0.02
49 52 0.39
50 1 0.01
51 1 0.01
52 39 0.29
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (49 bp):
TTTTCAAACAAGATTTTAAAATTTCAAAGCCTCTATTTAGGAGGAGCCA
Found at i:8893834 original size:44 final size:45
Alignment explanation
Indices: 8893715--8893850 Score: 175
Period size: 44 Copynumber: 3.0 Consensus size: 45
8893705 TTATTTTAAG
*
8893715 TTTCAAAGCCTCTATTTAGGGGGAGCTATTTTCAAACAAGATTTTAAAA
1 TTTCAAAGCCTCTATTTAGGGGGAGCCATTTTCAAACAAGA-TTT---A
* ** *
8893764 TTTCAAAGCCTCTATATAGGATGAGCCATTTTCAAAGAAGATTT-
1 TTTCAAAGCCTCTATTTAGGGGGAGCCATTTTCAAACAAGATTTA
*
8893808 TTTCAAAGCCCCTATTTAGGGGGAGCCATTTTCAAACAAGATT
1 TTTCAAAGCCTCTATTTAGGGGGAGCCATTTTCAAACAAGATT
8893851 AAAAAAAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
44 38 0.49
48 3 0.04
49 36 0.47
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (45 bp):
TTTCAAAGCCTCTATTTAGGGGGAGCCATTTTCAAACAAGATTTA
Found at i:8894764 original size:11 final size:12
Alignment explanation
Indices: 8894732--8894758 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8894722 AAACCTTAAG
8894732 AAAAGAGAAAAA
1 AAAAGAGAAAAA
8894744 AAAAGAGAAAAA
1 AAAAGAGAAAAA
8894756 AAA
1 AAA
8894759 TGGAAAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAGAAAAA
Found at i:8903965 original size:15 final size:16
Alignment explanation
Indices: 8903934--8903966 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8903924 ATTTTGAAAA
*
8903934 TGTTATATAATAGTTT
1 TGTTATATAATACTTT
8903950 TGTTAT-TAATACTTT
1 TGTTATATAATACTTT
8903965 TG
1 TG
8903967 AACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (16 bp):
TGTTATATAATACTTT
Found at i:8906310 original size:39 final size:39
Alignment explanation
Indices: 8906266--8906353 Score: 176
Period size: 39 Copynumber: 2.3 Consensus size: 39
8906256 TTTTAATATC
8906266 ATTAGGAATAGATCTTTAATAGCACTTATGTGAAATTTT
1 ATTAGGAATAGATCTTTAATAGCACTTATGTGAAATTTT
8906305 ATTAGGAATAGATCTTTAATAGCACTTATGTGAAATTTT
1 ATTAGGAATAGATCTTTAATAGCACTTATGTGAAATTTT
8906344 ATTAGGAATA
1 ATTAGGAATA
8906354 AAATTATAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (39 bp):
ATTAGGAATAGATCTTTAATAGCACTTATGTGAAATTTT
Found at i:8907909 original size:143 final size:143
Alignment explanation
Indices: 8907618--8907966 Score: 323
Period size: 143 Copynumber: 2.4 Consensus size: 143
8907608 TCAAGGTTTT
8907618 TTTTTTTGCAAAACACTTTAAATCATGGTTTTATATTATTTCATGATTTTTGGTGCATTAAAACC
1 TTTTTTTGCAAAACACTTTAAATCATGGTTTTATATTATTTCATGATTTTTGGTGCATTAAAACC
* * * * * * * *
8907683 ATTGATTACACTTTAAAAGGTGTGAAACTACCAAAATACCATTAGATATATTTTTGTAATTTGAC
66 ATTGATTACACCTCAAAAGGTATGAAACTACCAAAATAACATTAAAGATATATTCGTAATTTGAC
8907748 ATTTTTTAGTCAA
131 ATTTTTTAGTCAA
* * * *
8907761 TTTTTTTGCAAAACATTTTAAATCATGACTTTTTATATTATTTCGTGATTTTTTGTGCATTAAAA
1 TTTTTTTGCAAAACACTTTAAATCATG--GTTTTATATTATTTCATGATTTTTGGTGCATTAAAA
* * * ** * * *
8907826 CC-TTGATTGCACCTCAGAATGTATGAATTTACTAAAATAAC-TTAAAGGGTA-ATTCGTTATTT
64 CCATTGATTACACCTCAAAAGGTATGAAACTACCAAAATAACATTAAA-GATATATTCGTAATTT
* *
8907888 GA-TTTTTTTGAGGTCGA
128 GACATTTTTT-A-GTCAA
** * ** * * * *
8907905 -TTTTTCACAAAA-ACTTCTAGATCATAATTTCATATTATTTTAGGATTTTTGGTGCTTTAAAA
1 TTTTTTTGCAAAACACTT-TAAATCATGGTTTTATATTATTTCATGATTTTTGGTGCATTAAAA
8907967 TCATAAAAAT
Statistics
Matches: 166, Mismatches: 34, Indels: 14
0.78 0.16 0.07
Matches are distributed among these distances:
141 29 0.17
142 9 0.05
143 58 0.35
144 35 0.21
145 35 0.21
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (143 bp):
TTTTTTTGCAAAACACTTTAAATCATGGTTTTATATTATTTCATGATTTTTGGTGCATTAAAACC
ATTGATTACACCTCAAAAGGTATGAAACTACCAAAATAACATTAAAGATATATTCGTAATTTGAC
ATTTTTTAGTCAA
Found at i:8914599 original size:17 final size:17
Alignment explanation
Indices: 8914572--8914604 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
8914562 ATTTCTAAAC
8914572 TTTCTCTTTATTTATTTG
1 TTTCTCTTTA-TTATTTG
8914590 TTTC-CTTTATTATTT
1 TTTCTCTTTATTATTT
8914605 ATGTAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTCTCTTTATTATTTG
Found at i:8917021 original size:17 final size:17
Alignment explanation
Indices: 8916999--8917033 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8916989 TTGTTAATGT
8916999 TGTTGTAGCAATTAAAG
1 TGTTGTAGCAATTAAAG
8917016 TGTTGTAGCAATTAAAG
1 TGTTGTAGCAATTAAAG
8917033 T
1 T
8917034 ATAGATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (17 bp):
TGTTGTAGCAATTAAAG
Found at i:8917021 original size:20 final size:18
Alignment explanation
Indices: 8916994--8917031 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
8916984 TTTATTTGTT
8916994 AATGTTGTTGTAGCAATTA
1 AATG-TGTTGTAGCAATTA
8917013 AA-GTGTTGTAGCAATTA
1 AATGTGTTGTAGCAATTA
8917030 AA
1 AA
8917032 GTATAGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 1 0.05
19 2 0.11
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (18 bp):
AATGTGTTGTAGCAATTA
Found at i:8920317 original size:103 final size:103
Alignment explanation
Indices: 8920127--8920321 Score: 279
Period size: 103 Copynumber: 1.9 Consensus size: 103
8920117 TAAAAAGGCT
* *
8920127 TTTATTTGTGAAAATAATTTATTTTCATAAATATCTTTCAATATATTGGTAAGACTTTCTGTCAA
1 TTTATTTGTGAAAATAATTTATTTTCAAAAATATCTTTCAATATATTGGTAAAACTTTCTGTCAA
*
8920192 AGATTATTCTTCAATATGTTGATAGGACTGAAAATTTA
66 AGATTATTCTTCAATATATTGATAGGACTGAAAATTTA
* * *
8920230 TTTATTTGTGAAAATAATTTATTTTCAAAAATATCTTTTAATATGTTGGTAAAATTTTCCT-TC-
1 TTTATTTGTGAAAATAATTTATTTTCAAAAATATCTTTCAATATATTGGTAAAACTTT-CTGTCA
*
8920293 AAGAATTA-TCTTCCAATGTATTGATAGGA
65 AAG-ATTATTCTT-CAATATATTGATAGGA
8920322 TTTTTAAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
102 7 0.09
103 73 0.89
104 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (103 bp):
TTTATTTGTGAAAATAATTTATTTTCAAAAATATCTTTCAATATATTGGTAAAACTTTCTGTCAA
AGATTATTCTTCAATATATTGATAGGACTGAAAATTTA
Found at i:8920490 original size:15 final size:14
Alignment explanation
Indices: 8920470--8920503 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
8920460 AAGAAAATAA
8920470 ACAAAAATTATCAT
1 ACAAAAATTATCAT
8920484 ACAAAAATTATCAT
1 ACAAAAATTATCAT
*
8920498 GCAAAA
1 ACAAAA
8920504 TAATATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (14 bp):
ACAAAAATTATCAT
Found at i:8920524 original size:17 final size:15
Alignment explanation
Indices: 8920478--8920524 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
8920468 AAACAAAAAT
* *
8920478 TATCATACAAAA-AT
1 TATCATGCAAAATAA
8920492 TATCATGCAAAATAA
1 TATCATGCAAAATAA
8920507 TATCATGCGAACAATAA
1 TATCATGC-AA-AATAA
8920524 T
1 T
8920525 TTACTATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.39
15 9 0.32
16 2 0.07
17 6 0.21
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (15 bp):
TATCATGCAAAATAA
Found at i:8921563 original size:28 final size:28
Alignment explanation
Indices: 8921531--8921589 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
8921521 TATAGAATTT
*
8921531 TTAACAAG-AATTTTAAGGATTTCATTGA
1 TTAAC-AGTAATTTTAAGGATTCCATTGA
**
8921559 TTAACAGTAATTTTTGGGATTCCATTGA
1 TTAACAGTAATTTTAAGGATTCCATTGA
8921587 TTA
1 TTA
8921590 TCAGAGATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (28 bp):
TTAACAGTAATTTTAAGGATTCCATTGA
Found at i:8922590 original size:17 final size:17
Alignment explanation
Indices: 8922554--8922604 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
8922544 ATTTAATAAA
* * *
8922554 AAATATTATAAAAATAT
1 AAATATTTTAAAATTTT
8922571 AAATATTTTAAAATTTT
1 AAATATTTTAAAATTTT
*
8922588 AAA-A-TTTAAACTTTT
1 AAATATTTTAAAATTTT
8922603 AA
1 AA
8922605 TTAAAGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 17 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATTTTAAAATTTT
Found at i:8924988 original size:36 final size:38
Alignment explanation
Indices: 8924923--8924997 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 38
8924913 TTTGACTTCG
* * *
8924923 AATTTAAATTTGAGTT-GAATTAAATTTTAATT-TTTA
1 AATTTAAATTTGAGTTAAAATAAAATTTAAATTATTTA
* *
8924959 AATTTAAGTTTGATTTAAAATAAAATTTAAATTATTTA
1 AATTTAAATTTGAGTTAAAATAAAATTTAAATTATTTA
8924997 A
1 A
8924998 TTATATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 14 0.44
37 13 0.41
38 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (38 bp):
AATTTAAATTTGAGTTAAAATAAAATTTAAATTATTTA
Found at i:8925055 original size:19 final size:20
Alignment explanation
Indices: 8925026--8925073 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
8925016 TAAAAAATAA
*
8925026 ATTTAATTTTTA-TATTTGAT
1 ATTTAAATTTTATTATTT-AT
8925046 -TTTAAATTTTATTATTTAT
1 ATTTAAATTTTATTATTTAT
8925065 ATTTAAATT
1 ATTTAAATT
8925074 CAAATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTAAATTTTATTATTTAT
Found at i:8925078 original size:26 final size:25
Alignment explanation
Indices: 8925024--8925079 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
8925014 AATAAAAAAT
* * *
8925024 AAATTTAATTTTTATATTTGATTTT
1 AAATTTAATTTTTATATTTAAATTC
*
8925049 AAATTTTATTATTTATATTTAAATTC
1 AAATTTAATT-TTTATATTTAAATTC
8925075 AAATT
1 AAATT
8925080 AATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
AAATTTAATTTTTATATTTAAATTC
Found at i:8930010 original size:18 final size:18
Alignment explanation
Indices: 8929982--8930031 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
8929972 ATAGATGACT
*
8929982 TAAATAAATAAAAATAAAA
1 TAAA-AAATAAAAAGAAAA
**
8930001 TAAAAAATAAAGGGAAAA
1 TAAAAAATAAAAAGAAAA
*
8930019 TAGAAAATAAAAA
1 TAAAAAATAAAAA
8930032 CCAAAAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (18 bp):
TAAAAAATAAAAAGAAAA
Found at i:8931826 original size:38 final size:38
Alignment explanation
Indices: 8931781--8931882 Score: 116
Period size: 38 Copynumber: 2.7 Consensus size: 38
8931771 AACTAAAGTT
* *
8931781 TGAAACTTTAAATAAATTGCTCCCCCACAATTGAGGCA
1 TGAAACTTTAAATAAATTGCTCCCCCAAAAATGAGGCA
* * * * **
8931819 TGGAACTTTAACTAAATTGCTTCCCAAAAAATGAGGTT
1 TGAAACTTTAAATAAATTGCTCCCCCAAAAATGAGGCA
*
8931857 TGAAACTTTAAAT-AATTGCTGCCCCA
1 TGAAACTTTAAATAAATTGCTCCCCCA
8931883 TAACTAAAAC
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
37 11 0.21
38 41 0.79
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (38 bp):
TGAAACTTTAAATAAATTGCTCCCCCAAAAATGAGGCA
Found at i:8932055 original size:22 final size:22
Alignment explanation
Indices: 8931961--8932074 Score: 94
Period size: 21 Copynumber: 5.3 Consensus size: 22
8931951 GAAGTCTTAT
*
8931961 AAATTATG-TCTGGAGGTCTT-G
1 AAATTATGCTCT-GAGGTTTTAG
* *
8931982 AAATTATGCTCGGAGGTCTT-G
1 AAATTATGCTCTGAGGTTTTAG
* *
8932003 AAATTATGCTC-GAAGTTCTTAC
1 AAATTATGCTCTGAGGTT-TTAG
*
8932025 AAATCATGCTCTGAGGTTTTAG
1 AAATTATGCTCTGAGGTTTTAG
* * *
8932047 AGATTATGC-CAGAGGTTTTAT
1 AAATTATGCTCTGAGGTTTTAG
8932068 AAATTAT
1 AAATTAT
8932075 TTTCACATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
20 4 0.05
21 46 0.60
22 22 0.29
23 5 0.06
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (22 bp):
AAATTATGCTCTGAGGTTTTAG
Found at i:8932731 original size:16 final size:16
Alignment explanation
Indices: 8932706--8932745 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
8932696 TAATCAAGGG
8932706 TCAAAATCTCATA-TTT
1 TCAAAATCTC-TACTTT
*
8932722 TCAAATTCTCTACTTT
1 TCAAAATCTCTACTTT
8932738 TCAAAATC
1 TCAAAATC
8932746 AAAATCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TCAAAATCTCTACTTT
Found at i:8933931 original size:10 final size:10
Alignment explanation
Indices: 8933873--8933940 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
8933863 ACATTTTTCA
*
8933873 CCTTTTTTTC
1 CCTTTTTTTT
8933883 CCTTTTTTTT
1 CCTTTTTTTT
*
8933893 -CTCTTTTTT
1 CCTTTTTTTT
*
8933902 -CTTTTCATTT
1 CCTTTT-TTTT
*
8933912 -CTTTCCTTTT
1 CCTTT-TTTTT
8933922 CCTTTTTTTT
1 CCTTTTTTTT
8933932 CCTTTTTTT
1 CCTTTTTTT
8933941 CTTTCTTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 12 0.25
10 32 0.67
11 4 0.08
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (10 bp):
CCTTTTTTTT
Found at i:8933934 original size:16 final size:15
Alignment explanation
Indices: 8933896--8933937 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
8933886 TTTTTTTCTC
8933896 TTTTTT-CTTTTCAT
1 TTTTTTCCTTTTCAT
* *
8933910 TTCTTTCCTTTTCCTT
1 TTTTTTCCTTTT-CAT
8933926 TTTTTTCCTTTT
1 TTTTTTCCTTTT
8933938 TTTCTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 13 0.57
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTCCTTTTCAT
Found at i:8937901 original size:20 final size:20
Alignment explanation
Indices: 8937878--8937949 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
8937868 CAAATTATAC
8937878 AAATA-AATAATAAATCATGT
1 AAATATAATAA-AAATCATGT
*
8937898 AAATATATTAAAAATCATG-
1 AAATATAATAAAAATCATGT
* *
8937917 CAAT-TAATAAATAATCATGC
1 AAATATAATAAA-AATCATGT
*
8937937 AAATATATTAAAA
1 AAATATAATAAAA
8937950 CTTATACAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 17 0.40
21 10 0.23
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (20 bp):
AAATATAATAAAAATCATGT
Found at i:8942250 original size:76 final size:76
Alignment explanation
Indices: 8942124--8942276 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
8942114 CTACGCACCT
*
8942124 TTCTTTATCGCATTAAGGATACTATGCCAACATGCCCAATTTGCCTAGCACACCATCTATATTTC
1 TTCTTTATCGCATTAAGGATACTACGCCAACATGCCCAATTTGCCTAGCACACCATCTATATTTC
8942189 AAACCCATAAC
66 AAACCCATAAC
8942200 TTCTTTATCGCATTAAGGATACTACGCCAACATGCCCAATTTGCCTAGCACACCATCTATATTTC
1 TTCTTTATCGCATTAAGGATACTACGCCAACATGCCCAATTTGCCTAGCACACCATCTATATTTC
8942265 AAACCCATAAC
66 AAACCCATAAC
8942276 T
1 T
8942277 CCTCTATCAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.30
Consensus pattern (76 bp):
TTCTTTATCGCATTAAGGATACTACGCCAACATGCCCAATTTGCCTAGCACACCATCTATATTTC
AAACCCATAAC
Found at i:8951908 original size:9 final size:9
Alignment explanation
Indices: 8951894--8951941 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
8951884 ATTATTATTA
8951894 TTTTTTCTT
1 TTTTTTCTT
*
8951903 TTTTTTATTT
1 TTTTTT-CTT
*
8951913 TTTTTTATT
1 TTTTTTCTT
8951922 TTTTTTC-T
1 TTTTTTCTT
*
8951930 TTCTTTCTT
1 TTTTTTCTT
8951939 TTT
1 TTT
8951942 CCTTCTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 7 0.22
9 17 0.53
10 8 0.25
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:8951910 original size:19 final size:19
Alignment explanation
Indices: 8951888--8951927 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8951878 TTTAAAATTA
*
8951888 TTATTATTTTTTCTTTTTT
1 TTATTATTTTTTATTTTTT
*
8951907 TTATTTTTTTTTATTTTTT
1 TTATTATTTTTTATTTTTT
8951926 TT
1 TT
8951928 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (19 bp):
TTATTATTTTTTATTTTTT
Found at i:8951914 original size:10 final size:10
Alignment explanation
Indices: 8951888--8951927 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
8951878 TTTAAAATTA
*
8951888 TTATTATTTT
1 TTATTTTTTT
*
8951898 TT-CTTTTTT
1 TTATTTTTTT
8951907 TTATTTTTTT
1 TTATTTTTTT
8951917 TTATTTTTTT
1 TTATTTTTTT
8951927 T
1 T
8951928 CTTTCTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:8952884 original size:21 final size:23
Alignment explanation
Indices: 8952849--8952895 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
8952839 AAAAGATTTT
* *
8952849 TTTTATATATATTATTTTTGTTA
1 TTTTATATATATTATTATTGATA
8952872 TTTTA-AT-TATTATTATTGATA
1 TTTTATATATATTATTATTGATA
8952893 TTT
1 TTT
8952896 ATGTATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTATATATATTATTATTGATA
Found at i:8954138 original size:18 final size:18
Alignment explanation
Indices: 8954117--8954151 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
8954107 AAAAGAAAGT
8954117 AAAAA-AAAAAAACAAATC
1 AAAAATAAAAAAA-AAATC
8954135 AAAAATAAAAAAAAAAT
1 AAAAATAAAAAAAAAAT
8954152 TTCACACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.09
Consensus pattern (18 bp):
AAAAATAAAAAAAAAATC
Found at i:8965301 original size:46 final size:46
Alignment explanation
Indices: 8965141--8965784 Score: 644
Period size: 46 Copynumber: 13.5 Consensus size: 46
8965131 AAATGAGATT
* *
8965141 TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGTTTTTTCCAAGATGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-C-A-A-GAGAA
* * *
8965191 TTTTAAAGTTG-TGAAGCCTCTGCTAAAAGGAGCTTTTCTAAAATGAGAA
1 TTTTAAAGTTGTTG-AGCCTCTGCTGAGAGGAGCTTTT-T-CAA-GAGAA
* *
8965240 TTTTAAAGTTGTTGAGCCTTTGTTGAGAGGAGCTTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * *
8965286 TTTTAAAGTTATTGAGCCTTTGCTGAGATGAGCTTTTTCAAGATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-GA-A
* * *
8965334 TTTTTTAAAGTTATTGAGCCTCTACTGAGAGGAACTTTTTCAAGAGAA
1 --TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * * *
8965382 TTTTAAAGTTGTTGAGCCTCTACTAAGATGAGCTTTTTTTAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGAGAA
* * * * *
8965429 TTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGCTTTTTTAAAAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * * *
8965475 ATTTAAAATTGTTGAGCTTCTGCTGAAAGGAGCTTTTTCAAAATGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC--AA-GAGAA
* *
8965524 TTTTAAAAGTTGTTGAGCCTCTG-TCGAGAGGAGCTTTTCCAAGATAAGATTT
1 TTTT-AAAGTTGTTGAGCCTCTGCT-GAGAGGAGCTTTTTCAAG---AGA--A
* ** *
8965576 TTTTAAAGTTATTGAGCCTCTAATGAAAGGAGCTTTTTCAAGATGAGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-GA-A
* * *
8965624 TTTTTTAAAGTTGTTGAGCCTCTACTAAGAGGAGTTTTTTCAAGAGAA
1 --TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * **
8965672 TTTTAAAGTTGTTGAGCATCTACTGAGACAAGCTTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* *
8965718 TTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCTTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* *
8965764 TTTCAAAGTTATTGAGCCTCT
1 TTTTAAAGTTGTTGAGCCTCT
8965785 ACTTAAATGA
Statistics
Matches: 506, Mismatches: 66, Indels: 48
0.82 0.11 0.08
Matches are distributed among these distances:
46 220 0.43
47 45 0.09
48 9 0.02
49 52 0.10
50 142 0.28
51 33 0.07
52 5 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (46 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
Found at i:8965372 original size:96 final size:95
Alignment explanation
Indices: 8965133--8965801 Score: 665
Period size: 96 Copynumber: 7.0 Consensus size: 95
8965123 TCGAGAACAA
* * *
8965133 ATGAGATTTTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGTTTTTTCCAAGATGAGAATTTTAAA
1 ATGAGA-TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTT-C-A-A-GAGAATTTTAAA
* * * *
8965198 GTT-GTGAAGCCTCTGCTAAAAGGAGC-TTTTCTAAA
61 GTTATTG-AGCCTCTACTGAAAGGAGCTTTTTC-AAG
* * **
8965233 ATGAGAATTTTAAAGTTGTTGAGCCTTTGTTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTAT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTAT
* * * *
8965298 TGAGCCTTTGCTGAGATGAGCTTTTTCAAG
66 TGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* * *
8965328 ATGAGATTTTTTAAAGTTATTGAGCCTCTACTGAGAGGAACTTTTTCAAGAGAATTTTAAAGTTG
1 ATGAGA-TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTA
* *
8965393 TTGAGCCTCTACT-AAGATGAGCTTTTTTTAAG
65 TTGAGCCTCTACTGAA-AGGAGC-TTTTTCAAG
* ** * * * * * *
8965425 A-GA-A-TTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGCTTTTTTAAAAAAAATTTAAAATTGT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTAT
* * *
8965487 TGAGCTTCTGCTGAAAGGAGCTTTTTCAAA
66 TGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* * * *
8965517 ATGAGAATTTTAAAAGTTGTTGAGCCTCT-GTCGAGAGGAGCTTTTCCAAGATAAGATTTTTTTA
1 ATGAG-ATTTTTAAAGTTGTTGAGCCTCTACT-GAGAGGAGCTTTTTCAAG---AGA--ATTTTA
*
8965581 AAGTTATTGAGCCTCTAATGAAAGGAGCTTTTTCAAG
59 AAGTTATTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* * *
8965618 ATGAGATTTTTTAAAGTTGTTGAGCCTCTACTAAGAGGAGTTTTTTCAAGAGAATTTTAAAGTTG
1 ATGAGA-TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTA
* * **
8965683 TTGAGCATCTACTGAGACAAGCTTTTTCAAG
65 TTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* *
8965714 A-GA-A-TTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCTTTTTCAAGAGAATTTCAAAGTTAT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTAT
* * *
8965776 TGAGCCTCTACTTAAATGAGTTTTTT
66 TGAGCCTCTACTGAAAGGAGCTTTTT
8965802 TAAATTTTCA
Statistics
Matches: 478, Mismatches: 73, Indels: 44
0.80 0.12 0.07
Matches are distributed among these distances:
92 81 0.17
93 67 0.14
94 3 0.01
95 44 0.09
96 149 0.31
97 10 0.02
98 4 0.01
99 36 0.08
100 7 0.01
101 76 0.16
102 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (95 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTAT
TGAGCCTCTACTGAAAGGAGCTTTTTCAAG
Found at i:8965620 original size:290 final size:286
Alignment explanation
Indices: 8965141--8965763 Score: 855
Period size: 290 Copynumber: 2.2 Consensus size: 286
8965131 AAATGAGATT
* * *
8965141 TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAG-TTTTTTCCAAGATGAGAATTTTAAAGTTGTGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTT-CAAGA-GAAAAATTTAAAATTGTGA
* *
8965205 AGCCTCTGCTAAAAGGAGCTTTTCTAAAATGAGAATTTTAAAGTTGTTGAGCCTTTGTTGAGAGG
64 AGCCTCTGCTAAAAGGAGCTTTTCTAAAATGAGAATTTTAAAGTTGTTGAGCCTCTGTCGAGAGG
* * ** * *
8965270 AGCTTTTTCAAGAGAATTTTAAAGTTATTGAGCCTTTGCTGAGATGAGCTTTTTCAAGATGAGAT
129 AGCTTTTCCAAGAGAATTTTAAAGTTATTGAGCCTCTAATGAAAGGAGCTTTTTCAAGATGAGAT
* *
8965335 TTTTTAAAGTTATTGAGCCTCTACTGAGAGGAACTTTTTCAAGAGAATTTTAAAGTTGTTGAGCC
194 TTTTTAAAGTTATTGAGCCTCTACTAAGAGGAACTTTTTCAAGAGAATTTTAAAGTTGTTGAGCA
** *
8965400 TCTACTAAGATGAGCTTTTTTTAAGAGAA
259 TCTACTAAGACAAGC-TTTTTCAAGAGAA
* * *
8965429 TTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGCTTTTTT-AA-A-AAAAATTTAAAATTGTTG-A
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTTCAAGAGAAAAATTTAAAATTG-TGAA
* *
8965490 GCTTCTGCTGAAAGGAGCTTTT-TCAAAATGAGAATTTTAAAAGTTGTTGAGCCTCTGTCGAGAG
65 GCCTCTGCTAAAAGGAGCTTTTCT-AAAATGAGAATTTT-AAAGTTGTTGAGCCTCTGTCGAGAG
*
8965554 GAGCTTTTCCAAGATAAGATTTTTTTAAAGTTATTGAGCCTCTAATGAAAGGAGCTTTTTCAAGA
128 GAGCTTTTCCAAG---AGA--ATTTTAAAGTTATTGAGCCTCTAATGAAAGGAGCTTTTTCAAGA
* **
8965619 TGAGATTTTTTAAAGTTGTTGAGCCTCTACTAAGAGGAGTTTTTTCAAGAGAATTTTAAAGTTGT
188 TGAGATTTTTTAAAGTTATTGAGCCTCTACTAAGAGGAACTTTTTCAAGAGAATTTTAAAGTTGT
*
8965684 TGAGCATCTACTGAGACAAGCTTTTTCAAGAGAA
253 TGAGCATCTACTAAGACAAGCTTTTTCAAGAGAA
*
8965718 TTTTAAAGTTGTTGAGCCTCTACTGAGATGAGC-TTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTTCAAGAGAA
8965764 TTTCAAAGTT
Statistics
Matches: 293, Mismatches: 30, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
283 1 0.00
284 47 0.16
285 37 0.13
286 1 0.00
287 2 0.01
288 37 0.13
289 49 0.17
290 117 0.40
291 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (286 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTTCAAGAGAAAAATTTAAAATTGTGAAG
CCTCTGCTAAAAGGAGCTTTTCTAAAATGAGAATTTTAAAGTTGTTGAGCCTCTGTCGAGAGGAG
CTTTTCCAAGAGAATTTTAAAGTTATTGAGCCTCTAATGAAAGGAGCTTTTTCAAGATGAGATTT
TTTAAAGTTATTGAGCCTCTACTAAGAGGAACTTTTTCAAGAGAATTTTAAAGTTGTTGAGCATC
TACTAAGACAAGCTTTTTCAAGAGAA
Found at i:8966046 original size:19 final size:19
Alignment explanation
Indices: 8966015--8966076 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
8966005 AAAATTTTCA
*
8966015 TTTTTCA-TTTTTTATTTT
1 TTTTTCATTTTTTTCTTTT
8966033 TTTTTCATTTTTTTCTTTCT
1 TTTTTCATTTTTTTCTTT-T
* *
8966053 TCTTTC-TTTTTTTCTTTC
1 TTTTTCATTTTTTTCTTTT
8966071 TTTTTC
1 TTTTTC
8966077 CTTCTTCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 12 0.32
19 20 0.53
20 6 0.16
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTCATTTTTTTCTTTT
Found at i:8966055 original size:7 final size:7
Alignment explanation
Indices: 8966045--8966088 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
8966035 TTTCATTTTT
8966045 TTCTTTC
1 TTCTTTC
8966052 TTCTTTC
1 TTCTTTC
8966059 TT-TTT-
1 TTCTTTC
8966064 TTCTTTC
1 TTCTTTC
8966071 TT-TTTCC
1 TTCTTT-C
8966078 TTC-TTC
1 TTCTTTC
8966084 TTCTT
1 TTCTT
8966089 CCTTACCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
5 2 0.06
6 13 0.41
7 17 0.53
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTCTTTC
Found at i:8966074 original size:29 final size:28
Alignment explanation
Indices: 8966031--8966085 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
8966021 ATTTTTTATT
*
8966031 TTTTTTTCATTTTTTTCTTTCTTCTTTC
1 TTTTTTTCATTTTTTTCCTTCTTCTTTC
*
8966059 TTTTTTTCTTTCTTTTTCCTTCTTCTT
1 TTTTTTTCATT-TTTTTCCTTCTTCTT
8966086 CTTCCTTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTTTCATTTTTTTCCTTCTTCTTTC
Found at i:8966085 original size:32 final size:31
Alignment explanation
Indices: 8966029--8966088 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
8966019 TCATTTTTTA
8966029 TTTTTTTTTCATTTTTTTCTTTCTTCTTTCT
1 TTTTTTTTTCATTTTTTTCTTTCTTCTTTCT
8966060 TTTTTTCTTTC-TTTTTCCTTC-TTCTTCTT
1 TTTTTT-TTTCATTTTT--TTCTTTCTTCTT
8966089 CCTTACCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 11 0.42
32 12 0.46
33 3 0.12
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTTTTTCATTTTTTTCTTTCTTCTTTCT
Found at i:8967029 original size:21 final size:23
Alignment explanation
Indices: 8966993--8967040 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
8966983 TTTTTAAAAA
* *
8966993 ATTTTATATATATTATTTTTGTT
1 ATTTTATATATATTATTATTGAT
8967016 ATTTTA-AT-TATTATTATTGAT
1 ATTTTATATATATTATTATTGAT
8967037 ATTT
1 ATTT
8967041 ATGCATGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 2 0.09
23 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
ATTTTATATATATTATTATTGAT
Found at i:8981735 original size:15 final size:16
Alignment explanation
Indices: 8981703--8981736 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8981693 ACTTCAAATA
*
8981703 TAAGTTATATTTTTAT
1 TAAGTTATATTCTTAT
8981719 TAAGTTATA-TCTTAT
1 TAAGTTATATTCTTAT
8981734 TAA
1 TAA
8981737 CACTTGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (16 bp):
TAAGTTATATTCTTAT
Found at i:8983461 original size:17 final size:17
Alignment explanation
Indices: 8983439--8983482 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
8983429 GGCTTTAGAA
8983439 AGAGAAAATAAAATTTT
1 AGAGAAAATAAAATTTT
* *
8983456 AGAGAAAGTATGAACTTTT
1 AGAGAAA--ATAAAATTTT
8983475 AGAGAAAA
1 AGAGAAAA
8983483 AATATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.55, C:0.02, G:0.18, T:0.25
Consensus pattern (17 bp):
AGAGAAAATAAAATTTT
Found at i:8983494 original size:19 final size:19
Alignment explanation
Indices: 8983472--8983509 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
8983462 AGTATGAACT
8983472 TTTAGA-GAAAAAATATAAA
1 TTTAGATGAAAAAA-ATAAA
8983491 TTTAGATGAAAAAAATAAA
1 TTTAGATGAAAAAAATAAA
8983510 AAAAGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (19 bp):
TTTAGATGAAAAAAATAAA
Found at i:8984254 original size:29 final size:29
Alignment explanation
Indices: 8984230--8984313 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
8984220 AAAAATCATC
8984230 AAAATTAAAAATATAATGACAAAATTCAAT
1 AAAATT-AAAATATAATGACAAAATTCAAT
* **
8984260 AAAATTAAATTATAATGACAATTTTCAAT
1 AAAATTAAAATATAATGACAAAATTCAAT
* * * *
8984289 AAAATTGAATTACAATGAGAAAATT
1 AAAATTAAAATATAATGACAAAATT
8984314 AAAATATATT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
29 40 0.87
30 6 0.13
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAATTAAAATATAATGACAAAATTCAAT
Found at i:8986564 original size:23 final size:26
Alignment explanation
Indices: 8986524--8986576 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 26
8986514 TGTACATAAT
*
8986524 AATATTACTAATAATTTTCAAAAT-A
1 AATATTACTAATAATTTTAAAAATCA
*
8986549 AATA-TAC-AATATTTTTAAAAATCA
1 AATATTACTAATAATTTTAAAAATCA
8986573 AATA
1 AATA
8986577 AATAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 8 0.32
25 4 0.16
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATTACTAATAATTTTAAAAATCA
Found at i:8986693 original size:24 final size:24
Alignment explanation
Indices: 8986666--8986711 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
8986656 TTAAGATAAA
8986666 AACAAATAATGAAAAAAAAAAACT
1 AACAAATAATGAAAAAAAAAAACT
8986690 AACAAATAATGAAAAAAAAAAA
1 AACAAATAATGAAAAAAAAAAA
8986712 AAAACTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (24 bp):
AACAAATAATGAAAAAAAAAAACT
Found at i:8998686 original size:26 final size:26
Alignment explanation
Indices: 8998664--8998738 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 26
8998654 ATAATGAAAT
*
8998664 TATATTTATTTTAAATAACATGATAA
1 TATATTTATTTTAAATAACATGACAA
*
8998690 CATATTATATGTTTGAAACTAA-AT-ACAA
1 TATATT-TAT-TTT-AAA-TAACATGACAA
8998718 TATATTTATTTTAAATAACAT
1 TATATTTATTTTAAATAACAT
8998739 TTACAATGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
24 3 0.07
25 5 0.12
26 8 0.20
27 6 0.15
28 11 0.27
29 5 0.12
30 3 0.07
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (26 bp):
TATATTTATTTTAAATAACATGACAA
Found at i:8999764 original size:26 final size:26
Alignment explanation
Indices: 8999709--8999765 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
8999699 AAAATATTTT
*
8999709 TTTTTTATTTTACATTGAAAATAAAT
1 TTTTTTATTTTACATTGAAAATAAAA
8999735 TTTTTTATTTTACA-T-AAAATGTAAAA
1 TTTTTTATTTTACATTGAAAA--TAAAA
8999761 TTTTT
1 TTTTT
8999766 AATAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 1 0.04
26 23 0.82
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TTTTTTATTTTACATTGAAAATAAAA
Found at i:8999991 original size:18 final size:18
Alignment explanation
Indices: 8999951--8999989 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
8999941 TAATTTTTTA
*
8999951 AAAAT-TTATTTTCTAGT
1 AAAATATTATTTTCTAAT
8999968 AAAATATTATTTTACTAAT
1 AAAATATTATTTT-CTAAT
8999987 AAA
1 AAA
8999990 TAATATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
AAAATATTATTTTCTAAT
Found at i:9000800 original size:13 final size:13
Alignment explanation
Indices: 9000784--9000814 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
9000774 GCAACGCCCG
9000784 CACGCAGCTTCCA
1 CACGCAGCTTCCA
9000797 CACGCAGCTTCCA
1 CACGCAGCTTCCA
9000810 CACGC
1 CACGC
9000815 CTGCGCTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.16, T:0.13
Consensus pattern (13 bp):
CACGCAGCTTCCA
Found at i:9001983 original size:1 final size:1
Alignment explanation
Indices: 9001972--9002002 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
9001962 GGGAAAACAG
*
9001972 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9002003 GAAAGAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9003470 original size:15 final size:15
Alignment explanation
Indices: 9003452--9003485 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9003442 CTTTTTACTT
9003452 TTTTTCAT-TTTCAA
1 TTTTTCATCTTTCAA
*
9003466 ATTTTCATCTTTCAA
1 TTTTTCATCTTTCAA
9003481 TTTTT
1 TTTTT
9003486 TTATTCACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTCATCTTTCAA
Found at i:9004401 original size:23 final size:25
Alignment explanation
Indices: 9004375--9004427 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 25
9004365 AATAAAAACT
* *
9004375 ATTTTTACT-TTTTTAAAA-AATTA
1 ATTTTTACTGTTTTGAAAATAATCA
9004398 A--TTTACTGTTTTGAAAATAATCA
1 ATTTTTACTGTTTTGAAAATAATCA
9004421 ATTTTTA
1 ATTTTTA
9004428 AATTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 6 0.25
25 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (25 bp):
ATTTTTACTGTTTTGAAAATAATCA
Found at i:9004402 original size:21 final size:23
Alignment explanation
Indices: 9004378--9004424 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
9004368 AAAAACTATT
* *
9004378 TTTACT-TTTTTAAAA-AATTAA
1 TTTACTGTTTTGAAAATAATCAA
9004399 TTTACTGTTTTGAAAATAATCAA
1 TTTACTGTTTTGAAAATAATCAA
9004422 TTT
1 TTT
9004425 TTAAATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTACTGTTTTGAAAATAATCAA
Found at i:9004784 original size:20 final size:20
Alignment explanation
Indices: 9004740--9004784 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
9004730 TTTAAATTAT
* *
9004740 AAAAATAAAGAAAATAGATA
1 AAAAAGAAAGAAAATAGAAA
9004760 AAAAAGAAAGAAAATA-AAA
1 AAAAAGAAAGAAAATAGAAA
9004779 AGAAAA
1 A-AAAA
9004785 AAGTGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAAAGAAAGAAAATAGAAA
Found at i:9006594 original size:23 final size:23
Alignment explanation
Indices: 9006568--9006626 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
9006558 ATCCAATAAA
*
9006568 TTTATTAGTATTTCTTTGGTATT
1 TTTATTGGTATTTCTTTGGTATT
*
9006591 TTTATTGGTATTTCTTTGGTGTT
1 TTTATTGGTATTTCTTTGGTATT
9006614 TTTATTGGTATTT
1 TTTATTGGTATTT
9006627 GTTTTCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.14, C:0.03, G:0.17, T:0.66
Consensus pattern (23 bp):
TTTATTGGTATTTCTTTGGTATT
Found at i:9006600 original size:12 final size:12
Alignment explanation
Indices: 9006568--9006626 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
9006558 ATCCAATAAA
*
9006568 TTTATTAGTATT
1 TTTATTGGTATT
*
9006580 TCT-TTGGTATT
1 TTTATTGGTATT
9006591 TTTATTGGTATT
1 TTTATTGGTATT
* *
9006603 TCT-TTGGTGTT
1 TTTATTGGTATT
9006614 TTTATTGGTATT
1 TTTATTGGTATT
9006626 T
1 T
9006627 GTTTTCTGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 18 0.47
12 20 0.53
ACGTcount: A:0.14, C:0.03, G:0.17, T:0.66
Consensus pattern (12 bp):
TTTATTGGTATT
Found at i:9006726 original size:76 final size:76
Alignment explanation
Indices: 9006591--9006732 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 76
9006581 CTTTGGTATT
* * * * * * *
9006591 TTTATTGGTATTTCTTTGGTGTTTTTATTGGTATTTGTTTTCTGATATTTTCTTGGTGTGATTGT
1 TTTATTGGTATTTCTTAGGTGTTTTTACTAGAATTTATTTACTGATATTTTCTTAGTGTGATTGT
9006656 AAGCTGATAAA
66 AAGCTGATAAA
*
9006667 TTTATTGGTATTTCTTAGGTGTTTTTGCTAGAATTTATTTACTGATA-TTTCTTTAGTGTGATTG
1 TTTATTGGTATTTCTTAGGTGTTTTTACTAGAATTTATTTACTGATATTTTC-TTAGTGTGATTG
9006731 TA
65 TA
9006733 TAGCACTGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 4 0.07
76 53 0.93
ACGTcount: A:0.18, C:0.06, G:0.20, T:0.56
Consensus pattern (76 bp):
TTTATTGGTATTTCTTAGGTGTTTTTACTAGAATTTATTTACTGATATTTTCTTAGTGTGATTGT
AAGCTGATAAA
Found at i:9007440 original size:46 final size:47
Alignment explanation
Indices: 9007373--9007468 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
9007363 TCAGAAATAC
9007373 TTTTAATAACCCCATTAA-TTTTTTTTTTGAGATTATTCAAGATATT
1 TTTTAATAACCCCATTAATTTTTTTTTTTGAGATTATTCAAGATATT
9007419 TTTTAATAACCCCATTAATTTTTTTTTTTGAGATTATTCAAGATATT
1 TTTTAATAACCCCATTAATTTTTTTTTTTGAGATTATTCAAGATATT
9007466 TTT
1 TTT
9007469 GGTCAAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 18 0.37
47 31 0.63
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (47 bp):
TTTTAATAACCCCATTAATTTTTTTTTTTGAGATTATTCAAGATATT
Found at i:9012981 original size:17 final size:16
Alignment explanation
Indices: 9012959--9013010 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
9012949 TTGTTTTTAA
9012959 AATTATTATAATAATTT
1 AATTATTA-AATAATTT
9012976 AATTATTAAAGTAATTT
1 AATTATTAAA-TAATTT
* *
9012993 TACTATTAAGATAATTT
1 AATTATTAA-ATAATTT
9013010 A
1 A
9013011 TCATTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 2 0.07
17 27 0.90
18 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (16 bp):
AATTATTAAATAATTT
Found at i:9013246 original size:34 final size:34
Alignment explanation
Indices: 9013207--9013272 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
9013197 AAAATATTAG
9013207 TAATATTTTATGTACTTCATAATAAATATAATAC
1 TAATATTTTATGTACTTCATAATAAATATAATAC
9013241 TAATATTTTATGTACTTCATAATAAATATAAT
1 TAATATTTTATGTACTTCATAATAAATATAAT
9013273 TAAATTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (34 bp):
TAATATTTTATGTACTTCATAATAAATATAATAC
Found at i:9018704 original size:161 final size:157
Alignment explanation
Indices: 9018366--9018811 Score: 713
Period size: 152 Copynumber: 2.8 Consensus size: 157
9018356 TAGTTGTTGG
* *
9018366 AAATGATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACTTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
9018431 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAG-----AAA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAAAA
* * *
9018491 AATCAAAATCATCCAATTAATTATTGG
131 AATCAAAATCACCCAATTAATTATCGA
* *
9018518 AAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
*
9018583 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCATCGGATTAATTAAAGAAAAAAAA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAAAA
9018648 AATCAAAATCAGCCCAGTAATTAATTATCGA
131 AATCAAAATCA-CCC---AATTAATTATCGA
9018679 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
* * *
9018744 TATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCATCGTCGGATTAATTAAAGAAAAAAA
66 TATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAAA
9018809 AAA
130 AAA
9018812 AATCAAGATC
Statistics
Matches: 270, Mismatches: 14, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
152 117 0.43
157 14 0.05
158 2 0.01
161 93 0.34
162 44 0.16
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (157 bp):
AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAAAA
AATCAAAATCACCCAATTAATTATCGA
Found at i:9018852 original size:1 final size:1
Alignment explanation
Indices: 9018841--9018881 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
9018831 GTCAAATAAC
*
9018841 AAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9018882 CCTGGAGCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.98, C:0.00, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:9019340 original size:31 final size:31
Alignment explanation
Indices: 9019302--9019360 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
9019292 ACTGGGCAGG
*
9019302 TCGCCGGAAACTTCAATGTTGGCCGGAATTT
1 TCGCCGGAAACTTCAAGGTTGGCCGGAATTT
9019333 TCGCCGGAAACTTCAAGGTTGGCCGGAA
1 TCGCCGGAAACTTCAAGGTTGGCCGGAA
9019361 AATTCAACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (31 bp):
TCGCCGGAAACTTCAAGGTTGGCCGGAATTT
Found at i:9019716 original size:12 final size:12
Alignment explanation
Indices: 9019699--9019732 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
9019689 CTAGCCCTCC
9019699 AAAATAAAAATT
1 AAAATAAAAATT
9019711 AAAAT-AAAATT
1 AAAATAAAAATT
*
9019722 AAAAAAAAAAT
1 AAAATAAAAAT
9019733 CTAGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:9019991 original size:25 final size:26
Alignment explanation
Indices: 9019935--9019995 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
9019925 AATACATAAT
* * *
9019935 AATAAATAATAAAATACACAAGAGAA
1 AATAAAAAATAAAATACAAAAGAAAA
*
9019961 AA-AAAAAATAAAATA-AAAATAAAA
1 AATAAAAAATAAAATACAAAAGAAAA
9019985 AATAAAAAATA
1 AATAAAAAATA
9019996 CGGGTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 8 0.27
25 20 0.67
26 2 0.07
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (26 bp):
AATAAAAAATAAAATACAAAAGAAAA
Found at i:9020087 original size:20 final size:20
Alignment explanation
Indices: 9020032--9020090 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
9020022 CCATTTGGGG
*
9020032 CAGGCCCAGA-TGATCTGGGT
1 CAGGCCCA-ATTGATCCGGGT
9020052 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
9020072 CAGGCCCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
9020091 CCCGGACCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:9024788 original size:17 final size:16
Alignment explanation
Indices: 9024757--9024790 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
9024747 ATAATATTGA
*
9024757 TAAAATAATCAAAATG
1 TAAAATAAACAAAATG
9024773 TAAAACTAAACAAAATG
1 TAAAA-TAAACAAAATG
9024790 T
1 T
9024791 GTGTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (16 bp):
TAAAATAAACAAAATG
Found at i:9027850 original size:3 final size:3
Alignment explanation
Indices: 9027844--9027875 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
9027834 ATTTTACTAC
*
9027844 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9027876 CACCATGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:9047183 original size:17 final size:18
Alignment explanation
Indices: 9047161--9047194 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9047151 TGGATACCAT
*
9047161 TTTTTTATTA-TTAAATA
1 TTTTTTAATATTTAAATA
9047178 TTTTTTAATATTTAAAT
1 TTTTTTAATATTTAAAT
9047195 TAATAAATAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTTAATATTTAAATA
Found at i:9048466 original size:23 final size:23
Alignment explanation
Indices: 9048418--9048465 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9048408 AGCACTTAAT
* *
9048418 AAATAAAATTTATGTATAAATTA
1 AAATAAAATATATGTATAAATAA
*
9048441 AAATAAAATATATG-GTAAATAA
1 AAATAAAATATATGTATAAATAA
9048463 AAA
1 AAA
9048466 AGTTGAGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (23 bp):
AAATAAAATATATGTATAAATAA
Found at i:9049413 original size:55 final size:55
Alignment explanation
Indices: 9049350--9049459 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
9049340 ATAAAAACCG
* *
9049350 CCAATATCCAAAAATCAACCATTAATACCATTGTTTTGTATCGTTGTCCAAAGCA
1 CCAATATCCAAAAATCAACCATTAATACCATTGTTTAGTATCATTGTCCAAAGCA
* *
9049405 CCAATATCCAAAAATCGACCATTAATATCATTGTTTAGTATCATTGTCCAAAGCA
1 CCAATATCCAAAAATCAACCATTAATACCATTGTTTAGTATCATTGTCCAAAGCA
9049460 AAATTATGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (55 bp):
CCAATATCCAAAAATCAACCATTAATACCATTGTTTAGTATCATTGTCCAAAGCA
Found at i:9049757 original size:12 final size:13
Alignment explanation
Indices: 9049726--9049758 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
9049716 CCAATAAAGT
9049726 AATAAAATAGATA
1 AATAAAATAGATA
9049739 AAT-AAATA-ATA
1 AATAAAATAGATA
9049750 AATAAAATA
1 AATAAAATA
9049759 TTTTGGGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 10 0.53
13 3 0.16
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AATAAAATAGATA
Found at i:9050860 original size:18 final size:18
Alignment explanation
Indices: 9050834--9050868 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9050824 TACTATAATT
*
9050834 ATTAATTTTATTTTTATC
1 ATTAATTTTAATTTTATC
*
9050852 ATTATTTTTAATTTTAT
1 ATTAATTTTAATTTTAT
9050869 TAAAATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTAATTTTAATTTTATC
Found at i:9051758 original size:28 final size:29
Alignment explanation
Indices: 9051667--9051758 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 29
9051657 ATAATAGTTT
*
9051667 ATTATATAATAGTAAAATTTATTTATT-A
1 ATTATATAATAATAAAATTTATTTATTAA
* * **
9051695 GTTCT-TAATAAATAAGTTTTATTTATTAA
1 ATTATATAAT-AATAAAATTTATTTATTAA
9051724 TTTATTATATAATAATAAAATTTA-TTATTAA
1 ---ATTATATAATAATAAAATTTATTTATTAA
9051755 ATTA
1 ATTA
9051759 ATTTAGCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 4 0.08
28 21 0.43
29 1 0.02
31 7 0.14
32 12 0.24
33 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTATATAATAATAAAATTTATTTATTAA
Found at i:9053651 original size:14 final size:15
Alignment explanation
Indices: 9053626--9053654 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9053616 TTAATTTTAT
9053626 TTATATTTTAAATAA
1 TTATATTTTAAATAA
9053641 TTATA-TTTAAATAA
1 TTATATTTTAAATAA
9053655 AAATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATATTTTAAATAA
Found at i:9064125 original size:30 final size:31
Alignment explanation
Indices: 9064075--9064172 Score: 130
Period size: 30 Copynumber: 3.3 Consensus size: 31
9064065 AATGCACAGA
* *
9064075 GACTAAATTCCTTAAAAAATAATATTATAAG
1 GACTAAATTTCTTTAAAAATAATATTATAAG
* *
9064106 AACTAAATTT-TTTAAAAATAATATTACAAG
1 GACTAAATTTCTTTAAAAATAATATTATAAG
*
9064136 GATTAAATTTCTTT--AAATAATATTATAAG
1 GACTAAATTTCTTTAAAAATAATATTATAAG
9064165 GACTAAAT
1 GACTAAAT
9064173 CTTAAAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.36
30 26 0.45
31 11 0.19
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (31 bp):
GACTAAATTTCTTTAAAAATAATATTATAAG
Found at i:9064889 original size:20 final size:22
Alignment explanation
Indices: 9064831--9064891 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
9064821 TAGTAAAAGC
*
9064831 ATAAAGATCAAATCCACATATT
1 ATAAAGTTCAAATCCACATATT
*
9064853 ATAAAGTT-AAATTCACATCA-T
1 ATAAAGTTCAAATCCACAT-ATT
9064874 A-AAA-TTCAAATCCACATA
1 ATAAAGTTCAAATCCACATA
9064892 AATTCCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
21 11 0.32
22 8 0.24
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAAAGTTCAAATCCACATATT
Found at i:9066128 original size:17 final size:17
Alignment explanation
Indices: 9066106--9066139 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9066096 CATCATTGGG
*
9066106 TAATTATAAAATATTTT
1 TAATTAAAAAATATTTT
9066123 TAATTAAAAAATATTTT
1 TAATTAAAAAATATTTT
9066140 GTTTTTTCTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAAAAAATATTTT
Found at i:9067568 original size:43 final size:43
Alignment explanation
Indices: 9067486--9068351 Score: 774
Period size: 43 Copynumber: 20.1 Consensus size: 43
9067476 TTTCTAAAAA
* * *
9067486 CTCCTCTAAATAGAGGCTTC-ACGACTTTTGAAAAATAAATAAAG
1 CTCCTCTAAACAGAGGC-TCAACAAC-TTTGAAAAATAAATAAGG
* ** * * *
9067530 CTCCTATAAACTTAGGCTCAACAATTTTAAAAAATAAATATGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* ** *
9067573 CTCCTTTAAACAGAGGCTCAATGACTTTTGAAAAAATAAATATGG
1 CTCCTCTAAACAGAGGCTCAACAAC-TTTG-AAAAATAAATAAGG
** * * * **
9067618 CTTTTTTATACAAAGGCTCAACAACTTT-AAAAATAAATAAAA
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * ** *
9067660 CTCCTTTAAACA-AGGGCTTAATGACTTT-AAAAATAAATAAAG
1 CTCCTCTAAACAGA-GGCTCAACAACTTTGAAAAATAAATAAGG
* * ** * *
9067702 CTCCTATAATCAGAGGCTTTACGACTTTGGAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * *
9067745 CTCCTCTAAATAGAGGCTCAACAACTTTGAAAGACAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* *
9067788 CTCCTCTAGACAGAGGCTCAACAACTTTAAAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * * *
9067831 CTCTTCTAATCAGAGGCTCTATAACTTTGAAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* *
9067874 CTCCTCTAAATAGAGGCTCAACAACTTTGGAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* ** ** *
9067917 CTTCTCTAAACAGAGGCAAAATGACTTTAAAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * * *
9067960 CTCATCTAATCAGAGGCTCTACAACTTTGAAAAATAAATAATG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* *
9068003 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAGGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * * * *
9068046 CTCTTTTAAATAGAGGCTTAACAACTTTGAAAAATAAATAATG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* ** * *
9068089 CTCTTCTAAACAGAGGCTCAATGATTTTGAAAAATAAATAATG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * * * * **
9068132 CTCCTTTAAATAGAGGTTTAACGACTTTGAAAAAATAAATAATA
1 CTCCTCTAAACAGAGGCTCAACAACTTTG-AAAAATAAATAAGG
* * * **
9068176 CTCCTCTAAATAGAGGCTCAACGACTTTAAAAAAATAAATAACA
1 CTCCTCTAAACAGAGGCTCAACAACTTT-GAAAAATAAATAAGG
* * * * *
9068220 CTCCTTTAATCAAAGGCTCAACAACTTTTGGAAAA-CAAT--GG
1 CTCCTCTAAACAGAGGCTCAACAAC-TTTGAAAAATAAATAAGG
* * ** *
9068261 CTCCTCTAAATAGAAGCTCAATGACTTTGGAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
* * * ** * *
9068304 CTTCTTTAAGCAGACACTCAACAATTTTGAAAAATAAATAAAG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
9068347 CTCCT
1 CTCCT
9068352 TGACAATCAT
Statistics
Matches: 666, Mismatches: 144, Indels: 25
0.80 0.17 0.03
Matches are distributed among these distances:
40 9 0.01
41 22 0.03
42 66 0.10
43 436 0.65
44 97 0.15
45 36 0.05
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (43 bp):
CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAGG
Found at i:9067866 original size:172 final size:171
Alignment explanation
Indices: 9067486--9068351 Score: 872
Period size: 172 Copynumber: 5.0 Consensus size: 171
9067476 TTTCTAAAAA
* * **
9067486 CTCCTCTAAATAGAGGCTTC-ACGACTTTTGAAAAATAAATAAAGCTCCTATAAACTTAGGCTCA
1 CTCCTCTAAACAGAGGC-TCAACGAC-TTTGAAAAATAAATAAAGCTCCTATAATCAGAGGCTCA
* ** * *
9067550 ACAATTTTAAAAAATAAATATGGCTCCTTTAAACAGAGGCTCAATGACTTTTGAAAAAATAAATA
64 ACAACTTTGGAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGAC-TTTG-AAAAATAAATA
* ** * *
9067615 TGGCTTTTTTATACAAAGGCTCAACAACTTT-AAAAATAAATAAAA
127 AGGCTCCTTTA-ACAGAGGCTCAACAACTTTAAAAAATAAATAAAG
* * * **
9067660 CTCCTTTAAACA-AGGGCTTAATGACTTT-AAAAATAAATAAAGCTCCTATAATCAGAGGCTTTA
1 CTCCTCTAAACAGA-GGCTCAACGACTTTGAAAAATAAATAAAGCTCCTATAATCAGAGGCTCAA
* * ** * *
9067723 CGACTTTGGAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAACAACTTTGAAAGACAAATAAGG
65 CAACTTTGGAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAGG
* *
9067788 CTCCTCTAGACAGAGGCTCAACAACTTTAAAAAATAAATAAGG
130 CTCCTTTA-ACAGAGGCTCAACAACTTTAAAAAATAAATAAAG
* * * ** * *
9067831 CTCTTCTAATCAGAGGCTCTATAACTTTGAAAAATAAATAAGGCTCCTCTAAAT-AGAGGCTCAA
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTAT-AATCAGAGGCTCAA
* ** *
9067895 CAACTTTGGAAAATAAATAAGGCTTCTCTAAACAGAGGCAAAATGACTTTAAAAAATAAATAAGG
65 CAACTTTGGAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAGG
* * * * *
9067960 CTCATCTAATCAGAGGCTCTACAACTTTGAAAAATAAATAATG
130 CTCCTTTAA-CAGAGGCTCAACAACTTTAAAAAATAAATAAAG
** * * *
9068003 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAGGGCTCTTTTAAAT-AGAGGCTTAA
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTAT-AATCAGAGGCTCAA
* * * * *
9068067 CAACTTTGAAAAATAAATAATGCTCTTCTAAACAGAGGCTCAATGATTTTGAAAAATAAATAATG
65 CAACTTTGGAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAGG
* * * *
9068132 CTCCTTTAAATAGAGGTTTAACGACTTTGAAAAAATAAATAATA-
130 CTCCTTT-AACAGAGGCTCAACAACTTT-AAAAAATAAATAA-AG
* * * *
9068176 CTCCTCTAAATAGAGGCTCAACGACTTTAAAAAAATAAATAACA-CTCCTTTAATCAAAGGCTCA
1 CTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAATAA-AGCTCCTATAATCAGAGGCTCA
* * * *
9068240 ACAACTTTTGGAAAA-CAAT--GGCTCCTCTAAATAGAAGCTCAATGACTTTGGAAAATAAATAA
64 ACAAC-TTTGGAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAA
* ** * *
9068302 GGCTTCTTTAAGCAGACACTCAACAATTTTGAAAAATAAATAAAG
128 GGCTCCTTTAA-CAGAGGCTCAACAACTTTAAAAAATAAATAAAG
9068347 CTCCT
1 CTCCT
9068352 TGACAATCAT
Statistics
Matches: 572, Mismatches: 104, Indels: 35
0.80 0.15 0.05
Matches are distributed among these distances:
170 35 0.06
171 56 0.10
172 372 0.65
173 52 0.09
174 49 0.09
175 8 0.01
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (171 bp):
CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTATAATCAGAGGCTCAAC
AACTTTGGAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAGGC
TCCTTTAACAGAGGCTCAACAACTTTAAAAAATAAATAAAG
Found at i:9070251 original size:21 final size:21
Alignment explanation
Indices: 9070194--9070262 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 21
9070184 AATTTGAGTC
*
9070194 TTTTTTTTTC-TTTTTTTACA
1 TTTTTTTTTCATTTTTTTTCA
9070214 TTATTTCATTCTTTCATTTTTTTTCA
1 -T-TTT--TT-TTTCATTTTTTTTCA
9070240 TTTTTTTTTCATTTTTTTTCA
1 TTTTTTTTTCATTTTTTTTCA
9070261 TT
1 TT
9070263 ATTGACATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
21 18 0.43
22 5 0.12
24 5 0.12
25 5 0.12
26 9 0.21
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTTTTCATTTTTTTTCA
Found at i:9070260 original size:10 final size:10
Alignment explanation
Indices: 9070225--9070262 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
9070215 TATTTCATTC
9070225 TTTCATTTTT
1 TTTCATTTTT
9070235 TTTCATTTTTT
1 TTTCA-TTTTT
9070246 TTTCATTTTT
1 TTTCATTTTT
9070256 TTTCATT
1 TTTCATT
9070263 ATTGACATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:9072489 original size:19 final size:19
Alignment explanation
Indices: 9072465--9072506 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
9072455 AGCTTTTGAG
*
9072465 CCTTTTAAAGTTTTCTTTT
1 CCTTTTAAAGTTTTCTTCT
9072484 CCTTTTAAAGTTTTCTTCT
1 CCTTTTAAAGTTTTCTTCT
9072503 CCTT
1 CCTT
9072507 ATGCTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.21, G:0.05, T:0.60
Consensus pattern (19 bp):
CCTTTTAAAGTTTTCTTCT
Found at i:9072749 original size:37 final size:37
Alignment explanation
Indices: 9072697--9072771 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
9072687 AGATTGAGTT
* *
9072697 TGATGTAGCCCAAAACTAGGAGGGTACAAAGGGTCAA
1 TGATGTAGCCCAAAACTAAGAGAGTACAAAGGGTCAA
* * *
9072734 TGATGTAGCCTAAAACTAAGAGAGTGCAGAGGGTCAA
1 TGATGTAGCCCAAAACTAAGAGAGTACAAAGGGTCAA
9072771 T
1 T
9072772 CACCTTCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19
Consensus pattern (37 bp):
TGATGTAGCCCAAAACTAAGAGAGTACAAAGGGTCAA
Found at i:9075597 original size:21 final size:21
Alignment explanation
Indices: 9075571--9075610 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9075561 TCACAAACCA
9075571 AGAAAAGAAAGA-AGAAAAGCC
1 AGAAAA-AAAGAGAGAAAAGCC
*
9075592 AGAAAAATAGAGAGAAAAG
1 AGAAAAAAAGAGAGAAAAG
9075611 GTAGAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.03
Consensus pattern (21 bp):
AGAAAAAAAGAGAGAAAAGCC
Found at i:9078192 original size:31 final size:30
Alignment explanation
Indices: 9078157--9078225 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
9078147 AATTTTAAAA
* *
9078157 TTTAATTTATAATCCAAATAAG-TTATTAACT
1 TTTAATTTAT-AGCCAAATAAGCTT-TCAACT
* *
9078188 TTTAATTTGTAGCCACATAAGCTTTCAACT
1 TTTAATTTATAGCCAAATAAGCTTTCAACT
9078218 TTTAATTT
1 TTTAATTT
9078226 GAACGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (30 bp):
TTTAATTTATAGCCAAATAAGCTTTCAACT
Found at i:9079010 original size:25 final size:25
Alignment explanation
Indices: 9078950--9079011 Score: 65
Period size: 28 Copynumber: 2.4 Consensus size: 25
9078940 AATATTAAAC
9078950 ATAAATATT-TTTAATATTTTAATA
1 ATAAATATTATTTAATATTTTAATA
*
9078974 ATAAAAAGTATTATGTT-ATATTTTCATA
1 AT--AAA-TATTAT-TTAATATTTTAATA
9079002 ATAAATATTA
1 ATAAATATTA
9079012 ATACAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
24 2 0.06
25 5 0.16
26 6 0.19
27 4 0.12
28 13 0.41
29 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
ATAAATATTATTTAATATTTTAATA
Found at i:9079291 original size:20 final size:20
Alignment explanation
Indices: 9079268--9079306 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9079258 GTATTATAGT
9079268 AATAGAAATAATATTTTAAG
1 AATAGAAATAATATTTTAAG
* *
9079288 AATAGTAATATTATTTTAA
1 AATAGAAATAATATTTTAA
9079307 ATATTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
AATAGAAATAATATTTTAAG
Found at i:9082072 original size:4 final size:4
Alignment explanation
Indices: 9082065--9082093 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
9082055 TTAATCATAA
9082065 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
9082094 TATGATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:9082746 original size:24 final size:24
Alignment explanation
Indices: 9082717--9082762 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9082707 AATTTAAAAT
*
9082717 ACGATAC-AATGATATGATACGAAA
1 ACGATACGAAT-AAATGATACGAAA
9082741 ACGATACGAATAAATGATACGA
1 ACGATACGAATAAATGATACGA
9082763 TAATAACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (24 bp):
ACGATACGAATAAATGATACGAAA
Found at i:9104053 original size:16 final size:16
Alignment explanation
Indices: 9104017--9104058 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
9104007 TTTTCTTTAA
*
9104017 AGAAGCTTTTCAAATG
1 AGAATCTTTTCAAATG
9104033 AGAATCTTTTCAAATG
1 AGAATCTTTTCAAATG
* *
9104049 TGAATATTTT
1 AGAATCTTTT
9104059 TAACTTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (16 bp):
AGAATCTTTTCAAATG
Found at i:9104128 original size:44 final size:43
Alignment explanation
Indices: 9104039--9104381 Score: 274
Period size: 44 Copynumber: 7.8 Consensus size: 43
9104029 AATGAGAATC
* * ** * * *
9104039 TTTTCAAATGTGAATATTTTTAACTTTGGATGTAAATCTTTAAA
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAATC-TAAAA
** * *
9104083 TTTTTGAATGAGAATCTCTGGAATTTTGGATGTGAATCGTAAAA
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAATC-TAAAA
* * * * *
9104127 TTTTCAAATAAGAATTTTTGAAAATTTGGATGTGAATCTTTAAT
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAATC-TAAAA
** *
9104171 TTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAATCCAAAAA
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAAT-CTAAAA
* * * * *
9104215 TTTTCAAATGAAAATCTTTAAAATTTTAGATGTGAATCCATAA
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAATCTAAAA
* * * *
9104258 TTTTCAAATGAGAATCTTTGAAATTTTGAATATGAATCTTTAAT
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAATC-TAAAA
* *** * *
9104302 TTTTCGAATGAGAATCTTTGAAATTTCATATGTAAATCCCAAAA
1 TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAAT-CTAAAA
* * * *
9104346 TTTTTCAAATGAAAATATTT-AACTTTTGGATATGAA
1 -TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAA
9104382 ACCTTGAAAA
Statistics
Matches: 232, Mismatches: 63, Indels: 8
0.77 0.21 0.03
Matches are distributed among these distances:
43 37 0.16
44 177 0.76
45 18 0.08
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (43 bp):
TTTTCAAATGAGAATCTTTGAAATTTTGGATGTGAATCTAAAA
Found at i:9104157 original size:88 final size:89
Alignment explanation
Indices: 9104063--9104324 Score: 316
Period size: 88 Copynumber: 3.0 Consensus size: 89
9104053 TATTTTTAAC
* * * *
9104063 TTTGGATGTAAATCTTTAAATTTTTGAATGAGAATCTCTGGAATTTTGGATGTGAATCGTAAAAT
1 TTTGGATGTGAATCTTTAAATTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAATCCTAAAAT
*
9104128 TTTCAAATAAGAATTTTTGAAAA-
66 TTTCAAATAAGAATCTTTGAAAAT
* *
9104151 TTTGGATGTGAATCTTTAATTTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAATCCAAAAAT
1 TTTGGATGTGAATCTTTAAATTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAATCCTAAAAT
9104216 TTTCAAATGAA-AATCTTT-AAAAT
66 TTTCAAAT-AAGAATCTTTGAAAAT
* ** ** * * * * *
9104239 TTTAGATGTGAATCCAT-AATTTTCAAATGAGAATCTTTGAAATTTTGAATATGAATCTTTAATT
1 TTTGGATGTGAATCTTTAAATTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAATCCTAAAAT
* *
9104303 TTTCGAATGAGAATCTTTGAAA
66 TTTCAAATAAGAATCTTTGAAA
9104325 TTTCATATGT
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
86 1 0.01
87 56 0.38
88 90 0.60
89 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (89 bp):
TTTGGATGTGAATCTTTAAATTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAATCCTAAAAT
TTTCAAATAAGAATCTTTGAAAAT
Found at i:9104311 original size:131 final size:133
Alignment explanation
Indices: 9104104--9104367 Score: 379
Period size: 131 Copynumber: 2.0 Consensus size: 133
9104094 GAATCTCTGG
* * * * *
9104104 AATTTTGGATGTGAATCGTAAAATTTTCAAATAAGAATTTTTGAAAATTTGGATGTGAATCTTTA
1 AATTTTAGATGTGAATCGCAAAATTTTCAAATAAGAATCTTTGAAAATTTGAATATGAATCTTTA
* ** * *
9104169 ATTTTTTGAATGAGAATCTTTGAAATTTTGGATGTGAAT-CCAAAAATTTTCAAATGAAAATCTT
66 ATTTTTCGAATGAGAATCTTTGAAATTTCAGATGTAAATCCCAAAAATTTTCAAATGAAAATATT
9104233 TAA
131 TAA
* * *
9104236 AATTTTAGATGTGAATC-CATAATTTTCAAATGAGAATCTTTGAAATTTTGAATATGAATCTTTA
1 AATTTTAGATGTGAATCGCAAAATTTTCAAATAAGAATCTTTGAAAATTTGAATATGAATCTTTA
* *
9104300 ATTTTTCGAATGAGAATCTTTGAAATTTCATATGTAAATCCCAAAATTTTTCAAATGAAAATATT
66 ATTTTTCGAATGAGAATCTTTGAAATTTCAGATGTAAATCCCAAAAATTTTCAAATGAAAATATT
9104365 TAA
131 TAA
9104368 CTTTTGGATA
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 74 0.64
132 42 0.36
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (133 bp):
AATTTTAGATGTGAATCGCAAAATTTTCAAATAAGAATCTTTGAAAATTTGAATATGAATCTTTA
ATTTTTCGAATGAGAATCTTTGAAATTTCAGATGTAAATCCCAAAAATTTTCAAATGAAAATATT
TAA
Found at i:9104328 original size:22 final size:22
Alignment explanation
Indices: 9104073--9104328 Score: 89
Period size: 22 Copynumber: 11.7 Consensus size: 22
9104063 TTTGGATGTA
*
9104073 AATCTTT-AAATTTTTGAATGAG
1 AATCTTTGAAA-TTTCGAATGAG
* * * * *
9104095 AATCTCTGGAATTTTGGATGTG
1 AATCTTTGAAATTTCGAATGAG
* * * *
9104117 AATC-GTAAAATTTTCAAATAAG
1 AATCTTTGAAA-TTTCGAATGAG
* * *
9104139 AATTTTTGAAAATTT-GGATGTG
1 AATCTTTG-AAATTTCGAATGAG
* *
9104161 AATCTTT-AATTTTTTGAATGAG
1 AATCTTTGAA-ATTTCGAATGAG
* * *
9104183 AATCTTTGAAATTTTGGATGTG
1 AATCTTTGAAATTTCGAATGAG
*** * *
9104205 AATC-CAAAAATTTTCAAATGAA
1 AATCTTTGAAA-TTTCGAATGAG
* * *
9104227 AATCTTTAAAATTT-TAGATGTG
1 AATCTTTGAAATTTCGA-ATGAG
** * *
9104249 AATCCAT-AATTTTCAAATGAG
1 AATCTTTGAAATTTCGAATGAG
*
9104270 AATCTTTGAAATTTTGAAT-ATG
1 AATCTTTGAAATTTCGAATGA-G
*
9104292 AATCTTT-AATTTTTCGAATGAG
1 AATCTTTGAA-ATTTCGAATGAG
9104314 AATCTTTGAAATTTC
1 AATCTTTGAAATTTC
9104329 ATATGTAAAT
Statistics
Matches: 166, Mismatches: 52, Indels: 32
0.66 0.21 0.13
Matches are distributed among these distances:
20 2 0.01
21 27 0.16
22 119 0.72
23 15 0.09
24 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (22 bp):
AATCTTTGAAATTTCGAATGAG
Found at i:9104660 original size:16 final size:16
Alignment explanation
Indices: 9104635--9104665 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9104625 ATGAACTTGA
*
9104635 AATTATTGCAAATCTG
1 AATTAGTGCAAATCTG
9104651 AATTAGTGCAAATCT
1 AATTAGTGCAAATCT
9104666 AAATCTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
AATTAGTGCAAATCTG
Found at i:9104859 original size:18 final size:18
Alignment explanation
Indices: 9104838--9105021 Score: 125
Period size: 18 Copynumber: 10.5 Consensus size: 18
9104828 TTTTTTTTTT
*
9104838 TTTGTGAATCTTGTAACC
1 TTTGTGAATCTTGGAACC
**
9104856 TTTGTGAATCTTAAAACC
1 TTTGTGAATCTTGGAACC
* * *
9104874 TTTG-CATATCTT-AAATTC
1 TTTGTGA-ATCTTGGAA-CC
* *
9104892 TTTGTGAACCTTAGAACC
1 TTTGTGAATCTTGGAACC
*
9104910 TTTGTGAAACTTGGAACC
1 TTTGTGAATCTTGGAACC
*
9104928 -TTGTGAATC-TGAAACC
1 TTTGTGAATCTTGGAACC
* *
9104944 TTTGCGAAGCTTGGAACC
1 TTTGTGAATCTTGGAACC
*
9104962 TTCTATGAAAT-TTGGAACC
1 TT-TGTG-AATCTTGGAACC
**
9104981 -TTGTGAATC-CAGAACC
1 TTTGTGAATCTTGGAACC
*
9104997 TTTGCGAAT-TTGGAA-C
1 TTTGTGAATCTTGGAACC
9105013 TTTGTGAAT
1 TTTGTGAAT
9105022 TTGAAATCTC
Statistics
Matches: 130, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
16 23 0.18
17 32 0.25
18 60 0.46
19 13 0.10
20 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTGAATCTTGGAACC
Found at i:9104928 original size:54 final size:51
Alignment explanation
Indices: 9104838--9104989 Score: 144
Period size: 54 Copynumber: 2.9 Consensus size: 51
9104828 TTTTTTTTTT
* * ** * *
9104838 TTTGTGAATCTTGTAACCTTTGTGAATCTTAAAACCTT-TGCATATCTTAAATTC
1 TTTGTGAACCTTG-AACCTTTGTGAAACTTGGAACCTTGTG-A-ATCTGAAA-CC
9104892 TTTGTGAACCTTAGAACCTTTGTGAAACTTGGAACCTTGTGAATCTGAAACC
1 TTTGTGAACCTT-GAACCTTTGTGAAACTTGGAACCTTGTGAATCTGAAACC
* * * *
9104944 TTTGCGAAGCTTGGAACCTTCTATGAAATTTGGAACCTTGTGAATC
1 TTTGTGAACCTT-GAACCTT-TGTGAAACTTGGAACCTTGTGAATC
9104990 CAGAACCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
52 18 0.21
53 30 0.36
54 33 0.39
55 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (51 bp):
TTTGTGAACCTTGAACCTTTGTGAAACTTGGAACCTTGTGAATCTGAAACC
Found at i:9104979 original size:53 final size:51
Alignment explanation
Indices: 9104891--9105020 Score: 147
Period size: 53 Copynumber: 2.5 Consensus size: 51
9104881 ATCTTAAATT
* * * *
9104891 CTTTGTGAACCTTAGAACCTTTGTGAAACTTGGAACCTTGTGAAT-CTGAAAC
1 CTTTGCGAA-CTTGGAACCTTTATGAAACTTGGAACCTTGTGAATCCAG-AAC
*
9104943 CTTTGCGAAGCTTGGAACCTTCTATGAAATTTGGAACCTTGTGAATCCAGAAC
1 CTTTGCGAA-CTTGGAACCTT-TATGAAACTTGGAACCTTGTGAATCCAGAAC
* *
9104996 CTTTGCGAATTTGGAA-CTTTGTGAA
1 CTTTGCGAACTTGGAACCTTTATGAA
9105021 TTTGAAATCT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 5 0.07
51 3 0.04
52 24 0.35
53 34 0.50
54 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (51 bp):
CTTTGCGAACTTGGAACCTTTATGAAACTTGGAACCTTGTGAATCCAGAAC
Found at i:9105012 original size:17 final size:17
Alignment explanation
Indices: 9104891--9105024 Score: 94
Period size: 16 Copynumber: 7.8 Consensus size: 17
9104881 ATCTTAAATT
* *
9104891 CTTTGTGAACCTTAGAAC
1 CTTTGTGAA-TTTGGAAC
*
9104909 CTTTGTGAAACTTGGAAC
1 CTTTGTG-AATTTGGAAC
* *
9104927 C-TTGTGAATCTGAAAC
1 CTTTGTGAATTTGGAAC
* *
9104943 CTTTGCGAAGCTTGGAAC
1 CTTTGTGAA-TTTGGAAC
*
9104961 CTTCTATGAAATTTGGAAC
1 CTT-TGTG-AATTTGGAAC
***
9104980 C-TTGTGAATCCAGAAC
1 CTTTGTGAATTTGGAAC
*
9104996 CTTTGCGAATTTGGAA-
1 CTTTGTGAATTTGGAAC
9105012 CTTTGTGAATTTG
1 CTTTGTGAATTTG
9105025 AAATCTCCAT
Statistics
Matches: 90, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
16 28 0.31
17 24 0.27
18 24 0.27
19 12 0.13
20 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (17 bp):
CTTTGTGAATTTGGAAC
Found at i:9116663 original size:14 final size:12
Alignment explanation
Indices: 9116646--9116689 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
9116636 GCCCACTTTG
9116646 TTTTTTTTTCTTCC
1 TTTTTTTTT-TT-C
*
9116660 TTTTTTTTTTTT
1 TTTTTTTTTTTC
9116672 TTTTTTTTTTTGC
1 TTTTTTTTTTT-C
9116685 TTTTT
1 TTTTT
9116690 CACCATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 7 0.26
14 9 0.33
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:9119943 original size:3 final size:3
Alignment explanation
Indices: 9119935--9119975 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9119925 GTTGTTTTAT
9119935 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9119976 TCTTTTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9122586 original size:22 final size:22
Alignment explanation
Indices: 9122561--9122614 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
9122551 CTTACGAATC
*
9122561 ATGCCCAGAGAACTTAGAGATT
1 ATGCCCAGAGAACTAAGAGATT
* *
9122583 ATGCGCGGAGAACTAAGAGATT
1 ATGCCCAGAGAACTAAGAGATT
*
9122605 ATGCCTAGAG
1 ATGCCCAGAG
9122615 GTCTTACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (22 bp):
ATGCCCAGAGAACTAAGAGATT
Found at i:9122715 original size:22 final size:20
Alignment explanation
Indices: 9122694--9122757 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
9122684 ATTTTACCCA
9122694 AAAGTCTTACAAATTATGCCC
1 AAAGTCTTA-AAATTATGCCC
*
9122715 AAAGATCTTAAAGATTATGTCCG
1 AAAG-TCTTAAA-ATTATG-CCC
* *
9122738 AAGGTCTTAGAGATTATGCC
1 AAAGTCTTA-AAATTATGCC
9122758 GACTAAACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.22
22 22 0.61
23 6 0.17
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
AAAGTCTTAAAATTATGCCC
Found at i:9122878 original size:22 final size:22
Alignment explanation
Indices: 9122819--9122974 Score: 80
Period size: 22 Copynumber: 7.0 Consensus size: 22
9122809 ATCATCTAGT
* *
9122819 TGCCAGTTAAACTAGGCTTAGG
1 TGCCAGTTAATCTGGGCTTAGG
** *
9122841 TGCCAACTAATTTGGGCTTAGG
1 TGCCAGTTAATCTGGGCTTAGG
* *
9122863 TGCCAGTTACTCTGGGCTTAAAG
1 TGCCAGTTAATCTGGGCTT-AGG
* * * **
9122886 TGCTAGCTAGA-CTAGATTTAAGG
1 TGCCAGTTA-ATCTGGGCTT-AGG
**
9122909 TGCCAACTAATCTGGGCTTAAGG
1 TGCCAGTTAATCTGGGCTT-AGG
*** * *
9122932 TTTTAGCTAATATGGGCTTAGG
1 TGCCAGTTAATCTGGGCTTAGG
* *
9122954 TGCCAGCTAATCTAGGCTTAG
1 TGCCAGTTAATCTGGGCTTAG
9122975 TTATTATTTT
Statistics
Matches: 99, Mismatches: 32, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
22 52 0.53
23 47 0.47
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (22 bp):
TGCCAGTTAATCTGGGCTTAGG
Found at i:9124915 original size:13 final size:13
Alignment explanation
Indices: 9124897--9124925 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9124887 TTTCTTAGCT
9124897 CTTTCTTTTTTTG
1 CTTTCTTTTTTTG
9124910 CTTTCTTTTTTTG
1 CTTTCTTTTTTTG
9124923 CTT
1 CTT
9124926 ATCCTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (13 bp):
CTTTCTTTTTTTG
Found at i:9129056 original size:464 final size:464
Alignment explanation
Indices: 9128188--9129116 Score: 1642
Period size: 464 Copynumber: 2.0 Consensus size: 464
9128178 TTTTTTTCAT
*
9128188 TCCCAAAAGTTTCAAGTTTACACATCAAGAACCATCTTAGGGCTAGGCCTAAAAAGTACTAGGCC
1 TCCCAAAAGTTTCAAGTTTACACATCAAGAACCATCTTAGGGCTAGGCCTAAAAAGCACTAGGCC
* *
9128253 TATTCTTACTCCCCATTACCTTGCCTAAGAAATCCAAAAGCAGTTGACTATGATCGATGGTGAGG
66 TATTCTTACTCCCCATTACCTTGCCTAAGAAATCCAAAAGCAGTTGACTATGACCGATGATGAGG
* **
9128318 ATAACCTTTTGTTTTAAAGCTTCTTCCTTTTATTCATCATCCTGGCCAACCATACTAATGCCTAC
131 ACAACCTTTTGTTTTAAAGCTTCTTCCTTTTATTCATCATCCTAACCAACCATACTAATGCCTAC
* *
9128383 AGCACTGTCTGCTATCTTGGCATGGATCAATGAAGGATTCCTATAAACAACTGGCTTTATTTCAA
196 AGCACTGTCTGCTATCTTAGCATGGATCAATGAAGGATTCCTATAAACAACTAGCTTTATTTCAA
* * *
9128448 CATTAAAACCCAAATATCTAATTTTTATCAGTCTCTATAGCCTATATTTAAAGGACATGCAGTCC
261 CATCAAAACCCAAATATCCAATTTTTATCAGTCCCTATAGCCTATATTTAAAGGACATGCAGTCC
* *
9128513 TTCAAAGAATAGCCTACAACATCAAAATGGTATTCTCATTGGGCATTAGGGTTGTACCATTTGGG
326 TTCAAAGAATAACCTACAACATCAAAATGGTATTCTCATTGGGCATTAGGGTTATACCATTTGGG
9128578 ATAAGGTAGTTTGAGGTGTTCAATATGGATAGGGCCAATGAGGTAGTTTTTCAAGAGCAATAGGT
391 ATAAGGTAGTTTGAGGTGTTCAATATGGATAGGGCCAATGAGGTAGTTTTTCAAGAGCAATAGGT
9128643 ATAAATCTA
456 ATAAATCTA
* *
9128652 TCCCAAAAGTTTCAAGTTTACACATCATGAACCATCTTAGGGCTAGGCTTAAAAAGCACTAGGCC
1 TCCCAAAAGTTTCAAGTTTACACATCAAGAACCATCTTAGGGCTAGGCCTAAAAAGCACTAGGCC
* *
9128717 TATTCTTACTCCCCATTGCCTTGCCTAAGAAATCCAAAGGCAGTTGACTATGACCGATGATGAGG
66 TATTCTTACTCCCCATTACCTTGCCTAAGAAATCCAAAAGCAGTTGACTATGACCGATGATGAGG
** *
9128782 ACAACCTTTTGTTTTAAAGCTTCTTTTTTTTATTCATCATCCTAACCAACCATACTAATGCCTAT
131 ACAACCTTTTGTTTTAAAGCTTCTTCCTTTTATTCATCATCCTAACCAACCATACTAATGCCTAC
*
9128847 AGTACTGTCTGCTATCTTAGCATGGATCAATGAAGGATTCCTATAAACAACTAGCTTTATTTCAA
196 AGCACTGTCTGCTATCTTAGCATGGATCAATGAAGGATTCCTATAAACAACTAGCTTTATTTCAA
* *
9128912 CATCAAAACCCAAATATCCAGTTTTTATCAGTCCCTATAGCCTATATTTAAAGGACATGTAGTCC
261 CATCAAAACCCAAATATCCAATTTTTATCAGTCCCTATAGCCTATATTTAAAGGACATGCAGTCC
9128977 TTCAAAGAATAACCTACAACATCAAAATGGTATTCTCATTGGGCATTAGGGTTATACCATTTGGG
326 TTCAAAGAATAACCTACAACATCAAAATGGTATTCTCATTGGGCATTAGGGTTATACCATTTGGG
*
9129042 ATAAGGTAGTTTGAGGTGTTCAATATGGATAGGGCCAATGAGGTAGTTTTTCAAGAGCAATGGGT
391 ATAAGGTAGTTTGAGGTGTTCAATATGGATAGGGCCAATGAGGTAGTTTTTCAAGAGCAATAGGT
9129107 ATAAATCTA
456 ATAAATCTA
9129116 T
1 T
9129117 GTAAGACTTG
Statistics
Matches: 441, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
464 441 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (464 bp):
TCCCAAAAGTTTCAAGTTTACACATCAAGAACCATCTTAGGGCTAGGCCTAAAAAGCACTAGGCC
TATTCTTACTCCCCATTACCTTGCCTAAGAAATCCAAAAGCAGTTGACTATGACCGATGATGAGG
ACAACCTTTTGTTTTAAAGCTTCTTCCTTTTATTCATCATCCTAACCAACCATACTAATGCCTAC
AGCACTGTCTGCTATCTTAGCATGGATCAATGAAGGATTCCTATAAACAACTAGCTTTATTTCAA
CATCAAAACCCAAATATCCAATTTTTATCAGTCCCTATAGCCTATATTTAAAGGACATGCAGTCC
TTCAAAGAATAACCTACAACATCAAAATGGTATTCTCATTGGGCATTAGGGTTATACCATTTGGG
ATAAGGTAGTTTGAGGTGTTCAATATGGATAGGGCCAATGAGGTAGTTTTTCAAGAGCAATAGGT
ATAAATCTA
Found at i:9131309 original size:146 final size:145
Alignment explanation
Indices: 9131091--9131398 Score: 422
Period size: 146 Copynumber: 2.1 Consensus size: 145
9131081 GGGAATTATA
* * *
9131091 AAATTACTAAAATGCCCTTTTAGGGGTATTTTTGTAATTTAGCCTTCTCAAACTCAGATTTTCAT
1 AAATTACCAAAATACCCTTTTAGGGGTATTTTCGTAATTTAGCCTTCTCAAACTCAGATTTTCAT
*
9131156 GAAATTTTTCAGATCTAAATTTCATAATATTTCATGATTTTTGG-G-ACATTTGAAATCACAGCA
66 AAAATTTTTCAGATCTAAATTTCATAATATTTCATGATTTTTGGTGTA-A-TTGAAATCACAGCA
* * *
9131219 TTACCTCAAAAGATGTC
129 ATACCCCAAAAGATATC
* * *
9131236 AAATTACCAAAATACCCTTTTTATGGGTATTTTCGTAATTTGGCCTTCTCAAGCTCAGATTTTCA
1 AAATTACCAAAATACCC-TTTTAGGGGTATTTTCGTAATTTAGCCTTCTCAAACTCAGATTTTCA
* * *
9131301 TAAAATTTTTTAGATCTCAATTTCATAATATTTCATGATTTTTGGTGTAATTGAAATCATAGCAA
65 TAAAATTTTTCAGATCTAAATTTCATAATATTTCATGATTTTTGGTGTAATTGAAATCACAGCAA
** * *
9131366 TACCCCAGGAGGTATG
130 TACCCCAAAAGATATC
9131382 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
9131399 CTAAGGGTTT
Statistics
Matches: 143, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
145 15 0.10
146 125 0.87
147 2 0.01
148 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (145 bp):
AAATTACCAAAATACCCTTTTAGGGGTATTTTCGTAATTTAGCCTTCTCAAACTCAGATTTTCAT
AAAATTTTTCAGATCTAAATTTCATAATATTTCATGATTTTTGGTGTAATTGAAATCACAGCAAT
ACCCCAAAAGATATC
Found at i:9131862 original size:19 final size:20
Alignment explanation
Indices: 9131830--9131867 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
9131820 ATTTGAAAAA
9131830 AAAAGGAGAAAAAAAAGAAG
1 AAAAGGAGAAAAAAAAGAAG
9131850 AAAAGGA-AAAAAAAAGAA
1 AAAAGGAGAAAAAAAAGAA
9131868 CCTTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAGGAGAAAAAAAAGAAG
Found at i:9134494 original size:24 final size:25
Alignment explanation
Indices: 9134462--9134509 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
9134452 TCATCAATGA
9134462 TTATCA-TTTACAAAGAATGTTATT
1 TTATCATTTTACAAAGAATGTTATT
* * *
9134486 TTATTATTTTAGAATGAATGTTAT
1 TTATCATTTTACAAAGAATGTTAT
9134510 GATAAACCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.50
Consensus pattern (25 bp):
TTATCATTTTACAAAGAATGTTATT
Found at i:9145252 original size:8 final size:9
Alignment explanation
Indices: 9145238--9145292 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
9145228 TTTCTTAATT
9145238 AAAAAAATC
1 AAAAAAATC
9145247 AAAAAAATC
1 AAAAAAATC
*
9145256 AAATTAAAATA
1 AAA--AAAATC
9145267 AAAAAAATC
1 AAAAAAATC
*
9145276 AAATCAAAT-
1 AAA-AAAATC
9145285 AAAAAAAT
1 AAAAAAAT
9145293 AATCAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 4 0.10
9 23 0.59
10 4 0.10
11 8 0.21
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATC
Found at i:9145271 original size:19 final size:19
Alignment explanation
Indices: 9145241--9145291 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
9145231 CTTAATTAAA
*
9145241 AAAATCAAAAAAATCAAATT
1 AAAATAAAAAAAATCAAA-T
9145261 AAAATAAAAAAAATCAAAT
1 AAAATAAAAAAAATCAAAT
*
9145280 CAAATAAAAAAA
1 AAAATAAAAAAA
9145292 TAATCAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAATAAAAAAAATCAAAT
Found at i:9145290 original size:21 final size:20
Alignment explanation
Indices: 9145247--9145299 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
9145237 TAAAAAAATC
* *
9145247 AAAAAAATCAAATTAAAATA
1 AAAAAAATCAAATCAAAAAA
9145267 AAAAAAATCAAATCAAATAAA
1 AAAAAAATCAAATCAAA-AAA
*
9145288 AAAATAATCAAA
1 AAAAAAATCAAA
9145300 AGAAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAAAATCAAATCAAAAAA
Found at i:9145296 original size:16 final size:16
Alignment explanation
Indices: 9145262--9145320 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
9145252 AATCAAATTA
9145262 AAATAAAAAAAATCAAATC
1 AAAT-AAAAAAAT--AATC
9145281 AAATAAAAAAATAATC
1 AAATAAAAAAATAATC
* *
9145297 AAA-AGAAAAAAGAA-G
1 AAATA-AAAAAATAATC
9145312 AAATAAAAA
1 AAATAAAAA
9145321 GGAAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 8 0.22
16 16 0.44
18 8 0.22
19 4 0.11
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (16 bp):
AAATAAAAAAATAATC
Found at i:9145426 original size:100 final size:100
Alignment explanation
Indices: 9145268--9145459 Score: 275
Period size: 101 Copynumber: 1.9 Consensus size: 100
9145258 ATTAAAATAA
* *
9145268 AAAAAATCAAATCAAATAAAAAAATAATCAAAAGAAAAAAGAAG-AAATAAAAAGGAAAAAGAAA
1 AAAAAATCAAATCAAATAAAAAAATAATCAAAAGAAAAAAGAAGAAAAAAAAAAGAAAAAAGAAA
*
9145332 CAATT-ATGACTAAAAA-CCA-AAAAAGAGCGGTCT
66 CAATTCA-AACTAAAAACCCAGAAAAAGAGCGGTCT
* *
9145365 AAAAAATCAAAAATCAAATAAAAAAGTCAATCAAAAGAAAAAAGTAGAAAAAAAAAAGAAAAAAG
1 AAAAAATC--AAATCAAATAAAAAAAT-AATCAAAAGAAAAAAGAAGAAAAAAAAAAGAAAAAAG
9145430 AAACAATTCAAACTAAAAACCCAGAAAAAG
63 AAACAATTCAAACTAAAAACCCAGAAAAAG
9145460 GCGATGTAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
97 8 0.10
99 16 0.19
100 18 0.22
101 31 0.37
102 4 0.05
103 6 0.07
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.11
Consensus pattern (100 bp):
AAAAAATCAAATCAAATAAAAAAATAATCAAAAGAAAAAAGAAGAAAAAAAAAAGAAAAAAGAAA
CAATTCAAACTAAAAACCCAGAAAAAGAGCGGTCT
Found at i:9146840 original size:36 final size:36
Alignment explanation
Indices: 9146800--9146890 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 36
9146790 CAATCATTTT
9146800 TATTTTTTTGACTTGCAGTATTGTCTAGGTCATATA
1 TATTTTTTTGACTTGCAGTATTGTCTAGGTCATATA
* * * * * * *
9146836 TATTTTTTTCTGAGTTGCATTGTTGTTTTGGTCATTTT
1 TA-TTTTTT-TGACTTGCAGTATTGTCTAGGTCATATA
*
9146874 TATTTTTTTGACCTGCA
1 TATTTTTTTGACTTGCA
9146891 ATGTTGTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
36 9 0.20
37 12 0.27
38 23 0.52
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.56
Consensus pattern (36 bp):
TATTTTTTTGACTTGCAGTATTGTCTAGGTCATATA
Found at i:9146896 original size:36 final size:36
Alignment explanation
Indices: 9146793--9146917 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
9146783 ATTGTCTCAA
* * * *
9146793 TCATTTTTATTTTTTTGACTTGCAGTATTGTCTAGG
1 TCATTTTTATTTTTTTGACTTGCAATGTTGTTTTGG
* * * *
9146829 TCATATATATTTTTTTCTGAGTTGCATTGTTGTTTTGG
1 TCATTTTTA-TTTTTT-TGACTTGCAATGTTGTTTTGG
* *
9146867 TCATTTTTATTTTTTTGACCTGCAATGTTGTTTAT-A
1 TCATTTTTATTTTTTTGACTTGCAATGTTGTTT-TGG
*
9146903 TCACTTTTATTTTTT
1 TCATTTTTATTTTTT
9146918 GATCTACACT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
36 36 0.50
37 13 0.18
38 23 0.32
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.59
Consensus pattern (36 bp):
TCATTTTTATTTTTTTGACTTGCAATGTTGTTTTGG
Found at i:9147236 original size:13 final size:14
Alignment explanation
Indices: 9147219--9147265 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
9147209 ATTTAAAAAA
9147219 AAAAATCAAAC-AAC
1 AAAAA-CAAACAAAC
9147233 AAAAACAAACAAAC
1 AAAAACAAACAAAC
*
9147247 AAAAAATAAAACAAAC
1 -AAAAA-CAAACAAAC
9147263 AAA
1 AAA
9147266 CAAAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.17
14 8 0.28
15 8 0.28
16 8 0.28
ACGTcount: A:0.79, C:0.17, G:0.00, T:0.04
Consensus pattern (14 bp):
AAAAACAAACAAAC
Found at i:9147259 original size:20 final size:20
Alignment explanation
Indices: 9147234--9147271 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9147224 TCAAACAACA
9147234 AAAACAAACAAACAAAAAAT
1 AAAACAAACAAACAAAAAAT
9147254 AAAACAAACAAACAAAAA
1 AAAACAAACAAACAAAAA
9147272 TTAAGAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.03
Consensus pattern (20 bp):
AAAACAAACAAACAAAAAAT
Done.