Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 22 of 22
Found at i:10659044 original size:24 final size:24
Alignment explanation
Indices: 10659017--10659071 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
10659007 ATACATACAC
10659017 ATACATACATGTGTATGTGTATAT
1 ATACATACATGTGTATGTGTATAT
10659041 ATACATACATGTGTATGTGTATAT
1 ATACATACATGTGTATGTGTATAT
10659065 ATACATA
1 ATACATA
10659072 GACACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (24 bp):
ATACATACATGTGTATGTGTATAT
Found at i:10659165 original size:24 final size:24
Alignment explanation
Indices: 10659138--10659191 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
10659128 CGCGCGCACA
* *
10659138 TATATATGTATGTATAT-TGATTTG
1 TATATATGTACGTATATAT-ATATG
*
10659162 TATATGTGTACGTATATATATATG
1 TATATATGTACGTATATATATATG
10659186 TATATA
1 TATATA
10659192 CACACACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (24 bp):
TATATATGTACGTATATATATATG
Found at i:10661710 original size:14 final size:15
Alignment explanation
Indices: 10661685--10661715 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
10661675 ATCATGCTCT
10661685 AATTATAAAAATTAA
1 AATTATAAAAATTAA
10661700 AATTA-AAAAATTAA
1 AATTATAAAAATTAA
10661714 AA
1 AA
10661716 AATTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATTATAAAAATTAA
Found at i:10662003 original size:28 final size:28
Alignment explanation
Indices: 10661946--10662143 Score: 220
Period size: 28 Copynumber: 7.0 Consensus size: 28
10661936 AATTGAAACA
* * *
10661946 AAACATGTTATCTTGTCTAAATTGAGAC
1 AAACATATTTTCTTGTCTAAATTAAGAC
* * *
10661974 AAATATATTTTCTTGTCTAGATTAATAC
1 AAACATATTTTCTTGTCTAAATTAAGAC
10662002 AAAACATATTTTTCTTGTCTTAAATTAA-AGC
1 -AAACATA-TTTTCTTGTC-TAAATTAAGA-C
*
10662033 AAACATGTTTTCTTGTCTAAATTAAGAC
1 AAACATATTTTCTTGTCTAAATTAAGAC
*
10662061 AAACATGACTTT-TTGTCTAAATTAAGAC
1 AAACAT-ATTTTCTTGTCTAAATTAAGAC
* * * *
10662089 AAATATGTTTTCTTTTCTAAAGTAAGAC
1 AAACATATTTTCTTGTCTAAATTAAGAC
*
10662117 AAACATATTTTCTTATCTAAATTAAGA
1 AAACATATTTTCTTGTCTAAATTAAGA
10662144 TAAAACATGT
Statistics
Matches: 143, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.02
28 95 0.66
29 20 0.14
30 17 0.12
31 8 0.06
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (28 bp):
AAACATATTTTCTTGTCTAAATTAAGAC
Found at i:10663178 original size:47 final size:47
Alignment explanation
Indices: 10663109--10663203 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
10663099 TATTTTAATA
10663109 TCTTAATAGAATCATGGTATCTTAATAACTAGATAATGAATGCTTAC
1 TCTTAATAGAATCATGGTATCTTAATAACTAGATAATGAATGCTTAC
10663156 TCTTAATAGAATCATGGTATCTTAATAACTAGATAATGAATGCTTAC
1 TCTTAATAGAATCATGGTATCTTAATAACTAGATAATGAATGCTTAC
10663203 T
1 T
10663204 TAAAACAAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (47 bp):
TCTTAATAGAATCATGGTATCTTAATAACTAGATAATGAATGCTTAC
Found at i:10663581 original size:19 final size:16
Alignment explanation
Indices: 10663552--10663596 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 16
10663542 ACTCAATTTC
*
10663552 AAATGATTAATTAAACT
1 AAATAATTAATT-AACT
10663569 ATGAATAATTAATTAACT
1 A--AATAATTAATTAACT
10663587 AAATAATTAA
1 AAATAATTAA
10663597 CAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 5 0.20
19 10 0.40
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (16 bp):
AAATAATTAATTAACT
Found at i:10664640 original size:29 final size:30
Alignment explanation
Indices: 10664593--10664686 Score: 154
Period size: 30 Copynumber: 3.2 Consensus size: 30
10664583 AGAGCTCAGT
*
10664593 GCTGCAGCGCTGGAGAAGTAGCGCCGCAGC
1 GCTGCAGCACTGGAGAAGTAGCGCCGCAGC
10664623 GCTGCAGCAC-GGAGAAGTAGCGCCGCAGC
1 GCTGCAGCACTGGAGAAGTAGCGCCGCAGC
*
10664652 GCTGCGGCACTGGAGAAGTAGCGCCGCAGC
1 GCTGCAGCACTGGAGAAGTAGCGCCGCAGC
*
10664682 TCTGC
1 GCTGC
10664687 GCGACTTCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 28 0.47
30 32 0.53
ACGTcount: A:0.20, C:0.31, G:0.38, T:0.11
Consensus pattern (30 bp):
GCTGCAGCACTGGAGAAGTAGCGCCGCAGC
Found at i:10664793 original size:12 final size:13
Alignment explanation
Indices: 10664778--10664813 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
10664768 AGAGATTTTT
10664778 GAGGCAGCAAGA-
1 GAGGCAGCAAGAG
10664790 GAGGCAGCAA-AG
1 GAGGCAGCAAGAG
10664802 GAGGCAGCAAGA
1 GAGGCAGCAAGA
10664814 AACTATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GAGGCAGCAAGAG
Found at i:10668797 original size:36 final size:35
Alignment explanation
Indices: 10668750--10668831 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
10668740 TGCTCTTGGT
*
10668750 AAAAGTCATTGTAAAGGTTTTTGCTTGAGCTCGG-TA
1 AAAAGTCATTGT-AAGGGTTTTGCTTGAGC-CGGTTA
* * *
10668786 AAAAGTGATTGTGAGGGTTTTGCTTGATCCGGTTA
1 AAAAGTCATTGTAAGGGTTTTGCTTGAGCCGGTTA
10668821 AAAAGTACATT
1 AAAAGT-CATT
10668832 CCTTTGGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
34 3 0.08
35 22 0.56
36 14 0.36
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (35 bp):
AAAAGTCATTGTAAGGGTTTTGCTTGAGCCGGTTA
Found at i:10682114 original size:62 final size:62
Alignment explanation
Indices: 10682017--10682148 Score: 264
Period size: 62 Copynumber: 2.1 Consensus size: 62
10682007 GGTGGGGGTC
10682017 TCACATGTTTCCCACTAACTTCTCCTTTTTGGCATATAATAGTTTGCATGTAATAGTGAGTT
1 TCACATGTTTCCCACTAACTTCTCCTTTTTGGCATATAATAGTTTGCATGTAATAGTGAGTT
10682079 TCACATGTTTCCCACTAACTTCTCCTTTTTGGCATATAATAGTTTGCATGTAATAGTGAGTT
1 TCACATGTTTCCCACTAACTTCTCCTTTTTGGCATATAATAGTTTGCATGTAATAGTGAGTT
10682141 TCACATGT
1 TCACATGT
10682149 ACATCTCATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (62 bp):
TCACATGTTTCCCACTAACTTCTCCTTTTTGGCATATAATAGTTTGCATGTAATAGTGAGTT
Found at i:10682914 original size:29 final size:28
Alignment explanation
Indices: 10682863--10683075 Score: 237
Period size: 29 Copynumber: 7.3 Consensus size: 28
10682853 ATACATTGTT
10682863 TCTTAATTTAGACAAGAAAACATGTTTG
1 TCTTAATTTAGACAAGAAAACATGTTTG
* *
10682891 TCTTAATTTATGAGAAGAAAACATGCTTTTT
1 TCTTAATTTA-GACAAGAAAACATG--TTTG
* * *
10682922 TTTTAAAATTTAGATAAGAAAACATACTTTG
1 TCTT--AATTTAGACAAGAAAACAT-GTTTG
*
10682953 TCTTAATTTAGACAAGAAAACATGCTTG
1 TCTTAATTTAGACAAGAAAACATGTTTG
*
10682981 TCTTAATTTAAGACAAGAAAATATGTTTTG
1 TCTTAATTT-AGACAAGAAAACATG-TTTG
* * *
10683011 TCTTAATCTAGACAAAAAAATATGTTTG
1 TCTTAATTTAGACAAGAAAACATGTTTG
* *
10683039 TCTCAATTTAGACAAGATAACATGCTTTG
1 TCTTAATTTAGACAAGAAAACATG-TTTG
10683068 TCTTAATT
1 TCTTAATT
10683076 AAAGATAAGA
Statistics
Matches: 156, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
28 45 0.29
29 70 0.45
30 11 0.07
31 12 0.08
32 12 0.08
33 6 0.04
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (28 bp):
TCTTAATTTAGACAAGAAAACATGTTTG
Found at i:10682982 original size:90 final size:86
Alignment explanation
Indices: 10682863--10683085 Score: 268
Period size: 90 Copynumber: 2.5 Consensus size: 86
10682853 ATACATTGTT
* * * * *
10682863 TCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTATGAGAAGAAAACATGCTTTTTTTTTAA
1 TCTTAATTTAGACAAGAAAACATGCTTGTCTTAATTTAAGACAAGAAAACATG-TTTTGTCTT--
* *
10682928 AATTTAGATAAGAAAACATA-CTTTG
63 AATCTAGACAA-AAAA-ATATCTTTG
*
10682953 TCTTAATTTAGACAAGAAAACATGCTTGTCTTAATTTAAGACAAGAAAATATGTTTTGTCTTAAT
1 TCTTAATTTAGACAAGAAAACATGCTTGTCTTAATTTAAGACAAGAAAACATGTTTTGTCTTAAT
*
10683018 CTAGACAAAAAAATATGTTTG
66 CTAGACAAAAAAATATCTTTG
* * * *
10683039 TCTCAATTTAGACAAGATAACATGCTTTGTCTTAATTAAAGATAAGA
1 TCTTAATTTAGACAAGAAAACATGC-TTGTCTTAATTTAAGACAAGA
10683086 GTTGTCTTAA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
85 3 0.03
86 31 0.26
87 28 0.24
89 7 0.06
90 49 0.42
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (86 bp):
TCTTAATTTAGACAAGAAAACATGCTTGTCTTAATTTAAGACAAGAAAACATGTTTTGTCTTAAT
CTAGACAAAAAAATATCTTTG
Found at i:10692305 original size:26 final size:23
Alignment explanation
Indices: 10692252--10692306 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
10692242 CTTCTCAAAA
*
10692252 CCTTTTATAATAAAATGTATATG
1 CCTTTTATAATAAAATGTATATC
* *
10692275 GCTTTTATTTATATAAATGTATAGTC
1 CCTTTTA-TAATA-AAATGTATA-TC
10692301 CCTTTT
1 CCTTTT
10692307 GCTCTTTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 6 0.24
24 4 0.16
25 9 0.36
26 6 0.24
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (23 bp):
CCTTTTATAATAAAATGTATATC
Found at i:10705279 original size:17 final size:15
Alignment explanation
Indices: 10705258--10705297 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
10705248 GTTTCCATTA
10705258 ATTAATTTAGTGTTTAC
1 ATTAATTTAGT-TTT-C
*
10705275 TTTAATTTAGTTTTC
1 ATTAATTTAGTTTTC
10705290 ATTAATTT
1 ATTAATTT
10705298 TCTAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 3 0.14
17 10 0.48
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (15 bp):
ATTAATTTAGTTTTC
Found at i:10708063 original size:68 final size:68
Alignment explanation
Indices: 10707937--10708063 Score: 164
Period size: 68 Copynumber: 1.9 Consensus size: 68
10707927 ATCTCATAAG
* * * *
10707937 GTATATGGAAAATACATTATCAACATAATCTCATGGTATTCATCATGCTTTCTCAATCATTTCAT
1 GTATATGGAAAATACATCATCAACATAATCTCATGGCATTCATCATGCATACTCAATCATTTCAT
10708002 GTA
66 GTA
* ** * * *
10708005 GTATATGGAATATACATCATTTATATAATCTCATGGCATTTATCATGCATACTTAATCA
1 GTATATGGAAAATACATCATCAACATAATCTCATGGCATTCATCATGCATACTCAATCA
10708064 CCTTATATGG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 49 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (68 bp):
GTATATGGAAAATACATCATCAACATAATCTCATGGCATTCATCATGCATACTCAATCATTTCAT
GTA
Found at i:10708089 original size:68 final size:67
Alignment explanation
Indices: 10707959--10708186 Score: 201
Period size: 68 Copynumber: 3.3 Consensus size: 67
10707949 TACATTATCA
* * * * ** * * *
10707959 ACATAATCTCATGGTATTCATCATGCTTTCTCAATCATTTCATGTAG-TATATGGAATATACATC
1 ACATAATCT-ATGGCATTCATCATGCATACTTAATCACCTCATAT-GCTATATGAAATTTACATC
*
10708023 ATTT
64 ATAT
* * * * *
10708027 ATATAATCTCATGGCATTTATCATGCATACTTAATCACCTTATATGGTCTATGAAATTTACATCA
1 ACATAATCT-ATGGCATTCATCATGCATACTTAATCACCTCATATGCTATATGAAATTTACATCA
10708092 TAT
65 TAT
* * *
10708095 ACACAATCT-TGG-AGTATACATCATGCATACTTAATCATCTCATATGCTATATAAAATTTACAT
1 ACATAATCTATGGCA-T-T-CATCATGCATACTTAATCACCTCATATGCTATATGAAATTTACAT
10708158 CATAT
63 CATAT
*
10708163 ACATAATCTTATGACATTCATCAT
1 ACATAATC-TATGGCATTCATCAT
10708187 ACCAAACATG
Statistics
Matches: 129, Mismatches: 24, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
65 1 0.01
66 4 0.03
67 2 0.02
68 116 0.90
69 2 0.02
70 3 0.02
71 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (67 bp):
ACATAATCTATGGCATTCATCATGCATACTTAATCACCTCATATGCTATATGAAATTTACATCAT
AT
Found at i:10713833 original size:43 final size:42
Alignment explanation
Indices: 10713724--10713850 Score: 141
Period size: 42 Copynumber: 3.0 Consensus size: 42
10713714 CAATGGTTAC
* *
10713724 TTTTGATAT-ACTTATGACCCATGCCTCTAGGGTTAATTATGG
1 TTTTGATATGA-TTATGACCAATGCCACTAGGGTTAATTATGG
* *
10713766 TTTTGATATGAGTATGACCAATGCCACTAGGGTTAATTGTGG
1 TTTTGATATGATTATGACCAATGCCACTAGGGTTAATTATGG
* * * *
10713808 TTTTTGTTATGATTATAACCTATGCCA-TAGGGGTTAAGTATGG
1 -TTTTGATATGATTATGACCAATGCCACTA-GGGTTAATTATGG
10713851 CCATAGTATG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 38 0.53
43 34 0.47
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (42 bp):
TTTTGATATGATTATGACCAATGCCACTAGGGTTAATTATGG
Found at i:10713839 original size:42 final size:42
Alignment explanation
Indices: 10713744--10713850 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 42
10713734 CTTATGACCC
* *
10713744 ATGCCTCTAGGGTTAATTATGGTTTTGATATGAGTATGACCA
1 ATGCCACTAGGGTTAATTATGGTTTTGATATGAGTATAACCA
* * * *
10713786 ATGCCACTAGGGTTAATTGTGGTTTTTGTTATGATTATAACCT
1 ATGCCACTAGGGTTAATTATGG-TTTTGATATGAGTATAACCA
*
10713829 ATGCCA-TAGGGGTTAAGTATGG
1 ATGCCACTA-GGGTTAATTATGG
10713851 CCATAGTATG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 22 0.40
43 33 0.60
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (42 bp):
ATGCCACTAGGGTTAATTATGGTTTTGATATGAGTATAACCA
Found at i:10719836 original size:19 final size:18
Alignment explanation
Indices: 10719790--10719837 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
10719780 TTAAAATCAT
10719790 AATTAATTCATTTAAATG
1 AATTAATTCATTTAAATG
* *
10719808 AATCATATTCATTATAAATT
1 AATTA-ATTCATT-TAAATG
*
10719828 AGTTAATTCA
1 AATTAATTCA
10719838 ATTCCATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 12 0.50
20 8 0.33
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (18 bp):
AATTAATTCATTTAAATG
Found at i:10721027 original size:31 final size:31
Alignment explanation
Indices: 10720930--10721027 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
10720920 GAATAAAAGA
* * *
10720930 ATAACCTTACAACTACCTTTTCTC-TAGAGGA
1 ATAACCTT-TAACTACCTTTTCTCTTGGAGGT
* **
10720961 ATAACC-TTATACTA-CTTTT-TCTATGAACAT
1 ATAACCTTTA-ACTACCTTTTCTCT-TGGAGGT
*
10720991 TTAACCTTTAACTACCTTTTCTCTTGGAGGT
1 ATAACCTTTAACTACCTTTTCTCTTGGAGGT
10721022 ATAACC
1 ATAACC
10721028 AACAACAACA
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
28 2 0.04
29 6 0.12
30 16 0.32
31 23 0.46
32 3 0.06
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (31 bp):
ATAACCTTTAACTACCTTTTCTCTTGGAGGT
Found at i:10724602 original size:306 final size:306
Alignment explanation
Indices: 10724049--10724662 Score: 1147
Period size: 306 Copynumber: 2.0 Consensus size: 306
10724039 ATGCTGAGCT
*
10724049 TAGATTGACATAAAGCTAAAGGTTCTCAAATTATTTCCCACTATTGTCTATTTTTGGACTAGTAA
1 TAGATTGACATAAAGCTAAAGGTTCTCAAATTATTTCCCACTATCGTCTATTTTTGGACTAGTAA
10724114 GGCATCCCAATACTCACTTATTATAGAATGCCAGCGGAAAAGGTTCAATATAAGTGGAAGCATTT
66 GGCATCCCAATACTCACTTATTATAGAATGCCAGCGGAAAAGGTTCAATATAAGTGGAAGCATTT
* *
10724179 CATTAGCCCATGCGTAAGTTATCACCTCATGTGAGTAAAGATACTCTACTTCTTTTTAAAACGGA
131 CATTAGCCAATGCGTAAGTTATCACCTCATGTGAGTAAAGATACTCTACTTCTTTTTAAAAAGGA
*
10724244 TGGAGTCTAGGAAGAAGGTTTATGCATGCATGTGTAGTGAGTGTGTGAAAAGGCATATTATATAA
196 TGGAGTCTAGGAAGAAGGTTTATGCATGCATGTGTAGTGAGTGTGTGAAAAGGCATATTACATAA
*
10724309 AGAAAAGAAACAAGAAAGTAAAACAAACTAAAAAATTGAACTAGTG
261 AGAAAAGAAACAAGAAAATAAAACAAACTAAAAAATTGAACTAGTG
*
10724355 TAGATTGACATAGAGCTAAAGGTTCTCAAATTATTTCCCACTATCGTCTATTTTTGGACTAGTAA
1 TAGATTGACATAAAGCTAAAGGTTCTCAAATTATTTCCCACTATCGTCTATTTTTGGACTAGTAA
*
10724420 GGCATCCTAATACTCACTTATTATAGAATGCCAGCGGAAAAGGTTCAATATAAGTGGAAGCATTT
66 GGCATCCCAATACTCACTTATTATAGAATGCCAGCGGAAAAGGTTCAATATAAGTGGAAGCATTT
10724485 CATTAGCCAATGCGTAAGTTATCACCTCATGTGAGTAAAGATACTCTACTTCTTTTTAAAAAGGA
131 CATTAGCCAATGCGTAAGTTATCACCTCATGTGAGTAAAGATACTCTACTTCTTTTTAAAAAGGA
*
10724550 TGGAGTCTAGGAAGAAGGTTTATGCATGCATGTGTAGTGAGTGTGTGAAAAGGCCTATTACATAA
196 TGGAGTCTAGGAAGAAGGTTTATGCATGCATGTGTAGTGAGTGTGTGAAAAGGCATATTACATAA
*
10724615 AGAAAAGAAACAAGAAAATAAAACAAACTAAAAAATTGAATTAGTG
261 AGAAAAGAAACAAGAAAATAAAACAAACTAAAAAATTGAACTAGTG
10724661 TA
1 TA
10724663 ACTGTAAGGC
Statistics
Matches: 299, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
306 299 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (306 bp):
TAGATTGACATAAAGCTAAAGGTTCTCAAATTATTTCCCACTATCGTCTATTTTTGGACTAGTAA
GGCATCCCAATACTCACTTATTATAGAATGCCAGCGGAAAAGGTTCAATATAAGTGGAAGCATTT
CATTAGCCAATGCGTAAGTTATCACCTCATGTGAGTAAAGATACTCTACTTCTTTTTAAAAAGGA
TGGAGTCTAGGAAGAAGGTTTATGCATGCATGTGTAGTGAGTGTGTGAAAAGGCATATTACATAA
AGAAAAGAAACAAGAAAATAAAACAAACTAAAAAATTGAACTAGTG
Found at i:10727395 original size:17 final size:17
Alignment explanation
Indices: 10727337--10727401 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
10727327 CTTGATATTT
* *
10727337 TTATTTATTATTATCTA
1 TTATTTATAATTATCTC
* *
10727354 TTATATAAAATTATCTC
1 TTATTTATAATTATCTC
* *
10727371 -AATATTATTATTATCTC
1 TTAT-TTATAATTATCTC
10727388 TTATTTATAATTAT
1 TTATTTATAATTAT
10727402 TTGTTAGGAG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
16 2 0.06
17 32 0.89
18 2 0.06
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTTATAATTATCTC
Found at i:10727937 original size:18 final size:20
Alignment explanation
Indices: 10727914--10727961 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
10727904 ATAAATAATC
*
10727914 ATAAATATAA-AAAAAT-AG
1 ATAAATATAAGAAAAATGAA
10727932 ATAAATTAATAAGAAAAATGAA
1 ATAAA-T-ATAAGAAAAATGAA
10727954 ATAAATAT
1 ATAAATAT
10727962 TACCTTCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.20
19 1 0.04
20 6 0.24
21 7 0.28
22 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
ATAAATATAAGAAAAATGAA
Found at i:10727957 original size:22 final size:20
Alignment explanation
Indices: 10727920--10727959 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
10727910 AATCATAAAT
*
10727920 ATAAAAAAATAGATAAATTA
1 ATAAAAAAATAAATAAATTA
10727940 ATAAGAAAAATGAAATAAAT
1 ATAA-AAAAAT-AAATAAAT
10727960 ATTACCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
ATAAAAAAATAAATAAATTA
Found at i:10728513 original size:15 final size:15
Alignment explanation
Indices: 10728493--10728535 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
10728483 CTACCTTATT
*
10728493 AAAAACCTTATTAAG
1 AAAAACCTTAATAAG
*
10728508 AAAAACC-TAATGAG
1 AAAAACCTTAATAAG
*
10728522 AAAAACCTTGATAA
1 AAAAACCTTAATAA
10728536 AGGAAAAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAACCTTAATAAG
Found at i:10743702 original size:2 final size:2
Alignment explanation
Indices: 10743697--10743727 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10743687 ATATATATAT
10743697 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
10743728 GAGACAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10743855 original size:32 final size:32
Alignment explanation
Indices: 10743819--10743883 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
10743809 TAAAGACTTT
*
10743819 TCCAAATAGTATTACTTGAAATATGGAGAATA
1 TCCAAATACTATTACTTGAAATATGGAGAATA
*
10743851 TCCAAATACTATTTCTTGAAATATGGAGAATA
1 TCCAAATACTATTACTTGAAATATGGAGAATA
10743883 T
1 T
10743884 TCTTGCTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (32 bp):
TCCAAATACTATTACTTGAAATATGGAGAATA
Found at i:10748254 original size:30 final size:31
Alignment explanation
Indices: 10748200--10748260 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
10748190 AATCATAAGA
10748200 CTTATTTGACTCAAAATAAAAAGTACAAAGG
1 CTTATTTGACTCAAAATAAAAAGTACAAAGG
*
10748231 CTTATTTGACTCAAAAT-AAAAGTATAAAGG
1 CTTATTTGACTCAAAATAAAAAGTACAAAGG
10748261 TTTGACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (31 bp):
CTTATTTGACTCAAAATAAAAAGTACAAAGG
Found at i:10748591 original size:2 final size:2
Alignment explanation
Indices: 10748584--10748619 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10748574 TAGTTTAGTT
*
10748584 TA TA TA TA TA TA TA TA AA 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
10748620 AACCACCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10753170 original size:36 final size:36
Alignment explanation
Indices: 10753082--10753162 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
10753072 CAAATCAACG
* **
10753082 GGCAGAGAACAGATCATGCACAACATCTACGCAATT
1 GGCAGAGAACAGATCATGCACAACATCAAAACAATT
*
10753118 GGCAGAGAACAGATCATGCACAACGTCAAAACAATT
1 GGCAGAGAACAGATCATGCACAACATCAAAACAATT
*
10753154 GGTAGAGAA
1 GGCAGAGAA
10753163 TGGATCATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (36 bp):
GGCAGAGAACAGATCATGCACAACATCAAAACAATT
Found at i:10757625 original size:22 final size:22
Alignment explanation
Indices: 10757600--10757643 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
10757590 TTATCAAACA
10757600 CTTTATTATTT-TTTATTTTAAT
1 CTTT-TTATTTCTTTATTTTAAT
* *
10757622 CTTTTTCTTTCTTTTTTTTAAT
1 CTTTTTATTTCTTTATTTTAAT
10757644 ATTCAACACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (22 bp):
CTTTTTATTTCTTTATTTTAAT
Found at i:10762172 original size:24 final size:23
Alignment explanation
Indices: 10762145--10762206 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 23
10762135 AAATTTGGAT
*
10762145 AACTAATTAAACTAAAAACTAATC
1 AACTAATTAAAAT-AAAACTAATC
*
10762169 AACTAAATTAAAATAAAACTAATT
1 AACT-AATTAAAATAAAACTAATC
10762193 AACATTAATTAAAA
1 AAC--TAATTAAAA
10762207 AATCTAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 16 0.48
25 16 0.48
26 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (23 bp):
AACTAATTAAAATAAAACTAATC
Found at i:10762206 original size:25 final size:25
Alignment explanation
Indices: 10762148--10762206 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
10762138 TTTGGATAAC
*
10762148 TAATTAAACTAAAAACTAATCAACT
1 TAATTAAAATAAAAACTAATCAACT
* *
10762173 AAATTAAAAT-AAAACTAATTAACAT
1 TAATTAAAATAAAAACTAATCAAC-T
10762198 TAATTAAAA
1 TAATTAAAA
10762207 AATCTAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (25 bp):
TAATTAAAATAAAAACTAATCAACT
Found at i:10775925 original size:21 final size:21
Alignment explanation
Indices: 10775899--10775950 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
10775889 GTTCATTCAA
* *
10775899 TTCATGACAAAGATAGATGCC
1 TTCATGACAAAGACAAATGCC
*
10775920 TTCATGACAAAGACAAATGCT
1 TTCATGACAAAGACAAATGCC
10775941 TTCATGACAA
1 TTCATGACAA
10775951 GGACTGATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGACAAATGCC
Found at i:10775960 original size:21 final size:21
Alignment explanation
Indices: 10775899--10775966 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
10775889 GTTCATTCAA
10775899 TTCATGACAAAGA-TAGATGCC
1 TTCATGACAAAGACT-GATGCC
** *
10775920 TTCATGACAAAGACAAATGCT
1 TTCATGACAAAGACTGATGCC
*
10775941 TTCATGACAAGGACTGATGCC
1 TTCATGACAAAGACTGATGCC
*
10775962 ATCAT
1 TTCAT
10775967 TCAATGTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGACTGATGCC
Found at i:10780104 original size:35 final size:35
Alignment explanation
Indices: 10780064--10780267 Score: 169
Period size: 35 Copynumber: 5.8 Consensus size: 35
10780054 NNNNNNNTGT
*
10780064 GCCTAATTCATTAAATTATTTAATTAAGTCATTAG
1 GCCTAATTGATTAAATTATTTAATTAAGTCATTAG
* *** * *
10780099 GCCTAATTTATTAAATTAAACAATTAAGTTAGTAG
1 GCCTAATTGATTAAATTATTTAATTAAGTCATTAG
* * * * * *
10780134 GCCTAACTGATTAAATTTGTTTAATGAAATGATTGG
1 GCCTAATTGATTAAA-TTATTTAATTAAGTCATTAG
*
10780170 GCCTAATTGATTAAATTATTTAATTAAGTTATT-G
1 GCCTAATTGATTAAATTATTTAATTAAGTCATTAG
* * * *
10780204 GATCTAATTGATTAAATTTGTTTAATCAAGTTC-TTGG
1 G-CCTAATTGATTAAA-TTATTTAATTAAG-TCATTAG
* **
10780241 GCCTAATTTATTAAATTAAATAATTAA
1 GCCTAATTGATTAAATTATTTAATTAA
10780268 ATTAATTTGG
Statistics
Matches: 132, Mismatches: 32, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
34 2 0.02
35 77 0.58
36 50 0.38
37 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.42
Consensus pattern (35 bp):
GCCTAATTGATTAAATTATTTAATTAAGTCATTAG
Found at i:10780176 original size:71 final size:71
Alignment explanation
Indices: 10780098--10780267 Score: 225
Period size: 71 Copynumber: 2.4 Consensus size: 71
10780088 TAAGTCATTA
* *
10780098 GGCCTAATTTATTAAATTAAACAATTAAGTTAGTAGG-CCTAACTGATTAAATTTGTTTAATGAA
1 GGCCTAATTTATTAAATTAAATAATTAAGTTA-TAGGACCTAACTGATTAAATTTGTTTAATCAA
10780162 ATGATTG
65 ATGATTG
* ** * * * *
10780169 GGCCTAATTGATTAAATTATTTAATTAAGTTATTGGATCTAATTGATTAAATTTGTTTAATCAAG
1 GGCCTAATTTATTAAATTAAATAATTAAGTTATAGGACCTAACTGATTAAATTTGTTTAATCAAA
**
10780234 TTCTTG
66 TGATTG
10780240 GGCCTAATTTATTAAATTAAATAATTAA
1 GGCCTAATTTATTAAATTAAATAATTAA
10780268 ATTAATTTGG
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
70 3 0.04
71 81 0.96
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (71 bp):
GGCCTAATTTATTAAATTAAATAATTAAGTTATAGGACCTAACTGATTAAATTTGTTTAATCAAA
TGATTG
Found at i:10781498 original size:19 final size:20
Alignment explanation
Indices: 10781453--10781500 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
10781443 ATTTACCATT
* *
10781453 TAATTTTAGTTTTAGTTTAT
1 TAATTTTAATTTTAGTTTAA
* *
10781473 TAGTTTTAATTTT-TTTTAA
1 TAATTTTAATTTTAGTTTAA
10781492 TAATTTTAA
1 TAATTTTAA
10781501 ATTATTTGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (20 bp):
TAATTTTAATTTTAGTTTAA
Found at i:10796983 original size:35 final size:35
Alignment explanation
Indices: 10796955--10797139 Score: 214
Period size: 35 Copynumber: 5.3 Consensus size: 35
10796945 CTTAATTGTT
*
10796955 TAATTTAATCAATTAGGCCTAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * *
10796990 CAACTTAATCAATGAGGCCCAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* ***
10797025 TAATTTAATCAATTAGGCCCAGTAACTTAATTGTT
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * *
10797060 TAATTTAATTAACTAGACCCAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
10797095 TAATTTAATGAATTAGG--C-ACAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
10797127 CAATTTTAATCAA
1 TAA-TTTAATCAA
10797140 GTGCTTGAGA
Statistics
Matches: 125, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
32 15 0.12
33 9 0.07
35 101 0.81
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:10797057 original size:105 final size:103
Alignment explanation
Indices: 10796942--10797139 Score: 272
Period size: 105 Copynumber: 1.9 Consensus size: 103
10796932 GAAGCTCAAT
* * *
10796942 TAACTTAATTGTTTAATTTAATCAATTAGGCCTAATAACTTAATTAAACAACTTAATCAATGAGG
1 TAACTTAATTGTTTAATTTAATCAACTAGACCCAATAACTTAATTAAACAACTTAATCAATGAGG
* *
10797007 CCCAATAACTTAATTAAATAA-TTTAATCAATTAGGCCCAG
66 --C-ACAACTTAATTAAACAATTTTAATCAATTAGGCCCAG
* * * * *
10797047 TAACTTAATTGTTTAATTTAATTAACTAGACCCAATAACTTAATTAAATAATTTAATGAATTAGG
1 TAACTTAATTGTTTAATTTAATCAACTAGACCCAATAACTTAATTAAACAACTTAATCAATGAGG
10797112 CACAACTTAATTAAACAATTTTAATCAA
66 CACAACTTAATTAAACAATTTTAATCAA
10797140 GTGCTTGAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
102 15 0.18
103 10 0.12
105 57 0.70
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (103 bp):
TAACTTAATTGTTTAATTTAATCAACTAGACCCAATAACTTAATTAAACAACTTAATCAATGAGG
CACAACTTAATTAAACAATTTTAATCAATTAGGCCCAG
Found at i:10799325 original size:2 final size:2
Alignment explanation
Indices: 10799318--10799342 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10799308 AATCATGAGA
10799318 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
10799343 AGGATTGTTC
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:10804934 original size:18 final size:19
Alignment explanation
Indices: 10804908--10804955 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
10804898 GTAACAAGTA
*
10804908 AAAAGAATATTTT-TAAAT
1 AAAATAATATTTTATAAAT
*
10804926 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
10804945 AAAATAATATT
1 AAAATAATATT
10804956 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:10815862 original size:26 final size:21
Alignment explanation
Indices: 10815803--10815853 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
10815793 CTTTCTACTT
10815803 GAAATCTATCATTAGATTAGG
1 GAAATCTATCATTAGATTAGG
10815824 GAAATCTATCATTAGATTAGG
1 GAAATCTATCATTAGATTAGG
10815845 GAAATCTAT
1 GAAATCTAT
10815854 TAATACATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (21 bp):
GAAATCTATCATTAGATTAGG
Found at i:10815970 original size:61 final size:61
Alignment explanation
Indices: 10815886--10816024 Score: 170
Period size: 61 Copynumber: 2.3 Consensus size: 61
10815876 CTTATAGTTC
* * * * * * * ***
10815886 AAATTTATTGATACATTTGGACAATGTATTGATAGAAATTACACAGAATGGTCCCTTTTTT
1 AAATCTATTGATACATTTAGACAATGTATCGATAAAAATCACACAAAATGCTCCCCAATTT
10815947 AAATCTATTGATACATTTAGACAATGTATCGATAAAAATCACACAAAATGCTCCCCAATTT
1 AAATCTATTGATACATTTAGACAATGTATCGATAAAAATCACACAAAATGCTCCCCAATTT
* *
10816008 AACTCTATCGATACATT
1 AAATCTATTGATACATT
10816025 CTTGAATTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (61 bp):
AAATCTATTGATACATTTAGACAATGTATCGATAAAAATCACACAAAATGCTCCCCAATTT
Found at i:10822788 original size:17 final size:17
Alignment explanation
Indices: 10822736--10822790 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
10822726 ACTAATAAAT
10822736 AAAATATTAATTTT-TTA
1 AAAATATT-ATTTTATTA
*
10822753 ATAATATT-TTATTCA-TA
1 AAAATATTATT-TT-ATTA
10822770 AAAATATTATTTTATTA
1 AAAATATTATTTTATTA
10822787 AAAA
1 AAAA
10822791 ATACTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 2 0.06
16 3 0.10
17 24 0.77
18 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATATTATTTTATTA
Found at i:10822800 original size:18 final size:20
Alignment explanation
Indices: 10822752--10822800 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
10822742 TTAATTTTTT
*
10822752 AATAATATTTTATTCATAAA
1 AATACTATTTTATTCATAAA
*
10822772 AATATTATTTTATT-A-AAA
1 AATACTATTTTATTCATAAA
*
10822790 AATACTCTTTT
1 AATACTATTTT
10822801 TACTTGTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 13 0.50
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (20 bp):
AATACTATTTTATTCATAAA
Found at i:10826153 original size:18 final size:19
Alignment explanation
Indices: 10826114--10826162 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
10826104 TTAATATTTT
*
10826114 AATAATATTTTATTCATAAA
1 AATATTATTTTATT-ATAAA
10826134 AATATTATTTTATT-TAAA
1 AATATTATTTTATTATAAA
*
10826152 AATATTCTTTT
1 AATATTATTTT
10826163 TACTTGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTATAAA
Found at i:10832199 original size:99 final size:99
Alignment explanation
Indices: 10832028--10832238 Score: 377
Period size: 99 Copynumber: 2.1 Consensus size: 99
10832018 CATTTAACAA
*
10832028 ATGCATTATCTATGCATATCACACTAAAATACAAGGCATAGATTTTATTGCAAACATCGTGAAAG
1 ATGCATTATCTATGCATATCACACTAAAATACAAGGCATAGATTTTATTGCAAACATCATGAAAG
*
10832093 GCTTGTTTCTCGATTTCTAAAGCTCTTTACATAT
66 GCTTGTTTCTCGATTTATAAAGCTCTTTACATAT
*
10832127 ATGCATTATCTATGCGTATCACACTAAAATACAAGGCATAGATTTTATTGCAAACATCATGAAAG
1 ATGCATTATCTATGCATATCACACTAAAATACAAGGCATAGATTTTATTGCAAACATCATGAAAG
10832192 GCTTGTTTCTCGATTTATAAAGCTCTTTACATAT
66 GCTTGTTTCTCGATTTATAAAGCTCTTTACATAT
**
10832226 ATGGTTTATCTAT
1 ATGCATTATCTAT
10832239 AGTTATATCC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 107 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (99 bp):
ATGCATTATCTATGCATATCACACTAAAATACAAGGCATAGATTTTATTGCAAACATCATGAAAG
GCTTGTTTCTCGATTTATAAAGCTCTTTACATAT
Found at i:10840228 original size:11 final size:11
Alignment explanation
Indices: 10840212--10840252 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
10840202 TATAACAAAG
10840212 AAGAAAAGAGA
1 AAGAAAAGAGA
*
10840223 AAGAAAAGGGA
1 AAGAAAAGAGA
10840234 AA-AGAAAGA-A
1 AAGA-AAAGAGA
10840244 AAGAAAAGA
1 AAGAAAAGA
10840253 AACATGCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAGA
Found at i:10840241 original size:4 final size:5
Alignment explanation
Indices: 10840212--10840254 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
10840202 TATAACAAAG
10840212 AAGAA AAGAGA AAGAA AAGGGAA AAG-A AAGAA AAGAA AAGAA A
1 AAGAA AAGA-A AAGAA AA--GAA AAGAA AAGAA AAGAA AAGAA A
10840255 CATGCAAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.12
5 20 0.59
6 5 0.15
7 5 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:10840241 original size:16 final size:14
Alignment explanation
Indices: 10840220--10840254 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
10840210 AGAAGAAAAG
10840220 AGAAAGAAAAGGGAAA
1 AGAAAGAAAA--GAAA
10840236 AGAAAGAAAAGAAA
1 AGAAAGAAAAGAAA
10840250 AGAAA
1 AGAAA
10840255 CATGCAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
16 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAGAAA
Found at i:10850249 original size:76 final size:77
Alignment explanation
Indices: 10850089--10850251 Score: 197
Period size: 76 Copynumber: 2.1 Consensus size: 77
10850079 TGAATTTCTC
* * *
10850089 AAATTAAAATACTATCCTTAGTTTTAAAACTTTCTTTTAAAATAGGAAACAATTTCCTATTTTTA
1 AAATTAAAATACTATACTTAATTTTAAAACTTTCATTTAAAATAGGAAACAATTTCCTATTTTTA
**
10850154 TGAATCACTTAG
66 TGAATCACCCAG
* * * * *
10850166 AAA-TAAAATTCTATACTTAATTTTAGGAA-TTTCATTTAAAGTGGGAAACAATTTTCTATTTTT
1 AAATTAAAATACTATACTTAATTTTA-AAACTTTCATTTAAAATAGGAAACAATTTCCTATTTTT
*
10850229 ATGGATCACCCA-
65 ATGAATCACCCAG
10850241 AAATTAAAATA
1 AAATTAAAATA
10850252 AATGGTGTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
75 3 0.04
76 64 0.89
77 5 0.07
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (77 bp):
AAATTAAAATACTATACTTAATTTTAAAACTTTCATTTAAAATAGGAAACAATTTCCTATTTTTA
TGAATCACCCAG
Found at i:10852125 original size:175 final size:176
Alignment explanation
Indices: 10851824--10852175 Score: 553
Period size: 175 Copynumber: 2.0 Consensus size: 176
10851814 TGTCAAATTC
* * *
10851824 ATCATGCTTTCACCAAAGACTTTATACTAGTTAATCAAGAATTAAGAACAAGTGCGATACATCCC
1 ATCATGCTTTCACCAAAGACTTTATACCAGTTAATCAAGAATTAAAAACAAGTGAGATACATCCC
* *
10851889 CACATATCACTTGGGGTGATGAATCCTCTCTTAACCAGTCATTCACCTTCGCTTACTTCATGGCA
66 CACATATCACTTGGGGTGATAAATCCTCTCTTAACCAGTCATTCACCTTCGCATACTTCATGGCA
* * *
10851954 TA-CCAAAAACATCCTGTTTAGGAATTTGGTTGCATTCAAACCCGT
131 TACCCAAAAACACCCTGTTTAGGAATTTAGTTGCATCCAAACCCGT
** *
10851999 ATCATGCTTTGGCCAAAGACTTTATACCAGTTAATCAATAATTAAAAACAAGTGAGATACATCCC
1 ATCATGCTTTCACCAAAGACTTTATACCAGTTAATCAAGAATTAAAAACAAGTGAGATACATCCC
* * * *
10852064 CACATATCACTTGGGGTGATAAATCCTCTTTTAACTAGTCATTCACCTTTGCATGCTTCATGGCA
66 CACATATCACTTGGGGTGATAAATCCTCTCTTAACCAGTCATTCACCTTCGCATACTTCATGGCA
*
10852129 TACCCAAAAACACCCTGTTTAGGCATTTAGTTGCATCCAAACCCGT
131 TACCCAAAAACACCCTGTTTAGGAATTTAGTTGCATCCAAACCCGT
10852175 A
1 A
10852176 GGGGTGAAAT
Statistics
Matches: 160, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
175 120 0.75
176 40 0.25
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (176 bp):
ATCATGCTTTCACCAAAGACTTTATACCAGTTAATCAAGAATTAAAAACAAGTGAGATACATCCC
CACATATCACTTGGGGTGATAAATCCTCTCTTAACCAGTCATTCACCTTCGCATACTTCATGGCA
TACCCAAAAACACCCTGTTTAGGAATTTAGTTGCATCCAAACCCGT
Found at i:10859425 original size:36 final size:37
Alignment explanation
Indices: 10859356--10859433 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
10859346 GATGATTTGC
*
10859356 TCTCTGTTAGTTGCTTTAACATTATGCGAGATCTAAT
1 TCTCTGCTAGTTGCTTTAACATTATGCGAGATCTAAT
* *
10859393 TCTCTGCTCGTTGCTTTAACA-TATGC-ATGATCTATT
1 TCTCTGCTAGTTGCTTTAACATTATGCGA-GATCTAAT
10859429 TCTCT
1 TCTCT
10859434 ACCAATGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.03
36 17 0.46
37 19 0.51
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (37 bp):
TCTCTGCTAGTTGCTTTAACATTATGCGAGATCTAAT
Found at i:10864031 original size:77 final size:72
Alignment explanation
Indices: 10863908--10864112 Score: 195
Period size: 77 Copynumber: 2.8 Consensus size: 72
10863898 AATACCATTT
* * *
10863908 ATTTTAATTTTAGGTAATTCATAAAAAAAATTATTTCCTACTTTAAAAGCAAA-TCCTAAAATTA
1 ATTTTAATTTTAGGTAATTCATAAAAAAAATTATTTCCTACGTTAAAA-AAAATTCCTAAAACTA
10863972 AGGATAGA
65 AGGATAGA
* * *
10863980 ATTTTAATTTTGGGTGATTCATGAAAATTAGGAAATTGTTTCCTACGTTAAAAAAAATTCCTAAA
1 ATTTTAATTTTAGGTAATTCAT-AAAA--A--AAATTATTTCCTACGTTAAAAAAAATTCCTAAA
*
10864045 ACTAAGGATAGT
61 ACTAAGGATAGA
* * * * * * *
10864057 ATTTTAATTTGA-GAAATTCAT--AGAAAATAATTTCCTAC-TTTATAAAGATTCCTAAA
1 ATTTTAATTTTAGGTAATTCATAAAAAAAATTATTTCCTACGTTAAAAAAAATTCCTAAA
10864113 GTTATGTGAT
Statistics
Matches: 110, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
68 15 0.14
69 12 0.11
71 1 0.01
72 20 0.18
73 5 0.05
75 1 0.01
76 10 0.09
77 46 0.42
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (72 bp):
ATTTTAATTTTAGGTAATTCATAAAAAAAATTATTTCCTACGTTAAAAAAAATTCCTAAAACTAA
GGATAGA
Found at i:10873009 original size:24 final size:24
Alignment explanation
Indices: 10872982--10873031 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
10872972 TTTGCTAGCC
10872982 CTCGAGCAAAATATAGATAAGAAA
1 CTCGAGCAAAATATAGATAAGAAA
10873006 CTCGAGCAAAATATAGATAAGAAA
1 CTCGAGCAAAATATAGATAAGAAA
10873030 CT
1 CT
10873032 AACTTACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (24 bp):
CTCGAGCAAAATATAGATAAGAAA
Found at i:10875072 original size:21 final size:21
Alignment explanation
Indices: 10875047--10875102 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
10875037 GATGGAATCA
10875047 ATCTTTGTCATGAAGGCAGCT
1 ATCTTTGTCATGAAGGCAGCT
* * * *
10875068 GTCTTTCTCATAAAGGCATCT
1 ATCTTTGTCATGAAGGCAGCT
10875089 ATCTTTGTCATGAA
1 ATCTTTGTCATGAA
10875103 TTGCATGAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
ATCTTTGTCATGAAGGCAGCT
Found at i:10879643 original size:25 final size:25
Alignment explanation
Indices: 10879615--10879710 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
10879605 ACTTTCATAT
* * *
10879615 AGATAATAGTCACACAATGCCCTAC
1 AGATAACAATCACGCAATGCCCTAC
* * *
10879640 AGATAACAATCATGCAACGACCTAC
1 AGATAACAATCACGCAATGCCCTAC
* * **
10879665 ATATAATC-GTCACGCAATGCAATAC
1 AGATAA-CAATCACGCAATGCCCTAC
10879690 AGATAACAATCACGCAATGCC
1 AGATAACAATCACGCAATGCC
10879711 TTATCAAGTA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
24 1 0.02
25 51 0.96
26 1 0.02
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (25 bp):
AGATAACAATCACGCAATGCCCTAC
Found at i:10880271 original size:14 final size:14
Alignment explanation
Indices: 10880252--10880287 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10880242 CTCAGTGAGA
* *
10880252 AATGCTTTCGCTAG
1 AATGCTTTCACGAG
10880266 AATGCTTTCACGAG
1 AATGCTTTCACGAG
10880280 AATGCTTT
1 AATGCTTT
10880288 ATAAAGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (14 bp):
AATGCTTTCACGAG
Found at i:10886864 original size:42 final size:42
Alignment explanation
Indices: 10886818--10886948 Score: 110
Period size: 41 Copynumber: 3.2 Consensus size: 42
10886808 AAATTAGACC
10886818 AATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATA
1 AATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATA
* * ** * * * * ** **
10886860 AATC-AAAATAATTTAGAGATAAT---ATTTATATTTTGACC
1 AATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATA
*
10886898 AATCAAATATTAGTTATTGGTCATCCAATTTATCTCTAAATA
1 AATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATA
10886940 AAT-AAAAAT
1 AATCAAAAAT
10886949 AATTTGGAGA
Statistics
Matches: 59, Mismatches: 26, Indels: 9
0.63 0.28 0.10
Matches are distributed among these distances:
38 13 0.22
39 12 0.20
41 18 0.31
42 16 0.27
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (42 bp):
AATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATA
Found at i:10886910 original size:80 final size:79
Alignment explanation
Indices: 10886797--10887040 Score: 291
Period size: 80 Copynumber: 3.1 Consensus size: 79
10886787 GATTATTTGA
* *
10886797 AGATAATATTTA-AATTAGACCAATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATAA
1 AGATAATATTTATATTTTGACCAATC-AAAATTAGTTATTGGTCATCCAATTTATCTCTAAATAA
*
10886861 ATCAAAATAATTTAG
65 ATAAAAATAATTTAG
10886876 AGATAATATTTATATTTTGACCAATCAAATATTAGTTATTGGTCATCCAATTTATCTCTAAATAA
1 AGATAATATTTATATTTTGACCAATCAAA-ATTAGTTATTGGTCATCCAATTTATCTCTAAATAA
*
10886941 ATAAAAATAATTTGG
65 ATAAAAATAATTTAG
* * ** *
10886956 AGATAATCTTCGTAT-TTTTGAACAATCAAAATTTCA-TTATTGGTCATTTAAATTATCTCT-AA
1 AGATAATATT--TATATTTTGACCAATCAAAA-TT-AGTTATTGGTCATCCAATTTATCTCTAAA
* * *
10887018 T-AATTATATTAATTTAG
62 TAAATAAAAATAATTTAG
10887035 AGATAA
1 AGATAA
10887041 AAATCAAATT
Statistics
Matches: 146, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
79 33 0.23
80 72 0.49
81 37 0.25
82 4 0.03
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (79 bp):
AGATAATATTTATATTTTGACCAATCAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATAAA
TAAAAATAATTTAG
Found at i:10898115 original size:24 final size:22
Alignment explanation
Indices: 10898088--10898144 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
10898078 TATGGTATAA
*
10898088 TATTTATAAGAATTCTAATTAAAT
1 TATTTATAA-AATT-TAAATAAAT
10898112 TATTTATAAAATTTAAATAAAT
1 TATTTATAAAATTTAAATAAAT
*
10898134 T-TTTTTAAAAT
1 TATTTATAAAAT
10898145 AAAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.29
22 9 0.29
23 4 0.13
24 9 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTATAAAATTTAAATAAAT
Found at i:10898140 original size:23 final size:24
Alignment explanation
Indices: 10898088--10898134 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
10898078 TATGGTATAA
*
10898088 TATTTATAAGAATTCTAATTAAAT
1 TATTTATAAGAATTCTAAATAAAT
10898112 TATTTATAA-AATT-TAAATAAAT
1 TATTTATAAGAATTCTAAATAAAT
10898134 T
1 T
10898135 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 4 0.18
24 9 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTTATAAGAATTCTAAATAAAT
Found at i:10903814 original size:61 final size:60
Alignment explanation
Indices: 10903717--10903847 Score: 208
Period size: 61 Copynumber: 2.2 Consensus size: 60
10903707 TATCTTTTTC
* * *
10903717 TTTTTTTTTGACTTTAACTTTTGCCTAAGTCGTCCTGTTAAGGATTTTCAACTTAGCAGGT
1 TTTTTTTTTGACCTTAACTTTTGCCTAAGCCATCCTGTTAAGGATTTTCAACTTAGCA-GT
* *
10903778 TTTTTTTTTTACCTTAACTTTTGCCTAAGCCATCCTGTTAAGGATTTTCAACTTAGTAGT
1 TTTTTTTTTGACCTTAACTTTTGCCTAAGCCATCCTGTTAAGGATTTTCAACTTAGCAGT
10903838 TTTTTTTTTG
1 TTTTTTTTTG
10903848 GTGTAGTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
60 11 0.17
61 53 0.83
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (60 bp):
TTTTTTTTTGACCTTAACTTTTGCCTAAGCCATCCTGTTAAGGATTTTCAACTTAGCAGT
Found at i:10908613 original size:63 final size:62
Alignment explanation
Indices: 10908535--10908665 Score: 208
Period size: 63 Copynumber: 2.1 Consensus size: 62
10908525 AAACTGCACC
* * * * *
10908535 AAAAAAAAAATCCTGCTAAGTTGAAAATCCTTAACAGGATGGCTTAGGCAAAATTTAAGGCA
1 AAAAAAAAAAGCCTGCTAAGTTGAAAATCCTTAACAGAACGACTCAGGCAAAATTTAAGGCA
10908597 AAAAAAAAAAGGCCTGCTAAGTTGAAAATCCTTAACAGAACGACTCAGGCAAAATTTAAGGCA
1 AAAAAAAAAA-GCCTGCTAAGTTGAAAATCCTTAACAGAACGACTCAGGCAAAATTTAAGGCA
10908660 AAAAAA
1 AAAAAA
10908666 GAAGAAGATA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 10 0.16
63 53 0.84
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (62 bp):
AAAAAAAAAAGCCTGCTAAGTTGAAAATCCTTAACAGAACGACTCAGGCAAAATTTAAGGCA
Found at i:10910647 original size:40 final size:40
Alignment explanation
Indices: 10910589--10910800 Score: 149
Period size: 40 Copynumber: 5.5 Consensus size: 40
10910579 NGATCAATAA
*
10910589 GTGCTATTATAAAGAGCACCCTCCAAGGATAATGAATTAT
1 GTGCTATTATAAAGAGCACCCTCCAAGGATAATAAATTAT
* * * *
10910629 GTGCTAGTATAAAAAGCA-CTTCCCAAGGATCAA-CAA--A-
1 GTGCTATTATAAAGAGCACCCT-CCAAGGAT-AATAAATTAT
* *
10910666 -TGCTATTATAAAGAGCACCCTCCGAGGATAATAAATTGT
1 GTGCTATTATAAAGAGCACCCTCCAAGGATAATAAATTAT
* * *
10910705 GTGTTATTTTAAAGAGCACCCCCCAAGGATCAAT--A--A-
1 GTGCTATTATAAAGAGCACCCTCCAAGGAT-AATAAATTAT
* * * ** * * *
10910741 GTGCTATTGTAAATAGCACCATCTGAGGATAACAAATCAC
1 GTGCTATTATAAAGAGCACCCTCCAAGGATAATAAATTAT
*
10910781 GTGCTATTGTAAAGAGCACC
1 GTGCTATTATAAAGAGCACC
10910801 ACTTTAAGTT
Statistics
Matches: 134, Mismatches: 24, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
35 4 0.03
36 47 0.35
37 3 0.02
38 1 0.01
39 4 0.03
40 70 0.52
41 5 0.04
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (40 bp):
GTGCTATTATAAAGAGCACCCTCCAAGGATAATAAATTAT
Found at i:10910723 original size:76 final size:76
Alignment explanation
Indices: 10910580--10910800 Score: 253
Period size: 76 Copynumber: 2.9 Consensus size: 76
10910570 NNNNNNNNNN
* *
10910580 GATCAATAAGTGCTATTATAAAGAGCACCCTCCAAGGATAATGAATTATGTGCTAGTATAAAAAG
1 GATCAATAAGTGCTATTATAAAGAGCACCCTCCGAGGATAATAAATTATGTGCTAGTATAAAAAG
**
10910645 CACTTCCCAAG
66 CACCCCCCAAG
* * * * * * *
10910656 GATCAACAAATGCTATTATAAAGAGCACCCTCCGAGGATAATAAATTGTGTGTTATTTTAAAGAG
1 GATCAATAAGTGCTATTATAAAGAGCACCCTCCGAGGATAATAAATTATGTGCTAGTATAAAAAG
10910721 CACCCCCCAAG
66 CACCCCCCAAG
* * * * * * * * * *
10910732 GATCAATAAGTGCTATTGTAAATAGCACCATCTGAGGATAACAAATCACGTGCTATTGTAAAGAG
1 GATCAATAAGTGCTATTATAAAGAGCACCCTCCGAGGATAATAAATTATGTGCTAGTATAAAAAG
10910797 CACC
66 CACC
10910801 ACTTTAAGTT
Statistics
Matches: 122, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 122 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (76 bp):
GATCAATAAGTGCTATTATAAAGAGCACCCTCCGAGGATAATAAATTATGTGCTAGTATAAAAAG
CACCCCCCAAG
Found at i:10912288 original size:35 final size:35
Alignment explanation
Indices: 10912242--10912317 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
10912232 GACTAATCAA
*
10912242 AAATTAGTTATTGGTCATCCAATTTATCTCTAAAT
1 AAATTACTTATTGGTCATCCAATTTATCTCTAAAT
10912277 AAATTACTTATTGGTCATCCAATTTATCTCTAAAT
1 AAATTACTTATTGGTCATCCAATTTATCTCTAAAT
10912312 AAATTA
1 AAATTA
10912318 AAATAATTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (35 bp):
AAATTACTTATTGGTCATCCAATTTATCTCTAAAT
Found at i:10912822 original size:20 final size:20
Alignment explanation
Indices: 10912797--10912842 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
10912787 CCTTGAAGTG
*
10912797 AAGATCAAGTGTTCGTGATC
1 AAGATCAAATGTTCGTGATC
10912817 AAGATCAAATGTTCGTGATC
1 AAGATCAAATGTTCGTGATC
10912837 AAGATC
1 AAGATC
10912843 GAGTCATGAA
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:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (20 bp):
AAGATCAAATGTTCGTGATC
Found at i:10912835 original size:69 final size:68
Alignment explanation
Indices: 10912754--10912900 Score: 201
Period size: 69 Copynumber: 2.2 Consensus size: 68
10912744 CAAGTGGCAA
* * * * *
10912754 CAAAGTTTGTGATCAAGATCAAGTCGTGAAGAGCC-TTGAAGTGAAGATCAAGTGTTCGTGATCA
1 CAAAGTTCGTGATCAAGATCAAGTCATGAAGA-CCTTTAAAGTGAAGATCAAATGTTCGTAATCA
10912818 AGAT
65 AGAT
*
10912822 CAAATGTTCGTGATCAAGATCGAGTCATGAAGACCTTTAAAGTGAAGATCAAATGTTCGTAATCA
1 CAAA-GTTCGTGATCAAGATCAAGTCATGAAGACCTTTAAAGTGAAGATCAAATGTTCGTAATCA
10912887 AGAT
65 AGAT
10912891 C-AAG-TCGTGA
1 CAAAGTTCGTGA
10912901 AGACCCTTGA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
66 6 0.08
67 1 0.01
68 8 0.11
69 56 0.79
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (68 bp):
CAAAGTTCGTGATCAAGATCAAGTCATGAAGACCTTTAAAGTGAAGATCAAATGTTCGTAATCAA
GAT
Found at i:10912870 original size:49 final size:49
Alignment explanation
Indices: 10912817--10912970 Score: 209
Period size: 49 Copynumber: 3.1 Consensus size: 49
10912807 GTTCGTGATC
* * * *
10912817 AAGATCAAATGTTCGTGATCAAGATCGAGTCATGAAGACCTTTAAAGTG
1 AAGATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCG
* *
10912866 AAGATCAAATGTTCGTAATCAAGATCAAGTCGTGAAGACCCTTGAAGCG
1 AAGATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCG
* * *
10912915 AAGATATCAATTGTTCGTGATTAAGATTAAGTCGTGAAGACCCTTAAAGCG
1 AAG--ATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCG
10912966 AAGAT
1 AAGAT
10912971 TATGTGAAGT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
49 48 0.52
51 44 0.48
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (49 bp):
AAGATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCG
Found at i:10912941 original size:51 final size:51
Alignment explanation
Indices: 10912820--10912970 Score: 207
Period size: 51 Copynumber: 3.0 Consensus size: 51
10912810 CGTGATCAAG
* * * *
10912820 ATCAAATGTTCGTGATCAAGATCGAGTCATGAAGACCTTTAAAGTGAAG--
1 ATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCGAAGAT
* *
10912869 ATCAAATGTTCGTAATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGAT
1 ATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCGAAGAT
* * *
10912920 ATCAATTGTTCGTGATTAAGATTAAGTCGTGAAGACCCTTAAAGCGAAGAT
1 ATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCGAAGAT
10912971 TATGTGAAGT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 43 0.48
51 46 0.52
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (51 bp):
ATCAAATGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGCGAAGAT
Found at i:10913566 original size:22 final size:25
Alignment explanation
Indices: 10913534--10913578 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
10913524 AAATTTTAGG
10913534 TAAAAACCAAACT-CT-TCCATCTC
1 TAAAAACCAAACTACTCTCCATCTC
10913557 TAAAAA-CAAACTACTCTCCATC
1 TAAAAACCAAACTACTCTCCATC
10913579 CATTTGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (25 bp):
TAAAAACCAAACTACTCTCCATCTC
Found at i:10914355 original size:86 final size:86
Alignment explanation
Indices: 10914265--10914431 Score: 235
Period size: 86 Copynumber: 1.9 Consensus size: 86
10914255 TGATATGTTA
* * *
10914265 TTAAGTTTGCATCATAATCCAAATAATATAAATTAATTTTGCATTTGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAATCCAAATAATACAAATTAATTTTACATTTGTTAGTTTACAAATTCAAC
*
10914330 TAATACAAAAATTTTATATAT
66 TAATACAAAAAATTTATATAT
* * * ** *
10914351 TTAAGTTTGCATCATAATTCAAGTAATACAAATTAATTTTACATTTTTTAGTTTTTAAATTCAAT
1 TTAAGTTTGCATCATAATCCAAATAATACAAATTAATTTTACATTTGTTAGTTTACAAATTCAAC
*
10914416 TAATATAAAAAATTTA
66 TAATACAAAAAATTTA
10914432 CAAGTAATAT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 70 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (86 bp):
TTAAGTTTGCATCATAATCCAAATAATACAAATTAATTTTACATTTGTTAGTTTACAAATTCAAC
TAATACAAAAAATTTATATAT
Found at i:10914413 original size:42 final size:42
Alignment explanation
Indices: 10914288--10914420 Score: 117
Period size: 42 Copynumber: 3.1 Consensus size: 42
10914278 ATAATCCAAA
* * * * *
10914288 TAATATAAATTAATTTTGCATTTGTTAGTTTACAAGTTCAAC
1 TAATACAAATTAATTTTACATTTTTTAGTTTTCAAATTCAAC
* * * *
10914330 TAATACAAA--AATTTTATATATTTAAGTTTGCATCATAATTCAAG
1 TAATACAAATTAATTTTACATTTTTTAGTTT---TCA-AATTCAAC
* *
10914374 TAATACAAATTAATTTTACATTTTTTAGTTTTTAAATTCAAT
1 TAATACAAATTAATTTTACATTTTTTAGTTTTCAAATTCAAC
10914416 TAATA
1 TAATA
10914421 TAAAAAATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
40 15 0.21
42 20 0.28
43 4 0.06
44 15 0.21
46 17 0.24
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (42 bp):
TAATACAAATTAATTTTACATTTTTTAGTTTTCAAATTCAAC
Found at i:10915971 original size:30 final size:31
Alignment explanation
Indices: 10915923--10915993 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 31
10915913 AAGCAGCTAA
10915923 AGAGGACGAGGAAGAAAGAGCTGGTGGTGAC
1 AGAGGACGAGGAAGAAAGAGCTGGTGGTGAC
*
10915954 AGAGGACGAGG-AGAAAGAGGTGGTGGTGAC
1 AGAGGACGAGGAAGAAAGAGCTGGTGGTGAC
10915984 AGAGGACGAG
1 AGAGGACGAG
10915994 AAGGAACCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 28 0.72
31 11 0.28
ACGTcount: A:0.35, C:0.08, G:0.48, T:0.08
Consensus pattern (31 bp):
AGAGGACGAGGAAGAAAGAGCTGGTGGTGAC
Found at i:10921339 original size:31 final size:31
Alignment explanation
Indices: 10921301--10921359 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
10921291 AGATTTTCAA
*
10921301 TTCATTTGTTTTTTTGAGGATGATACTACAG
1 TTCATTTGCTTTTTTGAGGATGATACTACAG
10921332 TTCATTTGCTTTTTTGAGGATGATACTA
1 TTCATTTGCTTTTTTGAGGATGATACTA
10921360 AGTGTTTCAG
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:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (31 bp):
TTCATTTGCTTTTTTGAGGATGATACTACAG
Found at i:10929092 original size:29 final size:30
Alignment explanation
Indices: 10929039--10929103 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
10929029 CTAGTTATTA
10929039 TGGATATTTAATATATCTTACTTAGCTACTG
1 TGGATATTT-ATATATCTTACTTAGCTACTG
** *
10929070 TGGATATTT-TATATCTTGTTTAGCTATTG
1 TGGATATTTATATATCTTACTTAGCTACTG
10929099 TGGAT
1 TGGAT
10929104 GTTATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 22 0.71
31 9 0.29
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (30 bp):
TGGATATTTATATATCTTACTTAGCTACTG
Found at i:10934838 original size:27 final size:27
Alignment explanation
Indices: 10934788--10934840 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
10934778 TTGCAATGCT
*
10934788 TGCTTCAAAATGACTTAGATGAATAGC
1 TGCTTCAAAATGACTTAGAAGAATAGC
* * *
10934815 TGCTTGAAAATGATTTGGAAGAATAG
1 TGCTTCAAAATGACTTAGAAGAATAG
10934841 TCATTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (27 bp):
TGCTTCAAAATGACTTAGAAGAATAGC
Found at i:10938813 original size:17 final size:17
Alignment explanation
Indices: 10938783--10938821 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
10938773 CAAGCCAGGG
*
10938783 ATAAAAAATTTGAATAT
1 ATAAAAAATATGAATAT
10938800 -TAAAAACATATGAATAT
1 ATAAAAA-ATATGAATAT
10938817 ATAAA
1 ATAAA
10938822 CTGTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (17 bp):
ATAAAAAATATGAATAT
Found at i:10940651 original size:83 final size:82
Alignment explanation
Indices: 10940553--10940800 Score: 345
Period size: 83 Copynumber: 3.0 Consensus size: 82
10940543 GCATAACAAA
* * *
10940553 AATAAGTTTAGCATTCAAATATCATCAACAATCCATCAACAATTAAAATAATAAGTTGCCATGAA
1 AATAAGTTTAGCATTCAAATATCATCAACAATCCATCAGCAATTAAAATAATATGTTGTCATGAA
10940618 GAACCCGACATCATCAAC
66 GAACCC-ACATCATCAAC
* * *
10940636 AATAAGTTTAGCATTCAGATATCATCAACAATCCATCAGCAATTAAAATAATATGCTATCATG-A
1 AATAAGTTTAGCATTCAAATATCATCAACAATCCATCAGCAATTAAAATAATATGTTGTCATGAA
*
10940700 GCAACCCAGCATCATCTAC
66 G-AACCCA-CATCATCAAC
* * *
10940719 AATATGTTCAGCATTCAAATATCATCAACAATCCATCAGCAACTAAAATAATATGTTGTCATGAA
1 AATAAGTTTAGCATTCAAATATCATCAACAATCCATCAGCAATTAAAATAATATGTTGTCATGAA
* *
10940784 CAACCTAACATCATCAA
66 GAACC-CACATCATCAA
10940801 AGTCAAATTC
Statistics
Matches: 145, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
82 3 0.02
83 140 0.97
84 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (82 bp):
AATAAGTTTAGCATTCAAATATCATCAACAATCCATCAGCAATTAAAATAATATGTTGTCATGAA
GAACCCACATCATCAAC
Found at i:10946550 original size:25 final size:23
Alignment explanation
Indices: 10946499--10946552 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
10946489 CCCCTTCCTA
10946499 GCTTT-TCTTTTTTCTTCTCTTT
1 GCTTTCTCTTTTTTCTTCTCTTT
*
10946521 CCTTTCTCTTTTCTTCTTTCTCTTT
1 GCTTTCTCTTTT-TTC-TTCTCTTT
10946546 GCTTTCT
1 GCTTTCT
10946553 TCTTGGGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.22
24 3 0.11
25 14 0.52
ACGTcount: A:0.00, C:0.28, G:0.04, T:0.69
Consensus pattern (23 bp):
GCTTTCTCTTTTTTCTTCTCTTT
Found at i:10946555 original size:21 final size:19
Alignment explanation
Indices: 10946500--10946556 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 19
10946490 CCCTTCCTAG
*
10946500 CTTTTCTTT-TTTCTTC-T
1 CTTTCCTTTCTTTCTTCTT
10946517 CTTTCCTTTCTCTT-TTCTT
1 CTTTCCTTTCT-TTCTTCTT
10946536 CTTTCTCTTTGCTTTCTTCTT
1 CTTTC-CTTT-CTTTCTTCTT
10946557 GGGTGCAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 8 0.24
20 6 0.18
21 7 0.21
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (19 bp):
CTTTCCTTTCTTTCTTCTT
Found at i:10953579 original size:21 final size:21
Alignment explanation
Indices: 10953553--10953596 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10953543 ATTTATTTTG
10953553 ATTGATATGACCTAAACGCAA
1 ATTGATATGACCTAAACGCAA
10953574 ATTGATATGACCTAAACGCAA
1 ATTGATATGACCTAAACGCAA
10953595 AT
1 AT
10953597 GTCATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (21 bp):
ATTGATATGACCTAAACGCAA
Found at i:10977766 original size:28 final size:27
Alignment explanation
Indices: 10977712--10977875 Score: 125
Period size: 28 Copynumber: 5.6 Consensus size: 27
10977702 TTAAGACAAC
*
10977712 TCTTGTCTTTAATTAAGATAAAAATATTTT
1 TCTTGTC-TAAATTAAG--AAAAATATTTT
*
10977742 ATCTTGTCTAAATTGAGAAAAATATGTTT
1 -TCTTGTCTAAATTAAGAAAAATAT-TTT
**
10977771 TCTTGTCTAGGTTAGGAGAAAAAGTAATTTT
1 TCTTGTCTAAATTA--AGAAAAA-T-ATTTT
*
10977802 T-TTGTTTTAAATTAAGACAAACATA-TTT
1 TCTTG-TCTAAATTAAGA-AAA-ATATTTT
* *
10977830 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-AAAATAT-TTT
10977859 TCTTGTCTAAATTAAGA
1 TCTTGTCTAAATTAAGA
10977876 CAAACATGTT
Statistics
Matches: 111, Mismatches: 11, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
27 2 0.02
28 37 0.33
29 30 0.27
30 21 0.19
31 19 0.17
32 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (27 bp):
TCTTGTCTAAATTAAGAAAAATATTTT
Found at i:10977851 original size:29 final size:28
Alignment explanation
Indices: 10977712--10977882 Score: 144
Period size: 29 Copynumber: 5.9 Consensus size: 28
10977702 TTAAGACAAC
* * *
10977712 TCTTGTCTTTAATTAAGATAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAACATA-TTT
* * * *
10977742 ATCTTGTCTAAATTGAGAAAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
** * * *
10977771 TCTTGTCTAGGTTAGGAGAAAAAGTAATTT
1 TCTTGTCTAAATTAAGACAAACA-T-ATTT
* *
10977801 TTTTGTTTTAAATTAAGACAAACATATTT
1 TCTTG-TCTAAATTAAGACAAACATATTT
*
10977830 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
10977859 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
10977883 GTTAAAGTTG
Statistics
Matches: 114, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
28 35 0.31
29 39 0.34
30 21 0.18
31 19 0.17
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:10977894 original size:29 final size:28
Alignment explanation
Indices: 10977743--10977885 Score: 142
Period size: 28 Copynumber: 5.0 Consensus size: 28
10977733 AAATATTTTA
* * *
10977743 TCTTGTCTAAATTGAGAAAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
** * * * *
10977771 TCTTGTCTAGGTTAGGAGAAAAAGTAATTT
1 TCTTGTCTAAATTAAGACAAACA-T-GTTT
* * *
10977801 TTTTGTTTTAAATTAAGACAAACATATTT
1 TCTTG-TCTAAATTAAGACAAACATGTTT
10977830 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
10977859 TCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
10977886 AAAGTTGTCA
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
28 38 0.40
29 36 0.38
30 8 0.09
31 12 0.13
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:10982340 original size:168 final size:166
Alignment explanation
Indices: 10982031--10982347 Score: 517
Period size: 168 Copynumber: 1.9 Consensus size: 166
10982021 CAAAATCTCC
* * *
10982031 AGGTACATTCTCAAAACCTTTGAGTGCATTCTTATAAAACCTCCGAGTATATTCTCCAAAACCTC
1 AGGTACATTCTCAAAACCTATGAGTACATTCTTATAAAACATCCGAGTATATTCTCCAAAACCTC
* *
10982096 TGGGCAATTAGTTTTAAGATTCTTTAAAGTTATGTAGCCTTATTTAGAGATGAAGAGCAACCTTT
66 TGGGCAATTAGTTTCAAGATTCTTTAAAGTTATGTAGCCTCATTTAGAGATGAAGAGCAACCTTT
10982161 TCTTATAAAACCTCCGAGTTCATCTCTAAAACTTTT
131 TCTTATAAAACCTCCGAGTTCATCTCTAAAACTTTT
* * * *
10982197 AGGTACATTCTCAAACCCTATGAGTACATTCTTATAAAACATCTGGGTATATTCTCCAAAACCTT
1 AGGTACATTCTCAAAACCTATGAGTACATTCTTATAAAACATCCGAGTATATTCTCCAAAACCTC
* *
10982262 TGAGGTAATTAGTTTCAAGATTTCTTTAAAGTTATGTAGCCTCATTTAGAGATGAGGAGCAACCT
66 TG-GGCAATTAGTTTCAAGA-TTCTTTAAAGTTATGTAGCCTCATTTAGAGATGAAGAGCAACCT
10982327 TTTCTTATAAAACCTCCGAGT
129 TTTCTTATAAAACCTCCGAGT
10982348 ACATTTTTAA
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
166 60 0.43
167 15 0.11
168 63 0.46
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (166 bp):
AGGTACATTCTCAAAACCTATGAGTACATTCTTATAAAACATCCGAGTATATTCTCCAAAACCTC
TGGGCAATTAGTTTCAAGATTCTTTAAAGTTATGTAGCCTCATTTAGAGATGAAGAGCAACCTTT
TCTTATAAAACCTCCGAGTTCATCTCTAAAACTTTT
Found at i:10983036 original size:60 final size:60
Alignment explanation
Indices: 10982954--10983289 Score: 231
Period size: 60 Copynumber: 5.6 Consensus size: 60
10982944 CATGAGAGAA
* *
10982954 TTTCAAAATATTAAATCAAACCTACTGTAAGATAGGTTGACCTTAGATTAAGTTTAAGAG
1 TTTCAAAATATCAAATCAAACCTATTGTAAGATAGGTTGACCTTAGATTAAGTTTAAGAG
* ** * * *
10983014 TTTCAAAATATCATATTGAACCTATTGTGAGATAGGTAGA-GTCTAGATTAAGTTTAAGAG
1 TTTCAAAATATCAAATCAAACCTATTGTAAGATAGGTTGACCT-TAGATTAAGTTTAAGAG
* * * * * *
10983074 TTTAAAAATATCAAATCAAATCTGTTTTAAGATAGGTTGAGCC-TAGATTAAATCTAAGAG
1 TTTCAAAATATCAAATCAAACCTATTGTAAGATAGGTTGA-CCTTAGATTAAGTTTAAGAG
* * * * * *
10983134 -TTCAAAATATCAAATCGAATCTGTTTTGAA-ATA-ATTCGAGCC-TAGATTAAGTCTAAGA-
1 TTTCAAAATATCAAATCAAACCTATTGT-AAGATAGGTT-GA-CCTTAGATTAAGTTTAAGAG
* * * * * * * * * *
10983192 TTTCCAAAGTTGTTAAATCAAACTTGTTGCAAGATAAGTCGAGCC-TAGATTAAGTCTAGGAG
1 TTT-CAAA-ATATCAAATCAAACCTATTGTAAGATAGGTTGA-CCTTAGATTAAGTTTAAGAG
* * * *
10983254 -TTCAAAATATCAAATCGAATCTATTATGAGATAGGT
1 TTTCAAAATATCAAATCAAACCTATTGTAAGATAGGT
10983290 CAAGCCAAGA
Statistics
Matches: 219, Mismatches: 46, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
58 2 0.01
59 70 0.32
60 108 0.49
61 38 0.17
62 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTCAAAATATCAAATCAAACCTATTGTAAGATAGGTTGACCTTAGATTAAGTTTAAGAG
Found at i:10983175 original size:59 final size:59
Alignment explanation
Indices: 10982955--10983434 Score: 396
Period size: 59 Copynumber: 8.1 Consensus size: 59
10982945 ATGAGAGAAT
* * * * * * * *
10982955 TTCAAAATATTAAATCAAACCTACTGTAAGATAGGTTGA-CCTTAGATTAAGTTTAAGAG
1 TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCC-TAGATTAAGTCTAAGAG
* * * * * * *
10983014 TTTCAAAATATCATATTGAACCTATTGTGAGATAGGTAGAGTCTAGATTAAGTTTAAGAG
1 -TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAG
* * * * * *
10983074 TTTAAAAATATCAAATCAAATCTGTTTTAAGATAGGTTGAGCCTAGATTAAATCTAAGAG
1 -TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAG
* * ** *
10983134 TTCAAAATATCAAATCGAATCTGTTTTGAAATAATTCGAGCCTAGATTAAGTCTAAGAT
1 TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAG
* * * * * * *
10983193 TTCCAAAGTTGTTAAATC-AAACT-TGTTGCAAGATAAGTCGAGCCTAGATTAAGTCTAGGAG
1 TT-CAAA-ATATCAAATCGAATCTATTTTG--AGATAGGTCGAGCCTAGATTAAGTCTAAGAG
* * * * *
10983254 TTCAAAATATCAAATCGAATCTATTATGAGATAGGTCAAGCCAAGATTTAGTCCAAGAG
1 TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAG
* * * * * * *
10983313 TTCTAAACTTTTTAAATCGAA-CT-TGTCGCTAGATAAGTCGAGCCTAGATTGAGTCTAAGAG
1 TTC-AAA-ATATCAAATCGAATCTATTTTG--AGATAGGTCGAGCCTAGATTAAGTCTAAGAG
* *
10983374 TTCAAAATATTAAATCGAATCTATTTTGAGATAGGTTGAGCCTAGATTAA-TCTAAGAG
1 TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAG
10983432 TTC
1 TTC
10983435 TGAACCTTTT
Statistics
Matches: 339, Mismatches: 68, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
58 11 0.03
59 123 0.36
60 123 0.36
61 82 0.24
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (59 bp):
TTCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAG
Found at i:10983210 original size:120 final size:119
Alignment explanation
Indices: 10982953--10983487 Score: 487
Period size: 120 Copynumber: 4.5 Consensus size: 119
10982943 ACATGAGAGA
* ** * * * *
10982953 ATTTCAAAA-TATTAAATCAAACCTACTGTAAGATAGGTTGA-CCTTAGATTAAGTTTAAGAGTT
1 ATTTCAAAATTATTAAATCAAACTTGTTCTAAGATAAGTCGAGCC-TAGATTAAGTCTAAGAG-T
* * * * * * *
10983016 TCAAAATATCATATTGAACCTATTGTGAGATAGGTAGAGTCTAGATTAAGTTTAAG
64 TCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAG
* * * * * *
10983072 AGTTT-AAAAATATCAAATCAAA-TCTGTTTTAAGATAGGTTGAGCCTAGATTAAATCTAAGAGT
1 A-TTTCAAAATTATTAAATCAAACT-TGTTCTAAGATAAGTCGAGCCTAGATTAAGTCTAAGAGT
* * **
10983135 TCAAAATATCAAATCGAATCTGTTTTGAAATAATTCGAGCCTAGATTAAGTCTAAG
64 TCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAG
* * *
10983191 ATTTCCAAAGTTGTTAAATCAAACTTGTTGC-AAGATAAGTCGAGCCTAGATTAAGTCTAGGAGT
1 ATTT-CAAAATTATTAAATCAAACTTGTT-CTAAGATAAGTCGAGCCTAGATTAAGTCTAAGAGT
* * * * *
10983255 TCAAAATATCAAATCGAATCTATTATGAGATAGGTCAAGCCAAGATTTAGTCCAAG
64 TCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAG
* * * * * *
10983311 AGTTCTAAACTTTTTAAATCGAACTTGTCGCT-AGATAAGTCGAGCCTAGATTGAGTCTAAGAGT
1 ATTTC-AAAATTATTAAATCAAACTTGT-TCTAAGATAAGTCGAGCCTAGATTAAGTCTAAGAGT
* *
10983375 TCAAAATATTAAATCGAATCTATTTTGAGATAGGTTGAGCCTAGATTAA-TCTAAG
64 TCAAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAG
* ** * * *
10983430 AGTTCTGAACCTT-TTAAATCAAACTTGTTGTCA-AT-AGATCAAGCCTAGATTAAGTCTA
1 A-TT-TCAAAATTATTAAATCAAACTTGTTCTAAGATAAG-TCGAGCCTAGATTAAGTCTA
10983488 GGATCTTTGA
Statistics
Matches: 343, Mismatches: 58, Indels: 31
0.79 0.13 0.07
Matches are distributed among these distances:
117 2 0.01
118 24 0.07
119 74 0.22
120 239 0.70
121 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (119 bp):
ATTTCAAAATTATTAAATCAAACTTGTTCTAAGATAAGTCGAGCCTAGATTAAGTCTAAGAGTTC
AAAATATCAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGATTAAGTCTAAG
Found at i:10983242 original size:61 final size:59
Alignment explanation
Indices: 10983056--10983487 Score: 267
Period size: 59 Copynumber: 7.2 Consensus size: 59
10983046 TAGGTAGAGT
* ** * * ** * *
10983056 CTAGATTAAGTTTAAGAGTTTAAAAATATCAAATCAAA-TCTGTTTTAAGATAGGTTGAGC
1 CTAGATTAAGTCTAAGAGTTCCAAATTATTAAATCAAACT-TG-TTGCAGATAAGTCGAGC
* * * * * * *
10983116 CTAGATTAAATCTAAGAGTT-CAAAATATCAAATCGAATCTGTTTTG-AAATAATTCGAGC
1 CTAGATTAAGTCTAAGAGTTCCAAATTATTAAATC-AAACT-TGTTGCAGATAAGTCGAGC
* *
10983175 CTAGATTAAGTCTAAGATTTCCAAAGTTGTTAAATCAAACTTGTTGCAAGATAAGTCGAGC
1 CTAGATTAAGTCTAAGAGTTCCAAA-TTATTAAATCAAACTTGTTGC-AGATAAGTCGAGC
* * * * * *
10983236 CTAGATTAAGTCTAGGAGTT-CAAAATATCAAATCGAATCTAT-TATG-AGATAGGTCAAGC
1 CTAGATTAAGTCTAAGAGTTCCAAATTATTAAATC-AAACT-TGT-TGCAGATAAGTCGAGC
* * * * * * *
10983295 CAAGATTTAGTCCAAGAGTTCTAAACTTTTTAAATCGAACTTGTCGCTAGATAAGTCGAGC
1 CTAGATTAAGTCTAAGAGTTCCAAA-TTATTAAATCAAACTTGTTGC-AGATAAGTCGAGC
* * * * * *
10983356 CTAGATTGAGTCTAAGAGTT-CAAAATATTAAATCGAATCTATTTTG-AGATAGGTTGAGC
1 CTAGATTAAGTCTAAGAGTTCCAAATTATTAAATC-AAACT-TGTTGCAGATAAGTCGAGC
* * *
10983415 CTAGATTAA-TCTAAGAGTTCTGAACCTT-TTAAATCAAACTTGTTGTCA-AT-AGATCAAGC
1 CTAGATTAAGTCTAAGAGTTC-CAA-ATTATTAAATCAAACTTGTTG-CAGATAAG-TCGAGC
10983474 CTAGATTAAGTCTA
1 CTAGATTAAGTCTA
10983488 GGATCTTTGA
Statistics
Matches: 287, Mismatches: 62, Indels: 46
0.73 0.16 0.12
Matches are distributed among these distances:
58 15 0.05
59 126 0.44
60 66 0.23
61 80 0.28
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (59 bp):
CTAGATTAAGTCTAAGAGTTCCAAATTATTAAATCAAACTTGTTGCAGATAAGTCGAGC
Found at i:10998677 original size:2 final size:2
Alignment explanation
Indices: 10998670--10998695 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10998660 GTTACATTTA
10998670 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
10998696 CACGCGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:11000672 original size:73 final size:72
Alignment explanation
Indices: 11000495--11000678 Score: 192
Period size: 73 Copynumber: 2.5 Consensus size: 72
11000485 AAACAAGATG
* * *
11000495 CTCTTAGTCAACTAACATTGCTACTTAGTTGATTAAGTCATTTATGTCTTCGTACATAGTTTTTG
1 CTCTTAGTCAACTAACAATGCT-CTTAGTCGATTAAGTCATTTATGTCTTCGAACATAGTTTTTG
**
11000560 ACAATAGG
65 ACAATAAA
* * *
11000568 CTCTTAATCAACTAACAATACTTCTTAGTCGATTAAGTCATTTTTGTC-TCGGAAC-TCAGTTTT
1 CTCTTAGTCAACTAACAATGC-TCTTAGTCGATTAAGTCATTTATGTCTTC-GAACAT-AGTTTT
* *
11000631 TGGCAGTAAA
63 TGACAATAAA
* * *
11000641 CTCTTAGTCGACTAACAATGTCTCTTGGTCGACTAAGT
1 CTCTTAGTCAACTAACAATG-CTCTTAGTCGATTAAGT
11000679 GTTCTCTGTT
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
72 3 0.03
73 87 0.95
74 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (72 bp):
CTCTTAGTCAACTAACAATGCTCTTAGTCGATTAAGTCATTTATGTCTTCGAACATAGTTTTTGA
CAATAAA
Found at i:11009577 original size:73 final size:72
Alignment explanation
Indices: 11009380--11009583 Score: 196
Period size: 73 Copynumber: 2.8 Consensus size: 72
11009370 GTGCTTAAAT
*
11009380 TCAAATTTTCAGACAG-AATGCTCTTAGTCGACTAA-AATTGCTACTTAGTCGATTAAGTCGTTT
1 TCAAATTTT-A-ACAGTAA-GCTCTTAGTCGACTAACAATT-CT-CTTAGTCGATTAAGTCATTT
11009443 ATGTCTCTGAAC
61 ATGTCTCTGAAC
* ** *** * * * * *
11009455 CCAGTTTTTGGTAGTAGGCTTTTAGTTGACTAACAATACTTCTTAGTCGATTAAGTCATTTTTGT
1 TCAAATTTTAACAGTAAGCTCTTAGTCGACTAACAATTC-TCTTAGTCGATTAAGTCATTTATGT
11009520 CTCTGAAC
65 CTCTGAAC
* * *
11009528 TCAAATTTTAACAGTAAGCTCTTGGTCGACTAACAATGTCTCTTGGTCGACTAAGT
1 TCAAATTTTAACAGTAAGCTCTTAGTCGACTAACAAT-TCTCTTAGTCGATTAAGT
11009584 GTTTTATATT
Statistics
Matches: 100, Mismatches: 25, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
73 88 0.88
74 6 0.06
75 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (72 bp):
TCAAATTTTAACAGTAAGCTCTTAGTCGACTAACAATTCTCTTAGTCGATTAAGTCATTTATGTC
TCTGAAC
Found at i:11025164 original size:28 final size:28
Alignment explanation
Indices: 11025104--11025165 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
11025094 TTTATTTTAA
*
11025104 ATATTTAATAAATTTAATTAATAATTTT
1 ATATTTAATAAATTTAATCAATAATTTT
*
11025132 TTATTTAATAAATTTAA-CAA-AACTTTCT
1 ATATTTAATAAATTTAATCAATAA-TTT-T
11025160 ATATTT
1 ATATTT
11025166 TATTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 5 0.17
28 22 0.76
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATTTAATAAATTTAATCAATAATTTT
Found at i:11031045 original size:77 final size:79
Alignment explanation
Indices: 11030936--11031103 Score: 234
Period size: 77 Copynumber: 2.1 Consensus size: 79
11030926 TGAATTTCAT
*
11030936 AAATTAAAAATACTATCCTTAATTTTAAGAATTTCTTTTAAAAT-GGAAAACAATTTCCTAT-TC
1 AAATT-AAAATACTATCCTTAATTTTAAGAATTACTTTTAAAATAGG-AAACAATTTCCTATCTC
* *
11030999 TTTT-TGAATCATCCA
64 TTTTATAAATCACCCA
* * * *
11031014 CAATTAAAATTCTATCCTTAATTTTATGAATTACTTTTAAAATAGGAAACAATTTCCTTTCTCTT
1 AAATTAAAATACTATCCTTAATTTTAAGAATTACTTTTAAAATAGGAAACAATTTCCTATCTCTT
11031079 TTATAAATCACCCA
66 TTATAAATCACCCA
11031093 AAATTAAAATA
1 AAATTAAAATA
11031104 GATGGCATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
77 48 0.62
78 12 0.15
79 18 0.23
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (79 bp):
AAATTAAAATACTATCCTTAATTTTAAGAATTACTTTTAAAATAGGAAACAATTTCCTATCTCTT
TTATAAATCACCCA
Found at i:11031538 original size:32 final size:35
Alignment explanation
Indices: 11031501--11031622 Score: 126
Period size: 36 Copynumber: 3.5 Consensus size: 35
11031491 CACTTGATTA
11031501 AAATTGTTTAATTAAGTT-GT-G-CCTAATTCATT
1 AAATTGTTTAATTAAGTTAGTGGACCTAATTCATT
* *
11031533 AAATTGTTTAATTAAGTTATTGGACCTAATTGATT
1 AAATTGTTTAATTAAGTTAGTGGACCTAATTCATT
* * * * * *
11031568 AAATTTGTTTAATCAAGTTATTGGGCTTAATTGATCA
1 AAA-TTGTTTAATTAAGTTAGTGGACCTAATTCAT-T
11031605 AAATT-TTTAATTAAGTTA
1 AAATTGTTTAATTAAGTTA
11031623 TTAGGCCTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
32 18 0.23
33 1 0.01
34 1 0.01
35 25 0.32
36 30 0.38
37 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTAGTGGACCTAATTCATT
Found at i:11031569 original size:35 final size:34
Alignment explanation
Indices: 11031494--11031737 Score: 190
Period size: 35 Copynumber: 7.3 Consensus size: 34
11031484 TCTCAAGCAC
*
11031494 TTGATTAAAATTGTTTAATTAAGTT-GT-GCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGCCTAA
*
11031527 TTCATTAAATTGTTTAATTAAGTTATTGGACCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGG-CCTAA
* *
11031562 TTGATTAAATTTGTTTAATCAAGTTATTGGGCTTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATT-GGCCTAA
* *
11031598 TTGATCAAAATT-TTTAATTAAGTTATTAGGCCTCA
1 TTGAT-TAAATTGTTTAATTAAGTTATT-GGCCTAA
* ****
11031633 TTGACTAAATTAAACAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATT-GGCCTAA
11031668 TTGATTAAA-----T--TT--G-TATTGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGCCTAA
* *
11031692 TTAATTAAATTGTTTAATTAAGTTATTAGGCTTAA
1 TTGATTAAATTGTTTAATTAAGTTATT-GGCCTAA
* *
11031727 ATAATTAAATT
1 TTGATTAAATT
11031738 AAACAATTAA
Statistics
Matches: 171, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
24 15 0.09
25 4 0.02
26 1 0.01
28 2 0.01
29 1 0.01
31 2 0.01
32 18 0.11
33 7 0.04
34 10 0.06
35 78 0.46
36 28 0.16
37 5 0.03
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (34 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGCCTAA
Found at i:11031692 original size:24 final size:25
Alignment explanation
Indices: 11031656--11031702 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
11031646 ACAATTAAGT
*
11031656 TATTGGGCCTAATTGATTAAATTTG
1 TATTGGGCCTAATTAATTAAATTTG
11031681 TATT-GGCCTAATTAATTAAATT
1 TATTGGGCCTAATTAATTAAATT
11031703 GTTTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (25 bp):
TATTGGGCCTAATTAATTAAATTTG
Found at i:11033827 original size:21 final size:21
Alignment explanation
Indices: 11033803--11033872 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
11033793 ACATCCTTTG
11033803 TCTTAATTAAGACAACATATA
1 TCTTAATTAAGACAACATATA
* *
11033824 TCTTTATCTAAATTAAGACAAC-TCTTG
1 TC----T-T-AATTAAGACAACAT-ATA
11033851 TCTTAATTAAGACAACATATA
1 TCTTAATTAAGACAACATATA
11033872 T
1 T
11033873 ATCTTTGTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
21 16 0.43
22 2 0.05
23 1 0.03
25 1 0.03
26 2 0.05
27 15 0.41
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (21 bp):
TCTTAATTAAGACAACATATA
Found at i:11033898 original size:50 final size:50
Alignment explanation
Indices: 11033800--11033959 Score: 234
Period size: 50 Copynumber: 3.2 Consensus size: 50
11033790 AGGACATCCT
*
11033800 TTGTCTTAATTAAGACAAC--ATATATCTTTATCTAAATTAAGACAACTC
1 TTGTCTTAATTAAGACAACATATATATCTTTGTCTAAATTAAGACAACTC
* *
11033848 TTGTCTTAATTAAGACAACATATATATCTTTGTCCAAATTAAGACGACTC
1 TTGTCTTAATTAAGACAACATATATATCTTTGTCTAAATTAAGACAACTC
* * * *
11033898 TTCTCTTAATTAAGACAACATCTACATCCTTGTCTAAATTAAGACAACTC
1 TTGTCTTAATTAAGACAACATATATATCTTTGTCTAAATTAAGACAACTC
*
11033948 TTATCTTAATTA
1 TTGTCTTAATTA
11033960 TGATAAAATA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 19 0.19
50 81 0.81
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.38
Consensus pattern (50 bp):
TTGTCTTAATTAAGACAACATATATATCTTTGTCTAAATTAAGACAACTC
Found at i:11036112 original size:60 final size:60
Alignment explanation
Indices: 11036019--11036138 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
11036009 GATGTTTATG
11036019 TTACGAACTCTATATCTTGGATATACATTCCTTGATGCTCACCTCAATTATCATAGATCA
1 TTACGAACTCTATATCTTGGATATACATTCCTTGATGCTCACCTCAATTATCATAGATCA
11036079 TTACGAACTCTATATCTTGGATATACATTCCTTGATGCTCACCTCAATTATCATAGATCA
1 TTACGAACTCTATATCTTGGATATACATTCCTTGATGCTCACCTCAATTATCATAGATCA
11036139 ATATATTATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (60 bp):
TTACGAACTCTATATCTTGGATATACATTCCTTGATGCTCACCTCAATTATCATAGATCA
Found at i:11040393 original size:16 final size:15
Alignment explanation
Indices: 11040372--11040403 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
11040362 TTCAATCCTT
11040372 TTTTTTTCTTTCTTTC
1 TTTTTTTCTTT-TTTC
11040388 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
11040403 T
1 T
11040404 ATTTCATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:11053278 original size:30 final size:31
Alignment explanation
Indices: 11053243--11053309 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
11053233 ATCATAAAAT
** *
11053243 GCCCAAG-GGCAATGGGGATATACGTTGCCA
1 GCCCAAGAGGCAATACGGATATACATTGCCA
* *
11053273 GCCCAAGATGCAATACGGATGTACATTGCCA
1 GCCCAAGAGGCAATACGGATATACATTGCCA
11053304 GCCCAA
1 GCCCAA
11053310 AGATGATGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (31 bp):
GCCCAAGAGGCAATACGGATATACATTGCCA
Found at i:11058756 original size:13 final size:13
Alignment explanation
Indices: 11058738--11058764 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11058728 TGGAGGTTAA
11058738 TCATTTGAATGCC
1 TCATTTGAATGCC
11058751 TCATTTGAATGCC
1 TCATTTGAATGCC
11058764 T
1 T
11058765 TGGCGCACTA
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:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (13 bp):
TCATTTGAATGCC
Found at i:11064279 original size:55 final size:55
Alignment explanation
Indices: 11064116--11064280 Score: 267
Period size: 55 Copynumber: 3.0 Consensus size: 55
11064106 ATTTCCATAC
* * * *
11064116 TTTCTTATCGAATGGCATCAACTGAGTTAAAAGAGCTAAAATGGCAACTAGAGCA
1 TTTCTTATCGAATGGCACCAACTGAGTTAAAGGAGCTAAAAGGGCAACTAGAGGA
* *
11064171 TTTCTTATCGAATGGCACCAACTGAGTTAAAGGAGCTAAAAGGGAAAATAGAGGA
1 TTTCTTATCGAATGGCACCAACTGAGTTAAAGGAGCTAAAAGGGCAACTAGAGGA
*
11064226 TTTCTTATCGAATGGCACCAACTAAGTTAAAGGAGCTAAAAGGGCAACTAGAGGA
1 TTTCTTATCGAATGGCACCAACTGAGTTAAAGGAGCTAAAAGGGCAACTAGAGGA
11064281 CTTATTGAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 101 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (55 bp):
TTTCTTATCGAATGGCACCAACTGAGTTAAAGGAGCTAAAAGGGCAACTAGAGGA
Found at i:11069862 original size:25 final size:25
Alignment explanation
Indices: 11069834--11069882 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11069824 TGGTTATAGA
*
11069834 TGGCAAGGCCACGAGTTGTTATACT
1 TGGCAAGGCCACGAGTTGATATACT
*
11069859 TGGCAAGGCCACGGGTTGATATAC
1 TGGCAAGGCCACGAGTTGATATAC
11069883 GTGGTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (25 bp):
TGGCAAGGCCACGAGTTGATATACT
Found at i:11072544 original size:28 final size:28
Alignment explanation
Indices: 11072500--11072684 Score: 183
Period size: 28 Copynumber: 6.5 Consensus size: 28
11072490 AATATTTATG
** *
11072500 TTGTCTAAATTGGGACAAATATGTTTTC
1 TTGTCTAAATTAAGACAAACATGTTTTC
* * * *
11072528 TTATCTAGATTAAGACAAAAAATATTTTTC
1 TTGTCTAAATTAAGAC-AAACAT-GTTTTC
* *
11072558 TTGTCTTAAATTAAGACAAACATATTTTA
1 TTGTC-TAAATTAAGACAAACATGTTTTC
* * *
11072587 TGGTCCAAATTAAGACTAAACATGATTTC
1 TTGTCTAAATTAAGAC-AAACATGTTTTC
11072616 TTGTCTAAATTAAGACAAACATGTTTTC
1 TTGTCTAAATTAAGACAAACATGTTTTC
* * *
11072644 TTATCAAAATTAAGAC-AACATGTTTTT
1 TTGTCTAAATTAAGACAAACATGTTTTC
*
11072671 TTGTCTCAATTAAG
1 TTGTCTAAATTAAG
11072685 TCTTGGATTA
Statistics
Matches: 128, Mismatches: 25, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
27 21 0.16
28 47 0.37
29 36 0.28
30 14 0.11
31 10 0.08
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (28 bp):
TTGTCTAAATTAAGACAAACATGTTTTC
Found at i:11072634 original size:57 final size:55
Alignment explanation
Indices: 11072554--11072684 Score: 163
Period size: 57 Copynumber: 2.3 Consensus size: 55
11072544 AAAAAATATT
* *
11072554 TTTCTTGTCTTAAATTAAGACAAACATATTTTATGGTCCAAATTAAGACTAAACATGA
1 TTTCTTGTC-TAAATTAAGACAAACATATTTTATGATCAAAATTAAGAC--AACATGA
* * * *
11072612 TTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCAAAATTAAGACAACATGT
1 TTTCTTGTCTAAATTAAGACAAACATATTTTATGATCAAAATTAAGACAACATGA
* *
11072667 TTTTTTGTCTCAATTAAG
1 TTTCTTGTCTAAATTAAG
11072685 TCTTGGATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
55 22 0.34
57 34 0.52
58 9 0.14
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (55 bp):
TTTCTTGTCTAAATTAAGACAAACATATTTTATGATCAAAATTAAGACAACATGA
Found at i:11074961 original size:11 final size:11
Alignment explanation
Indices: 11074945--11074978 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
11074935 CGTACGTTAG
*
11074945 AAAATAATATT
1 AAAATAATAAT
11074956 AAAATAATAAT
1 AAAATAATAAT
11074967 AAAATAATAAT
1 AAAATAATAAT
11074978 A
1 A
11074979 TTTTATCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:11077964 original size:25 final size:25
Alignment explanation
Indices: 11077922--11077974 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
11077912 TGATCATACA
* * * *
11077922 TGGCAAGGCCATGGGTTGTTATAAG
1 TGGCAACGCCACGAGTTGATATAAG
*
11077947 TGGCAACGCCACGAGTTGATATACG
1 TGGCAACGCCACGAGTTGATATAAG
11077972 TGG
1 TGG
11077975 TTGCAACCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.25
Consensus pattern (25 bp):
TGGCAACGCCACGAGTTGATATAAG
Found at i:11084490 original size:24 final size:24
Alignment explanation
Indices: 11084463--11084517 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
11084453 ATCAGTAAAT
11084463 CAAAATAGATTTTGAAAGTTTTCA
1 CAAAATAGATTTTGAAAGTTTTCA
11084487 CAAAATAGATTTTGAAAGTTTTCA
1 CAAAATAGATTTTGAAAGTTTTCA
11084511 CAAAATA
1 CAAAATA
11084518 AGGAATTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (24 bp):
CAAAATAGATTTTGAAAGTTTTCA
Found at i:11089946 original size:171 final size:170
Alignment explanation
Indices: 11089660--11090036 Score: 442
Period size: 171 Copynumber: 2.2 Consensus size: 170
11089650 GTAAGCTTGT
* *
11089660 GTTTTAAAGAAGAATGTAAAAGAATTCAACCTAAAATCAATTATGAGATTATAAAACTATTTAAA
1 GTTTTAAAGAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
* * * * * ** *
11089725 GCAAGTAATAAGCCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCAATCAATGACT
65 CCAAGTAATAAGCCGTTCGAAAGAATGAGTGACTAGAAATGGACTTTTCTTCTCAATCAATGACT
* *
11089790 TTTTCTACACATT-TCTCGA-G-ATAGACATTCAATTATTGTCC
130 TTTTCTACACATTACCT-GAGGCAT-G-CATTCAATTATAGTCC
*
11089831 GTTTTAAAGAAAAATGTAAAAAAGTTCTACTTAAAATCAATTATGAGATTATAAAA-TCATTTAA
1 GTTTTAAAGAAAAATGTAAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAA
* * *
11089895 TCCGAGTAATAAAG-CGTTCGAAAGAATGAGTGACTAGAAATGG-CTTTTTCTTCTCAATGAATG
64 ACCAAGTAAT-AAGCCGTTCGAAAGAATGAGTGACTAGAAATGGAC-TTTTCTTCTCAATCAATG
* * * *
11089958 GCTTTTTCTACACCTTACCTGAGGCATGCTTTCAATTATAGTCT
127 ACTTTTTCTACACATTACCTGAGGCATGCATTCAATTATAGTCC
*
11090002 GTTTTAAAGAAAAATATAAAAAAATTCAACTTAAA
1 GTTTTAAAGAAAAATGT-AAAAAATTCAACTTAAA
11090037 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
170 4 0.02
171 157 0.89
172 13 0.07
173 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
GTTTTAAAGAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAC
CAAGTAATAAGCCGTTCGAAAGAATGAGTGACTAGAAATGGACTTTTCTTCTCAATCAATGACTT
TTTCTACACATTACCTGAGGCATGCATTCAATTATAGTCC
Found at i:11090545 original size:172 final size:171
Alignment explanation
Indices: 11090255--11090648 Score: 515
Period size: 172 Copynumber: 2.3 Consensus size: 171
11090245 NNNNNNNNNN
* * * *
11090255 AAGAATGGGTGACTAAAAATAGATTTTTCTTCTCAATGAATGGCTTTTTCCATACCTTTCGTGAG
1 AAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTCCATACCTTTCGTGAG
* *
11090320 ATAGGCTTTCAATTATAGTATGTTTTAATCAAAAATGTAAAAATAATCAACTTAAAATCAATTAT
66 ACAGGCTTTCAATTATAGTATGTTTTAACCAAAAATGTAAAAATAATCAACTTAAAATCAATTAT
* * * * *
11090385 GAGATTATAAGACTATTTAAAGCGAGTATTAAACCTTTTGA
131 GAGATTATAAAACCATTTAAACCGAGTAATAAACATTTTGA
* ** *
11090426 AAGAATGGGTGTCTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTT-TTTGCACCTTTCTTG
1 AAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTCCAT--ACCTTTCGTG
* *
11090490 AGGCAGGCATTT-AATTATAGTTTGTTTTAACCAAAAATGTAAAAA-AATGCAACTTAAAATCAA
64 AGACAGGC-TTTCAATTATAGTATGTTTTAACCAAAAATGTAAAAATAAT-CAACTTAAAATCAA
*
11090553 TTATGAGATTATAAAACCATTTAAACCGAGTAATAAAGATTTTGA
127 TTATGAGATTATAAAACCATTTAAACCGAGTAATAAACATTTTGA
* * * * *
11090598 AGGAATAGGTGACTATAAATGGACTTTTTTTCTCAATAAACAAGCTTTTTC
1 AAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAA-TAGCTTTTTC
11090649 TGCACATTTC
Statistics
Matches: 193, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
170 1 0.01
171 47 0.24
172 134 0.69
173 11 0.06
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTCCATACCTTTCGTGAG
ACAGGCTTTCAATTATAGTATGTTTTAACCAAAAATGTAAAAATAATCAACTTAAAATCAATTAT
GAGATTATAAAACCATTTAAACCGAGTAATAAACATTTTGA
Found at i:11095020 original size:2 final size:2
Alignment explanation
Indices: 11095013--11095037 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11095003 TGTAATGTAA
11095013 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
11095038 AGTTAAGCAT
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
Done.