Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 59 of 335
Found at i:20757799 original size:12 final size:12
Alignment explanation
Indices: 20757770--20757801 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20757760 ATATATTTTT
20757770 AAATT-ATATAA
1 AAATTAATATAA
20757781 AAA-TAATATAA
1 AAATTAATATAA
20757792 AAATTAATAT
1 AAATTAATAT
20757802 GGACAGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 12 0.63
12 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:20758603 original size:31 final size:31
Alignment explanation
Indices: 20758545--20758603 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
20758535 AGTGCAATTT
* *
20758545 TATACATGAAACTTTGATTGTGGTTCAAACG
1 TATACATAAAACTTTGATTGTGATTCAAACG
*
20758576 TATACATAAAACTTT-AGTTTTGATTCAA
1 TATACATAAAACTTTGA-TTGTGATTCAA
20758604 TTATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39
Consensus pattern (31 bp):
TATACATAAAACTTTGATTGTGATTCAAACG
Found at i:20759211 original size:19 final size:20
Alignment explanation
Indices: 20759189--20759273 Score: 95
Period size: 19 Copynumber: 4.2 Consensus size: 20
20759179 AAAATTACAA
20759189 AAAAATT-AAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
20759208 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
* *
20759228 -AAATTTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTTT
*
20759246 AAAAATTTCAAAACCTTATTTTT
1 AAAAA-TTCAAAA--TAATTTTT
20759269 AAAAA
1 AAAAA
20759274 AAAATTATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.09
19 21 0.38
20 19 0.34
22 1 0.02
23 10 0.18
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:20759211 original size:20 final size:21
Alignment explanation
Indices: 20759188--20759274 Score: 85
Period size: 20 Copynumber: 4.3 Consensus size: 21
20759178 AAAAATTACA
20759188 AAAAAATT-AAAATAATTTTT
1 AAAAAATTCAAAATAATTTTT
20759208 -AAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTT
* *
20759228 --AAATTTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTTTT
* *
20759246 AAAAATTTCAAAACCTTATTTTT
1 AAAAAATTCAAAA--TAATTTTT
20759269 AAAAAA
1 AAAAAA
20759275 AAATTATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
18 5 0.09
19 18 0.32
20 23 0.40
22 1 0.02
23 10 0.18
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTT
Found at i:20764602 original size:47 final size:48
Alignment explanation
Indices: 20764516--20764626 Score: 120
Period size: 47 Copynumber: 2.3 Consensus size: 48
20764506 AAACTTAAAT
* *
20764516 CCGTGATCATATAACCACTTTCAACTAGGCTCCTGAGTTATGCTCCAAC
1 CCGTGATCATATAA-CACTGTCAACTAGGCTCCTGAGTTATACTCCAAC
* * *
20764565 TCGTGACCATATAACA-TGTCAACTAGAAGC-CCT-AGTTATACTTCAAC
1 CCGTGATCATATAACACTGTCAACTAG--GCTCCTGAGTTATACTCCAAC
*
20764612 CCGTGATCGTATAAC
1 CCGTGATCATATAAC
20764627 CACCGTAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
47 33 0.63
48 5 0.10
49 14 0.27
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (48 bp):
CCGTGATCATATAACACTGTCAACTAGGCTCCTGAGTTATACTCCAAC
Found at i:20773038 original size:21 final size:21
Alignment explanation
Indices: 20773012--20773056 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
20773002 GTTAAAGTAG
20773012 TAAGAAACAAAATGTACCATC
1 TAAGAAACAAAATGTACCATC
20773033 TAAGAAACAAAATGTACCATC
1 TAAGAAACAAAATGTACCATC
20773054 TAA
1 TAA
20773057 CTATAGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.20
Consensus pattern (21 bp):
TAAGAAACAAAATGTACCATC
Found at i:20775762 original size:2 final size:2
Alignment explanation
Indices: 20775755--20775783 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20775745 GAAAATGAAC
20775755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20775784 AGGAGCAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20776743 original size:16 final size:17
Alignment explanation
Indices: 20776716--20776753 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
20776706 ATTTAAACTT
20776716 TATTATTTAAAAAATAA
1 TATTATTTAAAAAATAA
20776733 TATTA-TTAAAAAATAA
1 TATTATTTAAAAAATAA
*
20776749 AATTA
1 TATTA
20776754 CGAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATTATTTAAAAAATAA
Found at i:20781645 original size:4 final size:4
Alignment explanation
Indices: 20781636--20781663 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
20781626 AAGGCTCGCT
20781636 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
20781664 ATATAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:20783555 original size:13 final size:13
Alignment explanation
Indices: 20783539--20783566 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20783529 ATTCAAGTCT
20783539 ATAATTCATATTA
1 ATAATTCATATTA
20783552 ATAATTCATATTA
1 ATAATTCATATTA
20783565 AT
1 AT
20783567 TATTATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTCATATTA
Found at i:20786725 original size:43 final size:44
Alignment explanation
Indices: 20786661--20786795 Score: 155
Period size: 46 Copynumber: 3.0 Consensus size: 44
20786651 AGTGTGCTCT
* *
20786661 CTGATATGAAATGTGTCAGACCATGGTTGATA-ACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAGATACCATGGCAAC
*
20786704 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTG--AGATACCATGGCAAC
* * * **
20786750 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTG--AGATACCATGGCAAC
20786796 ATGACGGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 27 0.34
45 2 0.03
46 51 0.64
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (44 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAGATACCATGGCAAC
Found at i:20786769 original size:46 final size:46
Alignment explanation
Indices: 20786719--20786839 Score: 172
Period size: 46 Copynumber: 2.6 Consensus size: 46
20786709 ATGAGATGTG
* *
20786719 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA-GAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-GGAAAATGAA
*
20786765 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGAAAATGAA
* * *
20786811 TAAGACCATAGTTGAAAGACACTATGGCA
1 TAAGACCATGGTTGAAAGATACCATGGCA
20786840 TCACGTCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 5 0.07
46 63 0.93
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGAAAATGAA
Found at i:20787145 original size:23 final size:25
Alignment explanation
Indices: 20787100--20787146 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
20787090 AATAAATATA
*
20787100 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
20787125 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
20787147 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:20787577 original size:7 final size:7
Alignment explanation
Indices: 20787561--20788010 Score: 215
Period size: 7 Copynumber: 62.1 Consensus size: 7
20787551 AAATCTTATA
*
20787561 AAACCTT
1 AAACCCT
20787568 AAACCCT
1 AAACCCT
*
20787575 AAACCAT
1 AAACCCT
20787582 AAACCCT
1 AAACCCT
*
20787589 AGACCCT
1 AAACCCT
*
20787596 AGACCCT
1 AAACCCT
* *
20787603 AGACCTT
1 AAACCCT
*
20787610 AAACCAT
1 AAACCCT
*
20787617 AAAACACT
1 -AAACCCT
*
20787625 AAAACCT
1 AAACCCT
*
20787632 AAATCCT
1 AAACCCT
**
20787639 AAAACCAA
1 -AAACCCT
*
20787647 AAACCAT
1 AAACCCT
*
20787654 AAACCAT
1 AAACCCT
*
20787661 AAACTCT
1 AAACCCT
* *
20787668 AAAAGCAT
1 -AAACCCT
*
20787676 AAACCCC
1 AAACCCT
*
20787683 AAACCCC
1 AAACCCT
20787690 AAACCCAT
1 AAACCC-T
**
20787698 AAACTTT
1 AAACCCT
20787705 AAACCCT
1 AAACCCT
*
20787712 AAA-CTT
1 AAACCCT
*
20787718 AAACCAT
1 AAACCCT
*
20787725 GAAACCAT
1 -AAACCCT
*
20787733 AAACCTT
1 AAACCCT
* *
20787740 AAATCAT
1 AAACCCT
*
20787747 AAACACT
1 AAACCCT
20787754 AAACCCT
1 AAACCCT
20787761 AAACCCT
1 AAACCCT
*
20787768 AAACCAT
1 AAACCCT
*
20787775 -AACCTT
1 AAACCCT
*
20787781 AAACCAT
1 AAACCCT
* *
20787788 AAAACAT
1 AAACCCT
20787795 AAACCCT
1 AAACCCT
*
20787802 AAACTCT
1 AAACCCT
*
20787809 AAACCTT
1 AAACCCT
*
20787816 AAACCCCA
1 AAA-CCCT
*
20787824 AAACACT
1 AAACCCT
*
20787831 AAACCAT
1 AAACCCT
*
20787838 AAAACCT
1 AAACCCT
*
20787845 AAAAACACT
1 --AAACCCT
*
20787854 AAACCTT
1 AAACCCT
*
20787861 AAACCAT
1 AAACCCT
20787868 AAACCCT
1 AAACCCT
*
20787875 AAAACCTT
1 -AAACCCT
*
20787883 AAACCAT
1 AAACCCT
* * *
20787890 -TATCAT
1 AAACCCT
20787896 AAACCAC-
1 AAACC-CT
20787903 AAACCCT
1 AAACCCT
20787910 AAACCCT
1 AAACCCT
20787917 AAACCCT
1 AAACCCT
20787924 AAACCCT
1 AAACCCT
*
20787931 AAAAAACCTT
1 ---AAACCCT
20787941 AAACCTCAT
1 AAACC-C-T
**
20787950 AAAACTAT
1 -AAACCCT
*
20787958 AAACCAT
1 AAACCCT
20787965 AAACCCT
1 AAACCCT
*
20787972 AAATCCT
1 AAACCCT
20787979 AAACCTCAT
1 AAACC-C-T
* *
20787988 AAAGACAT
1 AAA-CCCT
20787996 AAACCCT
1 AAACCCT
20788003 AAACCCT
1 AAACCCT
20788010 A
1 A
20788011 TAAAATACTA
Statistics
Matches: 340, Mismatches: 80, Indels: 46
0.73 0.17 0.10
Matches are distributed among these distances:
6 15 0.04
7 263 0.77
8 41 0.12
9 10 0.03
10 11 0.03
ACGTcount: A:0.50, C:0.32, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:20787945 original size:24 final size:24
Alignment explanation
Indices: 20787625--20787770 Score: 54
Period size: 22 Copynumber: 6.0 Consensus size: 24
20787615 ATAAAACACT
* *
20787625 AAAACC-TAAATCCTAAAACC--A
1 AAAACCATAAACCCTAAACCCTAA
* *
20787646 AAAACCATAAACCATAAACTCT--
1 AAAACCATAAACCCTAAACCCTAA
* * *
20787668 AAAAGCATAAACCCCAAACCC--C
1 AAAACCATAAACCCTAAACCCTAA
* **
20787690 AAACCCATAAACTTTAAACCCTAA
1 AAAACCATAAACCCTAAACCCTAA
* *
20787714 ACTTAAACCATGAAACCATAAACCTTAA
1 A---AAACCAT-AAACCCTAAACCCTAA
*
20787742 ATCATAAACACTAAACCCTAAACCCTAA
1 A--A-AACCA-TAAACCCTAAACCCTAA
20787770 A
1 A
20787771 CCATAACCTT
Statistics
Matches: 92, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
21 6 0.07
22 43 0.47
24 1 0.01
27 8 0.09
28 33 0.36
29 1 0.01
ACGTcount: A:0.52, C:0.30, G:0.01, T:0.16
Consensus pattern (24 bp):
AAAACCATAAACCCTAAACCCTAA
Found at i:20787982 original size:38 final size:39
Alignment explanation
Indices: 20787916--20788010 Score: 131
Period size: 38 Copynumber: 2.4 Consensus size: 39
20787906 CCCTAAACCC
20787916 TAAACCCTAAACCCTAAAAAACCTTAAACCTCATAAA-ACTA
1 TAAACCCTAAACCCT--AAAACCTTAAACCTCATAAAGAC-A
* *
20787957 TAAACCATAAACCCTAAATCC-TAAACCTCATAAAGACA
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAGACA
20787995 TAAACCCTAAACCCTA
1 TAAACCCTAAACCCTA
20788011 TAAAATACTA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 29 0.58
39 7 0.14
41 14 0.28
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.19
Consensus pattern (39 bp):
TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAGACA
Found at i:20788000 original size:62 final size:60
Alignment explanation
Indices: 20787894--20788024 Score: 140
Period size: 62 Copynumber: 2.1 Consensus size: 60
20787884 AACCATTATC
* *
20787894 ATAAACCACAAACCCTAAACCCTAAACCCTAAACCCTAAAAAACCTTAAA-CCTCATAAAACT
1 ATAAACCACAAACCCTAAACCCTAAACCCTAAACAC-AAAAAACCCTAAACCCT-ATAAAA-T
* * * *
20787956 ATAAACCATAAACCCTAAATCCTAAACCTCATAAAGAC-ATAAACCCTAAACCCTATAAAAT
1 ATAAACCACAAACCCTAAACCCTAAACC-C-TAAACACAAAAAACCCTAAACCCTATAAAAT
20788017 ACTAAACC
1 A-TAAACC
20788025 CTCAACCATA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
61 2 0.03
62 48 0.81
63 4 0.07
64 5 0.08
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (60 bp):
ATAAACCACAAACCCTAAACCCTAAACCCTAAACACAAAAAACCCTAAACCCTATAAAAT
Found at i:20788003 original size:24 final size:23
Alignment explanation
Indices: 20787962--20788053 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 23
20787952 AACTATAAAC
* * *
20787962 CATAAACCCTAAATCCTAAACCT
1 CATAAAACATAAACCCTAAACCT
20787985 CATAAAGACATAAACCCTAAACC-
1 CATAAA-ACATAAACCCTAAACCT
* *
20788008 CTATAAAATACTAAACCCTCAACCAT
1 C-ATAAAACA-TAAACCCTAAACC-T
*
20788034 -ATAAAACTTTAAACCCTAAA
1 CATAAAAC-ATAAACCCTAAA
20788054 ACCTAAACCC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
23 9 0.16
24 46 0.84
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (23 bp):
CATAAAACATAAACCCTAAACCT
Found at i:20788005 original size:149 final size:143
Alignment explanation
Indices: 20787640--20788007 Score: 351
Period size: 141 Copynumber: 2.5 Consensus size: 143
20787630 CTAAATCCTA
* * * * * *
20787640 AAACCAAAAACCATAAACCATAAACTCTAAAAGCATAAACCCC-AAACCCCAAACCCAT-AAA-C
1 AAACCAAAAAACATAAACCCTAAACTAT-AAACCATAAACCCCAAAACACTAAA-CCATAAAACC
* *
20787702 TTTAAACCCTAAA-CTTAAACCATGAAACCATAAACCTTAAATCATAAACACTAAACCCTAAACC
64 TATAAACCCTAAACCTTAAACCATGAAACCATAAACCTTAAACCATAAACACTAAACCCTAAACC
*
20787766 CTAAACCATAACCTT
129 CTAAACCATAACCCT
* * *
20787781 AAACCATAAAACATAAACCCTAAACTCTAAACCTTAAACCCCAAAACACTAAACCATAAAACCTA
1 AAACCAAAAAACATAAACCCTAAACTATAAACCATAAACCCCAAAACACTAAACCATAAAACCTA
* * * * *
20787846 AAAACACTAAACCTTAAACCAT-AAACCCTAAAACCTTAAACCATTATCA-TAAACCAC-AAACC
66 TAAACCCTAAACCTTAAACCATGAAACCAT-AAACCTTAAACCATAAACACTAAACC-CTAAACC
*
20787908 CTAAACCCTAAACCCT
129 CTAAACCAT-AACCCT
* * *
20787924 AAACCCTAAAAAACCTTAAACCTCATAAAACTATAAACCATAAACCCTAAATC-CTAAACCTCAT
1 AAA-CC-AAAAAA-CATAAACC-C-T-AAACTATAAACCATAAACCCCAAAACACTAAA-C-CAT
20787988 AAAGA-C-ATAAACCCTAAACC
58 AAA-ACCTATAAACCCTAAACC
20788008 CTATAAAATA
Statistics
Matches: 187, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
140 16 0.09
141 36 0.19
142 36 0.19
143 35 0.19
144 2 0.01
145 5 0.03
146 7 0.04
147 1 0.01
148 6 0.03
149 35 0.19
150 7 0.04
151 1 0.01
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.17
Consensus pattern (143 bp):
AAACCAAAAAACATAAACCCTAAACTATAAACCATAAACCCCAAAACACTAAACCATAAAACCTA
TAAACCCTAAACCTTAAACCATGAAACCATAAACCTTAAACCATAAACACTAAACCCTAAACCCT
AAACCATAACCCT
Found at i:20795193 original size:46 final size:45
Alignment explanation
Indices: 20795095--20795185 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 45
20795085 AACTCGCCCC
* *
20795095 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-ATGCGCAACCA
*
20795141 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCA
20795185 T
1 T
20795186 CCTAGTGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 9 0.21
46 33 0.79
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCA
Found at i:20795629 original size:30 final size:30
Alignment explanation
Indices: 20795595--20795654 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20795585 ATTTAATACG
20795595 AACTTTGGAAAAATTACACT-TTTGCCCCTA
1 AACTTTGGAAAAATTACACTATTT-CCCCTA
* * *
20795625 AACTTTTGCATAATTACACTATTTCCCCTA
1 AACTTTGGAAAAATTACACTATTTCCCCTA
20795655 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTATTTCCCCTA
Found at i:20810185 original size:28 final size:30
Alignment explanation
Indices: 20810140--20810278 Score: 93
Period size: 28 Copynumber: 4.9 Consensus size: 30
20810130 TAATGTTTTT
20810140 TCATAAAAAATATTTAAAAATA-AAAAATA
1 TCATAAAAAATATTTAAAAATATAAAAATA
*
20810169 TCATCAAAAAT-TTTAAAAATATAAAAAGTA
1 TCATAAAAAATATTTAAAAATATAAAAA-TA
* * * *
20810199 T-TTAAAAAACA--TAAAATTTTAAAAAT-
1 TCATAAAAAATATTTAAAAATATAAAAATA
* *
20810225 TC-TAAGAAAT-TATAAAAA-ATATAAAAT-
1 TCATAAAAAATATTTAAAAATATA-AAAATA
** *
20810252 TCATAAAACTTATTT-AAAATTTAAAAA
1 TCATAAAAAATATTTAAAAATATAAAAA
20810279 AAACATATTG
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
26 9 0.11
27 13 0.15
28 35 0.41
29 25 0.29
30 3 0.04
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (30 bp):
TCATAAAAAATATTTAAAAATATAAAAATA
Found at i:20810188 original size:9 final size:9
Alignment explanation
Indices: 20810174--20810278 Score: 56
Period size: 9 Copynumber: 11.6 Consensus size: 9
20810164 AAATATCATC
*
20810174 AAAAATTTT
1 AAAAATTAT
20810183 AAAAA-TAT
1 AAAAATTAT
*
20810191 AAAAAGTATTT
1 AAAAA-T-TAT
**
20810202 AAAAAACAT
1 AAAAATTAT
*
20810211 -AAAATTTT
1 AAAAATTAT
*
20810219 AAAAATTCT
1 AAAAATTAT
20810228 AAGAAATTAT
1 AA-AAATTAT
*
20810238 AAAAAATAT
1 AAAAATTAT
20810247 -AAAATTCAT
1 AAAAATT-AT
*
20810256 AAAACTTATT
1 AAAAATTA-T
*
20810266 TAAAATT-T
1 AAAAATTAT
20810274 AAAAA
1 AAAAA
20810279 AAACATATTG
Statistics
Matches: 72, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
8 22 0.31
9 24 0.33
10 19 0.26
11 7 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20810241 original size:36 final size:36
Alignment explanation
Indices: 20810175--20810252 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
20810165 AATATCATCA
*
20810175 AAAATTTTAAAAATATAAAAAGTATTTAAAAAACAT
1 AAAATTTTAAAAATATAAAAAGTATATAAAAAACAT
* *
20810211 AAAATTTTAAAAATTCTAAGAAA-T-TATAAAAAATAT
1 AAAATTTTAAAAA-TATAA-AAAGTATATAAAAAACAT
20810247 AAAATT
1 AAAATT
20810253 CATAAAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 29 0.78
37 5 0.14
38 3 0.08
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (36 bp):
AAAATTTTAAAAATATAAAAAGTATATAAAAAACAT
Found at i:20810250 original size:45 final size:44
Alignment explanation
Indices: 20810174--20810278 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 44
20810164 AAATATCATC
* *
20810174 AAAAATTTTAAAAATATAAAAAGTATTTAAAAAACATAAAATTTT
1 AAAAATTCTAAAAATATAAAAAG-ATATAAAAAACATAAAATTTT
**
20810219 AAAAATTCTAAGAAATTATAAAAA-ATATAAAATTCATAAAACTTATT
1 AAAAATTCTAA-AAA-TATAAAAAGATATAAAAAACATAAAA-TT-TT
*
20810266 TAAAATT-TAAAAA
1 AAAAATTCTAAAAA
20810279 AAACATATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
45 27 0.53
46 8 0.16
47 16 0.31
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (44 bp):
AAAAATTCTAAAAATATAAAAAGATATAAAAAACATAAAATTTT
Found at i:20810675 original size:12 final size:11
Alignment explanation
Indices: 20810646--20810672 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20810636 ATCAAAAAAT
20810646 AAAAATTTTAA
1 AAAAATTTTAA
20810657 AAAAATTTTAA
1 AAAAATTTTAA
20810668 AAAAA
1 AAAAA
20810673 ATTGGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:20810802 original size:12 final size:12
Alignment explanation
Indices: 20810785--20810810 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20810775 CCACTTCAAG
20810785 TTTTTATAATTT
1 TTTTTATAATTT
20810797 TTTTTATAATTT
1 TTTTTATAATTT
20810809 TT
1 TT
20810811 ATAAGCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:20810873 original size:10 final size:10
Alignment explanation
Indices: 20810840--20810886 Score: 62
Period size: 9 Copynumber: 4.8 Consensus size: 10
20810830 AATAAGTTCT
20810840 TTTTTATA-A
1 TTTTTATAGA
20810849 TTTTTAT-GA
1 TTTTTATAGA
20810858 TTTTTATAGA
1 TTTTTATAGA
*
20810868 TTTTTAATACA
1 TTTTT-ATAGA
20810879 TTTTTATA
1 TTTTTATA
20810887 AAGGTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 15 0.44
10 10 0.29
11 9 0.26
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (10 bp):
TTTTTATAGA
Found at i:20811006 original size:20 final size:21
Alignment explanation
Indices: 20810983--20811030 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
20810973 TTTTTAAATA
20810983 TTTAATAGTATTTAT-ATTTT
1 TTTAATAGTATTTATGATTTT
*
20811003 TTT-ATAATTATTTATGATTTT
1 TTTAAT-AGTATTTATGATTTT
*
20811024 TTAAATA
1 TTTAATA
20811031 AATTTTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 8 0.35
22 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTAATAGTATTTATGATTTT
Found at i:20816173 original size:15 final size:16
Alignment explanation
Indices: 20816126--20816176 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
20816116 ATGTATAAGT
20816126 AAGATAAATTTTATTAA
1 AAGA-AAATTTTATTAA
*
20816143 GAAGAAAATTTAATTAA
1 -AAGAAAATTTTATTAA
*
20816160 AA-AATATTTTATTAA
1 AAGAAAATTTTATTAA
20816175 AA
1 AA
20816177 TTAAAAGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.43
16 2 0.07
17 11 0.37
18 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
AAGAAAATTTTATTAA
Found at i:20817653 original size:27 final size:26
Alignment explanation
Indices: 20817592--20817654 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
20817582 ACTCTATTTT
20817592 ATTTATATTAGGATCATTAATATTAAG
1 ATTT-TATTAGGATCATTAATATTAAG
* * * *
20817619 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGATCA-TTAATATTAAG
20817647 ATTTTATT
1 ATTTTATT
20817655 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATCATTAATATTAAG
Found at i:20824449 original size:13 final size:13
Alignment explanation
Indices: 20824431--20824461 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
20824421 TATTGGTCAG
20824431 TTCAAAGAAAAAA
1 TTCAAAGAAAAAA
20824444 TTCAAAGAAAAAA
1 TTCAAAGAAAAAA
20824457 TTCAA
1 TTCAA
20824462 GCTCATGCTG
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:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (13 bp):
TTCAAAGAAAAAA
Found at i:20840149 original size:20 final size:20
Alignment explanation
Indices: 20840113--20840150 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20840103 TGGAAAATAA
* *
20840113 TTTTTAAAAATTGATTTATT
1 TTTTTAAAAAATAATTTATT
20840133 TTTTTAAAAAATAATTTA
1 TTTTTAAAAAATAATTTA
20840151 CTAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTAAAAAATAATTTATT
Found at i:20840273 original size:20 final size:20
Alignment explanation
Indices: 20840250--20840288 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20840240 ATTTTTACAT
20840250 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
20840270 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
20840289 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:20848608 original size:20 final size:21
Alignment explanation
Indices: 20848573--20848611 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20848563 AATTAAAAAT
*
20848573 CCAAATTATTTTTTTAAAGCG
1 CCAAATTATATTTTTAAAGCG
20848594 CCAAATTA-ATTTTTAAAG
1 CCAAATTATATTTTTAAAG
20848612 TCGAAGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (21 bp):
CCAAATTATATTTTTAAAGCG
Found at i:20851260 original size:16 final size:18
Alignment explanation
Indices: 20851241--20851273 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
20851231 CATACGAATT
20851241 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
20851257 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
20851274 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:20851901 original size:43 final size:43
Alignment explanation
Indices: 20851757--20852087 Score: 365
Period size: 43 Copynumber: 7.8 Consensus size: 43
20851747 TTTTATCAAA
* ** *
20851757 TCACCGGCATTA-AGCCTGCTAGGTTTTAAACCCGA-AT--TC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATC
* * ** * *
20851796 ATCACCGGCATGA-AGCCTGCTAGACTTTAAGTCTGA-ACTCAT-
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATA-TCATC
* * *
20851838 TCACCGGTATT-TCGCCTGCTAGGCTCGAAGCCTGATATCATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATC
* * *
20851880 TTACCGGCATTATCGTCTGCTAGG-TCCGAAGCCCGATATCATC
1 TCACCGGCATTATAGCCTGCTAGGCT-CGAAGCCCGATATCATC
* *
20851923 TCACCGGCATTATAGCCTGCTAAGCTCGAAGCCTGATATCATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATC
* * *
20851966 TCACCGGCATTATAGCTTACTAGGCCCGAAGCCCGATATCATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATC
*
20852009 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCACC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATC
*
20852052 TCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGA
20852088 ATGTCACATT
Statistics
Matches: 250, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.12
41 32 0.13
42 11 0.04
43 176 0.70
44 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATC
Found at i:20852625 original size:3 final size:3
Alignment explanation
Indices: 20852617--20852666 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
20852607 AAATAAACTC
20852617 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
20852665 TC
1 TC
20852667 ACATCAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:20852991 original size:17 final size:17
Alignment explanation
Indices: 20852941--20852991 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
20852931 TTATAACTTG
20852941 AATATTATAAATT-TTA
1 AATATTATAAATTCTTA
* * *
20852957 GA-ATTAGAAAAATCTTA
1 AATATTA-TAAATTCTTA
20852974 AATATTATAAATTCTTA
1 AATATTATAAATTCTTA
20852991 A
1 A
20852992 TTCCAACTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 13 0.50
18 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (17 bp):
AATATTATAAATTCTTA
Found at i:20853559 original size:16 final size:16
Alignment explanation
Indices: 20853538--20853569 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20853528 GATAAGAGAA
20853538 TATTTAATATATTCTC
1 TATTTAATATATTCTC
20853554 TATTTAATATATTCTC
1 TATTTAATATATTCTC
20853570 GGGATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAATATATTCTC
Found at i:20858778 original size:11 final size:11
Alignment explanation
Indices: 20858764--20858794 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
20858754 AGATAAATAT
20858764 TATTTTATTAA
1 TATTTTATTAA
*
20858775 TATTTTATTAT
1 TATTTTATTAA
20858786 TATTTTATT
1 TATTTTATT
20858795 GGTATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:20860977 original size:46 final size:46
Alignment explanation
Indices: 20860925--20861022 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
20860915 AGTGTGCTCT
20860925 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20860971 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20861017 CTGATA
1 CTGATA
20861023 AGACCATGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20861032 original size:35 final size:35
Alignment explanation
Indices: 20860986--20861057 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
20860976 ATGAAATGTG
20860986 TAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGA
*
20861021 TAAGACCATGGTTGAAAGCTACCATGGCAACCTGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGA
20861056 TA
1 TA
20861058 TGAAATGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (35 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGA
Found at i:20861075 original size:81 final size:81
Alignment explanation
Indices: 20860940--20861103 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 81
20860930 ATGAAATGTG
*
20860940 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGATTGAAAGA
20861005 TACCATGGCAACCTGA
66 TACCATGGCAACCTGA
* *
20861021 TAAGACCATGGTTGAAAGCTACCATGGCAACCTGATATGAAATGTGTAAGACCATGATTGAAAGG
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGATTGAAAGA
20861086 TACCATGGCAACCTGA
66 TACCATGGCAACCTGA
20861102 TA
1 TA
20861104 TAAAATGAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (81 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGATTGAAAGA
TACCATGGCAACCTGA
Found at i:20861090 original size:46 final size:46
Alignment explanation
Indices: 20861020--20861233 Score: 277
Period size: 46 Copynumber: 4.7 Consensus size: 46
20861010 TGGCAACCTG
* * *
20861020 ATAAGACCATGGTTGAAAGCTACCATGGCAACCTGATATGAAATGT
1 ATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
* * * * *
20861066 GTAAGACCATGATTGAAAGGTACCATGGCAACCTGATATAAAATGA
1 ATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
* *
20861112 ATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGA
1 ATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
*
20861158 ATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
1 ATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAATGA
* * * *
20861204 GTAAGACCATAGTTGAAAGACACTATGGCA
1 ATAAGACCATGGTTGAAAGATACCATGGCA
20861234 TCATGTCAAA
Statistics
Matches: 149, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 148 0.99
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (46 bp):
ATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
Found at i:20863108 original size:52 final size:52
Alignment explanation
Indices: 20863051--20863168 Score: 125
Period size: 51 Copynumber: 2.3 Consensus size: 52
20863041 ATAGAAATGG
**
20863051 TGAAAATGAAGAAATGAGAAACATTTGAAAATGATTATGGGTTTCTCCAAAA
1 TGAAAATGAAGAAATGAGAAACATTTGAAAATGAACATGGGTTTCTCCAAAA
* * ** ** * *
20863103 TGAAAATGGAGAAAT-TGAATTATTTGGCAATGAACGTGGTTTTCTCCAAAA
1 TGAAAATGAAGAAATGAGAAACATTTGAAAATGAACATGGGTTTCTCCAAAA
20863154 TGAAAAT-AA-AAATGA
1 TGAAAATGAAGAAATGA
20863169 AAATGAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
49 4 0.08
50 1 0.02
51 34 0.64
52 14 0.26
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (52 bp):
TGAAAATGAAGAAATGAGAAACATTTGAAAATGAACATGGGTTTCTCCAAAA
Found at i:20863179 original size:13 final size:12
Alignment explanation
Indices: 20863150--20863187 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
20863140 GGTTTTCTCC
20863150 AAAATGAAAATA
1 AAAATGAAAATA
20863162 AAAATGAAAATGA
1 AAAATGAAAAT-A
20863175 AAAATGAAAATA
1 AAAATGAAAATA
20863187 A
1 A
20863188 CTTAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:20874731 original size:2 final size:2
Alignment explanation
Indices: 20874724--20874760 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20874714 TTATATCCAA
20874724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20874761 AAATCAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20880437 original size:21 final size:21
Alignment explanation
Indices: 20880413--20880453 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20880403 AAAATGATAC
20880413 TTAGAGCATAAATTTCTCGCT
1 TTAGAGCATAAATTTCTCGCT
20880434 TTAGAGCATAAATTTCTCGC
1 TTAGAGCATAAATTTCTCGC
20880454 CATAGGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (21 bp):
TTAGAGCATAAATTTCTCGCT
Found at i:20881335 original size:2 final size:2
Alignment explanation
Indices: 20881328--20881352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20881318 TGTATCAATA
20881328 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
20881353 CCATGATTGA
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:20885399 original size:14 final size:15
Alignment explanation
Indices: 20885375--20885403 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20885365 AATAATTGAG
20885375 TATTATTATTTATTT
1 TATTATTATTTATTT
20885390 TATT-TTATTTATTT
1 TATTATTATTTATTT
20885404 ATAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTATTATTTATTT
Found at i:20885640 original size:14 final size:13
Alignment explanation
Indices: 20885610--20885663 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
20885600 AACACCAGAA
20885610 AAAAATCATCTTTT
1 AAAAATCAT-TTTT
*
20885624 AAAAACCATTTTCT
1 AAAAATCATTTT-T
20885638 AAAAATCATTTTT
1 AAAAATCATTTTT
*
20885651 CAAAAATTATTTT
1 -AAAAATCATTTT
20885664 ACTGACAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.11
14 31 0.89
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAAATCATTTTT
Found at i:20894663 original size:10 final size:9
Alignment explanation
Indices: 20894648--20894675 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20894638 CCCTCAACTG
20894648 AAAAAAAAT
1 AAAAAAAAT
20894657 AAAAAAAAT
1 AAAAAAAAT
20894666 AAAAAAAAT
1 AAAAAAAAT
20894675 A
1 A
20894676 CAGAAAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:20898515 original size:29 final size:29
Alignment explanation
Indices: 20898482--20898538 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
20898472 AAGGTCTTAC
*
20898482 CAGATTTGCTTAATAATTTATCTCTGAAT
1 CAGATATGCTTAATAATTTATCTCTGAAT
20898511 CAGATATGCTTAATAATTTATCTCTGAA
1 CAGATATGCTTAATAATTTATCTCTGAA
20898539 ATTGTGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (29 bp):
CAGATATGCTTAATAATTTATCTCTGAAT
Found at i:20900341 original size:44 final size:45
Alignment explanation
Indices: 20900235--20900368 Score: 144
Period size: 46 Copynumber: 3.0 Consensus size: 45
20900225 ACAGGACAGA
* * *
20900235 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
20900281 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATTGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * *
20900325 ACAGGAATAATTCATGTAAGTCCATGTCAAAGATATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20900369 CAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 35 0.48
45 1 0.01
46 37 0.51
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:20904510 original size:74 final size:74
Alignment explanation
Indices: 20904371--20904512 Score: 250
Period size: 74 Copynumber: 1.9 Consensus size: 74
20904361 CTATTATCTT
* *
20904371 CAGTGTTATATTTATTTTGATTTTTTATCTCTAAGTCAAACCTTTTTTTGACTTAAAATGTTTTC
1 CAGTGTTATATTTATTTTGATTTTTGATCTCTAAGCCAAACCTTTTTTTGACTTAAAATGTTTTC
20904436 TTTTTTTGG
66 TTTTTTTGG
20904445 CAGTGTTATATTTATTTTGATTTTTGATCTCTAAGCCAAACCTTTCTTTTGACTTAAAATG-TTT
1 CAGTGTTATATTTATTTTGATTTTTGATCTCTAAGCCAAACCTTT-TTTTGACTTAAAATGTTTT
20904509 CTTT
65 CTTT
20904513 AATTTTTGGT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 50 0.77
75 15 0.23
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.54
Consensus pattern (74 bp):
CAGTGTTATATTTATTTTGATTTTTGATCTCTAAGCCAAACCTTTTTTTGACTTAAAATGTTTTC
TTTTTTTGG
Found at i:20914138 original size:17 final size:16
Alignment explanation
Indices: 20914118--20914153 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
20914108 AAGAACAATT
*
20914118 AACAAAAATGAACTAGA
1 AACAAAAATAAACTA-A
20914135 AACAAAAATAAACTAA
1 AACAAAAATAAACTAA
20914151 AAC
1 AAC
20914154 TGATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (16 bp):
AACAAAAATAAACTAA
Found at i:20932170 original size:90 final size:90
Alignment explanation
Indices: 20932017--20932204 Score: 279
Period size: 90 Copynumber: 2.1 Consensus size: 90
20932007 AAATTGAAAT
* * *
20932017 TTTTTTGGGTTGCTTTTTTCGATTATCTAGAAACAATAAATGATTAACAGAGGGAAAGGGATAGT
1 TTTTTTGGGTTGCTTTTTTCGATGATCTAGAAACAAGAAATGATTAACAGAGGAAAAGGGATAGT
20932082 GGGGGAGAG-GGAGAGAGCCGAATTC
66 GGGGGAGAGCGG-GAGAGCCGAATTC
* * *
20932107 TTTTTTGGGTTGCTTTTTTTGGTGATCTAGAAACAAGAAATTATTAACAGAGGAAAAGGGATAGT
1 TTTTTTGGGTTGCTTTTTTCGATGATCTAGAAACAAGAAATGATTAACAGAGGAAAAGGGATAGT
* *
20932172 GGGGGAGAGCGGGAGAGTCTAATTC
66 GGGGGAGAGCGGGAGAGCCGAATTC
*
20932197 TATTTTGG
1 TTTTTTGG
20932205 CAAAGCAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 86 0.98
91 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.31, T:0.31
Consensus pattern (90 bp):
TTTTTTGGGTTGCTTTTTTCGATGATCTAGAAACAAGAAATGATTAACAGAGGAAAAGGGATAGT
GGGGGAGAGCGGGAGAGCCGAATTC
Found at i:20938112 original size:23 final size:23
Alignment explanation
Indices: 20938086--20938135 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20938076 AAAGTGTTCC
20938086 AAAAGCATT-TTTTTAAGAAGTTG
1 AAAA-CATTATTTTTAAGAAGTTG
**
20938109 AAAATTTTATTTTTAAGAAGTTG
1 AAAACATTATTTTTAAGAAGTTG
20938132 AAAA
1 AAAA
20938136 TTTTAACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (23 bp):
AAAACATTATTTTTAAGAAGTTG
Found at i:20938136 original size:23 final size:23
Alignment explanation
Indices: 20938095--20938140 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20938085 CAAAAGCATT
20938095 TTTTTAAGAAGTTGAAAATTTTA
1 TTTTTAAGAAGTTGAAAATTTTA
20938118 TTTTTAAGAAGTTGAAAATTTTA
1 TTTTTAAGAAGTTGAAAATTTTA
20938141 ACTTCTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTTTAAGAAGTTGAAAATTTTA
Found at i:20939348 original size:6 final size:6
Alignment explanation
Indices: 20939337--20939369 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
20939327 GTTTTAACTT
*
20939337 CTCTCC CTCTCC CTCTCC CTCTCG CTCTCC CTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC
20939370 GGCTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.64, G:0.03, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:20940223 original size:31 final size:31
Alignment explanation
Indices: 20940166--20940224 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
20940156 CAATCCAGTA
** *
20940166 ACTTAAATAAAAACTTTTGAATAGTTTAATG
1 ACTTAAATAAAAACTTTCAAACAGTTTAATG
*
20940197 ACTTAAATGAAAACTTTCAAACAGTTTA
1 ACTTAAATAAAAACTTTCAAACAGTTTA
20940225 GTTACCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAACAGTTTAATG
Found at i:20982436 original size:3 final size:3
Alignment explanation
Indices: 20982430--20982456 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20982420 TAAGAAGAAG
20982430 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
20982457 CTGACAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20984756 original size:23 final size:23
Alignment explanation
Indices: 20984715--20984765 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
20984705 AAACAAAATT
20984715 TCATTTTTATACTATTAAAATAC
1 TCATTTTTATACTATTAAAATAC
* *
20984738 TCATATTTTATATTA-TAAAATAT
1 TCAT-TTTTATACTATTAAAATAC
20984761 TCATT
1 TCATT
20984766 AGTAAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
24 9 0.36
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (23 bp):
TCATTTTTATACTATTAAAATAC
Found at i:20984896 original size:17 final size:16
Alignment explanation
Indices: 20984856--20984894 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
20984846 TAATTTTAAT
* *
20984856 TTTAAATATTCTTAAA
1 TTTAAATATTATAAAA
20984872 TATTAAATATTATAAAA
1 T-TTAAATATTATAAAA
20984889 TTTAAA
1 TTTAAA
20984895 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAAATATTATAAAA
Found at i:20985291 original size:10 final size:10
Alignment explanation
Indices: 20985261--20985294 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
20985251 ATTCCGTAAT
20985261 TAATTTTAAA
1 TAATTTTAAA
20985271 TAATATATTAAA
1 TAAT-T-TTAAA
20985283 TAATTTTAAA
1 TAATTTTAAA
20985293 TA
1 TA
20985295 CTTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 11 0.50
11 2 0.09
12 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATTTTAAA
Found at i:20986918 original size:14 final size:14
Alignment explanation
Indices: 20986899--20986925 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20986889 GATTATACAT
20986899 ATATACATACATAC
1 ATATACATACATAC
20986913 ATATACATACATA
1 ATATACATACATA
20986926 TATGTTGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATACATACATAC
Found at i:20995857 original size:12 final size:13
Alignment explanation
Indices: 20995828--20995861 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
20995818 ACATTAATCT
*
20995828 AAATATTCATTAA
1 AAATATTAATTAA
20995841 AAATATTAATTAA
1 AAATATTAATTAA
20995854 AATATATT
1 AA-ATATT
20995862 GATACAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATTAATTAA
Found at i:20996713 original size:16 final size:16
Alignment explanation
Indices: 20996694--20996729 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20996684 AACCTAACCC
*
20996694 AAAAAAAAA-ACAAAG
1 AAAAAAAAAGAAAAAG
20996709 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
20996725 AAAAA
1 AAAAA
20996730 CCTACCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:20996758 original size:42 final size:44
Alignment explanation
Indices: 20996681--20996765 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 44
20996671 AGCCCCCAAA
20996681 AAAAACCTAACCCAAAAAAAAAACAAAGAAAAAAAAAGAAAAAG
1 AAAAACCTAACCCAAAAAAAAAACAAAGAAAAAAAAAGAAAAAG
* *
20996725 AAAAACCT-ACCCCAAAAAAAAA-AAAGAAGAAAAAAGAAAAA
1 AAAAACCTAACCCAAAAAAAAAACAAAGAAAAAAAAAGAAAAA
20996766 CCTAACAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 18 0.46
43 13 0.33
44 8 0.21
ACGTcount: A:0.76, C:0.14, G:0.07, T:0.02
Consensus pattern (44 bp):
AAAAACCTAACCCAAAAAAAAAACAAAGAAAAAAAAAGAAAAAG
Found at i:20996775 original size:18 final size:18
Alignment explanation
Indices: 20996719--20996777 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
20996709 AAAAAAAAAG
*
20996719 AAAAAGAAAAACCTACCCCA
1 AAAAAGAAAAACCTA--ACA
** *
20996739 AAAAA-AAAAA-AGAAGA
1 AAAAAGAAAAACCTAACA
20996755 AAAAAGAAAAACCTAACA
1 AAAAAGAAAAACCTAACA
20996773 AAAAA
1 AAAAA
20996778 AGATAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 6 0.20
17 5 0.17
18 9 0.30
19 5 0.17
20 5 0.17
ACGTcount: A:0.75, C:0.15, G:0.07, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAAACCTAACA
Found at i:20996778 original size:36 final size:36
Alignment explanation
Indices: 20996699--20996788 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
20996689 AACCCAAAAA
*
20996699 AAAAACAAAGAAAAAAAAAGAAAAAGAAAAACCTACC
1 AAAAA-AAAGAAAAAAAAAGAAAAAGAAAAACCTAAC
** *
20996736 CCAAAAAA-AAAAAAGAAGAAAAAAGAAAAACCTAAC
1 AAAAAAAAGAAAAAAAAAG-AAAAAGAAAAACCTAAC
*
20996772 -AAAAAAAGATAAAAAAA
1 AAAAAAAAGAAAAAAAAA
20996789 CCTAGCCACC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
35 15 0.34
36 26 0.59
37 3 0.07
ACGTcount: A:0.78, C:0.11, G:0.08, T:0.03
Consensus pattern (36 bp):
AAAAAAAAGAAAAAAAAAGAAAAAGAAAAACCTAAC
Found at i:20997061 original size:11 final size:11
Alignment explanation
Indices: 20997045--20997083 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20997035 TTCTTTCGAA
20997045 TCTTTTTTCTT
1 TCTTTTTTCTT
*
20997056 TCTTTTTTGTGT
1 TCTTTTTTCT-T
*
20997068 TTTTTTTTCTT
1 TCTTTTTTCTT
20997079 TCTTT
1 TCTTT
20997084 ATATATACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:20997572 original size:3 final size:3
Alignment explanation
Indices: 20997534--20997559 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20997524 TTTTTGTAGA
20997534 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
20997560 CATACTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20999318 original size:12 final size:12
Alignment explanation
Indices: 20999301--20999336 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
20999291 ATTCATTTGA
20999301 CATTCATGCATT
1 CATTCATGCATT
20999313 CATTCATGCATT
1 CATTCATGCATT
*
20999325 CATTCATACATT
1 CATTCATGCATT
20999337 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:21004450 original size:72 final size:72
Alignment explanation
Indices: 21004330--21004549 Score: 255
Period size: 72 Copynumber: 3.0 Consensus size: 72
21004320 CTTTTCAAGG
* * * * * *
21004330 AAAATAAACTCATATT--GAAAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCT
21004393 GTTTTTC
66 GTTTTTC
* * *
21004400 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCT
***
21004465 GTTCATAAAA
66 GTT--T-TTC
* * *
21004475 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAATCACGCGCTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA-GACACGCTGAGGTATTTTCAATTTC
21004540 TGTTTTTC
65 TGTTTTTC
21004548 AA
1 AA
21004550 TTTCTGTTCG
Statistics
Matches: 123, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
70 15 0.12
72 42 0.34
73 2 0.02
74 2 0.02
75 37 0.30
76 25 0.20
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (72 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCT
GTTTTTC
Found at i:21004502 original size:75 final size:74
Alignment explanation
Indices: 21004330--21004705 Score: 330
Period size: 76 Copynumber: 4.9 Consensus size: 74
21004320 CTTTTCAAGG
* * * * * * *
21004330 AAAATAAACTCATATT--GAAAGATGAGTTGAGCCTCAAG-ACACGTTGAGGTATTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCACACGCTGAGGTAATTTCAATTTC
***
21004392 TGTT--TTTC
65 TGTTCATAAA
* *
21004400 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCACACGCTGAGGTAATTTCAATTTCT
21004465 GTTCATAAAA
66 GTTCAT-AAA
* * * *
21004475 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAATCACGCGCTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCACACGCTGAGGTAATTTCAATTTC
***
21004540 TGTTTTTCAATTTCTGTTCGTC
65 TG---TTC-A-------T-AAA
* * *
21004562 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTAATTTTAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCACACGCTGAGGTAATTTCAATTTCT
*
21004627 GTTCATCAA
66 GTTCATAAA
* * *
21004636 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGCTCACGCGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--CACACGCTGAGGTAATTTCAATTT
21004701 CTGTT
64 CTGTT
21004706 TTTCAATTTC
Statistics
Matches: 249, Mismatches: 37, Indels: 34
0.78 0.12 0.11
Matches are distributed among these distances:
70 15 0.06
71 2 0.01
72 40 0.16
74 39 0.16
75 37 0.15
76 48 0.19
79 3 0.01
80 1 0.00
82 1 0.00
83 3 0.01
86 23 0.09
87 37 0.15
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCACACGCTGAGGTAATTTCAATTTCT
GTTCATAAA
Found at i:21004548 original size:14 final size:14
Alignment explanation
Indices: 21004529--21004557 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21004519 CGCTGAGGTA
21004529 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
21004543 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
21004557 T
1 T
21004558 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:21004667 original size:74 final size:73
Alignment explanation
Indices: 21004543--21004705 Score: 231
Period size: 74 Copynumber: 2.2 Consensus size: 73
21004533 CAATTTCTGT
* *
21004543 TTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACG
1 TTTTCAATTTCTGTTCATCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCCACACG
*
21004607 TTGAGGTAA
66 CTGAGGT-A
*
21004616 TTTT-AATTTCTGTTCATCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGCTCAC
1 TTTTCAATTTCTGTTCATC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGC-CAC
*
21004680 GCGCTGAGGTA
63 ACGCTGAGGTA
21004691 TTTTCAATTTCTGTT
1 TTTTCAATTTCTGTT
21004706 TTTCAATTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
72 13 0.16
73 4 0.05
74 38 0.47
75 5 0.06
76 20 0.25
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (73 bp):
TTTTCAATTTCTGTTCATCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCCACACG
CTGAGGTA
Found at i:21004682 original size:162 final size:162
Alignment explanation
Indices: 21004381--21004793 Score: 652
Period size: 162 Copynumber: 2.5 Consensus size: 162
21004371 CGTTGAGGTA
* ** *
21004381 TTTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATG
1 TTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
21004445 CTGAGGTAATTTCAATTTCTGTTCATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC
66 CTGAGGTAATTTCAATTTCTGTTCATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC
21004510 TCAATCACGCGCTGAGGTATTTTCAATTTCTG
131 TCAATCACGCGCTGAGGTATTTTCAATTTCTG
21004542 TTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
* * * * *
21004607 TTGAGGTAATTTTAATTTCTGTTCAT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCT
66 CTGAGGTAATTTCAATTTCTGTTCATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC
*
21004671 TCAGCTCACGCGCTGAGGTATTTTCAATTTCTG
131 TCA-ATCACGCGCTGAGGTATTTTCAATTTCTG
*
21004704 TTTTTCAATTTCTGTTCGTCAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCAC
1 TTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---AC
* *
21004768 GCGCTGAGGTATTTTCAATTTCTGTT
63 ACGCTGAGGTAATTTCAATTTCTGTT
21004794 TTTCAATTTC
Statistics
Matches: 232, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
161 45 0.19
162 163 0.70
164 24 0.10
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (162 bp):
TTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
CTGAGGTAATTTCAATTTCTGTTCATAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC
TCAATCACGCGCTGAGGTATTTTCAATTTCTG
Found at i:21004710 original size:14 final size:14
Alignment explanation
Indices: 21004691--21004719 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21004681 CGCTGAGGTA
21004691 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
21004705 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
21004719 T
1 T
21004720 CGTCAAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:21004771 original size:88 final size:88
Alignment explanation
Indices: 21004616--21004844 Score: 361
Period size: 88 Copynumber: 2.6 Consensus size: 88
21004606 GTTGAGGTAA
* * *
21004616 TTTT-AATTTCTGTTCATCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGCTCAC
1 TTTTCAATTTCTGTTCGTC--AAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCAC
21004680 GCGCTGAGGTATTTTCAATTTCTGT
64 GCGCTGAGGTATTTTCAATTTCTGT
*
21004705 TTTTCAATTTCTGTTCGTCAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACGC
1 TTTTCAATTTCTGTTCGTCAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACGC
21004770 GCTGAGGTATTTTCAATTTCTGT
66 GCTGAGGTATTTTCAATTTCTGT
* * *
21004793 TTTTCAATTTCTGTTTGTCAAGAATCAACTCACATTGCGAGAGGTGGGTTGA
1 TTTTCAATTTCTGTTCGTCAAG-ATCAACTCATATTGCGAGAGGTGAGTTGA
21004845 ACCTTTTAAT
Statistics
Matches: 131, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
88 87 0.66
89 31 0.24
90 13 0.10
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (88 bp):
TTTTCAATTTCTGTTCGTCAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACGC
GCTGAGGTATTTTCAATTTCTGT
Found at i:21004798 original size:14 final size:14
Alignment explanation
Indices: 21004779--21004813 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21004769 CGCTGAGGTA
21004779 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
21004793 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
*
21004807 TTGTCAA
1 TTTTCAA
21004814 GAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:21004873 original size:54 final size:55
Alignment explanation
Indices: 21004793--21004898 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 55
21004783 CAATTTCTGT
* *
21004793 TTTTCAATTTCTGTTTGTCAAGAATCAACTCACATTGCGAGAGGTGGGTTGAACC
1 TTTTCAATTTCTCTTTGTCAAGAATCAACTCACATTGCGAGAGGTGAGTTGAACC
* * * *
21004848 TTTT-AATTTCTACTTTTTCAA-AATCAGCTCATATTGTGAGAGGTGAGTTGA
1 TTTTCAATTTCT-CTTTGTCAAGAATCAACTCACATTGCGAGAGGTGAGTTGA
21004899 GCCTCAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (55 bp):
TTTTCAATTTCTCTTTGTCAAGAATCAACTCACATTGCGAGAGGTGAGTTGAACC
Found at i:21005155 original size:70 final size:69
Alignment explanation
Indices: 21005036--21005740 Score: 432
Period size: 72 Copynumber: 10.1 Consensus size: 69
21005026 GAGTTAAGCC
*
21005036 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
21005100 TGAGGTA
63 TGAGGTA
* * ** * *
21005107 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG
21005172 AGGTA
65 AGGTA
* * *
21005177 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACT
1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
21005242 GAGGTA
64 GAGGTA
* * * ** * * *
21005248 TTTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTT
1 -TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG
21005304 A---A
65 AGGTA
*** ** *
21005306 TTTTTGTTTTTCA----AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
21005367 GGTA
66 GGTA
* * *
21005371 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
21005436 TGAGGTA
63 TGAGGTA
* * ** * * * * ** * *** * *
21005443 TTTTCAATTTCTGTTTTCAATTTACGT--TGTT-CAAGA-ATCAACTCATATTGCGAGAGGTAGG
1 TTTTCAATTTTTGTTTTAAATCAAC-TCATATTGCGAGAGGTGAGTTGAGCCT-CG-G-GGCACG
* ***
21005504 TTGA-ACC
62 CTGAGGTA
* * *
21005511 TTTT-AATTTCTACT-TTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTTCAATTT-T--TGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
21005574 GCTGAGGTA
61 GCTGAGGTA
* * * * *
21005583 ATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTTCAATTTTTGTT-T----TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
21005648 GCTGAGGTA
61 GCTGAGGTA
* * * **
21005657 TTTTCAATTTTTATGTTTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCAC
*
21005722 GCCGAGGTA
61 GCTGAGGTA
21005731 TTTTCAATTT
1 TTTTCAATTT
21005741 CCGTTTTTCA
Statistics
Matches: 475, Mismatches: 109, Indels: 98
0.70 0.16 0.14
Matches are distributed among these distances:
53 31 0.07
57 8 0.02
58 1 0.00
61 2 0.00
62 2 0.00
65 5 0.01
66 9 0.02
67 10 0.02
68 8 0.02
69 16 0.03
70 100 0.21
71 69 0.15
72 116 0.24
73 14 0.03
74 76 0.16
75 4 0.01
76 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (69 bp):
TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
GGTA
Found at i:21005230 original size:71 final size:69
Alignment explanation
Indices: 21005036--21005300 Score: 316
Period size: 70 Copynumber: 3.7 Consensus size: 69
21005026 GAGTTAAGCC
* *
21005036 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
21005101 GAGGTAT
63 GAGGTAT
* * ** * *
21005108 TTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTAATTTTTGT-TTTAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGCTG
21005172 AGGTAT
64 AGGTAT
*
21005178 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
1 TTTTAATTTTTGTTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
21005243 AGGTATT
64 AGGTA-T
* * ** * *
21005250 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
21005301 TTTAATTTTT
Statistics
Matches: 166, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
69 4 0.02
70 87 0.52
71 44 0.27
72 31 0.19
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAG
GTAT
Found at i:21005346 original size:123 final size:124
Alignment explanation
Indices: 21005178--21005425 Score: 383
Period size: 123 Copynumber: 2.0 Consensus size: 124
21005168 GTTGAGGTAT
21005178 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
** *
21005243 AGGTATTTTTTA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
* * *
21005300 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACT
* * * *
21005365 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
21005425 T
1 T
21005426 CAGGTCACGC
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
122 12 0.11
123 60 0.53
124 13 0.12
125 28 0.25
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (124 bp):
TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:21005351 original size:264 final size:257
Alignment explanation
Indices: 21004869--21005462 Score: 999
Period size: 264 Copynumber: 2.3 Consensus size: 257
21004859 ACTTTTTCAA
* * * *
21004869 AATCAGCTCATATTGTGAGAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
*
21004934 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAGT
21004999 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
131 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
21005064 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
196 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
* * * *
21005126 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
*
21005191 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTGAGGTATTTTTTAG
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTA----TT--
21005256 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
125 TTTA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
21005321 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTG
189 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTG
21005386 TTTT
254 TTTT
* *
21005390 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT
1 AA--TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCT
21005455 GTTTTCAA
64 GTTTTCAA
21005463 TTTACGTTGT
Statistics
Matches: 312, Mismatches: 16, Indels: 9
0.93 0.05 0.03
Matches are distributed among these distances:
257 112 0.36
261 2 0.01
263 4 0.01
264 131 0.42
266 63 0.20
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (257 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAGT
TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
Found at i:21005723 original size:74 final size:74
Alignment explanation
Indices: 21005530--21005741 Score: 250
Period size: 74 Copynumber: 2.9 Consensus size: 74
21005520 CTACTTTTTC
* *
21005530 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
21005595 GTTGTCAAA
66 GTTGTCAAA
* * * *
21005604 AAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTT-T
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
***
21005668 -TATGT-TTT
66 GT-TGTCAAA
** * * *
21005676 AATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTT
21005741 C
64 C
21005742 CGTTTTTCAA
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
72 34 0.29
73 4 0.03
74 78 0.67
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTGTCAAA
Found at i:21005750 original size:14 final size:14
Alignment explanation
Indices: 21005731--21005765 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21005721 CGCCGAGGTA
21005731 TTTTCAATTTCCGT
1 TTTTCAATTTCCGT
*
21005745 TTTTCAATTTCTGT
1 TTTTCAATTTCCGT
*
21005759 CTTTCAA
1 TTTTCAA
21005766 AAAAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCCGT
Found at i:21005904 original size:76 final size:76
Alignment explanation
Indices: 21005745--21006462 Score: 342
Period size: 74 Copynumber: 9.1 Consensus size: 76
21005735 CAATTTCCGT
* *
21005745 TTTTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
1 TTTTCAATTTCTGTCTGTC-AAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGA
*
21005810 CACGCTGAGGTA
65 CACGCCGAGGTA
* * *
21005822 ATTTCAATTTCTGT-TGTC-AAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG--
21005885 ACACGCCGAGGTA
64 ACACGCCGAGGTA
* * * *
21005898 TTTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
1 TTTTCAATTTCTGTCTGTCAA------------AAAAAATCAACTCATATTGCGAGAGGCGAGTT
*
21005963 GAGCCTCAGGACACGCTGAGGTA
54 GAGCCTCAGGACACGCCGAGGTA
* * * * *
21005986 ATTTCAATTTCTGT-TGTC-AAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG--G
*
21006049 ACACGTCGAGGTA
64 ACACGCCGAGGTA
* *** * * * * *
21006062 TTTTCAATTTCCATTTTTCAATTTCTGCCTTTCAAAAAA-AAAATCA-ACT-C-ATATTGCGAGA
1 TTTTC-A-----A--TTTC--TGTCTG--TCAAAAAAAATCAACTCATATTGCGAGA--G-G-C-
* *
21006123 GGTGAGTTGAGCCTCGGGACACGCTGAGGTA
49 ---GAGTTGAGCCTCAGGACACGCCGAGGTA
* * *** *
21006154 ATTTCAATTTCTGT-T-TC---AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
**
21006214 ACGTTGAGGTA
66 ACGCCGAGGTA
* * * * * *
21006225 TTTTCAATTTCTGT-TTTC--AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCT
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-A
* *
21006286 CATGCGCTGAGCTA
65 CA--CGCCGAGGTA
* * * *
21006300 TTTTCAATTTCTATCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCA-GAT
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGA-
*
21006363 CACACACAGAGGTA
65 CACGC-C-GAGGTA
* * * * * * * *
21006377 TTTTTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGG
1 --TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG
* *
21006441 TTACATGTCGAGGTA
64 --ACACGCCGAGGTA
21006456 TTTTCAA
1 TTTTCAA
21006463 AATCTATTTT
Statistics
Matches: 502, Mismatches: 79, Indels: 120
0.72 0.11 0.17
Matches are distributed among these distances:
71 39 0.08
72 3 0.01
73 34 0.07
74 79 0.16
75 27 0.05
76 51 0.10
77 69 0.14
78 3 0.01
79 62 0.12
80 2 0.00
81 3 0.01
82 4 0.01
84 8 0.02
86 6 0.01
87 6 0.01
88 27 0.05
89 6 0.01
90 44 0.09
91 1 0.00
92 15 0.03
94 13 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (76 bp):
TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
ACGCCGAGGTA
Found at i:21006017 original size:164 final size:165
Alignment explanation
Indices: 21005584--21006241 Score: 933
Period size: 164 Copynumber: 4.0 Consensus size: 165
21005574 GCTGAGGTAA
* * * *
21005584 TTTCAATTTCTG--TTGTCAAAAAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCA
1 TTTCAATTTCTGCCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* *** *
21005647 CGCTGAGGTATTTTCAATTT-T-TATGT-TTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAG
65 CGCTGAGGTAATTTCAATTTCTGT-TGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAG
21005709 CCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
129 CCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
*
21005746 TTTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 TTTCAATTTCTGCCTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
* *
21005811 ACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAG
64 ACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAG
21005876 CCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
129 CCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
*
21005913 TTTCAATTTTTGCCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
21005977 GCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCC
66 GCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCC
* * *
21006042 TCAGATCACACGTCGAGGTATTTTCAATTTCCATT
131 TCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
*
21006077 TTTCAATTTCTGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
1 TTTCAATTTCTGCCTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* ***
21006142 CACGCTGAGGTAATTTCAATTTCTGTT-TC--AAAATTCAACTCATATTGCGAGAAATGAGTTGA
63 CACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGA
* ** *
21006204 GCCTCAAG--ACACGTTGAGGTATTTTCAATTTCTGTT
128 GCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
21006240 TT
1 TT
21006242 CAAAAAATCA
Statistics
Matches: 455, Mismatches: 30, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
162 12 0.03
163 29 0.06
164 159 0.35
165 96 0.21
166 4 0.01
167 86 0.19
168 69 0.15
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (165 bp):
TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCC
TCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
Found at i:21006402 original size:79 final size:77
Alignment explanation
Indices: 21006098--21006603 Score: 422
Period size: 79 Copynumber: 6.5 Consensus size: 77
21006088 GCCTTTCAAA
** *
21006098 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
21006161 TTTC--TGTTTC
66 TTTCTATTTTTC
* ** * *
21006171 --AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
21006232 TTTCT-GTTTTC
66 TTTCTATTTTTC
* * ** * ** *
21006243 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
21006307 TTTCTATCTTTC
66 TTTCTATTTTTC
* * *
21006319 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACAGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC
*
21006384 AATTTATATTTTTC
64 AATTTCTATTTTTC
* * * * * *
21006398 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA
**
21006462 AAATCTATTTTTC
65 ATTTCTATTTTTC
* ** * **
21006475 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
* *
21006540 GCTATTTTCAATTTCTGTTTTTTTTC
55 GGTATTTTCAATTTC---TATTTTTC
21006566 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
21006604 TTTTTAATTT
Statistics
Matches: 348, Mismatches: 58, Indels: 46
0.77 0.13 0.10
Matches are distributed among these distances:
71 58 0.17
72 4 0.01
73 32 0.09
75 21 0.06
76 4 0.01
77 62 0.18
78 2 0.01
79 65 0.19
80 5 0.01
81 29 0.08
88 56 0.16
89 1 0.00
90 2 0.01
91 7 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (77 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
TTTCTATTTTTC
Found at i:21006621 original size:30 final size:30
Alignment explanation
Indices: 21006585--21006646 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
21006575 CAACTCATAT
21006585 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
21006615 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
21006645 TG
1 TG
21006647 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:21006747 original size:253 final size:247
Alignment explanation
Indices: 21006237--21006814 Score: 740
Period size: 253 Copynumber: 2.3 Consensus size: 247
21006227 TTCAATTTCT
* * *
21006237 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
* *
21006302 TTCAATTTC---TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
66 TTCAATTTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
*
21006364 ACACACAGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAG
131 ACACACAGAGGTATTTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAG
* ** * * * **
21006429 TTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTATTTTTCAAATTCT
195 TTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
* *
21006482 GTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
*
21006546 TTCAATTTCTGTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-
66 TTCAATTTCTGTTTTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCAG
** * * * * * * * *
21006610 ATTTCTGC-GAGAGTTGAGTTGAGTCTTTTAATTTCTGTTTTTC-AAAAATTAACTCATATTGCG
128 ATCAC-ACACAGAGGT-A-TT---T-TTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCG
* *
21006673 AGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA
186 AGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
21006735 G-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
21006799 TTCAATTTCTGTTTTT
66 TTCAATTTCTGTTTTT
21006815 AATGTCTGTT
Statistics
Matches: 288, Mismatches: 31, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
244 62 0.22
245 6 0.02
247 13 0.05
248 30 0.10
249 8 0.03
250 5 0.02
251 2 0.01
252 4 0.01
253 142 0.49
254 1 0.00
255 15 0.05
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (247 bp):
GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
TTCAATTTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
ACACACAGAGGTATTTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGT
TGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
Found at i:21007453 original size:17 final size:17
Alignment explanation
Indices: 21007431--21007520 Score: 68
Period size: 17 Copynumber: 5.7 Consensus size: 17
21007421 CATTAAGCCC
21007431 CCCAAAAAAAAACCTAA
1 CCCAAAAAAAAACCTAA
*
21007448 CCCAAAAAAAAAAC-AA
1 CCCAAAAAAAAACCTAA
** **
21007464 -AGAAAAAAAAA-AGAA
1 CCCAAAAAAAAACCTAA
*
21007479 ---AAAGAAAAACCT-A
1 CCCAAAAAAAAACCTAA
*
21007492 CCCCAAAAAAAACCTAA
1 CCCAAAAAAAAACCTAA
21007509 CCCAAAAAAAAA
1 CCCAAAAAAAAA
21007521 AAGAAGAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 9 0.16
15 11 0.19
16 12 0.21
17 25 0.44
ACGTcount: A:0.71, C:0.22, G:0.03, T:0.03
Consensus pattern (17 bp):
CCCAAAAAAAAACCTAA
Found at i:21007486 original size:11 final size:11
Alignment explanation
Indices: 21007454--21007487 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
21007444 CTAACCCAAA
21007454 AAAAAAACAAAG
1 AAAAAAA-AAAG
21007466 AAAAAAAAAAG
1 AAAAAAAAAAG
21007477 AAAAAGAAAAA
1 AAAAA-AAAAA
21007488 CCTACCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:21007502 original size:16 final size:16
Alignment explanation
Indices: 21007483--21007519 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
21007473 AAAGAAAAAG
*
21007483 AAAAACCTACCCCAAA
1 AAAAACCTAACCCAAA
21007499 AAAAACCTAACCCAAA
1 AAAAACCTAACCCAAA
21007515 AAAAA
1 AAAAA
21007520 AAAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.30, G:0.00, T:0.05
Consensus pattern (16 bp):
AAAAACCTAACCCAAA
Found at i:21008359 original size:3 final size:3
Alignment explanation
Indices: 21008314--21008345 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21008304 TTATTGTAGA
21008314 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21008346 CATACTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21008412 original size:27 final size:27
Alignment explanation
Indices: 21008193--21008412 Score: 71
Period size: 27 Copynumber: 8.4 Consensus size: 27
21008183 TATATTAGTG
*
21008193 TATATT-TTATGTACATATGTA-TA-TA
1 TATATTATTATGTACATAT-TATTATTT
*
21008218 TATA-TATT-TGTACATATCATTATTT
1 TATATTATTATGTACATATTATTATTT
* * *
21008243 TATATTATTGTTGTA-A-ATTTTTATGTA
1 TATATTATT-ATGTACATATTATTAT-TT
* * * *
21008270 TATATTTTTTATGTACGTTTCCTAATATTT
1 TATA-TTATTATGTACATAT--TATTATTT
* * *
21008300 TCTTTTA-T-TGTAGATATTATTATTAT
1 TATATTATTATGTACATATTATTATT-T
* * *
21008326 TATTATTATTAT-TA-TTATTACATACTT
1 TA-TATTATTATGTACATATTA-TTATTT
*
21008353 T-TATTA-TATG--CATA-TATATATATG
1 TATATTATTATGTACATATTAT-TAT-TT
21008377 TAT-TT-TTATGTACATATTATTATTT
1 TATATTATTATGTACATATTATTATTT
21008402 TATATTATTAT
1 TATATTATTAT
21008413 TACCAAATAT
Statistics
Matches: 138, Mismatches: 29, Indels: 54
0.62 0.13 0.24
Matches are distributed among these distances:
23 5 0.04
24 25 0.18
25 27 0.20
26 21 0.15
27 34 0.25
28 15 0.11
29 4 0.03
30 3 0.02
31 4 0.03
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (27 bp):
TATATTATTATGTACATATTATTATTT
Found at i:21011362 original size:40 final size:37
Alignment explanation
Indices: 21011300--21011429 Score: 162
Period size: 35 Copynumber: 3.6 Consensus size: 37
21011290 GCAAAGTGTG
**
21011300 AAATGTAGGTATGGTA--TCATCCATACTGAGTTGTG
1 AAATGTAGGTATGGTATTTCATCCATACTGAGTTGAA
21011335 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AA
1 AAATGTAGGTATGGTATT-TC--ATCCATACTGAGTTGAA
* *
21011374 AAATGTAGGTATGGCATTTC--CCATACCGAGTTGAA
1 AAATGTAGGTATGGTATTTCATCCATACTGAGTTGAA
21011409 AAATGTAGGTATGGTATTTCA
1 AAATGTAGGTATGGTATTTCA
21011430 ATGAGGAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
34 11 0.13
35 37 0.45
38 4 0.05
39 17 0.20
40 14 0.17
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (37 bp):
AAATGTAGGTATGGTATTTCATCCATACTGAGTTGAA
Found at i:21018756 original size:35 final size:35
Alignment explanation
Indices: 21018717--21018881 Score: 181
Period size: 35 Copynumber: 4.6 Consensus size: 35
21018707 CCATGGAAAG
21018717 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
* *
21018752 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
21018787 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGT
** * * *
21018827 T-AAAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGT
**
21018861 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
21018882 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
33 1 0.01
34 11 0.10
35 69 0.61
36 2 0.02
38 3 0.03
39 14 0.12
40 13 0.12
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
Found at i:21018869 original size:74 final size:75
Alignment explanation
Indices: 21018721--21018886 Score: 204
Period size: 74 Copynumber: 2.3 Consensus size: 75
21018711 GGAAAGTGTG
** *
21018721 AAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCCATA
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
* **
21018781 CTGAGCTGTG
66 CCGAGCTGAA
21018791 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AAAAATGTAGGTATGGCATT-TCCCAT
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTAT-CCAT
*
21018854 ACCGAGTTGAA
65 ACCGAGCTGAA
21018865 AAATGTAGGTATGGTATT-TCAA
1 AAATGTAGGTATGGTATTATCAA
21018887 TGAGGAAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
70 14 0.17
73 9 0.11
74 46 0.55
75 14 0.17
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
CCGAGCTGAA
Found at i:21023554 original size:25 final size:25
Alignment explanation
Indices: 21023487--21023560 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
21023477 TAAGCTTTTC
21023487 CGAGCTGAATAACG-GGAAGCTCATG
1 CGAGCTGAATAA-GAGGAAGCTCATG
*
21023512 CGAGCTGAATAAGGGGAAGCTCATG
1 CGAGCTGAATAAGAGGAAGCTCATG
* **
21023537 CGAGCTGAGTATTAGGAAGCTCAT
1 CGAGCTGAATAAGAGGAAGCTCAT
21023561 AAGAGCTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 1 0.02
25 43 0.98
ACGTcount: A:0.31, C:0.18, G:0.32, T:0.19
Consensus pattern (25 bp):
CGAGCTGAATAAGAGGAAGCTCATG
Found at i:21024632 original size:13 final size:14
Alignment explanation
Indices: 21024614--21024648 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
21024604 TGTAAATGAT
21024614 AAAATTTCTTA-AC
1 AAAATTTCTTATAC
21024627 AAAATTT-TTATAC
1 AAAATTTCTTATAC
21024640 AAAATTTCT
1 AAAATTTCT
21024649 ATTATACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTTCTTATAC
Found at i:21026373 original size:3 final size:3
Alignment explanation
Indices: 21026365--21026395 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21026355 GAATAAGACT
21026365 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
21026396 ACTCTTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:21034131 original size:18 final size:18
Alignment explanation
Indices: 21034105--21034139 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21034095 AAACTATTTT
21034105 CTTAAAATTAAAATTATA
1 CTTAAAATTAAAATTATA
* *
21034123 CTTATAATTATAATTAT
1 CTTAAAATTAAAATTAT
21034140 TATATTAAAA
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:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTAAAATTAAAATTATA
Found at i:21034863 original size:18 final size:18
Alignment explanation
Indices: 21034842--21034876 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21034832 AAATATATGT
21034842 AAAAAAGAAAAAAAGAAA
1 AAAAAAGAAAAAAAGAAA
*
21034860 AAAAAAGAAAAGAAGAA
1 AAAAAAGAAAAAAAGAA
21034877 TCACAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAGAAA
Found at i:21041114 original size:15 final size:15
Alignment explanation
Indices: 21041094--21041135 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
21041084 TTAATACACG
21041094 TAATATAATTTTATT
1 TAATATAATTTTATT
*
21041109 TAATAT-ATCATTATT
1 TAATATAAT-TTTATT
21041124 TAATATAATTTT
1 TAATATAATTTT
21041136 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATAATTTTATT
Found at i:21041138 original size:13 final size:13
Alignment explanation
Indices: 21041094--21041141 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
21041084 TTAATACACG
21041094 TAATATAATTTTATT
1 TAATATAA-TTT-TT
*
21041109 TAATATATCATTATT
1 TAATATA--ATTTTT
21041124 TAATATAATTTTT
1 TAATATAATTTTT
21041137 TAATA
1 TAATA
21041142 AAAATAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 10 0.34
15 16 0.55
16 2 0.07
17 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATAATTTTT
Found at i:21042697 original size:45 final size:45
Alignment explanation
Indices: 21042647--21042748 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 45
21042637 AACCCCGGTT
* * * * *
21042647 CCACCATTGCCTATGCCTCCCCCTCTGCCGAAACCTCCACCAAGA
1 CCACCATTGCCTATACCTCCCCCCCTGCCAAAACCACCACCAACA
*
21042692 CCACCATTGCCTATACCTCCCCCCCTGCCAAAACCACCACCACCA
1 CCACCATTGCCTATACCTCCCCCCCTGCCAAAACCACCACCAACA
*
21042737 CCACCGTTGCCT
1 CCACCATTGCCT
21042749 GCACATCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.23, C:0.52, G:0.09, T:0.17
Consensus pattern (45 bp):
CCACCATTGCCTATACCTCCCCCCCTGCCAAAACCACCACCAACA
Found at i:21043711 original size:21 final size:21
Alignment explanation
Indices: 21043687--21043726 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21043677 AGATTTCAGC
*
21043687 ATTTATTTATAATTAAATATT
1 ATTTAATTATAATTAAATATT
**
21043708 ATTTAATTATGTTTAAATA
1 ATTTAATTATAATTAAATA
21043727 GAGTTATTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTAATTATAATTAAATATT
Found at i:21046325 original size:5 final size:5
Alignment explanation
Indices: 21046304--21046344 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
21046294 TGTTAAAATA
* *
21046304 TATAT TAAAT TATTAT TATAT TATAG TATAT TATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
21046345 AAATAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:21047681 original size:18 final size:19
Alignment explanation
Indices: 21047660--21047698 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
21047650 ATATATAGAT
21047660 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
21047678 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
21047697 AT
1 AT
21047699 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:21048047 original size:39 final size:39
Alignment explanation
Indices: 21047937--21048071 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
21047927 GACCTCGAGT
* * * *
21047937 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
21047978 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
21048016 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
21048055 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
21048072 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:21048215 original size:18 final size:19
Alignment explanation
Indices: 21048194--21048234 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
21048184 AATGAAATGA
21048194 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
21048212 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
21048231 GAAA
1 GAAA
21048235 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:21053420 original size:22 final size:21
Alignment explanation
Indices: 21053372--21053423 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
21053362 TGCGCTAATA
*
21053372 AACAGAGAGCACTAAAGTGCT
1 AACAGAGAGCACGAAAGTGCT
* *
21053393 ATACAGAGAGCACGAATGTGTT
1 A-ACAGAGAGCACGAAAGTGCT
21053415 CAACAGAGA
1 -AACAGAGA
21053424 ACATTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.15
Consensus pattern (21 bp):
AACAGAGAGCACGAAAGTGCT
Found at i:21066859 original size:20 final size:19
Alignment explanation
Indices: 21066834--21066877 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
21066824 CTTTGATTTT
*
21066834 TATATTTCGGGCTTATATAA
1 TATATTT-GGACTTATATAA
*
21066854 TATA-TTGGACTTATCTAA
1 TATATTTGGACTTATATAA
21066872 TATATT
1 TATATT
21066878 GAGCCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 14 0.67
19 3 0.14
20 4 0.19
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (19 bp):
TATATTTGGACTTATATAA
Found at i:21070802 original size:53 final size:54
Alignment explanation
Indices: 21070730--21070886 Score: 200
Period size: 53 Copynumber: 3.0 Consensus size: 54
21070720 ACAACATATC
* *
21070730 ATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAA-TCACATTATCACATT
1 ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAAGTCACATTATCACATT
21070783 ATACCGATGCCATAGCCCAGCTATGGTCTTATAC-GAAGTCACATTATCACATT
1 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAGTCACATTATCACATT
** * *
21070836 GCACCGATGCCATAGCTCAGCTATGGTCTTAAACGG--G-CACACTTATCACAT
1 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAGTCACA-TTATCACAT
21070887 ATTTTTCGTC
Statistics
Matches: 94, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
51 4 0.04
52 14 0.15
53 75 0.80
54 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (54 bp):
ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAGTCACATTATCACATT
Found at i:21073733 original size:39 final size:40
Alignment explanation
Indices: 21073690--21073801 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 40
21073680 TCGGATAGTT
*
21073690 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** * ** * *
21073729 CGAAGTAA-AGTTGGTACCCAATACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
21073768 CGAAGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATCGA
21073802 CTCGAGGTCG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
38 18 0.33
39 20 0.36
40 1 0.02
41 16 0.29
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Done.