Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 50 of 100
Found at i:12137532 original size:2 final size:2
Alignment explanation
Indices: 12137527--12137556 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12137517 TGTGTGTGTG
12137527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12137557 AACAGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12138098 original size:22 final size:22
Alignment explanation
Indices: 12138050--12138102 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
12138040 CTAAACAAAT
* *
12138050 AAATAAAATAAATATTAGAATT
1 AAATATAATAAATATTAGAATA
12138072 AAATATAATAAATA-TAGAATA
1 AAATATAATAAATATTAGAATA
12138093 ACAATATAAT
1 A-AATATAAT
12138103 TTTAATCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATATAATAAATATTAGAATA
Found at i:12143568 original size:17 final size:17
Alignment explanation
Indices: 12143548--12143586 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12143538 TTATTTTTCC
*
12143548 TTAAAAATTATATTTTT
1 TTAAAAATTATACTTTT
*
12143565 TTAAAAATTATCCTTTT
1 TTAAAAATTATACTTTT
12143582 TTAAA
1 TTAAA
12143587 GACATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAAATTATACTTTT
Found at i:12144700 original size:16 final size:17
Alignment explanation
Indices: 12144639--12144700 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
12144629 AAAGATAAAG
12144639 AATAGGATAAATAAAAT
1 AATAGGATAAATAAAAT
*
12144656 AA-AAGATAAATAAAGAT
1 AATAGGATAAATAAA-AT
*
12144673 AAATAGG-CAAAT-AAAT
1 -AATAGGATAAATAAAAT
12144689 AATAGGATAAAT
1 AATAGGATAAAT
12144701 TAAGGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.16
16 17 0.46
17 6 0.16
18 6 0.16
19 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.21
Consensus pattern (17 bp):
AATAGGATAAATAAAAT
Found at i:12147261 original size:30 final size:31
Alignment explanation
Indices: 12147227--12147284 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
12147217 AACTTGTTGA
*
12147227 AAAATT-AAACTTTGCCTAAAAACTCATTGG
1 AAAATTCAAACTTTGCCGAAAAACTCATTGG
* *
12147257 AAAATTCAACCTTTGTCGAAAAACTCAT
1 AAAATTCAAACTTTGCCGAAAAACTCAT
12147285 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (31 bp):
AAAATTCAAACTTTGCCGAAAAACTCATTGG
Found at i:12147834 original size:26 final size:25
Alignment explanation
Indices: 12147805--12147861 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
12147795 ATGGATAATC
*
12147805 AAATAATTAAA-GATAAAGAATAGGAT
1 AAATAAATAAATGATAAAGAA-A-GAT
*
12147831 AAATAAAATAAATGATAAATAAAGAT
1 AAAT-AAATAAATGATAAAGAAAGAT
12147857 AAATA
1 AAATA
12147862 GGGAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 1 0.04
26 11 0.41
27 7 0.26
28 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.23
Consensus pattern (25 bp):
AAATAAATAAATGATAAAGAAAGAT
Found at i:12147847 original size:16 final size:17
Alignment explanation
Indices: 12147828--12147860 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12147818 TAAAGAATAG
12147828 GATAAATAAA-ATAAAT
1 GATAAATAAAGATAAAT
12147844 GATAAATAAAGATAAAT
1 GATAAATAAAGATAAAT
12147861 AGGGAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
GATAAATAAAGATAAAT
Found at i:12147852 original size:11 final size:10
Alignment explanation
Indices: 12147807--12147893 Score: 56
Period size: 12 Copynumber: 8.5 Consensus size: 10
12147797 GGATAATCAA
*
12147807 ATAATTAAAG
1 ATAAATAAAG
*
12147817 ATAAAGAATAGG
1 ATAAATAA-A-G
12147829 ATAAATAAA-
1 ATAAATAAAG
12147838 ATAAAT---G
1 ATAAATAAAG
12147845 ATAAATAAAG
1 ATAAATAAAG
*
12147855 ATAAATAGGGAG
1 ATAAATA--AAG
12147867 ATAAATAATAGG
1 ATAAATAA-A-G
*
12147879 ATAAATTAAG
1 ATAAATAAAG
12147889 ATAAA
1 ATAAA
12147894 AAAAATAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
7 6 0.10
9 6 0.10
10 20 0.33
11 4 0.07
12 25 0.41
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:12150040 original size:15 final size:15
Alignment explanation
Indices: 12150022--12150070 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
12150012 TTTGGAACCC
12150022 TTTTTTTGTTCTTGT
1 TTTTTTTGTTCTTGT
* *
12150037 TTTTCTTGTTCTTAT
1 TTTTTTTGTTCTTGT
12150052 TCTTATTCTTGTTCTTGT
1 T-TT-TT-TTGTTCTTGT
12150070 T
1 T
12150071 CTTATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 14 0.52
16 2 0.07
17 1 0.04
18 10 0.37
ACGTcount: A:0.04, C:0.12, G:0.10, T:0.73
Consensus pattern (15 bp):
TTTTTTTGTTCTTGT
Found at i:12150048 original size:6 final size:6
Alignment explanation
Indices: 12150027--12150073 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
12150017 AACCCTTTTT
* *
12150027 TTGTTC TTG-T- TT-TTC TTGTTC TTATTC TTATTC TTGTTC TTGTTC
1 TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC
12150072 TT
1 TT
12150074 ATTATTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 3 0.08
5 3 0.08
6 30 0.83
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.70
Consensus pattern (6 bp):
TTGTTC
Found at i:12150062 original size:18 final size:18
Alignment explanation
Indices: 12150039--12150096 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
12150029 GTTCTTGTTT
12150039 TTCTTGTTCTTATTCTTA
1 TTCTTGTTCTTATTCTTA
*
12150057 TTCTTGTTCTTGTTCTTA
1 TTCTTGTTCTTATTCTTA
* *
12150075 TTATT-TTCCTTATTCTGA
1 TTCTTGTT-CTTATTCTTA
12150093 TTCT
1 TTCT
12150097 CCTTTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 2 0.06
18 32 0.94
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.66
Consensus pattern (18 bp):
TTCTTGTTCTTATTCTTA
Found at i:12150114 original size:9 final size:9
Alignment explanation
Indices: 12150098--12150166 Score: 102
Period size: 9 Copynumber: 7.4 Consensus size: 9
12150088 TCTGATTCTC
12150098 CTTTTTTTT
1 CTTTTTTTT
12150107 CCTTTTTTTT
1 -CTTTTTTTT
12150117 CTTTTTTTT
1 CTTTTTTTT
12150126 CTTTTTTTT
1 CTTTTTTTT
12150135 CTTTTTTTTT
1 C-TTTTTTTT
* *
12150145 CTTCTTATT
1 CTTTTTTTT
12150154 CTTTTTTTT
1 CTTTTTTTT
12150163 CTTT
1 CTTT
12150167 AATTGAAACC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
9 36 0.67
10 18 0.33
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:12150122 original size:19 final size:19
Alignment explanation
Indices: 12150098--12150163 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
12150088 TCTGATTCTC
12150098 CTTTTTTTTCCTTTTTTTT
1 CTTTTTTTTCCTTTTTTTT
12150117 CTTTTTTTT-CTTTTTTTT
1 CTTTTTTTTCCTTTTTTTT
* * *
12150135 CTTTTTTTTTCTTCTTATT
1 CTTTTTTTTCCTTTTTTTT
12150154 CTTTTTTTTC
1 CTTTTTTTTC
12150164 TTTAATTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 18 0.42
19 25 0.58
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTTTTCCTTTTTTTT
Found at i:12150164 original size:28 final size:28
Alignment explanation
Indices: 12150098--12150166 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
12150088 TCTGATTCTC
* * *
12150098 CTTTTTTTTCCTTTTTTTTCTTTTTTTT
1 CTTTTTTTTCTTTTTTTTTCTTCTTATT
12150126 CTTTTTTTTCTTTTTTTTTCTTCTTATT
1 CTTTTTTTTCTTTTTTTTTCTTCTTATT
12150154 CTTTTTTTTCTTT
1 CTTTTTTTTCTTT
12150167 AATTGAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (28 bp):
CTTTTTTTTCTTTTTTTTTCTTCTTATT
Found at i:12153429 original size:3 final size:3
Alignment explanation
Indices: 12153421--12153465 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12153411 CATAATCAAG
12153421 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12153466 AAGTATAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12154311 original size:29 final size:29
Alignment explanation
Indices: 12154268--12154326 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
12154258 TGCATACTTA
12154268 ATAAGTTTCAGCTAAGATTCAATTCCAAG
1 ATAAGTTTCAGCTAAGATTCAATTCCAAG
12154297 ATAAGTTTC-GACTAAGATTCAATTCCAAG
1 ATAAGTTTCAG-CTAAGATTCAATTCCAAG
12154326 A
1 A
12154327 CCATGTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (29 bp):
ATAAGTTTCAGCTAAGATTCAATTCCAAG
Found at i:12156662 original size:49 final size:49
Alignment explanation
Indices: 12156599--12156696 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
12156589 AATGTTTCAG
*
12156599 TATACCACATCTTAGCTACATGACAACATTTATAAACATCAGATTTATA
1 TATACCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATA
* * *
12156648 TATACCATACCTTAGCTGCATGACAACATTTATAAACGTCAGATTTATA
1 TATACCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATA
12156697 CTAGATCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (49 bp):
TATACCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATA
Found at i:12159793 original size:16 final size:17
Alignment explanation
Indices: 12159766--12159799 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12159756 GAGAATTAAA
12159766 AATTTAAAATATAATTT
1 AATTTAAAATATAATTT
*
12159783 AATTT-AAATATATTTT
1 AATTTAAAATATAATTT
12159799 A
1 A
12159800 TTAGTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAAATATAATTT
Found at i:12162109 original size:13 final size:13
Alignment explanation
Indices: 12162091--12162125 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
12162081 TAAGGAATCC
12162091 AAAAAAAATTAAA
1 AAAAAAAATTAAA
* *
12162104 AAAAAAAAGTATA
1 AAAAAAAATTAAA
12162117 AAAAAAAAT
1 AAAAAAAAT
12162126 GCTTACCCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTAAA
Found at i:12162111 original size:15 final size:15
Alignment explanation
Indices: 12162091--12162124 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12162081 TAAGGAATCC
12162091 AAAAAAAAT-TAAAA
1 AAAAAAAATATAAAA
*
12162105 AAAAAAAGTATAAAA
1 AAAAAAAATATAAAA
12162120 AAAAA
1 AAAAA
12162125 TGCTTACCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAAAAAATATAAAA
Found at i:12168583 original size:12 final size:12
Alignment explanation
Indices: 12168566--12168611 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
12168556 TCGTTTAGAA
12168566 ACACCATTCAGC
1 ACACCATTCAGC
*
12168578 ACACCATTCAAC
1 ACACCATTCAGC
*
12168590 ATACCATTCAGC
1 ACACCATTCAGC
12168602 ACACCATTCA
1 ACACCATTCA
12168612 ACAATATGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.37, C:0.39, G:0.04, T:0.20
Consensus pattern (12 bp):
ACACCATTCAGC
Found at i:12168595 original size:24 final size:24
Alignment explanation
Indices: 12168568--12168614 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12168558 GTTTAGAAAC
12168568 ACCATTCAGCACACCATTCAACAT
1 ACCATTCAGCACACCATTCAACAT
12168592 ACCATTCAGCACACCATTCAACA
1 ACCATTCAGCACACCATTCAACA
12168615 ATATGCTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.38, G:0.04, T:0.19
Consensus pattern (24 bp):
ACCATTCAGCACACCATTCAACAT
Found at i:12169973 original size:221 final size:221
Alignment explanation
Indices: 12169590--12170000 Score: 565
Period size: 221 Copynumber: 1.9 Consensus size: 221
12169580 TTATGTGGCA
* ** **** ***
12169590 GTATATTGAAGGTATTTTACAGTAGAAGATGCCTTTAATAATTTTTAAAATTTTTTGAGAAAAAA
1 GTATATTAAAGGTATTTTACAGTAGAAGACACCTTTAATAATGCCCAAAATTTTAAAAGAAAAAA
* *
12169655 TATTGAAGGCAGCTATTATTAACAAATACATTCAGTAATGGATTACTAAGTTTAAAGGTGTATTG
66 TATTGAAGGCAGCTATTATTAACAAATACATTCAGTAATGGATTACTAAGTTTAAAGGTATATTA
** *
12169720 AAGATGCTTTTTCAAACAAACACCTTCTATAACCATCGTGGTATATTAAAGGCATTTTATAATAA
131 AAGACACTTTTTCAAACAAACACCTTCTATAACCATCGTAGTATATTAAAGGCATTTTATAATAA
12169785 AAGATGCATTTAACAATTTCATCGTG
196 AAGATGCATTTAACAATTTCATCGTG
12169811 GTATATTAAAGGTATTTTACAGTAGAAGACACCTTTAATAATGCCCAAAATTTTAAAAGAAAAAA
1 GTATATTAAAGGTATTTTACAGTAGAAGACACCTTTAATAATGCCCAAAATTTTAAAAGAAAAAA
* * * * * *
12169876 TATTGAAGGC-GTCTGTTATTAACAAATGCCTTCTGTAATGGATTACTAAGTTTAAGGGTATGTT
66 TATTGAAGGCAG-CTATTATTAACAAATACATTCAGTAATGGATTACTAAGTTTAAAGGTATATT
* * * *
12169940 AAAGGCACATTTTT-TAATAAACACCTTCTATAACCATCGTAGTATATTGAAGGCATTTTAT
130 AAAGACAC-TTTTTCAAACAAACACCTTCTATAACCATCGTAGTATATTAAAGGCATTTTAT
12170001 TGTAGAAGAC
Statistics
Matches: 163, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
220 1 0.01
221 157 0.96
222 5 0.03
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (221 bp):
GTATATTAAAGGTATTTTACAGTAGAAGACACCTTTAATAATGCCCAAAATTTTAAAAGAAAAAA
TATTGAAGGCAGCTATTATTAACAAATACATTCAGTAATGGATTACTAAGTTTAAAGGTATATTA
AAGACACTTTTTCAAACAAACACCTTCTATAACCATCGTAGTATATTAAAGGCATTTTATAATAA
AAGATGCATTTAACAATTTCATCGTG
Found at i:12171088 original size:29 final size:29
Alignment explanation
Indices: 12171046--12171105 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12171036 GTGTAAGTAC
12171046 TGATCTTGTTATTGTCTATGATAATTCTA
1 TGATCTTGTTATTGTCTATGATAATTCTA
12171075 TGATCTTGTTATTGTCTATGATAATTCTA
1 TGATCTTGTTATTGTCTATGATAATTCTA
12171104 TG
1 TG
12171106 GATTACTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (29 bp):
TGATCTTGTTATTGTCTATGATAATTCTA
Found at i:12175861 original size:15 final size:15
Alignment explanation
Indices: 12175841--12175887 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
12175831 ATACTCATTC
12175841 TGTCCAATTTTTTTT
1 TGTCCAATTTTTTTT
12175856 TGTCCAATTTTTTTT
1 TGTCCAATTTTTTTT
* *
12175871 GGTTCAATTTTTCTTT
1 TGTCCAATTTTT-TTT
12175887 T
1 T
12175888 TAGGATGTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 25 0.89
16 3 0.11
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.66
Consensus pattern (15 bp):
TGTCCAATTTTTTTT
Found at i:12176036 original size:21 final size:21
Alignment explanation
Indices: 12175969--12176037 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
12175959 TATGATTTTT
12175969 TTAATTTTTAATATTAAAAATCA
1 TTAA-TTTTAATATTAAAAA-CA
* * *
12175992 TGAAACTTTAAT-TTAAAAAAA
1 T-TAATTTTAATATTAAAAACA
*
12176013 TTAATTTTAATATTAAATACA
1 TTAATTTTAATATTAAAAACA
12176034 TTAA
1 TTAA
12176038 AGTCAAAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 8 0.22
21 13 0.35
22 7 0.19
23 7 0.19
24 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (21 bp):
TTAATTTTAATATTAAAAACA
Found at i:12177170 original size:16 final size:16
Alignment explanation
Indices: 12177140--12177212 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
12177130 TCTTTTGTAT
*
12177140 TTTATGTATTGTATTA
1 TTTATGTATTTTATTA
12177156 TTTAT-TATTATTATTA
1 TTTATGTATT-TTATTA
* * *
12177172 TGTAT-TAATTTATTT
1 TTTATGTATTTTATTA
*
12177187 TTTGTGTATTTTATTA
1 TTTATGTATTTTATTA
12177203 TTTATGTATT
1 TTTATGTATT
12177213 ATTACTAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.26
16 34 0.74
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (16 bp):
TTTATGTATTTTATTA
Found at i:12177672 original size:25 final size:25
Alignment explanation
Indices: 12177643--12177695 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
12177633 GGGAGTGAGA
* *
12177643 AAAAAT-TTTTTAGAAATTTTTGGCG
1 AAAAATATTTCTAGAAATTTCTGG-G
*
12177668 AAAAATATTTCTGGAAATTTCTGGG
1 AAAAATATTTCTAGAAATTTCTGGG
12177693 AAA
1 AAA
12177696 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (25 bp):
AAAAATATTTCTAGAAATTTCTGGG
Found at i:12178308 original size:25 final size:25
Alignment explanation
Indices: 12178244--12178327 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 25
12178234 TTATTGTTTA
* *
12178244 TTTATTTATTTTTATATTAGGTTTATT
1 TTTATTT-TTTTTA-CTTAGCTTTATT
*
12178271 TAATAGTTCTTTTTTATCTTAGCTTTATT
1 T-TTA-TT-TTTTTTA-CTTAGCTTTATT
**
12178300 TTTATTTTTTTTACTTTTCTTTATT
1 TTTATTTTTTTTACTTAGCTTTATT
12178325 TTT
1 TTT
12178328 TATTATTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 13 0.27
26 7 0.15
27 3 0.06
28 4 0.08
29 20 0.42
30 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (25 bp):
TTTATTTTTTTTACTTAGCTTTATT
Found at i:12178317 original size:10 final size:9
Alignment explanation
Indices: 12178298--12178353 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
12178288 CTTAGCTTTA
12178298 TTTTTATTT
1 TTTTTATTT
12178307 TTTTTACTTT
1 TTTTTA-TTT
*
12178317 TCTTTATTT
1 TTTTTATTT
12178326 TTTATTATTT
1 TTT-TTATTT
* *
12178336 ATTATATTT
1 TTTTTATTT
12178345 TTTATTATT
1 TTT-TTATT
12178354 GCTTTTGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 18 0.47
10 20 0.53
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTATTT
Found at i:12178343 original size:19 final size:18
Alignment explanation
Indices: 12178295--12178353 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
12178285 TATCTTAGCT
*
12178295 TTATTTTTATTTTTTTTA
1 TTATTTTTATATTTTTTA
*
12178313 CTT-TTCTT-TATTTTTTA
1 -TTATTTTTATATTTTTTA
12178330 TTATTTATTATATTTTTTA
1 TTATTT-TTATATTTTTTA
12178349 TTATT
1 TTATT
12178354 GCTTTTGCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 6 0.18
19 16 0.47
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTTTTATATTTTTTA
Found at i:12178513 original size:60 final size:60
Alignment explanation
Indices: 12178369--12178729 Score: 523
Period size: 60 Copynumber: 6.0 Consensus size: 60
12178359 TGCTTTCAAA
*
12178369 TAAAAATCAAAATTTTCCAAAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCCATTTTCCT
1 TAAAAATC-AAATTTT-C--AAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* * *
12178433 T-AAGATCAAAGTTTCAAAAAAAATAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
12178492 TAAAAAT-AAATTTTCAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAATTTTC-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
12178552 TAAAAATCAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * *
12178612 TGAAAATCAAAATTTCAAAAAAATTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* **
12178672 TAGAAAT-AAATTTTCAAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATCAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
12178730 CTACAAAAAA
Statistics
Matches: 272, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
59 94 0.35
60 158 0.58
61 8 0.03
62 6 0.02
63 5 0.02
64 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (60 bp):
TAAAAATCAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:12183874 original size:18 final size:19
Alignment explanation
Indices: 12183853--12183893 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
12183843 ATTTTTCCTT
12183853 AAAAATTAT-ATTTTTTTA
1 AAAAATTATCATTTTTTTA
*
12183871 AAAAATTATCCCTTTTTTTA
1 AAAAATTAT-CATTTTTTTA
12183891 AAA
1 AAA
12183894 GACATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAAATTATCATTTTTTTA
Found at i:12185007 original size:16 final size:17
Alignment explanation
Indices: 12184946--12185007 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
12184936 AAAGATAAAG
12184946 AATAGGATAAATAAAAT
1 AATAGGATAAATAAAAT
*
12184963 AA-AAGATAAATAAAGAT
1 AATAGGATAAATAAA-AT
*
12184980 AAATAGG-CAAAT-AAAT
1 -AATAGGATAAATAAAAT
12184996 AATAGGATAAAT
1 AATAGGATAAAT
12185008 TAAGGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.16
16 17 0.46
17 6 0.16
18 6 0.16
19 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.21
Consensus pattern (17 bp):
AATAGGATAAATAAAAT
Found at i:12187415 original size:23 final size:23
Alignment explanation
Indices: 12187372--12187416 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12187362 AATTTTTTTT
*
12187372 TCTTTCAGACTTTCTTTTCCCTC
1 TCTTTCAGACTTTCTTCTCCCTC
*
12187395 TCTTTCGAGA-TTTGTTCTCCCT
1 TCTTTC-AGACTTTCTTCTCCCT
12187417 TGTTTCTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.09, C:0.31, G:0.09, T:0.51
Consensus pattern (23 bp):
TCTTTCAGACTTTCTTCTCCCTC
Found at i:12188121 original size:26 final size:25
Alignment explanation
Indices: 12188090--12188146 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
12188080 AAGGATAATC
*
12188090 AAATAATTAAA-GATAAAGAATAGGAT
1 AAATAAATAAATGATAAAGAA-A-GAT
*
12188116 AAATAAAATAAATGATAAATAAAGAT
1 AAAT-AAATAAATGATAAAGAAAGAT
12188142 AAATA
1 AAATA
12188147 GGGAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 1 0.04
26 11 0.41
27 7 0.26
28 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.23
Consensus pattern (25 bp):
AAATAAATAAATGATAAAGAAAGAT
Found at i:12188132 original size:16 final size:17
Alignment explanation
Indices: 12188113--12188145 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12188103 TAAAGAATAG
12188113 GATAAATAAA-ATAAAT
1 GATAAATAAAGATAAAT
12188129 GATAAATAAAGATAAAT
1 GATAAATAAAGATAAAT
12188146 AGGGAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
GATAAATAAAGATAAAT
Found at i:12188137 original size:11 final size:10
Alignment explanation
Indices: 12188092--12188178 Score: 56
Period size: 12 Copynumber: 8.5 Consensus size: 10
12188082 GGATAATCAA
*
12188092 ATAATTAAAG
1 ATAAATAAAG
*
12188102 ATAAAGAATAGG
1 ATAAATAA-A-G
12188114 ATAAATAAA-
1 ATAAATAAAG
12188123 ATAAAT---G
1 ATAAATAAAG
12188130 ATAAATAAAG
1 ATAAATAAAG
*
12188140 ATAAATAGGGAG
1 ATAAATA--AAG
12188152 ATAAATAATAGG
1 ATAAATAA-A-G
*
12188164 ATAAATTAAG
1 ATAAATAAAG
12188174 ATAAA
1 ATAAA
12188179 AAAAAAATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
7 6 0.10
9 6 0.10
10 20 0.33
11 4 0.07
12 25 0.41
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:12189095 original size:20 final size:20
Alignment explanation
Indices: 12189070--12189108 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12189060 ACAAGTGATG
*
12189070 CAAATATAAATTAAAAGATA
1 CAAATACAAATTAAAAGATA
*
12189090 CAAATACAAATTTAAAGAT
1 CAAATACAAATTAAAAGAT
12189109 GCAATGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (20 bp):
CAAATACAAATTAAAAGATA
Found at i:12194469 original size:16 final size:16
Alignment explanation
Indices: 12194450--12194503 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
12194440 TTTTCACATT
12194450 GCCATTTTTTGCTTTA
1 GCCATTTTTTGCTTTA
**
12194466 GCCA-TTTGAGCTTT-
1 GCCATTTTTTGCTTTA
*
12194480 --TATTTTTTGCTTTA
1 GCCATTTTTTGCTTTA
12194494 GCCATTTTTT
1 GCCATTTTTT
12194504 TCACATAGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
12 1 0.04
13 8 0.29
15 8 0.29
16 11 0.39
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (16 bp):
GCCATTTTTTGCTTTA
Found at i:12195764 original size:49 final size:49
Alignment explanation
Indices: 12195692--12195785 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
12195682 TTTCAGTATC
12195692 CCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATATATA
1 CCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATATATA
* * *
12195741 CCACACCTTAGTTGCATGACAACATTTATAAACGTCAGATTTATA
1 CCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATA
12195786 CTAGATCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (49 bp):
CCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATATATA
Found at i:12200556 original size:60 final size:61
Alignment explanation
Indices: 12200487--12200764 Score: 240
Period size: 60 Copynumber: 4.4 Consensus size: 61
12200477 TATTTTACGA
* *
12200487 AAAAGTTGAAAGTATCAATTTTTCACGAAAATAAAAATTTC-AAAAATCATATTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTTCTCGAAAATAAAAATTTCAAAAAATGATATTTTTGAGG
* * * * *
12200547 AAAAGTTGAAAATATCAATTTTCCT-TAAAA-AATCAATTTTCTTTGAAAATAAAAATTTTAAAA
1 AAAAGTTGAAAGTATCAATTTTTCTCGAAAATAA--AAATTTC-------A-AAAAA---T--GA
* *
12200610 AATATTTTAAGG
51 TAT-TTTTGAGG
* ** * *
12200622 AAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAAATTTTCAAAAAA-GATATTTTTGAAG
1 AAAAGTTGAAAGTATCAATTTTTCTCGAAAATAAAAATTTCAAAAAATGATATTTTTGAGG
* *
12200682 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATGGTATTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTTCTCGAAAATAAAAATTTCAAAAAATGATATTTTTGAGG
12200743 AAAAGTTGAAAGTATCAATTTT
1 AAAAGTTGAAAGTATCAATTTT
12200765 CCTTATTTAA
Statistics
Matches: 177, Mismatches: 21, Indels: 39
0.75 0.09 0.16
Matches are distributed among these distances:
58 2 0.01
59 4 0.02
60 78 0.44
61 36 0.20
67 5 0.03
68 1 0.01
69 5 0.03
72 1 0.01
74 3 0.02
75 36 0.20
76 4 0.02
77 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (61 bp):
AAAAGTTGAAAGTATCAATTTTTCTCGAAAATAAAAATTTCAAAAAATGATATTTTTGAGG
Found at i:12200595 original size:18 final size:19
Alignment explanation
Indices: 12200552--12200597 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
12200542 TGAGGAAAAG
12200552 TTGAAAATATCAATTTTCC
1 TTGAAAATATCAATTTTCC
* *
12200571 TT-AAAAAATCAATTTTCT
1 TTGAAAATATCAATTTTCC
12200589 TTGAAAATA
1 TTGAAAATA
12200598 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (19 bp):
TTGAAAATATCAATTTTCC
Found at i:12200612 original size:135 final size:136
Alignment explanation
Indices: 12200456--12200712 Score: 372
Period size: 135 Copynumber: 1.9 Consensus size: 136
12200446 ACCAAAAAAT
* * * *
12200456 AAAAGTAAAATTTTTCAAAAATATTTTACGAAAAAGTTGAAAGTATCAATTTTTCACGAAAATAA
1 AAAAGTAAAAATTTTAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCACAAAAATAA
* *
12200521 AAATTTCAAAAATCATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAAATCAATTT
66 AAATTTCAAAAAACATATTTTTGAAGAAAAGTTGAAAATATCAATTTTCCTTAAAAAATCAATTT
12200586 TCTTTG
131 TCTTTG
* * **
12200592 AAAA-TAAAAATTTTAAAAAATATTTTAAGGAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAA
1 AAAAGTAAAAATTTTAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCACAAAAATAA
* * * * *
12200656 AATTTTCAAAAAAGATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAA
66 AAATTTCAAAAAACATATTTTTGAAGAAAAGTTGAAAATATCAATTTTCCTTAAAAA
12200713 TAAAAATTTC
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
135 102 0.96
136 4 0.04
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (136 bp):
AAAAGTAAAAATTTTAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCACAAAAATAA
AAATTTCAAAAAACATATTTTTGAAGAAAAGTTGAAAATATCAATTTTCCTTAAAAAATCAATTT
TCTTTG
Found at i:12200660 original size:75 final size:77
Alignment explanation
Indices: 12200513--12200662 Score: 207
Period size: 75 Copynumber: 2.0 Consensus size: 77
12200503 AATTTTTCAC
*
12200513 GAAAATAAAAATTTCAAAAATCATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAA
1 GAAAATAAAAATTTCAAAAA-CATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAA
*
12200578 ATCAATTTTCTTT
65 ATAAATTTTCTTT
* * * *
12200591 GAAAATAAAAATTTTAAAAA-ATA-TTTTAAGGAAAAGTTGAAAGTATTAATTTTTCTT-AAAAA
1 GAAAATAAAAATTTCAAAAACATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAAA
12200653 TAAAATTTTC
66 T-AAATTTTC
12200663 AAAAAAGATA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
74 6 0.09
75 37 0.57
76 3 0.05
78 19 0.29
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (77 bp):
GAAAATAAAAATTTCAAAAACATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAAA
TAAATTTTCTTT
Found at i:12200765 original size:60 final size:59
Alignment explanation
Indices: 12200578--12200764 Score: 263
Period size: 60 Copynumber: 3.2 Consensus size: 59
12200568 TCCTTAAAAA
* *
12200578 ATCAA-TTTTCTTTGAAAATAAAAATTTTAAAAAA-TA-TTTTAAGGAAAAGTTGAAAGT
1 ATCAATTTTTC-TTGAAAATAAAAATTTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGT
* * * *
12200635 ATTAATTTTTCTTAAAAATAAAATTTTCAAAAAAGATATTTTTGAAGAAAAGTTGAAAGT
1 ATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAG-TATTTTTGAGGAAAAGTTGAAAGT
12200695 ATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATGGTATTTTTGAGGAAAAGTTGAAAGT
1 ATCAATTTTTCTTGAAAATAAAAATTTCAAAAAA--GTATTTTTGAGGAAAAGTTGAAAGT
12200756 ATCAATTTT
1 ATCAATTTT
12200765 CCTTATTTAA
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
57 24 0.21
58 5 0.04
59 2 0.02
60 50 0.44
61 32 0.28
62 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (59 bp):
ATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGT
Found at i:12213514 original size:221 final size:221
Alignment explanation
Indices: 12213131--12213529 Score: 554
Period size: 221 Copynumber: 1.8 Consensus size: 221
12213121 TATGTTAAAG
* * ** *
12213131 GTATTTTACAGTAGAAGATACCTTTAATAATTTCCAAAATTTTTTGAAGAAAAATATTGAAGGCG
1 GTATTTTACAGTAGAAGACACCTTTAATAATTCCCAAAATTTTTAAAAGAAAAATATTGAAGGCA
* * *
12213196 TTTATTATTAACAAATGCCTTTAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGATGCCTTT
66 TCTATTATTAACAAATGCCTTTAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGACGCCTTT
**
12213261 TGAAACAAACGTCTTCTATAACCATCGTGGTATATTAAAGGCATTTTATAATAAAAGACGCCTTT
131 TGAAACAAACACCTTCTATAACCATCGTGGTATATTAAAGGCATTTTATAATAAAAGACGCCTTT
12213326 AACAATTTCATCGTGGTATATTGAAA
196 AACAATTTCATCGTGGTATATTGAAA
* *
12213352 GTATTTTACAGTAGAAGACGCCTTTAAT-ATTGCCCAAAA-TTTTAAAAGGGAAAATATTGAAGG
1 GTATTTTACAGTAGAAGACACCTTTAATAATT-CCCAAAATTTTTAAAA-GAAAAATATTGAAGG
* * * *
12213415 TATCTGTTATTAACAAATGCCTTCT-GTAATGGATTACTAAGTTTAAAGGTATGTTAAAGGCGCA
64 CATCTATTATTAACAAATGCCTT-TAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGACGC-
* * * *
12213479 TTTTTG-AATAAACACCTTTTATAACCATCGTGGTATATTGAAGGCATTTTA
127 CTTTTGAAACAAACACCTTCTATAACCATCGTGGTATATTAAAGGCATTTTA
12213530 CTGTAGAAGA
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
220 9 0.06
221 139 0.90
222 6 0.04
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (221 bp):
GTATTTTACAGTAGAAGACACCTTTAATAATTCCCAAAATTTTTAAAAGAAAAATATTGAAGGCA
TCTATTATTAACAAATGCCTTTAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGACGCCTTT
TGAAACAAACACCTTCTATAACCATCGTGGTATATTAAAGGCATTTTATAATAAAAGACGCCTTT
AACAATTTCATCGTGGTATATTGAAA
Found at i:12215510 original size:291 final size:295
Alignment explanation
Indices: 12214942--12215548 Score: 976
Period size: 292 Copynumber: 2.1 Consensus size: 295
12214932 CCACTAGAGT
* * * *
12214942 TTTTTCAACTTCAAAGGCTTCCTAATAGCAACATGATTTCTTTTATAACAGATGACATTGAAGGC
1 TTTTTC-ACTTGAAAGGCTTCCTAATAACAACATGATCTCTTTTATAACAGATAACATTGAAGGC
12215007 ATGTTATGAGATACTTTTAACATTCATAACCAACATTTTCATAATCTTTCTCCTTAAATGAAGGA
65 ATGTTATGAGATACTTTTAACATTCATAACCAACATTTTCATAATCTTTCTCCTTAAATGAAGGA
* *
12215072 TTTAATCAGTCCAATGTTGAAATGCATGAATTTGGTGAACCTGGGATAGGTGTACGTGACCAACA
130 TTTAATCAATCCAATGTTGAAATGCATGAATTTGGTGAACCTGAGATAGGTGTACGTGACCAACA
* *
12215137 ACCTAGAAGAGAAGCATCAAAGTTTTATAAGTTGCTTGAAGAGATGAATGAAGAACTTTTTGAAA
195 ACCTAAAAGAGAAGCATCAAAATTTTATAAGTTGCTTGAAGAGATGAATGAAGAACTTTTTGAAA
12215202 GGATCGAAGCATTCAAGGATT-TC-T-T-TGTTCATC
260 GGATCGAAGCATTCAAGG-TTGTCTTCTGTGTTCATC
*
12215235 TTTTTCACTTGAAAGGCTTCCTAATAACAACATGATCT-TTTTATAACAGATAATATTGAAGGCA
1 TTTTTCACTTGAAAGGCTTCCTAATAACAACATGATCTCTTTTATAACAGATAACATTGAAGGCA
* *
12215299 TGTTATGAGATGCTTTTAACATTCATAACCAACATTTTTATAATCTTTCTCCTTGAAATGAAGGA
66 TGTTATGAGATACTTTTAACATTCATAACCAACATTTTCATAATCTTTCTCCTT-AAATGAAGGA
* *
12215364 TTTAATCAATTCAATGTTGAAATGCATGAATTTGGTGAACTTGAGATAGGTGTACGTGACCAACA
130 TTTAATCAATCCAATGTTGAAATGCATGAATTTGGTGAACCTGAGATAGGTGTACGTGACCAACA
*
12215429 ACCTAAAAGAGAAGCATCAAAATTTTATAAGTTGCTTGAAGAGATGAATGAA-AATTTTTTTG-A
195 ACCTAAAAGAGAAGCATCAAAATTTTATAAGTTGCTTGAAGAGATGAATGAAGAA-CTTTTTGAA
*
12215492 GGGATCGAAGCATTCAAGGTTGTCTTTCTGTGTTCATC
259 AGGATCGAAGCATTCAAGGTTGTC-TTCTGTGTTCATC
*
12215530 TTTTTCACTTGAAATGCTT
1 TTTTTCACTTGAAAGGCTT
12215549 ATGTGGATGG
Statistics
Matches: 291, Mismatches: 16, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
290 2 0.01
291 99 0.34
292 156 0.54
293 7 0.02
294 1 0.00
295 26 0.09
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (295 bp):
TTTTTCACTTGAAAGGCTTCCTAATAACAACATGATCTCTTTTATAACAGATAACATTGAAGGCA
TGTTATGAGATACTTTTAACATTCATAACCAACATTTTCATAATCTTTCTCCTTAAATGAAGGAT
TTAATCAATCCAATGTTGAAATGCATGAATTTGGTGAACCTGAGATAGGTGTACGTGACCAACAA
CCTAAAAGAGAAGCATCAAAATTTTATAAGTTGCTTGAAGAGATGAATGAAGAACTTTTTGAAAG
GATCGAAGCATTCAAGGTTGTCTTCTGTGTTCATC
Found at i:12226187 original size:26 final size:24
Alignment explanation
Indices: 12226156--12226215 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 24
12226146 ATGGATAATC
*
12226156 AAATAATTAAAGATAAAGAATAGGAT
1 AAATAATAAAAGATAAAGAA-A-GAT
*
12226182 AAATAAAATAAAAGATAAATAAAGAT
1 AAAT--AATAAAAGATAAAGAAAGAT
12226208 AAATAATA
1 AAATAATA
12226216 GGATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.13
26 11 0.37
27 1 0.03
28 14 0.47
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (24 bp):
AAATAATAAAAGATAAAGAAAGAT
Found at i:12226188 original size:22 final size:22
Alignment explanation
Indices: 12226158--12226237 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
12226148 GGATAATCAA
* *
12226158 ATAATTAAAGATAAAGAATAGG
1 ATAAATAAAGATAAATAATAGG
12226180 ATAAATAAA-AT--A-AA-A-G
1 ATAAATAAAGATAAATAATAGG
12226196 ATAAATAAAGATAAATAATAGG
1 ATAAATAAAGATAAATAATAGG
* *
12226218 ATAAATTAAGGTAAATAATA
1 ATAAATAAAGATAAATAATA
12226238 ATAATAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
16 10 0.20
17 3 0.06
18 2 0.04
19 2 0.04
20 2 0.04
21 3 0.06
22 27 0.55
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (22 bp):
ATAAATAAAGATAAATAATAGG
Found at i:12226198 original size:16 final size:17
Alignment explanation
Indices: 12226179--12226210 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12226169 TAAAGAATAG
12226179 GATAAATAAA-ATAAAA
1 GATAAATAAAGATAAAA
12226195 GATAAATAAAGATAAA
1 GATAAATAAAGATAAA
12226211 TAATAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (17 bp):
GATAAATAAAGATAAAA
Found at i:12226207 original size:10 final size:10
Alignment explanation
Indices: 12226158--12226235 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
12226148 GGATAATCAA
*
12226158 ATAATTAAAG
1 ATAAATAAAG
*
12226168 ATAAAGAATAGG
1 ATAAATAA-A-G
12226180 ATAAATAAA-
1 ATAAATAAAG
12226189 AT--A-AAAG
1 ATAAATAAAG
12226196 ATAAATAAAG
1 ATAAATAAAG
12226206 ATAAATAATAGG
1 ATAAATAA-A-G
*
12226218 ATAAATTAAG
1 ATAAATAAAG
*
12226228 GTAAATAA
1 ATAAATAA
12226236 TAATAATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
9 3 0.06
10 25 0.46
11 4 0.07
12 16 0.30
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:12226241 original size:38 final size:36
Alignment explanation
Indices: 12226156--12226241 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 36
12226146 ATGGATAATC
12226156 AAATAATTAAAGATAAAGAATAGGATAAATAAAATAA
1 AAATAA-TAAAGATAAAGAATAGGATAAATAAAATAA
* **
12226193 AAGATAAATAAAGATAAATAATAGGATAAATTAAGGTAA
1 AA-AT-AATAAAGATAAAGAATAGGATAAA-TAAAATAA
12226232 ATAATAATAA
1 A-AATAATAA
12226242 TAATAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 2 0.05
38 28 0.67
39 11 0.26
40 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (36 bp):
AAATAATAAAGATAAAGAATAGGATAAATAAAATAA
Found at i:12227681 original size:143 final size:142
Alignment explanation
Indices: 12227505--12227795 Score: 564
Period size: 143 Copynumber: 2.0 Consensus size: 142
12227495 AAGAATTTTT
12227505 AAAATTATTACTTTGGTATTTCACATTTATTATTAATGCATGAAATGCATATATGACAACATGAA
1 AAAATTATTACTTTGGTATTTCACATTTATTATTAATGCATGAAATGCATATATGACAACATGAA
12227570 TATAAATTAAATGGTGCATATAGTTACATTTATTTGTTTTTATCAAATTGATTTTATTTAGGATG
66 TATAAATTAAATGGTGCATATAGTTACATTTATTTGTTTTTATCAAATTGATTTTATTTAGGATG
12227635 AAAATTTTATAA
131 AAAATTTTATAA
12227647 AAAATTATTACTTTTGGTATTTCACATTTATTATTAATGCATGAAATGCATATATGACAACATGA
1 AAAATTATTAC-TTTGGTATTTCACATTTATTATTAATGCATGAAATGCATATATGACAACATGA
12227712 ATATAAATTAAATGGTGCATATAGTTACATTTATTTGTTTTTATCAAATTGATTTTATTTAGGAT
65 ATATAAATTAAATGGTGCATATAGTTACATTTATTTGTTTTTATCAAATTGATTTTATTTAGGAT
*
12227777 GAAAATTTTATCA
130 GAAAATTTTATAA
12227790 AAAATT
1 AAAATT
12227796 CTATACATTG
Statistics
Matches: 147, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
142 11 0.07
143 136 0.93
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (142 bp):
AAAATTATTACTTTGGTATTTCACATTTATTATTAATGCATGAAATGCATATATGACAACATGAA
TATAAATTAAATGGTGCATATAGTTACATTTATTTGTTTTTATCAAATTGATTTTATTTAGGATG
AAAATTTTATAA
Found at i:12229436 original size:30 final size:30
Alignment explanation
Indices: 12229402--12229459 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
12229392 TAAAGCTTTA
12229402 ATTTTAG-GATATGGA-ATGTTTAGGGTTTTG
1 ATTTTAGAG-TATGGAGAT-TTTAGGGTTTTG
*
12229432 ATTTTAGAGTTTGGAGATTTTAGGGTTT
1 ATTTTAGAGTATGGAGATTTTAGGGTTT
12229460 GGGGTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.48
Consensus pattern (30 bp):
ATTTTAGAGTATGGAGATTTTAGGGTTTTG
Found at i:12229452 original size:16 final size:16
Alignment explanation
Indices: 12229431--12229461 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12229421 TTAGGGTTTT
12229431 GATTTTAGAGTTTGGA
1 GATTTTAGAGTTTGGA
*
12229447 GATTTTAGGGTTTGG
1 GATTTTAGAGTTTGG
12229462 GGTTTTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GATTTTAGAGTTTGGA
Found at i:12229498 original size:37 final size:37
Alignment explanation
Indices: 12229419--12229491 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
12229409 GATATGGAAT
* *
12229419 GTTTAGGGTTTTGATTTTAGAGTTTGGAGATTTTAGG
1 GTTTGGGGTTTTGATTTAAGAGTTTGGAGATTTTAGG
*
12229456 GTTTGGGGTTTTGATTTAAGGGTTT-GA-ATTTTAGG
1 GTTTGGGGTTTTGATTTAAGAGTTTGGAGATTTTAGG
12229491 G
1 G
12229492 ATTTTGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 9 0.27
36 2 0.06
37 22 0.67
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (37 bp):
GTTTGGGGTTTTGATTTAAGAGTTTGGAGATTTTAGG
Found at i:12229502 original size:16 final size:16
Alignment explanation
Indices: 12229478--12229670 Score: 101
Period size: 16 Copynumber: 12.2 Consensus size: 16
12229468 GATTTAAGGG
*
12229478 TTTGAATTTTAGGGAT
1 TTTGGATTTTAGGGAT
*
12229494 TTTGGATTTT-GGG-G
1 TTTGGATTTTAGGGAT
* *
12229508 TTTGGA-TTTA-AGAG
1 TTTGGATTTTAGGGAT
** ** *
12229522 TTTAAAGGTTAGAGAT
1 TTTGGATTTTAGGGAT
* * *
12229538 TTCGGATTTTGGGGGGT
1 TTTGGATTTT-AGGGAT
*
12229555 TTTGGATTTTAGGGGT
1 TTTGGATTTTAGGGAT
* **
12229571 TTTGGACTTTAGGGGG
1 TTTGGATTTTAGGGAT
*
12229587 TTTGGATTTAAGGGAT
1 TTTGGATTTTAGGGAT
12229603 TTTGGATTTTTAAGGG-T
1 TTTGGA-TTTT-AGGGAT
* *
12229620 TTCGAATTTTA-GGAT
1 TTTGGATTTTAGGGAT
*
12229635 TTTGGATTTTGGGAGAT
1 TTTGGATTTTAGG-GAT
** *
12229652 TTTTTATTTTAGGGGT
1 TTTGGATTTTAGGGAT
12229668 TTT
1 TTT
12229671 AGAAACCTAG
Statistics
Matches: 134, Mismatches: 33, Indels: 20
0.72 0.18 0.11
Matches are distributed among these distances:
13 4 0.03
14 13 0.10
15 16 0.12
16 64 0.48
17 33 0.25
18 4 0.03
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.48
Consensus pattern (16 bp):
TTTGGATTTTAGGGAT
Found at i:12229563 original size:17 final size:16
Alignment explanation
Indices: 12229541--12229670 Score: 75
Period size: 17 Copynumber: 8.0 Consensus size: 16
12229531 TAGAGATTTC
12229541 GGATTTTGGGGGGTTTT
1 GGATTTT-GGGGGTTTT
*
12229558 GGATTTTAGGGGTTTT
1 GGATTTTGGGGGTTTT
*
12229574 GGACTTTAGGGGG-TTT
1 GGA-TTTTGGGGGTTTT
** *
12229590 GGATTTAAGGGATTTT
1 GGATTTTGGGGGTTTT
** *
12229606 GGATTTTTAAGGGTTTC
1 GGA-TTTTGGGGGTTTT
* * *
12229623 GAATTTT-AGGATTTT
1 GGATTTTGGGGGTTTT
*
12229638 GGATTTTGGGAGATTTT
1 GGATTTTGGG-GGTTTT
** *
12229655 TTATTTTAGGGGTTTT
1 GGATTTTGGGGGTTTT
12229671 AGAAACCTAG
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
15 19 0.21
16 33 0.37
17 38 0.42
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (16 bp):
GGATTTTGGGGGTTTT
Found at i:12229955 original size:3 final size:3
Alignment explanation
Indices: 12229949--12229978 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12229939 AATAATATTC
12229949 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12229979 CTTAAGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12231158 original size:14 final size:14
Alignment explanation
Indices: 12231122--12231169 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
12231112 CACCAGCCAC
12231122 CCTATTTTCTATTT
1 CCTATTTTCTATTT
* *
12231136 -CTTTTTTCTTTTT
1 CCTATTTTCTATTT
*
12231149 CCTATTTTCTCTTT
1 CCTATTTTCTATTT
12231163 CCT-TTTT
1 CCTATTTT
12231170 TTAACAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 15 0.52
14 14 0.48
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (14 bp):
CCTATTTTCTATTT
Found at i:12231170 original size:14 final size:14
Alignment explanation
Indices: 12231126--12231170 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
12231116 AGCCACCCTA
12231126 TTTTCTATTT-CTT
1 TTTTCTATTTCCTT
* *
12231139 TTTTCTTTTTCCTA
1 TTTTCTATTTCCTT
*
12231153 TTTTCTCTTTCCTT
1 TTTTCTATTTCCTT
12231167 TTTT
1 TTTT
12231171 TAACAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTATTTCCTT
Found at i:12231562 original size:23 final size:23
Alignment explanation
Indices: 12231529--12231574 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
12231519 CACCGCAAAT
* *
12231529 CAAAATTATGCTCGGAGGTCTTA
1 CAAAATCATGCCCGGAGGTCTTA
12231552 CAAAATCATGCCCGGAGGTCTTA
1 CAAAATCATGCCCGGAGGTCTTA
12231575 TAGATTCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
CAAAATCATGCCCGGAGGTCTTA
Found at i:12231704 original size:110 final size:110
Alignment explanation
Indices: 12231416--12232022 Score: 767
Period size: 110 Copynumber: 5.5 Consensus size: 110
12231406 GATGATCGCA
* * * * *
12231416 AATCGAAA-TTATGCCCGGAGGTATTAGAAATCATG-TCCAGAGGTCTTACAGAATTGACTGGGA
1 AATC-AAATTTATGCCCGAAGGTTTTAGAAATCATGCT-CGGAGGTCTTACAGAATCGATTGGGA
* * * * *
12231479 TAACATCTCAAGTCGAAAGATAAAGAATCGATC-CAGATAACACCGCA
64 TAACACCACAAGTCAAAAGATAAAGAATCGATCAC-GATAGCACCGCG
* * * * * * * * **
12231526 AATCAAAATTATGCTCGGAGGTCTTACAAAATCATGCCCGGAGGTCTTATAGATTCGATTAAGAT
1 AATCAAATTTATGCCCGAAGGTTTTA-GAAATCATGCTCGGAGGTCTTACAGAATCGATTGGGAT
* *
12231591 AACACCACAAGTCAAAAGATAAACAATTGATCACGATAGCACCGCG
65 AACACCACAAGTCAAAAGATAAAGAATCGATCACGATAGCACCGCG
* *
12231637 AATCGAATTTATGCCCGAAGGTTTTAGAAATCATG-TCCGGAGGTCTTACAGAATCGATTGAGAT
1 AATCAAATTTATGCCCGAAGGTTTTAGAAATCATGCT-CGGAGGTCTTACAGAATCGATTGGGAT
***
12231701 AACACCACAAGTCAAAAGATAAAGAATCGATTGGGATAGCACCGCG
65 AACACCACAAGTCAAAAGATAAAGAATCGATCACGATAGCACCGCG
* *
12231747 AATCAAATTTATGCTCGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATA
1 AATCAAATTTATGCCCGAAGGTTTTAGAAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATA
*
12231812 ACACCACAAGTTAAAAGATAAAGAATCGATCGA-GATAGCACCGCG
66 ACACCACAAGTCAAAAGATAAAGAATCGATC-ACGATAGCACCGCG
* *
12231857 AATCAAATTTATGCCCGGAGGTTTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGAT
1 AATCAAATTTATGCCCGAAGGTTTTAGA-AATCATGCTCGGAGGTCTTACAGAATCGATTGGGAT
* ** *
12231922 AACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAGCACTACA
65 AACACCACAAGTCAAAAGATAAAGAATCGATCACGATAGCACCGCG
*
12231968 AATCGAATTTATGCCC-AGAGGTTTTAGAAATCATGCTCGGAGGTCTTACAGAATC
1 AATCAAATTTATGCCCGA-AGGTTTTAGAAATCATGCTCGGAGGTCTTACAGAATC
12232023 ATGCTTGAAG
Statistics
Matches: 436, Mismatches: 51, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
109 3 0.01
110 245 0.56
111 187 0.43
112 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (110 bp):
AATCAAATTTATGCCCGAAGGTTTTAGAAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATA
ACACCACAAGTCAAAAGATAAAGAATCGATCACGATAGCACCGCG
Found at i:12231892 original size:221 final size:220
Alignment explanation
Indices: 12231416--12232265 Score: 924
Period size: 221 Copynumber: 3.8 Consensus size: 220
12231406 GATGATCGCA
* * * *
12231416 AATCGAAA-TTATGCCCGGAGGTATTAGAAATCATGTCCAGAGGTCTTACAGAATTGACTGGGAT
1 AATC-AAATTTATGCCCGGAGGTTTTAGAAATCATGTCCGGAGGTCTTACAGAATCGATTGGGAT
* * * * * *
12231480 AACATCTCAAGTCGAAAGATAAAGAATCGATCCA-GATAACACCGCAAATCAAAATTATGCTCGG
65 AACACCACAAGTCAAAAGATAAAGAATCGAT-CAGGATAGCACCGCAAATCAAATTTATGCTCGA
* * * *
12231544 AGGTCTTACAAAATCATGCCCGGAGGTCTTATAGATTCGATTAAGATAACACCACAAGTCAAAAG
129 AGGTCTTA-GAAATCATGCTCGGAGGTCTTACAGAATCGATTAAGATAACACCACAAGTCAAAAG
*
12231609 ATAAACAATTGATCACGATAGCACCGCG
193 ATAAACAATCGATCACGATAGCACCGCG
* * *
12231637 AATCGAATTTATGCCCGAAGGTTTTAGAAATCATGTCCGGAGGTCTTACAGAATCGATTGAGATA
1 AATCAAATTTATGCCCGGAGGTTTTAGAAATCATGTCCGGAGGTCTTACAGAATCGATTGGGATA
** *
12231702 ACACCACAAGTCAAAAGATAAAGAATCGATTGGGATAGCACCGCGAATCAAATTTATGCTCGAAG
66 ACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAGCACCGCAAATCAAATTTATGCTCGAAG
** *
12231767 GTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTTAAAAGATA
131 GTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGATTAAGATAACACCACAAGTCAAAAGATA
*
12231832 AAGAATCGATCGA-GATAGCACCGCG
196 AACAATCGATC-ACGATAGCACCGCG
*
12231857 AATCAAATTTATGCCCGGAGGTTTTACAGAATCATG-CTCGGAGGTCTTACAGAATCGATTGGGA
1 AATCAAATTTATGCCCGGAGGTTTTAGA-AATCATGTC-CGGAGGTCTTACAGAATCGATTGGGA
** * *
12231921 TAACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAGCACTACAAATCGAATTTATGC-CCA
64 TAACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAGCACCGCAAATCAAATTTATGCTCGA
*
12231985 GAGGTTTTAGAAATCATGCTCGGAGGTCTTACAGAATCATGCTTGAAGGTCTTACAGAATCGATT
129 -AGGTCTTAGAAATCATGCTCGGAGGTCTTACAG-A--AT-C--G-A----TTA-AG-AT--A--
* * * *** *
12232050 GGGATAACACCATAAGTCAAAAGATAAATAATCGATTGGGATAGCACCGCA
176 ---ACA---CCACAAGTCAAAAGATAAACAATCGATCACGATAGCACCGCG
* * * * *
12232101 AATCAAATTTATGCTCAGAGGTCTTAGAAATCATG-CCTAGAGATCTTACAGAATCGATTGGGAT
1 AATCAAATTTATGCCCGGAGGTTTTAGAAATCATGTCC-GGAGGTCTTACAGAATCGATTGGGAT
* ** *
12232165 AACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAACACCGTGAATCAAATTTATG-TCCGG
65 AACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAGCACCGCAAATCAAATTTATGCT-CGA
12232229 AGGTCTTAGAAATCATGC-CTGGAGGTCTTACAGAATC
129 AGGTCTTAGAAATCATGCTC-GGAGGTCTTACAGAATC
12232266 AAAATCTTTG
Statistics
Matches: 534, Mismatches: 61, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
220 103 0.19
221 236 0.44
222 1 0.00
224 2 0.00
225 1 0.00
227 1 0.00
228 1 0.00
232 2 0.00
233 1 0.00
234 2 0.00
236 1 0.00
239 1 0.00
240 2 0.00
241 2 0.00
242 3 0.01
243 115 0.22
244 60 0.11
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (220 bp):
AATCAAATTTATGCCCGGAGGTTTTAGAAATCATGTCCGGAGGTCTTACAGAATCGATTGGGATA
ACACCACAAGTCAAAAGATAAAGAATCGATCAGGATAGCACCGCAAATCAAATTTATGCTCGAAG
GTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCGATTAAGATAACACCACAAGTCAAAAGATA
AACAATCGATCACGATAGCACCGCG
Found at i:12231898 original size:23 final size:23
Alignment explanation
Indices: 12231867--12231912 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
12231857 AATCAAATTT
*
12231867 ATGCCCGGAGGTTTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
*
12231890 ATGCTCGGAGGTCTTACAGAATC
1 ATGCCCGGAGGTCTTACAGAATC
12231913 GATTGGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
ATGCCCGGAGGTCTTACAGAATC
Found at i:12232023 original size:133 final size:132
Alignment explanation
Indices: 12231871--12232155 Score: 426
Period size: 133 Copynumber: 2.1 Consensus size: 132
12231861 AAATTTATGC
* *
12231871 CCGGAGGTTTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCA
1 CCGGAGGTCTTACAGAATCATGCTCGAAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCA
* * *
12231936 AAAGATAAAGAATCGATCAGGATAGCACTACAAATCGAATTTATGCCCAGAGGTTTTAGAAATCA
66 AAAGATAAAGAATCGATCAGGATAGCACCACAAATCAAATTTATGCCCAGAGGTCTTAGAAATCA
12232001 TG
131 TG
* *
12232003 CTCGGAGGTCTTACAGAATCATGCTTGAAGGTCTTACAGAATCGATTGGGATAACACCATAAGTC
1 C-CGGAGGTCTTACAGAATCATGCTCGAAGGTCTTACAGAATCGATTGGGATAACACCACAAGTC
* ** * *
12232068 AAAAGATAAATAATCGATTGGGATAGCACCGCAAATCAAATTTATGCTCAGAGGTCTTAGAAATC
65 AAAAGATAAAGAATCGATCAGGATAGCACCACAAATCAAATTTATGCCCAGAGGTCTTAGAAATC
12232133 ATG
130 ATG
* *
12232136 CCTAGAGATCTTACAGAATC
1 CC-GGAGGTCTTACAGAATC
12232156 GATTGGGATA
Statistics
Matches: 137, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
132 2 0.01
133 135 0.99
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (132 bp):
CCGGAGGTCTTACAGAATCATGCTCGAAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCA
AAAGATAAAGAATCGATCAGGATAGCACCACAAATCAAATTTATGCCCAGAGGTCTTAGAAATCA
TG
Found at i:12232025 original size:23 final size:23
Alignment explanation
Indices: 12231996--12232045 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
12231986 AGGTTTTAGA
*
12231996 AATCATGCTCGGAGGTCTTACAG
1 AATCATGCTCGAAGGTCTTACAG
*
12232019 AATCATGCTTGAAGGTCTTACAG
1 AATCATGCTCGAAGGTCTTACAG
12232042 AATC
1 AATC
12232046 GATTGGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (23 bp):
AATCATGCTCGAAGGTCTTACAG
Found at i:12232162 original size:110 final size:110
Alignment explanation
Indices: 12232000--12232265 Score: 383
Period size: 110 Copynumber: 2.4 Consensus size: 110
12231990 TTTAGAAATC
* * *
12232000 ATGCTCGGAGGTCTTACAGAATCATG-CTTGAAGGTCTTACAGAATCGATTGGGATAACACCATA
1 ATGCTCGGAGGTCTTAGA-AATCATGCCTAG-AGGTCTTACAGAATCGATTGGGATAACACCACA
* ** *
12232064 AGTCAAAAGATAAATAATCGATTGGGATAGCACCGCAAATCAAATTT
64 AGTCAAAAGATAAAGAATCGATCAGGATAACACCGCAAATCAAATTT
* *
12232111 ATGCTCAGAGGTCTTAGAAATCATGCCTAGAGATCTTACAGAATCGATTGGGATAACACCACAAG
1 ATGCTCGGAGGTCTTAGAAATCATGCCTAGAGGTCTTACAGAATCGATTGGGATAACACCACAAG
**
12232176 TCAAAAGATAAAGAATCGATCAGGATAACACCGTGAATCAAATTT
66 TCAAAAGATAAAGAATCGATCAGGATAACACCGCAAATCAAATTT
*
12232221 ATG-TCCGGAGGTCTTAGAAATCATGCCTGGAGGTCTTACAGAATC
1 ATGCT-CGGAGGTCTTAGAAATCATGCCTAGAGGTCTTACAGAATC
12232266 AAAATCTTTG
Statistics
Matches: 139, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
109 1 0.01
110 119 0.86
111 19 0.14
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (110 bp):
ATGCTCGGAGGTCTTAGAAATCATGCCTAGAGGTCTTACAGAATCGATTGGGATAACACCACAAG
TCAAAAGATAAAGAATCGATCAGGATAACACCGCAAATCAAATTT
Found at i:12232904 original size:65 final size:66
Alignment explanation
Indices: 12232820--12233150 Score: 355
Period size: 65 Copynumber: 5.1 Consensus size: 66
12232810 TTTGAAACTC
* * * * * * *
12232820 TAAAACTTCCTTTGGGGCCAAATAAACTGGGCTTAAA-TTTTATTGAAGGCCAGCTAAATTGGGC
1 TAAAACTTCATTTGAGGCCAGATAAACTGGGCTTAAAGTCTCATTGAAGGCCAGATAAACTGGGC
12232884 T
66 T
* * * * *
12232885 TAAAACCTCATTTGAGGCCAGATAAACTGGGCTTAAA-TATCATTGATGGCTAGATAAACTAGGC
1 TAAAACTTCATTTGAGGCCAGATAAACTGGGCTTAAAGTCTCATTGAAGGCCAGATAAACTGGGC
12232949 T
66 T
* * * * *
12232950 TAAATCTTCATTTGAGGCTAGATAAACTAGGCTTAAAGCCTCATTG-AGGCCAGATAAACTGGGT
1 TAAAACTTCATTTGAGGCCAGATAAACTGGGCTTAAAGTCTCATTGAAGGCCAGATAAACTGGGC
12233014 T
66 T
* * * * * * * *
12233015 TAAAGCTTCA-TTGATGGTCAGATAAACTGGGCATAAAGTTTCATTGAGGGTCAGGTAAACTGAG
1 TAAAACTTCATTTGA-GGCCAGATAAACTGGGCTTAAAGTCTCATTGAAGGCCAGATAAACTGGG
12233079 CT
65 CT
* * * * *
12233081 TAAATCTTTATTTGAGGCCAGATAAACTGGGTTTAAAGCCTCATTGATGGCCAGATAAACTGGGC
1 TAAAACTTCATTTGAGGCCAGATAAACTGGGCTTAAAGTCTCATTGAAGGCCAGATAAACTGGGC
12233146 T
66 T
12233147 TAAA
1 TAAA
12233151 GGTTTTTTTT
Statistics
Matches: 218, Mismatches: 44, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
64 4 0.02
65 136 0.62
66 74 0.34
67 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (66 bp):
TAAAACTTCATTTGAGGCCAGATAAACTGGGCTTAAAGTCTCATTGAAGGCCAGATAAACTGGGC
T
Found at i:12233151 original size:33 final size:32
Alignment explanation
Indices: 12232835--12233151 Score: 316
Period size: 33 Copynumber: 9.7 Consensus size: 32
12232825 CTTCCTTTGG
* * *
12232835 GGCCAAATAAACTGGGCTTAAA-TTTTATTGAA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTG-A
* * * *
12232867 GGCCAGCTAAATTGGGCTTAAAACCTCATTTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCA-TTGA
12232900 GGCCAGATAAACTGGGCTTAAA--TATCATTGA
1 GGCCAGATAAACTGGGCTTAAAGCT-TCATTGA
* * *
12232931 TGGCTAGATAAACTAGGCTTAAATCTTCATTTGA
1 -GGCCAGATAAACTGGGCTTAAAGCTTCA-TTGA
* * *
12232965 GGCTAGATAAACTAGGCTTAAAGCCTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTGA
*
12232997 GGCCAGATAAACTGGGTTTAAAGCTTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTGA
* * *
12233029 TGGTCAGATAAACTGGGCATAAAGTTTCATTGA
1 -GGCCAGATAAACTGGGCTTAAAGCTTCATTGA
* * * * *
12233062 GGGTCAGGTAAACTGAGCTTAAATCTTTATTTGA
1 -GGCCAGATAAACTGGGCTTAAAGCTTCA-TTGA
* *
12233096 GGCCAGATAAACTGGGTTTAAAGCCTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTGA
12233128 TGGCCAGATAAACTGGGCTTAAAG
1 -GGCCAGATAAACTGGGCTTAAAG
12233152 GTTTTTTTTT
Statistics
Matches: 239, Mismatches: 36, Indels: 19
0.81 0.12 0.06
Matches are distributed among these distances:
31 4 0.02
32 78 0.33
33 145 0.61
34 12 0.05
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (32 bp):
GGCCAGATAAACTGGGCTTAAAGCTTCATTGA
Found at i:12240957 original size:15 final size:14
Alignment explanation
Indices: 12240934--12240985 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
12240924 GGTTTGGGGT
*
12240934 TTTG-ATTTAAGGG
1 TTTGAATTTTAGGG
12240947 TTTGAATTTTAGGG
1 TTTGAATTTTAGGG
*
12240961 ATTTTGAATTTTGGGG
1 --TTTGAATTTTAGGG
*
12240977 TTTGGATTT
1 TTTGAATTT
12240986 AACAGTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 4 0.12
14 16 0.48
16 13 0.39
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (14 bp):
TTTGAATTTTAGGG
Found at i:12240968 original size:16 final size:16
Alignment explanation
Indices: 12240947--12241089 Score: 54
Period size: 16 Copynumber: 9.2 Consensus size: 16
12240937 GATTTAAGGG
12240947 TTTGAATTTTAGGGAT
1 TTTGAATTTTAGGGAT
*
12240963 TTTGAATTTT-GGG-G
1 TTTGAATTTTAGGGAT
* ** *
12240977 TTTGGA-TTTA-ACAG
1 TTTGAATTTTAGGGAT
* *
12240991 TTTAAAGGTTT-GGGAT
1 TTTGAA-TTTTAGGGAT
*
12241007 TTTGGATTTTTAGGGA-
1 TTT-GAATTTTAGGGAT
*
12241023 TTTCAGATTTTAGGG-T
1 TTTGA-ATTTTAGGGAT
*
12241039 TTTCG-ATTTTA-AGAT
1 TTT-GAATTTTAGGGAT
*
12241054 TTTCG-ATTTTGAGAGAT
1 TTT-GAATTTT-AGGGAT
*
12241071 TTTGAATTTTAGGGGT
1 TTTGAATTTTAGGGAT
12241087 TTT
1 TTT
12241090 AGAAACCTAG
Statistics
Matches: 95, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
13 3 0.03
14 11 0.12
15 21 0.22
16 43 0.45
17 17 0.18
ACGTcount: A:0.22, C:0.03, G:0.26, T:0.50
Consensus pattern (16 bp):
TTTGAATTTTAGGGAT
Found at i:12240973 original size:51 final size:51
Alignment explanation
Indices: 12240874--12240981 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
12240864 GATACGAAAT
* * **
12240874 GTTTAGGGTTTTGATTTTAGAGTTTGGAGATTTTAGGGTTAGGGTTTTGAG
1 GTTTGGGGTTTTGATTTAAGAGTTTGGAGATTTTAGGGTTAGAATTTTGAG
* * *
12240925 GTTTGGGGTTTTGATTTAAGGGTTT-GA-ATTTTAGGGATTTTGAATTTTGGG
1 GTTTGGGGTTTTGATTTAAGAGTTTGGAGATTTTAGGG--TTAGAATTTTGAG
12240976 GTTTGG
1 GTTTGG
12240982 ATTTAACAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 9 0.19
50 2 0.04
51 37 0.77
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (51 bp):
GTTTGGGGTTTTGATTTAAGAGTTTGGAGATTTTAGGGTTAGAATTTTGAG
Found at i:12240985 original size:14 final size:14
Alignment explanation
Indices: 12240926--12240985 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
12240916 GGTTTTGAGG
12240926 TTTGGGGTTTTG-AT
1 TTTGGGG-TTTGAAT
**
12240940 TTAAGGGTTTGAAT
1 TTTGGGGTTTGAAT
*
12240954 TTTAGGGATTTTGAAT
1 TTT-GGG-GTTTGAAT
*
12240970 TTTGGGGTTTGGAT
1 TTTGGGGTTTGAAT
12240984 TT
1 TT
12240986 AACAGTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 4 0.11
14 17 0.47
15 5 0.14
16 10 0.28
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.52
Consensus pattern (14 bp):
TTTGGGGTTTGAAT
Found at i:12241006 original size:44 final size:44
Alignment explanation
Indices: 12240912--12241016 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
12240902 GATTTTAGGG
** * ** * *
12240912 TTAGGG-TTTTGAGGTTTGGGGTTTTGATTTAAGGGTTTGAATT
1 TTAGGGATTTTGAATTTTGGGGTTTGGATTTAACAGTTTAAAGT
12240955 TTAGGGATTTTGAATTTTGGGGTTTGGATTTAACAGTTTAAAGGT
1 TTAGGGATTTTGAATTTTGGGGTTTGGATTTAACAGTTTAAA-GT
*
12241000 TT-GGGATTTTGGATTTT
1 TTAGGGATTTTGAATTTT
12241017 TAGGGATTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
43 6 0.12
44 43 0.83
45 3 0.06
ACGTcount: A:0.19, C:0.01, G:0.31, T:0.49
Consensus pattern (44 bp):
TTAGGGATTTTGAATTTTGGGGTTTGGATTTAACAGTTTAAAGT
Found at i:12241024 original size:17 final size:16
Alignment explanation
Indices: 12241002--12241089 Score: 76
Period size: 16 Copynumber: 5.5 Consensus size: 16
12240992 TTAAAGGTTT
*
12241002 GGGATTTTGGATTTTTA
1 GGGATTTTCGA-TTTTA
12241019 GGGA-TTTCAGATTTTA
1 GGGATTTTC-GATTTTA
12241035 GGG-TTTTCGATTTTA
1 GGGATTTTCGATTTTA
*
12241050 -AGATTTTCGATTTTGA
1 GGGATTTTCGATTTT-A
*
12241066 GAGATTTT-GAATTTTA
1 GGGATTTTCG-ATTTTA
*
12241082 GGGGTTTT
1 GGGATTTT
12241090 AGAAACCTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
14 1 0.02
15 18 0.30
16 24 0.39
17 18 0.30
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.50
Consensus pattern (16 bp):
GGGATTTTCGATTTTA
Found at i:12241048 original size:15 final size:15
Alignment explanation
Indices: 12241014--12241063 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
12241004 GATTTTGGAT
*
12241014 TTTTAGGGATTTCAGA
1 TTTTAGGGTTTTC-GA
12241030 TTTTAGGGTTTTCGA
1 TTTTAGGGTTTTCGA
* *
12241045 TTTTAAGATTTTCGA
1 TTTTAGGGTTTTCGA
12241060 TTTT
1 TTTT
12241064 GAGAGATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (15 bp):
TTTTAGGGTTTTCGA
Found at i:12242632 original size:3 final size:3
Alignment explanation
Indices: 12242626--12242652 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12242616 AAATATATAC
12242626 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
12242653 ATGTTAATCT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12250389 original size:49 final size:47
Alignment explanation
Indices: 12250336--12250488 Score: 146
Period size: 49 Copynumber: 3.1 Consensus size: 47
12250326 TCTTAATTTT
* *
12250336 CAAAATCCTAAGTTTCTAAAACCCCTAAAATAAAAAATCTCCCAAAATC
1 CAAAATCCTAAG-TTC-AAAACCCCTAAAATCAAAAATCTCCTAAAATC
* * * * *
12250385 CAAAATCCTAAAATTCGAAACCCTTAAAAATCCAAAATC-CCTTAAATC
1 CAAAATCCT-AAGTTCAAAACCCCT-AAAATCAAAAATCTCCTAAAATC
** * *
12250433 CAAACCCCCTAAAGTCCAAAACCCCTAAAATCAAAAACCTCCTAAAATC
1 CAAA-ATCCT-AAGTTCAAAACCCCTAAAATCAAAAATCTCCTAAAATC
12250482 CAAAATC
1 CAAAATC
12250489 TCAAACCTTT
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
48 30 0.37
49 50 0.61
50 2 0.02
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (47 bp):
CAAAATCCTAAGTTCAAAACCCCTAAAATCAAAAATCTCCTAAAATC
Found at i:12250431 original size:16 final size:16
Alignment explanation
Indices: 12250353--12250486 Score: 119
Period size: 16 Copynumber: 8.2 Consensus size: 16
12250343 CTAAGTTTCT
**
12250353 AAAACCCCTAAAATAA
1 AAAACCCCTAAAATCC
12250369 AAAATCTCCC-AAAATCC
1 AAAA-C-CCCTAAAATCC
* *
12250386 AAAA-TCCTAAAATTC
1 AAAACCCCTAAAATCC
* *
12250401 GAAACCCTTAAAAATCC
1 AAAACCCCT-AAAATCC
* *
12250418 AAAATCCCTTAAATCC
1 AAAACCCCTAAAATCC
* *
12250434 AAACCCCCTAAAGTCC
1 AAAACCCCTAAAATCC
*
12250450 AAAACCCCTAAAATCA
1 AAAACCCCTAAAATCC
12250466 AAAACCTCCTAAAATCC
1 AAAACC-CCTAAAATCC
12250483 AAAA
1 AAAA
12250487 TCTCAAACCT
Statistics
Matches: 92, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
14 2 0.02
15 9 0.10
16 43 0.47
17 35 0.38
18 3 0.03
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.17
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:12250583 original size:16 final size:15
Alignment explanation
Indices: 12250562--12250622 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 15
12250552 AATCAAAACC
12250562 CCAAACCCTAAAATCT
1 CCAAACCCTAAAAT-T
*
12250578 CCAAACTCTAAAA-T
1 CCAAACCCTAAAATT
*
12250592 CAAAACCCTAAACATT
1 CCAAACCCTAAA-ATT
* *
12250608 CCATATCCTAAAATT
1 CCAAACCCTAAAATT
12250623 AAAGCTTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 11 0.30
15 4 0.11
16 22 0.59
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (15 bp):
CCAAACCCTAAAATT
Found at i:12250583 original size:37 final size:35
Alignment explanation
Indices: 12250532--12250604 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 35
12250522 AATCCAAAAT
*
12250532 CCCTAAAATTCAAACCCTTAAATCAAAACCCCAAA
1 CCCTAAAATTCAAACCCTAAAATCAAAACCCCAAA
* *
12250567 CCCTAAAATCTCCAAACTCTAAAATCAAAACCCTAAA
1 CCCTAAAAT-T-CAAACCCTAAAATCAAAACCCCAAA
12250604 C
1 C
12250605 ATTCCATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 9 0.27
36 1 0.03
37 23 0.70
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (35 bp):
CCCTAAAATTCAAACCCTAAAATCAAAACCCCAAA
Found at i:12252438 original size:142 final size:142
Alignment explanation
Indices: 12252230--12252519 Score: 571
Period size: 142 Copynumber: 2.0 Consensus size: 142
12252220 CAATGTATAG
12252230 AATTTTTGATAAAATTTTCATCCTAAATAAAATCAATTTGATAAAAACAAATAAATGTAACTATA
1 AATTTTTGATAAAATTTTCATCCTAAATAAAATCAATTTGATAAAAACAAATAAATGTAACTATA
12252295 TGCACCATTTAATTTATATTCATGTTGTCATATATGCATTTCATGCATTAATAATAAATGTGAAA
66 TGCACCATTTAATTTATATTCATGTTGTCATATATGCATTTCATGCATTAATAATAAATGTGAAA
12252360 TACCAAAGTAAT
131 TACCAAAGTAAT
*
12252372 AATTTTTTATAAAATTTTCATCCTAAATAAAATCAATTTGATAAAAACAAATAAATGTAACTATA
1 AATTTTTGATAAAATTTTCATCCTAAATAAAATCAATTTGATAAAAACAAATAAATGTAACTATA
12252437 TGCACCATTTAATTTATATTCATGTTGTCATATATGCATTTCATGCATTAATAATAAATGTGAAA
66 TGCACCATTTAATTTATATTCATGTTGTCATATATGCATTTCATGCATTAATAATAAATGTGAAA
12252502 TACCAAAGTAAT
131 TACCAAAGTAAT
12252514 AATTTT
1 AATTTT
12252520 AAAAATTCTT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 147 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (142 bp):
AATTTTTGATAAAATTTTCATCCTAAATAAAATCAATTTGATAAAAACAAATAAATGTAACTATA
TGCACCATTTAATTTATATTCATGTTGTCATATATGCATTTCATGCATTAATAATAAATGTGAAA
TACCAAAGTAAT
Found at i:12253779 original size:3 final size:3
Alignment explanation
Indices: 12253773--12253798 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12253763 GTATATATCT
12253773 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12253799 TACCTTAATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12265169 original size:291 final size:291
Alignment explanation
Indices: 12264603--12265169 Score: 974
Period size: 291 Copynumber: 1.9 Consensus size: 291
12264593 AGAAAGATAA
* * *
12264603 CCTTGAATGCTTCGATCCCTCAAAAAGTTTTTCATTCATCTCTTTAAGCACCTTATAAAACTTTG
1 CCTTGAATGCTTCGATCCCTCAAAAAGTTCTTCATTCATCTCTTCAAGCAACTTATAAAACTTTG
*
12264668 ATGCTTCTCTTCTAGGTTGTTGGTCACGTACACCTATCTCAAGTTCACCAAATTCATGCATTTCA
66 ATGCTTCTCTTCTAGGTTGTTGGTCACGTACACCTATCCCAAGTTCACCAAATTCATGCATTTCA
* *
12264733 ACATTGGATTGATTAAATCCTTCATTTCAAGGAGAAAGATTATGAAAATGTTGGTTATGAATGTT
131 ACATTGGACTGATTAAATCATTCATTTCAAGGAGAAAGATTATGAAAATGTTGGTTATGAATGTT
* * *
12264798 AAAAGCATCTTATAACATGCCTTCAATATTATCTGCTATAAAAGGATCATGTTGCTATTAGAAAG
196 AAAAGCATCTCATAACATGCCTTCAATATCATCTACTATAAAAGGATCATGTTGCTATTAGAAAG
12264863 CCTTTCAAGTGAAAAAGATTAACAAATAAAT
261 CCTTTCAAGTGAAAAAGATTAACAAATAAAT
12264894 CCTTGAATGCTTCGATCCCTCAAAAAGTTCTTCATTCATCTCTTCAAGCAACTTATAAAACTTTG
1 CCTTGAATGCTTCGATCCCTCAAAAAGTTCTTCATTCATCTCTTCAAGCAACTTATAAAACTTTG
* *
12264959 ATGCTTCTCTTTTAGGTTGTTGGTCACGTACACCTATCCCAGGTTCACCAAATTCATGCATTTCA
66 ATGCTTCTCTTCTAGGTTGTTGGTCACGTACACCTATCCCAAGTTCACCAAATTCATGCATTTCA
*
12265024 ATATTGGACTGATTAAATCATTCATTT-AAGGAGAAAGATTATGAAAATGTTGGTTATGAATGTT
131 ACATTGGACTGATTAAATCATTCATTTCAAGGAGAAAGATTATGAAAATGTTGGTTATGAATGTT
* * *
12265088 AAAAGTATCTCATAACATGCCTTCAATGTCATCTACTATAAAAGGATCATGTTGCTATTAGGAAG
196 AAAAGCATCTCATAACATGCCTTCAATATCATCTACTATAAAAGGATCATGTTGCTATTAGAAAG
*
12265153 CCTTTGAAGTTGAAAAA
261 CCTTTCAAG-TGAAAAA
12265170 CTCTAGTGAA
Statistics
Matches: 259, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
290 104 0.40
291 155 0.60
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (291 bp):
CCTTGAATGCTTCGATCCCTCAAAAAGTTCTTCATTCATCTCTTCAAGCAACTTATAAAACTTTG
ATGCTTCTCTTCTAGGTTGTTGGTCACGTACACCTATCCCAAGTTCACCAAATTCATGCATTTCA
ACATTGGACTGATTAAATCATTCATTTCAAGGAGAAAGATTATGAAAATGTTGGTTATGAATGTT
AAAAGCATCTCATAACATGCCTTCAATATCATCTACTATAAAAGGATCATGTTGCTATTAGAAAG
CCTTTCAAGTGAAAAAGATTAACAAATAAAT
Found at i:12267934 original size:84 final size:84
Alignment explanation
Indices: 12267783--12267937 Score: 197
Period size: 84 Copynumber: 1.8 Consensus size: 84
12267773 AATATTGTGA
* * *
12267783 TTTGCTGAACCTTGTAGTCTGATATTGTAATGCCGAATGGTATTGTATGATATTAGGGGTCTAAA
1 TTTGCTCAACCTTGTAGTCTGATATTATAATGCCGAATGGTATTGTATGAAATTAGGGGTCTAAA
12267848 TCATATATATGTTGAATGG
66 TCATATATATGTTGAATGG
* ** ** *
12267867 TTTGCTCAACCTTGTTGTCTGATATTATTTTGTTGAATGGGT-TTGTATGAAATT-GGGGTGCTG
1 TTTGCTCAACCTTGTAGTCTGATATTATAATGCCGAAT-GGTATTGTATGAAATTAGGGGT-CTA
12267930 AATCATAT
64 AATCATAT
12267938 GCTGAATGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
83 5 0.08
84 52 0.87
85 3 0.05
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.42
Consensus pattern (84 bp):
TTTGCTCAACCTTGTAGTCTGATATTATAATGCCGAATGGTATTGTATGAAATTAGGGGTCTAAA
TCATATATATGTTGAATGG
Found at i:12273349 original size:18 final size:18
Alignment explanation
Indices: 12273328--12273377 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
12273318 TAAGGAAAAT
12273328 AATAAGAACAAGAACAAG
1 AATAAGAACAAGAACAAG
* *
12273346 AATAAGAATAAGGACAAG
1 AATAAGAACAAGAACAAG
12273364 -A-AA-AACAAGAACAA
1 AATAAGAACAAGAACAA
12273378 AAAAAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.32
16 2 0.07
17 1 0.04
18 16 0.57
ACGTcount: A:0.68, C:0.10, G:0.16, T:0.06
Consensus pattern (18 bp):
AATAAGAACAAGAACAAG
Found at i:12273433 original size:8 final size:8
Alignment explanation
Indices: 12273417--12273451 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
12273407 GGCAACTAAG
*
12273417 AAGAGAAA
1 AAGAAAAA
12273425 AAGAAAAA
1 AAGAAAAA
12273433 AAG-AAAA
1 AAGAAAAA
12273440 AAGAAAAA
1 AAGAAAAA
12273448 AAGA
1 AAGA
12273452 GGTAAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:12273442 original size:15 final size:16
Alignment explanation
Indices: 12273417--12273452 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
12273407 GGCAACTAAG
12273417 AAGAGAAAAAGAAAAA
1 AAGAGAAAAAGAAAAA
12273433 AAGA-AAAAAGAAAAA
1 AAGAGAAAAAGAAAAA
12273448 AAGAG
1 AAGAG
12273453 GTAAATTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAGAGAAAAAGAAAAA
Found at i:12274680 original size:20 final size:20
Alignment explanation
Indices: 12274642--12274680 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12274632 TGATCATTGC
*
12274642 ATCTTTAAATTTGTATTTGT
1 ATCTTTAAATTTATATTTGT
* *
12274662 ATCTTTTAATTTATGTTTG
1 ATCTTTAAATTTATATTTG
12274681 CATCACTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (20 bp):
ATCTTTAAATTTATATTTGT
Found at i:12275627 original size:11 final size:10
Alignment explanation
Indices: 12275571--12275657 Score: 56
Period size: 12 Copynumber: 8.5 Consensus size: 10
12275561 TTATTATTTT
*
12275571 TTTATCTTAA
1 TTTATCTTTA
12275581 TTTATCCTATTA
1 TTTAT-CT-TTA
*
12275593 TTTATCTCCCTA
1 TTTATCT--TTA
12275605 TTTATCTTTA
1 TTTATCTTTA
12275615 TTTATC---A
1 TTTATCTTTA
12275622 TTTAT-TTTA
1 TTTATCTTTA
*
12275631 TTTATCCTATTC
1 TTTAT-CT-TTA
12275643 TTTATCTTTA
1 TTTATCTTTA
*
12275653 ATTAT
1 TTTAT
12275658 TTGATTATCC
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
7 6 0.10
9 6 0.10
10 19 0.31
11 7 0.11
12 23 0.38
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:12275632 original size:16 final size:17
Alignment explanation
Indices: 12275604--12275636 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12275594 TTATCTCCCT
12275604 ATTTATCTTTATTTATC
1 ATTTATCTTTATTTATC
12275621 ATTTAT-TTTATTTATC
1 ATTTATCTTTATTTATC
12275637 CTATTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTATCTTTATTTATC
Found at i:12275657 original size:26 final size:26
Alignment explanation
Indices: 12275603--12275659 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
12275593 TTTATCTCCC
*
12275603 TATTTATCTTTATTTATCATTTATTT
1 TATTTATCTTTATTTATCATTTATAT
*
12275629 TATTTATCCTATTCTTTATC-TTTA-AT
1 TATTTAT-CT-TTATTTATCATTTATAT
12275655 TATTT
1 TATTT
12275660 GATTATCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.48
27 6 0.22
28 8 0.30
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTATCTTTATTTATCATTTATAT
Found at i:12278813 original size:16 final size:17
Alignment explanation
Indices: 12278786--12278817 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12278776 TATTTGCCTA
12278786 TTTATCTTTATTTATCT
1 TTTATCTTTATTTATCT
12278803 TTTAT-TTTATTTATC
1 TTTATCTTTATTTATC
12278818 CTATTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATCTTTATTTATCT
Found at i:12281057 original size:12 final size:13
Alignment explanation
Indices: 12281033--12281061 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12281023 GACTAAGCTC
12281033 TCCTTTTTCTTTT
1 TCCTTTTTCTTTT
12281046 TCCTTTTT-TTTT
1 TCCTTTTTCTTTT
12281058 TCCT
1 TCCT
12281062 CCGCGGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCCTTTTTCTTTT
Found at i:12293990 original size:60 final size:60
Alignment explanation
Indices: 12293879--12294196 Score: 412
Period size: 60 Copynumber: 5.4 Consensus size: 60
12293869 TTAAATAAGG
*
12293879 AAAATTGATACTTTCAACTTTTCCTCAAAAATACCATTTTTTGAAATTTTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATC-TTTTTTGAAATTTTTATTTTCAAGA
* *
12293940 AAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAATTTTTATTTTCAAGA
* *
12294000 AAAATTGATACTTTCAACTTTTCCT--TAAA-ATGTTTTTTGAAATTTTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAATTTTTATTTTCAAGA
* * * ** *
12294057 AAAATTAATATTTTCAACTTTTCCTAAAAAATATGGTTTTTGAAATTTTTATTTTCATGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAATTTTTATTTTCAAGA
* * * * * ** **
12294117 AAAGTTGATACTTTCAATTTTTTCTCAAAAGTATATTTTTTTTAA-TTGGA-TTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAATTTTTATTTTCAAGA
12294175 AAAATTGATACTTTCAACTTTT
1 AAAATTGATACTTTCAACTTTT
12294197 TCGTAAAATA
Statistics
Matches: 226, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
57 48 0.21
58 30 0.13
59 6 0.03
60 108 0.48
61 34 0.15
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAATTTTTATTTTCAAGA
Found at i:12294056 original size:117 final size:116
Alignment explanation
Indices: 12293874--12294227 Score: 414
Period size: 117 Copynumber: 3.0 Consensus size: 116
12293864 TGCCTTTAAA
*
12293874 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACCATTTTTTGAAATTTTTATTTTCAAG
1 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT---ATTTTTTGAAATTTTTATTTTCAAG
12293939 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAATTTTATTTT
63 AAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTGAAAATTTTATTTT
* *
12293995 TAAGAAAAATTGATACTTTCAACTTTTCCT-TAAAATGTTTTTTGAAATTTTTATTTTCAAGAAA
1 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATTTTCAAGAAA
* * * *
12294059 AATTAATATTTTCAACTTTTCCTAAAAAATATGGTTTTTGAAATTTTTATTTT
66 AATTGATACTTTCAACTTTTCCTCAAAAATAT--TTTTTGAAAATTTTATTTT
* * * * * ** **
12294112 CATGAAAAGTTGATACTTTCAATTTTTTCTCAAAAGTATATTTTTTTTAA-TTGGA-TTTCAAGA
1 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA--ATATTTTTTGAAATTTTTATTTTCAAGA
* *
12294175 AAAATTGATACTTTCAACTTTT--TCGTAAAATA-TTTTTGAAAATTTTACTTT
64 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTGAAAATTTTATTTT
12294226 TA
1 TA
12294228 TTTTTTGGTT
Statistics
Matches: 202, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
114 18 0.09
115 1 0.00
116 1 0.00
117 104 0.51
118 31 0.15
119 3 0.01
120 15 0.07
121 29 0.14
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (116 bp):
TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATTTTCAAGAAA
AATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTATTTT
Found at i:12295606 original size:52 final size:52
Alignment explanation
Indices: 12295539--12295695 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 52
12295529 TATAATCATA
* * *
12295539 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * *
12295591 CAAACTTGCCTATTAAGAATCCATTTCCTTTTAGAATTCTTTTCTTACAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * *
12295643 CAAACTTACCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
12295695 C
1 C
12295696 TTCTTGTCCA
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 90 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:12296041 original size:50 final size:50
Alignment explanation
Indices: 12295987--12296081 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
12295977 AAACTCTTCC
* * * * *
12295987 CACATCTCGAACCTTTGACTCTTTTCACGTTTTGAACCTTTAGCTTTTTT
1 CACATCTCGAACCTTTAACTCTTCTCACATTTCGAACCTTCAGCTTTTTT
* *
12296037 CACATCTTGAATCTTTAACTCTTCTCACATTTCGAACCTTCAGCT
1 CACATCTCGAACCTTTAACTCTTCTCACATTTCGAACCTTCAGCT
12296082 CTGATACCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.21, C:0.28, G:0.08, T:0.42
Consensus pattern (50 bp):
CACATCTCGAACCTTTAACTCTTCTCACATTTCGAACCTTCAGCTTTTTT
Found at i:12296083 original size:25 final size:25
Alignment explanation
Indices: 12295980--12296083 Score: 86
Period size: 25 Copynumber: 4.2 Consensus size: 25
12295970 TCAAACCAAA
* *
12295980 CTCTTCCCACATCTCGAACCTTT-G
1 CTCTTCTCACATTTCGAACCTTTAG
* * *
12296004 ACTCTTTTCACGTTTTGAACCTTTAG
1 -CTCTTCTCACATTTCGAACCTTTAG
* * * *
12296030 CTTTTTTCACATCTT-GAATCTTTAA
1 CTCTTCTCACAT-TTCGAACCTTTAG
*
12296055 CTCTTCTCACATTTCGAACCTTCAG
1 CTCTTCTCACATTTCGAACCTTTAG
12296080 CTCT
1 CTCT
12296084 GATACCACTT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
24 2 0.03
25 57 0.92
26 3 0.05
ACGTcount: A:0.19, C:0.31, G:0.08, T:0.42
Consensus pattern (25 bp):
CTCTTCTCACATTTCGAACCTTTAG
Found at i:12296696 original size:52 final size:52
Alignment explanation
Indices: 12296610--12296754 Score: 204
Period size: 52 Copynumber: 2.8 Consensus size: 52
12296600 TATAATCATA
* * * * *
12296610 CAAACTTGCCCATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
12296662 CAAACTTACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
*
12296714 CAAACTTA-CTATTAAGAAT-CCTTTTCTCTTAGAATTCTTCT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCT
12296755 TTTCAAGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
50 20 0.24
51 11 0.13
52 53 0.63
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:12296803 original size:11 final size:11
Alignment explanation
Indices: 12296787--12296827 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
12296777 AGTAATATTT
*
12296787 AACAAATCTCA
1 AACAAATCCCA
12296798 AACAAATCCCA
1 AACAAATCCCA
12296809 AACAAATCCCA
1 AACAAATCCCA
*
12296820 AACTAATC
1 AACAAATC
12296828 TCTTATGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.15
Consensus pattern (11 bp):
AACAAATCCCA
Found at i:12300816 original size:48 final size:49
Alignment explanation
Indices: 12300732--12300828 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 49
12300722 TTGGATCTAG
12300732 TATAAATCTGACGTTTATAAATGTTGTCATGCAGCTAAGGTGTGGTATA
1 TATAAATCTGACGTTTATAAATGTTGTCATGCAGCTAAGGTGTGGTATA
* *
12300781 TATAAATCTGATGTTTA-AAATGTTGTCATGTAGCTAAGGTGTGGTATA
1 TATAAATCTGACGTTTATAAATGTTGTCATGCAGCTAAGGTGTGGTATA
12300829 CTGAAACATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 30 0.65
49 16 0.35
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (49 bp):
TATAAATCTGACGTTTATAAATGTTGTCATGCAGCTAAGGTGTGGTATA
Found at i:12302044 original size:16 final size:17
Alignment explanation
Indices: 12302004--12302045 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
12301994 ATTCTAGACT
12302004 ATGTGAAAAAATGGCTA
1 ATGTGAAAAAATGGCTA
* *
12302021 AAG-CAAAAAATGGC-A
1 ATGTGAAAAAATGGCTA
12302036 ATGTGAAAAA
1 ATGTGAAAAA
12302046 CAATGCTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
15 3 0.15
16 15 0.75
17 2 0.10
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.17
Consensus pattern (17 bp):
ATGTGAAAAAATGGCTA
Found at i:12303101 original size:28 final size:29
Alignment explanation
Indices: 12303056--12303113 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 29
12303046 ACTACATTGG
12303056 TCTTGGAATTGAATCTTAG-TCGAAACTTA
1 TCTTGGAATTGAATCTTAGCT-GAAACTTA
12303085 TCTTGGAA-TGAATCTTAGCTGAAACTTA
1 TCTTGGAATTGAATCTTAGCTGAAACTTA
12303113 T
1 T
12303114 TAAGTATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (29 bp):
TCTTGGAATTGAATCTTAGCTGAAACTTA
Found at i:12309127 original size:25 final size:25
Alignment explanation
Indices: 12309073--12309123 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
12309063 ATCTTTACTA
12309073 TTATTATTTTTTACCTTAATTTATC
1 TTATTATTTTTTACCTTAATTTATC
* *
12309098 CTATTATTTATTTGCC-T-ATTTATC
1 TTATTATTT-TTTACCTTAATTTATC
12309122 TT
1 TT
12309124 TATTTATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
24 8 0.36
25 9 0.41
26 5 0.23
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTATTTTTTACCTTAATTTATC
Found at i:12309143 original size:16 final size:17
Alignment explanation
Indices: 12309116--12309147 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12309106 TATTTGCCTA
12309116 TTTATCTTTATTTATCT
1 TTTATCTTTATTTATCT
12309133 TTTAT-TTTATTTATC
1 TTTATCTTTATTTATC
12309148 CTATTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATCTTTATTTATCT
Found at i:12309157 original size:16 final size:16
Alignment explanation
Indices: 12309091--12309158 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
12309081 TTTTACCTTA
*
12309091 ATTTATCCTATTATTT
1 ATTTATCCTATTCTTT
*
12309107 ATTT-GCCTATTTATCTTT
1 ATTTATCCTA--T-TCTTT
* *
12309125 ATTTAT-CTTTTATTTT
1 ATTTATCCTATT-CTTT
12309141 ATTTATCCTATTCTTT
1 ATTTATCCTATTCTTT
12309157 AT
1 AT
12309159 CTTTAATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
15 5 0.13
16 19 0.49
17 5 0.13
18 10 0.26
ACGTcount: A:0.21, C:0.13, G:0.01, T:0.65
Consensus pattern (16 bp):
ATTTATCCTATTCTTT
Found at i:12320934 original size:29 final size:29
Alignment explanation
Indices: 12320892--12320947 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
12320882 ATACTTAATA
12320892 AGTTTCAGCTAAGATTCAATTCCAAGATG
1 AGTTTCAGCTAAGATTCAATTCCAAGATG
12320921 AGTTTC-GACTAAGATTCAATTCCAAGA
1 AGTTTCAG-CTAAGATTCAATTCCAAGA
12320948 CCATGTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (29 bp):
AGTTTCAGCTAAGATTCAATTCCAAGATG
Found at i:12323266 original size:49 final size:50
Alignment explanation
Indices: 12323209--12323307 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
12323199 AATGTTTCAG
12323209 TATACCACACCTTAGC-TACATGACAACATTTATAAACATCAGATTTATA
1 TATACCACACCTTAGCTTACATGACAACATTTATAAACATCAGATTTATA
* *
12323258 TATACCACACCTTAGCTTGCATGACAACATTTATAAACGTCAGATTTATA
1 TATACCACACCTTAGCTTACATGACAACATTTATAAACATCAGATTTATA
12323308 CTGAAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 16 0.34
50 31 0.66
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.31
Consensus pattern (50 bp):
TATACCACACCTTAGCTTACATGACAACATTTATAAACATCAGATTTATA
Found at i:12327194 original size:11 final size:11
Alignment explanation
Indices: 12327176--12327207 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12327166 AATCCTATAA
12327176 GAGATTTGTTT
1 GAGATTTGTTT
*
12327187 GGGATTTGTTT
1 GAGATTTGTTT
12327198 GAGATTTGTT
1 GAGATTTGTT
12327208 AAATATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:12327387 original size:52 final size:52
Alignment explanation
Indices: 12327232--12327387 Score: 204
Period size: 52 Copynumber: 3.0 Consensus size: 52
12327222 GGATAAGAAT
* * * * * *
12327232 ACTTGCAAAAGAAGAATTCTAAGAGAAAAGAGATTCTTAATAGGTAAGTTTA
1 ACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
* * * *
12327284 ACTTGCAAGAGAATAATTCTAAAAAGAAAGGGATTCTTAATAGGCAAGTTTG
1 ACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
* *
12327336 ACTTACAGGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATGGGCAAGTTTG
1 ACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
12327388 TATGATTATA
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 90 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (52 bp):
ACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
Found at i:12327964 original size:25 final size:25
Alignment explanation
Indices: 12327926--12328024 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 25
12327916 ATCAGAGCTG
*
12327926 AAGGTTCGAA-ATGTGAGAAGAGTTA
1 AAGGTTC-AAGATGTGAAAAGAGTTA
* * *
12327951 AAGATTCAAGATGTGAAAAAAGCTA
1 AAGGTTCAAGATGTGAAAAGAGTTA
* * *
12327976 AAGGTTCAAAACGTGAAAAGAGTCA
1 AAGGTTCAAGATGTGAAAAGAGTTA
* **
12328001 AAGGTTCGAGATGTGGGAAGAGTT
1 AAGGTTCAAGATGTGAAAAGAGTT
12328025 TGGTTTGAGA
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 2 0.04
25 55 0.96
ACGTcount: A:0.42, C:0.07, G:0.29, T:0.21
Consensus pattern (25 bp):
AAGGTTCAAGATGTGAAAAGAGTTA
Found at i:12328013 original size:50 final size:50
Alignment explanation
Indices: 12327921--12328015 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
12327911 GTGGTATCAG
* * * * *
12327921 AGCTGAAGGTTCGAAATGTGAGAAGAGTTAAAGATTCAAGATGTGAAAAA
1 AGCTAAAGGTTCAAAACGTGAAAAGAGTCAAAGATTCAAGATGTGAAAAA
* *
12327971 AGCTAAAGGTTCAAAACGTGAAAAGAGTCAAAGGTTCGAGATGTG
1 AGCTAAAGGTTCAAAACGTGAAAAGAGTCAAAGATTCAAGATGTG
12328016 GGAAGAGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.28, T:0.21
Consensus pattern (50 bp):
AGCTAAAGGTTCAAAACGTGAAAAGAGTCAAAGATTCAAGATGTGAAAAA
Found at i:12328277 original size:11 final size:11
Alignment explanation
Indices: 12328259--12328290 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12328249 AATCCCATAA
12328259 GAGATTTGTTT
1 GAGATTTGTTT
*
12328270 GGGATTTGTTT
1 GAGATTTGTTT
12328281 GAGATTTGTT
1 GAGATTTGTT
12328291 AAGTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:12328402 original size:52 final size:52
Alignment explanation
Indices: 12328314--12328470 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
12328304 TGGACAAGAA
* *
12328314 GACTTGCAAAAGAAGAATTCTAAGA-GAAATGAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAATG-GATTCTTAATAGGCAAGTTT
* * *
12328366 GACTTGTAAGAGAAGCATTCTAAAAGGAAATGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAATGGATTCTTAATAGGCAAGTTT
* * * *
12328418 GACTTACAAGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAATGGATTCTTAATAGGCAAGTTT
12328470 G
1 G
12328471 TATGATTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 86 0.93
53 6 0.07
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAATGGATTCTTAATAGGCAAGTTT
Found at i:12329047 original size:25 final size:25
Alignment explanation
Indices: 12329019--12329067 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12329009 AAGGTTCGAA
* *
12329019 ATGTGAGAAGAGTTGAAGATTCAAG
1 ATGTGAAAAAAGTTGAAGATTCAAG
*
12329044 ATGTGAAAAAAGTTGAAGGTTCAA
1 ATGTGAAAAAAGTTGAAGATTCAA
12329068 AACATGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.24
Consensus pattern (25 bp):
ATGTGAAAAAAGTTGAAGATTCAAG
Found at i:12329075 original size:25 final size:25
Alignment explanation
Indices: 12329029--12329077 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12329019 ATGTGAGAAG
* **
12329029 AGTTGAAGATTCAAGATGTGAAAAA
1 AGTTGAAGATTCAAAACATGAAAAA
*
12329054 AGTTGAAGGTTCAAAACATGAAAA
1 AGTTGAAGATTCAAAACATGAAAA
12329078 GAGTCAAAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.22
Consensus pattern (25 bp):
AGTTGAAGATTCAAAACATGAAAAA
Found at i:12329479 original size:52 final size:52
Alignment explanation
Indices: 12329387--12329542 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
12329377 GGACAAGAAA
* * *
12329387 ACTTGCAAAAGAAGAATTCTAAGA-GAAAGGAGATTTTTAATAGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGGAAAGG-GATTCTTAATAGGCAAGTTTG
* * *
12329439 ACTTGCAAGAGAAGCATTCTAAAAGGAAATGGATTCTTAATAGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
** *
12329491 ACTTATAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAGA-GGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTA-ATAGGCAAGTTTG
12329543 TGTGATTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
52 84 0.93
53 6 0.07
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (52 bp):
ACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
Done.