Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 30 of 147
Found at i:6209207 original size:32 final size:32
Alignment explanation
Indices: 6209161--6209225 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
6209151 AGCTATTTTG
*
6209161 ACTGCAAAAAAAGAATGAAATCAAGGTTAGCA
1 ACTGCAAAAAAAGAATGAAATCAAGATTAGCA
*
6209193 ACTGTAAAAAAAGAATGAAATCAAGATTAGCA
1 ACTGCAAAAAAAGAATGAAATCAAGATTAGCA
6209225 A
1 A
6209226 GAGGTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (32 bp):
ACTGCAAAAAAAGAATGAAATCAAGATTAGCA
Found at i:6210344 original size:16 final size:16
Alignment explanation
Indices: 6210319--6210356 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6210309 ATTATTCAAA
6210319 TTTTTGTGAGTTTTTT
1 TTTTTGTGAGTTTTTT
*
6210335 TTTTTTTGAGTTTTTT
1 TTTTTGTGAGTTTTTT
*
6210351 TGTTTG
1 TTTTTG
6210357 CAATTAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.00, G:0.18, T:0.76
Consensus pattern (16 bp):
TTTTTGTGAGTTTTTT
Found at i:6213573 original size:13 final size:13
Alignment explanation
Indices: 6213553--6213597 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6213543 CTGATAATTT
6213553 AAAATATGATA-A
1 AAAATATGATACA
6213565 AATAATATGATACA
1 AA-AATATGATACA
* *
6213579 AAAATAAGATATA
1 AAAATATGATACA
6213592 AAAATA
1 AAAATA
6213598 ATATAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 24 0.83
14 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (13 bp):
AAAATATGATACA
Found at i:6213656 original size:29 final size:28
Alignment explanation
Indices: 6213591--6213657 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
6213581 AATAAGATAT
**
6213591 AAAAATA-ATATAATTTAAAATTTTAAC
1 AAAAATATATATAATTTAAAAAATTAAC
*
6213618 AATAACTATATATAAGTTTAATAAAATTAA-
1 AA-AAATATATATAA-TTTAA-AAAATTAAC
6213648 AAAAATATAT
1 AAAAATATAT
6213658 TTTATGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.06
28 4 0.12
29 13 0.41
30 7 0.22
31 6 0.19
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATATATATAATTTAAAAAATTAAC
Found at i:6217165 original size:27 final size:27
Alignment explanation
Indices: 6217120--6217175 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
6217110 TAAAAGGAAG
* * *
6217120 ATAATGGGAGTGAGGAAGAGAGAGAAT
1 ATAATGGAAGAGAGAAAGAGAGAGAAT
6217147 ATAATGGAAGAGAGAAAGAGAGAGAAT
1 ATAATGGAAGAGAGAAAGAGAGAGAAT
6217174 AT
1 AT
6217176 GGGTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (27 bp):
ATAATGGAAGAGAGAAAGAGAGAGAAT
Found at i:6219032 original size:22 final size:21
Alignment explanation
Indices: 6219002--6219051 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6218992 TAGCTAATCT
* * *
6219002 AATTGGATTAAGATAAAATTTA
1 AATTTGATTAA-ATAAAACTCA
*
6219024 AATTTGATTAAATTAAACTCA
1 AATTTGATTAAATAAAACTCA
6219045 AATTTGA
1 AATTTGA
6219052 ATAATTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTTGATTAAATAAAACTCA
Found at i:6225698 original size:21 final size:21
Alignment explanation
Indices: 6225672--6225717 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6225662 ATATATTATT
6225672 TTATATTTA-AAAAATAATATC
1 TTATA-TTACAAAAATAATATC
* *
6225693 TTATATTACAAAATTAATATT
1 TTATATTACAAAAATAATATC
6225714 TTAT
1 TTAT
6225718 TAATTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATTACAAAAATAATATC
Found at i:6235004 original size:2 final size:2
Alignment explanation
Indices: 6234997--6235021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6234987 TCTATGTTTG
6234997 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
6235022 AAGGATAAGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6236640 original size:22 final size:22
Alignment explanation
Indices: 6236612--6236655 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6236602 ATTTTTTGTT
* *
6236612 CTTAATTTTAGGGACACAAATA
1 CTTAATTCTAGAGACACAAATA
*
6236634 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGACACAAATA
6236656 TAAATACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGACACAAATA
Found at i:6240697 original size:22 final size:22
Alignment explanation
Indices: 6240672--6240715 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6240662 ATTTTTTGTC
*
6240672 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
6240694 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
6240716 TAAATACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:6240727 original size:22 final size:22
Alignment explanation
Indices: 6240679--6240727 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
6240669 GTCCTTAATT
* * *
6240679 CTAGGGATACAAATACTTAATT
1 CTAGAGATACAAATACTAAATA
6240701 CTAGAGATACAAATA-TAAATA
1 CTAGAGATACAAATACTAAATA
6240722 CATAGA
1 C-TAGA
6240728 TTACAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (22 bp):
CTAGAGATACAAATACTAAATA
Found at i:6247608 original size:30 final size:30
Alignment explanation
Indices: 6247573--6247629 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6247563 TTTAATATCT
*
6247573 GATTTGGATAATTTATGAA-TTTAATTATTC
1 GATTTGAATAATTTAT-AAGTTTAATTATTC
6247603 GATTTGAATAATTTATAAGTTTAATTA
1 GATTTGAATAATTTATAAGTTTAATTA
6247630 AATTTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (30 bp):
GATTTGAATAATTTATAAGTTTAATTATTC
Found at i:6247633 original size:18 final size:18
Alignment explanation
Indices: 6247612--6247669 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
6247602 CGATTTGAAT
6247612 AATTTATAAGTTTAATTA
1 AATTTATAAGTTTAATTA
*
6247630 AATTTTTAAGTATTAATATA
1 AATTTATAAGT-TTAAT-TA
** * *
6247650 TTTTTATTATTTTAATTA
1 AATTTATAAGTTTAATTA
6247668 AA
1 AA
6247670 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
18 12 0.40
19 10 0.33
20 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
AATTTATAAGTTTAATTA
Found at i:6247765 original size:18 final size:16
Alignment explanation
Indices: 6247719--6247766 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
6247709 TTACAAATTT
*
6247719 AATTATTAAATTTAAAT
1 AATT-TTAAATTTAAAA
6247736 AATTTATAAATTTAATTAA
1 AATTT-TAAATTTAA--AA
6247755 AATTTTAAATTT
1 AATTTTAAATTT
6247767 TAATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 1 0.04
17 13 0.48
18 7 0.26
19 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTAAATTTAAAA
Found at i:6248310 original size:11 final size:11
Alignment explanation
Indices: 6248294--6248320 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6248284 CTGAGAGAGA
6248294 CAAAGAAAGAT
1 CAAAGAAAGAT
6248305 CAAAGAAAGAT
1 CAAAGAAAGAT
6248316 CAAAG
1 CAAAG
6248321 TCGTTTCATT
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:0.63, C:0.11, G:0.19, T:0.07
Consensus pattern (11 bp):
CAAAGAAAGAT
Found at i:6260789 original size:17 final size:19
Alignment explanation
Indices: 6260744--6260792 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
6260734 TAAAAATGTC
*
6260744 TTTTAATATTAT-AAATAA
1 TTTTAATATAATAAAATAA
6260762 TTTTAAATATAATAAAAT-A
1 TTTT-AATATAATAAAATAA
6260781 -TTTAATATAATA
1 TTTTAATATAATA
6260793 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 8 0.29
20 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTAATATAATAAAATAA
Found at i:6272533 original size:22 final size:22
Alignment explanation
Indices: 6272500--6272541 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
6272490 TTTGTATTTT
6272500 TGAAGCCTATAAAT-TAATGAAA
1 TGAAGCCTAT-AATCTAATGAAA
6272522 TGAAG-CTCATAATCTAATGA
1 TGAAGCCT-ATAATCTAATGA
6272542 GCCAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (22 bp):
TGAAGCCTATAATCTAATGAAA
Found at i:6289813 original size:5 final size:5
Alignment explanation
Indices: 6289796--6289833 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
6289786 AGCATATAAA
* *
6289796 CATGT CATAT CATGT CATGT CATGT CATGT CACGT CAT
1 CATGT CATGT CATGT CATGT CATGT CATGT CATGT CAT
6289834 CTTTATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (5 bp):
CATGT
Found at i:6290843 original size:13 final size:14
Alignment explanation
Indices: 6290815--6290843 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6290805 AAATAGTAAT
6290815 TTATAATCTATAAC
1 TTATAATCTATAAC
6290829 TTATAATCT-TAAC
1 TTATAATCTATAAC
6290842 TT
1 TT
6290844 TTTTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATCTATAAC
Found at i:6292056 original size:25 final size:25
Alignment explanation
Indices: 6292031--6292089 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
6292021 ACTATCCTAT
*
6292031 AGCATATAGTTTTTGACCTAAATATA
1 AGCA-ATAGCTTTTGACCTAAATATA
* *
6292057 ATCAATGGCTTTTGACCTAAATATTA
1 AGCAATAGCTTTTGACCTAAATA-TA
*
6292083 ACCAATA
1 AGCAATA
6292090 ACTTATAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (25 bp):
AGCAATAGCTTTTGACCTAAATATA
Found at i:6293131 original size:76 final size:74
Alignment explanation
Indices: 6293051--6293228 Score: 189
Period size: 77 Copynumber: 2.4 Consensus size: 74
6293041 AAATATAACG
* * *
6293051 TATAATCTTTGACCTAACTTTTTATTTTTATTAACCTACTAACTATAACCTTTGGCTCAAATACT
1 TATAATCTTTGACCTAACTTTTT-TTTTTATTAACCTACTAACTATAAACTTTGGCCCAAAAACT
6293116 AACTTAT-AGC
65 AACTTATGA-C
* * * * **
6293126 TTATAATTTTTAACCTAATCTTTTCTTTTTTATTACCCTATTGGCTATAAACTTTGGCCCAAAAA
1 -TATAATCTTTGACCTAA-CTTTT-TTTTTTATTAACCTACTAACTATAAACTTTGGCCCAAAAA
*
6293191 GTAACTTATGAC
63 CTAACTTATGAC
* *
6293203 T-TAACCTTTGACCCAACTTTTTTTTT
1 TATAATCTTTGACCTAACTTTTTTTTT
6293229 CTACTAAACT
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
73 5 0.06
74 5 0.06
75 11 0.13
76 16 0.19
77 46 0.54
78 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (74 bp):
TATAATCTTTGACCTAACTTTTTTTTTTATTAACCTACTAACTATAAACTTTGGCCCAAAAACTA
ACTTATGAC
Found at i:6295502 original size:74 final size:76
Alignment explanation
Indices: 6295424--6295599 Score: 177
Period size: 74 Copynumber: 2.4 Consensus size: 76
6295414 CTTATTAGGC
**
6295424 ATAGCATTTGTTCCAAATAGTAACATAA-AGCT-TATAGTCTTTGACTTAA-CTTTT-TATTTAT
1 ATAGCATTTGTTCCAAATAGTAACATAATAGCTATA-AG-CTTTGACCCAACCTTTTCTATTTAT
*
6295485 TAA-CTTATTGACA
64 TAATCTT-TTAACA
** * * * *
6295498 ATAGCATTTGGCCCAAATGGTAACCTAATAGCTATAAGCTTTGGCCCAACCTTTTCTTTTTATTA
1 ATAGCATTTGTTCCAAATAGTAACATAATAGCTATAAGCTTTGACCCAACCTTTTCTATTTATTA
6295563 ATCTTTTAACA
66 ATCTTTTAACA
*
6295574 ATAGC-TTTGATT-TAAATAGTAACATA
1 ATAGCATTTG-TTCCAAATAGTAACATA
6295600 TAATATGTTG
Statistics
Matches: 82, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
74 32 0.39
75 26 0.32
76 21 0.26
77 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (76 bp):
ATAGCATTTGTTCCAAATAGTAACATAATAGCTATAAGCTTTGACCCAACCTTTTCTATTTATTA
ATCTTTTAACA
Found at i:6296895 original size:19 final size:20
Alignment explanation
Indices: 6296871--6296908 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6296861 TAAATTTGAC
6296871 ATATTA-ATAATATAAAAAA
1 ATATTACATAATATAAAAAA
*
6296890 ATATTACATATTATAAAAA
1 ATATTACATAATATAAAAA
6296909 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATTACATAATATAAAAAA
Found at i:6296898 original size:26 final size:26
Alignment explanation
Indices: 6296869--6296921 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6296859 AATAAATTTG
* *
6296869 ACATATTA-ATAATATAAAAAAATATT
1 ACATATTATA-AAAATAAAAAAAAATT
6296895 ACATATTATAAAAATAAAAAAAAATT
1 ACATATTATAAAAATAAAAAAAAATT
6296921 A
1 A
6296922 ATACTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (26 bp):
ACATATTATAAAAATAAAAAAAAATT
Found at i:6296958 original size:6 final size:6
Alignment explanation
Indices: 6296938--6296976 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
6296928 ATTTAATATG
*
6296938 TATTTAA TATATA TATTTA TATTTA TATTTA TA-TTA TAT
1 TATTT-A TATTTA TATTTA TATTTA TATTTA TATTTA TAT
6296977 AACTATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 5 0.17
6 20 0.69
7 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATTTA
Found at i:6296983 original size:25 final size:25
Alignment explanation
Indices: 6296938--6296985 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
6296928 ATTTAATATG
**
6296938 TATTTAATATATATATTTATATTTA
1 TATTTAATATATATAACTATATTTA
6296963 TATTT-ATATTATATAACTATATT
1 TATTTAATA-TATATAACTATATT
6296986 AATTTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTTAATATATATAACTATATTTA
Found at i:6298431 original size:76 final size:73
Alignment explanation
Indices: 6298351--6298768 Score: 211
Period size: 77 Copynumber: 5.5 Consensus size: 73
6298341 TAGCCTAATT
* *
6298351 TTTTCTTTTTATTAACATATTAGTTATGATCTTTAGCCCAAATAGTAATCTATATCCCATAGGCT
1 TTTTCTTTTTATTAACATATTAGTTAT-ACCTTTAGCCCAAATAGTAA-CTATATCCCATAGCCT
6298416 TTGGTCCAAC
64 TTGGTCCAAC
* * ** * * * * **
6298426 ATTTTCTTTTCATTAACATATTAGCTATAGTTTTTTA-TCTAAATACTAATATATATCATATAGC
1 -TTTTCTTTTTATTAACATATTAGTTATA--CCTTTAGCCCAAATAGTAA-CTATATCCCATAGC
*
6298490 CTTTGGTCCAAAAAAA
62 CTTTGGTCC----AAC
* * * * * *
6298506 ATTT-TTTTTATCAACAAATT-GCTATAACCTTTTGTCCAAATTA-TAACATATATCCCATAGCC
1 TTTTCTTTTTATTAACATATTAGTTAT-ACCTTTAGCCCAAA-TAGTAAC-TATATCCCATAGCC
**
6298568 TTTGGTTTAAC
63 TTTGGTCCAAC
* * * * * *
6298579 TTTTCATTTTATTAACATATCA-TTGATAACATTTCA-CCCAAATAGTAAACTATAACCAATACC
1 TTTTCTTTTTATTAACATATTAGTT-AT-ACCTTT-AGCCCAAATAGT-AACTATATCCCATAGC
*** *
6298642 CTTTAAACTAAC
62 CTTTGGTCCAAC
* * * *
6298654 TTTTTTCTTTTTATTAACTTATTAGTTATAGCCTTT-GTCCTAAATAGTAACTTATATCCTATAA
1 --TTTTCTTTTTATTAACATATTAGTTATA-CCTTTAG-CCCAAATAGTAAC-TATATCCCATAG
** *
6298718 TTTTTTGTCCAAC
61 CCTTTGGTCCAAC
* ** *
6298731 TTTTTTTTTTATTAACATATTAGCCATAGCTTTAGCCC
1 TTTTCTTTTTATTAACATATTAGTTATACCTTTAGCCC
6298769 CTAATAATAA
Statistics
Matches: 257, Mismatches: 61, Indels: 50
0.70 0.17 0.14
Matches are distributed among these distances:
73 5 0.02
74 21 0.08
75 58 0.23
76 64 0.25
77 86 0.33
78 18 0.07
79 3 0.01
80 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (73 bp):
TTTTCTTTTTATTAACATATTAGTTATACCTTTAGCCCAAATAGTAACTATATCCCATAGCCTTT
GGTCCAAC
Found at i:6301636 original size:20 final size:20
Alignment explanation
Indices: 6301611--6301651 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6301601 GTCCAATTAT
6301611 TTTTTTATTAATCTATTAAC
1 TTTTTTATTAATCTATTAAC
6301631 TTTTTTATTAATCTATTAAC
1 TTTTTTATTAATCTATTAAC
6301651 T
1 T
6301652 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTATTAATCTATTAAC
Found at i:6301872 original size:33 final size:32
Alignment explanation
Indices: 6301786--6301872 Score: 81
Period size: 33 Copynumber: 2.6 Consensus size: 32
6301776 TTTTTATTCT
*
6301786 TAATCTAGTGACTATAGCCTTGGTCCTAAATAG
1 TAATCTA-TAACTATAGCCTTGGTCCTAAATAG
*
6301819 TAATCTATAACGTATTGCCTTAGGAT-C-AAATAG
1 TAATCTATAAC-TATAGCCTT-GG-TCCTAAATAG
6301852 TAA-CTGATAAGCTATAGCCTT
1 TAATCT-ATAA-CTATAGCCTT
6301873 TACTCAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
32 5 0.11
33 36 0.78
34 4 0.09
35 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (32 bp):
TAATCTATAACTATAGCCTTGGTCCTAAATAG
Found at i:6304897 original size:114 final size:114
Alignment explanation
Indices: 6304695--6304920 Score: 382
Period size: 114 Copynumber: 2.0 Consensus size: 114
6304685 TCCGGTACTT
*
6304695 GAAATTTACCAGGTGTTAGCAACATTCTAAATGCAATAACACACAAGCAAAAACATTCCAAAGTA
1 GAAATTTACCAGGTATTAGCAACATTCTAAATGCAATAACACACAAGCAAAAACATTCCAAAGTA
6304760 CTTAAAAGAGTCAAGACAAGCTGTAGAGACTAAAATCTGCATTAAGTCC
66 CTTAAAAGAGTCAAGACAAGCTGTAGAGACTAAAATCTGCATTAAGTCC
*
6304809 GAAATTTACC-GGCTATTAGCAACATTCTAAATGCAATAACACACAAGTAAAAACATTCCAAAGT
1 GAAATTTACCAGG-TATTAGCAACATTCTAAATGCAATAACACACAAGCAAAAACATTCCAAAGT
* * * *
6304873 ACTTAAAAGAGTCGAGACAGGCTGTGGAGCCTAAAATCTGCATTAAGT
65 ACTTAAAAGAGTCAAGACAAGCTGTAGAGACTAAAATCTGCATTAAGT
6304921 TATAAACACA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 2 0.02
114 103 0.98
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (114 bp):
GAAATTTACCAGGTATTAGCAACATTCTAAATGCAATAACACACAAGCAAAAACATTCCAAAGTA
CTTAAAAGAGTCAAGACAAGCTGTAGAGACTAAAATCTGCATTAAGTCC
Found at i:6305817 original size:12 final size:11
Alignment explanation
Indices: 6305798--6305827 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
6305788 TTTTTGTTTT
6305798 AATTTTATTAA
1 AATTTTATTAA
6305809 AATTATTATTAA
1 AATT-TTATTAA
6305821 AATTTTA
1 AATTTTA
6305828 AGACATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTTATTAA
Found at i:6309903 original size:18 final size:18
Alignment explanation
Indices: 6309880--6309915 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6309870 ACTCTTTGTC
6309880 CTACTGAGTTCTGGCGCA
1 CTACTGAGTTCTGGCGCA
6309898 CTACTGAGTTCTGGCGCA
1 CTACTGAGTTCTGGCGCA
6309916 GGTTTGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (18 bp):
CTACTGAGTTCTGGCGCA
Found at i:6313798 original size:98 final size:98
Alignment explanation
Indices: 6313629--6313808 Score: 315
Period size: 98 Copynumber: 1.8 Consensus size: 98
6313619 ATAGGAACCT
* * *
6313629 TAAACTGGCAATCAAACGAAAAGAAAAACAACGAAGCAAAGCCTAAAGCATGATGATGTGTTGTC
1 TAAACTGACAATCAAACGAAAAGAAAAACAACAAAGCAAAGCCTAAAGCATGATGATGAGTTGTC
6313694 CTTATCGTTACCTTCGAGTATTGGAACCCTAAA
66 CTTATCGTTACCTTCGAGTATTGGAACCCTAAA
*
6313727 TAAACTGACAATCAAACGAAAAGAAAAACAACAAAGCAAAGCCTAAAGCTTGATGATGAGTTGTC
1 TAAACTGACAATCAAACGAAAAGAAAAACAACAAAGCAAAGCCTAAAGCATGATGATGAGTTGTC
*
6313792 GTTATCGTTACCTTCGA
66 CTTATCGTTACCTTCGA
6313809 TTGGAAGATA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (98 bp):
TAAACTGACAATCAAACGAAAAGAAAAACAACAAAGCAAAGCCTAAAGCATGATGATGAGTTGTC
CTTATCGTTACCTTCGAGTATTGGAACCCTAAA
Found at i:6315417 original size:18 final size:19
Alignment explanation
Indices: 6315394--6315459 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 19
6315384 ATAATTATTT
6315394 TTTTAATTAAATTTA-AAA
1 TTTTAATTAAATTTATAAA
6315412 TTTTAATTAAATTTATAAA
1 TTTTAATTAAATTTATAAA
6315431 TTATTTAAATTAAATATT-TAAA
1 -T-TTT-AATTAAAT-TTATAAA
6315453 TATTTAA
1 T-TTTAA
6315460 ATTTAACTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 15 0.35
19 3 0.07
20 3 0.07
21 8 0.19
22 12 0.28
23 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAATTAAATTTATAAA
Found at i:6315436 original size:22 final size:20
Alignment explanation
Indices: 6315398--6315462 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 20
6315388 TTATTTTTTT
*
6315398 AATTAAA-TTTAAA-ATTTT
1 AATTAAATTTTAAATATTTA
6315416 AATTAAATTTATAAATTATTTA
1 AATTAAATTT-TAAA-TATTTA
6315438 AATTAAATATTTAAATATTTA
1 AATTAAAT-TTTAAATATTTA
6315459 AATT
1 AATT
6315463 TAACTCACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
18 7 0.17
19 2 0.05
20 4 0.10
21 10 0.24
22 16 0.39
23 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAATTTTAAATATTTA
Found at i:6317815 original size:27 final size:28
Alignment explanation
Indices: 6317785--6317849 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
6317775 GTCATAAGAA
*
6317785 TAATTTAATAAAATTTTA-ATTATTTAT
1 TAATTTAATAAAATTTTATATTATGTAT
* *
6317812 TAATTTTAT-GAATTTTATATTATGTAT
1 TAATTTAATAAAATTTTATATTATGTAT
*
6317839 AAATTTTAATA
1 TAA-TTTAATA
6317850 TAATAACTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 7 0.23
27 18 0.60
28 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
TAATTTAATAAAATTTTATATTATGTAT
Found at i:6322969 original size:15 final size:13
Alignment explanation
Indices: 6322934--6322963 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6322924 TATCGAAAAA
*
6322934 AAATTTTGTTGAT
1 AAATTTTATTGAT
6322947 AAATTTTATTGAT
1 AAATTTTATTGAT
6322960 AAAT
1 AAAT
6322964 ATTTTAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (13 bp):
AAATTTTATTGAT
Found at i:6324064 original size:25 final size:25
Alignment explanation
Indices: 6324026--6324078 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
6324016 AGACATTAGA
6324026 TTAAATATTAAATA-TAATAAAAAT
1 TTAAATATTAAATATTAATAAAAAT
* *
6324050 TTAAATTATTTAATATTTATAAAAAT
1 TTAAA-TATTAAATATTAATAAAAAT
6324076 TTA
1 TTA
6324079 TTAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 8 0.32
26 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAAATATTAAATATTAATAAAAAT
Found at i:6324908 original size:21 final size:20
Alignment explanation
Indices: 6324882--6324923 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
6324872 ACACGATTTA
6324882 AAATTTAAAAAAATTATAAAT
1 AAATTTAAAAAAATTA-AAAT
*
6324903 AAATTTAATAAAATTAAAAT
1 AAATTTAAAAAAATTAAAAT
6324923 A
1 A
6324924 TTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTAAAAAAATTAAAAT
Found at i:6328181 original size:27 final size:27
Alignment explanation
Indices: 6328149--6328203 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6328139 AAAATTTTTA
*
6328149 TTATATCTAACTCAATTCCATTGCACC
1 TTATATCTAACTCAATTCCATTACACC
6328176 TTATATCTAACTCAATTCCATTACACC
1 TTATATCTAACTCAATTCCATTACACC
6328203 T
1 T
6328204 CTTTCGTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.38
Consensus pattern (27 bp):
TTATATCTAACTCAATTCCATTACACC
Found at i:6330034 original size:28 final size:28
Alignment explanation
Indices: 6329967--6330025 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
6329957 TATAATATAA
*
6329967 AAAATATTTAATAAGATACTTAAATTTT
1 AAAATATTTAATAAAATACTTAAATTTT
*
6329995 AAAATATTTAATAAAATACTTATATTTT
1 AAAATATTTAATAAAATACTTAAATTTT
6330023 AAA
1 AAA
6330026 TTTATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (28 bp):
AAAATATTTAATAAAATACTTAAATTTT
Found at i:6330053 original size:18 final size:18
Alignment explanation
Indices: 6330020--6330059 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6330010 ATACTTATAT
*
6330020 TTTAAATTTATTAATTTAA
1 TTTAAATTTATAAATTT-A
6330039 TTTAAA-TTATAAATTTA
1 TTTAAATTTATAAATTTA
6330056 TTTA
1 TTTA
6330060 TTAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATAAATTTA
Found at i:6347634 original size:11 final size:11
Alignment explanation
Indices: 6347606--6347656 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
6347596 ATTAAATTTG
*
6347606 ATAATTTAAAA
1 ATAATATAAAA
6347617 TATAATATAAAA
1 -ATAATATAAAA
6347629 ATAATATGAAAA
1 ATAATAT-AAAA
6347641 A-AATATAAAA
1 ATAATATAAAA
6347651 ATAATA
1 ATAATA
6347657 AAATTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 5 0.14
11 16 0.44
12 15 0.42
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:6348278 original size:2 final size:2
Alignment explanation
Indices: 6348273--6348306 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6348263 ATATATATAT
*
6348273 AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6348307 TTATAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6349247 original size:20 final size:20
Alignment explanation
Indices: 6349191--6349263 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
6349181 TAACTCAATA
* *
6349191 TTATATAAAAAAATTAT-TT
1 TTATATTAAAAAATAATATT
** *
6349210 TTA-ATTAATTAATTATA-T
1 TTATATTAAAAAATAATATT
6349228 TTATATTTAAAAAATAATATT
1 TTATA-TTAAAAAATAATATT
6349249 TTATATTAAAAAATA
1 TTATATTAAAAAATA
6349264 TTTTATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 14 0.32
19 4 0.09
20 20 0.45
21 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATATTAAAAAATAATATT
Found at i:6362017 original size:53 final size:53
Alignment explanation
Indices: 6361937--6362042 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
6361927 AAATAGTTAG
** *
6361937 AAAAAAATTAAGTACCAACAAAAATATATAGTCTCAGAAACAATAAGGTTGAC
1 AAAAAAAGGAAGTACCAACAAAAATATATAGCCTCAGAAACAATAAGGTTGAC
6361990 AAAAAAAGGAAGTACCAACAAAAATATATAGCCTCAGAAACAATAAGGTTGAC
1 AAAAAAAGGAAGTACCAACAAAAATATATAGCCTCAGAAACAATAAGGTTGAC
6362043 TTTAACAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.55, C:0.14, G:0.13, T:0.18
Consensus pattern (53 bp):
AAAAAAAGGAAGTACCAACAAAAATATATAGCCTCAGAAACAATAAGGTTGAC
Found at i:6366317 original size:2 final size:2
Alignment explanation
Indices: 6366310--6366347 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6366300 GGGTTTATTC
6366310 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6366348 GGAATCGACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6373522 original size:14 final size:15
Alignment explanation
Indices: 6373500--6373542 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
6373490 TTTATATTCA
6373500 TTTAGAATTTATTTG
1 TTTAGAATTTATTTG
6373515 TTTA-AATTTATTTG
1 TTTAGAATTTATTTG
* *
6373529 ATTATAATTTATTT
1 TTTAGAATTTATTT
6373543 ATTGTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTAGAATTTATTTG
Found at i:6373560 original size:19 final size:19
Alignment explanation
Indices: 6373520--6373561 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6373510 ATTTGTTTAA
*
6373520 ATTTATTTGATTATAATTT
1 ATTTATTTGATTATAATAT
*
6373539 ATTTA-TTGTTTATAAATAT
1 ATTTATTTGATTAT-AATAT
6373558 ATTT
1 ATTT
6373562 GTTTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
ATTTATTTGATTATAATAT
Found at i:6374923 original size:18 final size:18
Alignment explanation
Indices: 6374895--6374931 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6374885 CTGAATCAAA
6374895 ATTAATTATATAT-TTTT
1 ATTAATTATATATATTTT
6374912 ATTAATTTATATATATTTT
1 ATTAA-TTATATATATTTT
6374931 A
1 A
6374932 AATTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTAATTATATATATTTT
Found at i:6374981 original size:20 final size:21
Alignment explanation
Indices: 6374958--6375011 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
6374948 AATAATTATT
6374958 ATATATATAAAATTAT-TTAA
1 ATATATATAAAATTATATTAA
6374978 ATATAT-TAAAAATTATATTAA
1 ATATATAT-AAAATTATATTAA
6374999 A-ATAATATAAAAT
1 ATAT-ATATAAAAT
6375012 AACAAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 12 0.40
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATATAAAATTATATTAA
Found at i:6379948 original size:21 final size:22
Alignment explanation
Indices: 6379908--6379949 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6379898 TAATTTTAAT
6379908 TAATTTAAAATAATAATTTATA
1 TAATTTAAAATAATAATTTATA
6379930 TAATTTAACAA-AA-AATTTAT
1 TAATTTAA-AATAATAATTTAT
6379950 TTACTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTTAAAATAATAATTTATA
Found at i:6388753 original size:20 final size:20
Alignment explanation
Indices: 6388715--6388754 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6388705 TATATATTGT
*
6388715 TTTAATATAATTTTAATATA
1 TTTAATATAAATTTAATATA
6388735 TTTAA-ATAAATTTAGATATA
1 TTTAATATAAATTTA-ATATA
6388755 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTAATATAAATTTAATATA
Found at i:6388793 original size:17 final size:18
Alignment explanation
Indices: 6388773--6388813 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6388763 ATTTATATTT
*
6388773 TATAAAAA-ATTAAAATA
1 TATAAAAATAATAAAATA
6388790 TATACAAAATAATAAAATA
1 TATA-AAAATAATAAAATA
6388809 TATAA
1 TATAA
6388814 TTTAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 12 0.57
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TATAAAAATAATAAAATA
Found at i:6389555 original size:8 final size:8
Alignment explanation
Indices: 6389544--6389584 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
6389534 TTTAATAATA
6389544 TATAAAAT
1 TATAAAAT
6389552 TAT-AAAT
1 TATAAAAT
6389559 T-TAAAAT
1 TATAAAAT
6389566 TATAAATAT
1 TATAAA-AT
*
6389575 TAAAAAAT
1 TATAAAAT
6389583 TA
1 TA
6389585 ATTCAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
6 1 0.03
7 10 0.34
8 11 0.38
9 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TATAAAAT
Found at i:6389565 original size:14 final size:15
Alignment explanation
Indices: 6389540--6389579 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
6389530 ATTTTTTAAT
6389540 AATATATAAAATTATA
1 AATAT-TAAAATTATA
6389556 AAT-TTAAAATTATA
1 AATATTAAAATTATA
6389570 AATATTAAAA
1 AATATTAAAA
6389580 AATTAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.57
15 7 0.30
16 3 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATTAAAATTATA
Found at i:6389714 original size:20 final size:21
Alignment explanation
Indices: 6389676--6389714 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
6389666 TAAATATTAT
* *
6389676 TTTAATATAATTTTTAATACA
1 TTTAATATAAATTTAAATACA
6389697 TTTAA-ATAAATTTAAATA
1 TTTAATATAAATTTAAATA
6389715 TAAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAATATAAATTTAAATACA
Found at i:6390259 original size:2 final size:2
Alignment explanation
Indices: 6390252--6390284 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6390242 AAAGTGACTT
*
6390252 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6390285 TCGTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6391301 original size:22 final size:24
Alignment explanation
Indices: 6391256--6391301 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
6391246 TTTAAATTTT
*
6391256 AAATTTTTATATATTATTTTAATA
1 AAATTTTTATATATTATTTAAATA
6391280 AAATTTTTA-ATA-TATTTAAATA
1 AAATTTTTATATATTATTTAAATA
6391302 GATATGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 3 0.14
24 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AAATTTTTATATATTATTTAAATA
Found at i:6391354 original size:10 final size:10
Alignment explanation
Indices: 6391330--6391372 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
6391320 GTTTTTATTT
6391330 TATAAAAAT-
1 TATAAAAATA
*
6391339 TTTAAAAATA
1 TATAAAAATA
*
6391349 TATAAAATTA
1 TATAAAAATA
6391359 -ATAAAAATA
1 TATAAAAATA
6391368 TATAA
1 TATAA
6391373 TTCGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TATAAAAATA
Found at i:6391354 original size:19 final size:20
Alignment explanation
Indices: 6391330--6391372 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
6391320 GTTTTTATTT
*
6391330 TATAAAAATT-TTAAAAATA
1 TATAAAAATTAATAAAAATA
6391349 TAT-AAAATTAATAAAAATA
1 TATAAAAATTAATAAAAATA
6391368 TATAA
1 TATAA
6391373 TTCGATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:6396304 original size:79 final size:78
Alignment explanation
Indices: 6396197--6396420 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 78
6396187 AAACCATACG
* * *
6396197 GCATACGATTC-AGCCCCTCAATATCATACAAAACCATTTAGTAAAACAATATCAGATAACAAGA
1 GCATACG-TTCAAGCCCC-CAATATCATACAATACCATTTAG-AAAACAATATCAGACAACAAGG
6396261 TTTAGCAAA-TCATTCA
63 TTTAGCAAACT-ATTCA
* ** * * *
6396277 GCATATGATT-TGGCCCCCAATATCATACAATACCA-TTCGACAATACAATATCATACAATAAGG
1 GCATACG-TTCAAGCCCCCAATATCATACAATACCATTTAGA-AA-ACAATATCAGACAACAAGG
*
6396340 TTCAGCAAACTATTCA
63 TTTAGCAAACTATTCA
* *
6396356 GCATACGTTCAACCCCCCAATATCATACAATACCATTCAGCAAAA-AA-ATCAGACAACAAGGTT
1 GCATACGTTCAAGCCCCCAATATCATACAATACCATTTAG-AAAACAATATCAGACAACAAGGTT
6396419 TA
65 TA
6396421 ATAAACCATA
Statistics
Matches: 119, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
77 16 0.13
78 9 0.08
79 74 0.62
80 19 0.16
81 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (78 bp):
GCATACGTTCAAGCCCCCAATATCATACAATACCATTTAGAAAACAATATCAGACAACAAGGTTT
AGCAAACTATTCA
Found at i:6407067 original size:134 final size:134
Alignment explanation
Indices: 6406834--6407627 Score: 475
Period size: 134 Copynumber: 6.1 Consensus size: 134
6406824 GTAAACGACG
* * ** ** *
6406834 TTTTTCTCATAAAAATGCTATTAAATTAGTGGCGTCTCAAAGATACAAATGCCTCTAATATAGAG
1 TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
* * * *
6406899 GCATTTTCATATATAAACGCCTCTAAAGTAGTGACGTTTTTAATTACAAATACCACCAAAGCAAC
66 GCATTTTCAGATACAAACACCTCTAAAGTAGTGACGTTTTTAATTACAAACACCACCAAAGCAA-
*
6406964 GA-TA
130 GAGCA
* * *
6406968 TTTTTTTCATAAAAATGCCACTAAATTAACGGTGTCTCAAATATACAAACACCGCTAATATAGAG
1 TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
* * * * *
6407033 GTATTTTCAGATACAAACACCTCTAAAGTAGTGACGTTTTTAGTTACAAACGCCATCAAAGCAAT
66 GCATTTTCAGATACAAACACCTCTAAAGTAGTGACGTTTTTAATTACAAACACCACCAAAGCAAG
*
6407098 AGCG
131 AGCA
* * *
6407102 TTTTTCTCATAAAAACGTCACTAAATTAACGGCGTCTCAAAGATAC-AA-A---C-AATATAGAT
1 TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
* * * * * ** *
6407161 GCGTTCTCATATACAAACGCCACT--AGTA-TGGA-G----GCA-T-C--A-A--AGCAAA-CAA
66 GCATTTTCAGATACAAACACCTCTAAAGTAGT-GACGTTTTTAATTACAAACACCACCAAAGCAA
*
6407210 ---CG
130 GAGCA
* ** * * * ** *
6407212 TTTTTCTCATAAAAACGTTACTAAATTAACGACGTCTTAAAGATATAAATGCCGCTAATATGGAG
1 TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
* * * * ** *
6407277 GTATTTTCATATACAAACGCCTCTAAAGTAGTGACGTTTTTAGTTACAAACGTCATCAAAGCAAC
66 GCATTTTCAGATACAAACACCTCTAAAGTAGTGACGTTTTTAATTACAAACACCACCAAAGCAA-
**
6407342 G-TTA
130 GAGCA
* * * ** * ** *
6407346 TTTTTTTCATAAAAATGTCACTAAATTAATGATGTCTCAAATATATTAACACCGTTAATATAGAG
1 TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
* * * *** * * * * *
6407411 GCGTTTTTAGATACAAAAACGCCTCTAAAGTAACAACATTTTCAGTTACAAACATCATCAAAGCA
66 GCATTTTCAGATAC--AAACACCTCTAAAGTAGTGACGTTTTTAATTACAAACACCACCAAAGCA
*
6407476 ATAGCA
129 AGAGCA
*** * * * *
6407482 TTTTTCTCATAAAAACATCACTAAATTAGCAGTGTCTCAAAGATACATA-A-----AATATAGAG
1 TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
* ** *** * * * ** * *
6407541 GCGTTTTCAGATACAAACGTCTCTAAAGTAACAACATTTTTAGTTATAAATGCCACCAAAACAAT
66 GCATTTTCAGATACAAACACCTCTAAAGTAGTGACGTTTTTAATTACAAACACCACCAAAGCAAG
*
6407606 AGCG
131 AGCA
6407610 TTTTTCTCATAAAAATGC
1 TTTTTCTCATAAAAATGC
6407628 AGCTAATTTA
Statistics
Matches: 525, Mismatches: 105, Indels: 66
0.75 0.15 0.09
Matches are distributed among these distances:
110 44 0.08
111 2 0.00
113 3 0.01
114 5 0.01
115 1 0.00
116 27 0.05
117 1 0.00
118 6 0.01
119 3 0.01
120 1 0.00
124 1 0.00
125 3 0.01
126 6 0.01
127 1 0.00
128 87 0.17
129 1 0.00
130 27 0.05
131 3 0.01
132 1 0.00
133 3 0.01
134 215 0.41
135 1 0.00
136 83 0.16
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (134 bp):
TTTTTCTCATAAAAATGCCACTAAATTAACGGCGTCTCAAAGATACAAACACCGCTAATATAGAG
GCATTTTCAGATACAAACACCTCTAAAGTAGTGACGTTTTTAATTACAAACACCACCAAAGCAAG
AGCA
Found at i:6407469 original size:136 final size:132
Alignment explanation
Indices: 6407212--6407624 Score: 383
Period size: 136 Copynumber: 3.1 Consensus size: 132
6407202 GCAAACAACG
* * * * ** * *
6407212 TTTTTCTCATAAAAACGTTACTAAATTAACGACGTCTTAAAGATATAAATGCCGCTAATATGGAG
1 TTTTTCTCATAAAAACGTCACTAAATTAA-GATGTCTCAAA-ATATTAACACCGTTAATATAGAG
** * *** * *
6407277 GTATTTTCATATACAAACGCCTCTAAAGTAGTGACGTTTTTAGTTACAAACGTCATCAAAGCAA-
64 GCGTTTTCAGATACAAACGCCTCTAAAGTAACAACATTTTTAGTTACAAACATCATCAAAGCAAT
* *
6407341 CGTTA
129 AG-CA
* *
6407346 TTTTTTTCATAAAAATGTCACTAAATTAATGATGTCTCAAATATATTAACACCGTTAATATAGAG
1 TTTTTCTCATAAAAACGTCACTAAATTAA-GATGTCTCAAA-ATATTAACACCGTTAATATAGAG
* *
6407411 GCGTTTTTAGATACAAAAACGCCTCTAAAGTAACAACATTTTCAGTTACAAACATCATCAAAGCA
64 GCGTTTTCAGATAC--AAACGCCTCTAAAGTAACAACATTTTTAGTTACAAACATCATCAAAGCA
6407476 ATAGCA
127 ATAGCA
* * *
6407482 TTTTTCTCATAAAAACATCACTAAATT-AGCAGTGTCTC-AAAGA-T-ACA---TAAAATATAGA
1 TTTTTCTCATAAAAACGTCACTAAATTAAG-A-TGTCTCAAAATATTAACACCGT-TAATATAGA
* * *** * *
6407540 GGCGTTTTCAGATACAAACGTCTCTAAAGTAACAACATTTTTAGTTATAAATGCCACCAAAACAA
63 GGCGTTTTCAGATACAAACGCCTCTAAAGTAACAACATTTTTAGTTACAAACATCATCAAAGCAA
*
6407605 TAGCG
128 TAGCA
6407610 TTTTTCTCATAAAAA
1 TTTTTCTCATAAAAA
6407625 TGCAGCTAAT
Statistics
Matches: 234, Mismatches: 39, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
128 61 0.26
129 1 0.00
130 22 0.09
132 3 0.01
133 1 0.00
134 66 0.28
135 4 0.02
136 75 0.32
137 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (132 bp):
TTTTTCTCATAAAAACGTCACTAAATTAAGATGTCTCAAAATATTAACACCGTTAATATAGAGGC
GTTTTCAGATACAAACGCCTCTAAAGTAACAACATTTTTAGTTACAAACATCATCAAAGCAATAG
CA
Found at i:6407953 original size:1 final size:1
Alignment explanation
Indices: 6407947--6407972 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6407937 TGTTTCTTGT
6407947 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
6407973 TTGGCTAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6409732 original size:17 final size:18
Alignment explanation
Indices: 6409702--6409735 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6409692 AACTTGCCTA
*
6409702 TTAAGAATTTTTTTTCTC
1 TTAAGAATTCTTTTTCTC
6409720 TTAA-AATTCTTTTTCT
1 TTAAGAATTCTTTTTCT
6409736 ACAAGTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (18 bp):
TTAAGAATTCTTTTTCTC
Found at i:6409742 original size:52 final size:51
Alignment explanation
Indices: 6409639--6409742 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
6409629 TATAACCACA
* **
6409639 CAAACTTGCCTATTAAGAATCCTTTACTCTTAGAATTCTTTTTCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTTTACTCTTAAAATTCTTTTTCTACAAGT
** *
6409690 CAAACTTGCCTATTAAGAATTTTTTTTCTCTTAAAATTCTTTTTCTACAAGT
1 CAAACTTGCCTATTAAGAA-TCCTTTACTCTTAAAATTCTTTTTCTACAAGT
6409742 C
1 C
6409743 TTCTTATCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 19 0.41
52 27 0.59
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTTTACTCTTAAAATTCTTTTTCTACAAGT
Found at i:6414363 original size:2 final size:2
Alignment explanation
Indices: 6414347--6414381 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6414337 CAACCTCAAG
*
6414347 TA TA -A TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6414382 GAGGGCAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6416445 original size:14 final size:14
Alignment explanation
Indices: 6416426--6416455 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6416416 CAGAAGAAAG
6416426 AGCCAGTGACTACC
1 AGCCAGTGACTACC
6416440 AGCCAGTGACTACC
1 AGCCAGTGACTACC
6416454 AG
1 AG
6416456 TTGAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (14 bp):
AGCCAGTGACTACC
Found at i:6417425 original size:12 final size:12
Alignment explanation
Indices: 6417393--6417426 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6417383 TAATATAATA
*
6417393 TTAAATTTGAGT
1 TTAAATTTTAGT
*
6417405 TTAAATTTTATT
1 TTAAATTTTAGT
6417417 TTAAATTTTA
1 TTAAATTTTA
6417427 AATTTGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (12 bp):
TTAAATTTTAGT
Found at i:6418048 original size:10 final size:11
Alignment explanation
Indices: 6418036--6418066 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6418026 ATTCGTAAAT
6418036 AAATTTATTTA
1 AAATTTATTTA
*
6418047 AAATTCATTTA
1 AAATTTATTTA
6418058 AAATTTATT
1 AAATTTATT
6418067 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTTATTTA
Found at i:6418124 original size:11 final size:11
Alignment explanation
Indices: 6418101--6418130 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6418091 ATAAATTATA
6418101 ATTTTATATTTT
1 ATTTTA-ATTTT
6418113 ATTTTAATTTT
1 ATTTTAATTTT
6418124 ATTTTAA
1 ATTTTAA
6418131 AATTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:6418140 original size:11 final size:10
Alignment explanation
Indices: 6418110--6418182 Score: 56
Period size: 10 Copynumber: 6.9 Consensus size: 10
6418100 AATTTTATAT
*
6418110 TTTATTTTAAT
1 TTTA-TTTAAA
6418121 TTTATTTTAAAA
1 TTTA-TTT-AAA
*
6418133 TTTATTTATA
1 TTTATTTAAA
*
6418143 TTTATTTAGA
1 TTTATTTAAA
** *
6418153 TCCATTTATA
1 TTTATTTAAA
6418163 TTTATTTTAAA
1 TTTA-TTTAAA
6418174 TTTATTTAA
1 TTTATTTAA
6418183 TTATAATTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
10 25 0.49
11 20 0.39
12 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTATTTAAA
Found at i:6418147 original size:10 final size:10
Alignment explanation
Indices: 6418132--6418198 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
6418122 TTATTTTAAA
6418132 ATTTATTTAT
1 ATTTATTTAT
*
6418142 ATTTATTTAG
1 ATTTATTTAT
**
6418152 ATCCATTTAT
1 ATTTATTTAT
*
6418162 ATTTATTTTAA
1 ATTTA-TTTAT
6418173 ATTTATTTA-
1 ATTTATTTAT
*
6418182 ATTATAATT-T
1 ATT-TATTTAT
6418192 ATTTATT
1 ATTTATT
6418199 ATTCATAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 6 0.13
10 30 0.67
11 9 0.20
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (10 bp):
ATTTATTTAT
Found at i:6418181 original size:15 final size:16
Alignment explanation
Indices: 6418161--6418198 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
6418151 GATCCATTTA
6418161 TATTTATTTTA-AATT
1 TATTTATTTTATAATT
*
6418176 TATTTA-ATTATAATT
1 TATTTATTTTATAATT
6418191 TATTTATT
1 TATTTATT
6418199 ATTCATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTATTTTATAATT
Found at i:6418621 original size:18 final size:17
Alignment explanation
Indices: 6418592--6418641 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
6418582 CGACTCGAAA
6418592 TTAATA-AAAATATTTT
1 TTAATATAAAATATTTT
6418608 TTAAATATAAAATATTATT
1 TT-AATATAAAATATT-TT
6418627 TTAATAT-AAATATTT
1 TTAATATAAAATATTT
6418642 AAAAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.10
17 11 0.35
18 13 0.42
19 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATAAAATATTTT
Found at i:6421053 original size:21 final size:22
Alignment explanation
Indices: 6421029--6421075 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6421019 ATTTTGAGGG
6421029 AAAAACTAA-TGGTGGAATAAA
1 AAAAACTAAGTGGTGGAATAAA
** *
6421050 AAAATGTAAGTTGTGGAATAAA
1 AAAAACTAAGTGGTGGAATAAA
6421072 AAAA
1 AAAA
6421076 GTAAAGTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.19, T:0.21
Consensus pattern (22 bp):
AAAAACTAAGTGGTGGAATAAA
Found at i:6425521 original size:30 final size:30
Alignment explanation
Indices: 6425487--6425558 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
6425477 TTTGTACCTT
* * *
6425487 CAAAAGGTTTAGTAGCGATTTTTGCTGAAC
1 CAAAAGGTTTAGCACCGATTTTTGCTGAAA
* * **
6425517 CAAAAGGTCTAACACCTCTTTTTGCTGAAA
1 CAAAAGGTTTAGCACCGATTTTTGCTGAAA
6425547 CAAAAGGTTTAG
1 CAAAAGGTTTAG
6425559 GACCCAAAGC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
CAAAAGGTTTAGCACCGATTTTTGCTGAAA
Found at i:6437116 original size:5 final size:6
Alignment explanation
Indices: 6437066--6437114 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
6437056 AAAATAATTT
* ** *
6437066 TTTAAA TTTAAT TTTGTA TTTGAA TTTAAA TTTAAA TTTAAA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
6437113 TT
1 TT
6437115 AATATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:6437953 original size:23 final size:24
Alignment explanation
Indices: 6437923--6437974 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
6437913 TTTACATGTA
6437923 TTTATAAAATAGT-AAATTTATAT
1 TTTATAAAATAGTAAAATTTATAT
*
6437946 TTTATAAAATATTAAAATTTATAT
1 TTTATAAAATAGTAAAATTTATAT
*
6437970 ATTAT
1 TTTAT
6437975 TATATTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATAAAATAGTAAAATTTATAT
Found at i:6437983 original size:17 final size:17
Alignment explanation
Indices: 6437936--6437998 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
6437926 ATAAAATAGT
6437936 AAAT-TTATATTTTATA
1 AAATATTATATTTTATA
* *
6437952 AAATATTAAAATTTATA
1 AAATATTATATTTTATA
* *
6437969 TATTATTATATTTTACATA
1 AAATATTATATTTT--ATA
6437988 AAA-ATTATATT
1 AAATATTATATT
6437999 ATAACTTGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 4 0.11
17 20 0.56
18 8 0.22
19 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATATTATATTTTATA
Found at i:6438067 original size:22 final size:24
Alignment explanation
Indices: 6438042--6438100 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
6438032 TTTTTTGATT
*
6438042 TTATTAAATTTTTATA-TA-ATTA
1 TTATTAAATTTTTAAATTATATTA
*
6438064 TTATTAAAATTTTAAATTATATTA
1 TTATTAAATTTTTAAATTATATTA
* *
6438088 TTTTTATATTTTT
1 TTATTAAATTTTT
6438101 TTAATATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 14 0.47
23 2 0.07
24 14 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTAAATTTTTAAATTATATTA
Found at i:6441946 original size:31 final size:34
Alignment explanation
Indices: 6441894--6441959 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 34
6441884 AAATTTTAAT
6441894 TATAACTCTTCACCATATAGTACTTAA-TGATTC
1 TATAACTCTTCACCATATAGTACTTAACTGATTC
*
6441927 TATAAC-CTT-ACCATGTAGTACTTAACTGATTC
1 TATAACTCTTCACCATATAGTACTTAACTGATTC
6441959 T
1 T
6441960 TATGATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 15 0.48
32 10 0.32
33 6 0.19
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (34 bp):
TATAACTCTTCACCATATAGTACTTAACTGATTC
Found at i:6464047 original size:51 final size:51
Alignment explanation
Indices: 6463969--6464068 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
6463959 AATTTTGGGC
* * *
6463969 ATTATTAAAGGCGTCTTCTAATGTAAAATACCTTTAATATACCACGATGAG
1 ATTATTAAAGGCGTCTTCTAATATAAAACACCTTCAATATACCACGATGAG
* * * *
6464020 ATTATTAAAGGGGTCATT-TATTATAAAACGCCTTCAATATACGACGATG
1 ATTATTAAAGGCGTC-TTCTAATATAAAACACCTTCAATATACCACGATG
6464069 GTTATAGAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 39 0.95
52 2 0.05
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (51 bp):
ATTATTAAAGGCGTCTTCTAATATAAAACACCTTCAATATACCACGATGAG
Found at i:6465118 original size:84 final size:84
Alignment explanation
Indices: 6465027--6465180 Score: 202
Period size: 84 Copynumber: 1.8 Consensus size: 84
6465017 ATATATATTG
** * * *
6465027 TGGTTTGCTGAACCTTGTAGTCTGATATTGTAATGTCGAAT-GGTATTGTATGATATTGGGGGTC
1 TGGTTTGCACAACCTTGTAGTCTAATATTATAATGTCGAATGGGT-TTGTATGAAATTGGGGGTC
6465091 TGAATCATATATATGCTGAA
65 TGAATCATATATATGCTGAA
* ** * *
6465111 TGGTTTGCACAACCTTGTTGTCTAATATTATTTTGTTGAATGGGTTTGTATGAAATTGGGGGTTT
1 TGGTTTGCACAACCTTGTAGTCTAATATTATAATGTCGAATGGGTTTGTATGAAATTGGGGGTCT
6465176 GAATC
66 GAATC
6465181 GTATGCTAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 56 0.95
85 3 0.05
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (84 bp):
TGGTTTGCACAACCTTGTAGTCTAATATTATAATGTCGAATGGGTTTGTATGAAATTGGGGGTCT
GAATCATATATATGCTGAA
Found at i:6477160 original size:118 final size:118
Alignment explanation
Indices: 6476948--6477185 Score: 449
Period size: 118 Copynumber: 2.0 Consensus size: 118
6476938 ATAGATGTTT
* *
6476948 ATGACTTTGAGTTTTCATGTGGTCAATGTGGATGATTTGTATTTCAACGTGCATCAAGTCCAGTG
1 ATGACTTTGAGTGTTCATGTGGTCAATGTGGATGATTTGCATTTCAACGTGCATCAAGTCCAGTG
6477013 GGTTTATTCCTTGTAATTGTAGAGAGTCAAAATGGATGGTTGAATTTCTCAAG
66 GGTTTATTCCTTGTAATTGTAGAGAGTCAAAATGGATGGTTGAATTTCTCAAG
6477066 ATGACTTTGAGTGTTCATGTGGTCAATGTGGATGATTTGCATTTCAACGTGCATCAAGTCCAGTG
1 ATGACTTTGAGTGTTCATGTGGTCAATGTGGATGATTTGCATTTCAACGTGCATCAAGTCCAGTG
*
6477131 GGTTTATTCCTTGTAATTGTAGAGGGTCAAAATGGATGGTTGAATTTCTCAAG
66 GGTTTATTCCTTGTAATTGTAGAGAGTCAAAATGGATGGTTGAATTTCTCAAG
6477184 AT
1 AT
6477186 TTTTGTAAAA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (118 bp):
ATGACTTTGAGTGTTCATGTGGTCAATGTGGATGATTTGCATTTCAACGTGCATCAAGTCCAGTG
GGTTTATTCCTTGTAATTGTAGAGAGTCAAAATGGATGGTTGAATTTCTCAAG
Found at i:6480589 original size:14 final size:15
Alignment explanation
Indices: 6480565--6480593 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6480555 GAAGCTCGAG
6480565 ATTGATTTGAAATTT
1 ATTGATTTGAAATTT
6480580 ATTG-TTTGAAATTT
1 ATTGATTTGAAATTT
6480594 GGCTTTAGCA
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:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (15 bp):
ATTGATTTGAAATTT
Found at i:6480809 original size:20 final size:20
Alignment explanation
Indices: 6480757--6480814 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
6480747 ATTTATATAT
6480757 ATATATATATATAAAATAATA
1 ATATATATAT-TAAAATAATA
* *
6480778 AT-TTTTTAATTAAAATAATA
1 ATATATAT-ATTAAAATAATA
6480798 ATATATATATTAAAATA
1 ATATATATATTAAAATA
6480815 TAAAAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATATATTAAAATAATA
Found at i:6494033 original size:42 final size:41
Alignment explanation
Indices: 6493987--6494081 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 41
6493977 TTCTAATTAG
* * *
6493987 TATTTAAATAAAAAATTATTTAA-AAATTAAAATTTTATAATT
1 TATTTAAATAAAAAATGATATAATAAA-TAAAATTAT-TAATT
* *
6494029 TATTTAAATATCAAAATGATATAATAAATATAATTATTAATT
1 TATTTAAATA-AAAAATGATATAATAAATAAAATTATTAATT
6494071 T-TTTAAATAAA
1 TATTTAAATAAA
6494082 TTAAAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
40 1 0.02
41 8 0.18
42 16 0.36
43 17 0.38
44 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (41 bp):
TATTTAAATAAAAAATGATATAATAAATAAAATTATTAATT
Found at i:6494051 original size:26 final size:26
Alignment explanation
Indices: 6494002--6494053 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6493992 AAATAAAAAA
* **
6494002 TTATTTAAAAATTAAAATTTTATAAT
1 TTATTTAAAAATCAAAATGATATAAT
*
6494028 TTATTTAAATATCAAAATGATATAAT
1 TTATTTAAAAATCAAAATGATATAAT
6494054 AAATATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TTATTTAAAAATCAAAATGATATAAT
Found at i:6494380 original size:27 final size:26
Alignment explanation
Indices: 6494342--6494405 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
6494332 TATATATATG
*
6494342 AATTCAAA-TTTAAATTTGAACATAAA
1 AATT-AAATTTTAAATCTGAACATAAA
* *
6494368 TAATTAAATTTTAAGTCTGAGCATAAA
1 -AATTAAATTTTAAATCTGAACATAAA
*
6494395 AATAAAATTTT
1 AATTAAATTTT
6494406 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 13 0.41
27 19 0.59
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (26 bp):
AATTAAATTTTAAATCTGAACATAAA
Found at i:6499827 original size:15 final size:15
Alignment explanation
Indices: 6499809--6499839 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6499799 TTAAAACACA
6499809 TTTTTT-TAAATTTT
1 TTTTTTATAAATTTT
6499823 TTTTTTATAAATTTT
1 TTTTTTATAAATTTT
6499838 TT
1 TT
6499840 ATCTATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTATAAATTTT
Found at i:6508155 original size:2 final size:2
Alignment explanation
Indices: 6508148--6508184 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6508138 TTTTTGGTTA
*
6508148 AT AT AT AT AT AT AT AT AT AT TT 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
6508185 GTGCTTTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6510632 original size:2 final size:2
Alignment explanation
Indices: 6510614--6510647 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6510604 CAGCTATAAC
*
6510614 TA TA T- TA TA TT TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6510648 CTTCTTTCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:6516047 original size:17 final size:16
Alignment explanation
Indices: 6516025--6516058 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6516015 TATATTTGAG
6516025 TATTTGAATATATATTA
1 TATTTGAATATA-ATTA
*
6516042 TATTTGCATATAATTA
1 TATTTGAATATAATTA
6516058 T
1 T
6516059 TTTAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TATTTGAATATAATTA
Found at i:6519373 original size:24 final size:25
Alignment explanation
Indices: 6519341--6519387 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
6519331 CAGAGACAGG
*
6519341 ACATAAAACAAAAA-TACTTTTACT
1 ACATAAAACAAAAACAACTTTTACT
6519365 ACATAAAACAAAAACAACTTTTA
1 ACATAAAACAAAAACAACTTTTA
6519388 GGATCTGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (25 bp):
ACATAAAACAAAAACAACTTTTACT
Found at i:6522782 original size:2 final size:2
Alignment explanation
Indices: 6522775--6522804 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6522765 AAACAAATAA
6522775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6522805 TGTCAACACA
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):
AT
Found at i:6523639 original size:13 final size:13
Alignment explanation
Indices: 6523621--6523647 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6523611 AACGATTAAC
6523621 AAATAAATAACAA
1 AAATAAATAACAA
6523634 AAATAAATAACAA
1 AAATAAATAACAA
6523647 A
1 A
6523648 TGAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAATAACAA
Found at i:6532679 original size:13 final size:13
Alignment explanation
Indices: 6532661--6532687 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6532651 GAGTACAACA
6532661 AGTCTCTTGTAAT
1 AGTCTCTTGTAAT
6532674 AGTCTCTTGTAAT
1 AGTCTCTTGTAAT
6532687 A
1 A
6532688 AAATGCCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (13 bp):
AGTCTCTTGTAAT
Found at i:6532958 original size:24 final size:25
Alignment explanation
Indices: 6532931--6532986 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
6532921 ATTATTATTA
6532931 TTATAATTACAA-TTAAAAAAAATT
1 TTATAATTACAATTTAAAAAAAATT
* * **
6532955 TTATATTTATAATTTTTAAAAAATT
1 TTATAATTACAATTTAAAAAAAATT
6532980 TTCATAA
1 TT-ATAA
6532987 AAAATTTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 10 0.40
25 12 0.48
26 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
TTATAATTACAATTTAAAAAAAATT
Found at i:6536648 original size:97 final size:97
Alignment explanation
Indices: 6536482--6536665 Score: 296
Period size: 97 Copynumber: 1.9 Consensus size: 97
6536472 GTGCGACAGC
* * * *
6536482 AATGATTCGTTACGGTTAGTGGTGCGCTGGATGTGAACTCTTCCAAATTTACATGCCTTTATCAC
1 AATGATTCGTTACGGTTAGCGGTGCGCTGGATGAGAACGCTTCCAAATTCACATGCCTTTATCAC
*
6536547 CGTTCCTTATGCCGACTTTTTATTGCCAAAGT
66 CGTTCCTTATGCCGACATTTTATTGCCAAAGT
* *
6536579 AATGATTCGTTACGGTTAGCGGTGCGCTGGATGAGAGCGCTTCCAAATTCACGTGCCTTTATCAC
1 AATGATTCGTTACGGTTAGCGGTGCGCTGGATGAGAACGCTTCCAAATTCACATGCCTTTATCAC
*
6536644 CGTTCCTTATGTCGACATTTTA
66 CGTTCCTTATGCCGACATTTTA
6536666 CAGCGAATGC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (97 bp):
AATGATTCGTTACGGTTAGCGGTGCGCTGGATGAGAACGCTTCCAAATTCACATGCCTTTATCAC
CGTTCCTTATGCCGACATTTTATTGCCAAAGT
Found at i:6538833 original size:20 final size:21
Alignment explanation
Indices: 6538793--6538833 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6538783 AATATATATT
*
6538793 AATATATTATTTTTCAATTAA
1 AATATATTAATTTTCAATTAA
6538814 AATATATTAATTTT-AATTAA
1 AATATATTAATTTTCAATTAA
6538834 TCTAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATATTAATTTTCAATTAA
Found at i:6539637 original size:19 final size:19
Alignment explanation
Indices: 6539613--6539649 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6539603 AGTTTCAGGA
* *
6539613 TTTTTTATTTTTTATTTTG
1 TTTTTTATATATTATTTTG
6539632 TTTTTTATATATTATTTT
1 TTTTTTATATATTATTTT
6539650 AATATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTTTTATATATTATTTTG
Found at i:6540844 original size:15 final size:15
Alignment explanation
Indices: 6540812--6540859 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
6540802 ATTAATTTTA
* *
6540812 ATAAATAAATTAAAT
1 ATAAATAAATTTATT
6540827 ATAAATAAATTTATT
1 ATAAATAAATTTATT
**
6540842 ATATTTATAATTTATT
1 ATAAATA-AATTTATT
6540858 AT
1 AT
6540860 TTTAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAATAAATTTATT
Found at i:6540855 original size:16 final size:15
Alignment explanation
Indices: 6540834--6540863 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6540824 AATATAAATA
6540834 AATTTATTATATTTAT
1 AATTTATTAT-TTTAT
6540850 AATTTATTATTTTA
1 AATTTATTATTTTA
6540864 ATTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTATTATTTTAT
Found at i:6545046 original size:2 final size:2
Alignment explanation
Indices: 6545039--6545069 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6545029 TGTTATGGTC
6545039 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 A
6545070 CTACATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6546179 original size:5 final size:5
Alignment explanation
Indices: 6546169--6546194 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6546159 TATTACTTGG
6546169 ATCCT ATCCT ATCCT ATCCT ATCCT A
1 ATCCT ATCCT ATCCT ATCCT ATCCT A
6546195 GCCACTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (5 bp):
ATCCT
Found at i:6564859 original size:19 final size:19
Alignment explanation
Indices: 6564830--6564866 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6564820 AATTTTTAAA
6564830 TTATATTATATTCATTTTTT
1 TTATATTATATT-ATTTTTT
6564850 TTAT-TTATATTATTTTT
1 TTATATTATATTATTTTT
6564867 ATATCATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATATTATATTATTTTTT
Found at i:6573090 original size:19 final size:20
Alignment explanation
Indices: 6573068--6573124 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
6573058 AATTCACGAA
6573068 TTTAATTAAAATTTTA-AAT
1 TTTAATTAAAATTTTATAAT
* * *
6573087 TTTAA-TATATTTTTATGAT
1 TTTAATTAAAATTTTATAAT
6573106 TTTAATTATAAATTATTAT
1 TTTAATTA-AAATT-TTAT
6573125 TTTATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.28
19 12 0.41
20 2 0.07
21 3 0.10
22 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTAATTAAAATTTTATAAT
Found at i:6575506 original size:10 final size:10
Alignment explanation
Indices: 6575460--6575572 Score: 67
Period size: 10 Copynumber: 11.7 Consensus size: 10
6575450 AATAAAATTA
*
6575460 TATTTTTATT
1 TATTTATATT
6575470 T-TTTATATT
1 TATTTATATT
6575479 TATTT-TA-T
1 TATTTATATT
* *
6575487 T-TTAAGATT
1 TATTTATATT
6575496 TATTTATATT
1 TATTTATATT
* *
6575506 TATTTGTATA
1 TATTTATATT
*
6575516 TGTTTATATT
1 TATTTATATT
*
6575526 TGTTTATAGTT
1 TATTTATA-TT
*
6575537 TATTTGT-TT
1 TATTTATATT
* *
6575546 AAATT-TATT
1 TATTTATATT
*
6575555 TAGTTATAATT
1 TATTTAT-ATT
6575566 TATTTAT
1 TATTTAT
6575573 TGTTCATCAA
Statistics
Matches: 78, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
7 2 0.03
8 4 0.05
9 22 0.28
10 34 0.44
11 16 0.21
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (10 bp):
TATTTATATT
Found at i:6575527 original size:16 final size:17
Alignment explanation
Indices: 6575506--6575539 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6575496 TATTTATATT
6575506 TATTTGTATAT-GTTTA
1 TATTTGTATATAGTTTA
*
6575522 TATTTGTTTATAGTTTA
1 TATTTGTATATAGTTTA
6575539 T
1 T
6575540 TTGTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (17 bp):
TATTTGTATATAGTTTA
Found at i:6575542 original size:15 final size:15
Alignment explanation
Indices: 6575493--6575570 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
6575483 TTATTTTAAG
*
6575493 ATTTATTTAT-ATTT
1 ATTTGTTTATAATTT
* **
6575507 ATTTGTATATGTTTAT
1 ATTTGTTTATAATT-T
*
6575523 ATTTGTTTATAGTTT
1 ATTTGTTTATAATTT
6575538 ATTTGTTTA-AATTT
1 ATTTGTTTATAATTT
6575552 ATTTAG-TTATAATTT
1 ATTT-GTTTATAATTT
6575567 ATTT
1 ATTT
6575571 ATTGTTCATC
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
14 19 0.36
15 22 0.42
16 12 0.23
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (15 bp):
ATTTGTTTATAATTT
Found at i:6578008 original size:16 final size:16
Alignment explanation
Indices: 6577973--6578023 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
6577963 ATTATTTTAA
6577973 ATATGATATAA-AAA-T
1 ATAT-ATATAATAAATT
6577988 A-ATATATAATAAATT
1 ATATATATAATAAATT
*
6578003 ATATATATTATATAATT
1 ATATATATAATA-AATT
6578020 ATAT
1 ATAT
6578024 TTTGTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
15 3 0.10
16 9 0.29
17 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATATAATAAATT
Found at i:6578321 original size:19 final size:19
Alignment explanation
Indices: 6578294--6578330 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6578284 ATTATGTTAT
* *
6578294 AATTTTTGATTTAATATTG
1 AATTATTGATTAAATATTG
6578313 AATTATTGATTAAATATT
1 AATTATTGATTAAATATT
6578331 TTAGTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
AATTATTGATTAAATATTG
Found at i:6579578 original size:33 final size:33
Alignment explanation
Indices: 6579531--6579593 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
6579521 TTTAAAAATT
6579531 AAATTTTAATCAAATTCAAATT-AAATTTCGAC
1 AAATTTTAATCAAATTCAAATTAAAATTTCGAC
6579563 AAATTTTGAATCAAATTCAAATTAAAATTTC
1 AAATTTT-AATCAAATTCAAATTAAAATTTC
6579594 TCAATATCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 7 0.24
33 15 0.52
34 7 0.24
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (33 bp):
AAATTTTAATCAAATTCAAATTAAAATTTCGAC
Found at i:6589641 original size:32 final size:32
Alignment explanation
Indices: 6589605--6589669 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
6589595 TAAACTTAAA
*
6589605 TTGATAATAATAAAATTGAATTGAAATTTTAT
1 TTGATAATAATAAAATTAAATTGAAATTTTAT
* * *
6589637 TTGATAATAATTAATTTAAATTTAAATTTTAT
1 TTGATAATAATAAAATTAAATTGAAATTTTAT
6589669 T
1 T
6589670 CAAATTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (32 bp):
TTGATAATAATAAAATTAAATTGAAATTTTAT
Found at i:6590107 original size:13 final size:14
Alignment explanation
Indices: 6590089--6590117 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6590079 TAATCAACCT
6590089 TATAGAAAAAA-TA
1 TATAGAAAAAAGTA
6590102 TATAGAAAAAAGTA
1 TATAGAAAAAAGTA
6590116 TA
1 TA
6590118 CTACTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (14 bp):
TATAGAAAAAAGTA
Found at i:6591867 original size:20 final size:19
Alignment explanation
Indices: 6591826--6591868 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
6591816 TTAATTAATT
* *
6591826 ATTTTATTTTTATATATCA
1 ATTTTATTTTTATAAATAA
6591845 ATTTTATTTTTATTAAATAA
1 ATTTTATTTTTA-TAAATAA
6591865 ATTT
1 ATTT
6591869 AATAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTATTTTTATAAATAA
Found at i:6591922 original size:14 final size:15
Alignment explanation
Indices: 6591903--6591962 Score: 70
Period size: 16 Copynumber: 4.0 Consensus size: 15
6591893 ATTTTTATTT
6591903 TTAATTAAA-TTAAA
1 TTAATTAAATTTAAA
6591917 TTAATTAAATTTTAAA
1 TTAATTAAA-TTTAAA
*
6591933 -TAATAAAATTTAAA
1 TTAATTAAATTTAAA
*
6591947 TTAAATAAAATTTAAA
1 TT-AATTAAATTTAAA
6591963 ATTTTTATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
14 15 0.37
15 8 0.20
16 18 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAATTAAATTTAAA
Found at i:6591948 original size:30 final size:29
Alignment explanation
Indices: 6591904--6591962 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
6591894 TTTTTATTTT
* * *
6591904 TAATTAAATTAAATTAATTAAATTTTAAA
1 TAATAAAATTAAATTAAATAAAATTTAAA
6591933 TAATAAAATTTAAATTAAATAAAATTTAAA
1 TAATAAAA-TTAAATTAAATAAAATTTAAA
6591963 ATTTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATAAAATTAAATTAAATAAAATTTAAA
Done.