Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 65 of 160
Found at i:13509519 original size:18 final size:18
Alignment explanation
Indices: 13509487--13509530 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
13509477 AACATAAAAT
13509487 TCTTAC-AAACCTGGAAC
1 TCTTACAAAACCTGGAAC
* * *
13509504 TCTTGCAAAACTTGGAAT
1 TCTTACAAAACCTGGAAC
13509522 TCTTACAAA
1 TCTTACAAA
13509531 CCTTTGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (18 bp):
TCTTACAAAACCTGGAAC
Found at i:13509555 original size:18 final size:19
Alignment explanation
Indices: 13509518--13509562 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
13509508 GCAAAACTTG
13509518 GAATTCTTACAAACCTTTGT
1 GAATT-TTACAAACCTTTGT
*
13509538 GAATTTTA-AAATCTTTGT
1 GAATTTTACAAACCTTTGT
13509556 GAATTTT
1 GAATTTT
13509563 TTGCCAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
19 3 0.12
20 5 0.21
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
GAATTTTACAAACCTTTGT
Found at i:13509916 original size:66 final size:66
Alignment explanation
Indices: 13509787--13509927 Score: 156
Period size: 66 Copynumber: 2.1 Consensus size: 66
13509777 TTGATCTTGG
* * * * **
13509787 CTCGATCCTGATTTTTTTATTTTTTAGACCTACAATTTAATCTCGATCACTCATTTTTTATCTCA
1 CTCGATCCAGATTCTTTTATTTTTCAGACCTACAATTTAATCTCGATCACTCACTTTCGATCTCA
13509852 A
66 A
** * *** *
13509853 CTCGATCCAGATTCTTTTATTTTTCAGACCTACGGTTTAATCTCGGTTGTTCACTTTCGATCTCG
1 CTCGATCCAGATTCTTTTATTTTTCAGACCTACAATTTAATCTCGATCACTCACTTTCGATCTCA
*
13509918 G
66 A
13509919 CTCGATCCA
1 CTCGATCCA
13509928 ACTCTTGACT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (66 bp):
CTCGATCCAGATTCTTTTATTTTTCAGACCTACAATTTAATCTCGATCACTCACTTTCGATCTCA
A
Found at i:13513218 original size:3 final size:3
Alignment explanation
Indices: 13513212--13513241 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13513202 ATTACCGCTG
13513212 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13513242 CTACTACTAC
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):
TTA
Found at i:13518768 original size:16 final size:17
Alignment explanation
Indices: 13518743--13518779 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
13518733 GTTCAAGTAT
13518743 TTTTTATGTT-TTTT-A
1 TTTTTATGTTGTTTTAA
13518758 TTTTTATTGTTGTTTTAA
1 TTTTTA-TGTTGTTTTAA
13518776 TTTT
1 TTTT
13518780 CTTTATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 4 0.21
18 5 0.26
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (17 bp):
TTTTTATGTTGTTTTAA
Found at i:13519146 original size:10 final size:10
Alignment explanation
Indices: 13519133--13519166 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
13519123 GAAAGTAAAA
13519133 AAAAATTAAT
1 AAAAATTAAT
*
13519143 AAAAATGAA-
1 AAAAATTAAT
13519152 AAAAATTAAT
1 AAAAATTAAT
13519162 AAAAA
1 AAAAA
13519167 ATTTTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:13519518 original size:13 final size:12
Alignment explanation
Indices: 13519502--13519544 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
13519492 AAAAAAAGTG
*
13519502 AAAAGTAAAAAT
1 AAAAATAAAAAT
*
13519514 AAAAATAAATGAT
1 AAAAATAAA-AAT
13519527 AAAAATGAAAAAT
1 AAAAAT-AAAAAT
13519540 AAAAA
1 AAAAA
13519545 ACCAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 8 0.31
13 15 0.58
14 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:13519545 original size:7 final size:6
Alignment explanation
Indices: 13519502--13519544 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
13519492 AAAAAAAGTG
* *
13519502 AAAAGT AAAAAT AAAAAT AAATGAT AAAAAT GAAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT -AAAAAT AAAAA
13519545 ACCAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 21 0.66
7 11 0.34
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:13525410 original size:21 final size:22
Alignment explanation
Indices: 13525364--13525415 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
13525354 TTTTTTTGGT
* *
13525364 AAATCTTTGAAACCCTTGTGTC
1 AAATCTTTAAAACCCTTATGTC
13525386 -AATCTTTAAAACCCTTATG-C
1 AAATCTTTAAAACCCTTATGTC
13525406 AAATCTTTAA
1 AAATCTTTAA
13525416 GTCTTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATCTTTAAAACCCTTATGTC
Found at i:13525521 original size:20 final size:20
Alignment explanation
Indices: 13525493--13525531 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13525483 GAGTTTTTGC
* *
13525493 AAACCTTCAATGTAAATCTT
1 AAACATTCAATGAAAATCTT
13525513 AAACATTCAATGAAAATCT
1 AAACATTCAATGAAAATCT
13525532 CAAAATCCTT
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:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTCAATGAAAATCTT
Found at i:13525629 original size:37 final size:38
Alignment explanation
Indices: 13525588--13525672 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
13525578 GAATCCTTTT
* * *
13525588 AAATGCAAA-CCTTGGAGTTTT-AGATGTGAATCTCTTC
1 AAATGAAAATCCTT-GACTTTTAAGATGCGAATCTCTTC
*
13525625 AAATGAAAATCGTTGACTTTTAAGATGCGAATCTCTTC
1 AAATGAAAATCCTTGACTTTTAAGATGCGAATCTCTTC
*
13525663 AAATGTAAAT
1 AAATGAAAAT
13525673 TTTTCATTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 14 0.34
38 27 0.66
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (38 bp):
AAATGAAAATCCTTGACTTTTAAGATGCGAATCTCTTC
Found at i:13525850 original size:38 final size:38
Alignment explanation
Indices: 13525792--13526007 Score: 229
Period size: 38 Copynumber: 5.5 Consensus size: 38
13525782 TTTGCAAGTA
* * *
13525792 GAATCTCTTCATATGGGAATCTTTGACTTTTAAGATAT
1 GAATTTCTTCAAATGTGAATCTTTGACTTTTAAGATAT
* *
13525830 AAATTTCTTCAAATGTGAATCTTTGACTTTTAAGATGT
1 GAATTTCTTCAAATGTGAATCTTTGACTTTTAAGATAT
* * *
13525868 GAATCTCTTCAAATGAGAGTCTTTGA-TTTCT-AGATAT
1 GAATTTCTTCAAATGTGAATCTTTGACTTT-TAAGATAT
*
13525905 GAATCTCTGAATTTGTCAAATGTGAATCTTTGACTTTTAAGATAT
1 GAA--T-T---TCT-TCAAATGTGAATCTTTGACTTTTAAGATAT
* *
13525950 GAATCTCTTCAAATGTGAATCTTTGACTTTTAAGATGT
1 GAATTTCTTCAAATGTGAATCTTTGACTTTTAAGATAT
* *
13525988 GAATTTCCTCAAATGAGAAT
1 GAATTTCTTCAAATGTGAAT
13526008 ATTTTATTTC
Statistics
Matches: 148, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
37 11 0.07
38 102 0.69
39 3 0.02
43 3 0.02
44 17 0.11
45 12 0.08
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (38 bp):
GAATTTCTTCAAATGTGAATCTTTGACTTTTAAGATAT
Found at i:13525935 original size:44 final size:42
Alignment explanation
Indices: 13525875--13526073 Score: 145
Period size: 44 Copynumber: 4.8 Consensus size: 42
13525865 TGTGAATCTC
*
13525875 TTCAAATGAGAGTCTTTGATTTCTAGATATGAATCTCTGAATT
1 TTCAAATGAGAATCTTTGATTT-TAGATATGAATCTCTGAATT
*
13525918 TGTCAAATGTGAATCTTTGACTTTTAAGATATGAATCTC------
1 T-TCAAATGAGAATCTTTGA-TTTT-AGATATGAATCTCTGAATT
* *
13525957 TTCAAATGTGAATCTTTGACTTTT--A-A-G-A--TGTGAATT
1 TTCAAATGAGAATCTTTGA-TTTTAGATATGAATCTCTGAATT
* * * *
13525993 TCCTCAAATGAGAATATTTTATTTCTAGATGTGAATCTCTAAATTT
1 T--TCAAATGAGAATCTTTGATTT-TAGATATGAATCTCTGAA-TT
13526039 TTCAAATGAGAATCTTTGATTTTTAGATATGAATC
1 TTCAAATGAGAATCTTTGA-TTTTAGATATGAATC
13526074 GCTAAAATTT
Statistics
Matches: 123, Mismatches: 12, Indels: 41
0.70 0.07 0.23
Matches are distributed among these distances:
30 1 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
37 3 0.02
38 39 0.32
39 1 0.01
40 1 0.01
42 1 0.01
43 2 0.02
44 44 0.36
45 23 0.19
46 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (42 bp):
TTCAAATGAGAATCTTTGATTTTAGATATGAATCTCTGAATT
Found at i:13525949 original size:120 final size:120
Alignment explanation
Indices: 13525808--13526073 Score: 408
Period size: 120 Copynumber: 2.2 Consensus size: 120
13525798 CTTCATATGG
*
13525808 GAATCTTTGACTTTTAAGATATAAATTTCTTCAAATGTGAATCTTTGACTTTTAAGATGTGAATC
1 GAATCTTTGACTTTTAAGATATAAATCTCTTCAAATGTGAATCTTTGACTTTTAAGATGTGAATC
* * * * *
13525873 TCTTCAAATGAGAGTCTTTGATTTCTAGATATGAATCTCTGAATTTGTCAAATGT
66 TCCTCAAATGAGAATATTTGATTTCTAGATATGAATCTCTAAATTTGTCAAATGA
* *
13525928 GAATCTTTGACTTTTAAGATATGAATCTCTTCAAATGTGAATCTTTGACTTTTAAGATGTGAATT
1 GAATCTTTGACTTTTAAGATATAAATCTCTTCAAATGTGAATCTTTGACTTTTAAGATGTGAATC
* * *
13525993 TCCTCAAATGAGAATATTTTATTTCTAGATGTGAATCTCTAAATTTTTCAAATGA
66 TCCTCAAATGAGAATATTTGATTTCTAGATATGAATCTCTAAATTTGTCAAATGA
* *
13526048 GAATCTTTGA-TTTTTAGATATGAATC
1 GAATCTTTGACTTTTAAGATATAAATC
13526074 GCTAAAATTT
Statistics
Matches: 134, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 15 0.11
120 119 0.89
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (120 bp):
GAATCTTTGACTTTTAAGATATAAATCTCTTCAAATGTGAATCTTTGACTTTTAAGATGTGAATC
TCCTCAAATGAGAATATTTGATTTCTAGATATGAATCTCTAAATTTGTCAAATGA
Found at i:13525950 original size:45 final size:38
Alignment explanation
Indices: 13525920--13526032 Score: 140
Period size: 38 Copynumber: 3.0 Consensus size: 38
13525910 TCTGAATTTG
13525920 TCAAATGTGAATCTTTGACTTTTAAGATATGAATCTCT
1 TCAAATGTGAATCTTTGACTTTTAAGATATGAATCTCT
* * *
13525958 TCAAATGTGAATCTTTGACTTTTAAGATGTGAATTTCC
1 TCAAATGTGAATCTTTGACTTTTAAGATATGAATCTCT
* * * *
13525996 TCAAATGAGAATATTTTA-TTTCT-AGATGTGAATCTCT
1 TCAAATGTGAATCTTTGACTTT-TAAGATATGAATCTCT
13526033 AAATTTTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
37 15 0.23
38 51 0.77
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (38 bp):
TCAAATGTGAATCTTTGACTTTTAAGATATGAATCTCT
Found at i:13526079 original size:44 final size:44
Alignment explanation
Indices: 13525875--13526118 Score: 149
Period size: 45 Copynumber: 5.8 Consensus size: 44
13525865 TGTGAATCTC
* * * *
13525875 TTCAAATGAGAGTCTTTGATTTCTAGATATGAATCTCTGAATTT
1 TTCAAATGAGAATCTTTGATTTTTAGATATGAATCGCTAAATTT
* * * *
13525919 GTCAAATGTGAATCTTTGACTTTTAAGATATGAAT--C-----TC
1 TTCAAATGAGAATCTTTGA-TTTTTAGATATGAATCGCTAAATTT
* * *
13525957 TTCAAATGTGAATCTTTGACTTTT--A-A-G-AT-G-TGAATTT
1 TTCAAATGAGAATCTTTGATTTTTAGATATGAATCGCTAAATTT
* * * * * *
13525994 CCTCAAATGAGAATATTTTATTTCTAGATGTGAATCTCTAAATTT
1 -TTCAAATGAGAATCTTTGATTTTTAGATATGAATCGCTAAATTT
13526039 TTCAAATGAGAATCTTTGATTTTTAGATATGAATCGCTAAAATTT
1 TTCAAATGAGAATCTTTGATTTTTAGATATGAATCGCT-AAATTT
* * * **
13526084 TTTAAATAAGAA-CATTTAACCTTTAGATATGAATC
1 TTCAAATGAGAATC-TTTGATTTTTAGATATGAATC
13526119 TTTTCAAATA
Statistics
Matches: 153, Mismatches: 30, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
37 4 0.03
38 37 0.24
40 1 0.01
42 1 0.01
43 3 0.02
44 49 0.32
45 53 0.35
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (44 bp):
TTCAAATGAGAATCTTTGATTTTTAGATATGAATCGCTAAATTT
Found at i:13526742 original size:49 final size:48
Alignment explanation
Indices: 13526657--13526819 Score: 177
Period size: 49 Copynumber: 3.3 Consensus size: 48
13526647 AGTTGGCATA
* * * * * *
13526657 AGATGAGAATTTTAAAGTTTCAATGCTCCTAGTTAGAGGAGCCTTTTTT
1 AGATAAGATTTTTAAAATTTCAATCCTCTTA-TTAGAAGAGCCTTTTTT
*
13526706 AGATAAGATTTTTAAAATTTCAATACCTCTTATTAGAAGA-CCTTTTTCC
1 AGATAAGATTTTTAAAATTTCAAT-CCTCTTATTAGAAGAGCCTTTTT-T
* *
13526755 ACATAAGATTTTTAAAATTTCAATCCCTCTTATTAGATA-AGCCTTTTCT
1 AGATAAGATTTTTAAAATTTCAAT-CCTCTTATTAGA-AGAGCCTTTTTT
*
13526804 AGATGAGATTTTTAAA
1 AGATAAGATTTTTAAA
13526820 GTTTTTTAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
48 7 0.07
49 78 0.80
50 12 0.12
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (48 bp):
AGATAAGATTTTTAAAATTTCAATCCTCTTATTAGAAGAGCCTTTTTT
Found at i:13526972 original size:90 final size:91
Alignment explanation
Indices: 13526809--13526979 Score: 254
Period size: 90 Copynumber: 1.9 Consensus size: 91
13526799 TTTCTAGATG
* * * * * *
13526809 AGATTTTTAAAGTTTTTTAGCCTTTGTTTAGAAGAGCATTCATTAGTGTTGAGATTTGTAAGATC
1 AGATTTTTAAAGTTTCTTAGCCTTTGTTTAAAAGAGCACTCATTAGAGTTAAGATTTGTAAGACC
*
13526874 TCTAGGCATA-TCTCTATGCTTTGCA
66 ACTAGGCATAGTCTCTATGCTTTGCA
*
13526899 AGATTTTTAAAGTTTCTTAGCTTTTGTTTAAAAGAGCACTCATTAGAGTTAAGATTTGTAAGACC
1 AGATTTTTAAAGTTTCTTAGCCTTTGTTTAAAAGAGCACTCATTAGAGTTAAGATTTGTAAGACC
*
13526964 ACTGGGCATAGTCTCT
66 ACTAGGCATAGTCTCT
13526980 TAGTTCTTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 66 0.93
91 5 0.07
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (91 bp):
AGATTTTTAAAGTTTCTTAGCCTTTGTTTAAAAGAGCACTCATTAGAGTTAAGATTTGTAAGACC
ACTAGGCATAGTCTCTATGCTTTGCA
Found at i:13527591 original size:21 final size:21
Alignment explanation
Indices: 13527546--13527609 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
13527536 GTTCCCTAAA
*
13527546 CTACACCAG-CCTCCTTCTACCC
1 CTACACCAGTCC-CC-TCTACTC
13527568 CTACACCAGTCCCCTCTACTC
1 CTACACCAGTCCCCTCTACTC
13527589 CTACACCAGTCCCCTCTACTC
1 CTACACCAGTCCCCTCTACTC
13527610 TACCAACTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 27 0.68
22 11 0.28
23 2 0.05
ACGTcount: A:0.19, C:0.53, G:0.05, T:0.23
Consensus pattern (21 bp):
CTACACCAGTCCCCTCTACTC
Found at i:13528058 original size:20 final size:20
Alignment explanation
Indices: 13528017--13528058 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13528007 CCAAATAATC
* * *
13528017 AAGAAAACACCAACTAAAAA
1 AAGAAAAAACAAACAAAAAA
13528037 AAGAAAAAACAAACAAAAAA
1 AAGAAAAAACAAACAAAAAA
13528057 AA
1 AA
13528059 TCCACATCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02
Consensus pattern (20 bp):
AAGAAAAAACAAACAAAAAA
Found at i:13528809 original size:18 final size:17
Alignment explanation
Indices: 13528775--13528807 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13528765 AGTCGATTCA
13528775 AGTA-TTTTTGTGTTTT
1 AGTATTTTTTGTGTTTT
*
13528791 AGTATTTTTTGTATTTT
1 AGTATTTTTTGTGTTTT
13528808 TATTATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (17 bp):
AGTATTTTTTGTGTTTT
Found at i:13529599 original size:17 final size:17
Alignment explanation
Indices: 13529559--13529602 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
13529549 ACAAAAATGG
13529559 AAAATAAAAATTAAAAA
1 AAAATAAAAATTAAAAA
**
13529576 ATGATAAAAA-TAAAATA
1 AAAATAAAAATTAAAA-A
13529593 AAAATAAAAA
1 AAAATAAAAA
13529603 ACCAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAATAAAAATTAAAAA
Found at i:13531441 original size:20 final size:20
Alignment explanation
Indices: 13531400--13531441 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13531390 AAACTTGGTC
* **
13531400 AATAAAGTTAAAATTAGTCA
1 AATAAAGTCAAAATTACACA
13531420 AATAAAGTCAAAATTACACA
1 AATAAAGTCAAAATTACACA
13531440 AA
1 AA
13531442 ACTTGATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.24
Consensus pattern (20 bp):
AATAAAGTCAAAATTACACA
Found at i:13531807 original size:143 final size:144
Alignment explanation
Indices: 13531631--13531911 Score: 388
Period size: 143 Copynumber: 2.0 Consensus size: 144
13531621 AGATTGATTT
* *
13531631 TTTTCATAAAACTTTTCAATCTTAATTTCATAATATTTCATGATTTTTGGTGTG-TTTGAAATCA
1 TTTTCACAAAACTTTTCAATCTTAATTTCATAATATTTCATGATTTTTAGTG-GATTTGAAATCA
* * * *
13531695 CAACAGTA-CCTCGAGATGTGTGAAATTACCAAAATACCCCTAAAAGGTATTTTTATAATTT-GG
65 CAACAGTACCCT-AAGAGGTGTGAAAATACCAAAATACCCCTAAAAGGTATTTTCATAATTTAGG
*
13531758 CCTTCCCAAGTTTGAA
129 CATTCCCAAGTTTGAA
* *
13531774 TTTTCACAAAACTTTTCAATCTTAATTTCATAATATTTCATGATTTTTAGTGGATTTTAAATCTC
1 TTTTCACAAAACTTTTCAATCTTAATTTCATAATATTTCATGATTTTTAGTGGATTTGAAATCAC
* * ** * *
13531839 AATAGTACCCTAAGAGGTGTGAAAATATCAAAATACCTTTTAAGGGTATTTTCATAATTTAGGCA
66 AACAGTACCCTAAGAGGTGTGAAAATACCAAAATACCCCTAAAAGGTATTTTCATAATTTAGGCA
13531904 TTCCCAAG
131 TTCCCAAG
13531912 CTTAGATTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
142 1 0.01
143 105 0.88
144 14 0.12
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (144 bp):
TTTTCACAAAACTTTTCAATCTTAATTTCATAATATTTCATGATTTTTAGTGGATTTGAAATCAC
AACAGTACCCTAAGAGGTGTGAAAATACCAAAATACCCCTAAAAGGTATTTTCATAATTTAGGCA
TTCCCAAGTTTGAA
Found at i:13532241 original size:21 final size:23
Alignment explanation
Indices: 13532194--13532250 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
13532184 ATAAGAAGAA
*
13532194 AATAGAAAAAAAAAGGCTTTGGAGC
1 AATA-AAAAAAAAAGGC-TAGGAGC
13532219 AATAAAAAAAAAAGG-TAGG-GC
1 AATAAAAAAAAAAGGCTAGGAGC
13532240 AA-AAAAAAAAA
1 AATAAAAAAAAA
13532251 GATGAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 4 0.13
22 3 0.10
24 11 0.35
25 4 0.13
ACGTcount: A:0.65, C:0.05, G:0.19, T:0.11
Consensus pattern (23 bp):
AATAAAAAAAAAAGGCTAGGAGC
Found at i:13533342 original size:22 final size:22
Alignment explanation
Indices: 13533317--13533371 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
13533307 TATCTTACTT
*
13533317 TAATAAAAATTGTAAAAA-TAA
1 TAATAAAAATAGTAAAAAGTAA
13533338 GTAATAAGGATAATAGTAAAAAGTAA
1 -TAATAA--A-AATAGTAAAAAGTAA
13533364 TAATAAAA
1 TAATAAAA
13533372 TAAAAAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
22 7 0.25
23 1 0.04
24 1 0.04
25 16 0.57
26 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (22 bp):
TAATAAAAATAGTAAAAAGTAA
Found at i:13540296 original size:3 final size:3
Alignment explanation
Indices: 13540288--13540318 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13540278 TCCCAAGGTA
13540288 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13540319 CCCTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13540900 original size:25 final size:25
Alignment explanation
Indices: 13540872--13540920 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
13540862 CTTAAATGAG
*
13540872 TTTATTCCACATGACCCTTTTCTCC
1 TTTACTCCACATGACCCTTTTCTCC
* * *
13540897 TTTACTCCATATGATCTTTTTCTC
1 TTTACTCCACATGACCCTTTTCTC
13540921 GTAATAAATT
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:0.16, C:0.31, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTACTCCACATGACCCTTTTCTCC
Found at i:13541062 original size:23 final size:23
Alignment explanation
Indices: 13541021--13541072 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
13541011 TTTGGTCAAA
13541021 AAAAAAGGAAAAGAAAAAGA-AG
1 AAAAAAGGAAAAGAAAAAGAGAG
*
13541043 TAAAAAGGCAAAA-AGAAAAGAGAG
1 AAAAAAGG-AAAAGA-AAAAGAGAG
13541067 AAAAAA
1 AAAAAA
13541073 AATAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.32
23 10 0.40
24 7 0.28
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (23 bp):
AAAAAAGGAAAAGAAAAAGAGAG
Found at i:13541085 original size:24 final size:23
Alignment explanation
Indices: 13541019--13541085 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 23
13541009 GGTTTGGTCA
13541019 AAAAAAAAGGAAAAGAAAAAGAAGT
1 AAAAAAAA--AAAAGAAAAAGAAGT
**
13541044 AAAAAGGCAAAAAG-AAAAGAGAG-
1 AAAAA-AAAAAAAGAAAAAGA-AGT
13541067 AAAAAAAATAAAAGAAAAA
1 AAAAAAAA-AAAAGAAAAA
13541086 TGGTTATGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 16 0.47
24 11 0.32
25 5 0.15
26 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (23 bp):
AAAAAAAAAAAAGAAAAAGAAGT
Found at i:13542534 original size:32 final size:32
Alignment explanation
Indices: 13542471--13542535 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
13542461 ACCAATTTCC
* * *
13542471 AAGTTTTAAGCCTAGATTATCTAGTACCAATG
1 AAGTCTTAAGCCTAGATTAGCTAGCACCAATG
* * *
13542503 AAGTCTTAAGCCTAGTTTAGCTGGCATCAATG
1 AAGTCTTAAGCCTAGATTAGCTAGCACCAATG
13542535 A
1 A
13542536 GATTTAAACC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (32 bp):
AAGTCTTAAGCCTAGATTAGCTAGCACCAATG
Found at i:13542888 original size:33 final size:33
Alignment explanation
Indices: 13542841--13542915 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
13542831 CATTAATGAG
* *
13542841 ATTTAAACCTAGTTTATTTGGTACCAAAGAAAA
1 ATTTAAGCCCAGTTTATTTGGTACCAAAGAAAA
*
13542874 ATTTAAGCCCAGTTTATTTGGTACCAAAGAAAT
1 ATTTAAGCCCAGTTTATTTGGTACCAAAGAAAA
13542907 ATTTAAGCC
1 ATTTAAGCC
13542916 TAAATTATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTTAAGCCCAGTTTATTTGGTACCAAAGAAAA
Found at i:13543396 original size:140 final size:139
Alignment explanation
Indices: 13543217--13543539 Score: 323
Period size: 140 Copynumber: 2.3 Consensus size: 139
13543207 TCGACTTATG
* * * * * * *
13543217 GTTCAGTCTCAATCATATTTATTATTCGACTCGTAGTTCAATCCCAATTATTTTCATTTTTAAAC
1 GTTCAGTCTCAGTCATTTTTATTTTTTGACTTGTGGTTCAATCCCAATTATTTTCATTTCTAAAC
* *
13543282 TTGCGGTTCATTCTTGATCATTTTCATTGTTTGA-CT-CGATGTTCAAT-CTCAGTCA-TCTTTA
66 TTGCAGTTCAATCTTGATCATTTTCATT-TTTGATCTCCG--GTTCAATCCT-AGTCATTCTTTA
*
13543343 TTCTTTGACTTGC
127 TTCTTTGACTGGC
* * * * **
13543356 AGTTCAGTCTCAGTCATTTTTATTTTTTGACTTGTGGTTCAATCTCATTTGTTTTTATTTCTCGA
1 -GTTCAGTCTCAGTCATTTTTATTTTTTGACTTGTGGTTCAATCCCAATTATTTTCATTTCTAAA
* * * * *
13543421 CTTGCAGTTCAATCTTGGTCATTTTCATTTTTGATTTCCGGTTTAGTCCTAGTCATTTTTTATTC
65 CTTGCAGTTCAATCTTGATCATTTTCATTTTTGATCTCCGGTTCAATCCTAGTCATTCTTTATTC
13543486 TTTGACTGGC
130 TTTGACTGGC
* * * *
13543496 GATTCAATCTC-GATCATTTTCATTTCTTGACTTATGGTTCAATC
1 G-TTCAGTCTCAG-TCATTTTTATTTTTTGACTTGTGGTTCAATC
13543540 TCGATCATCT
Statistics
Matches: 152, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
139 17 0.11
140 133 0.88
141 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (139 bp):
GTTCAGTCTCAGTCATTTTTATTTTTTGACTTGTGGTTCAATCCCAATTATTTTCATTTCTAAAC
TTGCAGTTCAATCTTGATCATTTTCATTTTTGATCTCCGGTTCAATCCTAGTCATTCTTTATTCT
TTGACTGGC
Found at i:13543400 original size:70 final size:71
Alignment explanation
Indices: 13543280--13543667 Score: 282
Period size: 70 Copynumber: 5.5 Consensus size: 71
13543270 TCATTTTTAA
* * * * * *
13543280 ACTTGC-GGTTCATTCTTGATCATTTTCATTGTTTGACTCGAT-GTTCAATCTCAGTCATCTTTA
1 ACTTGCAGATTCAATCTCGATCATTTTCATTTTTTGACTTG-TGGTTCAATCTCAGTCATTTTTA
13543343 TTCTTTG
65 TTCTTTG
* * * **
13543350 ACTTGCAG-TTCAGTCTC-AGTCATTTTTATTTTTTGACTTGTGGTTCAATCTCATTTGTTTTTA
1 ACTTGCAGATTCAATCTCGA-TCATTTTCATTTTTTGACTTGTGGTTCAATCTCAGTCATTTTTA
*
13543413 TT-TCTCG
65 TTCT-TTG
* * * ** * *
13543420 ACTTGCAG-TTCAATCTTGGTCATTTTCA-TTTTTGATTTCCGGTTTAGTC-CTAGTCATTTTTT
1 ACTTGCAGATTCAATCTCGATCATTTTCATTTTTTGACTTGTGGTTCAATCTC-AGTCA-TTTTT
13543482 ATTCTTTG
64 ATTCTTTG
* * * *
13543490 ACTGGC-GATTCAATCTCGATCATTTTCATTTCTTGACTTATGGTTCAATCTC-GATCATCTTTA
1 ACTTGCAGATTCAATCTCGATCATTTTCATTTTTTGACTTGTGGTTCAATCTCAG-TCATTTTTA
*
13543553 TTCTTTA
65 TTCTTTG
* * * * ****
13543560 ACTT-AAGTTTCAATCCCGATCATTTTTATTTCCCAACTTGTGGTTCAATCTCAGTCATTTTTAT
1 ACTTGCAGATTCAATCTCGATCATTTTCATTTTTTGACTTGTGGTTCAATCTCAGTCATTTTTAT
*
13543624 TCTTCG
66 TCTTTG
* * *
13543630 ACTTACAG-CTCAATC-CTGATCATATTT-ATTCTTTGACT
1 ACTTGCAGATTCAATCTC-GATCAT-TTTCATTTTTTGACT
13543668 CGCACTTCAA
Statistics
Matches: 248, Mismatches: 53, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
68 1 0.00
69 23 0.09
70 197 0.79
71 26 0.10
72 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.12, T:0.48
Consensus pattern (71 bp):
ACTTGCAGATTCAATCTCGATCATTTTCATTTTTTGACTTGTGGTTCAATCTCAGTCATTTTTAT
TCTTTG
Found at i:13543431 original size:35 final size:35
Alignment explanation
Indices: 13543157--13543732 Score: 161
Period size: 35 Copynumber: 16.5 Consensus size: 35
13543147 TTTAATTTTG
* *
13543157 GTCATCTTTTATTT-TCTGACTTGTAGCTT-AGTCTCA
1 GTCAT-TTTTATTTCTC-GACTTGCAG-TTCAATCTCA
* *** *
13543193 ATCATTTTTATTTCTCGACTTATGGTTCAGTCTCA
1 GTCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
* * * * *
13543228 ATCATATTTATTAT-TCGACTCGTAGTTCAATCCCA
1 GTCATTTTTATT-TCTCGACTTGCAGTTCAATCTCA
* * * * ** * * *
13543263 ATTATTTTCATTTTTAAACTTGCGGTTCATTCT-T
1 GTCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
* * *
13543297 GATCATTTTCATTGT-TTGACTCG-ATGTTCAATCTCA
1 G-TCATTTTTATT-TCTCGACTTGCA-GTTCAATCTCA
* * *
13543333 GTCATCTTTA-TTCTTTGACTTGCAGTTCAGTCTCA
1 GTCATTTTTATTTC-TCGACTTGCAGTTCAATCTCA
* * **
13543368 GTCATTTTTATTTTTTGACTTGTGGTTCAATCTCA
1 GTCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
* ** **
13543403 TTTGTTTTTATTTCTCGACTTGCAGTTCAATCTTG
1 GTCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
* * * * * * *
13543438 GTCATTTTCATTT-TTGATTTCCGGTTTAGTC-CTA
1 GTCATTTTTATTTCTCGACTTGCAGTTCAATCTC-A
* *
13543472 GTCATTTTT-TATTCTTTGACTGGC-GATTCAATCTC-
1 GTCATTTTTAT-TTC-TCGACTTGCAG-TTCAATCTCA
* * ***
13543507 GATCATTTTCATTTCTTGACTTATGGTTCAATCTC-
1 G-TCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
* ** * *
13543542 GATCATCTTTA-TTCTTTAACTT-AAGTTTCAATC-CC
1 G-TCATTTTTATTTC-TCGACTTGCAG-TTCAATCTCA
* * **
13543577 GATCATTTTTATTTCCCAACTTGTGGTTCAATCTCA
1 G-TCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
* * *
13543613 GTCATTTTTA-TTCTTCGACTTACAGCTCAATC-CT
1 GTCATTTTTATTTC-TCGACTTGCAGTTCAATCTCA
* * * *
13543647 GATCATATTTA-TTCTTTGACTCGCACTTCAAT-TC-
1 G-TCATTTTTATTTC-TCGACTTGCAGTTCAATCTCA
* * * * *
13543681 GATCATTTTCATTTC-CTAACTCGTAGTTCAATCTAA
1 G-TCATTTTTATTTCTC-GACTTGCAGTTCAATCTCA
13543717 GTCATTTTTATTTCTC
1 GTCATTTTTATTTCTC
13543733 ATCTTGCGAC
Statistics
Matches: 405, Mismatches: 100, Indels: 70
0.70 0.17 0.12
Matches are distributed among these distances:
33 2 0.00
34 57 0.14
35 302 0.75
36 42 0.10
37 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (35 bp):
GTCATTTTTATTTCTCGACTTGCAGTTCAATCTCA
Found at i:13543431 original size:105 final size:103
Alignment explanation
Indices: 13543157--13543732 Score: 328
Period size: 105 Copynumber: 5.5 Consensus size: 103
13543147 TTTAATTTTG
* * * **
13543157 GTCATCTTTTATTTTCTGACTTGTAGCTT-AGTCTCAATCATTTTTATTTCTCGACTTATGGTTC
1 GTCAT-TTTTATTTTTTGACTTGT-GGTTCAATCTC-ATCATTTTTATTTCTCGACTTACAGTTC
* * * * * * * *
13543221 AGTCTCAATCATATTTATTATTCGACTCGTAGTTCAATCCCA
63 AATCTCGATCATCTTTATTCTTTGACTTGCAGTTCAGT-CCA
* * * ** * * * * *
13543263 ATTATTTTCATTTTTAAACTTGCGGTTCATTCTTGATCATTTTCATTGT-TTGAC-T-CGATGTT
1 GTCATTTTTATTTTTTGACTTGTGGTTCAATC-TCATCATTTTTATT-TCTCGACTTAC-A-GTT
13543325 CAATCTC-AGTCATCTTTATTCTTTGACTTGCAGTTCAGTCTCA
62 CAATCTCGA-TCATCTTTATTCTTTGACTTGCAGTTCAGTC-CA
** *
13543368 GTCATTTTTATTTTTTGACTTGTGGTTCAATCTCATTTGTTTTTATTTCTCGACTTGCAGTTCAA
1 GTCATTTTTATTTTTTGACTTGTGGTTCAATCTCA-TCATTTTTATTTCTCGACTTACAGTTCAA
* * * * * *
13543433 TCTTGGTCAT-TTTCATT-TTTGATTTCCGGTTTAGTCCTA
65 TCTCGATCATCTTT-ATTCTTTGACTTGCAGTTCAGTCC-A
* * * * * * **
13543472 GTCATTTTTTATTCTTTGACTGGCGATTCAATCTCGATCATTTTCATTTCTTGACTTATGGTTCA
1 GTCA-TTTTTATTTTTTGACTTGTGGTTCAATCTC-ATCATTTTTATTTCTCGACTTACAGTTCA
* * * *
13543537 ATCTCGATCATCTTTATTCTTTAACTT-AAGTTTCAATCCC
64 ATCTCGATCATCTTTATTCTTTGACTTGCAG-TTCAGTCCA
**** *
13543577 GATCATTTTTATTTCCCAACTTGTGGTTCAATCTCAGTCATTTTTA-TTCTTCGACTTACAGCTC
1 G-TCATTTTTATTTTTTGACTTGTGGTTCAATCTCA-TCATTTTTATTTC-TCGACTTACAGTTC
* * * * *
13543641 AATC-CTGATCATATTTATTCTTTGACTCGCACTTCAATTC-
63 AATCTC-GATCATCTTTATTCTTTGACTTGCAGTTCAGTCCA
* ** * * * *
13543681 GATCATTTTCATTTCCTAACTCGTAGTTCAATCTAAGTCATTTTTATTTCTC
1 G-TCATTTTTATTTTTTGACTTGTGGTTCAATCTCA-TCATTTTTATTTCTC
13543733 ATCTTGCGAC
Statistics
Matches: 362, Mismatches: 83, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
103 1 0.00
104 80 0.22
105 253 0.70
106 27 0.07
107 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (103 bp):
GTCATTTTTATTTTTTGACTTGTGGTTCAATCTCATCATTTTTATTTCTCGACTTACAGTTCAAT
CTCGATCATCTTTATTCTTTGACTTGCAGTTCAGTCCA
Found at i:13544166 original size:20 final size:20
Alignment explanation
Indices: 13544128--13544166 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13544118 CTTGGTCAAT
* **
13544128 AAAGTTAAAATTAGTCAAAC
1 AAAGTCAAAATTACACAAAC
13544148 AAAGTCAAAATTACACAAA
1 AAAGTCAAAATTACACAAA
13544167 ACTTGATCAA
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:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAGTCAAAATTACACAAAC
Found at i:13545942 original size:18 final size:17
Alignment explanation
Indices: 13545921--13545968 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
13545911 TCCCTATAAG
**
13545921 TTTAATTTTCATGTTTGT
1 TTTAATTTTCATG-TCAT
*
13545939 TTTAATTTTTATG-CAT
1 TTTAATTTTCATGTCAT
13545955 TTTAATTTTCATGT
1 TTTAATTTTCATGT
13545969 AGATTACTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (17 bp):
TTTAATTTTCATGTCAT
Found at i:13546388 original size:14 final size:14
Alignment explanation
Indices: 13546379--13546407 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13546369 CGAAACTTTT
13546379 AAATTAAAACCCTA
1 AAATTAAAACCCTA
13546393 AAATTAAAACCCTA
1 AAATTAAAACCCTA
13546407 A
1 A
13546408 GGTCAAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATTAAAACCCTA
Found at i:13546445 original size:25 final size:25
Alignment explanation
Indices: 13546413--13546472 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
13546403 CCTAAGGTCA
* *
13546413 AGACCCTAAATAAAGCCTTAAATTG
1 AGACCCTAAATAAAACCTTAAACTG
13546438 AGACCCTAAATAAAACCTTAAACTG
1 AGACCCTAAATAAAACCTTAAACTG
*
13546463 AAACCCTAAA
1 AGACCCTAAA
13546473 CTTGTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.20
Consensus pattern (25 bp):
AGACCCTAAATAAAACCTTAAACTG
Found at i:13547471 original size:27 final size:25
Alignment explanation
Indices: 13547441--13547492 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
13547431 TCATTTTTTT
13547441 ATTTTTATATTTTTATTAAAATTTTCA
1 ATTTTTATA-TTTTA-TAAAATTTTCA
* *
13547468 ATTTTTTTATTTTATCAAATTTTCA
1 ATTTTTATATTTTATAAAATTTTCA
13547493 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTTTATATTTTATAAAATTTTCA
Found at i:13547499 original size:35 final size:34
Alignment explanation
Indices: 13547433--13547501 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 34
13547423 TGATGTCATC
* *
13547433 ATTTTTTTATTTTTATATTTTTATTAAAATTTTCA
1 ATTTTTTTATTTTTAAATTTTCATT-AAATTTTCA
*
13547468 ATTTTTTTATTTTATCAAATTTTCATTAATTTTT
1 ATTTTTTTATTTT-T-AAATTTTCATTAAATTTT
13547502 TAAATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 7 0.24
37 9 0.31
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (34 bp):
ATTTTTTTATTTTTAAATTTTCATTAAATTTTCA
Found at i:13547623 original size:18 final size:17
Alignment explanation
Indices: 13547592--13547645 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
13547582 ATAGTTTCAA
13547592 AAATTTTTAGATTTTTT
1 AAATTTTTAGATTTTTT
*
13547609 AAATTTTTCATATTTTTT
1 AAATTTTT-AGATTTTTT
*
13547627 AAGTTTTTATGAATTTTTT
1 AAATTTTTA-G-ATTTTTT
13547646 TTAGTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 9 0.29
18 15 0.48
19 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (17 bp):
AAATTTTTAGATTTTTT
Found at i:13547644 original size:20 final size:19
Alignment explanation
Indices: 13547620--13547666 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13547610 AATTTTTCAT
*
13547620 ATTTTTTAAGTTTTTATGAA
1 ATTTTTTAAG-TTTTAAGAA
* *
13547640 TTTTTTTTAGTTTTAAGAA
1 ATTTTTTAAGTTTTAAGAA
13547659 ATTTTTTA
1 ATTTTTTA
13547667 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (19 bp):
ATTTTTTAAGTTTTAAGAA
Found at i:13547653 original size:19 final size:21
Alignment explanation
Indices: 13547621--13547665 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
13547611 ATTTTTCATA
*
13547621 TTTTTTAAGTTTTTATG-AAT
1 TTTTTTAAGTTTTTAAGAAAT
*
13547641 TTTTTTTAG-TTTTAAGAAAT
1 TTTTTTAAGTTTTTAAGAAAT
13547661 TTTTT
1 TTTTT
13547666 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTTTTAAGTTTTTAAGAAAT
Found at i:13547782 original size:19 final size:19
Alignment explanation
Indices: 13547750--13547801 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
13547740 AAGATTTTTA
13547750 TTTTTTAGAATTTTTT--GT
1 TTTTTTAG-ATTTTTTAAGT
13547768 TTTTATTAGATTTTTTAAGT
1 TTTT-TTAGATTTTTTAAGT
*
13547788 TTTTTTAAATTTTT
1 TTTTTTAGATTTTT
13547802 CATATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.37
19 13 0.43
20 6 0.20
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (19 bp):
TTTTTTAGATTTTTTAAGT
Found at i:13547809 original size:17 final size:18
Alignment explanation
Indices: 13547789--13547830 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
13547779 TTTTTAAGTT
*
13547789 TTTTTAAATTTTTC-ATA
1 TTTTTAAATTTTACAATA
13547806 TTTTT-AATTTTACAATA
1 TTTTTAAATTTTACAATA
13547823 TTTTTAAA
1 TTTTTAAA
13547831 AAATGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 13 0.59
18 2 0.09
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTAAATTTTACAATA
Found at i:13547890 original size:11 final size:11
Alignment explanation
Indices: 13547871--13547935 Score: 53
Period size: 11 Copynumber: 6.1 Consensus size: 11
13547861 CTTTTAGAAA
*
13547871 TTTTAAATTTT
1 TTTTGAATTTT
13547882 TTTTGAA-TTT
1 TTTTGAATTTT
** *
13547892 TTCAGAATTTG
1 TTTTGAATTTT
13547903 TTTTGAA-TTT
1 TTTTGAATTTT
*
13547913 TTTTGGATTTT
1 TTTTGAATTTT
* *
13547924 TATTAAATTTT
1 TTTTGAATTTT
13547935 T
1 T
13547936 GTTGTTTTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
10 16 0.39
11 25 0.61
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:13547892 original size:10 final size:10
Alignment explanation
Indices: 13547879--13547935 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
13547869 AATTTTAAAT
13547879 TTTTTTTGAA
1 TTTTTTTGAA
**
13547889 TTTTTCAGAA
1 TTTTTTTGAA
13547899 TTTGTTTTGAA
1 TTT-TTTTGAA
*
13547910 TTTTTTTGGA
1 TTTTTTTGAA
*
13547920 TTTTTATTAAA
1 TTTTT-TTGAA
13547931 TTTTT
1 TTTTT
13547936 GTTGTTTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
10 22 0.58
11 16 0.42
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.67
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:13551009 original size:19 final size:21
Alignment explanation
Indices: 13550985--13551028 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
13550975 TATTTTATTA
*
13550985 ATTTATATTTGATT-GATAT-
1 ATTTATATTTCATTAGATATG
13551004 ATTTATATTTCATTAGATATG
1 ATTTATATTTCATTAGATATG
13551025 ATTT
1 ATTT
13551029 CATTAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 5 0.23
21 4 0.18
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (21 bp):
ATTTATATTTCATTAGATATG
Found at i:13551492 original size:647 final size:635
Alignment explanation
Indices: 13550076--13551375 Score: 1674
Period size: 647 Copynumber: 2.0 Consensus size: 635
13550066 ACTTTCAATT
* * *
13550076 CAATTCATATTAAAAGTATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATCAATA
1 CAATTCATATTAAAAATATTAAAATTTTAAAATCTTCTTAATTTGACAAATCAAATCAATCAATA
* * ** * * *
13550141 TATAAGTAATAGATTAATAAATACAACAATTACAATTATAAAATAGTTGATTCTTTAATTAATTA
66 TATAATTAATA-ATTTATAAATATTACAATTACAATTAT-AAATAATTGATTCTCTAATCAATTA
* * * *
13550206 TTTGATACATTTATATTTGATTAAATAGAGTACCCCTTTGAGTAATTAATGTATTTCATGATGTA
129 TTTGATACATTTATATTTGATTAAGTATAGTATCCATTTGAG----T-A---A-TT-A--ATGTA
* *
13550271 TTTCATGTGTAAATATATAAAGCAAATATATCAAATTAATTCTCCATAATTAAATTAATGCAATA
182 TTTCATGTGTAAATATAGAAAGCAAATATATCAAATTAATTCTCCATAATTAAATTAATGAAATA
* *
13550336 AAATATTTTATTAATTTATATTTGATTGACACATTTATATTTTATTAAATATGATTTCATTTGAT
247 AAATATTTTATTAATTTATATTTGATTGACACATTTATATTTCATTAAATATGATTTCATTTCAT
** *
13550401 TAAATATTAATGCACGTTGATTTCATTTGTAACGTTTTATAATTTTATTATTTGATACTAACGCA
312 TAAATATTAATGCACGTTGATTTCATTTGTAACGTTTTATAATTTTAAAATTAGATACTAACGCA
* * *
13550466 CGTTGATTTAGTTAAAATTTAATTTATTTTATTGCCATTCTTAAATATAATAAAATCAATTTATT
377 CGTTGATTTAATTAAAATTTAATTTATTTTATTGCCATTATTAAATACAATAAAATCAATTTATT
* * *
13550531 TTACTGTTCTAAATTAAGGGATCTTTAAATGTTAATGGCAGAATAAAATATTTTAATATCAATCA
442 TTACTGTTCTAAATTAACGGATCTCTAAATGTTAATGGCAGAATAAAATATTTCAATATCAATCA
* * * *
13550596 ACTTGCCATTGTTAGATAATTATTTACTCATAATTTTTATTATTTCAATATTAACTTTCATAATT
507 ACTTGCCATTGTTAAACAATTATTCACTCATAATTTTTATTATCTCAATATTAACTTTCATAATT
* * * *** * * * ** * *
13550661 TAAAATTGTCTTATTAATTGACTATATTTATGTTTTTATTATTGACTTTAAATCACTCTTAATT
572 TAAAATTATCTTATTAATTAACTAAACACATGTTTTTATAATAGACTCTAAATCAAGCATAATG
* *
13550725 CAATTCATATTAAAAATATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATCAATA
1 CAATTCATATTAAAAATATTAAAATTTTAAAATCTTCTTAATTTGACAAATCAAATCAATCAATA
13550790 TATAATTAATAATTTAATAAATATTACAATTACAATTATAAATTAATTGATTCTCTAATCAATTA
66 TATAATTAATAATTT-ATAAATATTACAATTACAATTATAAA-TAATTGATTCTCTAATCAATTA
13550855 TTTGATACATTTATATTTGATTAAGTATAGTATCCATTTGAGTAATTAATGTATTT-ATGTGTAA
129 TTTGATACATTTATATTTGATTAAGTATAGTATCCATTTGAGTAATTAATGTATTTCATGTGTAA
13550919 ATATAGAAAGCAAATATATCAAATTAATTCTCCATAATTAAATTAATGAAATAAAATATTTTATT
194 ATATAGAAAGCAAATATATCAAATTAATTCTCCATAATTAAATTAATGAAATAAAATATTTTATT
* * *
13550984 AATTTATATTTGATTGATATATTTATATTTCATTAGATATGATTTCATTAATTTCATTTGGTAAA
259 AATTTATATTTGATTGACACATTTATATTTCATTAAATATGATTTC----ATTTCA--T--T-AA
* * *
13551049 ATATTAATGCACATTTGATTTCATTTGTAACGTTTTATAATTTTAAAATATAGATATTAATGCAC
315 ATATTAATGCAC-GTTGATTTCATTTGTAACGTTTTATAATTTTAAAAT-TAGATACTAACGCAC
* * * * *
13551114 GTTGATTTAATTAAAATTTATTTTATTTTACTT-TCATTATTAAATACAATAAATTTAATTTGTT
378 GTTGATTTAATTAAAATTTAATTTATTTTA-TTGCCATTATTAAATACAATAAAATCAATTTATT
* * *
13551178 TTATTGTTCTAAATTAACGGATCTCTAAATGTTAATGGCAGAATAAAATATTTCAATGTCAGTCA
442 TTACTGTTCTAAATTAACGGATCTCTAAATGTTAATGGCAGAATAAAATATTTCAATATCAATCA
** *
13551243 ACTTGGTATTGTTAAACCATTATTCACTCATAATTTTTATTATCTCAATATTAAC-TTCATAATT
507 ACTTGCCATTGTTAAACAATTATTCACTCATAATTTTTATTATCTCAATATTAACTTTCATAATT
** *
13551307 TAAAATTATCTTATTAATTAACCTACAACACACT-TTTTATATAAATAG-CTCTAGGTTAAGCAT
572 TAAAATTATCTTATTAATTAA-CTA-AACACA-TGTTTT-TAT-AATAGACTCTAAATCAAGCAT
13551370 AATG
632 AATG
13551374 CA
1 CA
13551376 TCTTTAACCA
Statistics
Matches: 570, Mismatches: 62, Indels: 38
0.85 0.09 0.06
Matches are distributed among these distances:
636 113 0.20
637 8 0.01
639 1 0.00
640 7 0.01
641 1 0.00
642 1 0.00
644 2 0.00
645 15 0.03
646 61 0.11
647 175 0.31
648 14 0.02
649 169 0.30
650 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (635 bp):
CAATTCATATTAAAAATATTAAAATTTTAAAATCTTCTTAATTTGACAAATCAAATCAATCAATA
TATAATTAATAATTTATAAATATTACAATTACAATTATAAATAATTGATTCTCTAATCAATTATT
TGATACATTTATATTTGATTAAGTATAGTATCCATTTGAGTAATTAATGTATTTCATGTGTAAAT
ATAGAAAGCAAATATATCAAATTAATTCTCCATAATTAAATTAATGAAATAAAATATTTTATTAA
TTTATATTTGATTGACACATTTATATTTCATTAAATATGATTTCATTTCATTAAATATTAATGCA
CGTTGATTTCATTTGTAACGTTTTATAATTTTAAAATTAGATACTAACGCACGTTGATTTAATTA
AAATTTAATTTATTTTATTGCCATTATTAAATACAATAAAATCAATTTATTTTACTGTTCTAAAT
TAACGGATCTCTAAATGTTAATGGCAGAATAAAATATTTCAATATCAATCAACTTGCCATTGTTA
AACAATTATTCACTCATAATTTTTATTATCTCAATATTAACTTTCATAATTTAAAATTATCTTAT
TAATTAACTAAACACATGTTTTTATAATAGACTCTAAATCAAGCATAATG
Found at i:13553340 original size:21 final size:20
Alignment explanation
Indices: 13553315--13553360 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
13553305 TAAATCTTAA
13553315 ATAAAAAAACCCTAAATGAAT
1 ATAAAAAAACCC-AAATGAAT
**
13553336 ATAAATGAACCCAAATGAAT
1 ATAAAAAAACCCAAATGAAT
13553356 ATAAA
1 ATAAA
13553361 CTAGCCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.20
Consensus pattern (20 bp):
ATAAAAAAACCCAAATGAAT
Found at i:13553353 original size:20 final size:21
Alignment explanation
Indices: 13553322--13553360 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
13553312 TAAATAAAAA
13553322 AACCCTAAATGAATATAAATG
1 AACCCTAAATGAATATAAATG
13553343 AACCC-AAATGAATATAAA
1 AACCCTAAATGAATATAAA
13553361 CTAGCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (21 bp):
AACCCTAAATGAATATAAATG
Found at i:13556324 original size:85 final size:85
Alignment explanation
Indices: 13556180--13556335 Score: 190
Period size: 85 Copynumber: 1.8 Consensus size: 85
13556170 ATTAAATATT
* * * * *
13556180 ATGGTTTGCTGAACCTTGTTAACTGATATTGCATTGTTGAATGGTATTATATGATATTAGGTGTC
1 ATGGTTTGCTGAACCTTATTAACTGATATTGCATTGCTGAATGGTATTATATGAAATTAGGGGGC
13556245 TGAATCATATTTCATGCTGA
66 TGAATCATATTTCATGCTGA
* ** **
13556265 ATGGTTTGCTTAACCTTATTGTCTGATATTGTTTTGCTGAATGGGT-TTCA-ATGAAATTAGGGG
1 ATGGTTTGCTGAACCTTATTAACTGATATTGCATTGCTGAAT-GGTATT-ATATGAAATTAGGGG
13556328 GCTGAATC
64 GCTGAATC
13556336 GTATGCTGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 55 0.93
86 4 0.07
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (85 bp):
ATGGTTTGCTGAACCTTATTAACTGATATTGCATTGCTGAATGGTATTATATGAAATTAGGGGGC
TGAATCATATTTCATGCTGA
Found at i:13561550 original size:3 final size:3
Alignment explanation
Indices: 13561526--13561574 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
13561516 TACTTATAAA
* *
13561526 TAT TAT T-T TTT TAT TAAG TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13561570 TAT TA
1 TAT TA
13561575 AGTCATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:13562122 original size:23 final size:22
Alignment explanation
Indices: 13562092--13562140 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
13562082 AATTTAGAAG
*
13562092 ATAATAATTATTTTTATATAAAA
1 ATAATAATTATATTTAT-TAAAA
*
13562115 ATAATAATTATATTTATTCAAA
1 ATAATAATTATATTTATTAAAA
13562137 ATAA
1 ATAA
13562141 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATAATTATATTTATTAAAA
Found at i:13563029 original size:17 final size:17
Alignment explanation
Indices: 13563007--13563039 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13562997 TGATAAAATA
13563007 AAATAAAATAATATTAC
1 AAATAAAATAATATTAC
*
13563024 AAATAAAATTATATTA
1 AAATAAAATAATATTA
13563040 AATAATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAATAATATTAC
Found at i:13563543 original size:27 final size:22
Alignment explanation
Indices: 13563481--13563541 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
13563471 TTCACAAGCT
*
13563481 ACTCGAATTCGATTCGAAGAAA
1 ACTCAAATTCGATTCGAAGAAA
13563503 ACTCAAATTCGATTCGAAGAAA
1 ACTCAAATTCGATTCGAAGAAA
13563525 ACTCAAATTCGATTCGA
1 ACTCAAATTCGATTCGA
13563542 TTATTATCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (22 bp):
ACTCAAATTCGATTCGAAGAAA
Found at i:13563967 original size:14 final size:15
Alignment explanation
Indices: 13563934--13563971 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
13563924 TAACACCCCT
*
13563934 AATCGCAAACATTAA
1 AATCTCAAACATTAA
13563949 AATCTCAAACATT-A
1 AATCTCAAACATTAA
13563963 AATCTCAAA
1 AATCTCAAA
13563972 TTAAACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.24
Consensus pattern (15 bp):
AATCTCAAACATTAA
Found at i:13565126 original size:15 final size:15
Alignment explanation
Indices: 13565106--13565316 Score: 92
Period size: 15 Copynumber: 14.9 Consensus size: 15
13565096 TATTTTTTAT
13565106 TATATTAATAAATAA
1 TATATTAATAAATAA
13565121 TATATTAATAAAT-A
1 TATATTAATAAATAA
** *
13565135 -ATATT-ATATTTAT
1 TATATTAATAAATAA
*
13565148 TATATAAATAATATAA
1 TATATTAATAA-ATAA
13565164 TAT-TT-AT--A-AA
1 TATATTAATAAATAA
*
13565174 TATATT-AT--ATTA
1 TATATTAATAAATAA
* *
13565186 TTTATTAA-AAATAT
1 TATATTAATAAATAA
* **
13565200 TTTATTAATATGTAA
1 TATATTAATAAATAA
* *
13565215 TATATTTATAAATAT
1 TATATTAATAAATAA
* *
13565230 TATATTACTACATAA
1 TATATTAATAAATAA
* *
13565245 TATATTAATATATTA
1 TATATTAATAAATAA
* *
13565260 T-TGTATAATATATTAA
1 TATAT-TAATA-AATAA
* * *
13565276 TAAATAAAT-AATAT
1 TATATTAATAAATAA
*
13565290 TATATTAAT-ATTAA
1 TATATTAATAAATAA
13565304 TATATTAATAAAT
1 TATATTAATAAAT
13565317 GTTATTATAT
Statistics
Matches: 141, Mismatches: 41, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
10 5 0.04
11 6 0.04
12 10 0.07
13 6 0.04
14 41 0.29
15 61 0.43
16 11 0.08
17 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
TATATTAATAAATAA
Found at i:13565142 original size:18 final size:18
Alignment explanation
Indices: 13565103--13565329 Score: 90
Period size: 18 Copynumber: 12.6 Consensus size: 18
13565093 TAATATTTTT
13565103 TATTATATTAATAAAT-A
1 TATTATATTAATAAATAA
13565120 -A-TATATTAATAAATAA
1 TATTATATTAATAAATAA
13565136 TATTATATTTATTATATAAATAA
1 TA-T-TA--TATTA-ATAAATAA
* *
13565159 TATAATATTTATAAAT-A
1 TATTATATTAATAAATAA
13565176 TATTATATTATTTATTAAA-AA
1 TATTATATTA---A-TAAATAA
* **
13565197 TATTTTATTAATATGTAA
1 TATTATATTAATAAATAA
13565215 TA-TAT-TT-ATAAATATTA
1 TATTATATTAATAAATA--A
* *
13565232 TATTACTACATAATATATTAA
1 TATTA-TA-TTAATA-AATAA
*
13565253 TA-TATTATT-GTATAAT-A
1 TATTA-TATTAATA-AATAA
*
13565270 TATTA-ATAAATAAATAA
1 TATTATATTAATAAATAA
13565287 TATTATATTAAT--AT--
1 TATTATATTAATAAATAA
* **
13565301 TAATATATTAATAAATGT
1 TATTATATTAATAAATAA
13565319 TATTATATTAA
1 TATTATATTAA
13565330 GATCATTATA
Statistics
Matches: 159, Mismatches: 21, Indels: 59
0.67 0.09 0.25
Matches are distributed among these distances:
14 11 0.07
15 18 0.11
16 13 0.08
17 28 0.18
18 35 0.22
19 6 0.04
20 7 0.04
21 19 0.12
22 9 0.06
23 13 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
TATTATATTAATAAATAA
Found at i:13565158 original size:23 final size:23
Alignment explanation
Indices: 13565090--13565170 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 23
13565080 TTATATGATA
13565090 AAATAATATT-T-TTTATTATAT
1 AAATAATATTATATTTATTATAT
* *
13565111 TAATAA-A-TA-ATATATTA-AT
1 AAATAATATTATATTTATTATAT
13565130 AAATAATATTATATTTATTATAT
1 AAATAATATTATATTTATTATAT
*
13565153 AAATAATATAATATTTAT
1 AAATAATATTATATTTAT
13565171 AAATATATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
19 8 0.16
20 8 0.16
21 7 0.14
22 7 0.14
23 19 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATAATATTATATTTATTATAT
Found at i:13565176 original size:38 final size:39
Alignment explanation
Indices: 13565091--13565301 Score: 112
Period size: 40 Copynumber: 5.2 Consensus size: 39
13565081 TATATGATAA
*
13565091 AATAATATTTTTTATTATATTAATAAATAATATATTAAT
1 AATAATATTTTTTATTATATAAATAAATAATATATTAAT
13565130 AAATAATATTATATTTATTATATAAATAATATAATAT-TT-AT
1 -AATAATATT-T-TTTATTATATAAATAA-ATAATATATTAAT
* * * *
13565171 AA-ATATATTATATTATT-TATTAA-AAATATTTTATTAAT
1 AATA-ATATT-TTTTATTATATAAATAAATAATATATTAAT
* * * *
13565209 ATGTAATATATTTATAAATATTATATTACTACATAATATATTAAT
1 A-ATAATAT-TTT-T---TATTATATAAATAAATAATATATTAAT
* * * * *
13565254 -ATATTATTGTATAATATATTAATAAATAAATAATATT-AT
1 AATAATATTTTTTATTATATAAATAAAT-AAT-ATATTAAT
*
13565293 ATTAATATT
1 AATAATATT
13565302 AATATATTAA
Statistics
Matches: 133, Mismatches: 20, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
36 5 0.04
37 4 0.03
38 21 0.16
39 16 0.12
40 32 0.24
41 3 0.02
42 19 0.14
43 16 0.12
44 5 0.04
45 12 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (39 bp):
AATAATATTTTTTATTATATAAATAAATAATATATTAAT
Found at i:13565186 original size:45 final size:42
Alignment explanation
Indices: 13565090--13565184 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 42
13565080 TTATATGATA
* *
13565090 AAATAATATT-T-TTTATTATATTAATAAATAATATATTAAT
1 AAATAATATTATATTTATTATATAAATAAATAATATATAAAT
*
13565130 AAATAATATTATATTTATTATATAAATAATATAATAT-T-TAT
1 AAATAATATTATATTTATTATATAAATAA-ATAATATATAAAT
13565171 AAAT-ATATTATATT
1 AAATAATATTATATT
13565185 ATTTATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
40 20 0.40
41 7 0.14
42 16 0.32
43 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
AAATAATATTATATTTATTATATAAATAAATAATATATAAAT
Found at i:13565230 original size:30 final size:29
Alignment explanation
Indices: 13565106--13565321 Score: 150
Period size: 30 Copynumber: 7.6 Consensus size: 29
13565096 TATTTTTTAT
*
13565106 TATATTAATAAATAATATATTAATA--AA
1 TATATTAATAAATATTATATTAATATTAA
** *
13565133 TAATATT-ATATTTATTATATAAATAATATAA
1 T-ATATTAATAAATATTATATTAAT-AT-TAA
13565164 TAT-TT-AT-AA-A-TATATT-ATATT-A
1 TATATTAATAAATATTATATTAATATTAA
* *
13565186 TTTATTAA-AAATATTTTATTAATATGTAA
1 TATATTAATAAATATTATATTAATAT-TAA
* * *
13565215 TATATTTATAAATATTATATTACTACATAA
1 TATATTAATAAATATTATATTAATA-TTAA
* * *
13565245 TATATTAATATATTATTGTATAATATATTAA
1 TATATTAATA-AATATTATATTA-ATATTAA
* *
13565276 TAAATAAAT-AATATTATATTAATATTAA
1 TATATTAATAAATATTATATTAATATTAA
*
13565304 TATATTAATAAATGTTAT
1 TATATTAATAAATATTAT
13565322 TATATTAAGA
Statistics
Matches: 143, Mismatches: 28, Indels: 34
0.70 0.14 0.17
Matches are distributed among these distances:
22 3 0.02
23 3 0.02
24 5 0.03
25 3 0.02
26 10 0.07
27 19 0.13
28 21 0.15
29 27 0.19
30 28 0.20
31 22 0.15
32 2 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TATATTAATAAATATTATATTAATATTAA
Found at i:13565258 original size:23 final size:22
Alignment explanation
Indices: 13565118--13565300 Score: 74
Period size: 23 Copynumber: 8.3 Consensus size: 22
13565108 TATTAATAAA
13565118 TAATATATTAAT-A-AATAATAT
1 TAATATATTAATAATAAT-ATAT
* *
13565139 TATATTTATTATATAAATAATATAA
1 TA-ATATATTA-AT-AATAATATAT
* * *
13565164 T-ATTTATAAAT-ATATTATAT
1 TAATATATTAATAATAATATAT
* * * *
13565184 T-ATTTATTAAAAATATTTTAT
1 TAATATATTAATAATAATATAT
* * *
13565205 TAATAT-GTAAT-ATATTTATAAA
1 TAATATATTAATAATA-ATAT-AT
* *
13565227 TATTATATTACTACATAATATAT
1 TAATATATTAATA-ATAATATAT
* *
13565250 TAATATATTATTGTATAATATAT
1 TAATATATTAAT-AATAATATAT
* * *
13565273 TAATAAATAAATAATATTATAT
1 TAATATATTAATAATAATATAT
13565295 TAATAT
1 TAATAT
13565301 TAATATATTA
Statistics
Matches: 122, Mismatches: 27, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
20 19 0.16
21 17 0.14
22 31 0.25
23 41 0.34
24 3 0.02
25 8 0.07
26 3 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
TAATATATTAATAATAATATAT
Found at i:13565259 original size:53 final size:51
Alignment explanation
Indices: 13565202--13565313 Score: 125
Period size: 53 Copynumber: 2.2 Consensus size: 51
13565192 AAAAATATTT
* * * *
13565202 TATTAATATGTAATATATTTATAAATATTATATTACTACATAATATATTAATA
1 TATTAATATATAATATATTAATAAATA-AATAATACTACATAA-ATATTAATA
* * * * *
13565255 TATTATTGTATAATATATTAATAAATAAATAATATTATATTAATATTAATA
1 TATTAATATATAATATATTAATAAATAAATAATACTACATAAATATTAATA
13565306 TATTAATA
1 TATTAATA
13565314 AATGTTATTA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
51 15 0.31
52 10 0.21
53 23 0.48
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (51 bp):
TATTAATATATAATATATTAATAAATAAATAATACTACATAAATATTAATA
Found at i:13565340 original size:32 final size:32
Alignment explanation
Indices: 13565278--13565352 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
13565268 TATATTAATA
* *
13565278 AATAAATAATATTATATTAATATTAATATATT
1 AATAAATAATATTATATTAAGATCAATATATT
** *
13565310 AATAAATGTTATTATATTAAGATCATTATATT
1 AATAAATAATATTATATTAAGATCAATATATT
*
13565342 -ATTAATAATAT
1 AATAAATAATAT
13565353 ATGGACTCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (32 bp):
AATAAATAATATTATATTAAGATCAATATATT
Found at i:13565346 original size:94 final size:92
Alignment explanation
Indices: 13565103--13565348 Score: 231
Period size: 94 Copynumber: 2.6 Consensus size: 92
13565093 TAATATTTTT
* * *
13565103 TATTATATTAATAAATAATATATTAATAAATAATATTATATT--T-ATTATATAAATAATATAAT
1 TATTATATTAAT-ATTAATATATTAATAAAT--TATTATATTAATCATTATATTATTAATATAAT
*
13565165 ATTTATAAATATATTATATTATTTATTAAAAA
63 ATTTATAAATATATTATATTA--TAATAAAAA
* * * * *
13565197 TATTTTATTAATATGTAATATATTTATAAA-TATTATATTACTACATAATA-TATTAATATATTA
1 TATTATATTAATAT-TAATATATTAATAAATTATTATATTAAT-CATTATATTATTAATATAATA
13565260 TTGTAT-AATATATTA-A-TA-AATAAATAA
64 TT-TATAAATATATTATATTATAATAAA-AA
13565287 TATTATATTAATATTAATATATTAATAAATGTTATTATATTAAGATCATTATATTATTAATA
1 TATTATATTAATATTAATATATTAATAAA--TTATTATATT-A-ATCATTATATTATTAATA
13565349 ATATATGGAC
Statistics
Matches: 127, Mismatches: 12, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
89 19 0.15
90 15 0.12
91 9 0.07
92 11 0.09
93 10 0.08
94 55 0.43
95 8 0.06
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (92 bp):
TATTATATTAATATTAATATATTAATAAATTATTATATTAATCATTATATTATTAATATAATATT
TATAAATATATTATATTATAATAAAAA
Found at i:13568163 original size:3 final size:3
Alignment explanation
Indices: 13568155--13568194 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13568145 TAAAAGAATT
13568155 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
13568195 TACTATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:13569073 original size:2 final size:2
Alignment explanation
Indices: 13569066--13569104 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
13569056 ATTGTGAATT
*
13569066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13569105 GAGTCCATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13569305 original size:24 final size:24
Alignment explanation
Indices: 13569284--13569334 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
13569274 TTAAATTATA
13569284 AAAAAAGTATTGAAATACATTAAG
1 AAAAAAGTATTGAAATACATTAAG
*
13569308 TAAAAAGTATTGAAATATC-TTAAG
1 AAAAAAGTATTGAAATA-CATTAAG
13569332 AAA
1 AAA
13569335 GAATTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (24 bp):
AAAAAAGTATTGAAATACATTAAG
Found at i:13576554 original size:19 final size:19
Alignment explanation
Indices: 13576530--13576568 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
13576520 TTACTTGATT
13576530 GGTTTTTATCCTTTTTTGA
1 GGTTTTTATCCTTTTTTGA
13576549 GGTTTTTATCCTTTTTTGA
1 GGTTTTTATCCTTTTTTGA
13576568 G
1 G
13576569 CTTTATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.62
Consensus pattern (19 bp):
GGTTTTTATCCTTTTTTGA
Found at i:13578725 original size:38 final size:38
Alignment explanation
Indices: 13578674--13578753 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
13578664 TAAAAACAAT
13578674 GCTTCAACAAGTTGATTTGAATCAGATTATATCTTTAA
1 GCTTCAACAAGTTGATTTGAATCAGATTATATCTTTAA
13578712 GCTTCAACAAGTTGATTTGAATCAGATTATATCTTTAA
1 GCTTCAACAAGTTGATTTGAATCAGATTATATCTTTAA
13578750 GCTT
1 GCTT
13578754 GAAGTATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (38 bp):
GCTTCAACAAGTTGATTTGAATCAGATTATATCTTTAA
Found at i:13579520 original size:30 final size:30
Alignment explanation
Indices: 13579444--13579520 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
13579434 TACTTTATAA
* * *
13579444 CCAAATAAGTTCTTAAACTTTAATTTGTAT
1 CCAAATAAGTCCTTAACCTTTAATTGGTAT
* *
13579474 CCAAATAAATCTTTAACCTTTAATTGGTA-
1 CCAAATAAGTCCTTAACCTTTAATTGGTAT
*
13579503 CCTAAATAAGCCCTTAAC
1 CC-AAATAAGTCCTTAAC
13579521 ACAAATCAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.36
Consensus pattern (30 bp):
CCAAATAAGTCCTTAACCTTTAATTGGTAT
Found at i:13580055 original size:15 final size:16
Alignment explanation
Indices: 13580037--13580066 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13580027 CGAAGACTGA
13580037 AATTTGAAAA-AATCC
1 AATTTGAAAATAATCC
13580052 AATTTGAAAATAATC
1 AATTTGAAAATAATC
13580067 TAAACCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AATTTGAAAATAATCC
Found at i:13582480 original size:17 final size:17
Alignment explanation
Indices: 13582454--13582506 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
13582444 AAAAAAGCCT
* *
13582454 AAATCAAAAATTATTTC
1 AAATCCAAAATTATTCC
* *
13582471 GAATCCAAAAATA-TCC
1 AAATCCAAAATTATTCC
13582487 AAATCCAAAATTATT-C
1 AAATCCAAAATTATTCC
13582503 AAAT
1 AAAT
13582507 AAAAAGAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (17 bp):
AAATCCAAAATTATTCC
Found at i:13588026 original size:19 final size:19
Alignment explanation
Indices: 13588002--13588068 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
13587992 CTCAAATTCC
13588002 AAACCCTAAACCACCTATG
1 AAACCCTAAACCACCTATG
**
13588021 AAACCCT-AACCACCCT-CC
1 AAACCCTAAACCA-CCTATG
13588039 AAACCCTAAACCA-CTCATG
1 AAACCCTAAACCACCT-ATG
*
13588058 AAACCTTAAAC
1 AAACCCTAAAC
13588069 TAAAATCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.05
18 12 0.31
19 25 0.64
ACGTcount: A:0.42, C:0.40, G:0.03, T:0.15
Consensus pattern (19 bp):
AAACCCTAAACCACCTATG
Found at i:13588093 original size:13 final size:13
Alignment explanation
Indices: 13588058--13588217 Score: 75
Period size: 13 Copynumber: 12.4 Consensus size: 13
13588048 ACCACTCATG
13588058 AAACCTTAAA-CT
1 AAACCTTAAACCT
*
13588070 AAA-ATCTAAACCTT
1 AAACCT-TAAACC-T
*
13588084 AATCC-TAAACCCT
1 AAACCTTAAA-CCT
*
13588097 AAACCATAAACCT
1 AAACCTTAAACCT
* *
13588110 AAACCCTACAATC-
1 AAACCTTA-AACCT
* * *
13588123 AAA-CTTTAGCTT
1 AAACCTTAAACCT
*
13588135 TAACCTTAAACC-
1 AAACCTTAAACCT
*
13588147 AAACCTTAACCCT
1 AAACCTTAAACCT
13588160 AAACCTTAAACCT
1 AAACCTTAAACCT
* * *
13588173 AGACCCTAACCCT
1 AAACCTTAAACCT
*
13588186 AAACATTAAAACC-
1 AAACCTT-AAACCT
13588199 AAATCC-TAAAGCCT
1 AAA-CCTTAAA-CCT
13588213 AAACC
1 AAACC
13588218 AAACCCCCAA
Statistics
Matches: 108, Mismatches: 26, Indels: 27
0.67 0.16 0.17
Matches are distributed among these distances:
11 2 0.02
12 24 0.22
13 62 0.57
14 20 0.19
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (13 bp):
AAACCTTAAACCT
Found at i:13588098 original size:20 final size:20
Alignment explanation
Indices: 13588075--13588117 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13588065 AAACTAAAAT
* *
13588075 CTAAACCTTAATCCTAAACC
1 CTAAACCATAAACCTAAACC
13588095 CTAAACCATAAACCTAAACC
1 CTAAACCATAAACCTAAACC
13588115 CTA
1 CTA
13588118 CAATCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (20 bp):
CTAAACCATAAACCTAAACC
Found at i:13590423 original size:37 final size:37
Alignment explanation
Indices: 13590377--13590565 Score: 177
Period size: 37 Copynumber: 5.1 Consensus size: 37
13590367 AAGTTAGAAA
* *
13590377 TAATAAGATAGTACATGCACTCTATTTCATGCACATAT
1 TAAT-AGATAGTACATGCATTCTATCTCATGCACATAT
* * * *
13590415 TAATAGATAGTACATGCATTTTATTTTATGCATATAT
1 TAATAGATAGTACATGCATTCTATCTCATGCACATAT
* * *
13590452 TAATAAATAGTACATGCATTC-ATCTCATGCAGATCT
1 TAATAGATAGTACATGCATTCTATCTCATGCACATAT
* * * *
13590488 TAATA-AGTGGTACATGCATTATATATCATGCATC-TCT
1 TAATAGA-TAGTACATGCATTCTATCTCATGCA-CATAT
* * * *
13590525 TAATAGATAGTATATGCATTCCATCTCATACACATTT
1 TAATAGATAGTACATGCATTCTATCTCATGCACATAT
13590562 TAAT
1 TAAT
13590566 GGTAGTGACA
Statistics
Matches: 125, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
35 1 0.01
36 29 0.23
37 90 0.72
38 5 0.04
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (37 bp):
TAATAGATAGTACATGCATTCTATCTCATGCACATAT
Found at i:13590491 original size:73 final size:73
Alignment explanation
Indices: 13590377--13590565 Score: 209
Period size: 73 Copynumber: 2.5 Consensus size: 73
13590367 AAGTTAGAAA
* * * *
13590377 TAATAAGATAGTACATGCACTCTATTTCATGCACATATTAAT-AGATAGTACATGCATTTTATTT
1 TAATAA-ATAGTACATGCATTC-ATCTCATGCACATATTAATAAG-TAGTACATGCATTATATAT
*
13590441 TATGCATATAT
63 CATGCATATAT
* * *
13590452 TAATAAATAGTACATGCATTCATCTCATGCAGATCTTAATAAGTGGTACATGCATTATATATCAT
1 TAATAAATAGTACATGCATTCATCTCATGCACATATTAATAAGTAGTACATGCATTATATATCAT
* *
13590517 GCATCTCT
66 GCATATAT
* * * *
13590525 TAATAGATAGTATATGCATTCCATCTCATACACATTTTAAT
1 TAATAAATAGTACATGCATT-CATCTCATGCACATATTAAT
13590566 GGTAGTGACA
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
73 58 0.60
74 33 0.34
75 6 0.06
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (73 bp):
TAATAAATAGTACATGCATTCATCTCATGCACATATTAATAAGTAGTACATGCATTATATATCAT
GCATATAT
Found at i:13596536 original size:140 final size:140
Alignment explanation
Indices: 13596291--13596554 Score: 377
Period size: 140 Copynumber: 1.9 Consensus size: 140
13596281 ATGGTTATAA
* ** *
13596291 GTATTTAATGAAACACAAATCTGAATCCTTTGAAAAGTTCAAAGAATTTAGAATGGTGGTTGAAA
1 GTATTTAATGAAACACAAATCTGAATCCTTTAAAAAGTTCAAAGAATTTAGAACAGAGGTTGAAA
* * * *
13596356 AGAAAACTGGTAAAAATATCATGACACTTAGATCTGATCGAGGTGATGAATACTTAAGCTATGGT
66 AAAAAAATGGTAAAAATATCATGACACTTAGATCGGATCGAGATGATGAATACTTAAGCTATGGT
13596421 ATAGTTATGT
131 ATAGTTATGT
* * * *
13596431 GTATTTAATGAAACACAAATTTGAATCTTTTAAAAAGTTTAAAGAATTTAGAACAGAGTTTGAAA
1 GTATTTAATGAAACACAAATCTGAATCCTTTAAAAAGTTCAAAGAATTTAGAACAGAGGTTGAAA
* * *
13596496 AAAAAAATGGTAAAAGTATCATGACACTTAGAGT-GGATCGAGATGGTGAATTCTTAAGC
66 AAAAAAATGGTAAAAATATCATGACACTTAGA-TCGGATCGAGATGATGAATACTTAAGC
13596555 CATGATTTTC
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
140 107 0.99
141 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.30
Consensus pattern (140 bp):
GTATTTAATGAAACACAAATCTGAATCCTTTAAAAAGTTCAAAGAATTTAGAACAGAGGTTGAAA
AAAAAAATGGTAAAAATATCATGACACTTAGATCGGATCGAGATGATGAATACTTAAGCTATGGT
ATAGTTATGT
Found at i:13602814 original size:14 final size:14
Alignment explanation
Indices: 13602766--13602832 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
13602756 TCCACTAAAA
*
13602766 AAAAATGAAATGAAAG
1 AAAAATGAAA--AAGG
*
13602782 AAAAATGAAAAGGG
1 AAAAATGAAAAAGG
13602796 AAAAATGAAAATAGG
1 AAAAATGAAAA-AGG
13602811 AAAAA--AAAAA-G
1 AAAAATGAAAAAGG
13602822 AACAAATGAAA
1 AA-AAATGAAA
13602833 GGACAGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 3 0.07
12 4 0.09
13 4 0.09
14 16 0.36
15 7 0.16
16 10 0.23
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAAATGAAAAAGG
Found at i:13604663 original size:43 final size:42
Alignment explanation
Indices: 13604616--13604697 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
13604606 AAATCTCAGT
* * *
13604616 GGTGATATCCGAGTCTTCAAAGTCTAAGTTTTCAAATCTTGAC
1 GGTGATATCCGAGTCTTCAAAATCCAAATTTT-AAATCTTGAC
** *
13604659 GGTGATATTTGAGTGTTCAAAATCCAAATTTTAAATCTT
1 GGTGATATCCGAGTCTTCAAAATCCAAATTTTAAATCTT
13604698 AATAATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 7 0.21
43 26 0.79
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (42 bp):
GGTGATATCCGAGTCTTCAAAATCCAAATTTTAAATCTTGAC
Found at i:13605048 original size:56 final size:57
Alignment explanation
Indices: 13604978--13605086 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
13604968 GCTTTTTAAA
* **
13604978 ATTTTCTTGATGGTGATAATTAAGT-TTTTTCAATAGTAATATCCAAAGTCATTTGC
1 ATTTACTTGATGGTGATAATTAAGTATTCGTCAATAGTAATATCCAAAGTCATTTGC
* * * * *
13605034 ATTTACTTGGTGGTGATATTTGAGTATTCGTCAATTGTGATATCCAAAGTCAT
1 ATTTACTTGATGGTGATAATTAAGTATTCGTCAATAGTAATATCCAAAGTCAT
13605087 CTGTATTCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
56 21 0.48
57 23 0.52
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (57 bp):
ATTTACTTGATGGTGATAATTAAGTATTCGTCAATAGTAATATCCAAAGTCATTTGC
Found at i:13607694 original size:49 final size:49
Alignment explanation
Indices: 13607624--13607719 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
13607614 ATGTATTTTT
13607624 CATGCATCAATAATTACATTTTTACCAAT-AGCACTTTT-GTTATTTGTCA
1 CATGCATCAATAATTACATTTTTACCAATGA-CA-TTTTAGTTATTTGTCA
*
13607673 CATGCATCAAT-ATTAATATTTTTACCAATGACATTTTAGTTATTTGT
1 CATGCATCAATAATT-ACATTTTTACCAATGACATTTTAGTTATTTGT
13607720 TTTTATCACA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
48 7 0.16
49 35 0.81
50 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (49 bp):
CATGCATCAATAATTACATTTTTACCAATGACATTTTAGTTATTTGTCA
Found at i:13607908 original size:19 final size:19
Alignment explanation
Indices: 13607757--13607935 Score: 152
Period size: 19 Copynumber: 9.6 Consensus size: 19
13607747 CCCACATTTC
*
13607757 AAACCCTAAACCACTCATG
1 AAACCCTAAACCACCCATG
*
13607776 -AACCCTAAACCACCC-TCT
1 AAACCCTAAACCACCCAT-G
* * * *
13607794 AAACCTTAAATCACCCTTC
1 AAACCCTAAACCACCCATG
* *
13607813 AAACCCTAAACCACCAATC
1 AAACCCTAAACCACCCATG
* *
13607832 AAA-CCT-TAGCACCCATG
1 AAACCCTAAACCACCCATG
*
13607849 AAA-CCTCAAACCACCTATG
1 AAACCCT-AAACCACCCATG
* *
13607868 AAACACTAAACCACCCTTG
1 AAACCCTAAACCACCCATG
* *
13607887 AAACCCTAAACCACTCACG
1 AAACCCTAAACCACCCATG
*
13607906 AAACCCTAAATCACCCATG
1 AAACCCTAAACCACCCATG
*
13607925 AAATCCTAAAC
1 AAACCCTAAAC
13607936 TAAACCCTAA
Statistics
Matches: 126, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
17 14 0.11
18 17 0.13
19 92 0.73
20 3 0.02
ACGTcount: A:0.41, C:0.39, G:0.04, T:0.16
Consensus pattern (19 bp):
AAACCCTAAACCACCCATG
Found at i:13607974 original size:20 final size:20
Alignment explanation
Indices: 13607951--13608065 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 20
13607941 CCTAAACCAT
**
13607951 AACCTTAAATTTTAAA-TCTA
1 AACCTTAAACCTTAAACT-TA
*
13607971 AACCCTAAACCTTAAACTTA
1 AACCTTAAACCTTAAACTTA
*
13607991 AACCTTAAACCCTAAACTTA
1 AACCTTAAACCTTAAACTTA
13608011 AATCC-T-AACCTTAAACCTTAA
1 AA-CCTTAAACCTTAAA-CTT-A
* *
13608032 AACC--AAATCTTAAATCCTA
1 AACCTTAAACCTTAAA-CTTA
13608051 AACC--AAACCTTAAAC
1 AACCTTAAACCTTAAAC
13608066 CCTAACCTGA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.01
19 22 0.28
20 51 0.64
21 6 0.08
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
AACCTTAAACCTTAAACTTA
Found at i:13607979 original size:13 final size:14
Alignment explanation
Indices: 13607969--13608084 Score: 90
Period size: 13 Copynumber: 8.9 Consensus size: 14
13607959 ATTTTAAATC
13607969 TAAACCCTAAACCT
1 TAAACCCTAAACCT
*
13607983 TAAA-CTTAAACCT
1 TAAACCCTAAACCT
13607996 TAAACCCTAAA-CT
1 TAAACCCTAAACCT
*
13608009 TAAATCCT-AACCT
1 TAAACCCTAAACCT
*
13608022 TAAACCTTAAAACC-
1 TAAACCCT-AAACCT
* *
13608036 -AAATCTTAAATCC-
1 TAAACCCTAAA-CCT
13608049 TAAA-CC-AAACCT
1 TAAACCCTAAACCT
13608061 TAAACCCT-AACC-
1 TAAACCCTAAACCT
*
13608073 TGAACCCTAAAC
1 TAAACCCTAAAC
13608085 TAAACCTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
11 2 0.02
12 19 0.23
13 47 0.56
14 12 0.14
15 4 0.05
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:13607999 original size:33 final size:31
Alignment explanation
Indices: 13607931--13608032 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 31
13607921 CATGAAATCC
**
13607931 TAAACTAAACCCTAAACCATAACCTTAAATTT
1 TAAACTAAACCCTAAACC-TAACCTTAAACCT
*
13607963 TAAATCTAAACCCTAAACCTTAAACTTAAACCT
1 TAAA-CTAAACCCTAAACC-TAACCTTAAACCT
*
13607996 TAAACCCTAAA-CTTAAATCCTAACCTTAAACCT
1 TAAA--CTAAACCCTAAA-CCTAACCTTAAACCT
13608029 TAAA
1 TAAA
13608033 ACCAAATCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
32 4 0.07
33 49 0.82
34 7 0.12
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.27
Consensus pattern (31 bp):
TAAACTAAACCCTAAACCTAACCTTAAACCT
Found at i:13608089 original size:5 final size:6
Alignment explanation
Indices: 13607963--13608100 Score: 70
Period size: 7 Copynumber: 21.5 Consensus size: 6
13607953 CCTTAAATTT
* * *
13607963 TAAATC TAAACCC TAAACC TTAAACT TAAACC TTAAACCC TAAACT TAAATCC
1 TAAACC TAAA-CC TAAACC -TAAACC TAAACC -TAAA-CC TAAACC TAAA-CC
*
13608016 T-AACC TTAAACC TTAAAACC -AAATCT TAAATCC TAAACC -AAACC TTAAACCC
1 TAAACC -TAAACC -T-AAACC TAAA-CC TAAA-CC TAAACC TAAACC -TAAA-CC
*
13608068 T-AACC TGAACCC TAAA-C TAAACC TAAATCC TAA
1 TAAACC T-AAACC TAAACC TAAACC TAAA-CC TAA
13608101 GCCAAACCCC
Statistics
Matches: 106, Mismatches: 9, Indels: 33
0.72 0.06 0.22
Matches are distributed among these distances:
5 18 0.17
6 31 0.29
7 48 0.45
8 9 0.08
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.24
Consensus pattern (6 bp):
TAAACC
Found at i:13608109 original size:30 final size:31
Alignment explanation
Indices: 13607974--13608129 Score: 122
Period size: 33 Copynumber: 5.0 Consensus size: 31
13607964 AAATCTAAAC
*
13607974 CCTAAACCTTAAACTTAAACCTTAAACCCTAAA
1 CCTAAACCCTAAAC-TAAACCTTAAACCCT-AA
* * * * *
13608007 CTTAAATCCTAACCTTAAACCTTAAAACCAAA
1 CCTAAACCCTAAAC-TAAACCTTAAACCCTAA
* * *
13608039 TCTTAAATCCTAAACCAAACCTTAAACCCTAA
1 -CCTAAACCCTAAACTAAACCTTAAACCCTAA
* *
13608071 CCTGAACCCTAAACTAAACC-TAAATCCTAA
1 CCTAAACCCTAAACTAAACCTTAAACCCTAA
* *
13608101 GCC-AAACCCCAAACTAATCC--AAACCCTAA
1 -CCTAAACCCTAAACTAAACCTTAAACCCTAA
13608130 ATTGAACCAC
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.08
30 23 0.23
31 18 0.18
32 16 0.16
33 37 0.36
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (31 bp):
CCTAAACCCTAAACTAAACCTTAAACCCTAA
Found at i:13609088 original size:24 final size:24
Alignment explanation
Indices: 13609061--13609111 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
13609051 ATATTAATTT
13609061 AATAAAAATAATAAATACAACACA
1 AATAAAAATAATAAATACAACACA
*
13609085 AATAAAAATAATAAATATAACACA
1 AATAAAAATAATAAATACAACACA
13609109 AAT
1 AAT
13609112 GATAACTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (24 bp):
AATAAAAATAATAAATACAACACA
Found at i:13611076 original size:3 final size:3
Alignment explanation
Indices: 13611068--13611095 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13611058 ATGCTTTGCA
13611068 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13611096 CTACTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:13615583 original size:4 final size:4
Alignment explanation
Indices: 13615576--13615601 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
13615566 GTGACAAACA
13615576 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
13615602 TGTCAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:13616406 original size:3 final size:3
Alignment explanation
Indices: 13616398--13616422 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13616388 CACATTTTAT
13616398 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
13616423 AAAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13616608 original size:161 final size:161
Alignment explanation
Indices: 13616414--13616737 Score: 578
Period size: 161 Copynumber: 2.0 Consensus size: 161
13616404 ATAATAATAA
13616414 TAATAATAAAAAATAAATAAATAAAGGATTGAAGTCCAAAACTTCAAAATTGTTTTACAATGTAC
1 TAATAATAAAAAATAAATAAATAAAGGATTGAAGTCCAAAACTTCAAAATTGTTTTACAATGTAC
* *
13616479 TTATATAATTTAAATGCAAGATGAAAAATACATACATGTTTTATATAAAAAAATTCTTAGTTTAA
66 TTATATAATTTAAATGCAAGATGAAAAATACATACATGTTTTATATAAAAAAATACTTAGGTTAA
*
13616544 TTTTAAATGAAATTTTATTTTTATTTTTTTAT
131 TTTTAAATGAAATCTTATTTTTA-TTTTTTAT
* *
13616576 TAATAAT-AATAATAAATAAATAAAGGATTGAAGTCCAAAACTTCAAAATTGTTTTATAATGTAC
1 TAATAATAAAAAATAAATAAATAAAGGATTGAAGTCCAAAACTTCAAAATTGTTTTACAATGTAC
*
13616640 TTATATAATTTAAATGCAAGATGAAAAATACATACATGTTTTCTATAAAAAAATACTTAGGTTAA
66 TTATATAATTTAAATGCAAGATGAAAAATACATACATGTTTTATATAAAAAAATACTTAGGTTAA
13616705 TTTTAAATGAAATCTTATTTTTATTTTTTAT
131 TTTTAAATGAAATCTTATTTTTATTTTTTAT
13616736 TA
1 TA
13616738 GAATAATCTC
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
160 10 0.06
161 139 0.89
162 7 0.04
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (161 bp):
TAATAATAAAAAATAAATAAATAAAGGATTGAAGTCCAAAACTTCAAAATTGTTTTACAATGTAC
TTATATAATTTAAATGCAAGATGAAAAATACATACATGTTTTATATAAAAAAATACTTAGGTTAA
TTTTAAATGAAATCTTATTTTTATTTTTTAT
Found at i:13617173 original size:17 final size:16
Alignment explanation
Indices: 13617148--13617189 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
13617138 AACAAGTTAT
*
13617148 TAAATAATATTTTAAA
1 TAAATAATATATTAAA
13617164 TAATATAATATATTAAA
1 TAA-ATAATATATTAAA
13617181 TAAATAATA
1 TAAATAATA
13617190 AAATATATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATAATATATTAAA
Found at i:13619407 original size:14 final size:14
Alignment explanation
Indices: 13619385--13619433 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
13619375 GATTTCTATT
13619385 AAAAA-AAAAAAAG
1 AAAAAGAAAAAAAG
13619398 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
*
13619412 -AAAAG-AAAAGAG
1 AAAAAGAAAAAAAG
13619424 AAGAAAGAAA
1 AA-AAAGAAA
13619434 GATGATATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 6 0.19
13 11 0.35
14 12 0.39
15 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:13619409 original size:19 final size:20
Alignment explanation
Indices: 13619385--13619425 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
13619375 GATTTCTATT
13619385 AAAAAAAAAAAAGAAAA-AG
1 AAAAAAAAAAAAGAAAAGAG
*
13619404 AAAAAAAGAAAAGAAAAGAG
1 AAAAAAAAAAAAGAAAAGAG
13619424 AA
1 AA
13619426 GAAAGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAGAAAAGAG
Found at i:13624000 original size:21 final size:21
Alignment explanation
Indices: 13623974--13624018 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13623964 GGATATAGGT
* * *
13623974 AGATATTTTGGCAAGAATGAA
1 AGATATATTAGCAAGAATAAA
*
13623995 AGATATATTAGCATGAATAAA
1 AGATATATTAGCAAGAATAAA
13624016 AGA
1 AGA
13624019 ATGTAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (21 bp):
AGATATATTAGCAAGAATAAA
Found at i:13624750 original size:21 final size:21
Alignment explanation
Indices: 13624711--13624750 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13624701 CAAATTTTCA
* * *
13624711 TTTTCGTCAACACATAATTGT
1 TTTTCATCAACAAAAAATTGT
13624732 TTTTCATCAACAAAAAATT
1 TTTTCATCAACAAAAAATT
13624751 TTACCTTCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTCATCAACAAAAAATTGT
Found at i:13626000 original size:63 final size:63
Alignment explanation
Indices: 13625932--13626068 Score: 150
Period size: 63 Copynumber: 2.2 Consensus size: 63
13625922 CTATGTTTTT
* * * **
13625932 CTTCAAAGAAATGCAATACTT-ATTATTTAAAAAAAAACTATTATGAATAATTATTGCATCTAG
1 CTTCAAAAAAATGCAAGAATTAATTATTT-AAAAAAAACTACAATGAATAATTATTGCATCTAG
* * * * * *
13625995 TTTCAAAAAAATGTAGGAATTAATTATTTTAAAAAAATTACAATGAATAATTATTGCATTTAG
1 CTTCAAAAAAATGCAAGAATTAATTATTTAAAAAAAACTACAATGAATAATTATTGCATCTAG
*
13626058 CTTCAACAAAA
1 CTTCAAAAAAA
13626069 CGTAGTAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
63 53 0.88
64 7 0.12
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (63 bp):
CTTCAAAAAAATGCAAGAATTAATTATTTAAAAAAAACTACAATGAATAATTATTGCATCTAG
Found at i:13626958 original size:20 final size:21
Alignment explanation
Indices: 13626920--13626968 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
13626910 TGCCTTACCC
13626920 GATCGATCTCTTGCTTTAGGG
1 GATCGATCTCTTGCTTTAGGG
* *
13626941 GATCGATCTGTT-CTTTAGGT
1 GATCGATCTCTTGCTTTAGGG
13626961 GATCGATC
1 GATCGATC
13626969 CCTTATATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (21 bp):
GATCGATCTCTTGCTTTAGGG
Found at i:13627710 original size:24 final size:24
Alignment explanation
Indices: 13627683--13627730 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
13627673 ATATCAAAGC
*
13627683 ATCATCAAATTTTCATACCAATAT
1 ATCATCAAATTTTCACACCAATAT
13627707 ATCATCAAATTTTCACACCAATAT
1 ATCATCAAATTTTCACACCAATAT
13627731 TTTTCTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (24 bp):
ATCATCAAATTTTCACACCAATAT
Found at i:13639029 original size:8 final size:8
Alignment explanation
Indices: 13639018--13639051 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
13639008 AATCAAAATC
13639018 AAAATCAA
1 AAAATCAA
13639026 AAAATCAA
1 AAAATCAA
13639034 AAAATCAA
1 AAAATCAA
13639042 AAAATCAA
1 AAAATCAA
13639050 AA
1 AA
13639052 TAAAAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATCAA
Found at i:13639588 original size:51 final size:52
Alignment explanation
Indices: 13639533--13639665 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 52
13639523 TTGATTTTCA
* * * **
13639533 TTTAATGAGAATTGATTCTAAAATCAAATCCCAAAAATCTCTCTTTATCA-T
1 TTTAATGTGAATTGATTCTGAAATTAAATCCCAAAAATCTCTCCATATCATT
* * * * *
13639584 TTTAATGTGAATTGATTATGGAATTAAATGCCGACAATCTCTCCATATCATT
1 TTTAATGTGAATTGATTCTGAAATTAAATCCCAAAAATCTCTCCATATCATT
*
13639636 TTTAATGTCAATTGATTCTGAAATTAAATC
1 TTTAATGTGAATTGATTCTGAAATTAAATC
13639666 TAAAAGATTT
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 40 0.60
52 27 0.40
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (52 bp):
TTTAATGTGAATTGATTCTGAAATTAAATCCCAAAAATCTCTCCATATCATT
Found at i:13640006 original size:65 final size:65
Alignment explanation
Indices: 13639874--13640010 Score: 186
Period size: 65 Copynumber: 2.1 Consensus size: 65
13639864 GCAAAATAAG
* * * *
13639874 AAATAAAATGATCTAGACTGAGACGAGATCAAAACAAGCGATTGGGATTGAACCGTGAGTTAGAA
1 AAATAAAATGATCTAGACTGAGACGAGATCAAAACAAGCGACTGAGATTGAACCGTGAGTCAAAA
* ** *
13639939 AAATAAAATGATCTAGACTGAGCCGAGATCAAAATGAGTGACTGAGATTGAACCGT-AGGTCAAA
1 AAATAAAATGATCTAGACTGAGACGAGATCAAAACAAGCGACTGAGATTGAACCGTGA-GTCAAA
13640003 A
65 A
13640004 AAATAAA
1 AAATAAA
13640011 GTTCACAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 1 0.02
65 62 0.98
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (65 bp):
AAATAAAATGATCTAGACTGAGACGAGATCAAAACAAGCGACTGAGATTGAACCGTGAGTCAAAA
Found at i:13640087 original size:28 final size:28
Alignment explanation
Indices: 13640008--13640077 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
13639998 TCAAAAAAAT
13640008 AAAG-TTCACAATTTCAACTTTAAATCC
1 AAAGATTCACAATTTCAACTTTAAATCC
13640035 AAAGATTCACAATTTCAACTTTAAATCC
1 AAAGATTCACAATTTCAACTTTAAATCC
13640063 AAAGATTCACAATTT
1 AAAGATTCACAATTT
13640078 GGATATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 4 0.10
28 38 0.90
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAGATTCACAATTTCAACTTTAAATCC
Found at i:13640347 original size:86 final size:86
Alignment explanation
Indices: 13640227--13640477 Score: 236
Period size: 86 Copynumber: 2.9 Consensus size: 86
13640217 GCAAAGGTAC
* * *** * ** *
13640227 TAGATTCGTAAAGATTTCAAGTTTGTAAGGACTTTCAGATGCGTAAGGAA-GAAGGATTCGTAAG
1 TAGATTTGAAAAGATTTCAAGTTCACAAGGACTTTCAAATGCACAA-GAATGAAAGATTCGTAAG
* * *
13640291 ATTCCAAGTTTCATAAAGGTTT
65 ATTCCAAGTTTCACAAAGATCT
* * * *
13640313 TAGATTTGTAAAGATTTTAGGTTCACAAGGACTTTCAAATTCACAAGAATGAAAGATTCGTAAGA
1 TAGATTTGAAAAGATTTCAAGTTCACAAGGACTTTCAAATGCACAAGAATGAAAGATTCGTAAGA
* **
13640378 TTTCAAGTTTTGCAAAGATCT
66 TTCCAAGTTTCACAAAGATCT
* * * * * *
13640399 TAGATTTGAAAAGATTTCAAGTTCACAAGGA-TGTTTAGATTCGCAAGACTGAAAGATTTGTAAG
1 TAGATTTGAAAAGATTTCAAGTTCACAAGGACT-TTCAAATGCACAAGAATGAAAGATTCGTAAG
*
13640463 ATTTCAAGTTTCACA
65 ATTCCAAGTTTCACA
13640478 GAGGTTAGAA
Statistics
Matches: 136, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
85 4 0.03
86 132 0.97
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (86 bp):
TAGATTTGAAAAGATTTCAAGTTCACAAGGACTTTCAAATGCACAAGAATGAAAGATTCGTAAGA
TTCCAAGTTTCACAAAGATCT
Found at i:13642349 original size:12 final size:13
Alignment explanation
Indices: 13642322--13642349 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13642312 TAAGTCTTCC
13642322 TTTTTCTTTCATT
1 TTTTTCTTTCATT
13642335 TTTTTCTTTCATT
1 TTTTTCTTTCATT
13642348 TT
1 TT
13642350 GCTTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCATT
Found at i:13642361 original size:22 final size:22
Alignment explanation
Indices: 13642333--13642384 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
13642323 TTTTCTTTCA
13642333 TTTTTTTCT-TTCATTTTGCTTC
1 TTTTTTTCTATTCATTTTG-TTC
* * *
13642355 TTTTTTTGTATTCTTTTTGTTG
1 TTTTTTTCTATTCATTTTGTTC
13642377 TTTTTTTC
1 TTTTTTTC
13642385 CCTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.04, C:0.12, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTTTCTATTCATTTTGTTC
Found at i:13642715 original size:13 final size:13
Alignment explanation
Indices: 13642697--13642740 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
13642687 TACCCAATCA
*
13642697 ATTTTTTTTCTTC
1 ATTTTTTTTCATC
*
13642710 ATTTTTTTTAATC
1 ATTTTTTTTCATC
13642723 -TTTTTTTTCATC
1 ATTTTTTTTCATC
13642735 ACTTTT
1 A-TTTT
13642741 CAAGAAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.42
13 11 0.42
14 4 0.15
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTTTTTCATC
Found at i:13646579 original size:36 final size:35
Alignment explanation
Indices: 13646539--13646637 Score: 103
Period size: 35 Copynumber: 2.8 Consensus size: 35
13646529 AAAATTGCTA
* *
13646539 AAAAAAAACAAAATATAATAAATAAAAAAAT-GAAAT
1 AAAAAAATCAAAATAT-A-AAATAAAAAAATCAAAAT
* * * *
13646575 AAAAAACTTAAAATATAAAATGATAAAATCAAAAT
1 AAAAAAATCAAAATATAAAATAAAAAAATCAAAAT
13646610 AAAAAAATCAAAATA-AAAATGAAAAAAA
1 AAAAAAATCAAAATATAAAAT-AAAAAAA
13646638 GAAAAACCTG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
34 15 0.29
35 23 0.45
36 13 0.25
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (35 bp):
AAAAAAATCAAAATATAAAATAAAAAAATCAAAAT
Found at i:13646610 original size:35 final size:34
Alignment explanation
Indices: 13646539--13646636 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 34
13646529 AAAATTGCTA
* * *
13646539 AAAAAAAACAAAATATAATAAATAAAAAAAT-GAAAT
1 AAAAAAATC-AAA-ATAA-AAATGAAAAAATCAAAAT
* * *
13646575 AAAAAACTTAAAATATAAAATGATAAAATCAAAAT
1 AAAAAAATCAAAATA-AAAATGAAAAAATCAAAAT
13646610 AAAAAAATCAAAATAAAAATGAAAAAA
1 AAAAAAATCAAAATAAAAATGAAAAAA
13646637 AGAAAAACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
34 24 0.47
35 21 0.41
36 6 0.12
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (34 bp):
AAAAAAATCAAAATAAAAATGAAAAAATCAAAAT
Found at i:13646622 original size:20 final size:21
Alignment explanation
Indices: 13646599--13646637 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
13646589 ATAAAATGAT
*
13646599 AAAATCAAAAT-AAAAAAATC
1 AAAATAAAAATGAAAAAAATC
13646619 AAAATAAAAATGAAAAAAA
1 AAAATAAAAATGAAAAAAA
13646638 GAAAAACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (21 bp):
AAAATAAAAATGAAAAAAATC
Found at i:13646636 original size:14 final size:13
Alignment explanation
Indices: 13646599--13646628 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
13646589 ATAAAATGAT
13646599 AAAATCAAAATAAA
1 AAAATCAAAAT-AA
13646613 AAAATCAAAATAA
1 AAAATCAAAATAA
13646626 AAA
1 AAA
13646629 TGAAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAATCAAAATAA
Found at i:13647190 original size:51 final size:51
Alignment explanation
Indices: 13647107--13647255 Score: 154
Period size: 51 Copynumber: 2.9 Consensus size: 51
13647097 ATTTGATTTC
* * ** * **
13647107 CATTTTAATGGGAATTGATTCTAAAATCAAATCCCGAAAATCTCTCCTTAT
1 CATTTTAATGCGAATTGATTATGGAATTAAATCCCGAAAATCTCTCCACAT
* * * *
13647158 CATTTTAATGTGAATTGATTATGGAATTAAATCTCGACAATCTTTCCACAT
1 CATTTTAATGCGAATTGATTATGGAATTAAATCCCGAAAATCTCTCCACAT
* * **
13647209 CATTTTTAATGCCAATTGATTTTGGAATTAAATCCAAAAAATCTCTC
1 CA-TTTTAATGCGAATTGATTATGGAATTAAATCCCGAAAATCTCTC
13647256 AATTACAGTT
Statistics
Matches: 79, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 43 0.54
52 36 0.46
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (51 bp):
CATTTTAATGCGAATTGATTATGGAATTAAATCCCGAAAATCTCTCCACAT
Found at i:13648873 original size:19 final size:18
Alignment explanation
Indices: 13648851--13648886 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
13648841 CCTTCTTTTT
13648851 TTTTTCTTTCACTTTTTCC
1 TTTTTC-TTCACTTTTTCC
13648870 TTTTTCTTCACTTTTTC
1 TTTTTCTTCACTTTTTC
13648887 ATTTCATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTCTTCACTTTTTCC
Done.