Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 28 of 30
Found at i:4625594 original size:38 final size:38
Alignment explanation
Indices: 4625567--4625643 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
4625557 ATAAGATTTT
4625567 GTGGATTGGTACAAAAAGGAGTTAAGGAAAGAGAGGAA
1 GTGGATTGGTACAAAAAGGAGTTAAGGAAAGAGAGGAA
4625605 GTGGATTGGTACAAAAAGGAGTTAAGGAAAGAGAGGAA
1 GTGGATTGGTACAAAAAGGAGTTAAGGAAAGAGAGGAA
4625643 G
1 G
4625644 AAGAGGAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.44, C:0.03, G:0.38, T:0.16
Consensus pattern (38 bp):
GTGGATTGGTACAAAAAGGAGTTAAGGAAAGAGAGGAA
Found at i:4627050 original size:22 final size:22
Alignment explanation
Indices: 4627022--4627065 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4627012 AATATGATTG
*
4627022 TAAATTTATTATT-TTATTATTT
1 TAAATTT-TTATTATTAATATTT
4627044 TAAATTTTTATTATTAATATTT
1 TAAATTTTTATTATTAATATTT
4627066 ATTATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TAAATTTTTATTATTAATATTT
Found at i:4627070 original size:16 final size:16
Alignment explanation
Indices: 4627034--4627077 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
4627024 AATTTATTAT
4627034 TTTATTATT-TTAA-A
1 TTTATTATTATTAATA
4627048 TTT-TTATTATTAATA
1 TTTATTATTATTAATA
*
4627063 TTTATTATAATTAAT
1 TTTATTATTATTAAT
4627078 GATGATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 4 0.15
16 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATTATTATTAATA
Found at i:4627640 original size:19 final size:18
Alignment explanation
Indices: 4627614--4627682 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 18
4627604 AAATTCAACG
4627614 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
4627632 ATGTTGTATCGAT--AT-A
1 AT-TTGTATCGATACATAA
4627648 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
4627664 GTATTGTATCGATACATAA
1 AT-TTGTATCGATACATAA
4627683 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.21
15 2 0.05
16 3 0.07
17 2 0.05
18 2 0.05
19 25 0.58
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:4627653 original size:32 final size:32
Alignment explanation
Indices: 4627617--4627677 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
4627607 TTCAACGATT
*
4627617 TGTATCGATACATAAATGTTGTATCGATATAA
1 TGTATCGATACATAAATATTGTATCGATATAA
*
4627649 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAATATTGTATCGATA
4627678 CATAATTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATATAA
Found at i:4641685 original size:14 final size:13
Alignment explanation
Indices: 4641666--4641695 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4641656 GTCCTTCGGC
*
4641666 AAAAAAAAAACCA
1 AAAAAAAAAAACA
4641679 AAAAAAAAAAACA
1 AAAAAAAAAAACA
4641692 AAAA
1 AAAA
4641696 GGGTCCAGAT
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:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:4643169 original size:28 final size:28
Alignment explanation
Indices: 4643129--4643420 Score: 327
Period size: 28 Copynumber: 10.1 Consensus size: 28
4643119 CATCCCTCAC
4643129 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
4643157 CCTTCAAAAGCCCACAAATCACTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
4643185 CCTTCAAAATCCCATAAATCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
4643213 CCTTCAAAAGTCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
4643241 CCTTTTCCAAAGCCCACAAATCAGTGGCGA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
4643271 CCTTCAAAAGCCCACAAGTCAGTGGC-A
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
4643298 CCTTTTTCCAAAGCCCACAAGTCAGTGGC-A
1 CC---TTCAAAAGCCCACAAGTCAGTGGCAA
* *
4643328 CCTTTTTCCAAAGCCCACAAGTCAGTGGCAC
1 CC---TTCAAAAGCCCACAAGTCAGTGGCAA
** *
4643359 CCTTTTCCGAAGCCCACAAATCAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
*
4643389 CCTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
4643417 CCTT
1 CCTT
4643421 TTCTGAAGCC
Statistics
Matches: 232, Mismatches: 26, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
27 3 0.01
28 124 0.53
30 103 0.44
31 2 0.01
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.19
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:4643265 original size:30 final size:30
Alignment explanation
Indices: 4643131--4643452 Score: 335
Period size: 30 Copynumber: 11.1 Consensus size: 30
4643121 TCCCTCACCC
*
4643131 TTCAAAAGCCCACAAGTCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* * *
4643159 TTCAAAAGCCCACAAATCACTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* * * *
4643187 TTCAAAATCCCATAAATCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
4643215 TTCAAAAGTCCACAAGTCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* *
4643245 TTCCAAAGCCCACAAATCAGTGGCGA-CC--
1 TTCAAAAGCCCACAAGTCAGTGGC-ACCCTT
*
4643273 TTCAAAAGCCCACAAGTCAGTGGCACCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* *
4643303 TTCCAAAGCCCACAAGTCAGTGGCACCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
4643333 TTCCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
** * *
4643363 TTCCGAAGCCCACAAATCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
4643391 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
** * *
4643421 TTCTGAAGCCCACAATTCCA-TGGCACCATT
1 TTCAAAAGCCCACAAGT-CAGTGGCACCCTT
4643451 TT
1 TT
4643453 GCTTTTTAAG
Statistics
Matches: 256, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.00
28 121 0.47
30 131 0.51
31 3 0.01
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTT
Found at i:4643445 original size:58 final size:58
Alignment explanation
Indices: 4643135--4643435 Score: 419
Period size: 58 Copynumber: 5.2 Consensus size: 58
4643125 TCACCCTTCA
* * * * *
4643135 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCACTGGCAACC--TTCA
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * *
4643191 AAATCCCATAAATCAGTGGCAACCTTCAAAAGTCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
4643249 AAAGCCCACAAATCAGTGGCGACCTTCAAAAGCCCACAAGTCAGTGGCACCTTTTTCC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
4643307 AAAGCCCACAAGTCAGTGGC-ACCTTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAATCAGTGGCAACC---TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
4643367 GAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCT
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
4643425 GAAGCCCACAA
1 AAAGCCCACAA
4643436 TTCCATGGCA
Statistics
Matches: 219, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
56 45 0.21
57 3 0.01
58 118 0.54
60 50 0.23
61 3 0.01
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (58 bp):
AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
Found at i:4643466 original size:34 final size:34
Alignment explanation
Indices: 4643426--4643582 Score: 217
Period size: 34 Copynumber: 4.6 Consensus size: 34
4643416 CCCTTTTCTG
* * *
4643426 AAGCCCACAATTCCATGGCAC-CATTTTGCTTTTT
1 AAGCCCACAACTCCGTGGCACTC-TTTTTCTTTTT
*
4643460 AAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
4643494 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* *
4643528 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* * *
4643562 AAGTCCACAAGTCTGTGGCAC
1 AAGCCCACAACTCCGTGGCAC
4643583 CCTTATCTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 111 0.99
35 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.34
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
Found at i:4643654 original size:43 final size:43
Alignment explanation
Indices: 4643589--4643680 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 43
4643579 GCACCCTTAT
*
4643589 CTTTAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
4643632 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
4643675 CTTTAA
1 CTTTAA
4643681 CATCCCTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:4643856 original size:52 final size:52
Alignment explanation
Indices: 4643635--4643880 Score: 180
Period size: 52 Copynumber: 4.8 Consensus size: 52
4643625 TTGGCACCTT
* * * * *
4643635 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTAACATCCC
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATCTTTAACATCCC
* * **
4643687 TAAGCCCAATGCCGTTGGCTTTGTCTCAGCACATTGACAT-TCTT--C-T-CC
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATCT-TTAACATCCC
* * * * * * ** **
4643735 -AAGTCTAATGCCGCTGACCGTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACAT-C--TTTAACATCCC
* * ** *
4643789 TAAGCCTAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCC
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATCTTTAACATCCC
**
4643841 TAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGACAT
1 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACAT
4643881 TCTTCTCTAA
Statistics
Matches: 145, Mismatches: 39, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
47 31 0.21
48 2 0.01
49 1 0.01
50 3 0.02
51 2 0.01
52 74 0.51
53 1 0.01
54 1 0.01
55 30 0.21
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (52 bp):
TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGACATCTTTAACATCCC
Found at i:4643915 original size:154 final size:150
Alignment explanation
Indices: 4643632--4643984 Score: 519
Period size: 154 Copynumber: 2.3 Consensus size: 150
4643622 ACATTGGCAC
4643632 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTAACATCCCTAAGCCCAAT
1 CTTTAAG-CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTAACATCCCTAAGCCCAAT
* **
4643697 GCCGTTGGCTTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGAATCA
65 GCCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGCAAATCA
* *
4643762 GCACATTGACATCCTTTTTCTCAT
130 GCACATTGACAT--TCTTT-ACAT
* *
4643786 CTTTAAGCCTAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAAT
1 CTTTAAGCC-AATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTAACATCCCTAAGCCCAAT
* * **
4643851 GTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCTAAGTCTAATGTTGCTGACCGCAAATCA
65 GCCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGCAAATCA
4643916 GCACATTGACATTCTTTACAT
130 GCACATTGACATTCTTTACAT
**
4643937 CTTTAAGCCCAATATCACTGGTCC-TGAATCAGCATATTGGCACCTTTA
1 CTTTAAG-CCAATATCGTTGG-CCTTGAATCAGCATATTGGCACCTTTA
4643985 TCACTTTTCT
Statistics
Matches: 181, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
151 41 0.23
152 8 0.04
153 2 0.01
154 130 0.72
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (150 bp):
CTTTAAGCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTAACATCCCTAAGCCCAATG
CCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGCAAATCAG
CACATTGACATTCTTTACAT
Found at i:4644667 original size:19 final size:18
Alignment explanation
Indices: 4644641--4644709 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 18
4644631 AAATTCAACG
4644641 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
4644659 ATGTTGTATCGAT--AT-A
1 AT-TTGTATCGATACATAA
4644675 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
4644691 GTATTGTATCGATACATAA
1 AT-TTGTATCGATACATAA
4644710 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.21
15 2 0.05
16 3 0.07
17 2 0.05
18 2 0.05
19 25 0.58
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:4644680 original size:32 final size:32
Alignment explanation
Indices: 4644644--4644704 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
4644634 TTCAACGATT
*
4644644 TGTATCGATACATAAATGTTGTATCGATATAA
1 TGTATCGATACATAAATATTGTATCGATATAA
*
4644676 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAATATTGTATCGATA
4644705 CATAATTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATATAA
Found at i:4648112 original size:33 final size:30
Alignment explanation
Indices: 4648021--4648123 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 30
4648011 AATTTACTTT
*
4648021 TTAAATAA-ATAAATTTAAAATTAAAATTAAA
1 TTAAATAATATAAATATAAAATT-AAA-TAAA
4648052 TTATAATAATA-AATATATAAAGTATTAAATAAA
1 TTA-AATAATATAA-ATATAAA--ATTAAATAAA
*
4648085 TTAAGATACTATATAAATATAAAATTAAAAATAA
1 TTAA-ATA--ATATAAATATAAAATTAAATA-AA
4648119 TTAAA
1 TTAAA
4648124 ATAAGGCAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
31 3 0.05
32 8 0.13
33 25 0.42
34 9 0.15
35 13 0.22
36 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (30 bp):
TTAAATAATATAAATATAAAATTAAATAAA
Found at i:4648766 original size:11 final size:11
Alignment explanation
Indices: 4648733--4648783 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
4648723 AAAAGAAAAA
4648733 ATAAAAAT-AT
1 ATAAAAATAAT
4648743 GATTAAAATATAAT
1 -A-TAAAA-ATAAT
4648757 ATAAAAATAAT
1 ATAAAAATAAT
**
4648768 ATAAATTTAAT
1 ATAAAAATAAT
4648779 ATAAA
1 ATAAA
4648784 TATATAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 20 0.57
12 10 0.29
13 3 0.09
14 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:4648784 original size:11 final size:11
Alignment explanation
Indices: 4648748--4648787 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
4648738 AATATGATTA
4648748 AAATATAATAT
1 AAATATAATAT
*
4648759 AAAAATAATAT
1 AAATATAATAT
*
4648770 AAATTTAATAT
1 AAATATAATAT
4648781 AAATATA
1 AAATATA
4648788 TAACATGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:4649582 original size:40 final size:37
Alignment explanation
Indices: 4649503--4649593 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 37
4649493 TACACAAATT
* *
4649503 TTTTTATCTTT-CTTCTCTTTCCTTTCTTCTTTCTATC
1 TTTTT-TCTTTCCTTCTCTTTCCTTTCTCCTTTATATC
* *
4649540 TTTTTTGTTTCCTTCTCTTTCCTCTCCTCTCCTTTATTTC
1 TTTTTTCTTTCCTTCTCTTTCCT-T--TCTCCTTTATATC
4649580 TTTTTTCTTTCCTT
1 TTTTTTCTTTCCTT
4649594 TCCTTTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 4 0.09
37 17 0.38
38 1 0.02
40 23 0.51
ACGTcount: A:0.03, C:0.29, G:0.01, T:0.67
Consensus pattern (37 bp):
TTTTTTCTTTCCTTCTCTTTCCTTTCTCCTTTATATC
Found at i:4649606 original size:25 final size:26
Alignment explanation
Indices: 4649557--4649621 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
4649547 TTTCCTTCTC
* *
4649557 TTTCCTCTCCTCTCCTTTATTTCTTT
1 TTTCCTTTCCTTTCCTTTATTTCTTT
4649583 TTT-CTTTCCTTTCCTTTATTTCTTT
1 TTTCCTTTCCTTTCCTTTATTTCTTT
*
4649608 TTTCCTTTTCTTTC
1 TTTCCTTTCCTTTC
4649622 TGTTCTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 23 0.66
26 12 0.34
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTCCTTTCCTTTCCTTTATTTCTTT
Found at i:4649627 original size:5 final size:4
Alignment explanation
Indices: 4649509--4649628 Score: 50
Period size: 4 Copynumber: 28.0 Consensus size: 4
4649499 AATTTTTTTA
* *
4649509 TCTT TCTT CTCTT TCCTT TC-T TCTT TCTA TCTT T-TT TGTT TCCTT CTCTT
1 TCTT TCTT -TCTT T-CTT TCTT TCTT TCTT TCTT TCTT TCTT T-CTT -TCTT
* * * *
4649559 TCCTCT CCTCT CCTT TATT TCTT T-TT TCTT TCCTT TCCTT TATT TCTT
1 T-CT-T TCT-T TCTT TCTT TCTT TCTT TCTT T-CTT T-CTT TCTT TCTT
4649607 T-TT TCCTTT TCTT TCTGT TCTT
1 TCTT T-C-TT TCTT TCT-T TCTT
4649629 AATAAACCAT
Statistics
Matches: 93, Mismatches: 9, Indels: 28
0.72 0.07 0.22
Matches are distributed among these distances:
3 12 0.13
4 40 0.43
5 36 0.39
6 5 0.05
ACGTcount: A:0.03, C:0.28, G:0.02, T:0.68
Consensus pattern (4 bp):
TCTT
Found at i:4654939 original size:16 final size:17
Alignment explanation
Indices: 4654883--4654945 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
4654873 TATTTAAAAT
**
4654883 ATTTTATATTTATATAA
1 ATTTTATACATATATAA
4654900 ATTTTGATACAT-TA-ATA
1 ATTTT-ATACATATATA-A
4654917 A-TTTATA-ATATATAA
1 ATTTTATACATATATAA
4654932 ATTTTATA-ATATAT
1 ATTTTATACATATAT
4654946 TTATATTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 2 0.05
15 7 0.18
16 17 0.44
17 9 0.23
18 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTATACATATATAA
Found at i:4654954 original size:16 final size:16
Alignment explanation
Indices: 4654919--4655006 Score: 56
Period size: 16 Copynumber: 5.6 Consensus size: 16
4654909 CATTAATAAT
** *
4654919 TTATAATATATAAATT
1 TTATAATATATTTATA
4654935 TTATAATATATTTATA
1 TTATAATATATTTATA
*
4654951 TTATATTATATTT-TAA
1 TTATAATATATTTAT-A
**
4654967 TTATTTTATATATTATA
1 TTATAATATAT-TTATA
* * *
4654984 TT-TTATATAATCATA
1 TTATAATATATTTATA
4654999 TT-TAATAT
1 TTATAATAT
4655007 TATTAAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
15 12 0.20
16 42 0.70
17 5 0.08
18 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATAATATATTTATA
Found at i:4654959 original size:21 final size:21
Alignment explanation
Indices: 4654935--4654991 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
4654925 TATATAAATT
4654935 TTATAATATATTTATATTATA
1 TTATAATATATTTATATTATA
* * * *
4654956 TTATATTTTAATTATTTTATA
1 TTATAATATATTTATATTATA
*
4654977 -TATTATAT-TTTATAT
1 TTATAATATATTTATAT
4654992 AATCATATTT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 17 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATAATATATTTATATTATA
Found at i:4654961 original size:32 final size:32
Alignment explanation
Indices: 4654880--4654956 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 32
4654870 TTATATTTAA
*
4654880 AATATTTTATATTTATATAAATTTTGATACATT
1 AATAATTTATA-TTATATAAATTTTGATACATT
*
4654913 AATAATTTATAATATATAAATTTT-ATA-A-T
1 AATAATTTATATTATATAAATTTTGATACATT
4654942 -AT-ATTTATATTATAT
1 AATAATTTATATTATAT
4654957 TATATTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.29
28 2 0.05
29 1 0.02
30 1 0.02
31 3 0.07
32 12 0.29
33 10 0.24
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTGATACATT
Found at i:4655001 original size:15 final size:14
Alignment explanation
Indices: 4654968--4655006 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4654958 ATATTTTAAT
*
4654968 TATTTTATATATTA
1 TATTTTATATATCA
4654982 TATTTTATATAATCA
1 TATTTTATAT-ATCA
*
4654997 TATTTAATAT
1 TATTTTATAT
4655007 TATTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTATATATCA
Found at i:4655833 original size:21 final size:21
Alignment explanation
Indices: 4655807--4655852 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
4655797 AACCTTGCTC
4655807 AAAGTTGTGCTGGTAAGAAGA
1 AAAGTTGTGCTGGTAAGAAGA
4655828 AAAGTTGTGCTGGTAAGAAGA
1 AAAGTTGTGCTGGTAAGAAGA
4655849 AAAG
1 AAAG
4655853 CCAATGCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (21 bp):
AAAGTTGTGCTGGTAAGAAGA
Found at i:4656584 original size:11 final size:12
Alignment explanation
Indices: 4656559--4656583 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4656549 TATATTTTAT
4656559 AATTAAATAAAA
1 AATTAAATAAAA
4656571 AATTAAATAAAA
1 AATTAAATAAAA
4656583 A
1 A
4656584 TATTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATTAAATAAAA
Found at i:4656584 original size:35 final size:35
Alignment explanation
Indices: 4656544--4656614 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
4656534 TACTCTTTCA
4656544 AAAAATA-TATTTTATAATTAAATAAAAAATTAAAT
1 AAAAATATTATTTTATAATTAAAT-AAAAATTAAAT
* *
4656579 AAAAATATTTTTTTATAATTAAATTAAAATTAAAT
1 AAAAATATTATTTTATAATTAAATAAAAATTAAAT
4656614 A
1 A
4656615 TTCTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 18 0.55
36 15 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAAATATTATTTTATAATTAAATAAAAATTAAAT
Found at i:4656953 original size:32 final size:30
Alignment explanation
Indices: 4656917--4656976 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
4656907 TGAAGAAAAC
4656917 CTAAAAATTCTATCAAAAATAATTATTTTTAA
1 CTAAAAATTC-ATCAAAAATAATT-TTTTTAA
**
4656949 CTAAATTTTCATCAAAAATAATTTTTTT
1 CTAAAAATTCATCAAAAATAATTTTTTT
4656977 GGTGAAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.19
31 13 0.50
32 8 0.31
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (30 bp):
CTAAAAATTCATCAAAAATAATTTTTTTAA
Found at i:4657719 original size:24 final size:24
Alignment explanation
Indices: 4657674--4657720 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4657664 TTTACATTAC
* *
4657674 AATTATAATTAATTTTTTAATATA
1 AATTATAAATAATTTTTAAATATA
4657698 AATT-TAAATAATTCTTTAAATAT
1 AATTATAAATAATT-TTTAAATAT
4657721 GTTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTATAAATAATTTTTAAATATA
Found at i:4657747 original size:16 final size:16
Alignment explanation
Indices: 4657705--4657747 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4657695 ATAAATTTAA
*
4657705 ATAATTCTTTAAATAT
1 ATAATTATTTAAATAT
* * *
4657721 GTTATTTTTTAAATAT
1 ATAATTATTTAAATAT
4657737 ATAATTATTTA
1 ATAATTATTTA
4657748 CGTTATTGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
ATAATTATTTAAATAT
Found at i:4662198 original size:61 final size:61
Alignment explanation
Indices: 4662103--4662225 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
4662093 TTTTTTCTCG
4662103 TTTTTAGTTTCCTTTTTTACATTTTTTTGTTAATTTATGACTAAAGTTTGACCTTGGTTCA
1 TTTTTAGTTTCCTTTTTTACATTTTTTTGTTAATTTATGACTAAAGTTTGACCTTGGTTCA
4662164 TTTTTAGTTTCCTTTTTTACATTTTTTTGTTAATTTATGACTAAAGTTTGACCTTGGTTCA
1 TTTTTAGTTTCCTTTTTTACATTTTTTTGTTAATTTATGACTAAAGTTTGACCTTGGTTCA
4662225 T
1 T
4662226 GGGTCATAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (61 bp):
TTTTTAGTTTCCTTTTTTACATTTTTTTGTTAATTTATGACTAAAGTTTGACCTTGGTTCA
Found at i:4662685 original size:32 final size:31
Alignment explanation
Indices: 4662631--4662708 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 31
4662621 AATTTTATTT
** * * *
4662631 ATTTTTAATATATTTTGATTTATTTAATTGTA
1 ATTTTT-ATATATTTACATTTATATAAATGCA
4662663 ATTTTTATATATTTACATTTTATATAAATGCA
1 ATTTTTATATATTTACA-TTTATATAAATGCA
* *
4662695 ATTTATATTTATTT
1 ATTTTTATATATTT
4662709 TTAAATTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 9 0.24
32 29 0.76
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (31 bp):
ATTTTTATATATTTACATTTATATAAATGCA
Found at i:4663731 original size:19 final size:20
Alignment explanation
Indices: 4663709--4663754 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
4663699 AAAGAAACTA
**
4663709 TATTTTATTTT-TTTAAAAT
1 TATTTTATTTTATAAAAAAT
4663728 TATTTATATTTTATAAAAAAT
1 TATTT-TATTTTATAAAAAAT
4663749 TATTTT
1 TATTTT
4663755 TTAATTACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTATTTTATAAAAAAT
Found at i:4664180 original size:15 final size:15
Alignment explanation
Indices: 4664151--4664225 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
4664141 ATTTGATTTG
*
4664151 TTAAATTTAATTTTTA
1 TTAAA-TTAAATTTTA
4664167 TTAAATTAAATTTTA
1 TTAAATTAAATTTTA
* **
4664182 ATAAA-TATTTTTTA
1 TTAAATTAAATTTTA
*
4664196 TTTAAATT-AATTTAA
1 -TTAAATTAAATTTTA
*
4664211 TTAGATTTAAATTTT
1 TTA-AATTAAATTTT
4664226 TATTTATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
14 10 0.22
15 24 0.53
16 11 0.24
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
TTAAATTAAATTTTA
Found at i:4664261 original size:18 final size:17
Alignment explanation
Indices: 4664151--4664264 Score: 64
Period size: 18 Copynumber: 6.8 Consensus size: 17
4664141 ATTTGATTTG
4664151 TTAAATTTAATT-TTTA-
1 TTAAA-TTAATTATTTAT
*
4664167 TTAAATTAAAT-TTTA-
1 TTAAATTAATTATTTAT
* *
4664182 ATAAA-T-ATTTTTTAT
1 TTAAATTAATTATTTAT
*
4664197 TTAAATTAATTTAATTAGAT
1 TTAAATTAA-TT-ATT-TAT
*
4664217 TTAAATT-TTTATTTAT
1 TTAAATTAATTATTTAT
4664233 TAATAAA-TAATTATTTAT
1 T--TAAATTAATTATTTAT
4664251 TTAAATTTAATTAT
1 TTAAA-TTAATTAT
4664265 AAAATATATA
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
13 2 0.03
14 5 0.06
15 17 0.22
16 13 0.17
17 5 0.06
18 24 0.31
19 2 0.03
20 9 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TTAAATTAATTATTTAT
Found at i:4664626 original size:22 final size:24
Alignment explanation
Indices: 4664597--4664666 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
4664587 TATTTTTTAT
* *
4664597 ATAAAAAAAGTATATAAT-TTAAAA
1 ATAAAAATATTATA-AATATTAAAA
4664621 ATAAAAATATTATAAATATTAAAA
1 ATAAAAATATTATAAATATTAAAA
* *
4664645 TTTAAAAT-TTA-AAATTATTAAA
1 ATAAAAATATTATAAA-TATTAAA
4664667 TATCAACACT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.08
23 13 0.32
24 24 0.60
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (24 bp):
ATAAAAATATTATAAATATTAAAA
Found at i:4664639 original size:9 final size:8
Alignment explanation
Indices: 4664615--4664666 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 8
4664605 AGTATATAAT
4664615 TTAAAA-A
1 TTAAAATA
*
4664622 TAAAAATA
1 TTAAAATA
4664630 TTATAAATA
1 TTA-AAATA
4664639 TTAAAAT-
1 TTAAAATA
4664646 TTAAAAT-
1 TTAAAATA
4664653 TTAAAATTA
1 TTAAAA-TA
4664662 TTAAA
1 TTAAA
4664667 TATCAACACT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 18 0.46
8 8 0.21
9 13 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TTAAAATA
Found at i:4665240 original size:17 final size:17
Alignment explanation
Indices: 4665220--4665257 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4665210 TTTTATTTTA
*
4665220 TTTTCAATATTATTATT
1 TTTTCAATATAATTATT
*
4665237 TTTTCATTATAATTATT
1 TTTTCAATATAATTATT
4665254 TTTT
1 TTTT
4665258 GTTTTGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCAATATAATTATT
Found at i:4666348 original size:16 final size:17
Alignment explanation
Indices: 4666327--4666360 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4666317 TTCAACAAGG
4666327 AGGAAA-AAAAAAGAAA
1 AGGAAAGAAAAAAGAAA
*
4666343 AGGAAAGAAAAAATAAA
1 AGGAAAGAAAAAAGAAA
4666360 A
1 A
4666361 ATTATTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AGGAAAGAAAAAAGAAA
Found at i:4666752 original size:23 final size:23
Alignment explanation
Indices: 4666719--4666774 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
4666709 TTTATGTCAT
* *
4666719 ATTTTTTTATCGTGTT-TTAATTA
1 ATTTTTATATCGTGTTCAT-ATTA
4666742 ATTTTTATATCGTGTTCATATTA
1 ATTTTTATATCGTGTTCATATTA
*
4666765 TTTTTTATAT
1 ATTTTTATAT
4666775 ATTTAAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.64
Consensus pattern (23 bp):
ATTTTTATATCGTGTTCATATTA
Found at i:4667679 original size:26 final size:27
Alignment explanation
Indices: 4667635--4667687 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
4667625 TTTGATACTT
*
4667635 TTTAATTTAAATTTATATAATTATTAA
1 TTTAATTTAAATTTATATAAATATTAA
4667662 TTTAA-TTAAATATT-TATAAATATTAA
1 TTTAATTTAAAT-TTATATAAATATTAA
4667688 AATTTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTAATTTAAATTTATATAAATATTAA
Found at i:4669882 original size:2 final size:2
Alignment explanation
Indices: 4669875--4669900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4669865 GCGTGCGTGC
4669875 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
4669901 TCTTGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:4673040 original size:12 final size:12
Alignment explanation
Indices: 4673023--4673047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4673013 AGTACATTTA
4673023 ACTTTTTTTTTT
1 ACTTTTTTTTTT
4673035 ACTTTTTTTTTT
1 ACTTTTTTTTTT
4673047 A
1 A
4673048 AATCATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (12 bp):
ACTTTTTTTTTT
Found at i:4675653 original size:16 final size:16
Alignment explanation
Indices: 4675628--4675658 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4675618 TATTTTTAAT
4675628 TTAATAAATTATTTTC
1 TTAATAAATTATTTTC
*
4675644 TTAATTAATTATTTT
1 TTAATAAATTATTTT
4675659 TTACTATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATAAATTATTTTC
Found at i:4677244 original size:22 final size:20
Alignment explanation
Indices: 4677194--4677251 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
4677184 TTGGAAAAGA
4677194 AATGTATCGATACATTTACT
1 AATGTATCGATACATTTACT
*
4677214 TATGTATCGATACATGCTTA-T
1 AATGTATCGATACAT--TTACT
4677235 AATTGTATCGATACATT
1 AA-TGTATCGATACATT
4677252 ATTCATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 15 0.45
21 2 0.06
22 16 0.48
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTACT
Found at i:4682630 original size:24 final size:24
Alignment explanation
Indices: 4682601--4682649 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
4682591 TATTGCAAAA
*
4682601 GGATAAGAATGGGAAGATTCATAG
1 GGATAAGAATAGGAAGATTCATAG
4682625 GGATAAGAATAGGAAGATTCATAG
1 GGATAAGAATAGGAAGATTCATAG
4682649 G
1 G
4682650 TGTGCTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (24 bp):
GGATAAGAATAGGAAGATTCATAG
Found at i:4691819 original size:16 final size:16
Alignment explanation
Indices: 4691798--4691829 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4691788 TCCCCAGGAA
4691798 AATAACGGGATTGGAG
1 AATAACGGGATTGGAG
4691814 AATAACGGGATTGGAG
1 AATAACGGGATTGGAG
4691830 TATCCCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.19
Consensus pattern (16 bp):
AATAACGGGATTGGAG
Found at i:4694972 original size:61 final size:61
Alignment explanation
Indices: 4694876--4695168 Score: 360
Period size: 61 Copynumber: 4.8 Consensus size: 61
4694866 AAATGGGTCT
* * * * *
4694876 TGCTCCTTGAAGACTAAAAAGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGGCATCT
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
4694937 TGCTCTTTGAAGACTGAAAAGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCC
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
4694998 TACTCTTTGAGGACTAAAAAAGTG-CACCAACTTGTGTGGGCTTTAAAAGAAAAAAGGCATCC
1 TGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-GAAAAGGCATCC
* * * * *
4695060 AGTTCTTTGAGGACTAGCAAAGTGCCACCAA-TT-TGTAGGCTTTAAAAGGAAAAGGCGTCC
1 TGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * *
4695120 TGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGTGCTTTGAAAGG
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
4695169 TGTCCTACTC
Statistics
Matches: 203, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
58 12 0.06
59 3 0.01
60 36 0.18
61 106 0.52
62 40 0.20
63 6 0.03
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (61 bp):
TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
Found at i:4695297 original size:100 final size:99
Alignment explanation
Indices: 4695114--4695403 Score: 360
Period size: 100 Copynumber: 3.0 Consensus size: 99
4695104 AAAGGAAAAG
* * *
4695114 GCGTCCTGCTCTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGTGCTTT----G-AAAGGTGTC
1 GCGTCCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTC
* *
4695173 CTACTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
66 CTACTCTTTGAGGACTAAAAGGTGAAAAGAGAGA
*
4695207 GCGTCCTGCTCTTTGAGGACTGAGAAGCGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGT
* *
4695272 CCTACTCTTTAAGGACTAAAAGGTGAAATGAGAGA
65 CCTACTCTTTGAGGACTAAAAGGTGAAAAGAGAGA
* * * * *
4695307 GTGTCTTGCTCTTTGAGGACTG-GAAAGTGTCACCAACTTGTGTGGACTTTAAAAGAGAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTGAG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT
* * * *
4695371 CATGCTCTTTGAGGACTGAAATGTGAAAAGAGA
65 CCTACTCTTTGAGGACTAAAAGGTGAAAAGAGA
4695404 AAGTTTAGAT
Statistics
Matches: 170, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
93 23 0.14
94 23 0.14
99 38 0.22
100 86 0.51
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (99 bp):
GCGTCCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTC
CTACTCTTTGAGGACTAAAAGGTGAAAAGAGAGA
Found at i:4696378 original size:9 final size:9
Alignment explanation
Indices: 4696356--4696415 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
4696346 CTTAAGTAGG
4696356 TTCTTTTCTT
1 TTCTTTT-TT
4696366 TTCTTTTTT
1 TTCTTTTTT
4696375 TTCTTTATTT
1 TTCTTT-TTT
4696385 TT-TTTATTT
1 TTCTTT-TTT
4696394 TT-TTTTATT
1 TTCTTTT-TT
*
4696403 TT-TTTGTT
1 TTCTTTTTT
4696411 TTCTT
1 TTCTT
4696416 AAAAAGAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
8 5 0.11
9 29 0.63
10 12 0.26
ACGTcount: A:0.05, C:0.08, G:0.02, T:0.85
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:4696378 original size:14 final size:13
Alignment explanation
Indices: 4696359--4696412 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
4696349 AAGTAGGTTC
4696359 TTTTCTTTTCTTTT
1 TTTTCTTTT-TTTT
*
4696373 TTTTCTTTATTTT
1 TTTTCTTTTTTTT
*
4696386 TTTTATTTTTTTT
1 TTTTCTTTTTTTT
4696399 TATTT-TTTTGTTTT
1 T-TTTCTTTT-TTTT
4696413 CTTAAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 20 0.57
14 15 0.43
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.87
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:4696385 original size:10 final size:10
Alignment explanation
Indices: 4696364--4696405 Score: 61
Period size: 9 Copynumber: 4.4 Consensus size: 10
4696354 GGTTCTTTTC
4696364 TTTTCTTT-T
1 TTTTCTTTAT
4696373 TTTTCTTTAT
1 TTTTCTTTAT
4696383 TTTT-TTTAT
1 TTTTCTTTAT
*
4696392 TTTTTTTTAT
1 TTTTCTTTAT
4696402 TTTT
1 TTTT
4696406 TTGTTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 17 0.55
10 14 0.45
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTCTTTAT
Found at i:4696406 original size:10 final size:10
Alignment explanation
Indices: 4696371--4696407 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
4696361 TTCTTTTCTT
4696371 TTTTTTCTTTA
1 TTTTTT-TTTA
4696382 -TTTTTTTTA
1 TTTTTTTTTA
4696391 TTTTTTTTTA
1 TTTTTTTTTA
4696401 TTTTTTT
1 TTTTTTT
4696408 GTTTTCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 4 0.16
10 21 0.84
ACGTcount: A:0.08, C:0.03, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:4698153 original size:22 final size:22
Alignment explanation
Indices: 4698122--4698178 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
4698112 GTAGTGATTT
4698122 TCGAA-TGCATTTGAAGCTCCA
1 TCGAAGTGCATTTGAAGCTCCA
4698143 TCGAAGTGCATTTGAAGCTCCA
1 TCGAAGTGCATTTGAAGCTCCA
*
4698165 TCGAAGTACATTTG
1 TCGAAGTGCATTTG
4698179 CCATGAGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (22 bp):
TCGAAGTGCATTTGAAGCTCCA
Found at i:4702462 original size:35 final size:35
Alignment explanation
Indices: 4702416--4702485 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
4702406 TTCGTTCGTC
4702416 ATATTCTTCATAGAATTTAATTTCTGATCGATCCA
1 ATATTCTTCATAGAATTTAATTTCTGATCGATCCA
*
4702451 ATATTCTTCATAGAATTTAATTTTTGATCGATCCA
1 ATATTCTTCATAGAATTTAATTTCTGATCGATCCA
4702486 TCATCCATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (35 bp):
ATATTCTTCATAGAATTTAATTTCTGATCGATCCA
Found at i:4708985 original size:79 final size:78
Alignment explanation
Indices: 4708811--4709189 Score: 302
Period size: 79 Copynumber: 4.8 Consensus size: 78
4708801 ACAATGGGGC
* * * * *
4708811 TGGAGTATCCCCTGATTATGGAAAATCGGTATTTTAGAAATAAAA-TCAGGGTTGGAGTATTCCC
1 TGGAGTATCCCC-GATTATGG-AAATCAGTGTTTTAGAAATAAAACT-GGGGTTAGAGTATCCCC
* * *
4708875 TCAGAAATAACAAGCT
63 TCAAAAATAACGAGGT
* * * * *
4708891 TGAAGCATCCTCGATTATAGGAAATCAGTGTTTT-GAAAATAAAATTGGGGTTAGATTATCCCCT
1 TGGAGTATCCCCGATTAT-GGAAATCAGTGTTTTAG-AAATAAAACTGGGGTTAGAGTATCCCCT
4708955 CAAAAATAACGAGGT
64 CAAAAATAACGAGGT
* * * * ** * * *
4708970 TAGAGTATCCCCGATTGTGGAAAATC-GAAGCTTTAGAAATAAGGCTAGGGTTGGAGTATCCCCA
1 TGGAGTATCCCCGATTATGG-AAATCAG-TGTTTTAGAAATAAAACTGGGGTTAGAGTATCCCCT
* *
4709034 CCAAAATAACGGGGT
64 CAAAAATAACGAGGT
* * * * * *
4709049 TGGAGTAT-CCCGATTGTAAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAGAGTATCCCCTC
1 TGGAGTATCCCCGATTAT-GGAAATCAGTGTTTTAGAAATAAAACTGGGGTTAGAGTATCCCCTC
*
4709113 AGAAATAACG-GGAT
65 AAAAATAACGAGG-T
* * * *
4709127 TGGAGTATCCCCTATTATGAAAAAT-TGATGTTTTGGAAATAAAACTGGGGTTAGAGTATCCCC
1 TGGAGTATCCCCGATTATG-GAAATCAG-TGTTTTAGAAATAAAACTGGGGTTAGAGTATCCCC
4709190 AAGATGAAAA
Statistics
Matches: 236, Mismatches: 51, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
77 2 0.01
78 64 0.27
79 157 0.67
80 13 0.06
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (78 bp):
TGGAGTATCCCCGATTATGGAAATCAGTGTTTTAGAAATAAAACTGGGGTTAGAGTATCCCCTCA
AAAATAACGAGGT
Found at i:4709216 original size:50 final size:50
Alignment explanation
Indices: 4709129--4709252 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
4709119 AACGGGATTG
** ** * * * *
4709129 GAGTATCCCCTATTATGAAAAATTGATGTTTTGGAAATAAAACTGGGGTTA
1 GAGTATCCCC-AAGATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTA
* *
4709180 GAGTATCCCCAAGATGAAAAATCAATATTTTAGAAATAAAGCCGAGGTTC
1 GAGTATCCCCAAGATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTA
**
4709230 GAGTATCTACAAGATGAAAAATC
1 GAGTATCCCCAAGATGAAAAATC
4709253 TGAAAATTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
50 51 0.84
51 10 0.16
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (50 bp):
GAGTATCCCCAAGATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTA
Found at i:4712736 original size:17 final size:17
Alignment explanation
Indices: 4712714--4712812 Score: 61
Period size: 17 Copynumber: 6.2 Consensus size: 17
4712704 CCCTTGTAAA
*
4712714 AAAACAACAAAAATAAG
1 AAAACAAAAAAAATAAG
4712731 AAAACAAAAAAAAT-A-
1 AAAACAAAAAAAATAAG
*
4712746 AAAGCAAAAAAAA-AAG
1 AAAACAAAAAAAATAAG
*
4712762 ----CAAAAAAAAGTAAA
1 AAAACAAAAAAAA-TAAG
* *
4712776 AAAATAAAAATAA-AAG
1 AAAACAAAAAAAATAAG
* *
4712792 AAACCAAAAAAGATAATG
1 AAAACAAAAAAAATAA-G
4712810 AAA
1 AAA
4712813 TGAAAATGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
12 9 0.15
14 2 0.03
15 13 0.21
16 12 0.19
17 15 0.24
18 11 0.18
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAACAAAAAAAATAAG
Found at i:4712738 original size:14 final size:12
Alignment explanation
Indices: 4712711--4712770 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 12
4712701 CATCCCTTGT
*
4712711 AAAAAAACAACA
1 AAAAAAAAAACA
4712723 AAAATAAGAAAACAA
1 AAAA-AA-AAAAC-A
4712738 AAAAAATAAAAGCA
1 AAAAAA-AAAA-CA
*
4712752 AAAAAAAAAGCA
1 AAAAAAAAAACA
4712764 AAAAAAA
1 AAAAAAA
4712771 GTAAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 13 0.32
13 5 0.12
14 17 0.41
15 6 0.15
ACGTcount: A:0.83, C:0.08, G:0.05, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:4712754 original size:28 final size:28
Alignment explanation
Indices: 4712721--4712776 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
4712711 AAAAAAACAA
*
4712721 CAAAAATAAGAAAACAAAAAAAA-TAAAAG
1 CAAAAA-AA-AAAGCAAAAAAAAGTAAAAG
4712750 CAAAAAAAAAAGCAAAAAAAAGTAAAA
1 CAAAAAAAAAAGCAAAAAAAAGTAAAA
4712777 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 7 0.28
29 6 0.24
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.05
Consensus pattern (28 bp):
CAAAAAAAAAAGCAAAAAAAAGTAAAAG
Found at i:4712759 original size:42 final size:42
Alignment explanation
Indices: 4712711--4712791 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
4712701 CATCCCTTGT
* *
4712711 AAAAAAACAACAAAAATAAG-AAAACAAA-AAAAATAAAAGCA
1 AAAAAAAAAACAAAAAAAAGTAAAA-AAATAAAAATAAAAGCA
*
4712752 AAAAAAAAAGCAAAAAAAAGTAAAAAAATAAAAATAAAAG
1 AAAAAAAAAACAAAAAAAAGTAAAAAAATAAAAATAAAAG
4712792 AAACCAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (42 bp):
AAAAAAAAAACAAAAAAAAGTAAAAAAATAAAAATAAAAGCA
Found at i:4712760 original size:12 final size:12
Alignment explanation
Indices: 4712738--4712770 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
4712728 AAGAAAACAA
4712738 AAAAAATAAAAGC
1 AAAAAA-AAAAGC
4712751 AAAAAAAAAAGC
1 AAAAAAAAAAGC
4712763 AAAAAAAA
1 AAAAAAAA
4712771 GTAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:4712784 original size:14 final size:13
Alignment explanation
Indices: 4712731--4712790 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 13
4712721 CAAAAATAAG
4712731 AAAACAAAAAAAAT
1 AAAA-AAAAAAAAT
4712745 AAAAGCAAAAAAAA-
1 AAAA--AAAAAAAAT
* *
4712759 AAGCAAAAAAAAGT
1 AA-AAAAAAAAAAT
4712773 AAAAAAATAAAAAT
1 AAAAAAA-AAAAAT
4712787 AAAA
1 AAAA
4712791 GAAACCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.29
14 17 0.45
15 10 0.26
ACGTcount: A:0.83, C:0.05, G:0.05, T:0.07
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:4712803 original size:42 final size:41
Alignment explanation
Indices: 4712711--4712791 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
4712701 CATCCCTTGT
* *
4712711 AAAAAAACAA-CAAAAATAAGAAAACAAAAAAAATAAAAGC
1 AAAAAAAAAAGCAAAAAAAAGAAAACAAAAAAAATAAAAGC
4712751 AAAAAAAAAAGCAAAAAAAAGTAAAA-AAATAAAAATAAAAG
1 AAAAAAAAAAGCAAAAAAAAG-AAAACAAA-AAAAATAAAAG
4712792 AAACCAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 9 0.25
41 12 0.33
42 15 0.42
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (41 bp):
AAAAAAAAAAGCAAAAAAAAGAAAACAAAAAAAATAAAAGC
Found at i:4713815 original size:14 final size:14
Alignment explanation
Indices: 4713796--4713833 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
4713786 AGACTTCACA
4713796 TCATGCATTCCACG
1 TCATGCATTCCACG
*
4713810 TCATGCATTCCATG
1 TCATGCATTCCACG
4713824 TCATGCATTC
1 TCATGCATTC
4713834 ACCTTACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (14 bp):
TCATGCATTCCACG
Found at i:4714336 original size:30 final size:30
Alignment explanation
Indices: 4714302--4714462 Score: 86
Period size: 30 Copynumber: 5.4 Consensus size: 30
4714292 CAACCCTCTC
4714302 AAAGTCCACAACTTCGTAGCATCTCTTTTT
1 AAAGTCCACAACTTCGTAGCATCTCTTTTT
* * * *
4714332 AAAGTCTACCAC-TCTGTAGTATGTCTTTTT
1 AAAGTCCACAACTTC-GTAGCATCTCTTTTT
* *
4714362 AAAG-CTCATGCAAGTCCGTAGCATCT-TTTTT
1 AAAGTC-CA--CAACTTCGTAGCATCTCTTTTT
* *
4714393 AAAGCTCACACAAGTT-GATGGCATC-CTTTTT
1 AAAG-TC-CACAACTTCG-TAGCATCTCTTTTT
* * * *
4714424 CAAAGCCCACAA-ATAGTGGCA-CTC-TTTT
1 -AAAGTCCACAACTTCGTAGCATCTCTTTTT
4714452 AAAGTCCACAA
1 AAAGTCCACAA
4714463 GTCGGTGGCA
Statistics
Matches: 103, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
27 10 0.10
28 5 0.05
29 10 0.10
30 35 0.34
31 26 0.25
32 13 0.13
33 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (30 bp):
AAAGTCCACAACTTCGTAGCATCTCTTTTT
Found at i:4714471 original size:28 final size:27
Alignment explanation
Indices: 4714389--4714529 Score: 113
Period size: 28 Copynumber: 4.9 Consensus size: 27
4714379 GTAGCATCTT
* *
4714389 TTTTAAAGCTCACACAAGTTGATGGCATCC
1 TTTTAAAGC-C-CACAAGTCGGTGGCA-CC
* *
4714419 TTTTTCAAAGCCCACAAAT-AGTGGCACTC
1 -TTTT-AAAGCCCACAAGTCGGTGGCAC-C
*
4714448 TTTTAAAGTCCACAAGTCGGTGGCAACC
1 TTTTAAAGCCCACAAGTCGGTGGC-ACC
* *
4714476 TTTTCAAAGCCCATAAGTCAGTGGCACCC
1 TTTT-AAAGCCCACAAGTCGGTGGCA-CC
* *
4714505 TTGTAAAGCCCACAAGTCGATGGCA
1 TTTTAAAGCCCACAAGTCGGTGGCA
4714530 GCCCTCTCAA
Statistics
Matches: 91, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
27 11 0.12
28 34 0.37
29 30 0.33
30 6 0.07
31 5 0.05
32 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (27 bp):
TTTTAAAGCCCACAAGTCGGTGGCACC
Found at i:4714472 original size:57 final size:57
Alignment explanation
Indices: 4714389--4714529 Score: 176
Period size: 57 Copynumber: 2.4 Consensus size: 57
4714379 GTAGCATCTT
* * *
4714389 TTTTAAAGCTCACACAAGTTGATGGCATCCTTTTTCAAAGCCCACAAAT-AGTGGCACTC
1 TTTTAAAG-TC-CACAAGTCGATGGCAACC-TTTTCAAAGCCCACAAATCAGTGGCACCC
* * *
4714448 TTTTAAAGTCCACAAGTCGGTGGCAACCTTTTCAAAGCCCATAAGTCAGTGGCACCC
1 TTTTAAAGTCCACAAGTCGATGGCAACCTTTTCAAAGCCCACAAATCAGTGGCACCC
* *
4714505 TTGTAAAGCCCACAAGTCGATGGCA
1 TTTTAAAGTCCACAAGTCGATGGCA
4714530 GCCCTCTCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
56 16 0.22
57 46 0.64
58 2 0.03
59 8 0.11
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (57 bp):
TTTTAAAGTCCACAAGTCGATGGCAACCTTTTCAAAGCCCACAAATCAGTGGCACCC
Found at i:4714494 original size:29 final size:28
Alignment explanation
Indices: 4714389--4714522 Score: 112
Period size: 29 Copynumber: 4.6 Consensus size: 28
4714379 GTAGCATCTT
* *
4714389 TTTTAAAGCTCACACAAGT-TGATGGCATCC
1 TTTTAAAGC-C-CACAAGTCAG-TGGCAACC
*
4714419 TTTTTCAAAGCCCACAAAT-AGTGGC-ACTC
1 -TTTT-AAAGCCCACAAGTCAGTGGCAAC-C
* *
4714448 TTTTAAAGTCCACAAGTCGGTGGCAACC
1 TTTTAAAGCCCACAAGTCAGTGGCAACC
* *
4714476 TTTTCAAAGCCCATAAGTCAGTGGCACCC
1 TTTT-AAAGCCCACAAGTCAGTGGCAACC
*
4714505 TTGTAAAGCCCACAAGTC
1 TTTTAAAGCCCACAAGTC
4714523 GATGGCAGCC
Statistics
Matches: 86, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
27 11 0.13
28 28 0.33
29 30 0.35
30 7 0.08
31 5 0.06
32 5 0.06
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (28 bp):
TTTTAAAGCCCACAAGTCAGTGGCAACC
Found at i:4714764 original size:52 final size:52
Alignment explanation
Indices: 4714684--4714931 Score: 221
Period size: 52 Copynumber: 4.8 Consensus size: 52
4714674 AAATCGTCTC
* * *
4714684 TCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCATATTGGCATTTCTATCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTCTATCA
* * * * *
4714736 TTTTTAAGCCCAATGTCGTTGGCCTTGAATTAGCACATTGGCA-CCCTTATCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTC-TATCA
* * * * * * * *
4714788 TCTTTAAATCCAATGTTGCTGGCTTTGAATTAACACATTGACACCTCTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTCTATCA
* * * * * *
4714840 TCTTTAAGTCCAATATTGTTGGCCTTGAATCATCATATTGGCAT-TCTTCTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTC-TATCA
* * * * *
4714892 TCTTCAAGTACAATGTCGCTAGCCTTAAATCAGCTCATTG
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
4714932 ACACTCTTCT
Statistics
Matches: 155, Mismatches: 38, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
51 3 0.02
52 150 0.97
53 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (52 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTCTATCA
Found at i:4714945 original size:104 final size:104
Alignment explanation
Indices: 4714680--4714945 Score: 263
Period size: 104 Copynumber: 2.6 Consensus size: 104
4714670 CATTAAATCG
* *
4714680 TCTC-TCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCAT-ATTGGCA-T-TTCTATCATTTTT
1 TCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGC-TCATTGACACTCTTC--TCATCTTT
* *
4714741 AAGCCCAATGTCGTTGGCCTTGAATTAGCACATTGGCACCCT
63 AAGCCCAATATCGTTGGCCTTGAATCAGCACATTGGCACCCT
* * * * * * * * *
4714783 TATCATCTTTAAATCCAATGTTGCTGGCTTTGAATTAACACATTGACAC-CTCTGTCATCTTTAA
1 TCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCTCATTGACACTCT-TCTCATCTTTAA
* * * * **
4714847 GTCCAATATTGTTGGCCTTGAATCATCATATTGGCATTCT
65 GCCCAATATCGTTGGCCTTGAATCAGCACATTGGCACCCT
* * *
4714887 TCTCATCTTCAAGTACAATGTCGCTAGCCTTAAATCAGCTCATTGACACTCTTCTCATC
1 TCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCTCATTGACACTCTTCTCATC
4714946 CTTATCATTT
Statistics
Matches: 126, Mismatches: 31, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
103 3 0.02
104 119 0.94
105 3 0.02
106 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (104 bp):
TCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCTCATTGACACTCTTCTCATCTTTAAG
CCCAATATCGTTGGCCTTGAATCAGCACATTGGCACCCT
Found at i:4715569 original size:20 final size:20
Alignment explanation
Indices: 4715538--4715653 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
4715528 ACAAATAGTA
*
4715538 AATGTTTCGATACATAAGTG
1 AATGTATCGATACATAAGTG
*
4715558 AATATATCGATACATAAGTG
1 AATGTATCGATACATAAGTG
* * ***
4715578 AATGTGTTGATACATGCCTG
1 AATGTATCGATACATAAGTG
4715598 AAATGTATCGATACATAAGTG
1 -AATGTATCGATACATAAGTG
* ***
4715619 AATGTATTGATACATGCCTG
1 AATGTATCGATACATAAGTG
4715639 AAATGTATCGATACA
1 -AATGTATCGATACA
4715654 AAACTGCTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
20 48 0.63
21 28 0.37
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATAAGTG
Found at i:4715607 original size:41 final size:41
Alignment explanation
Indices: 4715562--4715653 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
4715552 TAAGTGAATA
*
4715562 TATCGATACATAAGTGAATGTGTTGATACATGCCTGAAATG
1 TATCGATACATAAGTGAATGTATTGATACATGCCTGAAATG
4715603 TATCGATACATAAGTGAATGTATTGATACATGCCTGAAATG
1 TATCGATACATAAGTGAATGTATTGATACATGCCTGAAATG
4715644 TATCGATACA
1 TATCGATACA
4715654 AAACTGCTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (41 bp):
TATCGATACATAAGTGAATGTATTGATACATGCCTGAAATG
Found at i:4715610 original size:21 final size:21
Alignment explanation
Indices: 4715586--4715653 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
4715576 TGAATGTGTT
4715586 GATACATGCCTGAAATGTATC
1 GATACATGCCTGAAATGTATC
*** *
4715607 GATACATAAGTG-AATGTATT
1 GATACATGCCTGAAATGTATC
4715627 GATACATGCCTGAAATGTATC
1 GATACATGCCTGAAATGTATC
4715648 GATACA
1 GATACA
4715654 AAACTGCTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (21 bp):
GATACATGCCTGAAATGTATC
Found at i:4715962 original size:36 final size:36
Alignment explanation
Indices: 4715906--4715977 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
4715896 ATTAGAATTC
* * *
4715906 ATGTTAAGGTCAATTGTCAAACTTCATAATTAAGCT
1 ATGTCAAGGTCAATTATCAAACTTCATAATCAAGCT
4715942 ATGTCAAGGTCAATTATCAAACTTCATAATCAAGCT
1 ATGTCAAGGTCAATTATCAAACTTCATAATCAAGCT
4715978 TTAATCACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (36 bp):
ATGTCAAGGTCAATTATCAAACTTCATAATCAAGCT
Found at i:4721538 original size:20 final size:19
Alignment explanation
Indices: 4721513--4721574 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
4721503 TAAAATACAA
4721513 AAAATAATAACTTAGATAAC
1 AAAATAATAACTTAGAT-AC
4721533 AAAATAATAA-TTCCAAGATAC
1 AAAATAATAACTT---AGATAC
4721554 AAAA-AATAACTTAGATAC
1 AAAATAATAACTTAGATAC
4721572 AAA
1 AAA
4721575 GAATTAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 9 0.24
19 2 0.05
20 15 0.39
21 8 0.21
22 4 0.11
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAATAATAACTTAGATAC
Found at i:4721655 original size:25 final size:25
Alignment explanation
Indices: 4721625--4721673 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4721615 TTTAAACTAT
*
4721625 TAGTAACATAAAGTATATAGTAATA
1 TAGTAACATAAAATATATAGTAATA
**
4721650 TAGTAATGTAAAATATATAGTAAT
1 TAGTAACATAAAATATATAGTAAT
4721674 TTTATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (25 bp):
TAGTAACATAAAATATATAGTAATA
Found at i:4721820 original size:26 final size:27
Alignment explanation
Indices: 4721765--4721828 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
4721755 TATGATATGG
* *
4721765 TATAATATAATTACTTTATATGGTAGAT
1 TATAATAT-ATTACTTTATATGATAAAT
4721793 TATAATATATTA-TTTATAT-ATAAAAT
1 TATAATATATTACTTTATATGAT-AAAT
4721819 TATAA-ATATT
1 TATAATATATT
4721829 TATACATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 15 0.45
27 4 0.12
28 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
TATAATATATTACTTTATATGATAAAT
Found at i:4721828 original size:22 final size:19
Alignment explanation
Indices: 4721803--4721853 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
4721793 TATAATATAT
4721803 TATTTATATATAAAATTATAAA
1 TATTTATATAT-AAA-TA-AAA
*
4721825 TATTTATACATAAATAAAA
1 TATTTATATATAAATAAAA
4721844 TATTTATATA
1 TATTTATATA
4721854 ACTATTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 12 0.44
20 2 0.07
21 3 0.11
22 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTATATATAAATAAAA
Found at i:4724401 original size:20 final size:20
Alignment explanation
Indices: 4724376--4724428 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
4724366 AAACCCTTGA
4724376 ATGTATCGATACACACCCAG
1 ATGTATCGATACACACCCAG
4724396 ATGTATCGATACACACCCAG
1 ATGTATCGATACACACCCAG
4724416 ATGTATCGATACA
1 ATGTATCGATACA
4724429 TTATGCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (20 bp):
ATGTATCGATACACACCCAG
Found at i:4724479 original size:20 final size:19
Alignment explanation
Indices: 4724439--4724487 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
4724429 TTATGCTTTT
**
4724439 TATCGATACATGTTCATTG
1 TATCGATACATGGACATTG
4724458 TATCGATACATGGACAATTG
1 TATCGATACATGGAC-ATTG
4724478 TATCGATACA
1 TATCGATACA
4724488 AGAGATTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
TATCGATACATGGACATTG
Found at i:4730462 original size:12 final size:12
Alignment explanation
Indices: 4730447--4730478 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4730437 AATGTCAAAA
*
4730447 TTGGCGGCACAG
1 TTGGCAGCACAG
4730459 TTGGCAGCACAG
1 TTGGCAGCACAG
4730471 TTGGCAGC
1 TTGGCAGC
4730479 CTTTGTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:4735208 original size:12 final size:12
Alignment explanation
Indices: 4735193--4735224 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4735183 AATGTCAAAA
*
4735193 TTGGCGGCACAG
1 TTGGCAGCACAG
4735205 TTGGCAGCACAG
1 TTGGCAGCACAG
4735217 TTGGCAGC
1 TTGGCAGC
4735225 CTTTGTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:4735737 original size:27 final size:25
Alignment explanation
Indices: 4735695--4735770 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 25
4735685 CTTGATCTTA
4735695 ATTATTATTTAATAATTA-AAAAAT
1 ATTATTATTTAATAATTATAAAAAT
*
4735719 ATTATTATTTAAACTTAATTATGAAAAT
1 ATTATTATTT-AA--TAATTATAAAAAT
* *
4735747 A-TATTA-ATATTAATTATAAAAAT
1 ATTATTATTTAATAATTATAAAAAT
4735770 A
1 A
4735771 AAAATTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 13 0.30
24 10 0.23
25 3 0.07
26 1 0.02
27 11 0.25
28 6 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
ATTATTATTTAATAATTATAAAAAT
Found at i:4744392 original size:21 final size:21
Alignment explanation
Indices: 4744362--4744441 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
4744352 GATTACACTG
*
4744362 CCCTACTCGACATAAGATTGA
1 CCCTAGTCGACATAAGATTGA
* *
4744383 CCCTAGTCGACATAAAATTAA
1 CCCTAGTCGACATAAGATTGA
* *
4744404 CCTTGGTC-ATCATAAGATTGA
1 CCCTAGTCGA-CATAAGATTGA
*
4744425 CCCTGGTCGACATAAGA
1 CCCTAGTCGACATAAGA
4744442 CTAGCCTTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (21 bp):
CCCTAGTCGACATAAGATTGA
Found at i:4744434 original size:42 final size:42
Alignment explanation
Indices: 4744372--4744454 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
4744362 CCCTACTCGA
*
4744372 CATAAGATTGACCCTAGTCGACATAAAATTAACCTTGGTCAT
1 CATAAGATTGACCCTAGTCGACATAAAACTAACCTTGGTCAT
* * *
4744414 CATAAGATTGACCCTGGTCGACATAAGACTAGCCTTGGTCA
1 CATAAGATTGACCCTAGTCGACATAAAACTAACCTTGGTCA
4744455 CTTTATAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
CATAAGATTGACCCTAGTCGACATAAAACTAACCTTGGTCAT
Found at i:4744452 original size:21 final size:20
Alignment explanation
Indices: 4744368--4744453 Score: 57
Period size: 21 Copynumber: 4.1 Consensus size: 20
4744358 ACTGCCCTAC
* * *
4744368 TCGACATAAGATTGACCCTAG
1 TCGACATAAGATAG-CCTTGG
* *
4744389 TCGACATAAAATTAACCTTGG
1 TCGACATAAGA-TAGCCTTGG
* *
4744410 TC-ATCATAAGATTGACCCTGG
1 TCGA-CATAAGATAG-CCTTGG
4744431 TCGACATAAGACTAGCCTTGG
1 TCGACATAAGA-TAGCCTTGG
4744452 TC
1 TC
4744454 ACTTTATAAC
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
20 2 0.04
21 43 0.88
22 4 0.08
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGACATAAGATAGCCTTGG
Found at i:4748991 original size:13 final size:13
Alignment explanation
Indices: 4748973--4748998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4748963 TGTCATATTA
4748973 ATATTATTTTTTT
1 ATATTATTTTTTT
4748986 ATATTATTTTTTT
1 ATATTATTTTTTT
4748999 CACATCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATATTATTTTTTT
Found at i:4749477 original size:28 final size:29
Alignment explanation
Indices: 4749423--4749493 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
4749413 AAATAGATTT
*
4749423 AATAATTTTAAATATGATAAAGATATAAAA
1 AATAA-TTAAAATATGATAAAGATATAAAA
* *
4749453 AATAATTAAAATATGAT-ACGTTATAAAA
1 AATAATTAAAATATGATAAAGATATAAAA
4749481 AATACA-TAAAATA
1 AATA-ATTAAAATA
4749494 ATATGAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 20 0.54
29 12 0.32
30 5 0.14
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (29 bp):
AATAATTAAAATATGATAAAGATATAAAA
Found at i:4749909 original size:29 final size:28
Alignment explanation
Indices: 4749854--4749966 Score: 100
Period size: 29 Copynumber: 4.2 Consensus size: 28
4749844 ATATATTATG
*
4749854 AAATATATATTAT-A---TAAAAATAA-
1 AAATATATATTATAATTTTAAAATTAAT
*
4749877 AAATATGATATTATAATTTTAACATTAAT
1 AAATAT-ATATTATAATTTTAAAATTAAT
4749906 AAATATATTATTAT-ATTTTAAAATTTAAT
1 AAATATA-TATTATAATTTTAAAA-TTAAT
*
4749935 AAA-A-ATATTA-AATTATTAAAATTAAA
1 AAATATATATTATAATT-TTAAAATTAAT
4749961 AAATAT
1 AAATAT
4749967 TTTAAAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
23 6 0.08
24 7 0.09
25 1 0.01
26 15 0.20
27 8 0.11
28 17 0.23
29 20 0.27
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
AAATATATATTATAATTTTAAAATTAAT
Found at i:4750001 original size:30 final size:30
Alignment explanation
Indices: 4749967--4750038 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
4749957 TAAAAAATAT
*
4749967 TTTAAAAAAATTTAAAAATATAATTATAAA
1 TTTAAATAAATTTAAAAATATAATTATAAA
* ** *
4749997 TTTAAATAAATTTATACTTATATTTATAAA
1 TTTAAATAAATTTAAAAATATAATTATAAA
*
4750027 TATAAATAAATT
1 TTTAAATAAATT
4750039 AAATAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAATAAATTTAAAAATATAATTATAAA
Found at i:4750163 original size:401 final size:396
Alignment explanation
Indices: 4749697--4750546 Score: 1425
Period size: 401 Copynumber: 2.1 Consensus size: 396
4749687 GATTTGAACA
4749697 AAAATAATAATTTTAAAAAATGAGTTTAGGTAAAAAATAAGATTTGATTATGAAATAGACTAATC
1 AAAATAATAATTTTAAAAAATGAGTTTAGGTAAAAAATAAGATTTGATTATGAAATAGACTAATC
4749762 TTTGACTTCAATATTTAAAGCTTAAGTTCAACCGGACCTAATTTATTTTTTTAATTAAATAATAT
66 TTTGACTTCAATATTTAAAGCTTAAGTTCAACCGGACCTAATTTATTTTTTTAATTAAATAATAT
4749827 TTATTATTTTTATATTTATATATTATGAAATATATATTATATAAAAATAAAAATATGATATTATA
131 TTATTA-TTTTATATTTATATATTATG-AATATATATTATAT-AAAATAAAAATATGATATTATA
4749892 ATTTTAACATTAATAAATATATTATTATATTTTAAAATTTAATAAAAATATTAA-ATTATT-AAA
193 A-TTTAACATTAATAAATATA-TATTATATTTTAAAATTT-ATAAAAATATTAAGATT-TTAAAA
*
4749955 ATTAAAAAATATTTTAAAAAAATTTAAAAATATAAT-TATAAATTTAAATAAATTTATACT-TAT
254 ATTAAAAAATATTTTAAAAAAATTTAAAAATATAATAAATAAA-TTAAATAAATTTATACTATAT
4750018 ATTTATAAATATAAATAAA-TTAAATAAAATTT-CAAAACTAATATTTTTTAAATTAA-TTT-AA
318 ATTTATAAATATAAATAAATTTAAATAAAATTTACAAAACT-A-A--TTTTAAATTAATTTTAAA
4750079 TATAT-T-ATATTATTTTT
379 TATATATAATA-TATTTTT
*
4750096 AAAATAATTATTTTAAAAAATGAGTTTAGGTAAACAAAATAAGATTTGATTATGAAATAGACTAA
1 AAAATAATAATTTTAAAAAATGAGTTTAGGT-AA-AAAATAAGATTTGATTATGAAATAGACTAA
*
4750161 TCTTTGACTTTAATATTTAAAGCTTAAGTTCAACCGGACCTAATTTATTTTTTTAATTAAATAAT
64 TCTTTGACTTCAATATTTAAAGCTTAAGTTCAACCGGACCTAATTTATTTTTTTAATTAAATAAT
4750226 ATTTATTATTTTATATTTATATATTATGAATATATATTATATAAAATAAAAATATGATATTATAA
129 ATTTATTATTTTATATTTATATATTATGAATATATATTATATAAAATAAAAATATGATATTATAA
4750291 TTTAACATTAATAAATATATATTATATTTTAAAATTTATAAAAATATTAAGTATTTTAAAAATTA
194 TTTAACATTAATAAATATATATTATATTTTAAAATTTATAAAAATATTAAG-ATTTTAAAAATTA
*
4750356 AAAAATATTTTTAAAAAATTTAAAAATATAATAAAATAAATTAAATAAATTTATACTATATATTT
258 AAAAATATTTTAAAAAAATTTAAAAATATAAT-AAATAAATTAAATAAATTTATACTATATATTT
4750421 ATAAATATAAATAAATTTAAATAAAATTTACAAAACTAATTTTAAATTAATTTTAAATATATATA
322 ATAAATATAAATAAATTTAAATAAAATTTACAAAACTAATTTTAAATTAATTTTAAATATATATA
4750486 ATATATTTTT
387 ATATATTTTT
*
4750496 AAAATAATAATTTT-AAAAATGAGTTTAAGTAAAAAATAAGATTTGATTATG
1 AAAATAATAATTTTAAAAAATGAGTTTAGGTAAAAAATAAGATTTGATTATG
4750547 TAACATTAAT
Statistics
Matches: 431, Mismatches: 6, Indels: 30
0.92 0.01 0.06
Matches are distributed among these distances:
395 13 0.03
396 20 0.05
397 90 0.21
398 45 0.10
399 94 0.22
400 57 0.13
401 112 0.26
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (396 bp):
AAAATAATAATTTTAAAAAATGAGTTTAGGTAAAAAATAAGATTTGATTATGAAATAGACTAATC
TTTGACTTCAATATTTAAAGCTTAAGTTCAACCGGACCTAATTTATTTTTTTAATTAAATAATAT
TTATTATTTTATATTTATATATTATGAATATATATTATATAAAATAAAAATATGATATTATAATT
TAACATTAATAAATATATATTATATTTTAAAATTTATAAAAATATTAAGATTTTAAAAATTAAAA
AATATTTTAAAAAAATTTAAAAATATAATAAATAAATTAAATAAATTTATACTATATATTTATAA
ATATAAATAAATTTAAATAAAATTTACAAAACTAATTTTAAATTAATTTTAAATATATATAATAT
ATTTTT
Found at i:4750321 original size:27 final size:27
Alignment explanation
Indices: 4750254--4750363 Score: 99
Period size: 27 Copynumber: 4.2 Consensus size: 27
4750244 ATATATTATG
4750254 AATATATATTATA---TAAAA-TAA-A
1 AATATATATTATATTTTAAAATTAATA
* *
4750276 AATATGATATTATAATTTAACATTAATA
1 AATAT-ATATTATATTTTAAAATTAATA
*
4750304 AATATATATTATATTTTAAAATTTATA
1 AATATATATTATATTTTAAAATTAATA
*
4750331 AA-A-ATATTAAGTATTTTAAAAATTAAAA
1 AATATATATT-A-TATTTT-AAAATTAATA
4750359 AATAT
1 AATAT
4750364 TTTTAAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
22 5 0.07
23 8 0.11
25 5 0.07
26 6 0.08
27 30 0.42
28 16 0.23
29 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (27 bp):
AATATATATTATATTTTAAAATTAATA
Found at i:4750367 original size:20 final size:21
Alignment explanation
Indices: 4750344--4750384 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4750334 ATATTAAGTA
4750344 TTTT-AAAAATTAAAAAATAT
1 TTTTAAAAAATTAAAAAATAT
*
4750364 TTTTAAAAAATTTAAAAATAT
1 TTTTAAAAAATTAAAAAATAT
4750385 AATAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAAAATTAAAAAATAT
Found at i:4750467 original size:41 final size:39
Alignment explanation
Indices: 4750385--4750467 Score: 89
Period size: 42 Copynumber: 2.1 Consensus size: 39
4750375 TTAAAAATAT
* **
4750385 AATAAAATAAATTAAATAAATTTATACTATATATTTATA
1 AATAAAATAAATTAAATAAATTTACAAAATATATTTATA
4750424 AATATAAATAAATTTAAATAAAATTTACAAAACTA-ATTT-TA
1 AATA-AAATAAA-TTAAAT-AAATTTACAAAA-TATATTTATA
4750465 AAT
1 AAT
4750468 TAATTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
39 4 0.11
40 7 0.19
41 11 0.30
42 13 0.35
43 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (39 bp):
AATAAAATAAATTAAATAAATTTACAAAATATATTTATA
Found at i:4750514 original size:15 final size:16
Alignment explanation
Indices: 4750483--4750515 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4750473 TTAAATATAT
*
4750483 ATAATATATTTTTAAA
1 ATAATATATTTTAAAA
4750499 ATAATA-ATTTTAAAA
1 ATAATATATTTTAAAA
4750514 AT
1 AT
4750516 GAGTTTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATATATTTTAAAA
Found at i:4750646 original size:24 final size:23
Alignment explanation
Indices: 4750600--4750654 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
4750590 ATTAAATATT
* *
4750600 AAAAA-TTAAAAAATATTTTTAA
1 AAAAATTTAAAAAATATATATAA
4750622 AAAAATTTAAAAAATATAATATAA
1 AAAAATTTAAAAAATAT-ATATAA
*
4750646 ATAAATTTA
1 AAAAATTTA
4750655 TACTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 5 0.18
23 11 0.39
24 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAAATTTAAAAAATATATATAA
Found at i:4750713 original size:41 final size:42
Alignment explanation
Indices: 4750633--4750713 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
4750623 AAAATTTAAA
*
4750633 AAATATAATATAAATAAATTTATACTATATATTTATAAATAT
1 AAATATAATATAAATAAATTTAAACTATATATTTATAAATAT
*
4750675 AAATA-AATTTAAATAAAATTTAAAACTA-ATATTT-TAAAT
1 AAATATAATATAAAT-AAATTT-AAACTATATATTTATAAAT
4750714 TAATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 13 0.37
42 17 0.49
43 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (42 bp):
AAATATAATATAAATAAATTTAAACTATATATTTATAAATAT
Found at i:4751535 original size:17 final size:17
Alignment explanation
Indices: 4751513--4751549 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4751503 TTTAAAATAT
*
4751513 TATTTAATAAATTTAAA
1 TATTTAACAAATTTAAA
4751530 TATTTAACAAATTTAAA
1 TATTTAACAAATTTAAA
4751547 TAT
1 TAT
4751550 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAACAAATTTAAA
Found at i:4752884 original size:13 final size:13
Alignment explanation
Indices: 4752866--4752892 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4752856 ACATGCTGCT
4752866 TTGTATCGATACA
1 TTGTATCGATACA
4752879 TTGTATCGATACA
1 TTGTATCGATACA
4752892 T
1 T
4752893 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4752889 original size:33 final size:32
Alignment explanation
Indices: 4752847--4752911 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
4752837 TACACCCGGA
*
4752847 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
4752880 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
4752912 GGACAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:4752923 original size:21 final size:19
Alignment explanation
Indices: 4752876--4752933 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
4752866 TTGTATCGAT
*
4752876 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
4752895 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
4752914 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
4752934 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:4752994 original size:13 final size:13
Alignment explanation
Indices: 4752976--4753007 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4752966 ATCGATACAT
4752976 GATACAATGTATC
1 GATACAATGTATC
4752989 GATACAATGTATC
1 GATACAATGTATC
*
4753002 AATACA
1 GATACA
4753008 TGAAGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (13 bp):
GATACAATGTATC
Found at i:4753007 original size:33 final size:33
Alignment explanation
Indices: 4752963--4753027 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
4752953 TATCACTATT
* *
4752963 TGTATCGATACATGATA-CAATGTATCGATACAA
1 TGTATCAATACATGA-AGAAATGTATCGATACAA
4752996 TGTATCAATACATGAAGAAATGTATCGATACA
1 TGTATCAATACATGAAGAAATGTATCGATACA
4753028 TAGCTTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCAATACATGAAGAAATGTATCGATACAA
Found at i:4759126 original size:13 final size:13
Alignment explanation
Indices: 4759108--4759135 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4759098 AAAACCTAGA
4759108 TGTATCGATACAT
1 TGTATCGATACAT
4759121 TGTATCGATACAT
1 TGTATCGATACAT
4759134 TG
1 TG
4759136 GGTACTATTT
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:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4761024 original size:16 final size:17
Alignment explanation
Indices: 4760997--4761043 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
4760987 GAGATAATCG
4760997 TTTAAGGGGGAGAA-TTT
1 TTTAA-GGGGAGAATTTT
4761014 TTTAAGGGGAGAATTTT
1 TTTAAGGGGAGAATTTT
*
4761031 TTTTAGGGGAGAA
1 TTTAAGGGGAGAA
4761044 AAATAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (17 bp):
TTTAAGGGGAGAATTTT
Found at i:4761598 original size:13 final size:13
Alignment explanation
Indices: 4761580--4761606 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4761570 ACATGCTGCT
4761580 TTGTATCGATACA
1 TTGTATCGATACA
4761593 TTGTATCGATACA
1 TTGTATCGATACA
4761606 T
1 T
4761607 GTTCGTTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4761603 original size:33 final size:32
Alignment explanation
Indices: 4761561--4761624 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
4761551 CACACCTAGA
*
4761561 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCGTTGTATCGATACAT
*
4761594 TGTATCGATACATGTTCGTTGTATCGATACA
1 TGTATCGATACATGTGCGTTGTATCGATACA
4761625 ATTCATGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATGTGCGTTGTATCGATACAT
Found at i:4761718 original size:13 final size:13
Alignment explanation
Indices: 4761697--4761726 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4761687 CAGTACATGG
4761697 TACAATGTATCGA
1 TACAATGTATCGA
*
4761710 TACAGTGTATCGA
1 TACAATGTATCGA
4761723 TACA
1 TACA
4761727 TGAAGAAATG
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:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:4763369 original size:14 final size:16
Alignment explanation
Indices: 4763339--4763371 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4763329 TATTTCAAAA
4763339 TATCTCTCCCCCTTTT
1 TATCTCTCCCCCTTTT
4763355 TATCTCT-CCCCTTTT
1 TATCTCTCCCCCTTTT
4763370 TA
1 TA
4763372 CAAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.09, C:0.39, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTCTCCCCCTTTT
Found at i:4765261 original size:13 final size:13
Alignment explanation
Indices: 4765243--4765299 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
4765233 ATAGTGCCCT
4765243 TGTATCGATACAA
1 TGTATCGATACAA
4765256 TGTATCGATACTAA
1 TGTATCGATAC-AA
4765270 -G-ATC-AT----
1 TGTATCGATACAA
4765276 TGTATCGATACAA
1 TGTATCGATACAA
4765289 TGTATCGATAC
1 TGTATCGATAC
4765300 TAAGATCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 2 0.06
11 2 0.06
12 3 0.08
13 23 0.64
14 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4765280 original size:33 final size:33
Alignment explanation
Indices: 4765242--4765320 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
4765232 AATAGTGCCC
4765242 TTGTATCGATACAATGTATCGATACTAAGATCA
1 TTGTATCGATACAATGTATCGATACTAAGATCA
4765275 TTGTATCGATACAATGTATCGATACTAAGATCA
1 TTGTATCGATACAATGTATCGATACTAAGATCA
*
4765308 TTGTATTGATACA
1 TTGTATCGATACA
4765321 TCTGGGTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACAATGTATCGATACTAAGATCA
Found at i:4765281 original size:20 final size:20
Alignment explanation
Indices: 4765256--4765319 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
4765246 ATCGATACAA
4765256 TGTATCGATACTAAGATCAT
1 TGTATCGATACTAAGATCAT
4765276 TGTATCGATAC----A--A-
1 TGTATCGATACTAAGATCAT
4765289 TGTATCGATACTAAGATCAT
1 TGTATCGATACTAAGATCAT
*
4765309 TGTATTGATAC
1 TGTATCGATAC
4765320 ATCTGGGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 21 0.58
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
TGTATCGATACTAAGATCAT
Found at i:4765485 original size:24 final size:24
Alignment explanation
Indices: 4765453--4765532 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 24
4765443 AACATAATTC
4765453 ATTTAAAAACATTAAAACAACACA
1 ATTTAAAAACATTAAAACAACACA
* *
4765477 ATTTGAAAACCAAATTTAAACATA-ATTC-
1 ATTT-AAAA--ACATTAAAACA-ACA--CA
*
4765505 ATTTAAAAACATTAAAATAACACA
1 ATTTAAAAACATTAAAACAACACA
4765529 ATTT
1 ATTT
4765533 GAACACCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
23 1 0.02
24 9 0.21
25 13 0.30
27 14 0.33
28 5 0.12
29 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (24 bp):
ATTTAAAAACATTAAAACAACACA
Found at i:4765495 original size:28 final size:28
Alignment explanation
Indices: 4765464--4765546 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
4765454 TTTAAAAACA
*
4765464 TTAAAACAACACAATTTGAAAACCAAAT
1 TTAAAATAACACAATTTGAAAACCAAAT
** *
4765492 TTAAACATAATTC-ATTT-AAAA--ACA-
1 TTAAA-ATAACACAATTTGAAAACCAAAT
*
4765516 TTAAAATAACACAATTTGAACACCAAAT
1 TTAAAATAACACAATTTGAAAACCAAAT
4765544 TTA
1 TTA
4765547 TCTACAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
23 5 0.12
24 9 0.22
25 5 0.12
27 6 0.15
28 12 0.29
29 4 0.10
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (28 bp):
TTAAAATAACACAATTTGAAAACCAAAT
Found at i:4765498 original size:52 final size:52
Alignment explanation
Indices: 4765442--4765546 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
4765432 TGAATTAATC
4765442 AAACATAATTCATTTAAAAACATTAAAACAACACAATTTGAAAACCAAATTT
1 AAACATAATTCATTTAAAAACATTAAAACAACACAATTTGAAAACCAAATTT
* *
4765494 AAACATAATTCATTTAAAAACATTAAAATAACACAATTTGAACACCAAATTT
1 AAACATAATTCATTTAAAAACATTAAAACAACACAATTTGAAAACCAAATTT
4765546 A
1 A
4765547 TCTACAATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (52 bp):
AAACATAATTCATTTAAAAACATTAAAACAACACAATTTGAAAACCAAATTT
Found at i:4769897 original size:3 final size:3
Alignment explanation
Indices: 4769889--4769923 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4769879 TGAGTCAACT
*
4769889 TCA TCA TCA TTA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
4769924 TTTGATGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:4772311 original size:16 final size:19
Alignment explanation
Indices: 4772283--4772327 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 19
4772273 ATTTAATTTT
*
4772283 TATATTAAAAATATA-AT-
1 TATATTTAAAATATACATA
4772300 TAT-TTTAAAATATACATA
1 TATATTTAAAATATACATA
4772318 TATATTTAAA
1 TATATTTAAA
4772328 TATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 5 0.21
18 3 0.12
19 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATTTAAAATATACATA
Done.