Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 26 of 91
Found at i:4590716 original size:18 final size:18
Alignment explanation
Indices: 4590685--4590741 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 18
4590675 TTAAAAGCTT
* *
4590685 AATTTTTTCTTTATTTAAA
1 AATTTTTT-ATTATATAAA
*
4590704 AATTTTTTATTATATATA
1 AATTTTTTATTATATAAA
4590722 AA-TTTTTATTATATAAA
1 AATTTTTTATTATATAAA
4590739 AAT
1 AAT
4590742 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 16 0.48
18 9 0.27
19 8 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTTTTATTATATAAA
Found at i:4592693 original size:20 final size:19
Alignment explanation
Indices: 4592651--4592693 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
4592641 GGGGAAAATT
*
4592651 AATATTTTCATAAGATTTT
1 AATATTTTCATAAGATTTG
4592670 AATATTTTCTATATA-ATTTG
1 AATATTTTC-ATA-AGATTTG
4592690 AATA
1 AATA
4592694 AAATTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 11 0.52
21 1 0.05
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
AATATTTTCATAAGATTTG
Found at i:4593090 original size:20 final size:21
Alignment explanation
Indices: 4593047--4593090 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
4593037 ATTTTTTAAA
*
4593047 TATAAATATTTAAAAATATCAT
1 TATAAATATATAAAAATA-CAT
*
4593069 TATATATATATAAAAATA-AT
1 TATAAATATATAAAAATACAT
4593089 TA
1 TA
4593091 AATAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAAATATATAAAAATACAT
Found at i:4594704 original size:2 final size:2
Alignment explanation
Indices: 4594697--4594728 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4594687 TCAGAATTCA
4594697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4594729 TGTTGGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4595185 original size:31 final size:31
Alignment explanation
Indices: 4595118--4595186 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
4595108 AGATTTTATA
*
4595118 CACTAAT--AATAAATTAGATGATATTATCT
1 CACTAATGAAATAAATTAGATGATATCATCT
* * * *
4595147 CATTAATGAAATAAATTAGATGGTGTCATTT
1 CACTAATGAAATAAATTAGATGATATCATCT
4595178 CACTAATGA
1 CACTAATGA
4595187 GTAAATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 6 0.19
31 26 0.81
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
CACTAATGAAATAAATTAGATGATATCATCT
Found at i:4597927 original size:30 final size:30
Alignment explanation
Indices: 4597891--4597962 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
4597881 TATATTTTCA
*
4597891 TTACATCCAAATAAACCTTTAAACTTTAAT
1 TTACATCCAAATAAACCGTTAAACTTTAAT
** * *
4597921 TTACATCCAAATAATTCGTTAAATTTTATT
1 TTACATCCAAATAAACCGTTAAACTTTAAT
*
4597951 TTATATCCAAAT
1 TTACATCCAAAT
4597963 GATTATTTAG
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:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (30 bp):
TTACATCCAAATAAACCGTTAAACTTTAAT
Found at i:4598095 original size:29 final size:28
Alignment explanation
Indices: 4598024--4598092 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
4598014 CTTTTGTTTG
**
4598024 AAATAAGGGTTTATTTAAATATAACAAA
1 AAATAAGATTTTATTTAAATATAACAAA
*
4598052 AAATAAGATTTTATTTAAATATAATAAA
1 AAATAAGATTTTATTTAAATATAACAAA
4598080 AATATAGAGATTT
1 AA-ATA-AGATTT
4598093 ATTCAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 27 0.75
29 3 0.08
30 6 0.17
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (28 bp):
AAATAAGATTTTATTTAAATATAACAAA
Found at i:4599457 original size:1 final size:1
Alignment explanation
Indices: 4599451--4599483 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
4599441 ATGGGAGCAG
4599451 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4599484 AAATTAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4599676 original size:24 final size:26
Alignment explanation
Indices: 4599631--4599678 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
4599621 AATTTAATTT
*
4599631 AAATATATATGTATATATATTAATAA
1 AAATATATATGTATATACATTAATAA
*
4599657 AAATAT-TATTTA-ATACATTAAT
1 AAATATATATGTATATACATTAAT
4599679 TTAAGATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 5 0.25
26 6 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AAATATATATGTATATACATTAATAA
Found at i:4599696 original size:42 final size:38
Alignment explanation
Indices: 4599650--4599749 Score: 103
Period size: 42 Copynumber: 2.5 Consensus size: 38
4599640 TGTATATATA
*
4599650 TTAATAAAAATATTATTTAATACATTAATTTAAGATGTTAAC
1 TTAATAAAAATATTATTT-ATACA-TAA-TTAAAATG-TAAC
*
4599692 TTAATAAAAA-ATTACATTTATACATAATTAAAATGTAAT
1 TTAATAAAAATATT--ATTTATACATAATTAAAATGTAAC
*
4599731 TTATATAAAAATAATATTT
1 TTA-ATAAAAATATTATTT
4599750 TATAAATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
39 10 0.20
40 14 0.27
41 8 0.16
42 15 0.29
43 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (38 bp):
TTAATAAAAATATTATTTATACATAATTAAAATGTAAC
Found at i:4599752 original size:40 final size:42
Alignment explanation
Indices: 4599650--4599753 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 42
4599640 TGTATATATA
* *
4599650 TTAATAAAAATATTATTTAATACATTAATTTAAGATGTTAAC
1 TTAATAAAAATATTATTTTATACATTAATTTAAAATGTTAAC
* *
4599692 TTAATAAAAA-ATTACATTTATACA-TAA-TTAAAATG-TAAT
1 TTAATAAAAATATTA-TTTTATACATTAATTTAAAATGTTAAC
*
4599731 TTATATAAAAATAATATTTTATA
1 TTA-ATAAAAATATTATTTTATA
4599754 AATATTATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
39 6 0.11
40 20 0.38
41 10 0.19
42 17 0.32
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (42 bp):
TTAATAAAAATATTATTTTATACATTAATTTAAAATGTTAAC
Found at i:4600654 original size:32 final size:33
Alignment explanation
Indices: 4600613--4600681 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
4600603 GGTCAGGCAA
4600613 ACTTATTTTTAAATATTT-TAAGGGTTTTGTTG
1 ACTTATTTTTAAATATTTCTAAGGGTTTTGTTG
* *
4600645 ACTTATTTTTAAATGTTTCTAAGGTTTTTGTTG
1 ACTTATTTTTAAATATTTCTAAGGGTTTTGTTG
4600678 ACTT
1 ACTT
4600682 GATCTTGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (33 bp):
ACTTATTTTTAAATATTTCTAAGGGTTTTGTTG
Found at i:4601840 original size:13 final size:13
Alignment explanation
Indices: 4601822--4601872 Score: 63
Period size: 12 Copynumber: 4.1 Consensus size: 13
4601812 CATTTAAAGT
4601822 TTATATATTTATA
1 TTATATATTTATA
4601835 TTATAT-TTTATA
1 TTATATATTTATA
*
4601847 TTA-AAATTATATA
1 TTATATATT-TATA
4601860 TTATA-ATTTATA
1 TTATATATTTATA
4601872 T
1 T
4601873 AAATATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
11 1 0.03
12 16 0.47
13 16 0.47
14 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:4601848 original size:18 final size:18
Alignment explanation
Indices: 4601825--4601872 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
4601815 TTAAAGTTTA
*
4601825 TATATTTATATTATATTT
1 TATATTTATATTATATAT
* *
4601843 TATATTAAAATTATATAT
1 TATATTTATATTATATAT
4601861 TATAATTTATAT
1 TAT-ATTTATAT
4601873 AAATATAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTATATTATATAT
Found at i:4602007 original size:13 final size:13
Alignment explanation
Indices: 4601989--4602018 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4601979 ATTTTATTTG
*
4601989 ATATGATATAATA
1 ATATGATATAAAA
4602002 ATATGATATAAAA
1 ATATGATATAAAA
4602015 ATAT
1 ATAT
4602019 AAATTAAAAT
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:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATATGATATAAAA
Found at i:4602094 original size:36 final size:35
Alignment explanation
Indices: 4602007--4602095 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
4601997 TAATAATATG
**
4602007 ATATA-AAAATATAAATTAAAATTTTAATATAAATA
1 ATATATAAAATATAAATT-TTATTTTAATATAAATA
* *
4602042 ATATATAAAATTTAAATTTTATTTTTATATAAA-A
1 ATATATAAAATATAAATTTTATTTTAATATAAATA
*
4602076 ATATAGTATAATAATAAATT
1 ATATA-TAAAAT-ATAAATT
4602096 ATTAATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 17 0.38
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
ATATATAAAATATAAATTTTATTTTAATATAAATA
Found at i:4611957 original size:3 final size:3
Alignment explanation
Indices: 4611949--4611979 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4611939 ATAATTTTTA
4611949 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4611980 TAAGATAATT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4613536 original size:3 final size:3
Alignment explanation
Indices: 4613528--4613554 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4613518 GAATCTAACC
4613528 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
4613555 TTGTAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4613766 original size:19 final size:20
Alignment explanation
Indices: 4613732--4613771 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4613722 AAAGTTCTTC
*
4613732 TTTTTAATTGCAAAATTATT
1 TTTTTAATTGCAAAATCATT
*
4613752 TTTTTAATT-CCAAATCATT
1 TTTTTAATTGCAAAATCATT
4613771 T
1 T
4613772 GATTATTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTAATTGCAAAATCATT
Found at i:4617699 original size:101 final size:100
Alignment explanation
Indices: 4617539--4617814 Score: 376
Period size: 101 Copynumber: 2.8 Consensus size: 100
4617529 GAGAATTTCA
* **
4617539 TAATGAATTTTTT-AAAAAATAA-AATAAAATTTTTAATCCTACCAAACTATTTAAGGATTTAAA
1 TAATAAATTTTTTAAAAAAATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTAAA
* * * *
4617602 TCTTGAATTAAGTTTTACCAAACTATTAGAAGACT
66 TATTGAATTAAGTCTTACAAAAATATTAGAAGACT
* *
4617637 TAATAAATTTTTTAAAAATAATAATAATAGAATTTTTAATCCTACCAAACTATTGGATGATTTAA
1 TAATAAATTTTTTAAAAA-AATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTAA
* **
4617702 ATATTGAATTAAGTCTTATAAAAATATTAGGGGACT
65 ATATTGAATTAAGTCTTACAAAAATATTAGAAGACT
* * *
4617738 TAATGAAACTTTTGTAAAAAAATAATAATAAAATTTTCAATCATACCAAACTATTGGAGGATTTA
1 TAAT-AAA-TTTTTTAAAAAAATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTA
4617803 AATATTGAATTA
64 AATATTGAATTA
4617815 GATATTTTCA
Statistics
Matches: 156, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
98 12 0.08
99 4 0.03
100 5 0.03
101 69 0.44
102 56 0.36
103 10 0.06
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (100 bp):
TAATAAATTTTTTAAAAAAATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTAAA
TATTGAATTAAGTCTTACAAAAATATTAGAAGACT
Found at i:4617828 original size:102 final size:99
Alignment explanation
Indices: 4617539--4617836 Score: 359
Period size: 102 Copynumber: 3.0 Consensus size: 99
4617529 GAGAATTTCA
* * **
4617539 TAATGAATTTT-TTAAAAAATAA-AATAAAATTTTTAATCCTACCAAACTATTTAAGGATTTAAA
1 TAATAAATTTTGTAAAAAAATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTAAA
* * *
4617602 TCTTGAATTAAGTTTTACCAAACTATTAGAAGACT
66 TATTGAATTAAGTTTT-TCAAAATATTAGAAGACT
* * *
4617637 TAATAAATTTTTTAAAAATAATAATAATAGAATTTTTAATCCTACCAAACTATTGGATGATTTAA
1 TAATAAATTTTGTAAAAA-AATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTAA
* * **
4617702 ATATTGAATTAAGTCTTATAAAAATATTAGGGGACT
65 ATATTGAATTAAGT-TTTTCAAAATATTAGAAGACT
* *
4617738 TAATGAAACTTTTGTAAAAAAATAATAATAAAATTTTCAATCATACCAAACTATTGGAGGATTTA
1 TAAT-AAA-TTTTGTAAAAAAATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTA
*
4617803 AATATTGAATT-AGATATTTTCAAAATATTGGAAG
64 AATATTGAATTAAG-T-TTTTCAAAATATTAGAAG
4617837 GTTTAATTGA
Statistics
Matches: 169, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
98 10 0.06
99 5 0.03
100 5 0.03
101 68 0.40
102 71 0.42
103 10 0.06
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.37
Consensus pattern (99 bp):
TAATAAATTTTGTAAAAAAATAATAATAAAATTTTTAATCCTACCAAACTATTGGAGGATTTAAA
TATTGAATTAAGTTTTTCAAAATATTAGAAGACT
Found at i:4619607 original size:23 final size:24
Alignment explanation
Indices: 4619564--4619612 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4619554 ATTTTTAAAA
*
4619564 TTTTGGATGTGAATCTCTAAAATT
1 TTTTGAATGTGAATCTCTAAAATT
4619588 TTTTGAATGTGAA-CAT-TAAAATT
1 TTTTGAATGTGAATC-TCTAAAATT
4619611 TT
1 TT
4619613 GGTTGTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (24 bp):
TTTTGAATGTGAATCTCTAAAATT
Found at i:4619627 original size:22 final size:21
Alignment explanation
Indices: 4619558--4619667 Score: 76
Period size: 22 Copynumber: 5.0 Consensus size: 21
4619548 ATGAGAATTT
*
4619558 TTAAAATTTTGGATGTGAATC
1 TTAAAATTTTGGATGTGAATA
* *
4619579 TCTAAAATTTTTTGAATGTGAACA
1 T-TAAAA--TTTTGGATGTGAATA
*
4619603 TTAAAATTTTGGTTGTGAAATA
1 TTAAAATTTTGGATGTG-AATA
* ** *
4619625 TTAAAGTTTTTAAGTGTGAATTT
1 TTAAAATTTTGGA-TGTGAA-TA
* *
4619648 TTGAAATTTTTGATGTGAAT
1 TTAAAATTTTGGATGTGAAT
4619668 CTTTAGGTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
21 11 0.16
22 25 0.36
23 20 0.29
24 13 0.19
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (21 bp):
TTAAAATTTTGGATGTGAATA
Found at i:4619770 original size:21 final size:21
Alignment explanation
Indices: 4619744--4619789 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4619734 ATTTTGGCTG
4619744 TGAATCT-TGAAATCTTTGATA
1 TGAATCTATG-AATCTTTGATA
* *
4619765 TGAATCTATGAATTTTTTATA
1 TGAATCTATGAATCTTTGATA
4619786 TGAA
1 TGAA
4619790 ATTTTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (21 bp):
TGAATCTATGAATCTTTGATA
Found at i:4620121 original size:17 final size:17
Alignment explanation
Indices: 4620089--4620122 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4620079 ATTCTAAAAG
**
4620089 TCTTTGCGAATGTAGAA
1 TCTTTGCGAAACTAGAA
4620106 TCTTTGCGAAACTAGAA
1 TCTTTGCGAAACTAGAA
4620123 CCTCTGTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (17 bp):
TCTTTGCGAAACTAGAA
Found at i:4621307 original size:101 final size:101
Alignment explanation
Indices: 4621157--4621479 Score: 361
Period size: 101 Copynumber: 3.2 Consensus size: 101
4621147 GAGAATTTCA
* * * * * *
4621157 TAATGAATATT-TTGAAAATAATAATAATAAAAGTTTTGATCCTATCAAACTATTGGAGGATTTA
1 TAATGAATTTTCTTAAAAATAAAAATAATAAAA-TTTTAATTCTACCAAACTATTGGAGGATTTA
* *
4621221 AATATTGAATTAAATTTTACCAAACTATTGGAAGACT
65 AATATTGAATTAAATCTAACCAAACTATTGGAAGACT
* *
4621258 TAATGAATTTT-TTAAAAATAAAAATAATAAAATTTTTAATTTTACCAAACTATTGGACGATTTA
1 TAATGAATTTTCTTAAAAATAAAAATAATAAAA-TTTTAATTCTACCAAACTATTGGAGGATTTA
* * * **
4621322 AATATTGAATTAAGTCTAATCAAAATATTGGGGCGACT
65 AATATTGAATTAAATCTAACCAAACTATT-GGAAGACT
** * *
4621360 TAATGAATTTTGGTAAAAA-AAAAA-AATAAAATTTTAATTCTGCCAAACTATTAGAGGATTTAA
1 TAATGAATTTTCTTAAAAATAAAAATAATAAAATTTTAATTCTACCAAACTATTGGAGGATTTAA
* * * **
4621423 ATATTGAATTGAATCTCACAAAACTATT-GAAGGTT
66 ATATTGAATTAAATCTAACCAAACTATTGGAAGACT
4621458 TAATGAATTTTCTT-AAAATAAA
1 TAATGAATTTTCTTAAAAATAAA
4621480 TTTCATACAT
Statistics
Matches: 186, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
97 4 0.02
98 18 0.10
100 50 0.27
101 86 0.46
102 22 0.12
103 6 0.03
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (101 bp):
TAATGAATTTTCTTAAAAATAAAAATAATAAAATTTTAATTCTACCAAACTATTGGAGGATTTAA
ATATTGAATTAAATCTAACCAAACTATTGGAAGACT
Found at i:4624706 original size:2 final size:2
Alignment explanation
Indices: 4624699--4624738 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4624689 AATGTGTTAT
*
4624699 TG TG TG TG TT TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4624739 AGGGAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:4629612 original size:16 final size:16
Alignment explanation
Indices: 4629591--4629625 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4629581 ATGTAAGCTC
*
4629591 ATACCAATTGTTATAG
1 ATACCAATTGTTAAAG
4629607 ATACCAATTGTTAAAG
1 ATACCAATTGTTAAAG
4629623 ATA
1 ATA
4629626 TGTTATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (16 bp):
ATACCAATTGTTAAAG
Found at i:4634876 original size:21 final size:21
Alignment explanation
Indices: 4634852--4634906 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
4634842 GGTTCAAGGG
4634852 GGTGATCAATCCCCTCCATAA
1 GGTGATCAATCCCCTCCATAA
4634873 GGTGATCAATCCCCTCCATAA
1 GGTGATCAATCCCCTCCATAA
4634894 GGTGATCAATCCC
1 GGTGATCAATCCC
4634907 TTCTTCAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (21 bp):
GGTGATCAATCCCCTCCATAA
Found at i:4636895 original size:99 final size:100
Alignment explanation
Indices: 4636731--4636992 Score: 339
Period size: 99 Copynumber: 2.6 Consensus size: 100
4636721 TTCCAATAGT
* * * * * *
4636731 TTGATAAAATTTAATTTTCAGATTTAAATCCTCTAATAGATTGATAGGATTTATTTCAAAATTTT
1 TTGATAAGATTTAATTTTGAGATTTAAATCCTCCAATAGTTTGGTAGGATTAATTTCAAAATTTT
* *
4636796 ATTTTAAGAAAAAGATAATTAAA-CCTTTAAATAAC
66 ATTTTAAGAAAAAAATAATTAAATCCTCT-AATAAC
* * * * *
4636831 TTGGTAAGATTTAATTTTGAGATTTAAA-CTTCCAAGAGTTTGGTAGAATTCATTTCAAAATTTT
1 TTGATAAGATTTAATTTTGAGATTTAAATCCTCCAATAGTTTGGTAGGATTAATTTCAAAATTTT
**
4636895 ATTTTAAGAAAAAAATAATTAAATCCTCTAATAGT
66 ATTTTAAGAAAAAAATAATTAAATCCTCTAATAAC
* *
4636930 TTGATAAGATTTAATTTTGAAATTTAAATCCACCAATAGTTTGGTAGGATTAATTTTCAAAAT
1 TTGATAAGATTTAATTTTGAGATTTAAATCCTCCAATAGTTTGGTAGGATTAA-TTTCAAAAT
4636993 GAAAGAAATA
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
99 81 0.59
100 48 0.35
101 9 0.07
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (100 bp):
TTGATAAGATTTAATTTTGAGATTTAAATCCTCCAATAGTTTGGTAGGATTAATTTCAAAATTTT
ATTTTAAGAAAAAAATAATTAAATCCTCTAATAAC
Found at i:4637830 original size:26 final size:26
Alignment explanation
Indices: 4637801--4637897 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 26
4637791 TTAGGTAATA
*
4637801 ATAAAATAATAAAGATAAAGATTAAG
1 ATAAAATAATAAAAATAAAGATTAAG
*
4637827 AT-AAATGAGA-AATAAAGTAAA-ATAAAG
1 ATAAAAT-A-ATAA-AAA-TAAAGATTAAG
4637854 ATAAAA-AATAAAAAATAAAGA-TAA-
1 ATAAAATAAT-AAAAATAAAGATTAAG
4637878 ATAAAATAAATAAAAATAAA
1 ATAAAAT-AATAAAAATAAA
4637898 AATAACATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
24 6 0.10
25 20 0.34
26 13 0.22
27 12 0.21
28 7 0.12
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (26 bp):
ATAAAATAATAAAAATAAAGATTAAG
Found at i:4637851 original size:10 final size:9
Alignment explanation
Indices: 4637800--4637897 Score: 60
Period size: 10 Copynumber: 10.2 Consensus size: 9
4637790 ATTAGGTAAT
4637800 AATAAAAT-
1 AATAAAATA
4637808 AATAAAGATAA
1 AATAAA-AT-A
*
4637819 AGATTAAGATA
1 A-A-TAAAATA
4637830 AATGAGAAATA
1 AAT-A-AAATA
4637841 AAGTAAAATA
1 AA-TAAAATA
*
4637851 AAGATAAA-A
1 AATA-AAATA
4637860 AAT-AAA-A
1 AATAAAATA
4637867 AATAAAGATA
1 AATAAA-ATA
4637877 AATAAAATA
1 AATAAAATA
4637886 AATAAAAATA
1 AAT-AAAATA
4637896 AA
1 AA
4637898 AATAACATAA
Statistics
Matches: 73, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
7 7 0.10
8 8 0.11
9 14 0.19
10 27 0.37
11 10 0.14
12 4 0.05
13 3 0.04
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:4637870 original size:20 final size:19
Alignment explanation
Indices: 4637845--4637899 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
4637835 GAAATAAAGT
4637845 AAAATAAAGATAAAAAATAA
1 AAAATAAAGATAAAAAA-AA
*
4637865 AAAATAAAGATAAATAAAA
1 AAAATAAAGATAAAAAAAA
* *
4637884 TAAATAAAAATAAAAA
1 AAAATAAAGATAAAAA
4637900 TAACATAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAATAAAGATAAAAAAAA
Found at i:4637889 original size:39 final size:39
Alignment explanation
Indices: 4637800--4637899 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
4637790 ATTAGGTAAT
* * *
4637800 AATAAAAT-AATAAAGAT-AAAGATTAAGATAAATGAGA
1 AATAAAATAAATAAAGATAAAAAATAAAAATAAATGAGA
* *
4637837 AATAAAGTAAAATAAAGATAAAAAATAAAAAATAAA-GATA
1 AATAAAAT-AAATAAAGATAAAAAAT-AAAAATAAATGAGA
*
4637877 AATAAAATAAATAAAAATAAAAA
1 AATAAAATAAATAAAGATAAAAA
4637900 TAACATAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
37 7 0.13
39 23 0.44
40 15 0.29
41 7 0.13
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (39 bp):
AATAAAATAAATAAAGATAAAAAATAAAAATAAATGAGA
Found at i:4637894 original size:6 final size:6
Alignment explanation
Indices: 4637845--4637902 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
4637835 GAAATAAAGT
* *
4637845 AAAATA AAGATAA AAAATAA AAAATA AAGATA AATAA-A ATAAATA AAAATA
1 AAAATA AAAAT-A AAAAT-A AAAATA AAAATA AA-AATA A-AAATA AAAATA
4637896 AAAATA A
1 AAAATA A
4637903 CATAAAGACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 28 0.64
7 16 0.36
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:4637907 original size:26 final size:26
Alignment explanation
Indices: 4637845--4637908 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
4637835 GAAATAAAGT
*
4637845 AAAATAAAGATAAA-AAATAAAAAATA
1 AAAATAAATA-AAATAAATAAAAAATA
*
4637871 AAGATAAATAAAATAAAT-AAAAATA
1 AAAATAAATAAAATAAATAAAAAATA
4637896 AAAATAACATAAA
1 AAAATAA-ATAAA
4637909 GACACATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (26 bp):
AAAATAAATAAAATAAATAAAAAATA
Found at i:4637908 original size:30 final size:36
Alignment explanation
Indices: 4637838--4637909 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 36
4637828 TAAATGAGAA
*
4637838 ATAAAGTAAAATAAAGATAAAAAATAAAAAATAAAG
1 ATAAAGTAAAATAAAGATAAAAAATAAAAAATAAAC
4637874 ATAAA-TAAAAT-AA-AT-AAAAAT-AAAAAT-AAC
1 ATAAAGTAAAATAAAGATAAAAAATAAAAAATAAAC
4637904 ATAAAG
1 ATAAAG
4637910 ACACATAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
30 7 0.21
31 6 0.18
32 6 0.18
33 2 0.06
34 2 0.06
35 6 0.18
36 5 0.15
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (36 bp):
ATAAAGTAAAATAAAGATAAAAAATAAAAAATAAAC
Found at i:4638342 original size:33 final size:33
Alignment explanation
Indices: 4638303--4638367 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
4638293 GCTACTTGAC
4638303 TAAGCCTAAGTCTG-AAAATGAAATGAATTGGAT
1 TAAGCCTAAGTC-GAAAAATGAAATGAATTGGAT
* *
4638336 TAAGCCTAAGTCGAAAAATGATATGACTTGGA
1 TAAGCCTAAGTCGAAAAATGAAATGAATTGGA
4638368 CTGAGTTTGA
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:0.11, G:0.22, T:0.26
Consensus pattern (33 bp):
TAAGCCTAAGTCGAAAAATGAAATGAATTGGAT
Found at i:4638424 original size:34 final size:33
Alignment explanation
Indices: 4638349--4638424 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
4638339 GCCTAAGTCG
*** *
4638349 AAAAATGATATGACTTGGACTGAGTTTGAGTCA
1 AAAAATGATATGACTTGGACTGAGTAAAAGTAA
* *
4638382 AAAAATGATATGACTTGGATTTAGTCAAAAGTAA
1 AAAAATGATATGACTTGGACTGAGT-AAAAGTAA
4638416 AAAAATGAT
1 AAAAATGAT
4638425 GACTTGATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 23 0.64
34 13 0.36
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.29
Consensus pattern (33 bp):
AAAAATGATATGACTTGGACTGAGTAAAAGTAA
Found at i:4643052 original size:22 final size:22
Alignment explanation
Indices: 4643017--4643142 Score: 85
Period size: 22 Copynumber: 5.6 Consensus size: 22
4643007 GGGAGCCTTT
*
4643017 TTTTGAATGAGAATTTTTAAAA
1 TTTTGAATGTGAATTTTTAAAA
* * *
4643039 TTTTGGATGTGAATCTCTAAAA
1 TTTTGAATGTGAATTTTTAAAA
**
4643061 TTTTTTGAATGTGAA-CATTAAAA
1 --TTTTGAATGTGAATTTTTAAAA
** * * *
4643084 TTTTGGTTGTGAAATATTAAAG
1 TTTTGAATGTGAATTTTTAAAA
* *
4643106 TTTTTAAGTGTGAATTTTTGAAAT
1 TTTTGAA-TGTGAATTTTT-AAAA
4643130 TTTTG-ATGTGAAT
1 TTTTGAATGTGAAT
4643143 CTCTAGGTTT
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
21 11 0.14
22 35 0.43
23 16 0.20
24 19 0.23
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.47
Consensus pattern (22 bp):
TTTTGAATGTGAATTTTTAAAA
Found at i:4643083 original size:45 final size:46
Alignment explanation
Indices: 4643015--4643147 Score: 148
Period size: 45 Copynumber: 2.9 Consensus size: 46
4643005 AAGGGAGCCT
*
4643015 TTTTTTGAATGAGAATTTTTAAAATTTTGGATGTGAATCTCTAAAA
1 TTTTTTGAATGTGAATTTTTAAAATTTTGGATGTGAATCTCTAAAA
** * *
4643061 TTTTTTGAATGTGAA-CATTAAAATTTTGGTTGTGAAATAT-T-AAA
1 TTTTTTGAATGTGAATTTTTAAAATTTTGGATGTG-AATCTCTAAAA
* * *
4643105 GTTTTT-AAGTGTGAATTTTTGAAATTTTTGATGTGAATCTCTA
1 TTTTTTGAA-TGTGAATTTTTAAAATTTTGGATGTGAATCTCTA
4643148 GGTTTTTTGA
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
43 2 0.03
44 18 0.26
45 32 0.46
46 18 0.26
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (46 bp):
TTTTTTGAATGTGAATTTTTAAAATTTTGGATGTGAATCTCTAAAA
Found at i:4643245 original size:21 final size:21
Alignment explanation
Indices: 4643219--4643264 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4643209 ATTTTGGTTG
4643219 TGAATCT-TGAAATCTTTGATA
1 TGAATCTATG-AATCTTTGATA
* *
4643240 TGAATCTATGAATTTTTTATA
1 TGAATCTATGAATCTTTGATA
4643261 TGAA
1 TGAA
4643265 ATTTTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (21 bp):
TGAATCTATGAATCTTTGATA
Found at i:4643569 original size:17 final size:17
Alignment explanation
Indices: 4643537--4643570 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4643527 ATTCTAAAAG
**
4643537 TCTTTGCGAATGTAGAA
1 TCTTTGCGAAACTAGAA
4643554 TCTTTGCGAAACTAGAA
1 TCTTTGCGAAACTAGAA
4643571 CCTCTGTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (17 bp):
TCTTTGCGAAACTAGAA
Found at i:4644751 original size:101 final size:100
Alignment explanation
Indices: 4644601--4644919 Score: 399
Period size: 101 Copynumber: 3.2 Consensus size: 100
4644591 GAGAATTTCA
* * * * *
4644601 TAATGAATATTTTGAAAAAAATAATAATAAAAGTTTTGATCCTACCAAACTATTGGAGGATTTAA
1 TAATGAAT-TTTTTAAAAAAAAAATAATAAAATTTTTAATTCTACCAAACTATTGGAGGATTTAA
4644666 ATATTGAATTAAATCTTACTAAACTATTGGAAGACT
65 ATATTGAATTAAATCTTACTAAACTATTGGAAGACT
* * *
4644702 TAATGAATTTTTTAAAAATAAAAATAATAAAATTTTTAATTTTATCAAACTATTGGACGATTTAA
1 TAATGAATTTTTTAAAAA-AAAAATAATAAAATTTTTAATTCTACCAAACTATTGGAGGATTTAA
* * * **
4644767 ATATTGAATTAAGTC-TAATCAAAATATTGGGGGACT
65 ATATTGAATTAAATCTTACT-AAACTATTGGAAGACT
** * *
4644803 TAATGAATTTTTTGTAAAAGAAA-AATAAAATTTTTAATTCTACCAAACTATTAGAGGATTTAAA
1 TAATGAATTTTTTAAAAAAAAAATAATAAAATTTTTAATTCTACCAAACTATTGGAGGATTTAAA
* * **
4644867 TATTGAATTAAATCTCACAAAACTATTGGAAGGTT
66 TATTGAATTAAATCTTACTAAACTATTGGAAGACT
4644902 TAATGAATTTTCTTAAAA
1 TAATGAATTTT-TTAAAA
4644920 TAAATTTCAT
Statistics
Matches: 183, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
99 72 0.39
100 21 0.11
101 90 0.49
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (100 bp):
TAATGAATTTTTTAAAAAAAAAATAATAAAATTTTTAATTCTACCAAACTATTGGAGGATTTAAA
TATTGAATTAAATCTTACTAAACTATTGGAAGACT
Found at i:4651760 original size:13 final size:13
Alignment explanation
Indices: 4651742--4651770 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4651732 AGACAATTGC
4651742 AAAGTGTCTAGTA
1 AAAGTGTCTAGTA
4651755 AAAGTGTCTAGTA
1 AAAGTGTCTAGTA
4651768 AAA
1 AAA
4651771 ATTCAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (13 bp):
AAAGTGTCTAGTA
Found at i:4653055 original size:16 final size:16
Alignment explanation
Indices: 4653034--4653064 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4653024 AAGCTCATAC
*
4653034 CAATTGTTATAGATAG
1 CAATTGTTAAAGATAG
4653050 CAATTGTTAAAGATA
1 CAATTGTTAAAGATA
4653065 TATTATTAAG
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:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (16 bp):
CAATTGTTAAAGATAG
Found at i:4660328 original size:99 final size:100
Alignment explanation
Indices: 4660153--4660414 Score: 314
Period size: 99 Copynumber: 2.6 Consensus size: 100
4660143 TTCCAATATT
* * * * * * *
4660153 TTGATAAAATTTAATTTTCAGATTTAAATCCTT-TAATAGATTGATAGGATTTATTTTAAAATTT
1 TTGATAAGATTTAATTTTGAGATTTAAAT-CTTCCAATAGTTTGGTAGGATTAATTTCAAAATTT
* *
4660217 TATTTTAAGAAAAAGATAATTAAA-CCTTTAAATAAC
65 TATTTTAAGAAAAAAATAATTAAATCCTCT-AATAAC
* * * *
4660253 TTGGTAAGATTTAATTTTGAGATTTAAAT-TTCCAAGAGTTTGGTAGAATTGATTTCAAAATTTT
1 TTGATAAGATTTAATTTTGAGATTTAAATCTTCCAATAGTTTGGTAGGATTAATTTCAAAATTTT
**
4660317 ATTTTAAGAAAAAAATAATTAAATCCTCTAATAGT
66 ATTTTAAGAAAAAAATAATTAAATCCTCTAATAAC
* **
4660352 TTGATAAGATTTAATTTTGAAATTTAAATCCACCAATAGTTTGGTAGGATTAATTTTCAAAAT
1 TTGATAAGATTTAATTTTGAGATTTAAATCTTCCAATAGTTTGGTAGGATTAA-TTTCAAAAT
4660415 GAAAGAAATA
Statistics
Matches: 137, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
98 2 0.01
99 78 0.57
100 48 0.35
101 9 0.07
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.42
Consensus pattern (100 bp):
TTGATAAGATTTAATTTTGAGATTTAAATCTTCCAATAGTTTGGTAGGATTAATTTCAAAATTTT
ATTTTAAGAAAAAAATAATTAAATCCTCTAATAAC
Found at i:4661283 original size:57 final size:57
Alignment explanation
Indices: 4661222--4661346 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 57
4661212 ATTAGGTAAT
* * * * *
4661222 AATAAAATAATAAAGATAAAGATTAAGATAAATGAGAAATAAAGTAA-AATAAAGATA-
1 AATAAAATAATAAAAATAAA-AATAACATAAA-GACAAATAAAGCAAGAATAAAGATAG
*
4661279 AATAAAATAAATAAAAATAAAAATAACATAAAGACACATAAAGCAAGAATAAAGATAG
1 AATAAAAT-AATAAAAATAAAAATAACATAAAGACAAATAAAGCAAGAATAAAGATAG
4661337 AATAAAATAA
1 AATAAAATAA
4661347 GGATAAATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
56 11 0.19
57 29 0.49
58 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (57 bp):
AATAAAATAATAAAAATAAAAATAACATAAAGACAAATAAAGCAAGAATAAAGATAG
Found at i:4661351 original size:16 final size:15
Alignment explanation
Indices: 4661222--4661300 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 15
4661212 ATTAGGTAAT
4661222 AATAAA-AT-AATAA
1 AATAAAGATAAATAA
4661235 AGATAAAGATTAAGAT-A
1 A-ATAAAGA-TAA-ATAA
4661252 AATGAGAA-ATAAAGTAA
1 AAT-A-AAGATAAA-TAA
4661269 AATAAAGATAAATAA
1 AATAAAGATAAATAA
* *
4661284 AATAAATAAAAATAA
1 AATAAAGATAAATAA
4661299 AA
1 AA
4661301 ATAACATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 22 0.41
16 13 0.24
17 9 0.17
18 4 0.07
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (15 bp):
AATAAAGATAAATAA
Found at i:4661751 original size:33 final size:33
Alignment explanation
Indices: 4661712--4661811 Score: 101
Period size: 33 Copynumber: 3.0 Consensus size: 33
4661702 GCTACTTGAC
**
4661712 TAAGCCTAAGTCTGAAAATGAAATGAATTGGAT
1 TAAGCCTAAGTCAAAAAATGAAATGAATTGGAT
* * *
4661745 TAAGCCTAAGTCAAAAAATGATATGACTTGGAC
1 TAAGCCTAAGTCAAAAAATGAAATGAATTGGAT
* ** * * *
4661778 TGAGTTTGAGTCAAAAAATGATATGACTTGGAT
1 TAAGCCTAAGTCAAAAAATGAAATGAATTGGAT
4661811 T
1 T
4661812 TAGTCAAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (33 bp):
TAAGCCTAAGTCAAAAAATGAAATGAATTGGAT
Found at i:4661810 original size:66 final size:65
Alignment explanation
Indices: 4661717--4662079 Score: 202
Period size: 66 Copynumber: 5.5 Consensus size: 65
4661707 TTGACTAAGC
** * * * *
4661717 CTAAGTCTGAAAATGAAATGAATTGGATTAAGCCTAAGTCAAAAAATGATATGACTTGGACTGAG
1 CTAAGTCAAAAAATGATATGACTTGGATTAAGCCAAAGTCAAAAAATGAAATGACTTGGACTGAG
* * * * *
4661782 TTTGAGTCAAAAAATGATATGACTTGGATTTAGTCAAAAGTAAAAAAATG--ATGACTT-GATCT
1 -CTAAGTCAAAAAATGATATGACTTGGATTAAG-CCAAAGTCAAAAAATGAAATGACTTGGA-CT
*
4661844 TAG
63 GAG
* * * **
4661847 CTAAGGTCGAAAAATGCA-A-GAACTTGG-TCTTAGCTAAAGTCAAAAAACAAAATGACTTGGAC
1 CTAA-GTCAAAAAATG-ATATG-ACTTGGAT-TAAGCCAAAGTCAAAAAATGAAATGACTTGGAC
*
4661909 TTAG
62 TGAG
* * ** * * ** * * *
4661913 TTGATGTTGAAAAATGATATGATTTGGACTT-AGTCAAAGTCAGGTAAATGATATGACTTAGATT
1 CT-AAGTCAAAAAATGATATGACTTGGA-TTAAGCCAAAGTCA-AAAAATGAAATGACTTGGACT
*
4661977 GGG
63 GAG
* * * * * *
4661980 CCTAAGTCAAAAAAATGATATGACTTGGACTGAGCCAAACTC-AAAAATAAAATTACTTGAACTG
1 -CTAAGTC-AAAAAATGATATGACTTGGATTAAGCCAAAGTCAAAAAATGAAATGACTTGGACTG
4662044 AG
64 AG
** *
4662046 CCTAAACCAAAAAATGATATGACTTGGAATAAGC
1 -CTAAGTCAAAAAATGATATGACTTGGATTAAGC
4662080 TTAAATAGAA
Statistics
Matches: 225, Mismatches: 54, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
64 18 0.08
65 57 0.25
66 85 0.38
67 37 0.16
68 28 0.12
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.27
Consensus pattern (65 bp):
CTAAGTCAAAAAATGATATGACTTGGATTAAGCCAAAGTCAAAAAATGAAATGACTTGGACTGAG
Found at i:4661860 original size:32 final size:33
Alignment explanation
Indices: 4661818--4661893 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
4661808 GATTTAGTCA
* *
4661818 AAAGTAAAAAAATG-ATG-ACTTGATCTTAGCT
1 AAAGTCAAAAAATGCAAGAACTTGATCTTAGCT
* * *
4661849 AAGGTCGAAAAATGCAAGAACTTGGTCTTAGCT
1 AAAGTCAAAAAATGCAAGAACTTGATCTTAGCT
4661882 AAAGTCAAAAAA
1 AAAGTCAAAAAA
4661894 CAAAATGACT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 11 0.31
32 2 0.06
33 23 0.64
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (33 bp):
AAAGTCAAAAAATGCAAGAACTTGATCTTAGCT
Found at i:4661905 original size:33 final size:35
Alignment explanation
Indices: 4661832--4661912 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 35
4661822 TAAAAAAATG
* * * *
4661832 ATGACTTGATCTTAGCTAAGGTCGAAAAATGCAAG
1 ATGACTTGGTCTTAGCTAAAGTCGAAAAATACAAA
4661867 A--ACTTGGTCTTAGCTAAAGTC-AAAAA-ACAAA
1 ATGACTTGGTCTTAGCTAAAGTCGAAAAATACAAA
*
4661898 ATGACTTGGACTTAG
1 ATGACTTGGTCTTAG
4661913 TTGATGTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
31 4 0.10
32 5 0.13
33 29 0.74
35 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (35 bp):
ATGACTTGGTCTTAGCTAAAGTCGAAAAATACAAA
Found at i:4662024 original size:34 final size:34
Alignment explanation
Indices: 4661922--4662073 Score: 125
Period size: 34 Copynumber: 4.6 Consensus size: 34
4661912 GTTGATGTTG
* * * * *
4661922 AAAAATGATATGATTTGGACTTAGTCAAAGTCAG
1 AAAAATGATATGACTTGGACTGAGCCAAACTCAA
** * * * * *
4661956 GTAAATGATATGACTTAGATTGGGCCTAAGTCAA
1 AAAAATGATATGACTTGGACTGAGCCAAACTCAA
4661990 AAAAATGATATGACTTGGACTGAGCCAAACTCAA
1 AAAAATGATATGACTTGGACTGAGCCAAACTCAA
* *
4662024 AAATAA--A-ATTACTTGAACTGAGCCTAAAC-C-A
1 AAA-AATGATATGACTTGGACTGAGCC-AAACTCAA
4662055 AAAAATGATATGACTTGGA
1 AAAAATGATATGACTTGGA
4662074 ATAAGCTTAA
Statistics
Matches: 92, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
30 2 0.02
31 4 0.04
32 17 0.18
33 13 0.14
34 54 0.59
35 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (34 bp):
AAAAATGATATGACTTGGACTGAGCCAAACTCAA
Found at i:4663226 original size:10 final size:10
Alignment explanation
Indices: 4663213--4663237 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4663203 AAATGCTTAA
4663213 AAAAAAGAAT
1 AAAAAAGAAT
4663223 AAAAAAGAAT
1 AAAAAAGAAT
4663233 AAAAA
1 AAAAA
4663238 GAAATAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAGAAT
Found at i:4665255 original size:99 final size:99
Alignment explanation
Indices: 4665102--4665395 Score: 344
Period size: 99 Copynumber: 2.9 Consensus size: 99
4665092 TATATCTTTA
* * * * *
4665102 AATAGTTTAGTAGGATTGATTTCAAAAATTCATTTTCATGAAACAGATAATTAAAGATTCCAATA
1 AATAGTTTGGTAGGATTGA-TTCAAAAATTTATTTT-AAGAAAAAGATAATTAAACATTCCAATA
* * *
4665167 GTTTGGTAACATTTATTTTTGACT-TTTAAATTTTCT
64 GTTTGATAACATTTAATTTTGA-TATTTAAATTCTCT
* * * *
4665203 AATAGTTTGGTAGGATTTATTCAAAAATTTATTTTAAGAAAAAGATAATTAAACTTTCAAATAAT
1 AATAGTTTGGTAGGATTGATTCAAAAATTTATTTTAAGAAAAAGATAATTAAACATTCCAATAGT
**
4665268 TTGATATGATTTAATTTTGATATTTAAATTCTCT
66 TTGATAACATTTAATTTTGATATTTAAATTCTCT
* ** *
4665302 AATAATTTGGTAAAATTGATTCCAAAAATTTATTTTAAGAAAAAGATAATTAAACCTTCCAATAG
1 AATAGTTTGGTAGGATTGATT-CAAAAATTTATTTTAAGAAAAAGATAATTAAACATTCCAATAG
4665367 -TTGATAA-ATTTTAATTTTG-TGATTTAAAT
65 TTTGATAACA-TTTAATTTTGAT-ATTTAAAT
4665396 CCTCCATTAA
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
98 3 0.02
99 92 0.55
100 55 0.33
101 17 0.10
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.43
Consensus pattern (99 bp):
AATAGTTTGGTAGGATTGATTCAAAAATTTATTTTAAGAAAAAGATAATTAAACATTCCAATAGT
TTGATAACATTTAATTTTGATATTTAAATTCTCT
Found at i:4665430 original size:100 final size:100
Alignment explanation
Indices: 4665224--4665421 Score: 258
Period size: 99 Copynumber: 2.0 Consensus size: 100
4665214 AGGATTTATT
* * *
4665224 CAAAAATTTATTTTAAGAAAAAGATAATTAAACTTTCAAATAATTTGATATGATTTAATTTTGAT
1 CAAAAATTTATTTTAAGAAAAAGATAATTAAACCTTCAAATAAGTTGATATAATTTAATTTTGAT
* * * *
4665289 ATTTAAATTCTCTAATAATTTGGTAAAATTGATTC
66 ATTTAAATCCTCCAATAATTCGGTAAAATTAATTC
*
4665324 CAAAAATTTATTTTAAGAAAAAGATAATTAAACCTTCCAAT-AGTTGATA-AATTTTAATTTTG-
1 CAAAAATTTATTTTAAGAAAAAGATAATTAAACCTTCAAATAAGTTGATATAA-TTTAATTTTGA
* **
4665386 TGATTTAAATCCTCCATTAATTCGGTATGATTAATT
65 T-ATTTAAATCCTCCAATAATTCGGTAAAATTAATT
4665422 TTGAAAAATA
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
98 2 0.02
99 44 0.52
100 39 0.46
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (100 bp):
CAAAAATTTATTTTAAGAAAAAGATAATTAAACCTTCAAATAAGTTGATATAATTTAATTTTGAT
ATTTAAATCCTCCAATAATTCGGTAAAATTAATTC
Found at i:4667694 original size:24 final size:24
Alignment explanation
Indices: 4667667--4667746 Score: 101
Period size: 24 Copynumber: 3.3 Consensus size: 24
4667657 TTATAAAATC
4667667 ATTTATTTAACATTTTCATAATAT
1 ATTTATTTAACATTTTCATAATAT
**
4667691 ATTTATTTAACA-CATCAATAAT-T
1 ATTTATTTAACATTTTC-ATAATAT
*
4667714 GATTTATTTAACATTTTCGTAATAT
1 -ATTTATTTAACATTTTCATAATAT
4667739 ATTTATTT
1 ATTTATTT
4667747 TTTAACTTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 3 0.06
24 41 0.87
25 3 0.06
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (24 bp):
ATTTATTTAACATTTTCATAATAT
Found at i:4668992 original size:19 final size:19
Alignment explanation
Indices: 4668968--4669089 Score: 120
Period size: 19 Copynumber: 6.4 Consensus size: 19
4668958 TAAGGTTTTG
*
4668968 GGGTTTTACTTAGGGTTTA
1 GGGTTTTACCTAGGGTTTA
**
4668987 GGGTTTTATTTAGGGTTTA
1 GGGTTTTACCTAGGGTTTA
*
4669006 GGGTTTTACCTAGGATTTA
1 GGGTTTTACCTAGGGTTTA
* * * *
4669025 GAGTTTCACATAGAGTTTA
1 GGGTTTTACCTAGGGTTTA
*
4669044 GGGTTTTACCTAGAGTTTTA
1 GGGTTTTACCTAG-GGTTTA
**
4669064 -GGTTTTCACCTAAAGTTTA
1 GGGTTTT-ACCTAGGGTTTA
4669083 GGGTTTT
1 GGGTTTT
4669090 GTTTAATGTT
Statistics
Matches: 83, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
19 68 0.82
20 15 0.18
ACGTcount: A:0.20, C:0.08, G:0.26, T:0.45
Consensus pattern (19 bp):
GGGTTTTACCTAGGGTTTA
Found at i:4669025 original size:38 final size:38
Alignment explanation
Indices: 4668943--4669089 Score: 132
Period size: 38 Copynumber: 3.8 Consensus size: 38
4668933 TTAAGTTTTC
* * * *
4668943 ATTTAGGGTTTGCATTAAGGTTTTGGGGTTTTACTTAGG
1 ATTTAGGGTTT-CATTTAGGGTTTAGGGTTTTACCTAGG
* *
4668982 GTTTAGGGTTTTATTTAGGGTTTAGGGTTTTACCTAGG
1 ATTTAGGGTTTCATTTAGGGTTTAGGGTTTTACCTAGG
* ** *
4669020 ATTTAGAGTTTCACATAGAGTTTAGGGTTTTACCTAGAG
1 ATTTAGGGTTTCATTTAGGGTTTAGGGTTTTACCTAG-G
* * ** **
4669059 TTTTAGGTTTTCACCTAAAGTTTAGGGTTTT
1 ATTTAGGGTTTCATTTAGGGTTTAGGGTTTT
4669090 GTTTAATGTT
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
38 53 0.59
39 37 0.41
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.46
Consensus pattern (38 bp):
ATTTAGGGTTTCATTTAGGGTTTAGGGTTTTACCTAGG
Found at i:4669387 original size:8 final size:7
Alignment explanation
Indices: 4669368--4669397 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
4669358 TTAGTTCCTT
4669368 ATTTTTA
1 ATTTTTA
4669375 ATTTTTA
1 ATTTTTA
4669382 ATTTTTA
1 ATTTTTA
4669389 ATGTTTTA
1 AT-TTTTA
4669397 A
1 A
4669398 AGTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.73
8 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (7 bp):
ATTTTTA
Found at i:4671651 original size:9 final size:10
Alignment explanation
Indices: 4671618--4671662 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
4671608 CCTAAGGTAA
4671618 ATTTTT-TTT
1 ATTTTTGTTT
4671627 -TTTTTGCTTT
1 ATTTTTG-TTT
*
4671637 TTTTTTGTTT
1 ATTTTTGTTT
4671647 ATTTTTGTTT
1 ATTTTTGTTT
4671657 ATTTTT
1 ATTTTT
4671663 ACCTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 5 0.16
10 21 0.66
11 6 0.19
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (10 bp):
ATTTTTGTTT
Found at i:4671670 original size:31 final size:29
Alignment explanation
Indices: 4671618--4671678 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
4671608 CCTAAGGTAA
* * *
4671618 ATTTTTTTTTTTTTGCTTTTTTTTTGTTT
1 ATTTTTTTTTTTTTACCTTTTTTTTCTTT
4671647 ATTTTTGTTTATTTTTACCTTTTTTTTCTTT
1 ATTTTT-TTT-TTTTTACCTTTTTTTTCTTT
4671678 A
1 A
4671679 AGACTATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
30 3 0.11
31 18 0.67
ACGTcount: A:0.08, C:0.07, G:0.05, T:0.80
Consensus pattern (29 bp):
ATTTTTTTTTTTTTACCTTTTTTTTCTTT
Found at i:4672415 original size:22 final size:22
Alignment explanation
Indices: 4672310--4672431 Score: 88
Period size: 22 Copynumber: 5.6 Consensus size: 22
4672300 TATATTTTTT
*
4672310 CAACTAATTTGGGCTTATGTGC
1 CAACTAATCTGGGCTTATGTGC
* *
4672332 C-ACTAATCTAGGCTTATATGC
1 CAACTAATCTGGGCTTATGTGC
* ** *
4672353 TAGTTAATTTGGGCTTGCATGT--
1 CAACTAATCTGGGCTT--ATGTGC
* * *
4672375 TAGCTAATCTGGACTTATGTGC
1 CAACTAATCTGGGCTTATGTGC
*
4672397 CAACTAATATGGGCTTATGTGC
1 CAACTAATCTGGGCTTATGTGC
* *
4672419 TAACTAAACTGGG
1 CAACTAATCTGGG
4672432 TTTAAATTCT
Statistics
Matches: 76, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
20 4 0.05
21 17 0.22
22 52 0.68
24 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (22 bp):
CAACTAATCTGGGCTTATGTGC
Found at i:4673437 original size:24 final size:23
Alignment explanation
Indices: 4673403--4673483 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
4673393 TGTTTTTTTA
*
4673403 TTCTTTATTTCACTTTTTTCACTT
1 TTCTTTTTTTCA-TTTTTTCACTT
* *
4673427 TTCTTTTTTTCTTTTTCTTCACCT
1 TTCTTTTTTTCATTTT-TTCACTT
* *
4673451 TTC-CTTTTTCATTCTTTCACTT
1 TTCTTTTTTTCATTTTTTCACTT
4673473 CTTCTTTTTTT
1 -TTCTTTTTTT
4673484 TGAATGGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.13
23 16 0.35
24 24 0.52
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.69
Consensus pattern (23 bp):
TTCTTTTTTTCATTTTTTCACTT
Found at i:4673988 original size:22 final size:23
Alignment explanation
Indices: 4673960--4674014 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
4673950 ATCATAACTA
4673960 TTTTTTTATTCTTT-TCTTATCCT
1 TTTTTTTATT-TTTATCTTATCCT
* *
4673983 TTTTTTTATTTTTAT-TTTTTCT
1 TTTTTTTATTTTTATCTTATCCT
4674005 TTTTTTTATT
1 TTTTTTTATT
4674015 GACATGCCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTTATTTTTATCTTATCCT
Found at i:4675933 original size:23 final size:24
Alignment explanation
Indices: 4675884--4675933 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4675874 GATAAATCCC
** *
4675884 TCAAAGTATGAATTTGGTTGCTTT
1 TCAAAGTATGAATTAAGTAGCTTT
4675908 TCAAAGTATGAA-TAAGTAGCTTT
1 TCAAAGTATGAATTAAGTAGCTTT
4675931 TCA
1 TCA
4675934 TCACTAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (24 bp):
TCAAAGTATGAATTAAGTAGCTTT
Found at i:4676653 original size:19 final size:19
Alignment explanation
Indices: 4676631--4676669 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4676621 ATTTCCTTAT
*
4676631 ATTTATCTAATTTTTTAAA
1 ATTTATCTAATTATTTAAA
*
4676650 ATTTATCTAGTTATTTAAA
1 ATTTATCTAATTATTTAAA
4676669 A
1 A
4676670 AAAAGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTATCTAATTATTTAAA
Found at i:4678093 original size:11 final size:12
Alignment explanation
Indices: 4678077--4678136 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 12
4678067 GGAATGAAGC
4678077 AAAGAAAAAAA-
1 AAAGAAAAAAAG
4678088 AAAGAAAAAAAG
1 AAAGAAAAAAAG
* *
4678100 AATGAAAAATAAC
1 AAAGAAAAA-AAG
4678113 AAATGAAAATATAAG
1 AAA-GAAAA-A-AAG
4678128 AAATGAAAA
1 AAA-GAAAA
4678137 TGAGGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 4 0.10
14 5 0.12
15 13 0.32
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:4678131 original size:15 final size:15
Alignment explanation
Indices: 4678100--4678137 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
4678090 AGAAAAAAAG
4678100 AATGAAAA-ATAACA
1 AATGAAAATATAACA
*
4678114 AATGAAAATATAAGA
1 AATGAAAATATAACA
4678129 AATGAAAAT
1 AATGAAAAT
4678138 GAGGAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.03, G:0.11, T:0.18
Consensus pattern (15 bp):
AATGAAAATATAACA
Found at i:4679187 original size:31 final size:30
Alignment explanation
Indices: 4679152--4679250 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
4679142 GGTTATTTTC
* **
4679152 ATTTTTACCTTGGTTCAGTGTGGTCATCTTT
1 ATTTTTACTTTGGTTCAGT-CAGTCATCTTT
* *
4679183 ATTTTCGACTTTGGGTCAGTCAGTCATCTTT
1 ATTTT-TACTTTGGTTCAGTCAGTCATCTTT
* *
4679214 ATTTTTTACTTTGGTTCAGTTCAATCATTTTT
1 A-TTTTTACTTTGGTTCAG-TCAGTCATCTTT
4679246 ATTTT
1 ATTTT
4679251 CAACCTTGGC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
31 30 0.54
32 26 0.46
ACGTcount: A:0.16, C:0.15, G:0.15, T:0.54
Consensus pattern (30 bp):
ATTTTTACTTTGGTTCAGTCAGTCATCTTT
Found at i:4679265 original size:32 final size:32
Alignment explanation
Indices: 4679146--4679874 Score: 380
Period size: 32 Copynumber: 22.8 Consensus size: 32
4679136 CAATCTGGTT
* ****
4679146 ATTTTCATTTTT-ACCTTGGTTCAGTGTGGTC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * * * *
4679177 ATCTTTATTTTCGACTTTGGGTCAGT-CAGTC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * * *
4679208 ATCTTTATTTTTTACTTTGGTTCAGTTCAATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
** * **
4679240 ATTTTTATTTTCAACCTTGGCTCAGTCCAGCC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* ** *
4679272 ATTTTTATCTTTGACCTTATTTCAG-CTCGATC
1 ATTTTTATTTTTGACCTTGGTTCAGTC-CAATC
* * ** * *
4679304 ATTTTCATCTTCAACC-TGGTTTAGTCCAGTC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
*
4679335 -TTTTTCATTTTTGACCTTGGTTCAG-CTCAGTC
1 ATTTTT-ATTTTTGACCTTGGTTCAGTC-CAATC
* * *
4679367 ATTTTTATCTTCGACCTTGGTTCAGTCCAGTC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * * * **
4679399 ATTTTTATCTTCGACTTTGGTTTAGTCTGATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * * * *
4679431 ATTTTCATTTTTGTCATTGGCTCAATCCAATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * * * * *
4679463 ATTTTTA-TCTTCACCTTCGTTTAGTTCGATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* ** * * **
4679494 ATTTTCACCTTCGACCTTGGTTCAGTTCGGTC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
** *
4679526 ATTTTTATTTTTGATTTTGGTTCGGTTCAATCCAATC
1 ATTTTTATTTTTGA----CCTT-GGTTCAGTCCAATC
* * *
4679563 ATTTTTATTTTTGGCCTTGATTTAGTCCAATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * *
4679595 ATTTTCATTTTTGACCTTGGCTT-AGTCCAGTG
1 ATTTTTATTTTTGACCTTGG-TTCAGTCCAATC
* ** * **
4679627 ATTTTTATCTTCAACCTTAGCTT-AGTCTGATC
1 ATTTTTATTTTTGACCTT-GGTTCAGTCCAATC
* *
4679659 ATTTTTATTTTTGACCTTGGTTTAGTCCGATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * * * *
4679691 ATTTTCATTTTTAACCTTGGTTCAATTCGATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
** *
4679723 ATTTTTATTTTTGGTCTTGGTTCAGTCCGATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * **
4679755 ATTTTTATTTTTGACCTTAGCTT-AATCCGGTC
1 ATTTTTATTTTTGACCTT-GGTTCAGTCCAATC
* * * * * * ****
4679787 ACTTTCATCTTGGACTTTGGTTTAGTTTGGTC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* * *
4679819 ATTTTCATTTTTGACATTGGTTCAGTCTAATC
1 ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
* *
4679851 ATTTTCATCTTTGACCTTGGTTCA
1 ATTTTTATTTTTGACCTTGGTTCA
4679875 ATTCGGTCAC
Statistics
Matches: 531, Mismatches: 147, Indels: 39
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.01
31 78 0.15
32 410 0.77
33 14 0.03
36 2 0.00
37 23 0.04
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (32 bp):
ATTTTTATTTTTGACCTTGGTTCAGTCCAATC
Found at i:4679893 original size:96 final size:96
Alignment explanation
Indices: 4679271--4679872 Score: 466
Period size: 96 Copynumber: 6.2 Consensus size: 96
4679261 TCAGTCCAGC
* * * *
4679271 CATTTTTATCTTTGACCTT-ATTTCAG-CTCGATCATTTTCATCTTCAACC-TGGTTTAGTCCAG
1 CATTTTTATCTTTGACCTTGGTTT-AGTC-CGATCATTTTCATCTTCGACCTTGGTTTAGTTCGG
* * *
4679333 TCTTTTTCATTTTTGACCTTGGTTCAG-CTCAGT
64 TCATTTTCATTTTTGACATTGGTTCAGTCT-AAT
* * * * *
4679366 CATTTTTATCTTCGACCTTGGTTCAGTCC-AGTCATTTTTATCTTCGACTTTGGTTTAG-TCTGA
1 CATTTTTATCTTTGACCTTGGTTTAGTCCGA-TCATTTTCATCTTCGACCTTGGTTTAGTTC-GG
* * * *
4679429 TCATTTTCATTTTTGTCATTGGCTCAATCCAAT
64 TCATTTTCATTTTTGACATTGGTTCAGTCTAAT
* * * * *
4679462 CATTTTTATC-TTCACCTTCGTTTAGTTCGATCATTTTCACCTTCGACCTTGGTTCAGTTCGGTC
1 CATTTTTATCTTTGACCTTGGTTTAGTCCGATCATTTTCATCTTCGACCTTGGTTTAGTTCGGTC
* ** *
4679526 ATTTTTATTTTTGATTTTGGTTCGGTTCAATCCAAT
66 ATTTTCATTTTTGACATTGGTTCAG-TC--T--AAT
* * * * * * * * * *
4679562 CATTTTTATTTTTGGCCTTGATTTAGTCCAATCATTTTCATTTTTGACCTTGGCTTAGTCCAGTG
1 CATTTTTATCTTTGACCTTGGTTTAGTCCGATCATTTTCATCTTCGACCTTGGTTTAGTTCGGTC
* * ** * * *
4679627 ATTTTTATCTTCAACCTTAGCTT-AGTCTGAT
66 ATTTTCATTTTTGACATT-GGTTCAGTCTAAT
* * ** * * *
4679658 CATTTTTATTTTTGACCTTGGTTTAGTCCGATCATTTTCATTTTTAACCTTGGTTCAATTCGATC
1 CATTTTTATCTTTGACCTTGGTTTAGTCCGATCATTTTCATCTTCGACCTTGGTTTAGTTCGGTC
* * **
4679723 ATTTTTATTTTTGGTC-TTGGTTCAGTCCGAT
66 ATTTTCATTTTT-GACATTGGTTCAGTCTAAT
* * * * * * * * *
4679754 CATTTTTATTTTTGACCTTAGCTTAATCCGGTCACTTTCATCTTGGACTTTGGTTTAGTTTGGTC
1 CATTTTTATCTTTGACCTTGGTTTAGTCCGATCATTTTCATCTTCGACCTTGGTTTAGTTCGGTC
4679819 ATTTTCATTTTTGACATTGGTTCAGTCTAAT
66 ATTTTCATTTTTGACATTGGTTCAGTCTAAT
*
4679850 CATTTTCATCTTTGACCTTGGTT
1 CATTTTTATCTTTGACCTTGGTT
4679873 CAATTCGGTC
Statistics
Matches: 394, Mismatches: 95, Indels: 35
0.75 0.18 0.07
Matches are distributed among these distances:
94 1 0.00
95 99 0.25
96 220 0.56
97 2 0.01
98 1 0.00
100 14 0.04
101 54 0.14
102 3 0.01
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (96 bp):
CATTTTTATCTTTGACCTTGGTTTAGTCCGATCATTTTCATCTTCGACCTTGGTTTAGTTCGGTC
ATTTTCATTTTTGACATTGGTTCAGTCTAAT
Found at i:4681224 original size:24 final size:24
Alignment explanation
Indices: 4681197--4681246 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4681187 AATAAATAAT
*
4681197 AATTATCAATGATAAAATTT-TAGA
1 AATTATAAATGAT-AAATTTCTAGA
*
4681221 AATTATAAATGATTAATTTCTAGA
1 AATTATAAATGATAAATTTCTAGA
4681245 AA
1 AA
4681247 ATTTTTAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
AATTATAAATGATAAATTTCTAGA
Found at i:4681855 original size:53 final size:52
Alignment explanation
Indices: 4681784--4681887 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
4681774 TTTAGGAAAA
* * *
4681784 ATATTTTTAAATTTGGCCCAAATGATAAAAAATTTAAAGATGAAACTTGTAAG
1 ATATTTCTAAATTAGGCCCAAATGAT-AAAAATTTAAAAATGAAACTTGTAAG
* * **
4681837 ATATTTCTAACTTAGGCCCAAATGGTGGAAATTTAAAAATGAAACTTGTAA
1 ATATTTCTAAATTAGGCCCAAATGATAAAAATTTAAAAATGAAACTTGTAA
4681888 AATAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 22 0.50
53 22 0.50
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (52 bp):
ATATTTCTAAATTAGGCCCAAATGATAAAAATTTAAAAATGAAACTTGTAAG
Found at i:4684127 original size:37 final size:37
Alignment explanation
Indices: 4684078--4684153 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
4684068 ATATAATGCC
4684078 TATATAATGTATGCAACAAAGTTAAAGACTATACAAA
1 TATATAATGTATGCAACAAAGTTAAAGACTATACAAA
4684115 TATATAATGTATGCAACAAAGTTAAAGACTATACAAA
1 TATATAATGTATGCAACAAAGTTAAAGACTATACAAA
4684152 TA
1 TA
4684154 AAAATGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (37 bp):
TATATAATGTATGCAACAAAGTTAAAGACTATACAAA
Found at i:4685888 original size:19 final size:19
Alignment explanation
Indices: 4685810--4685945 Score: 96
Period size: 19 Copynumber: 7.2 Consensus size: 19
4685800 TAGGTTTTCA
*
4685810 TTTAGGGTTTGCAC-TAAGG
1 TTTAGGGTTT-CACTTAGGG
* * * *
4685829 TTTCAAGGTTTTACTTTGAG
1 TTT-AGGGTTTCACTTAGGG
* *
4685849 TTTAGGGTTT-ATTTAGTG
1 TTTAGGGTTTCACTTAGGG
4685867 TTTAGGGTTTCACTTAGGG
1 TTTAGGGTTTCACTTAGGG
* *
4685886 TTTAGGGTTTCACCTAAGG
1 TTTAGGGTTTCACTTAGGG
** *
4685905 TTTAAAGTTTTACTTAGGG
1 TTTAGGGTTTCACTTAGGG
* * * *
4685924 TTCAAGGTTTCATTTAGAG
1 TTTAGGGTTTCACTTAGGG
4685943 TTT
1 TTT
4685946 TTTTAGGGTT
Statistics
Matches: 90, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
18 15 0.17
19 64 0.71
20 11 0.12
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.46
Consensus pattern (19 bp):
TTTAGGGTTTCACTTAGGG
Found at i:4685920 original size:38 final size:37
Alignment explanation
Indices: 4685810--4685935 Score: 128
Period size: 38 Copynumber: 3.3 Consensus size: 37
4685800 TAGGTTTTCA
* *
4685810 TTTAGGGTTTGCACTAAGGTTTCAAGGTTTTACTTTGAG
1 TTTAGGGTTT-CACTAAGGTTT-AAGGTTTTACTTAGGG
* * * *
4685849 TTTAGGGTTT-ATTTAGTGTTTAGGGTTTCACTTAGGG
1 TTTAGGGTTTCACTAAG-GTTTAAGGTTTTACTTAGGG
*
4685886 TTTAGGGTTTCACCTAAGGTTTAAAGTTTTACTTAGGG
1 TTTAGGGTTTCA-CTAAGGTTTAAGGTTTTACTTAGGG
* *
4685924 TTCAAGGTTTCA
1 TTTAGGGTTTCA
4685936 TTTAGAGTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
37 26 0.37
38 32 0.45
39 13 0.18
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (37 bp):
TTTAGGGTTTCACTAAGGTTTAAGGTTTTACTTAGGG
Found at i:4685984 original size:23 final size:22
Alignment explanation
Indices: 4685936--4685994 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
4685926 CAAGGTTTCA
*
4685936 TTTAGAGTTTT-TTTAGGGTTG
1 TTTAGGGTTTTATTTAGGGTTG
* *
4685957 TTTAGGGTTTTATTTAGAGTTTT
1 TTTAGGGTTTTATTTAG-GGTTG
*
4685980 TTTAGGGTTTCATTT
1 TTTAGGGTTTTATTT
4685995 GGTATTTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 10 0.31
22 5 0.16
23 17 0.53
ACGTcount: A:0.15, C:0.02, G:0.24, T:0.59
Consensus pattern (22 bp):
TTTAGGGTTTTATTTAGGGTTG
Found at i:4685989 original size:11 final size:11
Alignment explanation
Indices: 4685936--4685989 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
4685926 CAAGGTTTCA
*
4685936 TTTAGAGTTTT
1 TTTAGGGTTTT
*
4685947 TTTAGGG-TTG
1 TTTAGGGTTTT
4685957 TTTAGGGTTTT
1 TTTAGGGTTTT
*
4685968 ATTTAGAGTTTT
1 -TTTAGGGTTTT
4685980 TTTAGGGTTT
1 TTTAGGGTTT
4685990 CATTTGGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 9 0.25
11 17 0.47
12 10 0.28
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (11 bp):
TTTAGGGTTTT
Found at i:4688088 original size:22 final size:20
Alignment explanation
Indices: 4688054--4688109 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 20
4688044 TGGTACAAGT
4688054 TTTTTTTATATTTATTATATA
1 TTTTTTTATATTTATTAT-TA
4688075 TATTTTATTA-ATTTATTATTA
1 T-TTTT-TTATATTTATTATTA
4688096 TTTTTTTATATTTA
1 TTTTTTTATATTTA
4688110 ATGATCAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.09
20 9 0.28
21 4 0.12
22 13 0.41
23 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTTATATTTATTATTA
Found at i:4689751 original size:6 final size:6
Alignment explanation
Indices: 4689740--4689769 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
4689730 GAGAAAATAT
4689740 TTTTTA TTTTTA TTTTCTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTT-TA TTTTTA TTTTT
4689770 TAGAAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:4689755 original size:13 final size:13
Alignment explanation
Indices: 4689737--4689771 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4689727 TTTGAGAAAA
4689737 TATTTTTTATTTT
1 TATTTTTTATTTT
*
4689750 TATTTTCTATTTT
1 TATTTTTTATTTT
4689763 TATTTTTTA
1 TATTTTTTA
4689772 GAAAATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:4692944 original size:62 final size:56
Alignment explanation
Indices: 4692742--4693034 Score: 248
Period size: 56 Copynumber: 4.9 Consensus size: 56
4692732 TTTGAAGGTT
* * * *
4692742 TTTATTTT-AAGAAAAATTGATAATTTCAACTTTTCCTTAAAAAAAATATTTTTCTCGATAA
1 TTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCC-T--CAAAAATATTTTT-T--TTAA
* * * *
4692803 TTTTTATTTTTAAGAAAAATTGGTACTTTCAACTTTTCCTCAAAATATTTTTTTTTTAAA
1 --TTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCCTCAAAA-ATATTTTTTTT-AA
* * *
4692863 TTTTAATTTCAAGAAAAATTGATACTTTTAACTTCCTCCTCTAAAATATACTTTTTTTTTA
1 -TTTATTTTCAAGAAAAATTGATACTTTCAACTT-CTCCTC-AAAA-ATA-TTTTTTTTAA
* * * * *
4692924 TTTGTGTGTTCAA-AAGAAATTGATACATTCAACTTTTCTTCAACAATATTTTTTTTAA
1 TTTAT-T-TTCAAGAA-AAATTGATACTTTCAACTTCTCCTCAAAAATATTTTTTTTAA
* *
4692982 TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCGTCAAAAATATTTTTTT
1 TTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCCTCAAAAATATTTTTTT
4693035 AGAAATTTTA
Statistics
Matches: 196, Mismatches: 24, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
56 41 0.21
57 3 0.02
58 13 0.07
59 34 0.17
60 13 0.07
61 20 0.10
62 37 0.19
63 9 0.05
64 26 0.13
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (56 bp):
TTTATTTTCAAGAAAAATTGATACTTTCAACTTCTCCTCAAAAATATTTTTTTTAA
Found at i:4693099 original size:12 final size:12
Alignment explanation
Indices: 4693060--4693099 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
4693050 GGAAAATCAT
4693060 TAAAA-TAAATAA
1 TAAAATTAAA-AA
4693072 T-AAATTAAAAA
1 TAAAATTAAAAA
4693083 TAAAATTAAAAA
1 TAAAATTAAAAA
4693095 TAAAA
1 TAAAA
4693100 AATTAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAAATTAAAAA
Found at i:4694383 original size:44 final size:44
Alignment explanation
Indices: 4694264--4694396 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 44
4694254 ATTTTTGGAG
* * *
4694264 AATAAATAAAATTTCTCTAAAT-AGAGGCTCAACAAC-TTTGAAAA
1 AATAAATAAAACTTCTCT-AATCAGAGGCTTAACGACTTTTG-AAA
* *
4694308 AATAAACAAAACCTTCTATAATCAGAGGCTTAACGACTTTTGAAA
1 AATAAATAAAA-CTTCTCTAATCAGAGGCTTAACGACTTTTGAAA
* * *
4694353 AATAAATAAAGCTCCTCTAATCAGAGGCTTAACGACTTTGGAAA
1 AATAAATAAAACTTCTCTAATCAGAGGCTTAACGACTTTTGAAA
4694397 GTAAATTGCT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
44 43 0.57
45 29 0.38
46 4 0.05
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (44 bp):
AATAAATAAAACTTCTCTAATCAGAGGCTTAACGACTTTTGAAA
Found at i:4694454 original size:42 final size:41
Alignment explanation
Indices: 4694400--4694524 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 41
4694390 TTGGAAAGTA
* *
4694400 AATTGCTCCTCTATACAGAAGCAACCACAACTTCAAAAAATT
1 AATTGCTTCTCTAAACAGAAGCAACCACAACTTCAAAAAA-T
*
4694442 AATTGCTTCTCTAAACAGAAGCAACCACGACTTCAAAAAAT
1 AATTGCTTCTCTAAACAGAAGCAACCACAACTTCAAAAAAT
* * * *
4694483 AAATGCTTCTCTAAATAG-AG-ACACCACAATTTAAAAAAAT
1 AATTGCTTCTCTAAACAGAAGCA-ACCACAACTTCAAAAAAT
4694523 AA
1 AA
4694525 AATGCTCCTC
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 19 0.26
41 17 0.23
42 37 0.50
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.23
Consensus pattern (41 bp):
AATTGCTTCTCTAAACAGAAGCAACCACAACTTCAAAAAAT
Found at i:4695022 original size:21 final size:20
Alignment explanation
Indices: 4694998--4695183 Score: 87
Period size: 21 Copynumber: 8.9 Consensus size: 20
4694988 GTTTCACATA
4694998 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTG-AAT
4695019 TCAAAGATTCTCATTTGAAT
1 TCAAAGATTCTCATTTGAAT
* * *
4695039 TCGAAGATTCACATTCG-A-
1 TCAAAGATTCTCATTTGAAT
* ** *
4695057 T--AA-ATTTTGGGTTTCACACCT
1 TCAAAGATTCT-CATTTGA-A--T
4695078 T-AAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTG-AAT
*
4695098 TCAAAGATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTG-AAT
* * *
4695119 TAAAAAATTATCATTTGAAAAT
1 TCAAAGATTCTCATTTG--AAT
* * *
4695141 GTCTTAAAGATTTTCATTTAGGAC
1 -TC--AAAGATTCTCATTT-GAAT
4695165 TCAAAGATTCTCATTTGAA
1 TCAAAGATTCTCATTTGAA
4695184 AACATTTTAA
Statistics
Matches: 125, Mismatches: 25, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
15 3 0.02
16 4 0.03
18 2 0.02
19 1 0.01
20 21 0.17
21 63 0.50
22 9 0.07
23 8 0.06
24 1 0.01
25 12 0.10
26 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
TCAAAGATTCTCATTTGAAT
Found at i:4695083 original size:79 final size:80
Alignment explanation
Indices: 4694958--4695116 Score: 248
Period size: 79 Copynumber: 2.0 Consensus size: 80
4694948 TTTTCATTAG
*
4694958 TTCGAAGATTCACACCCAACAAATTTTAGGGTTTCACATATCAAAGATTCTCATTTGAAATTCAA
1 TTCGAAGATTCACACCCAACAAATTTTAGGGTTTCACACATCAAAGATTCTCATTTGAAATTCAA
4695023 AGATTCTCATTTGAA
66 AGATTCTCATTTGAA
** * * * *
4695038 TTCGAAGATTCACATTCGATAAATTTT-GGGTTTCACACCTTAAAGATTCTCATTTGAAATTCAA
1 TTCGAAGATTCACACCCAACAAATTTTAGGGTTTCACACATCAAAGATTCTCATTTGAAATTCAA
4695102 AGATTCTCATTTGAA
66 AGATTCTCATTTGAA
4695117 ACTAAAAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 49 0.68
80 23 0.32
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (80 bp):
TTCGAAGATTCACACCCAACAAATTTTAGGGTTTCACACATCAAAGATTCTCATTTGAAATTCAA
AGATTCTCATTTGAA
Found at i:4695194 original size:46 final size:46
Alignment explanation
Indices: 4695079--4695772 Score: 478
Period size: 46 Copynumber: 14.9 Consensus size: 46
4695069 TTCACACCTT
* *
4695079 AAAGATTCTCATTTG--AA-AT-TCAAAGATTCTCATTTGAA-ACTA
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT-AAGACTC
* * ** * *
4695121 AAAAATTATCATTTGAAAATGTCTTAAAGATTTTCATTTAGGACTC
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAGACTC
* * * *
4695167 AAAGATTCTCATTTGAAAACATTTTAAAAATTCTCATTTAAGAAATGTTTT
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAG--A---CTC
* * ** * *
4695218 AAAGATTCTCATTT-AAGAC-TC--AAAGATTTTTTTTTGGAAATGTCTT
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT---AA-GACTC
* * *
4695264 AAAGATTCTCATTT---AAGA-CTTAAAGATTCTCATTTGAAAATGTCTT
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT---AA-GACTC
** * *
4695310 AAAGATTCTCATTT-ATGAAATGTCTTAAAGATTTTGATTTAAGACTC
1 AAAGATTCTCATTTGA--AAACATCTTAAAGATTCTCATTTAAGACTC
* ** * **
4695357 AAAGATTTTTTTTTTAGAAATGTCTTAAAGATTCTCATTTAAGACTC
1 AAAGATTCTCATTTGA-AAACATCTTAAAGATTCTCATTTAAGACTC
* *
4695404 AAAGATTCTCATTTGAAAACATCTTAAAGGTTCTCATTTAAGAAATGTCTT
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAG--A---CTC
* * * *
4695455 AAAGATTTTCATTT-AAAAC-TC--AAAGATTCTTATTTGAAAATGTCTT
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT---AA-GACTC
* *
4695501 AAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGAAAACGTC
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT-AAGAC-TC
* * *
4695545 TTAAAGATTCTCATTTAAGAAACGTCTTAAAGATTCTCATTTGAGACTC
1 --AAAGATTCTCATTTGA-AAACATCTTAAAGATTCTCATTTAAGACTC
* ** * *
4695594 AAAGATTTTTTTTTGCAAATATCTTAAAGATTCTCATTTAAGACTC
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAGACTC
**
4695640 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAGACTC
** * *
4695686 AAAGATTCTTTTTTGAAAATATCTTAAAGATTCTCATTTAAGACTT
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAGACTC
4695732 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
1 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
4695773 AAAACATCTT
Statistics
Matches: 528, Mismatches: 84, Indels: 76
0.77 0.12 0.11
Matches are distributed among these distances:
42 13 0.02
43 1 0.00
44 7 0.01
45 2 0.00
46 322 0.61
47 89 0.17
48 8 0.02
49 7 0.01
50 18 0.03
51 61 0.12
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (46 bp):
AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAGACTC
Found at i:4695225 original size:26 final size:26
Alignment explanation
Indices: 4695167--4695942 Score: 196
Period size: 21 Copynumber: 32.8 Consensus size: 26
4695157 TTTAGGACTC
*
4695167 AAAGATTCTCATTTGA-AAACATTTT
1 AAAGATTCTCATTTAAGAAACATTTT
* **
4695192 AAAAATTCTCATTTAAGAAATGTTTT
1 AAAGATTCTCATTTAAGAAACATTTT
*
4695218 AAAGATTCTCATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
** ** ** *
4695239 AAAGATT-TTTTTTTGGAAATGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
4695264 AAAGATTCTCATTTAAG--AC---TT
1 AAAGATTCTCATTTAAGAAACATTTT
4695285 AAAGATTCTCATTT--GAAA-ATGTCTT
1 AAAGATTCTCATTTAAGAAACAT-T-TT
* ** *
4695310 AAAGATTCTCATTTATGAAATGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* * *
4695336 AAAGATTTTGATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
* ** * ** *
4695357 AAAGATTTTTTTTTTAGAAATGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
*
4695383 AAAGATTCTCATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
* *
4695404 AAAGATTCTCATTTGA-AAACATCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* ** *
4695429 AAAGGTTCTCATTTAAGAAATGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* *
4695455 AAAGATTTTCATTT-A-AAAC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
*
4695476 AAAGATTCTTATTT--GAAA-ATGTCTT
1 AAAGATTCTCATTTAAGAAACAT-T-TT
*
4695501 AAAGATTCTCATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
* * *
4695522 AAAGATTCTCATTTGA-AAACGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* *
4695547 AAAGATTCTCATTTAAGAAACGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* *
4695573 AAAGATTCTCATTT--GAGAC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
* ** * *
4695594 AAAGATT-T-TTTTTTGCAAATATCTT
1 AAAGATTCTCATTTAAG-AAACATTTT
*
4695619 AAAGATTCTCATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
4695640 AAAGATTCTCATTT--GAAA-ATGTCTT
1 AAAGATTCTCATTTAAGAAACAT-T-TT
*
4695665 AAAGATTCTCATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
** * * *
4695686 AAAGATTCTTTTTTGA-AAATATCTT
1 AAAGATTCTCATTTAAGAAACATTTT
4695711 AAAGATTCTCATTTAAG--AC---TT
1 AAAGATTCTCATTTAAGAAACATTTT
* *
4695732 AAAGATTCTCATTTGA-AAACATCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* *
4695757 AAAGATTCTCATTTAAAAAACATCTT
1 AAAGATTCTCATTTAAGAAACATTTT
* * *
4695783 AAAGGTTTTCATTTAAG--AC---TC
1 AAAGATTCTCATTTAAGAAACATTTT
* * *
4695804 AAAGATTCTCATTT-GGAAATATCTT
1 AAAGATTCTCATTTAAGAAACATTTT
*
4695829 AAAAATTCTCATTTAAG--AC---TT
1 AAAGATTCTCATTTAAGAAACATTTT
*
4695850 AGAGATTCTCATTT--GAAA-ATGTCTT
1 AAAGATTCTCATTTAAGAAACAT-T-TT
* *
4695875 AAAAATTCTCATTTAAG--A-A--TC
1 AAAGATTCTCATTTAAGAAACATTTT
* * *
4695896 AAAGATTCTCATTTGA-AAACGTCTT
1 AAAGATTCTCATTTAAGAAACATTTT
*
4695921 AAAGATTTTCATTTAAGAAACA
1 AAAGATTCTCATTTAAGAAACA
4695943 AAGATTCTCA
Statistics
Matches: 555, Mismatches: 102, Indels: 187
0.66 0.12 0.22
Matches are distributed among these distances:
19 6 0.01
20 7 0.01
21 187 0.34
22 12 0.02
23 1 0.00
24 16 0.03
25 185 0.33
26 129 0.23
27 11 0.02
28 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (26 bp):
AAAGATTCTCATTTAAGAAACATTTT
Found at i:4695230 original size:72 final size:72
Alignment explanation
Indices: 4695076--4695960 Score: 471
Period size: 72 Copynumber: 12.6 Consensus size: 72
4695066 GGTTTCACAC
* * * * * *
4695076 CTTAAAGATTCTCATTT-GAAATTCAAAGATTCTCATTTG--AA-A-CTAAAAAATTATCATTTG
1 CTTAAAGATTCTCATTTAG-GACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTA
4695136 A-AAATGT
65 AGAAATGT
* * *
4695143 CTTAAAGATTTTCATTTAGGACTCAAAGATTCTCATTTGAAAACATTTTAAAAATTCTCATTTAA
1 CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
4695208 GAAATGT
66 GAAATGT
* * * ** * **
4695215 TTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTGGAAATGTCTTAAAGATTCTCATTTAA
1 CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
4695280 G--A---
66 GAAATGT
* * * ** * *
4695282 CTTAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTT-ATGAAATGTCTTAAAGATTTTG
1 CTTAAAGATTCTCATTT----AGGACTCAAAGATTCTCATTTGA--AAACATCTTAAAGATTCTC
4695346 ATTTAAG--A---
60 ATTTAAGAAATGT
* * ** * * *
4695354 CTCAAAGATTTTTTTTTTAGAAATGTCTTAAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCA
1 CTTAAAGA-TTCTCATTTAG----GACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCA
* **
4695415 TTTGA-AAACAT
61 TTTAAGAAATGT
* * * * *
4695426 CTTAAAGGTTCTCATTTAAGAAATGTCTTAAAGATTTTCATTT-AAAAC-TC--AAAGATTCTTA
1 CTTAAAGATTCTCATTT-AG----GACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCA
*
4695487 TTTGA-AAATGT
61 TTTAAGAAATGT
* *
4695498 CTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGTCTTAAAGATTCTCATTTAA
1 CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
*
4695563 GAAACGT
66 GAAATGT
* ** * *
4695570 CTTAAAGATTCTCATTT-GAGACTCAAAGATTTTTTTTTGCAAATATCTTAAAGATTCTCATTTA
1 CTTAAAGATTCTCATTTAG-GACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTA
4695634 AG--A---
65 AGAAATGT
* * * * * **
4695637 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTT-AAGAC-TC--AAAGATTCTTTT
1 CTTAAAGATTCTCATTT----AGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCAT
* *
4695698 TTGA-AAATAT
62 TTAAGAAATGT
* *
4695708 CTTAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
1 CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
* **
4695773 AAAACAT
66 GAAATGT
* * * * * *
4695780 CTTAAAGGTTTTCATTTAAGACTCAAAGATTCTCATTTGGAAATATCTTAAAAATTCTCATTTAA
1 CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
4695845 G--A---
66 GAAATGT
* * * * * *
4695847 CTTAGAGATTCTCATTTGAAAATGTCTTAAAAATTCTCATTT-AAGA-ATC--AAAGATTCTCAT
1 CTTAAAGATTCTCATTT----AGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCAT
* *
4695908 TTGA-AAACGT
62 TTAAGAAATGT
* * ** *
4695918 CTTAAAGATTTTCATTTAAGAAACAAAGATTCTCATGTGAAAA
1 CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAA
4695961 TGTAGGACTT
Statistics
Matches: 652, Mismatches: 112, Indels: 107
0.75 0.13 0.12
Matches are distributed among these distances:
67 156 0.24
68 28 0.04
69 13 0.02
70 10 0.02
71 128 0.20
72 291 0.45
73 26 0.04
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (72 bp):
CTTAAAGATTCTCATTTAGGACTCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAA
GAAATGT
Found at i:4695276 original size:118 final size:118
Alignment explanation
Indices: 4695076--4695682 Score: 893
Period size: 118 Copynumber: 5.2 Consensus size: 118
4695066 GGTTTCACAC
* * * **
4695076 CTTAAAGATTCTCATTT--GAAAT-TC--AAAGATTCTCATTTGAA-ACTAAAAAATTATCATTT
1 CTTAAAGATTCTCATTTAAGAAATGTCTTAAAGATTCTCATTT-AAGACTCAAAGATTTTTTTTT
* * *
4695135 GAAAATGTCTTAAAGATTTTCATTTAGGACTCAAAGATTCTCATTTGAAAACAT
65 GAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
* * *
4695189 TTTAAAAATTCTCATTTAAGAAATGTTTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTG
1 CTTAAAGATTCTCATTTAAGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTG
* * *
4695254 GAAATGTCTTAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAATGT
66 AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
* * * *
4695307 CTTAAAGATTCTCATTTATGAAATGTCTTAAAGATTTTGATTTAAGACTCAAAGATTTTTTTTTT
1 CTTAAAGATTCTCATTTAAGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTG
*
4695372 AGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACAT
66 A-AAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
* * * * *
4695426 CTTAAAGGTTCTCATTTAAGAAATGTCTTAAAGATTTTCATTTAAAACTCAAAGATTCTTATTTG
1 CTTAAAGATTCTCATTTAAGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTG
4695491 AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
66 AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
* *
4695544 CTTAAAGATTCTCATTTAAGAAACGTCTTAAAGATTCTCATTTGAGACTCAAAGATTTTTTTTTG
1 CTTAAAGATTCTCATTTAAGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTG
* * *
4695609 CAAATATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGT
66 AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
4695662 CTTAAAGATTCTCATTTAAGA
1 CTTAAAGATTCTCATTTAAGA
4695683 CTCAAAGATT
Statistics
Matches: 444, Mismatches: 43, Indels: 9
0.90 0.09 0.02
Matches are distributed among these distances:
113 15 0.03
115 5 0.01
116 1 0.00
117 2 0.00
118 313 0.70
119 108 0.24
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (118 bp):
CTTAAAGATTCTCATTTAAGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTG
AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGT
Found at i:4695693 original size:210 final size:210
Alignment explanation
Indices: 4695404--4695960 Score: 808
Period size: 210 Copynumber: 2.6 Consensus size: 210
4695394 TTTAAGACTC
* * * *
4695404 AAAGATTCTCATTTGAAAACATCTTAAAGGTTCTCATTTAAGAAATGTCTTAAAGATTTTCATTT
1 AAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGA-AAATGTCTTAAAGATTCTCATTT
*
4695469 AAAACTCAAAGATTCTTATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCAT
61 AAGACTCAAAGATTCTTATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCAT
* * * *
4695534 TTGAAAACGTCTTAAAGATTCTCATTTAAGAAACGTCTTAAAGATTCTCATTTGAGACTCAAAGA
126 TTGAAAACATCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCATTTAAGACTCAAAGA
* **
4695599 TTTTTTTTTGCAAATATCTT
191 TTCTCATTTGCAAATATCTT
4695619 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGAC
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGAC
* * *
4695684 TCAAAGATTCTTTTTTGAAAATATCTTAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAA
66 TCAAAGATTCTTATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAA
* *
4695749 AACATCTTAAAGATTCTCATTTAAAAAACATCTTAAAGGTTTTCATTTAAGACTCAAAGATTCTC
131 AACATCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTC
*
4695814 ATTTGGAAATATCTT
196 ATTTGCAAATATCTT
* * * * *
4695829 AAAAATTCTCATTTAAGACTTAGAGATTCTCATTTGAAAATGTCTTAAAAATTCTCATTTAAGAA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGAC
* * * ** *
4695894 TCAAAGATTCTCATTTGAAAACGTCTTAAAGATTTTCATTTAAGAAACAAAGATTCTCATGTGAA
66 TCAAAGATTCTTATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAA
4695959 AA
131 AA
4695961 TGTAGGACTT
Statistics
Matches: 310, Mismatches: 32, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
210 276 0.89
211 14 0.05
213 2 0.01
214 4 0.01
215 14 0.05
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (210 bp):
AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGAC
TCAAAGATTCTTATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAA
AACATCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTC
ATTTGCAAATATCTT
Found at i:4695786 original size:118 final size:117
Alignment explanation
Indices: 4695380--4695890 Score: 414
Period size: 118 Copynumber: 4.4 Consensus size: 117
4695370 TTAGAAATGT
* * *
4695380 CTTAAAGATTCTCATTT-AAGACTC--AAAGATTCTCATTT-GAAAACATCTTAAAGGTTCTCAT
1 CTTAAAGATTCTCATTTGAAAACTCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCAT
* * * * * *
4695441 TTAAGAAATGTCTTAAAGATTTTCATTT--AAA-A-CTCAAAGATTCTTATTTGAAAATGT
66 TTAAG--A---CTCAAAGATTCTCATTTGAAAATATCTTAAAAATTCTCATTT---AA-GA
* * *
4695498 CTTAAAGATTCTCATTT-AAGACTC--AAAGATTCTCATTT-GAAAACGTCTTAAAGATTCTCAT
1 CTTAAAGATTCTCATTTGAAAACTCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCAT
* * * * ** *
4695559 TTAAGAAACGTCTTAAAGATTCTCATTTG---AGA-CTCAAAGATTTTTTTTTGCAAATA
66 TTAAG--AC-TC--AAAGATTCTCATTTGAAAATATCTTAAAAATTCTCATTT---AAGA
* * **
4695615 TCTTAAAGATTCTCATTT-AAGACTC--AAAGATTCTCATTT-GAAAATGTCTTAAAGATTCTCA
1 -CTTAAAGATTCTCATTTGAAAACTCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCA
** *
4695676 TTTAAGACTCAAAGATTCTTTTTTGAAAATATCTTAAAGATTCTCATTTAAGA
65 TTTAAGACTCAAAGATTCTCATTTGAAAATATCTTAAAAATTCTCATTTAAGA
* *
4695729 CTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAAAAACATCTTAAAGGTTTTCA
1 CTTAAAGATTCTCATTTGAAAAC-TCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCA
*
4695794 TTTAAGACTCAAAGATTCTCATTTGGAAATATCTTAAAAATTCTCATTTAAGA
65 TTTAAGACTCAAAGATTCTCATTTGAAAATATCTTAAAAATTCTCATTTAAGA
* * *
4695847 CTTAGAGATTCTCATTTGAAAATGTCTTAAAAATTCTCATTTAA
1 CTTAAAGATTCTCATTTGAAAA-CTCTTAAAGATTCTCATTTAA
4695891 GAATCAAAGA
Statistics
Matches: 346, Mismatches: 31, Indels: 32
0.85 0.08 0.08
Matches are distributed among these distances:
113 30 0.09
114 7 0.02
115 5 0.01
116 5 0.01
117 28 0.08
118 271 0.78
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (117 bp):
CTTAAAGATTCTCATTTGAAAACTCTTAAAGATTCTCATTTAAAAAACATCTTAAAGATTCTCAT
TTAAGACTCAAAGATTCTCATTTGAAAATATCTTAAAAATTCTCATTTAAGA
Found at i:4695842 original size:46 final size:46
Alignment explanation
Indices: 4695216--4695960 Score: 413
Period size: 46 Copynumber: 15.9 Consensus size: 46
4695206 AAGAAATGTT
* ** * **
4695216 TTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTGGAAATGTC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
* **
4695262 TTAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAATGTC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
* * * * *
4695308 TTAAAGATTCTCATTTATGAAATGTCTTAAAGATTTTGATTT-AAGAC-TC
1 TTAAAGATTCTCA-TT-T--AA-GACTCAAAGATTCTCATTTGAAAACATC
* ** * * *
4695357 --AAAGATTTTTTTTTTAGAAATGTCTTAAAGATTCTCATTT-AAGAC-TC
1 TTAAAGA-TTCTCATTT---AA-GACTCAAAGATTCTCATTTGAAAACATC
* * * **
4695404 --AAAGATTCTCATTTGAAAACATCTTAAAGGTTCTCATTTAAGAAATGTC
1 TTAAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGA-AAACATC
* * * **
4695453 TTAAAGATTTTCATTTAAAACTCAAAGATTCTTATTTGAAAATGTC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
*
4695499 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACGTC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
*
4695545 TTAAAGATTCTCATTTAAGAAACGTCTTAAAGATTCTCATTTG-AGAC-TC
1 TTAAAGATTCTCATTTAAG--AC-TC--AAAGATTCTCATTTGAAAACATC
* ** * * *
4695594 --AAAGATTTTTTTTTGCAAATATCTTAAAGATTCTCATTT-AAGAC-TC
1 TTAAAGATTCTCATTT---AAGA-CTCAAAGATTCTCATTTGAAAACATC
* * *
4695640 --AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTT-AAGAC-TC
1 TTAAAGATTCTCATTT---AA-GACTCAAAGATTCTCATTTGAAAACATC
** * * *
4695686 --AAAGATTCTTTTTTGAAAATATCTTAAAGATTCTCATTT---AAGA-C
1 TTAAAGATTCTCATTT---AAGA-CTCAAAGATTCTCATTTGAAAACATC
* *
4695730 TTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAAAAACATC
1 TTAAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTT-GAAAACATC
* * * *
4695781 TTAAAGGTTTTCATTTAAGACTCAAAGATTCTCATTTGGAAATATC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
* * * **
4695827 TTAAAAATTCTCATTTAAGACTTAGAGATTCTCATTTGAAAATGTC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
* * *
4695873 TTAAAAATTCTCATTTAAGAATCAAAGATTCTCATTTGAAAACGTC
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
* ** *
4695919 TTAAAGATTTTCATTTAAGAAACAAAGATTCTCATGTGAAAA
1 TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAA
4695961 TGTAGGACTT
Statistics
Matches: 583, Mismatches: 78, Indels: 76
0.79 0.11 0.10
Matches are distributed among these distances:
43 2 0.00
44 9 0.02
46 386 0.66
47 82 0.14
48 10 0.02
49 13 0.02
50 22 0.04
51 59 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (46 bp):
TTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
Found at i:4695935 original size:164 final size:164
Alignment explanation
Indices: 4695196--4695942 Score: 888
Period size: 164 Copynumber: 4.5 Consensus size: 164
4695186 CATTTTAAAA
* * * ** * **
4695196 ATTCTCATTTAAGAAATGTTTTAAAGATTCTCATTTAAGACTCAAAGATTTTTTTTTGGAAATGT
1 ATTCTCATTTGA-AAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACAT
* *
4695261 CTTAAAGATTCTCATTTAAG----A-CTTAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCA
65 CTTAAAGATTCTCATTTAAGAAACATCTTAAAGATTCTCATTT---AA-GACTCAAAGATTCTCA
* *
4695321 TTT-ATGAAATGTCTTAAAGATTTTGATTTAAGACTCAAAG
126 TTTGA--AAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
* ** *
4695361 ATTTTTTTTTTAGAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACAT
1 ATTCTCATTTGA-AAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACAT
* ** * * *
4695426 CTTAAAGGTTCTCATTTAAGAAATGTCTTAAAGATTTTCATTTAAAACTCAAAGATTCTTATTTG
65 CTTAAAGATTCTCATTTAAGAAACATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTG
4695491 AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
130 AAAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
* *
4695526 ATTCTCATTTGAAAACGTCTTAAAGATTCTCATTTAAGAAACGTCTTAAAGATTCTCATTTG-AG
1 ATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAG--AC-TC--AAAGATTCTCATTTGAAA
* ** *
4695590 AC-TC--AAAGATT-T-TTTTTTGCAAATATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTC
61 ACATCTTAAAGATTCTCATTTAAG-AAACATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTC
4695650 ATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
125 ATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
** * *
4695690 ATTCTTTTTTGAAAATATCTTAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAACATC
1 ATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
* * * *
4695755 TTAAAGATTCTCATTTAAAAAACATCTTAAAGGTTTTCATTTAAGACTCAAAGATTCTCATTTGG
66 TTAAAGATTCTCATTTAAGAAACATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGA
* * * *
4695820 AAATATCTTAAAAATTCTCATTTAAGACTTAGAG
131 AAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
* * *
4695854 ATTCTCATTTGAAAATGTCTTAAAAATTCTCATTTAAGAATCAAAGATTCTCATTTGAAAACGTC
1 ATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
*
4695919 TTAAAGATTTTCATTTAAGAAACA
66 TTAAAGATTCTCATTTAAGAAACA
4695943 AAGATTCTCA
Statistics
Matches: 503, Mismatches: 61, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
159 15 0.03
160 3 0.01
161 3 0.01
162 2 0.00
163 11 0.02
164 289 0.57
165 122 0.24
166 17 0.03
167 7 0.01
168 3 0.01
169 15 0.03
170 16 0.03
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (164 bp):
ATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATC
TTAAAGATTCTCATTTAAGAAACATCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGA
AAATGTCTTAAAGATTCTCATTTAAGACTCAAAG
Found at i:4697140 original size:8 final size:8
Alignment explanation
Indices: 4697119--4697221 Score: 102
Period size: 8 Copynumber: 12.0 Consensus size: 8
4697109 ATTTTCTCTT
4697119 ATTTTTATC
1 ATTTTT-TC
4697128 -TTTTTTCC
1 ATTTTTT-C
4697136 ATTTTTTC
1 ATTTTTTC
4697144 ATTTTTTC
1 ATTTTTTC
4697152 ATTTTTTC
1 ATTTTTTC
4697160 ATTTTTTC
1 ATTTTTTC
4697168 ATTTTTCTCTC
1 A-TTTT-T-TC
4697179 ATTTTTTC
1 ATTTTTTC
*
4697187 TCTTTTTCTC
1 -ATTTTT-TC
4697197 ATTTTTTTTC
1 A--TTTTTTC
4697207 -TTTTTTC
1 ATTTTTTC
4697214 ATTTTTTC
1 ATTTTTTC
4697222 TTCCTCTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 21
0.78 0.02 0.20
Matches are distributed among these distances:
7 8 0.10
8 41 0.50
9 16 0.20
10 9 0.11
11 8 0.10
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTC
Found at i:4697140 original size:27 final size:25
Alignment explanation
Indices: 4697108--4697247 Score: 97
Period size: 27 Copynumber: 5.2 Consensus size: 25
4697098 TTTGAGTCTT
4697108 CATTTTCTCTTATTTTTATCTTTTTTC
1 CATTTTCTCTT-TTTTT-TCTTTTTTC
* *
4697135 CATTTTTTC-ATTTTTTCATTTTTT-
1 CATTTTCTCTTTTTTTTC-TTTTTTC
* *
4697159 CATTTTTTCATTTTTCTCTCATTTTTTC
1 CATTTTCTC-TTTTT-TTTC-TTTTTTC
*
4697187 TCTTTTTCTCATTTTTTTTCTTTTTT-
1 -CATTTTCTC-TTTTTTTTCTTTTTTC
*
4697213 CATTTTTTCTTCCTCTTTTTCTTTTTTC
1 CATTTTCTCTT--T-TTTTTCTTTTTTC
4697241 TCATTTT
1 -CATTTT
4697248 TTTCATTCTG
Statistics
Matches: 93, Mismatches: 9, Indels: 20
0.76 0.07 0.16
Matches are distributed among these distances:
24 13 0.14
25 18 0.19
26 4 0.04
27 36 0.39
28 3 0.03
29 19 0.20
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.73
Consensus pattern (25 bp):
CATTTTCTCTTTTTTTTCTTTTTTC
Found at i:4697141 original size:18 final size:18
Alignment explanation
Indices: 4697120--4697220 Score: 57
Period size: 18 Copynumber: 5.3 Consensus size: 18
4697110 TTTTCTCTTA
4697120 TTTTTATCTTTTTTCCAT
1 TTTTTATCTTTTTTCCAT
4697138 TTTTTCATTTTTTCATTTTTT-CAT
1 TTTTT-A-----TC-TTTTTTCCAT
*
4697162 TTTTTCAT-TTTTCTCTCAT
1 TTTTT-ATCTTTTTTC-CAT
*
4697181 TTTTTCTC-TTTTTCTCAT
1 TTTTTATCTTTTTTC-CAT
*
4697199 TTTTTTTCTTTTTT-CAT
1 TTTTTATCTTTTTTCCAT
4697216 TTTTT
1 TTTTT
4697221 CTTCCTCTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
17 13 0.19
18 22 0.32
19 15 0.22
24 12 0.18
25 6 0.09
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTATCTTTTTTCCAT
Found at i:4697155 original size:43 final size:44
Alignment explanation
Indices: 4697119--4697254 Score: 133
Period size: 46 Copynumber: 3.1 Consensus size: 44
4697109 ATTTTCTCTT
4697119 ATTTTTATC-TTTTT-TC-CATTTTTTC-ATTTTTTCATTTTTTC
1 ATTTTT-TCATTTTTCTCTCATTTTTTCTATTTTTTCATTTTTTC
*
4697160 ATTTTTTCATTTTTCTCTCATTTTTTCTCTTTTTCTCATTTTTTTTC
1 ATTTTTTCATTTTTCTCTCATTTTTTCTATTTTT-TCA--TTTTTTC
*
4697207 -TTTTTTCATTTTT-TCTTCCTCTTTTTCT-TTTTTCTCATTTTTTTC
1 ATTTTTTCATTTTTCTC-TCAT-TTTTTCTATTTTT-TCA-TTTTTTC
4697252 ATT
1 ATT
4697255 CTGCTTTTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 15
0.83 0.02 0.15
Matches are distributed among these distances:
40 2 0.02
41 11 0.13
42 2 0.02
43 9 0.11
44 5 0.06
45 13 0.16
46 27 0.33
47 14 0.17
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (44 bp):
ATTTTTTCATTTTTCTCTCATTTTTTCTATTTTTTCATTTTTTC
Found at i:4697216 original size:35 final size:35
Alignment explanation
Indices: 4697110--4697254 Score: 129
Period size: 35 Copynumber: 4.0 Consensus size: 35
4697100 TGAGTCTTCA
* *
4697110 TTTTCTCTTATTTTTATCTTTTTTCCATTTTTTCATT
1 TTTTCTCTT-TTTTCAT-TTTTTTTCATTTTTTCATT
*
4697147 TTTTC-ATTTTTTCA--TTTTTTCATTTTTCTCTCATT
1 TTTTCTCTTTTTTCATTTTTTTTCA-TTTT-T-TCATT
4697182 TTTTCTCTTTTTCTCATTTTTTTTC-TTTTTTCATT
1 TTTTCTCTTTTT-TCATTTTTTTTCATTTTTTCATT
*
4697217 TTTTCTTCCTCTTTTTC-TTTTTTCTCATTTTTTTCATT
1 TTTTC-T-CT-TTTTTCATTTTTTTTCA-TTTTTTCATT
4697255 CTGCTTTTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 23
0.76 0.04 0.19
Matches are distributed among these distances:
32 7 0.08
33 4 0.04
34 1 0.01
35 25 0.27
36 17 0.19
37 16 0.18
38 14 0.15
39 7 0.08
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (35 bp):
TTTTCTCTTTTTTCATTTTTTTTCATTTTTTCATT
Found at i:4697231 original size:19 final size:18
Alignment explanation
Indices: 4697139--4697241 Score: 76
Period size: 18 Copynumber: 5.8 Consensus size: 18
4697129 TTTTTCCATT
*
4697139 TTTTCATTTTTTCAT-T-
1 TTTTCATTTTTTCTTCTC
4697155 TTTTCATTTTTTCATT-T-
1 TTTTCATTTTTTC-TTCTC
*
4697172 TTCTCTCATTTTTTC-TCTT
1 TT-T-TCATTTTTTCTTCTC
*
4697191 TTTCTCATTTTTT-TTCTT
1 TTT-TCATTTTTTCTTCTC
4697209 TTTTCATTTTTTCTTCCTC
1 TTTTCATTTTTTCTT-CTC
4697228 TTTTTC-TTTTTTCT
1 -TTTTCATTTTTTCT
4697242 CATTTTTTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
16 13 0.17
17 14 0.18
18 22 0.29
19 22 0.29
20 5 0.07
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCATTTTTTCTTCTC
Found at i:4697239 original size:8 final size:8
Alignment explanation
Indices: 4697120--4697251 Score: 68
Period size: 8 Copynumber: 15.0 Consensus size: 8
4697110 TTTTCTCTTA
*
4697120 TTTTTATC
1 TTTTTTTC
*
4697128 TTTTTTCC
1 TTTTTTTC
*
4697136 ATTTTTTC
1 TTTTTTTC
*
4697144 ATTTTTTC
1 TTTTTTTC
*
4697152 ATTTTTTC
1 TTTTTTTC
*
4697160 ATTTTTTC
1 TTTTTTTC
4697168 ATTTTTCTCTC
1 -TTTTT-T-TC
4697179 ATTTTTTCTC
1 -TTTTTT-TC
*
4697189 TTTTTCTC
1 TTTTTTTC
4697197 ATTTTTTT-
1 -TTTTTTTC
4697205 TCTTTTTTC
1 T-TTTTTTC
4697214 ATTTTTTCTTCC
1 --TTTTT-TT-C
*
4697226 TCTTTTTC
1 TTTTTTTC
4697234 TTTTTTCTC
1 TTTTTT-TC
4697243 ATTTTTTTC
1 -TTTTTTTC
4697252 ATTCTGCTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
7 1 0.01
8 50 0.49
9 21 0.20
10 19 0.18
11 11 0.11
12 1 0.01
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTTC
Found at i:4697249 original size:18 final size:18
Alignment explanation
Indices: 4697119--4697251 Score: 93
Period size: 16 Copynumber: 7.5 Consensus size: 18
4697109 ATTTTCTCTT
*
4697119 ATTTTTATCTTTTTTC-C
1 ATTTTTTTCTTTTTTCTC
*
4697136 A-TTTTTTCATTTTT-TC
1 ATTTTTTTCTTTTTTCTC
*
4697152 A-TTTTTTCATTTTT-TC
1 ATTTTTTTCTTTTTTCTC
4697168 ATTTTTCTCTCATTTTTTCTC
1 ATTTTT-T-TC-TTTTTTCTC
* *
4697189 -TTTTTCTCATTTTTTTTC
1 ATTTTTTTC-TTTTTTCTC
4697207 --TTTTTTCATTTTTTCTTC
1 ATTTTTTTC-TTTTTTC-TC
* *
4697225 CTCTTTTTCTTTTTTCTC
1 ATTTTTTTCTTTTTTCTC
4697243 ATTTTTTTC
1 ATTTTTTTC
4697252 ATTCTGCTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
16 29 0.30
17 18 0.19
18 23 0.24
19 9 0.09
20 16 0.16
21 2 0.02
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTTCTTTTTTCTC
Found at i:4699316 original size:27 final size:26
Alignment explanation
Indices: 4699269--4699325 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
4699259 TTATTTCAGT
* *
4699269 ATAATATTAATAATTTTAAAAAATAA
1 ATAATATTAATAATATAAAAAAATAA
*
4699295 ATAATTATTAATTATATAAAAAAATAA
1 ATAA-TATTAATAATATAAAAAAATAA
4699322 ATAA
1 ATAA
4699326 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAATATTAATAATATAAAAAAATAA
Found at i:4700365 original size:19 final size:18
Alignment explanation
Indices: 4700341--4700378 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
4700331 AGGTAAAAAA
4700341 AAATTTTTTTGAATTTTTT
1 AAATTTTTTT-AATTTTTT
*
4700360 AAATTTTTTTATTTTTTT
1 AAATTTTTTTAATTTTTT
4700378 A
1 A
4700379 TTTTTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
AAATTTTTTTAATTTTTT
Found at i:4700374 original size:7 final size:8
Alignment explanation
Indices: 4700343--4700391 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
4700333 GTAAAAAAAA
4700343 ATTTTTTT
1 ATTTTTTT
*
4700351 GAATTTTTTAA
1 --ATTTTTT-T
4700362 ATTTTTTT
1 ATTTTTTT
4700370 ATTTTTTT
1 ATTTTTTT
4700378 ATTTTTGTT
1 ATTTTT-TT
4700387 ATTTT
1 ATTTT
4700392 GAGTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 14 0.40
9 14 0.40
10 7 0.20
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (8 bp):
ATTTTTTT
Found at i:4700467 original size:3 final size:3
Alignment explanation
Indices: 4700459--4700501 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
4700449 CTCATTGTTT
4700459 TAA 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 TAA T
4700502 TATTATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4700506 original size:3 final size:3
Alignment explanation
Indices: 4700500--4700536 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4700490 AATAATAATA
4700500 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4700537 AAAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4701421 original size:59 final size:59
Alignment explanation
Indices: 4701287--4701559 Score: 361
Period size: 60 Copynumber: 4.6 Consensus size: 59
4701277 TCTTGTGTAG
*
4701287 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCCTTTGTTTTTGAAAATTTATTTTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-CCCTT-TTTTTGAAAATTTA-TTTTT-AA
**
4701350 GGAAAATTGATACTTTCAACTTTTCCTTAAAAACCCTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAAATTTATTTTTAA
* * ** *
4701409 GGAAATTTGATACTTTCAACTTTTCCCTAAAAA-TATTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAAA-TTT-ATTTTTAA
* * *
4701469 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAAATTTATTTTTAA
* *
4701527 GAAAAATTGATACTTTCAACTTTTCCCAAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA
4701560 TATTTTTTGA
Statistics
Matches: 188, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
58 48 0.26
59 39 0.21
60 52 0.28
61 14 0.07
62 4 0.02
63 31 0.16
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCCTTTTTTTGAAAATTTATTTTTAA
Found at i:4701501 original size:119 final size:118
Alignment explanation
Indices: 4701287--4701567 Score: 429
Period size: 118 Copynumber: 2.3 Consensus size: 118
4701277 TCTTGTGTAG
* * * *
4701287 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCCTTTGTTTTTGAAAATTTATTTTTTCAAGG
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAAT--ATT-TTTTTGAAAATTTATATTTTCAAAG
*
4701352 AAAATTGATACTTTCAACTTTTCCTTAAAAACCCTTTTTTTGAAAATTTATTTTTAA
63 AAAATTGATACTTTCAACTTTTCCTCAAAAACCC-TTTTTTGAAAATTTATTTTTAA
* *
4701409 GGAAATTTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTT-TGATTTTCAAAGAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTGAAAATTTAT-ATTTTCAAAGAA
*
4701473 AATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTATTTTTAA
65 AATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAA
*
4701527 GAAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTT
4701568 GATCTTTATT
Statistics
Matches: 148, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
118 61 0.41
119 53 0.36
120 2 0.01
122 32 0.22
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTGAAAATTTATATTTTCAAAGAAA
ATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAA
Found at i:4702662 original size:17 final size:16
Alignment explanation
Indices: 4702631--4702694 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 16
4702621 ATATTACAAG
4702631 ATAA-AAAA-AATATA
1 ATAATAAAATAATATA
4702645 ATAAT--AATAATATA
1 ATAATAAAATAATATA
4702659 ATAATAAATATAACTAT-
1 ATAATAAA-ATAA-TATA
4702676 ATAAATAAAATACATATA
1 AT-AATAAAATA-ATATA
4702694 A
1 A
4702695 ATATTAACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.05
14 15 0.37
16 1 0.02
17 12 0.29
18 11 0.27
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATAAAATAATATA
Found at i:4702679 original size:14 final size:12
Alignment explanation
Indices: 4702638--4702765 Score: 66
Period size: 12 Copynumber: 10.2 Consensus size: 12
4702628 AAGATAAAAA
4702638 AAATATAATAAT
1 AAATATAATAAT
4702650 AATAATATAATAAT
1 -A-AATATAATAAT
4702664 AAATATAACTATAT
1 AAATATAA-TA-AT
*
4702678 AAATAAAATACAT
1 AAATATAATA-AT
* *
4702691 ATAA-ATATTAAC
1 A-AATATAATAAT
* *
4702703 AGAA-AAAAAAAT
1 A-AATATAATAAT
*
4702715 AAATA-AAGATAT
1 AAATATAATA-AT
* *
4702727 ACATATATTAAT
1 AAATATAATAAT
*
4702739 ACATAATAATAAT
1 AAAT-ATAATAAT
4702752 AAATA-AATAAT
1 AAATATAATAAT
4702763 AAA
1 AAA
4702766 ATACATAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
11 14 0.15
12 30 0.33
13 25 0.27
14 22 0.24
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:4702721 original size:41 final size:43
Alignment explanation
Indices: 4702658--4702795 Score: 103
Period size: 41 Copynumber: 3.3 Consensus size: 43
4702648 ATAATAATAT
* *
4702658 AATAATAAATATAACTATATAAATAAAATACATATAAATATTAACAG
1 AATAAT-AATA-AA-TAAATAAATAAAATACATATAAATAAT-ACAG
* * * *
4702705 AA-AA-AA-AAATAAATAAA-GATATACATAT-ATTAATACAT
1 AATAATAATAAATAAATAAATAAAATACATATAAATAATACAG
*
4702743 AATAATAATAAATAAAT-AATAAAATACATA-AAATACA-AAAG
1 AATAATAATAAATAAATAAATAAAATACATATAAATA-ATACAG
*
4702784 AATAAAAATAAA
1 AATAATAATAAA
4702796 AATAATACAA
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
38 5 0.07
39 6 0.08
40 13 0.18
41 39 0.53
42 3 0.04
43 1 0.01
44 2 0.03
46 2 0.03
47 2 0.03
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.25
Consensus pattern (43 bp):
AATAATAATAAATAAATAAATAAAATACATATAAATAATACAG
Found at i:4702777 original size:17 final size:17
Alignment explanation
Indices: 4702712--4702774 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
4702702 CAGAAAAAAA
*
4702712 AATAAATAAAGATATACAT
1 AATAAATAAATA-ATA-AT
* *
4702731 ATATTAATACATAATAAT
1 A-ATAAATAAATAATAAT
4702749 AATAAATAAATAATAA-
1 AATAAATAAATAATAAT
*
4702765 AATACATAAA
1 AATAAATAAA
4702775 ATACAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 9 0.24
17 13 0.35
18 3 0.08
19 4 0.11
20 8 0.22
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (17 bp):
AATAAATAAATAATAAT
Found at i:4702782 original size:16 final size:15
Alignment explanation
Indices: 4702743--4702814 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 15
4702733 ATTAATACAT
*
4702743 AATAATAATAAATAAA
1 AATAAAAAT-AATAAA
4702759 TAAT-AAAATACAT-AA
1 -AATAAAAATA-ATAAA
*
4702774 AATACAAAAGAATAAA
1 AATA-AAAATAATAAA
4702790 AATAAAAATAATACAA
1 AATAAAAATAATA-AA
4702806 AATAAAAAT
1 AATAAAAAT
4702815 TAAATTGGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.06
15 13 0.28
16 28 0.60
17 3 0.06
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:4703330 original size:22 final size:21
Alignment explanation
Indices: 4703305--4703347 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4703295 TCGATGATAA
4703305 AATA-TTTTATAATAAAAAAAAT
1 AATACTTTT-TAA-AAAAAAAAT
*
4703327 AATACTTTTTAAAAATAAAAT
1 AATACTTTTTAAAAAAAAAAT
4703348 TTTTTTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATACTTTTTAAAAAAAAAAT
Found at i:4706088 original size:57 final size:57
Alignment explanation
Indices: 4705833--4706139 Score: 176
Period size: 57 Copynumber: 5.1 Consensus size: 57
4705823 TTGTATAAGA
* * * * * **
4705833 AAAATTGATACTTTCAACTTTTTCTTAAAAAAATATTTTTCTCGATAATTTTTATTTTTAAAA
1 AAAATTGATACATTCAACTTTTCCTCAAAAATATA-TTTT-T---TAA-TTTTATTTTCAAGG
* * * * * *
4705896 AAAATTGGTAC-TTCTAACTTTTCCCCAAAATATTTTTTTTTCTAAAATTTTAATTTCAAGA
1 AAAATTGATACATTC-AACTTTTCCTCAAAA-ATATATTTTT-T--AATTTTATTTTCAAGG
* * * * * * *
4705957 AAAATTGATACTTTCAACTTCCCCCATCCCCCAAAATATACTTTTTCTATTTTTGTGTTCAAAGG
1 AAAATTGATACATTCAACTT-----TTCCTCAAAAATATA-TTTTT-TAATTTTATTTTC-AAGG
4706022 -AAATTGATACATTCAAC-TTTCCTTCAAAAATATATTTTTTAATTTTATTTTCAAGG
1 AAAATTGATACATTCAACTTTTCC-TCAAAAATATATTTTTTAATTTTATTTTCAAGG
*
4706078 AAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTGAAAATTTTATTTT--AGG
1 AAAATTGATACATTCAACTTTTCCTCAAAAATATATTTTTT---AATTTTATTTTCAAGG
4706135 AAAAT
1 AAAAT
4706140 CATTAAAAAA
Statistics
Matches: 197, Mismatches: 29, Indels: 42
0.74 0.11 0.16
Matches are distributed among these distances:
56 10 0.05
57 44 0.22
58 13 0.07
59 20 0.10
60 1 0.01
61 26 0.13
62 9 0.05
63 27 0.14
64 26 0.13
65 6 0.03
66 15 0.08
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (57 bp):
AAAATTGATACATTCAACTTTTCCTCAAAAATATATTTTTTAATTTTATTTTCAAGG
Found at i:4706786 original size:11 final size:11
Alignment explanation
Indices: 4706770--4706809 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
4706760 ATCTAGAAAT
4706770 TTTTCAAAAAA
1 TTTTCAAAAAA
*
4706781 TTTTC-AAAAT
1 TTTTCAAAAAA
4706791 TTTTCAAAAAA
1 TTTTCAAAAAA
4706802 TTTTCAAA
1 TTTTCAAA
4706810 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (11 bp):
TTTTCAAAAAA
Done.