Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 118 of 135
Found at i:39423812 original size:12 final size:12
Alignment explanation
Indices: 39423779--39423803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39423769 CCAGAGCAAC
39423779 AAGAAGAGGAGG
1 AAGAAGAGGAGG
39423791 AAGAAGAGGAGG
1 AAGAAGAGGAGG
39423803 A
1 A
39423804 TGAGGAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (12 bp):
AAGAAGAGGAGG
Found at i:39427193 original size:4 final size:4
Alignment explanation
Indices: 39427174--39427237 Score: 85
Period size: 4 Copynumber: 16.0 Consensus size: 4
39427164 ACACATTACG
* * *
39427174 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
39427222 TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC
39427238 CCATTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
3 3 0.06
4 47 0.89
5 3 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:39427440 original size:27 final size:27
Alignment explanation
Indices: 39427409--39427465 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
39427399 ACACCCCTTA
*
39427409 GTGCCGCCACTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCACTG
* *
39427436 GTGCCGCCACTTGGTGTTCCTCCACTG
1 GTGCCGCCACTTGATATTCCTCCACTG
39427463 GTG
1 GTG
39427466 TCAGGTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.33, G:0.25, T:0.32
Consensus pattern (27 bp):
GTGCCGCCACTTGATATTCCTCCACTG
Found at i:39429592 original size:20 final size:21
Alignment explanation
Indices: 39429554--39429592 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39429544 TCTACTGTTT
* *
39429554 TGTTGTTTTTCCATGTTTTGG
1 TGTTGTTTTCCCATCTTTTGG
39429575 TGTTGTTTTCCCA-CTTTT
1 TGTTGTTTTCCCATCTTTT
39429593 TGTTTCTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.05, C:0.15, G:0.18, T:0.62
Consensus pattern (21 bp):
TGTTGTTTTCCCATCTTTTGG
Found at i:39433934 original size:26 final size:28
Alignment explanation
Indices: 39433897--39433949 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
39433887 CAATAATTAT
39433897 ATTAATAATTTA-TA-AAAATTAAATAA
1 ATTAATAATTTAGTATAAAATTAAATAA
39433923 ATTAA-AATTTTATGTATAAAATTAAAT
1 ATTAATAA-TTTA-GTATAAAATTAAAT
39433950 CGAAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 2 0.09
26 9 0.39
28 2 0.09
29 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
ATTAATAATTTAGTATAAAATTAAATAA
Found at i:39436708 original size:28 final size:27
Alignment explanation
Indices: 39436592--39436709 Score: 78
Period size: 28 Copynumber: 4.1 Consensus size: 27
39436582 AAAACGGGAC
*
39436592 TTTTGGATACCCGAGGG-TAAAATGGTAA
1 TTTTGGATACTCG-GGGCTAAAATGGT-A
*
39436620 TTTTGGACT-CTCGAGGGCAAAAATGGTA
1 TTTTGGA-TACTCG-GGGCTAAAATGGTA
* * * *
39436648 TTTTGGGAAAATTTGGGGCTAAAAATGATA
1 TTTT-GG-ATACTCGGGGCT-AAAATGGTA
* *
39436678 TTTTGGATATTCGGGGGTAAAATGGTGA
1 TTTTGGATACTCGGGGCTAAAATGGT-A
39436706 TTTT
1 TTTT
39436710 TAGAAAAATC
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
27 7 0.10
28 33 0.46
29 17 0.24
30 15 0.21
ACGTcount: A:0.30, C:0.08, G:0.29, T:0.34
Consensus pattern (27 bp):
TTTTGGATACTCGGGGCTAAAATGGTA
Found at i:39436855 original size:28 final size:29
Alignment explanation
Indices: 39436761--39436975 Score: 169
Period size: 29 Copynumber: 7.6 Consensus size: 29
39436751 GGGTAAAACG
* * *
39436761 GTAATTTTTGGAAGTTTCGAAG-TCAAAAT
1 GTAATTTTTGGAAGTTTTG-GGTTAAAAAT
* * ** *
39436790 GGAATTCTTGGAAGTTCGAGGGGT-AAAAT
1 GTAATTTTTGGAAGTT-TTGGGTTAAAAAT
39436819 GTAATTTTTGGAAGTTTTGGGTTAAAAAT
1 GTAATTTTTGGAAGTTTTGGGTTAAAAAT
* * *
39436848 -TAAATTTTGAAAG-TTTGAGGGT-AAAAT
1 GTAATTTTTGGAAGTTTTG-GGTTAAAAAT
* *
39436875 GTAATTTTTAGAAGTTTTAGGGTCAAAAAT
1 GTAATTTTTGGAAGTTTT-GGGTTAAAAAT
* * *
39436905 G-AA-ATTTGGAAG-TTGGGGGTAAAAAT
1 GTAATTTTTGGAAGTTTTGGGTTAAAAAT
*
39436931 GTAATTTTTAGAAGTTTTGGGGTT-AAAAT
1 GTAATTTTTGGAAGTTTT-GGGTTAAAAAT
39436960 GTAATTTTTGGAAGTT
1 GTAATTTTTGGAAGTT
39436976 CAGAGGTCAA
Statistics
Matches: 146, Mismatches: 28, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
26 10 0.07
27 13 0.09
28 42 0.29
29 68 0.47
30 13 0.09
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTTTGGGTTAAAAAT
Found at i:39436889 original size:56 final size:57
Alignment explanation
Indices: 39436792--39436975 Score: 232
Period size: 56 Copynumber: 3.2 Consensus size: 57
39436782 GTCAAAATGG
* *
39436792 AATTCTTGGAAGTTCGAGGGGTAAAATGTAATTTTTGGAAGTTTT-GGGTTAAAAATTA
1 AATT-TTGGAAGTTTGA-GGGTAAAATGTAATTTTTAGAAGTTTTAGGGTTAAAAATTA
* * *
39436850 AATTTTGAAAGTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTAGGGTCAAAAATGA
1 AATTTTGGAAGTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTAGGGTTAAAAATTA
* *
39436907 AA-TTTGGAAG-TTGGGGGTAAAAATGTAATTTTTAGAAGTTTTGGGGTT-AAAATGTA
1 AATTTTGGAAGTTTGAGGGT-AAAATGTAATTTTTAGAAGTTTTAGGGTTAAAAAT-TA
*
39436963 ATTTTTGGAAGTT
1 AATTTTGGAAGTT
39436976 CAGAGGTCAA
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
55 12 0.11
56 62 0.56
57 31 0.28
58 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.39
Consensus pattern (57 bp):
AATTTTGGAAGTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTAGGGTTAAAAATTA
Found at i:39436984 original size:85 final size:86
Alignment explanation
Indices: 39436751--39436987 Score: 220
Period size: 85 Copynumber: 2.8 Consensus size: 86
39436741 GGACATCCGA
** * ** * * *
39436751 GGGTAAAACGGTAATTTTTGGAAGTTTCGAAGTCAAAATGGAATTCTTGGAAGTTCGAGGGGT--
1 GGGTAAAAATGTAATTTTT-GAAGTTTTGGGGTTAAAATGTAATTTTTGGAAGTTC-A-GGGTCA
* *
39436814 AAAATGTAATTTTTGGAAGTTTTG
63 AAAATGTAATATTTGGAAGTTTGG
* * * *
39436838 GGTTAAAAAT-TAAATTTTGAAAG-TTTGAGGG-TAAAATGTAATTTTTAGAAGTTTTAGGGTCA
1 GGGTAAAAATGTAATTTTTG-AAGTTTTG-GGGTTAAAATGTAATTTTTGGAAG-TTCAGGGTCA
39436900 AAAATG-AA-ATTTGGAAG-TTGG
63 AAAATGTAATATTTGGAAGTTTGG
39436921 GGGTAAAAATGTAATTTTTAGAAGTTTTGGGGTTAAAATGTAATTTTTGGAAGTTCAGAGGTCAA
1 GGGTAAAAATGTAATTTTT-GAAGTTTTGGGGTTAAAATGTAATTTTTGGAAGTTCAG-GGTCAA
39436986 AA
64 AA
39436988 TATAATTTAT
Statistics
Matches: 122, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
83 12 0.10
84 29 0.24
85 55 0.45
86 19 0.16
87 7 0.06
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (86 bp):
GGGTAAAAATGTAATTTTTGAAGTTTTGGGGTTAAAATGTAATTTTTGGAAGTTCAGGGTCAAAA
ATGTAATATTTGGAAGTTTGG
Found at i:39436987 original size:29 final size:29
Alignment explanation
Indices: 39436761--39437005 Score: 150
Period size: 29 Copynumber: 8.6 Consensus size: 29
39436751 GGGTAAAACG
*
39436761 GTAATTTTTGGAAGTTTC-GAAGTCAAAAT
1 GTAATTTTTGGAAG-TTCAGAGGTCAAAAT
* * *
39436790 GGAATTCTTGGAAGTTCGAGGGGT-AAAAT
1 GTAATTTTTGGAAGTTC-AGAGGTCAAAAT
** *
39436819 GTAATTTTTGGAAGTTTTG-GGTTAAAAAT
1 GTAATTTTTGGAAGTTCAGAGG-TCAAAAT
* * *
39436848 -TAAATTTTGAAAGTT-TGAGGGT-AAAAT
1 GTAATTTTTGGAAGTTCAGA-GGTCAAAAT
* *
39436875 GTAATTTTTAGAAGTTTTAG-GGTCAAAAAT
1 GTAATTTTTGGAAG-TTCAGAGGTC-AAAAT
* * * *
39436905 G-AA-ATTTGGAAGTT-GGGGGTAAAAAT
1 GTAATTTTTGGAAGTTCAGAGGTCAAAAT
* ** * *
39436931 GTAATTTTTAGAAGTTTTGGGGTTAAAAT
1 GTAATTTTTGGAAGTTCAGAGGTCAAAAT
39436960 GTAATTTTTGGAAGTTCAGAGGTCAAAAT
1 GTAATTTTTGGAAGTTCAGAGGTCAAAAT
* *
39436989 ATAATTTATGGATAGTT
1 GTAATTTTTGGA-AGTT
39437006 TAGGGACCTC
Statistics
Matches: 171, Mismatches: 29, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
26 7 0.04
27 16 0.09
28 48 0.28
29 86 0.50
30 14 0.08
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTCAGAGGTCAAAAT
Found at i:39438130 original size:3 final size:3
Alignment explanation
Indices: 39438122--39438203 Score: 87
Period size: 3 Copynumber: 27.3 Consensus size: 3
39438112 AATGTCATTA
* *
39438122 ATT ATT ATT AAT A-G ATT TATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
39438167 ATT ATT ATT ATT A-T AGTC ATT AAT ATT ATT AAT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
39438204 AAACGTTATT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
2 3 0.05
3 59 0.89
4 4 0.06
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:39438932 original size:17 final size:17
Alignment explanation
Indices: 39438912--39438983 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
39438902 TTTTAATATT
* *
39438912 AAATAATTTTTAATTCA
1 AAATAAATTTAAATTCA
*
39438929 AAATAAATTTAAATTTA
1 AAATAAATTTAAATTCA
** *
39438946 AAATAAATTCGAATTTA
1 AAATAAATTTAAATTCA
* *
39438963 AAATAAATTAAAATTTA
1 AAATAAATTTAAATTCA
39438980 AAAT
1 AAAT
39438984 TAAAAGTTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATAAATTTAAATTCA
Found at i:39439541 original size:12 final size:12
Alignment explanation
Indices: 39439524--39439548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39439514 TAAATAAATT
39439524 TGTGCTTTTTTA
1 TGTGCTTTTTTA
39439536 TGTGCTTTTTTA
1 TGTGCTTTTTTA
39439548 T
1 T
39439549 TAATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TGTGCTTTTTTA
Found at i:39449677 original size:20 final size:20
Alignment explanation
Indices: 39449654--39449731 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
39449644 ATTTATTAAC
*
39449654 TTAATTATACATAAAATAAT
1 TTAATTATAAATAAAATAAT
* *
39449674 TTAATTTTAAATATAATAAAT
1 TTAATTATAAATAAAAT-AAT
**
39449695 ATT-A-TATAAATAATTTAAT
1 -TTAATTATAAATAAAATAAT
* *
39449714 ATAATTATACATAAAATA
1 TTAATTATAAATAAAATA
39449732 TAGATTAATC
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
20 32 0.74
21 4 0.09
22 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTATAAATAAAATAAT
Found at i:39449765 original size:60 final size:58
Alignment explanation
Indices: 39449576--39449771 Score: 139
Period size: 60 Copynumber: 3.2 Consensus size: 58
39449566 TTTAGATGAT
* *
39449576 ATTTAAATAAGTCAATATAATTATACATAAAATATAAATT--TTAAATATTTTTAAAT-A
1 ATTTAAATAATTTAATATAATTATACATAAAATAT-AATTAATTAAA-ATTTTTAAATAA
* * * * **
39449633 ATTAATAAATTATTTATTAACTTAATTATACATAAAATA-ATTTAATTTTAAATATAATAAATAT
1 ATT--TAAATAATTTAAT-A--TAATTATACATAAAATATAATTAA-TTAAAAT-TTTTAAATA-
*
39449697 T
58 A
* **
39449698 ATATAAATAATTTAATATAATTATACATAAAATATAGATTAATCCAAATTTTTAAATACA
1 ATTTAAATAATTTAATATAATTATACATAAAATATA-ATTAATTAAAATTTTTAAATA-A
*
39449758 ATTTAAATAGTTTA
1 ATTTAAATAATTTA
39449772 TACAAATAAA
Statistics
Matches: 105, Mismatches: 21, Indels: 23
0.70 0.14 0.15
Matches are distributed among these distances:
57 3 0.03
59 9 0.09
60 40 0.38
61 6 0.06
62 24 0.23
63 21 0.20
65 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (58 bp):
ATTTAAATAATTTAATATAATTATACATAAAATATAATTAATTAAAATTTTTAAATAA
Found at i:39458617 original size:31 final size:30
Alignment explanation
Indices: 39458565--39458622 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
39458555 GTCGGGCCTG
*
39458565 CAAGTACTAAATTAAAGATTAAAGCCAAACT
1 CAAGTACTAAATGAAAGATTAAA-CCAAACT
* *
39458596 CAAGTACTAAATGATATATTAAACCAA
1 CAAGTACTAAATGAAAGATTAAACCAA
39458623 TAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.24
Consensus pattern (30 bp):
CAAGTACTAAATGAAAGATTAAACCAAACT
Found at i:39459215 original size:12 final size:13
Alignment explanation
Indices: 39459183--39459219 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
39459173 TTAATTAATA
39459183 TTTAAAAATTATC
1 TTTAAAAATTATC
39459196 TTTAAAAATTATC
1 TTTAAAAATTATC
39459209 TTTAAAAATTA
1 TTTAAAAATTA
39459220 AAATGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAAATTATC
Found at i:39459232 original size:16 final size:15
Alignment explanation
Indices: 39459211--39459244 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39459201 AAATTATCTT
39459211 TAAAAATTAAAATGTA
1 TAAAAATTAAAAT-TA
*
39459227 TAAAAATTATAATTA
1 TAAAAATTAAAATTA
39459242 TAA
1 TAA
39459245 TTCATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TAAAAATTAAAATTA
Found at i:39466266 original size:8 final size:9
Alignment explanation
Indices: 39466242--39466274 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39466232 TATTACTATG
39466242 TAAATTATA
1 TAAATTATA
39466251 TAAATTATA
1 TAAATTATA
*
39466260 T-AATTATG
1 TAAATTATA
39466268 TAAATTA
1 TAAATTA
39466275 CAGTTTGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (9 bp):
TAAATTATA
Found at i:39471861 original size:126 final size:126
Alignment explanation
Indices: 39471636--39471889 Score: 402
Period size: 126 Copynumber: 2.0 Consensus size: 126
39471626 TGAGCTGCAG
* * *
39471636 AATAAGCAGCAAGATGTTCAGGTTCCTTCACTTGATAGAAAGCTGGGGAAGGACCATTCCCATAG
1 AATAAGCAGCAAGATGTTCAGGTTCCTTCACTTGATAGAAAGCTAGGGAAGGACAATTCCCACAG
* * *
39471701 CCCTTCTAAGTTGGACGTGCTTGAAGGTGGAAATGATGAA-TCAGTGACAAAATCAGTTAGC
66 CCCTTCTAACTTGGACGTGCTTGAAGGAGGAAATGAT-AAGTCAGTGACAAAACCAGTTAGC
* *
39471762 AATAAGCAGCAAGATGTTCAGGTTCCTTCACTTGATGGAAAGCTAGGGAAGGACAATTTCCACAG
1 AATAAGCAGCAAGATGTTCAGGTTCCTTCACTTGATAGAAAGCTAGGGAAGGACAATTCCCACAG
* *
39471827 CCCTTCTAACTTGGATGTGGTTGAAGGAGGAAATGATAAGTCAGTGACAAAACCAGTTAGC
66 CCCTTCTAACTTGGACGTGCTTGAAGGAGGAAATGATAAGTCAGTGACAAAACCAGTTAGC
39471888 AA
1 AA
39471890 GAAGAAGCTT
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
125 2 0.02
126 115 0.98
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (126 bp):
AATAAGCAGCAAGATGTTCAGGTTCCTTCACTTGATAGAAAGCTAGGGAAGGACAATTCCCACAG
CCCTTCTAACTTGGACGTGCTTGAAGGAGGAAATGATAAGTCAGTGACAAAACCAGTTAGC
Found at i:39481131 original size:16 final size:16
Alignment explanation
Indices: 39481082--39481133 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
39481072 AAAGTGAAAA
* *
39481082 GAAAATTGAAAGAATA
1 GAAAATTGAAAGGATG
* *
39481098 GAAAATTGAAGGGGTG
1 GAAAATTGAAAGGATG
*
39481114 GAAAATTAAAAGGATG
1 GAAAATTGAAAGGATG
39481130 GAAA
1 GAAA
39481134 TGAAAAGCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (16 bp):
GAAAATTGAAAGGATG
Found at i:39491725 original size:18 final size:18
Alignment explanation
Indices: 39491685--39491727 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39491675 TTTTCAATTG
39491685 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
39491703 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
39491721 TAATTAA
1 TAATTAA
39491728 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:39495466 original size:14 final size:14
Alignment explanation
Indices: 39495444--39495479 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39495434 GATTGTTTTT
*
39495444 TAAACTTTAAATCC
1 TAAATTTTAAATCC
*
39495458 TAAATTTTAAATCT
1 TAAATTTTAAATCC
39495472 TAAATTTT
1 TAAATTTT
39495480 TTTATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTTAAATCC
Found at i:39496569 original size:21 final size:21
Alignment explanation
Indices: 39496540--39496579 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39496530 ATTTGATTTT
*
39496540 TTCAAGATGAAAATCTTAAAA
1 TTCAAGATGAAAATATTAAAA
*
39496561 TTCAGGATGAAAATATTAA
1 TTCAAGATGAAAATATTAA
39496580 TTTGACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (21 bp):
TTCAAGATGAAAATATTAAAA
Found at i:39499144 original size:29 final size:30
Alignment explanation
Indices: 39499054--39499145 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
39499044 ATGTAATGTG
* * *
39499054 TATAATTGAATCAAAATCAAAGTTTTTTGTA
1 TATAATTGAACCAAAATCAAA-ATTTGTGTA
* * *
39499085 TATATTTGAACCGAAATCAAAGTTTGATGTA
1 TATAATTGAACCAAAATCAAAATTTG-TGTA
*
39499116 TATAATTGCA-CAAAATCAAAATTTGTGTA
1 TATAATTGAACCAAAATCAAAATTTGTGTA
39499145 T
1 T
39499146 CAAATTGCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 5 0.10
30 16 0.31
31 30 0.59
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (30 bp):
TATAATTGAACCAAAATCAAAATTTGTGTA
Found at i:39499151 original size:29 final size:30
Alignment explanation
Indices: 39499049--39499154 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
39499039 CGTTTATGTA
* * * *
39499049 ATGTGTATAATTGAATCAAAATCAAAGTTTT
1 ATGTATATAATTGCA-CAAAATCAAAATTTG
* * * * *
39499080 TTGTATATATTTGAACCGAAATCAAAGTTTG
1 ATGTATATAATTGCA-CAAAATCAAAATTTG
39499111 ATGTATATAATTGCACAAAATCAAAATTTG
1 ATGTATATAATTGCACAAAATCAAAATTTG
39499141 -TGTATCA-AATTGCA
1 ATGTAT-ATAATTGCA
39499155 TATTTAATCA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 12 0.19
30 14 0.22
31 37 0.59
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (30 bp):
ATGTATATAATTGCACAAAATCAAAATTTG
Found at i:39500628 original size:36 final size:36
Alignment explanation
Indices: 39500582--39500655 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
39500572 TGGGACGATA
39500582 AAAAATCCGAACCCAACTTACTCCATTGTCATCCCT
1 AAAAATCCGAACCCAACTTACTCCATTGTCATCCCT
39500618 AAAAATCCGAACCCAACTTACTCCATTGTCATCCCT
1 AAAAATCCGAACCCAACTTACTCCATTGTCATCCCT
39500654 AA
1 AA
39500656 TCAGGCGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.24
Consensus pattern (36 bp):
AAAAATCCGAACCCAACTTACTCCATTGTCATCCCT
Found at i:39510084 original size:4 final size:4
Alignment explanation
Indices: 39510041--39510065 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39510031 TTTTAATTAC
39510041 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
39510066 TATCAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:39512529 original size:14 final size:13
Alignment explanation
Indices: 39512481--39512530 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
39512471 TGTGATACCT
*
39512481 GCAAAAAAAAGA-
1 GCAAAAAATAGAG
* *
39512493 GCAAAGAACAGAG
1 GCAAAAAATAGAG
39512506 GC-AAAAATAGAG
1 GCAAAAAATAGAG
39512518 GCAAAGAAATAGA
1 GCAAA-AAATAGA
39512531 ATTTTGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 20 0.65
13 4 0.13
14 7 0.23
ACGTcount: A:0.62, C:0.10, G:0.24, T:0.04
Consensus pattern (13 bp):
GCAAAAAATAGAG
Found at i:39514752 original size:32 final size:32
Alignment explanation
Indices: 39514688--39514753 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
39514678 TATATATATG
**
39514688 ATCCTTTGCATTTTCTATTAAATATTACGATA
1 ATCCTTTGCATTTTCTATTAAATACCACGATA
*
39514720 ATCCTTTGCATTTTCTATTAAATACCATGATA
1 ATCCTTTGCATTTTCTATTAAATACCACGATA
39514752 AT
1 AT
39514754 ATTACTGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (32 bp):
ATCCTTTGCATTTTCTATTAAATACCACGATA
Found at i:39517108 original size:23 final size:23
Alignment explanation
Indices: 39517073--39517120 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
39517063 CAATGCTTTG
*
39517073 TTGCATGCATTTCAT-CATTCAT
1 TTGCATGCATTTCATGCATTAAT
39517095 TTGCATTGCATTTCATGCATTAAT
1 TTGCA-TGCATTTCATGCATTAAT
39517119 TT
1 TT
39517121 TTAATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (23 bp):
TTGCATGCATTTCATGCATTAAT
Found at i:39518650 original size:59 final size:58
Alignment explanation
Indices: 39518579--39518773 Score: 250
Period size: 59 Copynumber: 3.3 Consensus size: 58
39518569 TGGTAAATAT
39518579 GTAAAATGGTAATTTTTGGTGAAACCAGGGTTGAAAAATGGAA-TTTGGAAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGTGAAACC-GGGTT-AAAAATGGAATTTTGGAAAGTTCGGGG
* *
39518638 GTAAAATGGTAATTTTTGGTGAAACTGGGGTT-AAAATGGAATTTTAGAAAGTTCGAGGG
1 GTAAAATGGTAATTTTTGGTGAAAC-CGGGTTAAAAATGGAATTTTGGAAAGTTCG-GGG
* * * * **
39518697 TTAAAATGGTATAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGG
1 GTAAAATGGTA-ATTTTTGGTGAAACCG-GGTTAAAAATGGAATTTTGGAAAGTTCGGGG
39518757 GTAAAATGGTAATTTTT
1 GTAAAATGGTAATTTTT
39518774 TGACAGTCTA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
57 9 0.08
58 12 0.10
59 49 0.42
60 28 0.24
61 20 0.17
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
GTAAAATGGTAATTTTTGGTGAAACCGGGTTAAAAATGGAATTTTGGAAAGTTCGGGG
Found at i:39518673 original size:30 final size:29
Alignment explanation
Indices: 39518580--39518682 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
39518570 GGTAAATATG
**
39518580 TAAAATGGTAATTTTTGGTGAAACCAGGGT
1 TAAAATGG-AATTTTTGGTGAAACTGGGGT
* *
39518610 TGAAAAATGGAA--TTT-G-GAAAGTTCGGGGG
1 T--AAAATGGAATTTTTGGTGAAA-CT-GGGGT
39518639 TAAAATGGTAATTTTTGGTGAAACTGGGGT
1 TAAAATGG-AATTTTTGGTGAAACTGGGGT
39518669 TAAAATGGAATTTT
1 TAAAATGGAATTTT
39518683 AGAAAGTTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
27 11 0.19
28 3 0.05
29 13 0.22
30 16 0.28
31 4 0.07
32 11 0.19
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGTGAAACTGGGGT
Found at i:39518697 original size:29 final size:30
Alignment explanation
Indices: 39518613--39518772 Score: 126
Period size: 29 Copynumber: 5.5 Consensus size: 30
39518603 CCAGGGTTGA
*
39518613 AAAATGG-AA-TTTGGAAAGTTCG-GGGGT
1 AAAATGGTAATTTTGGAAAGTTCGAGGGTT
*
39518640 AAAATGGTAATTTTTGGTGAAA-CT-G-GGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTCGAGGGTT
*
39518670 AAAATGG-AATTTTAGAAAGTTCGAGGGTT
1 AAAATGGTAATTTTGGAAAGTTCGAGGGTT
*
39518699 AAAATGGTATAATTTTGGTAAA-ATCGA-GGTT
1 AAAATGG--TAATTTTGG-AAAGTTCGAGGGTT
* *
39518730 AAAAATGG-AATTTTGGAAAGTT-TAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTCGAGGGTT
39518759 AAAATGGTAATTTT
1 AAAATGGTAATTTT
39518773 TTGACAGTCT
Statistics
Matches: 108, Mismatches: 9, Indels: 30
0.73 0.06 0.20
Matches are distributed among these distances:
26 4 0.04
27 8 0.07
28 18 0.17
29 32 0.30
30 15 0.14
31 6 0.06
32 22 0.20
33 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTGGAAAGTTCGAGGGTT
Found at i:39519148 original size:60 final size:59
Alignment explanation
Indices: 39519083--39519392 Score: 448
Period size: 59 Copynumber: 5.2 Consensus size: 59
39519073 TATGGAAAGG
39519083 AAATGGTAATTTTTGGTGAAATCAGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
1 AAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
* * * *
39519143 AAATGGTAATTTTT-GTAAAACCAGGGTTGAAAAATGGAATTTTGGAAAGTTCGGGGGTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTCAGGGGTA
* * *
39519202 AAATGGTAATTTTTGTTGAAA-CTGGGGTT-AAAATGGAATTTTAGAAAGTTC-GAGGTTA
1 AAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTCAG-GGGTA
* * *
39519260 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGGTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCAGGGGTA
*
39519320 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
39519379 AAATGGTAATTTTT
1 AAATGGTAATTTTT
39519393 TGACAGTCTA
Statistics
Matches: 224, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.00
58 54 0.24
59 92 0.41
60 76 0.34
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
Found at i:39519377 original size:30 final size:29
Alignment explanation
Indices: 39519083--39519391 Score: 189
Period size: 30 Copynumber: 10.4 Consensus size: 29
39519073 TATGGAAAGG
*
39519083 AAATGGTAATTTTTGGTGAAA-TCAGGGGTTAA
1 AAATGGTAA-TTTT-G-GAAAGTTAGGGGTT-A
39519115 AAATGG-AATTTTGGAAAGTTCAGGGG-TA
1 AAATGGTAATTTTGGAAAGTT-AGGGGTTA
* ***
39519143 AAATGGTAATTTTTGTAAAACCA-GGGTTGAA
1 AAATGGTAA-TTTTGGAAAGTTAGGGGTT--A
* *
39519174 AAATGG-AATTTTGGAAAGTTCGGGGGTA
1 AAATGGTAATTTTGGAAAGTTAGGGGTTA
*
39519202 AAATGGTAATTTTTGTTGAAA-CT-GGGGTTA
1 AAATGGTAA-TTTTG--GAAAGTTAGGGGTTA
* * *
39519232 AAATGG-AATTTTAGAAAGTTCGAGGTTA
1 AAATGGTAATTTTGGAAAGTTAGGGGTTA
* * *
39519260 AAATGGTAATTTTTGGTAAA-ATCGAGGTTAA
1 AAATGGTAA-TTTTGG-AAAGTTAGGGGTT-A
39519291 AAATGG-AATTTTGGAAAGTTTGAGGGG-TA
1 AAATGGTAATTTTGGAAAG-TT-AGGGGTTA
*
39519320 AAATGGTAATTTTTGGTGAAA--TCGGGGTTAA
1 AAATGGTAA-TTTT-G-GAAAGTTAGGGGTT-A
39519351 AAATGG-AATTTTGGAAAGTTTAGGGG-TA
1 AAATGGTAATTTTGGAAAG-TTAGGGGTTA
39519379 AAATGGTAATTTT
1 AAATGGTAATTTT
39519392 TTGACAGTCT
Statistics
Matches: 223, Mismatches: 23, Indels: 65
0.72 0.07 0.21
Matches are distributed among these distances:
26 4 0.02
27 5 0.02
28 48 0.22
29 49 0.22
30 68 0.30
31 34 0.15
32 11 0.05
33 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AAATGGTAATTTTGGAAAGTTAGGGGTTA
Found at i:39519405 original size:30 final size:29
Alignment explanation
Indices: 39519313--39519405 Score: 77
Period size: 30 Copynumber: 3.1 Consensus size: 29
39519303 GGAAAGTTTG
*
39519313 AGGGGTAAAATGGTAATTTTTGGTGAAATC-
1 AGGGGTAAAATGGTAATTTTT--TGAAGTCT
* *
39519343 -GGGGTTAAAAATGG-AA-TTTTGGAAAGTTT
1 AGGGG-T-AAAATGGTAATTTTTTG-AAGTCT
39519372 AGGGGTAAAATGGTAATTTTTTGACAGTCT
1 AGGGGTAAAATGGTAATTTTTTGA-AGTCT
39519402 AGGG
1 AGGG
39519406 ACTTATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 1 0.02
28 10 0.20
29 12 0.24
30 20 0.40
31 7 0.14
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
AGGGGTAAAATGGTAATTTTTTGAAGTCT
Found at i:39521238 original size:6 final size:6
Alignment explanation
Indices: 39521223--39521298 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
39521213 TTAAATTTGA
* * *
39521223 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT GAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
39521271 ATAAAT TTAAAT TTAAGA- -TAAAT TTAAA
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAA
39521299 ACCCTCTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 11 0.20
6 38 0.68
7 1 0.02
8 5 0.09
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:39521249 original size:17 final size:16
Alignment explanation
Indices: 39521212--39521298 Score: 88
Period size: 17 Copynumber: 5.4 Consensus size: 16
39521202 TTAATATTAT
* *
39521212 TTTAAATTTGATTAAA
1 TTTAAATTTAAGTAAA
*
39521228 CTTAAATTTAAAGTAAA
1 TTTAAATTT-AAGTAAA
*
39521245 TTTAAA--TGAGTAAA
1 TTTAAATTTAAGTAAA
*
39521259 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAGTAAA
39521276 TTTAAATTTAAGATAAA
1 TTTAAATTTAAG-TAAA
39521293 TTTAAA
1 TTTAAA
39521299 ACCCTCTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 11 0.19
17 34 0.59
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAGTAAA
Found at i:39521258 original size:14 final size:14
Alignment explanation
Indices: 39521239--39521265 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39521229 TTAAATTTAA
39521239 AGTAAATTTAAATG
1 AGTAAATTTAAATG
39521253 AGTAAATTTAAAT
1 AGTAAATTTAAAT
39521266 TTAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AGTAAATTTAAATG
Found at i:39521267 original size:31 final size:31
Alignment explanation
Indices: 39521224--39521282 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
39521214 TAAATTTGAT
*
39521224 TAAACTTAAATTTAAAGTAAATTTAAATGAG
1 TAAACTTAAATTTAAAATAAATTTAAATGAG
*
39521255 TAAATTTAAATTTAAAATAAATTTAAAT
1 TAAACTTAAATTTAAAATAAATTTAAAT
39521283 TTAAGATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (31 bp):
TAAACTTAAATTTAAAATAAATTTAAATGAG
Found at i:39521277 original size:11 final size:12
Alignment explanation
Indices: 39521230--39521298 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 12
39521220 TGATTAAACT
*
39521230 TAAATTTAAA-G
1 TAAATTTAAATA
39521241 TAAATTTAAATGA
1 TAAATTTAAAT-A
*
39521254 GTAAATTTAAATT
1 -TAAATTTAAATA
* *
39521267 TAAA-ATAAATT
1 TAAATTTAAATA
*
39521278 TAAATTT-AAGA
1 TAAATTTAAATA
39521289 TAAATTTAAA
1 TAAATTTAAA
39521299 ACCCTCTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
11 29 0.62
12 7 0.15
14 11 0.23
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:39526182 original size:42 final size:41
Alignment explanation
Indices: 39526123--39526252 Score: 156
Period size: 42 Copynumber: 3.2 Consensus size: 41
39526113 GGGGAAAGGG
*
39526123 CCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTCTAATAAGCA
1 CCGCTAAAGGT-TGGTCATTAGCGGCGCTTTTCTAATAAGCA
* * * *
39526165 CCGCTAAAGGTTAGGTCATTAACGGCACTTTTTTAATAAGCG
1 CCGCTAAAGGTT-GGTCATTAGCGGCGCTTTTCTAATAAGCA
* **
39526207 CCGCTAAAGG-TGGCCATTAGCGGCGC-TTTCCCATAAGCA
1 CCGCTAAAGGTTGGTCATTAGCGGCGCTTTTCTAATAAGCA
39526246 CCGCTAA
1 CCGCTAA
39526253 TTTATTTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 16 0.21
40 12 0.16
41 1 0.01
42 46 0.61
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (41 bp):
CCGCTAAAGGTTGGTCATTAGCGGCGCTTTTCTAATAAGCA
Found at i:39526183 original size:82 final size:81
Alignment explanation
Indices: 39526058--39526252 Score: 189
Period size: 82 Copynumber: 2.4 Consensus size: 81
39526048 AAAGGTAAAG
* * * * * * * *
39526058 CATTAGCAGCACTTTCCCACAAGCACCGCTAAAAGTCGAGTCATTAGCGGCGC-TTGGGGA-AAG
1 CATTAGCGGCGCTTTCCAATAAGCACCGCTAAAAGTAGAGTCATTAACGGCACTTTGGGAATAAG
* *
39526121 GGCCGCTAAAGGTCGGGT
66 CGCCGCTAAAGGT--GGC
* * ***
39526139 CATTAGCGGCGCTTTTCTAATAAGCACCGCTAAAGGTTAG-GTCATTAACGGCACTTTTTTAATA
1 CATTAGCGGCGC-TTTCCAATAAGCACCGCTAAAAG-TAGAGTCATTAACGGCACTTTGGGAATA
39526203 AGCGCCGCTAAAGGTGGC
64 AGCGCCGCTAAAGGTGGC
*
39526221 CATTAGCGGCGCTTTCCCATAAGCACCGCTAA
1 CATTAGCGGCGCTTTCCAATAAGCACCGCTAA
39526253 TTTATTTAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
81 28 0.30
82 45 0.48
83 5 0.05
84 15 0.16
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (81 bp):
CATTAGCGGCGCTTTCCAATAAGCACCGCTAAAAGTAGAGTCATTAACGGCACTTTGGGAATAAG
CGCCGCTAAAGGTGGC
Found at i:39527870 original size:64 final size:65
Alignment explanation
Indices: 39527769--39527921 Score: 245
Period size: 66 Copynumber: 2.4 Consensus size: 65
39527759 GCAAATTGCT
* * *
39527769 CAACTTAAAGAGGAGGCTACAGCGAGAGAAGCAGAGGCTC-AAAAAATATGATGAACTTCACCTA
1 CAACTTAAAGAGGAGGCTGCAGCCAGAGAAGCAGAGGCTCAAAAAAATATGATGAACTCCACCTA
39527833 CAACTTAAAGAGGAGGCTGCAGCCAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCACCT
1 CAACTTAAAGAGGAGGCTGCAGCCAGAGAAGCAGAGGCTC-AAAAAAATATGATGAACTCCACCT
39527898 A
65 A
* *
39527899 CAACTTAAAGTGGAGGCAGCAGC
1 CAACTTAAAGAGGAGGCTGCAGC
39527922 GAGGCAAGCG
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 38 0.46
66 44 0.54
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.14
Consensus pattern (65 bp):
CAACTTAAAGAGGAGGCTGCAGCCAGAGAAGCAGAGGCTCAAAAAAATATGATGAACTCCACCTA
Found at i:39527936 original size:21 final size:21
Alignment explanation
Indices: 39527910--39527962 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39527900 AACTTAAAGT
*
39527910 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCAAGGCAAGC
39527931 GGAGGCAGCAGCAAGGCAAGC
1 GGAGGCAGCAGCAAGGCAAGC
* *
39527952 GAAGGAAGCAG
1 GGAGGCAGCAG
39527963 AGGTTACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.45, T:0.00
Consensus pattern (21 bp):
GGAGGCAGCAGCAAGGCAAGC
Found at i:39530291 original size:31 final size:32
Alignment explanation
Indices: 39530234--39530315 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
39530224 AATTTACTAG
* *
39530234 AAGCACAAATCTTAAATTATCACATTGTTTTT
1 AAGCACAAATCTTAAATTATCACATTGCTCTT
* **
39530266 AAGCACAAATC-TAAATTGTTGCATTGCTCTT
1 AAGCACAAATCTTAAATTATCACATTGCTCTT
*
39530297 AAACACAAA-CTTAAATTAT
1 AAGCACAAATCTTAAATTAT
39530316 TTATTCGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 1 0.02
31 30 0.71
32 11 0.26
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (32 bp):
AAGCACAAATCTTAAATTATCACATTGCTCTT
Found at i:39531074 original size:25 final size:25
Alignment explanation
Indices: 39531046--39531093 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
39531036 GTGAGACTAC
39531046 ATCTATCTTCCATCAAGTTTCAACA
1 ATCTATCTTCCATCAAGTTTCAACA
*
39531071 ATCTATCTTGCATCAAGTTTCAA
1 ATCTATCTTCCATCAAGTTTCAA
39531094 AAATATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (25 bp):
ATCTATCTTCCATCAAGTTTCAACA
Found at i:39540958 original size:18 final size:17
Alignment explanation
Indices: 39540923--39540961 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
39540913 CTCTTAATTT
*
39540923 TTTAATTTATTTTTTTA
1 TTTAATTTATTATTTTA
39540940 TTTAATTTGATTATTTTA
1 TTTAATTT-ATTATTTTA
39540958 TTTA
1 TTTA
39540962 GATTCTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTAATTTATTATTTTA
Found at i:39544096 original size:21 final size:20
Alignment explanation
Indices: 39544066--39544116 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
39544056 TAAGTACAAA
39544066 CATG-TTTAAAATTTGATCCG
1 CATGTTTTAAAA-TTGATCCG
*
39544086 CATGTTTTAAAATTGATTCG
1 CATGTTTTAAAATTGATCCG
39544106 CATGTTTTAAA
1 CATGTTTTAAA
39544117 TTTATGTGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (20 bp):
CATGTTTTAAAATTGATCCG
Found at i:39546536 original size:20 final size:21
Alignment explanation
Indices: 39546498--39546536 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
39546488 CAGCCCTTTT
39546498 TTTTCAATTATTTTATTTTAA
1 TTTTCAATTATTTTATTTTAA
* *
39546519 TTTT-AATTTTTTTTTTTT
1 TTTTCAATTATTTTATTTT
39546537 TGGTCCCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTCAATTATTTTATTTTAA
Found at i:39547512 original size:19 final size:19
Alignment explanation
Indices: 39547471--39547508 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
39547461 CTTTTTTAGC
*
39547471 ATTTACATTATTAGGAATA
1 ATTTACATTATTAGCAATA
*
39547490 ATTTAC-TTATTAGCCATA
1 ATTTACATTATTAGCAATA
39547508 A
1 A
39547509 ATTTTTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (19 bp):
ATTTACATTATTAGCAATA
Found at i:39549778 original size:20 final size:20
Alignment explanation
Indices: 39549745--39549793 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
39549735 TTTCCAAATG
*
39549745 ATTTT-ATTTATCCAATTTT
1 ATTTTCATTTATCCAATTTC
* *
39549764 ATTTTCATTTCTCCACTTTC
1 ATTTTCATTTATCCAATTTC
39549784 ATTTTCATTT
1 ATTTTCATTT
39549794 TGGAGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTCATTTATCCAATTTC
Found at i:39551571 original size:30 final size:28
Alignment explanation
Indices: 39551531--39552115 Score: 126
Period size: 29 Copynumber: 20.6 Consensus size: 28
39551521 TGACTTCTAA
39551531 GGGTAAAAATGTAATTTTTGGTGAAATCG
1 GGGTAAAAATGTAA-TTTTGGTGAAATCG
** *
39551560 GGGTCAAAAATGGGATTTTAG-GAAATTCGG
1 GGGT-AAAAATGTAATTTTGGTGAAA-TC-G
*
39551590 GGGT-AAAATGGTAATTTTGATGAAATCG
1 GGGTAAAAAT-GTAATTTTGGTGAAATCG
**
39551618 GGGTTAAAAATGGGA--TT--T----T-G
1 GGG-TAAAAATGTAATTTTGGTGAAATCG
*
39551638 GGGTAAAATTGTAATCTTTGGTGAAATCG
1 GGGTAAAAATGTAAT-TTTGGTGAAATCG
** * *
39551667 AGATTAAAAGTGGAATTTT-G-GAAAGTTCG
1 -GGGTAAAAATGTAATTTTGGTGAAA--TCG
* *
39551696 GGGT-AAAATGGTAATTTTTGTGAAATTG
1 GGGTAAAAAT-GTAATTTTGGTGAAATCG
* ** * *
39551724 GGGTTAAAAGTGGGA-TTTAG-GAAAGTTTAG
1 GGG-TAAAAATGTAATTTTGGTGAAA---TCG
*
39551754 GGGT-AAAATGGTAATTTTGGTAAAATCG
1 GGGTAAAAAT-GTAATTTTGGTGAAATCG
* ** *
39551782 AGGTTAAAAATGGGA-TTTAG-GAAAGTTCG
1 -GGGTAAAAATGTAATTTTGGTGAAA--TCG
39551811 AGGGT-AAAATGGTAATTTTGGGTGAAATCG
1 -GGGTAAAAAT-GTAATTTT-GGTGAAATCG
* * *** *
39551841 GGTTAAAAGTGGGGTTTT-G-GAAAGTTTAG
1 GGGTAAAAATGTAATTTTGGTGAAA---TCG
*
39551870 GGGT-AAAATGGTAATTTTGGTAAAATCG
1 GGGTAAAAAT-GTAATTTTGGTGAAATCG
**
39551898 GGGTTAAAAATGGGATTTT-G-GAAAGTTCGG
1 GGG-TAAAAATGTAATTTTGGTGAAA--TC-G
39551928 GGGT-AAAATGGTAATTTTGGT-AATATCG
1 GGGTAAAAAT-GTAATTTTGGTGAA-ATCG
* **
39551956 GGTTAAAAATGGGATTTT-G-GAAAGTCCAG
1 GGGTAAAAATGTAATTTTGGTGAAA-T-C-G
*
39551985 GGGT-AAAATGGTAATTTTGGTGAAATTG
1 GGGTAAAAAT-GTAATTTTGGTGAAATCG
** *
39552013 GGGTTAAAAATGGGATTTT-G-GAAGTTCGG
1 GGG-TAAAAATGTAATTTTGGTGAA-ATC-G
* * *
39552042 GGGT-AAAATGGTGATTTTGGTAAAATCA
1 GGGTAAAAAT-GTAATTTTGGTGAAATCG
* **
39552070 GGGTTAAAATGGGATTTT-G-GAAATTCG
1 GGGTAAAAATGTAATTTTGGTGAAA-TCG
39552097 AGGGT-AAAATGGTAATTTT
1 -GGGTAAAAAT-GTAATTTT
39552116 TGGACAGTCC
Statistics
Matches: 403, Mismatches: 79, Indels: 149
0.64 0.13 0.24
Matches are distributed among these distances:
19 8 0.02
20 4 0.01
21 1 0.00
22 2 0.00
24 1 0.00
25 1 0.00
26 8 0.02
27 41 0.10
28 114 0.28
29 120 0.30
30 87 0.22
31 12 0.03
32 4 0.01
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTGGTGAAATCG
Found at i:39551627 original size:58 final size:58
Alignment explanation
Indices: 39551531--39552115 Score: 722
Period size: 58 Copynumber: 10.3 Consensus size: 58
39551521 TGACTTCTAA
*
39551531 GGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAATGGGATTTTAGGAAA-TTCGG
1 GGGT-AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTT-GGAAAGTTCGG
*
39551590 GGGTAAAATGGTAATTTTGATGAAATCGGGGTTAAAAATGGGA--TT------TT--G
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* * * * *
39551638 GGGTAAAATTGTAATCTTTGGTGAAATCGAGATTAAAAGTGGAATTTTGGAAAGTTC-G
1 GGGTAAAATGGTAAT-TTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* * * * **
39551696 GGGTAAAATGGTAATTTTTGTGAAATTGGGGTTAAAAGTGGGATTTAGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* * * *
39551754 GGGTAAAATGGTAATTTTGGTAAAATCGAGGTTAAAAATGGGATTTAGGAAAGTTCGA
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* * **
39551812 GGGTAAAATGGTAATTTTGGGTGAAATC-GGGTTAAAAGTGGGGTTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
*
39551870 GGGTAAAATGGTAATTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* *
39551928 GGGTAAAATGGTAATTTTGGT-AATATC-GGGTTAAAAATGGGATTTTGGAAAGTCCAG
1 GGGTAAAATGGTAATTTTGGTGAA-ATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
*
39551985 GGGTAAAATGGTAATTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGG-AAGTTCGG
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
* * * *
39552042 GGGTAAAATGGTGATTTTGGTAAAATCAGGGTT-AAAATGGGATTTTGGAAA-TTCGA
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
39552098 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
39552116 TGGACAGTCC
Statistics
Matches: 460, Mismatches: 48, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
48 15 0.03
49 23 0.05
50 2 0.00
51 2 0.00
56 38 0.08
57 134 0.29
58 230 0.50
59 16 0.03
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGG
Found at i:39551685 original size:49 final size:48
Alignment explanation
Indices: 39551589--39551687 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 48
39551579 AGGAAATTCG
* * *
39551589 GGGGTAAAATGGTAATTTTGATGAAATCGGGGTTAAAAATGGGATTTT
1 GGGGTAAAATGGTAATTTTGATGAAATCGAGATTAAAAATGGAATTTT
* * *
39551637 GGGGTAAAATTGTAATCTTTGGTGAAATCGAGATTAAAAGTGGAATTTT
1 GGGGTAAAATGGTAAT-TTTGATGAAATCGAGATTAAAAATGGAATTTT
39551686 GG
1 GG
39551688 AAAGTTCGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 15 0.34
49 29 0.66
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (48 bp):
GGGGTAAAATGGTAATTTTGATGAAATCGAGATTAAAAATGGAATTTT
Found at i:39553890 original size:6 final size:6
Alignment explanation
Indices: 39553870--39553939 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
39553860 ATAATATTAT
* *
39553870 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAGTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
*
39553917 TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
39553940 AATCTATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.04
5 12 0.23
6 33 0.63
8 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:39553915 original size:14 final size:15
Alignment explanation
Indices: 39553882--39553939 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 15
39553872 TAAATTTAAT
39553882 TAAATTTAAATTTAAAG
1 TAAATTTAAA--TAAAG
39553899 TAAATTTAAAT-AAG
1 TAAATTTAAATAAAG
*
39553913 TAAATTTAAATTTAAAA
1 TAAATTTAAA--TAAAG
39553930 TAAATTTAAA
1 TAAATTTAAA
39553940 AATCTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 13 0.35
15 1 0.03
16 1 0.03
17 22 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAAATTTAAATAAAG
Found at i:39565301 original size:31 final size:31
Alignment explanation
Indices: 39565265--39565325 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
39565255 GATATATATT
*
39565265 GGAATTAAAAGTTAAACCCAGTGAATCTCTG
1 GGAATTAAAAGTTAAAACCAGTGAATCTCTG
*
39565296 GGAATTAAAAGTTAAAATCAGTGAATCTCT
1 GGAATTAAAAGTTAAAACCAGTGAATCTCT
39565326 TAATTAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (31 bp):
GGAATTAAAAGTTAAAACCAGTGAATCTCTG
Found at i:39576761 original size:12 final size:12
Alignment explanation
Indices: 39576744--39576776 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39576734 TCACGAACAA
39576744 GCTCGTTTATTG
1 GCTCGTTTATTG
39576756 GCTCGTTTATTG
1 GCTCGTTTATTG
*
39576768 ACTCGTTTA
1 GCTCGTTTA
39576777 GTTATTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:39576906 original size:23 final size:23
Alignment explanation
Indices: 39576875--39576953 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
39576865 CATTATTCGC
39576875 GAACATGTTCAATTATATGCTCAT
1 GAACATGTTCAATTA-ATGCTCAT
* * *
39576899 GAA-ATGTTCATTTAATGTTCGT
1 GAACATGTTCAATTAATGCTCAT
* * *
39576921 GAACATGTTCGATTAA-GTTAAAT
1 GAACATGTTCAATTAATGCT-CAT
39576944 GAACATGTTC
1 GAACATGTTC
39576954 GTGAACATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 12 0.26
23 31 0.67
24 3 0.07
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (23 bp):
GAACATGTTCAATTAATGCTCAT
Found at i:39576964 original size:23 final size:23
Alignment explanation
Indices: 39576920--39576965 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39576910 TTAATGTTCG
* *
39576920 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
39576943 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
39576966 CAAAACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:39583529 original size:238 final size:238
Alignment explanation
Indices: 39583111--39583667 Score: 1105
Period size: 238 Copynumber: 2.3 Consensus size: 238
39583101 ATCAATTAAA
39583111 AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
1 AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
39583176 TAGGTTTGAGTTTTTTATTCGACCAAATAAGAAATTAAATTCAACTCGCCTCAAAATTCGATTTA
66 TAGGTTTGAGTTTTTTATTCGACCAAATAAGAAATTAAATTCAACTCGCCTCAAAATTCGATTTA
39583241 ACAAAATCTAATTGTCTATTAGGTTTGAGGGTTTTTTTTCCATTTGTAACAATATCCAATGCTAC
131 ACAAAATCTAATTGTCTATTAGGTTTGAGGGTTTTTTTTCCATTTGTAACAATATCCAATGCTAC
39583306 GAAGGATTTAACTTGTTAGGCATATTTTTTATCCGATTAATTG
196 GAAGGATTTAACTTGTTAGGCATATTTTTTATCCGATTAATTG
39583349 AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
1 AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
39583414 TAGGTTTGAGTTTTTTATTCGACCAAATAAGAAATTAAATTCAACTCGCCTCAAAATTCGATTTA
66 TAGGTTTGAGTTTTTTATTCGACCAAATAAGAAATTAAATTCAACTCGCCTCAAAATTCGATTTA
39583479 ACAAAATCTAATTGTCTATTAGGTTTGAGGGTTTTTTTTCCATTTGTAACAATATCCAATGCTAC
131 ACAAAATCTAATTGTCTATTAGGTTTGAGGGTTTTTTTTCCATTTGTAACAATATCCAATGCTAC
39583544 GAAGGATTTAACTTGTTAGGCATATTTTTTATCCGATTAATTG
196 GAAGGATTTAACTTGTTAGGCATATTTTTTATCCGATTAATTG
39583587 AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
1 AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
*
39583652 TAGGTTCGAGTTTTTT
66 TAGGTTTGAGTTTTTT
39583668 TCTCTCTTTT
Statistics
Matches: 318, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
238 318 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (238 bp):
AAAAATTAGATTTCACTTACCTCAAAATCCGATTTCAAATGGATTAAAAAAATCTAACCGCTTAT
TAGGTTTGAGTTTTTTATTCGACCAAATAAGAAATTAAATTCAACTCGCCTCAAAATTCGATTTA
ACAAAATCTAATTGTCTATTAGGTTTGAGGGTTTTTTTTCCATTTGTAACAATATCCAATGCTAC
GAAGGATTTAACTTGTTAGGCATATTTTTTATCCGATTAATTG
Found at i:39584114 original size:12 final size:12
Alignment explanation
Indices: 39584096--39584131 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39584086 TTCACGAACA
39584096 AGCTCGTTTATT
1 AGCTCGTTTATT
*
39584108 GGCTCGTTTATT
1 AGCTCGTTTATT
*
39584120 AACTCGTTTATT
1 AGCTCGTTTATT
39584132 TATTAATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (12 bp):
AGCTCGTTTATT
Found at i:39584248 original size:12 final size:12
Alignment explanation
Indices: 39584233--39584274 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39584223 GTACAATTAT
*
39584233 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
39584245 ATGTTCGTTTA-
1 ATGTTCGTGAAC
39584256 ATGTTCGTGAAC
1 ATGTTCGTGAAC
39584268 ATGTTCG
1 ATGTTCG
39584275 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:39584266 original size:23 final size:23
Alignment explanation
Indices: 39584210--39584279 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
39584200 TCATTAACAT
* * *
39584210 TGTTTGTGAACATGTACAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
39584234 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
39584257 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
39584280 GTTAAATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:39584289 original size:23 final size:23
Alignment explanation
Indices: 39584216--39584302 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
39584206 ACATTGTTTG
* * *
39584216 TGAACATGTACAATTATATGTTCA
1 TGAACATGTTCGATTA-ATGTTAA
* **
39584240 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGATTAATGTTAA
39584263 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-AA
* *
39584286 TGAATATGTTCAATTAA
1 TGAACATGTTCGATTAA
39584303 ACAAACGAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 37 0.70
24 13 0.25
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTAA
Found at i:39588345 original size:28 final size:27
Alignment explanation
Indices: 39588301--39588403 Score: 80
Period size: 28 Copynumber: 3.7 Consensus size: 27
39588291 GTGAACCTCT
* *
39588301 TAAAGAAAGCCTTTGTGGCTATCTTAA
1 TAAAGAAAGCCTGTGTGGCGATCTTAA
* * * *
39588328 TGAAAGGAAGCCTGTGTGACGATCTCAGT
1 T-AAAGAAAGCCTGTGTGGCGATCTTA-A
* * *
39588357 TAAAGGAAGTCTGTGTGGCGATCTCTAC
1 TAAAGAAAGCCTGTGTGGCGATCT-TAA
* *
39588385 TAAAAAAAGCCTTTGTGGC
1 TAAAGAAAGCCTGTGTGGC
39588404 TATTTCTGTT
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.02
28 56 0.95
29 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (27 bp):
TAAAGAAAGCCTGTGTGGCGATCTTAA
Found at i:39589832 original size:19 final size:20
Alignment explanation
Indices: 39589800--39589841 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
39589790 CTAAACATAC
39589800 AAACCCAAACCTCAAAAACA
1 AAACCCAAACCTCAAAAACA
* *
39589820 AAACCCTAA-CTCAAAAATA
1 AAACCCAAACCTCAAAAACA
39589839 AAA
1 AAA
39589842 ACATCTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.62, C:0.29, G:0.00, T:0.10
Consensus pattern (20 bp):
AAACCCAAACCTCAAAAACA
Found at i:39589842 original size:20 final size:20
Alignment explanation
Indices: 39589800--39589843 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39589790 CTAAACATAC
*
39589800 AAACCCAAACCTCAAAAACA
1 AAACCCAAACCTCAAAAAAA
*
39589820 AAACCCTAA-CTCAAAAATAA
1 AAACCCAAACCTCAAAAA-AA
39589840 AAAC
1 AAAC
39589844 ATCTCTATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.61, C:0.30, G:0.00, T:0.09
Consensus pattern (20 bp):
AAACCCAAACCTCAAAAAAA
Found at i:39599647 original size:122 final size:123
Alignment explanation
Indices: 39599455--39599689 Score: 391
Period size: 122 Copynumber: 1.9 Consensus size: 123
39599445 TAATTTTGAT
* * *
39599455 ATTTGATTTATAAAGTGTTGCAATCGGAGTTAAAATATCAAAATTTGAATTTGATTTAGCTTCTT
1 ATTTGATTTAGAAAGTGTTGCAATCGGAGTTAAAATATCAAAATCTGAATTTAATTTAGCTTCTT
* *
39599520 TTGTGCTGAATTTTTAACTTTTAATTTCAGTTCCAAGTTAGTATCTTTTTTAAAATTA
66 TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTAGTAACTTTTTTAAAATTA
* * *
39599578 ATTTGATTTAGAGAGTGTTGCAATCGGAGTT-AAATGTCAAAATCTGAATTTAATTTAGTTTCTT
1 ATTTGATTTAGAAAGTGTTGCAATCGGAGTTAAAATATCAAAATCTGAATTTAATTTAGCTTCTT
39599642 TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTAGTAACTTT
66 TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTAGTAACTTT
39599690 GAAAAAAAAT
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 75 0.72
123 29 0.28
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (123 bp):
ATTTGATTTAGAAAGTGTTGCAATCGGAGTTAAAATATCAAAATCTGAATTTAATTTAGCTTCTT
TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTAGTAACTTTTTTAAAATTA
Found at i:39609382 original size:20 final size:21
Alignment explanation
Indices: 39609354--39609392 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
39609344 TCTTTTCCAA
*
39609354 AAGTAAAAA-TCAAAATTATT
1 AAGTAAAAAGACAAAATTATT
*
39609374 AAGTTAAAAGACAAAATTA
1 AAGTAAAAAGACAAAATTA
39609393 CGTCATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (21 bp):
AAGTAAAAAGACAAAATTATT
Found at i:39618767 original size:38 final size:39
Alignment explanation
Indices: 39618677--39618766 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
39618667 ATAAATTACA
* *
39618677 TTTT-ATACAATAAAACATTTTATTATATTTATTTGTAT
1 TTTTAATATAATAAAACATTTTATTATATTTATTAGTAT
* *
39618715 TTTTAATATAATAAAATA-TTTATTATATTTATAGTAGTGTT
1 TTTTAATATAATAAAACATTTTATTATATTTAT--TAGT-AT
39618756 TTTTAATATAA
1 TTTTAATATAA
39618767 ATACTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 18 0.41
39 11 0.25
40 3 0.07
41 12 0.27
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (39 bp):
TTTTAATATAATAAAACATTTTATTATATTTATTAGTAT
Found at i:39619453 original size:69 final size:69
Alignment explanation
Indices: 39619337--39619829 Score: 583
Period size: 69 Copynumber: 7.1 Consensus size: 69
39619327 TGGTCGTGGG
* * * * * *
39619337 GTCATTTTAAGGCTCGCAGGTGAAGAGTCACAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCAC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
39619402 AGCT
66 AGCT
* * *
39619406 GTCATATTAAGGCTCACAGGTAAAGAGCCGCAGCCTCTAACACAGTTAGCGAGAGCAAATCTCCC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
**
39619471 AATT
66 AGCT
* ** * *
39619475 GTCATGTTAAGGCTCATAGGTAAAGAGCAGCAGCCTCCAACACAGTTAGCGAGAGCAAATCTCCC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
*
39619540 AACT
66 AGCT
* * * * * *
39619544 GTCATATTAAGACTCGCAGGTAATGAACCGCAACCTCCAACACAGTTAGCGAGAACAAAACTCCC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
*
39619609 AACT
66 AGCT
* * * * * * *
39619613 GTCATATTAAGGCTTGCAAGTGAAGAGCTGCAACCTCCAACACAATTAGCGAGAGTAAAGCTCCC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
39619678 AAG-T
66 -AGCT
* * *
39619682 GTCATATTAAGGCACGCAGGTCAAGAGCCGCAGCCTCCAACACAGTTAGCGAAAGCAAAGCTCCC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
39619747 AGCT
66 AGCT
* * * * * * * *
39619751 GTCATATTAAAGCTCACAAGTAAAGAGACGGAGCCTCTAACACAGTTAGTGAGAGCAAAGCTTCC
1 GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
39619816 AGCT
66 AGCT
*
39619820 ATCATATTAA
1 GTCATATTAA
39619830 TCATATTTGA
Statistics
Matches: 363, Mismatches: 59, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
68 2 0.01
69 360 0.99
70 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (69 bp):
GTCATATTAAGGCTCGCAGGTAAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
AGCT
Found at i:39626599 original size:41 final size:41
Alignment explanation
Indices: 39626554--39626927 Score: 446
Period size: 41 Copynumber: 9.1 Consensus size: 41
39626544 AAGTATCAAT
* *
39626554 GGAAGACTTAAGTCTCGGGATGAGCATGAGATTATATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
* * *** *
39626595 GGAAGACTCGTGACTCAAAATGAGCATGAGATTAAATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
*
39626636 GGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
* * *
39626677 GGAAGACTCATGTCTCGGGATAAGTAAGAGATTATATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
* * *** *
39626718 GGAAGACTCGTGACTCAAAATGAGCATGAGATTAAATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
**
39626759 GTTAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
* * *
39626800 GAAAGACTCATGTTTCGGGATGAGTATGAGATTATATTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
* *
39626841 GGAAGACTCGTGACTCGGGATGAGCATGAGATTATATTTAAA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATA-TTAAA
* * * * *
39626883 GGAAGACTTATGACTCGGTA-GAGCATAAGATTGT-TTAAGA
1 GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAA-A
39626923 GGAAG
1 GGAAG
39626928 GTCAACGACT
Statistics
Matches: 283, Mismatches: 48, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
39 4 0.01
40 6 0.02
41 251 0.89
42 22 0.08
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.26
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
Found at i:39626773 original size:123 final size:123
Alignment explanation
Indices: 39626554--39626899 Score: 539
Period size: 123 Copynumber: 2.8 Consensus size: 123
39626544 AAGTATCAAT
* * *
39626554 GGAAGACTTAAGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTCAAAATGAG
1 GGAAGACTCATGTCTCGGGATGAGTATGAGATTATATTAAAGGAAGACTCGTGACTCAAAATGAG
39626619 CATGAGATTAAATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAA
66 CATGAGATTAAATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAA
* *
39626677 GGAAGACTCATGTCTCGGGATAAGTAAGAGATTATATTAAAGGAAGACTCGTGACTCAAAATGAG
1 GGAAGACTCATGTCTCGGGATGAGTATGAGATTATATTAAAGGAAGACTCGTGACTCAAAATGAG
** *
39626742 CATGAGATTAAATTAAAGTTAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAA
66 CATGAGATTAAATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAA
* * ***
39626800 GAAAGACTCATGTTTCGGGATGAGTATGAGATTATATTAAAGGAAGACTCGTGACTCGGGATGAG
1 GGAAGACTCATGTCTCGGGATGAGTATGAGATTATATTAAAGGAAGACTCGTGACTCAAAATGAG
* * *
39626865 CATGAGATTATATTTAAAGGAAGACTTATGACTCG
66 CATGAGATTA-AATTAAAGGAAGACTCATGTCTCG
39626900 GTAGAGCATA
Statistics
Matches: 202, Mismatches: 20, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
123 183 0.91
124 19 0.09
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (123 bp):
GGAAGACTCATGTCTCGGGATGAGTATGAGATTATATTAAAGGAAGACTCGTGACTCAAAATGAG
CATGAGATTAAATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAA
Found at i:39629186 original size:19 final size:19
Alignment explanation
Indices: 39629162--39629198 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39629152 TTATTTATAT
39629162 TTAATAATATAATA-AATTA
1 TTAATAAT-TAATATAATTA
39629181 TTAATAATTAATATAATT
1 TTAATAATTAATATAATT
39629199 TATTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATAATTAATATAATTA
Found at i:39629196 original size:23 final size:22
Alignment explanation
Indices: 39629166--39629211 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
39629156 TTATATTTAA
39629166 TAATATAATAAATTATTAATAAT
1 TAATATAATAAATT-TTAATAAT
**
39629189 TAATATAATTTATTTTAATAAT
1 TAATATAATAAATTTTAATAAT
39629211 T
1 T
39629212 TTTTTGGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATAATAAATTTTAATAAT
Found at i:39629211 original size:22 final size:21
Alignment explanation
Indices: 39629154--39629211 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
39629144 TTGGTAAATT
39629154 ATTTATATTTAATAATATAATAA
1 ATTTAT-TTTAATAAT-TAATAA
39629177 A-TTA--TTAATAATTAATATA
1 ATTTATTTTAATAATTAATA-A
39629196 ATTTATTTTAATAATT
1 ATTTATTTTAATAATT
39629212 TTTTTGGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 5 0.16
19 10 0.32
20 3 0.10
22 12 0.39
23 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTATTTTAATAATTAATAA
Found at i:39629986 original size:28 final size:29
Alignment explanation
Indices: 39629954--39630016 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
39629944 GAAAATTTAG
*
39629954 AATTTAATTAATGTA-TTTTTA-TTTCCAA
1 AATTTAATTAATCTACTTTTTAGTTT-CAA
*
39629982 AATTTAGTTAATCTACTTTTTAGTTTCAA
1 AATTTAATTAATCTACTTTTTAGTTTCAA
39630011 AATTTA
1 AATTTA
39630017 CGTACAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 13 0.42
29 15 0.48
30 3 0.10
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (29 bp):
AATTTAATTAATCTACTTTTTAGTTTCAA
Found at i:39634121 original size:15 final size:15
Alignment explanation
Indices: 39634101--39634129 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39634091 GTGAATTTAA
39634101 ATAAATTTAAATTAG
1 ATAAATTTAAATTAG
39634116 ATAAATTTAAATTA
1 ATAAATTTAAATTA
39634130 TTTTCTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATAAATTTAAATTAG
Found at i:39638796 original size:19 final size:21
Alignment explanation
Indices: 39638764--39638806 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
39638754 TTATGTAATT
*
39638764 TATATTAAA-TTAAAT-TAAA
1 TATATTAAACTAAAATATAAA
*
39638783 TATATTATACTAAAATATAAA
1 TATATTAAACTAAAATATAAA
39638804 TAT
1 TAT
39638807 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATTAAACTAAAATATAAA
Found at i:39639807 original size:2 final size:2
Alignment explanation
Indices: 39639800--39639833 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39639790 TAATTCTATC
39639800 AT 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 AT
39639834 TACTAGATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39640182 original size:60 final size:60
Alignment explanation
Indices: 39640073--39640186 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
39640063 AATTTTCTAT
* * *
39640073 TAATCTCTATACTATGCGTAAGTTGTAGGTTTAGTCATTATAGTCCAATTTGATCGTTTG
1 TAATATCTATACTATGCATAAGTTGTAGGTTTAGTCATTATACTCCAATTTGATCGTTTG
* * *
39640133 TAATATCTATACTATGTATAAGTTGT-GGATTTAGTC-TCTGTACTTCAATTTGAT
1 TAATATCTATACTATGCATAAGTTGTAGG-TTTAGTCAT-TATACTCCAATTTGAT
39640187 TATTTTTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (60 bp):
TAATATCTATACTATGCATAAGTTGTAGGTTTAGTCATTATACTCCAATTTGATCGTTTG
Found at i:39644346 original size:24 final size:24
Alignment explanation
Indices: 39644296--39644349 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
39644286 CTTTTAGTTT
*
39644296 AACTCTGTTTATTTGTTTCAATTA
1 AACTCTGTTTATTTGTTTCAATCA
* *
39644320 AACTCTGTTTATTTGTTTGAGTCA
1 AACTCTGTTTATTTGTTTCAATCA
39644344 AACTCT
1 AACTCT
39644350 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (24 bp):
AACTCTGTTTATTTGTTTCAATCA
Found at i:39653052 original size:6 final size:6
Alignment explanation
Indices: 39653027--39653065 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39653017 ACAATTCATA
* * *
39653027 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
39653066 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:39657395 original size:28 final size:28
Alignment explanation
Indices: 39657336--39657395 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
39657326 TATATGGACC
* *
39657336 GATTATTTAATTAGTAGACGAAGTATAA
1 GATTATTTAATTAATAAACGAAGTATAA
39657364 GATTATTTAATTACATAAAC-AA-TATAA
1 GATTATTTAATTA-ATAAACGAAGTATAA
39657391 TGATT
1 -GATT
39657396 CTGGCTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (28 bp):
GATTATTTAATTAATAAACGAAGTATAA
Found at i:39662738 original size:30 final size:28
Alignment explanation
Indices: 39662668--39662745 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 28
39662658 TACTTTTCAC
*
39662668 AAATTTAAAATTTCGTCCTTATACTTTT
1 AAATTTAAAATTTAGTCCTTATACTTTT
** *
39662696 ATTTTTATAAATTTAGTCCTTCTACTTTTT
1 AAATTTA-AAATTTAGTCCTTATAC-TTTT
39662726 AAATTTCAAAATTTAAGTCC
1 AAATTT-AAAATTT-AGTCC
39662746 AACTATTAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.12
29 15 0.38
30 14 0.35
31 6 0.15
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (28 bp):
AAATTTAAAATTTAGTCCTTATACTTTT
Found at i:39669884 original size:42 final size:42
Alignment explanation
Indices: 39669777--39669929 Score: 189
Period size: 42 Copynumber: 3.6 Consensus size: 42
39669767 ATGAGGATTT
* *
39669777 ATTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGAATATG
1 ATTAAAGGAAGACTCATGACTCGGGATGAGAATGAGAATATG
* *
39669819 ATTAAAGGAAGACTTATGTCTCGGGATGAGAATGAGAATATG
1 ATTAAAGGAAGACTCATGACTCGGGATGAGAATGAGAATATG
* ** *
39669861 ATTAAAGGAAGACTCATGACTCGGAATGAGCGTGAGATTATG
1 ATTAAAGGAAGACTCATGACTCGGGATGAGAATGAGAATATG
* *
39669903 TTTAGAAAAGGAAGACTTATGACTCGG
1 ATT---AAAGGAAGACTCATGACTCGG
39669930 TAGAGCATAA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
42 78 0.80
45 20 0.20
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (42 bp):
ATTAAAGGAAGACTCATGACTCGGGATGAGAATGAGAATATG
Found at i:39671437 original size:25 final size:24
Alignment explanation
Indices: 39671391--39671439 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
39671381 AATTATTAAA
39671391 TATTAAATAAAGAAATAAAATAAT
1 TATTAAATAAAGAAATAAAATAAT
39671415 TATTGAAATAAA-AAATAATAATAAT
1 TATT-AAATAAAGAAATAA-AATAAT
39671440 ATGAACGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
TATTAAATAAAGAAATAAAATAAT
Found at i:39672347 original size:19 final size:21
Alignment explanation
Indices: 39672323--39672364 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39672313 TTATAATTTA
*
39672323 ATATTA-ATAAT-ATTTAAAT
1 ATATTACATAATAATATAAAT
39672342 ATATTACATAATAATATAAAT
1 ATATTACATAATAATATAAAT
39672363 AT
1 AT
39672365 TATAAAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTACATAATAATATAAAT
Found at i:39673370 original size:21 final size:21
Alignment explanation
Indices: 39673346--39673400 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
39673336 TCAGGTGCCG
**
39673346 CGGGTGTGGAATCAGTTGATT
1 CGGGTGTGGAATCAGGGGATT
* *
39673367 CGGGTGTTGAATCTGGGGATT
1 CGGGTGTGGAATCAGGGGATT
*
39673388 CAGGTGTGGAATC
1 CGGGTGTGGAATC
39673401 CGGTGACTCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.40, T:0.31
Consensus pattern (21 bp):
CGGGTGTGGAATCAGGGGATT
Found at i:39678760 original size:25 final size:25
Alignment explanation
Indices: 39678718--39678766 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39678708 TCATCATTTT
* *
39678718 TCATTCTTTCATTTTATTATTGTTC
1 TCATTCTTTCACTCTATTATTGTTC
*
39678743 TCATTCTTTCACTCTATTCTTGTT
1 TCATTCTTTCACTCTATTATTGTT
39678767 ATTTGAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.04, T:0.61
Consensus pattern (25 bp):
TCATTCTTTCACTCTATTATTGTTC
Found at i:39679205 original size:70 final size:69
Alignment explanation
Indices: 39679092--39679292 Score: 306
Period size: 63 Copynumber: 3.0 Consensus size: 69
39679082 CATTGCTGAG
*
39679092 ACCTCGAGCATGAACCTTATGCATACTGCAAATTTTCTGTTTGTTTGAAACGGGTAACGGGAAAC
1 ACCTCGAGCATGAACCTTATGCATACTGCAAATTTGCTGTTTGTTTGAAACGGG-AACGGGAAAC
39679157 GGGAA
65 GGGAA
*
39679162 ACCTCGAGCATGAACCTTATGCATTCTGCAAATTTGCTGTTTGTTTG--A----AACGGGAAACG
1 ACCTCGAGCATGAACCTTATGCATACTGCAAATTTGCTGTTTGTTTGAAACGGGAACGGGAAACG
*
39679221 GGAG
66 GGAA
*
39679225 ACCTCGAGCATGAACCTTATGCATACTGCAAATTTGCTGTTTGTTTGAAACGGGAAACGGGGAAC
1 ACCTCGAGCATGAACCTTATGCATACTGCAAATTTGCTGTTTGTTTGAAACGGG-AACGGGAAAC
39679290 GGG
65 GGG
39679293 GTTTGTTCTT
Statistics
Matches: 119, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
63 60 0.50
65 1 0.01
68 1 0.01
70 57 0.48
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (69 bp):
ACCTCGAGCATGAACCTTATGCATACTGCAAATTTGCTGTTTGTTTGAAACGGGAACGGGAAACG
GGAA
Found at i:39681816 original size:80 final size:80
Alignment explanation
Indices: 39681696--39681934 Score: 304
Period size: 80 Copynumber: 3.0 Consensus size: 80
39681686 TGGCATCCAA
* * * *
39681696 TGCCTAACGAATAGATCGCAAAAGGGAATCCAACTCTAATTGAATTAATCAACAAATATCCGTCA
1 TGCCTAATGAATAAATCGCAAAAGTGAGTCCAACTCTAATTGAATTAATCAACAAATATCCGTCA
39681761 AATCTTGACACTCAG
66 AATCTTGACACTCAG
* * * * * * **
39681776 TGCTTAATGAATAAATTGCAAAAGTGAG-CCTAATTTTAATTGGATTAATTAACAAATATCAATC
1 TGCCTAATGAATAAATCGCAAAAGTGAGTCC-AACTCTAATTGAATTAATCAACAAATATCCGTC
39681840 AAATCTTGACAC-CTAG
65 AAATCTTGACACTC-AG
* *
39681856 TGCCTAATGAATAAATCGCAAAAGTGAGTCCAACTCTAGTTGAATTAATCAA-AGAATATTCGTC
1 TGCCTAATGAATAAATCGCAAAAGTGAGTCCAACTCTAATTGAATTAATCAACA-AATATCCGTC
39681920 AAATCTTGACACTCA
65 AAATCTTGACACTCA
39681935 ATACTTAGCG
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
79 4 0.03
80 125 0.95
81 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (80 bp):
TGCCTAATGAATAAATCGCAAAAGTGAGTCCAACTCTAATTGAATTAATCAACAAATATCCGTCA
AATCTTGACACTCAG
Found at i:39685366 original size:20 final size:21
Alignment explanation
Indices: 39685328--39685366 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39685318 AAATTAGAGT
*
39685328 GAAATTGTTTGAGTTTTGATA
1 GAAATTGTTAGAGTTTTGATA
39685349 GAAATTGTTAGA-TTTTGA
1 GAAATTGTTAGAGTTTTGA
39685367 AGCTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
GAAATTGTTAGAGTTTTGATA
Found at i:39686542 original size:2 final size:2
Alignment explanation
Indices: 39686535--39686565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39686525 TATTTGATGA
39686535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39686566 CTTGAAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39710476 original size:6 final size:6
Alignment explanation
Indices: 39710465--39710502 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
39710455 ATTTGGACAA
39710465 AAATTT AAATTT AAATTTT AAA-TT AAA-TT AAATTT AAA
1 AAATTT AAATTT AAA-TTT AAATTT AAATTT AAATTT AAA
39710503 CAAATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.33
6 14 0.47
7 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:39710758 original size:31 final size:31
Alignment explanation
Indices: 39710723--39710789 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
39710713 TATAAAATGG
*
39710723 TCATTAAGCTATTCGAAAGTTTATATTTAAA
1 TCATTAAACTATTCGAAAGTTTATATTTAAA
* * * * *
39710754 TCATTAAATTATTTGAAAGTTTTTCTTTAAG
1 TCATTAAACTATTCGAAAGTTTATATTTAAA
39710785 TCATT
1 TCATT
39710790 GAGTTGTCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (31 bp):
TCATTAAACTATTCGAAAGTTTATATTTAAA
Found at i:39712333 original size:3 final size:3
Alignment explanation
Indices: 39712312--39712612 Score: 78
Period size: 3 Copynumber: 100.3 Consensus size: 3
39712302 TTGGGGACGA
* * * * * **
39712312 GGT GGT AGT GGT AGT GGT GGT GGT GGT GGT GGT GGA GGA GGA GGT GCA
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * * * * *
39712360 AGT GGT GGT GCT AGG- GGT GGT GGA GGT GCT GGA GGT GGT -GT AGGA
1 GGT GGT GGT GGT -GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT -GGT
* ** * * * * * *
39712405 GGA GGT GCA GGA GGA GGT GCT GGT GTT GG- GGTT GGT GGA GG- AGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG-T GGT GGT GGT GGT
* * ** * *
39712449 AGGT GGT GGT GGT GGT GGT GGT GGT GGT AGA GGT GGT GCA GGA GGA
1 -GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * ** * *
39712495 GGT GCT GG- AGT GGGT GCA GGT GTT GGT GGT GGT GTT GG- GGCT GGT
1 GGT GGT GGT GGT -GGT GGT GGT GGT GGT GGT GGT GGT GGT GG-T GGT
* * * * * * * **
39712540 GGA GGT GGA GCT GCT AGG- GGT GGT GGA GGT GCT GG- AGT GGGT GCA
1 GGT GGT GGT GGT GGT -GGT GGT GGT GGT GGT GGT GGT GGT -GGT GGT
*
39712585 GGT GGT GGT GGT GGT GGT GGA GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT G
39712613 TTGGCGGAGG
Statistics
Matches: 211, Mismatches: 71, Indels: 32
0.67 0.23 0.10
Matches are distributed among these distances:
2 13 0.06
3 185 0.88
4 13 0.06
ACGTcount: A:0.11, C:0.04, G:0.60, T:0.25
Consensus pattern (3 bp):
GGT
Found at i:39712412 original size:42 final size:42
Alignment explanation
Indices: 39712366--39712529 Score: 127
Period size: 42 Copynumber: 3.8 Consensus size: 42
39712356 TGCAAGTGGT
* *
39712366 GGTGCTAGG-GGTGGTGGAGGTGCTGGAGGTGGTGTAGGAGGA
1 GGTGCT-GGAGGTGGTGCAGGTGTTGGAGGTGGTGTAGGAGGA
* * * * *
39712408 GGTGCAGGAGGAGGTGCTGGTGTTGG-GGTTGGTGGAGGAGTA
1 GGTGCTGGAGGTGGTGCAGGTGTTGGAGG-TGGTGTAGGAGGA
* * ** * *
39712450 GGTGGTGGTGGTGGTGGTGGTGGTGGTAGAGGTGGTGCAGGAGGA
1 GGTGCTGGAGGTGGTGCAGGT-GT--TGGAGGTGGTGTAGGAGGA
*
39712495 GGTGCTGGA-GTGGGTGCAGGTGTTGGTGGTGGTGT
1 GGTGCTGGAGGT-GGTGCAGGTGTTGGAGGTGGTGT
39712530 TGGGGCTGGT
Statistics
Matches: 93, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
41 4 0.04
42 54 0.58
43 2 0.02
44 4 0.04
45 27 0.29
46 2 0.02
ACGTcount: A:0.12, C:0.04, G:0.59, T:0.25
Consensus pattern (42 bp):
GGTGCTGGAGGTGGTGCAGGTGTTGGAGGTGGTGTAGGAGGA
Found at i:39712540 original size:75 final size:74
Alignment explanation
Indices: 39712375--39713069 Score: 361
Period size: 75 Copynumber: 9.3 Consensus size: 74
39712365 TGGTGCTAGG
* * * * *
39712375 GGTGGTGGAGGTGCTGGAGGTGGT-GTAGGAGGAGGTGCAGGAGGAGGTGCTGGTGTTGGG-GTT
1 GGTGTTGG-GGTGGTGGAGGTGGTGGTA-GAGGAGGTGCAGGAGGAGGTGTTGGAG-TGGGTGTA
* *
39712438 GGTGGAGG-AGT
63 GGTGGTGGTGGT
* * * * *
39712449 AGGTGGTGGTGGTGGTGGTGGTGGTGGTAGAGGTGGTGCAGGAGGAGGTGCTGGAGTGGGTGCAG
1 -GGTGTTGG-GGTGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTAG
*
39712514 GTGTTGGTGGT
64 GTGGTGGTGGT
* * * * *
39712525 GGTGTTGGGGCTGGTGGAGGTGGAGCT-GCTAGG-GGT---GGTGGAGGTGCTGGAGTGGGTGCA
1 GGTGTTGGGG-TGGTGGAGGTGGTGGTAG--AGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTA
39712585 ---GGTGGTGGT
63 GGTGGTGGTGGT
* * * * *
39712594 -G-G-T--GGTGGTGGAGGTGGTGTTGGCGGAGGTGTAGGAGGAGGTGCTGGAGTGGGTGTAGGT
1 GGTGTTGGGGTGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTAGGT
39712654 GGTGGTGGTGTT
66 GGTGGT-G-G-T
* * * * * *
39712666 AGGGCTGTTGGAGGAGCAGGTGGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGCGTTGGAGTAGG
1 --GG-TGTT-G-GG-G-TGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGG
39712731 TGTAGGTGGTGGTGGT
59 TGTAGGTGGTGGTGGT
* * * * * ** * * * *
39712747 GGGGTTAGTGGAGGAGCAGGTGCCGGT---GGAGGTGGAGGTGGAGGTGTTAGGGGT-GGTGGAG
1 GGTGTT-GGGGTGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTT-GGAGTGGGTGTAG
*
39712808 GTGGTGTTAGTGGA
64 GTGGTG---GTGGT
** * ** * * * ** * * * * *
39712822 GGTGCAGGAGGAGGTGTTGG-AGTAGGTACAGGTGGTGGTGGTGGTGGTGTTGGGGTTGGTGGAG
1 GGTGTTGG-GGTGGTGGAGGTGGT-GGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTAG
* *
39712886 GTGGAGGTGGA
64 GTGGTGGTGGT
* * * * * * *
39712897 GGTGTTAGGGGTGGTAGAGGTGGTGTTGGCGGAGGTGCAGAAGGAGGTGTTGGAGTAGGTGCAGG
1 GGTGTT-GGGGTGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTAGG
39712962 TGGTGGTGGT
65 TGGTGGTGGT
* * * * *
39712972 GGTGTTGGGGTTGGTGGAGGTAGTGTTAGTGGAGGTGCAAGAGGAGGTGTTGGAGTAGGTGTAGG
1 GGTGTTGGGG-TGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTAGG
39713037 TGGTGGTGGT
65 TGGTGGTGGT
39713047 GGTGTTGGGGCTGGTGGAGGTGG
1 GGTGTTGGGG-TGGTGGAGGTGG
39713070 AGGAGCAGGT
Statistics
Matches: 493, Mismatches: 85, Indels: 84
0.74 0.13 0.13
Matches are distributed among these distances:
62 2 0.00
63 17 0.03
64 3 0.01
66 23 0.05
67 1 0.00
68 1 0.00
69 14 0.03
70 1 0.00
71 1 0.00
72 54 0.11
73 4 0.01
74 12 0.02
75 242 0.49
76 13 0.03
77 7 0.01
78 35 0.07
79 2 0.00
81 1 0.00
82 2 0.00
83 2 0.00
84 56 0.11
ACGTcount: A:0.13, C:0.04, G:0.58, T:0.25
Consensus pattern (74 bp):
GGTGTTGGGGTGGTGGAGGTGGTGGTAGAGGAGGTGCAGGAGGAGGTGTTGGAGTGGGTGTAGGT
GGTGGTGGT
Found at i:39712621 original size:15 final size:15
Alignment explanation
Indices: 39712591--39712624 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39712581 TGCAGGTGGT
*
39712591 GGTGGTGGTGGTGGA
1 GGTGGTGGTGGCGGA
*
39712606 GGTGGTGTTGGCGGA
1 GGTGGTGGTGGCGGA
39712621 GGTG
1 GGTG
39712625 TAGGAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.65, T:0.26
Consensus pattern (15 bp):
GGTGGTGGTGGCGGA
Found at i:39712630 original size:24 final size:24
Alignment explanation
Indices: 39712603--39712660 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
39712593 TGGTGGTGGT
* *
39712603 GGAGGTGGTGTTGGCG-GAGGTGTA
1 GGAGGTGGTGCTGGAGTG-GGTGTA
*
39712627 GGAGGAGGTGCTGGAGTGGGTGTA
1 GGAGGTGGTGCTGGAGTGGGTGTA
*
39712651 GGTGGTGGTG
1 GGAGGTGGTG
39712661 GTGTTAGGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.12, C:0.03, G:0.60, T:0.24
Consensus pattern (24 bp):
GGAGGTGGTGCTGGAGTGGGTGTA
Found at i:39712654 original size:84 final size:83
Alignment explanation
Indices: 39712512--39712747 Score: 210
Period size: 84 Copynumber: 2.8 Consensus size: 83
39712502 GAGTGGGTGC
* * * * * * * *
39712512 AGGTGTTGGTGGTGGTGTTGG-GGCTGGTGGAGGTGGAGCTGCTAGGGGTGGTGGAGGTGCTGGA
1 AGGTGGTGGAGGTGGTGTTGGCGG-AGGTGCAGGAGGAGGTGCT-GGAGTGGTGTAGGTGCT-G-
*
39712576 GTGG-GTGCA-GG-TGGTGGTGG
62 GTGGTGT-CAGGGCTGGTGGAGG
* * *
39712596 TGGTGGTGGAGGTGGTGTTGGCGGAGGTGTAGGAGGAGGTGCTGGAGTGGGTGTAGGTGGTGGTG
1 AGGTGGTGGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGCTGGAGT-GGTGTAGGTGCTGGTG
* *
39712661 GTGTTAGGGCTGTTGGAGG
65 GTGTCAGGGCTGGTGGAGG
** * * *
39712680 AGCAGGTGGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGCGTTGGAGTAGGTGTAGGTGGTGGTG
1 AGGTGGTGGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGCTGGAGT-GGTGTAGGTGCTGGTG
39712745 GTG
65 GTG
39712748 GGGTTAGTGG
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
82 5 0.04
83 9 0.07
84 111 0.87
85 2 0.02
ACGTcount: A:0.11, C:0.05, G:0.58, T:0.25
Consensus pattern (83 bp):
AGGTGGTGGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGCTGGAGTGGTGTAGGTGCTGGTGG
TGTCAGGGCTGGTGGAGG
Found at i:39712708 original size:72 final size:71
Alignment explanation
Indices: 39712478--39712714 Score: 222
Period size: 72 Copynumber: 3.4 Consensus size: 71
39712468 GGTGGTGGTA
*
39712478 GAGGTGGTGCAGGAGGAGGTGCTGGAGTGGGTGCAGGTGTTGGTGGTGGTGTTGGGGCTGGTGGA
1 GAGGTGGTGTAGGAGGAGGTGCTGGAGTGGGTGCA-G-G-TGGTGGTGGTGTT-GGGCTGGTGGA
39712543 GGTGGAGCTG
62 GGTGGAGCTG
* *
39712553 CTA-G-GG-GT-GGTGGAGGTGCTGGAGTGGGTGCAGGTGGTGGT-G-G-T-GG-TGGTGGAGGT
1 -GAGGTGGTGTAGGAGGAGGTGCTGGAGTGGGTGCAGGTGGTGGTGGTGTTGGGCTGGTGGAGGT
* *
39712609 GGTGTTG
65 GGAGCTG
* * * * *
39712616 GCGGAGGTGTAGGAGGAGGTGCTGGAGTGGGTGTAGGTGGTGGTGGTGTTAGGGCTGTTGGAGGA
1 GAGGTGGTGTAGGAGGAGGTGCTGGAGTGGGTGCAGGTGGTGGTGGTGTT-GGGCTGGTGGAGGT
* *
39712681 GCAGGTG
65 GGAGCTG
* * *
39712688 GAGGTGGTGTTGGCGGAGGTGCAGGAG
1 GAGGTGGTGTAGGAGGAGGTGCTGGAG
39712715 GAGGCGTTGG
Statistics
Matches: 132, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
63 16 0.12
64 4 0.03
65 2 0.02
66 32 0.24
67 2 0.02
68 2 0.02
69 8 0.06
70 1 0.01
71 3 0.02
72 57 0.43
73 1 0.01
74 2 0.02
75 1 0.01
76 1 0.01
ACGTcount: A:0.11, C:0.06, G:0.59, T:0.24
Consensus pattern (71 bp):
GAGGTGGTGTAGGAGGAGGTGCTGGAGTGGGTGCAGGTGGTGGTGGTGTTGGGCTGGTGGAGGTG
GAGCTG
Found at i:39712714 original size:24 final size:23
Alignment explanation
Indices: 39712687--39712841 Score: 75
Period size: 24 Copynumber: 6.6 Consensus size: 23
39712677 AGGAGCAGGT
*
39712687 GGAGGTGGTGTTGGCGGAGGTGCA
1 GGAGGAGGTGTTGG-GGAGGTGCA
* * *
39712711 GGAGGAGGCGTTGGAGTAGGTGTA
1 GGAGGAGGTGTTGG-GGAGGTGCA
* * * *
39712735 GGTGGTGGTGGTGGGGTTA-GTGGA
1 GGAGGAGGTGTTGGGG--AGGTGCA
* ** *
39712759 GGAGCAGGTGCCGGTGGAGGTGGA
1 GGAGGAGGTGTTGG-GGAGGTGCA
* *
39712783 GGTGGAGGTGTTAGGGGTGGT---
1 GGAGGAGGTGTT-GGGGAGGTGCA
* *
39712804 GGAGGTGGTGTTAGTGGAGGTGCA
1 GGAGGAGGTGTT-GGGGAGGTGCA
39712828 GGAGGAGGTGTTGG
1 GGAGGAGGTGTTGG
39712842 AGTAGGTACA
Statistics
Matches: 96, Mismatches: 27, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
21 17 0.18
23 3 0.03
24 71 0.74
25 5 0.05
ACGTcount: A:0.14, C:0.05, G:0.59, T:0.23
Consensus pattern (23 bp):
GGAGGAGGTGTTGGGGAGGTGCA
Found at i:39712780 original size:6 final size:6
Alignment explanation
Indices: 39712771--39712900 Score: 52
Period size: 6 Copynumber: 21.7 Consensus size: 6
39712761 AGCAGGTGCC
* * *
39712771 GGTGGA GGTGGA GGTGGA GGTGTTA GG-GGT GGTGGA GGTGGT GTTAGTGGA
1 GGTGGA GGTGGA GGTGGA GGTG-GA GGTGGA GGTGGA GGTGGA G---GTGGA
* * ** * * ** * * *
39712822 GGTGCA GGAGGA GGTGTT GGAGTA GGTACA GGTGGT GGTGGT GGTGGT
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
* *
39712870 GTTGG- GGT--T GGTGGA GGTGGA GGTGGA GGTG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTG
39712901 TTAGGGGTGG
Statistics
Matches: 93, Mismatches: 23, Indels: 16
0.70 0.17 0.12
Matches are distributed among these distances:
4 3 0.03
5 4 0.04
6 78 0.84
7 3 0.03
9 5 0.05
ACGTcount: A:0.13, C:0.02, G:0.60, T:0.25
Consensus pattern (6 bp):
GGTGGA
Found at i:39712802 original size:108 final size:106
Alignment explanation
Indices: 39712688--39712975 Score: 326
Period size: 108 Copynumber: 2.6 Consensus size: 106
39712678 GGAGCAGGTG
* *
39712688 GAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGCGTTGGAGTAGGTGTAGGTGGTGGTGGTGG-GGT
1 GAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGG-
* *
39712752 TAGTGGAGGAGCAGGTGCCGGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTG
65 T-GTGG-GG-GCAGGTG-C-----AGGTGGAGGTGGAGGTG-T-GAGGTGGTA
* * *
39712805 GAGGTGGTGTTAGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTACAGGTGGTGGTGGTGGTGGT
1 GAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGT
* ** * *
39712870 GTTGGGGTTGGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTA
66 GTGGGGGCAGGTGCAGGTGGAGGTGGAGGTG-T-GAGGTGGTA
*
39712913 GAGGTGGTGTTGGCGGAGGTGCAGAAGGAGGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTG
1 GAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTG
39712976 TTGGGGTTGG
Statistics
Matches: 156, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
108 87 0.56
114 5 0.03
115 2 0.01
116 3 0.02
117 57 0.37
118 2 0.01
ACGTcount: A:0.14, C:0.04, G:0.58, T:0.24
Consensus pattern (106 bp):
GAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGT
GTGGGGGCAGGTGCAGGTGGAGGTGGAGGTGTGAGGTGGTA
Found at i:39712855 original size:45 final size:45
Alignment explanation
Indices: 39712772--39712858 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
39712762 GCAGGTGCCG
* * * **
39712772 GTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTGGAGGTGGTGTTA
1 GTGGAGGTGCAGGAGGAGGTGTTAGGAGTGGTACAGGTGGTGTTA
39712817 GTGGAGGTGCAGGAGGAGGTGTT-GGAGTAGGTACAGGTGGTG
1 GTGGAGGTGCAGGAGGAGGTGTTAGGAGT-GGTACAGGTGGTG
39712859 GTGGTGGTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 4 0.11
45 32 0.89
ACGTcount: A:0.16, C:0.02, G:0.57, T:0.24
Consensus pattern (45 bp):
GTGGAGGTGCAGGAGGAGGTGTTAGGAGTGGTACAGGTGGTGTTA
Found at i:39712855 original size:63 final size:61
Alignment explanation
Indices: 39712684--39713236 Score: 256
Period size: 63 Copynumber: 9.2 Consensus size: 61
39712674 TGGAGGAGCA
* *
39712684 GGTGGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGCGTT-G-G-A-GT-AGGTGTA--GGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGAGGTGTAGGGGT
* * * * * ** ** * *
39712738 GGTGGTGGTGGGGTTAGTGGAGGAGCAGGTGCCGGTGGAGGTGGAGGTGGAGGTGTTAGGGGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGT-GAGGTG-TAGGGGT
* *
39712801 GGTGGAGGTGGTGTTAGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTACAGGTGGT-GGTGGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGT-GAGGT-GTAGG-GGT
* * * * * *
39712864 GGTGGTGTTGGGGTTGGTGGAGGTGGAGGTGGAGGTGTT--AG--GG-GTGGTAG-AGGTGGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGAGGT-GTAGG-GGT
* * * ** ** ** * ** * * *
39712921 GTTGGCGGAGGTGCAGAAGGAGGTGTTGGAGTAGGTGCAGGTGGT-GGTGGTGGTGTTGGGGTT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGG-AGTAGGT-GAGGTGTAGGGG-T
* * * *
39712984 GGTGGAGGTAGTGTTAGTGGAGGTGCAAGAGGAGGTGTTGGAGTAGGTGTAGGTG--GTGGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTG-AGGTGTAGGGGT
* * * * * * **
39713044 GGTGGTGTTGGGGCTGGTGGAGGTGGAGGAGCAGGTG-CCG-GT--G-GAGGTGCTAGGGGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGAGGTG-TAGGGGT
* * *
39713101 GGTAGAGGTGGTGTTGGCGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGCAGGTG--GTGGT
1 GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTG-AGGTGTAGGGGT
* * * *
39713161 GGTGGTGGTGGTGTTGG-GGTAGGTGGAGGTGGAGGTGGTGTTGGAGTAGGTGCAGGTGGTAGTG
1 GGTGGAGGTGGTGTTGGTGG-AGGTGCA---GGAGGAGGTGTTGGAGTAGGTG-AGGT-GTAGGG
39713225 GT
60 GT
*
39713227 GGTGGTGGTG
1 GGTGGAGGTG
39713237 TTGGGGTTGG
Statistics
Matches: 367, Mismatches: 94, Indels: 64
0.70 0.18 0.12
Matches are distributed among these distances:
54 33 0.09
55 2 0.01
56 2 0.01
57 68 0.19
58 5 0.01
59 7 0.02
60 60 0.16
61 10 0.03
62 9 0.02
63 154 0.42
64 2 0.01
66 15 0.04
ACGTcount: A:0.13, C:0.04, G:0.58, T:0.25
Consensus pattern (61 bp):
GGTGGAGGTGGTGTTGGTGGAGGTGCAGGAGGAGGTGTTGGAGTAGGTGAGGTGTAGGGGT
Found at i:39712861 original size:24 final size:24
Alignment explanation
Indices: 39712804--39712861 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
39712794 TAGGGGTGGT
* *
39712804 GGAGGTGGTGTTAGTGGAGGTGCA
1 GGAGGTGGTGTTAGAGGAGGTACA
* * *
39712828 GGAGGAGGTGTTGGAGTAGGTACA
1 GGAGGTGGTGTTAGAGGAGGTACA
*
39712852 GGTGGTGGTG
1 GGAGGTGGTG
39712862 GTGGTGGTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.03, G:0.55, T:0.24
Consensus pattern (24 bp):
GGAGGTGGTGTTAGAGGAGGTACA
Found at i:39712895 original size:30 final size:30
Alignment explanation
Indices: 39712855--39712919 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
39712845 AGGTACAGGT
* * *
39712855 GGTGGTGGTGGTGGTGTT-GGGGTTGGTGGA
1 GGTGGAGGTGGAGGTGTTAGGGG-TGGTAGA
39712885 GGTGGAGGTGGAGGTGTTAGGGGTGGTAGA
1 GGTGGAGGTGGAGGTGTTAGGGGTGGTAGA
39712915 GGTGG
1 GGTGG
39712920 TGTTGGCGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.09, C:0.00, G:0.63, T:0.28
Consensus pattern (30 bp):
GGTGGAGGTGGAGGTGTTAGGGGTGGTAGA
Found at i:39712933 original size:33 final size:31
Alignment explanation
Indices: 39712831--39712933 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 31
39712821 AGGTGCAGGA
* *
39712831 GGAGGTGTTGGAGTAGGTACAGGTGGTGGTGGT
1 GGAGGTGTTGGGGT-GGTAGAGGTGGT-GTGGT
* * *
39712864 GGTGGTGTTGGGGTTGGTGGAGGT-G-GAGGT
1 GGAGGTGTTGGGG-TGGTAGAGGTGGTGTGGT
*
39712894 GGAGGTGTTAGGGGTGGTAGAGGTGGTGTTGGC
1 GGAGGTGTT-GGGGTGGTAGAGGTGGTG-TGGT
39712927 GGAGGTG
1 GGAGGTG
39712934 CAGAAGGAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
30 21 0.38
31 5 0.09
32 2 0.04
33 27 0.48
34 1 0.02
ACGTcount: A:0.12, C:0.02, G:0.59, T:0.27
Consensus pattern (31 bp):
GGAGGTGTTGGGGTGGTAGAGGTGGTGTGGT
Found at i:39712969 original size:24 final size:24
Alignment explanation
Indices: 39712918--39713161 Score: 113
Period size: 24 Copynumber: 10.2 Consensus size: 24
39712908 TGGTAGAGGT
* * **
39712918 GGTGTTGGCGGAGGTGCAGAAGGA
1 GGTGTTGGAGTAGGTGCAGGTGGA
*
39712942 GGTGTTGGAGTAGGTGCAGGTGGT
1 GGTGTTGGAGTAGGTGCAGGTGGA
* * * * **
39712966 GGTGGTGGTGTTGGGGTTGGTGGA
1 GGTGTTGGAGTAGGTGCAGGTGGA
* * *
39712990 GGTAG-TGTTAGTGGAGGTGCAAGAGGA
1 GGT-GTTG-GAGT--AGGTGCAGGTGGA
* *
39713017 GGTGTTGGAGTAGGTGTAGGTGGT
1 GGTGTTGGAGTAGGTGCAGGTGGA
* * * * *
39713041 GGTGGTGGTGTTGGGGCTGGTGGA
1 GGTGTTGGAGTAGGTGCAGGTGGA
** * *
39713065 GGTGGAGGAGCAGGTGCCGGTGGA
1 GGTGTTGGAGTAGGTGCAGGTGGA
* *
39713089 GGTGCTAGGGGT-GGTAG-AGGT---
1 GGTG-TTGGAGTAGGT-GCAGGTGGA
* * *
39713110 GGTGTTGGCGGAGGTGCAGGAGGA
1 GGTGTTGGAGTAGGTGCAGGTGGA
*
39713134 GGTGTTGGAGTAGGTGCAGGTGGT
1 GGTGTTGGAGTAGGTGCAGGTGGA
39713158 GGTG
1 GGTG
39713162 GTGGTGGTGG
Statistics
Matches: 158, Mismatches: 50, Indels: 24
0.68 0.22 0.10
Matches are distributed among these distances:
20 5 0.03
21 10 0.06
24 119 0.75
25 8 0.05
26 4 0.03
27 12 0.08
ACGTcount: A:0.14, C:0.05, G:0.57, T:0.25
Consensus pattern (24 bp):
GGTGTTGGAGTAGGTGCAGGTGGA
Found at i:39713008 original size:108 final size:106
Alignment explanation
Indices: 39712771--39712992 Score: 374
Period size: 108 Copynumber: 2.1 Consensus size: 106
39712761 AGCAGGTGCC
* * *
39712771 GGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTGGAGGTGGTGTTAGTGGAGGTGCAGGAGGAGG
1 GGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTAGAGGTGGTGTTAGCGGAGGTGCAGAAGGAGG
39712836 TGTTGGAGTAGGTACAGGTGGTGGTGGTGGTGGTGTTGGGGTT
66 TGTTGGAGTAGGTACA-G-GGTGGTGGTGGTGGTGTTGGGGTT
*
39712879 GGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTAGAGGTGGTGTTGGCGGAGGTGCAGAAGGAGG
1 GGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTAGAGGTGGTGTTAGCGGAGGTGCAGAAGGAGG
*
39712944 TGTTGGAGTAGGTGCA-GGTGGTGGTGGTGGTGTTGGGGTT
66 TGTTGGAGTAGGTACAGGGTGGTGGTGGTGGTGTTGGGGTT
39712984 GGTGGAGGT
1 GGTGGAGGT
39712993 AGTGTTAGTG
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
105 33 0.30
108 76 0.70
ACGTcount: A:0.13, C:0.02, G:0.59, T:0.26
Consensus pattern (106 bp):
GGTGGAGGTGGAGGTGGAGGTGTTAGGGGTGGTAGAGGTGGTGTTAGCGGAGGTGCAGAAGGAGG
TGTTGGAGTAGGTACAGGGTGGTGGTGGTGGTGTTGGGGTT
Found at i:39713160 original size:3 final size:3
Alignment explanation
Indices: 39713152--39713308 Score: 72
Period size: 3 Copynumber: 52.3 Consensus size: 3
39713142 AGTAGGTGCA
* * *
39713152 GGT GGT GGT GGT GGT GGT GGT GTT GG- GGT AGGT GGA GGT GGA GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT -GGT GGT GGT GGT GGT
* * ** * *
39713197 GGT GTT GG- AGT AGGT GCA GGT GGT AGT GGT GGT GGT GGT GTT GG-
1 GGT GGT GGT GGT -GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * * * * *
39713241 GGTT GGT GGA GG- AGT AGGA GCT GGT GGT GGT GGA GGT GCT AGG- GGT
1 GG-T GGT GGT GGT GGT -GGT GGT GGT GGT GGT GGT GGT GGT -GGT GGT
* * *
39713287 AGT GGA GGT GCT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT G
39713309 CAGGTGTTGG
Statistics
Matches: 109, Mismatches: 35, Indels: 20
0.66 0.21 0.12
Matches are distributed among these distances:
2 8 0.07
3 92 0.84
4 9 0.08
ACGTcount: A:0.10, C:0.03, G:0.60, T:0.28
Consensus pattern (3 bp):
GGT
Found at i:39713167 original size:18 final size:18
Alignment explanation
Indices: 39713146--39713326 Score: 104
Period size: 18 Copynumber: 10.2 Consensus size: 18
39713136 TGTTGGAGTA
*
39713146 GGTGCAGGTGGTGGTGGT
1 GGTGGAGGTGGTGGTGGT
* *
39713164 GGTGGTGGTGTTGG-GGT
1 GGTGGAGGTGGTGGTGGT
*
39713181 AGGTGGAGGTGGAGGTGGT
1 -GGTGGAGGTGGTGGTGGT
* **
39713200 GTTGGA-GTAGGTGCAGGT
1 GGTGGAGGT-GGTGGTGGT
* *
39713218 GGTAGTGGTGGTGGTGGT
1 GGTGGAGGTGGTGGTGGT
* *
39713236 GTTGG-GGT--TGGTGGA
1 GGTGGAGGTGGTGGTGGT
* * * *
39713251 GGAGTAGGAGCTGGTGGT
1 GGTGGAGGTGGTGGTGGT
*
39713269 GGTGGAGGTGCTAGG-GGT
1 GGTGGAGGTGGT-GGTGGT
* *
39713287 AGTGGAGGTGCTGGTGGT
1 GGTGGAGGTGGTGGTGGT
* * *
39713305 GGTGCAGGTGTTGGTAGT
1 GGTGGAGGTGGTGGTGGT
39713323 GGTG
1 GGTG
39713327 TTGGAGCTGG
Statistics
Matches: 123, Mismatches: 31, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
15 8 0.07
16 2 0.02
17 10 0.08
18 96 0.78
19 7 0.06
ACGTcount: A:0.10, C:0.03, G:0.59, T:0.28
Consensus pattern (18 bp):
GGTGGAGGTGGTGGTGGT
Found at i:39713185 original size:12 final size:13
Alignment explanation
Indices: 39713133--39713240 Score: 50
Period size: 12 Copynumber: 8.7 Consensus size: 13
39713123 GTGCAGGAGG
*
39713133 AGGTGTTGG-AGT
1 AGGTGTTGGTGGT
**
39713145 AGGTGCAGGTGGT
1 AGGTGTTGGTGGT
*
39713158 -GGTGGTGGTGGT
1 AGGTGTTGGTGGT
39713170 -GGTGTTGG-GGT
1 AGGTGTTGGTGGT
**
39713181 AGGTGGAGGTGG-
1 AGGTGTTGGTGGT
* *
39713193 AGGTGGTGTTGGAGT
1 AGGTGTTGGT-G-GT
**
39713208 AGGTGCAGGTGGT
1 AGGTGTTGGTGGT
*
39713221 A-GTGGTGGTGGT
1 AGGTGTTGGTGGT
39713233 -GGTGTTGG
1 AGGTGTTGG
39713241 GGTTGGTGGA
Statistics
Matches: 73, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
11 3 0.04
12 53 0.73
13 8 0.11
14 2 0.03
15 7 0.10
ACGTcount: A:0.10, C:0.02, G:0.58, T:0.30
Consensus pattern (13 bp):
AGGTGTTGGTGGT
Found at i:39713185 original size:27 final size:27
Alignment explanation
Indices: 39713155--39713227 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
39713145 AGGTGCAGGT
* *
39713155 GGTGGTGGTGGTGGTGGTGTTGGGGTA
1 GGTGGAGGTGGTGGTGGTGTTGGAGTA
*
39713182 GGTGGAGGTGGAGGTGGTGTTGGAGTA
1 GGTGGAGGTGGTGGTGGTGTTGGAGTA
* *
39713209 GGTGCAGGTGGTAGTGGTG
1 GGTGGAGGTGGTGGTGGTG
39713228 GTGGTGGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.10, C:0.01, G:0.60, T:0.29
Consensus pattern (27 bp):
GGTGGAGGTGGTGGTGGTGTTGGAGTA
Done.