Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 23
Found at i:3813151 original size:33 final size:33
Alignment explanation
Indices: 3813109--3813201 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 33
3813099 GAAAATGGCT
*
3813109 ATCGCAATGCGAAATGAAAATCACAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
* *
3813142 ATCGCAATGCGAAATG-AAATCGCAACGGCAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
3813174 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
3813202 CGATTTGTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 28 0.52
33 26 0.48
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:3813193 original size:19 final size:19
Alignment explanation
Indices: 3813139--3813204 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
3813129 TCACAATGAC
*
3813139 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
3813158 -AAATCGCAACG-G----C
1 AAAATCGCAACGCGAAATG
3813171 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
3813190 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
3813205 TTTGTGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
17 1 0.03
18 10 0.27
19 14 0.38
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:3813256 original size:19 final size:19
Alignment explanation
Indices: 3813230--3813314 Score: 89
Period size: 19 Copynumber: 4.4 Consensus size: 19
3813220 GCGATTTTGC
*
3813230 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* **
3813249 CATTGCGATAACCATTTCG
1 CGTTGCGATATTCATTTCG
*
3813268 CGTTGCGATAGTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
3813287 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATATTCA-TTTCG
*
3813307 TGTTGCGA
1 CGTTGCGA
3813315 AAGTAAACTA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
19 42 0.78
20 12 0.22
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:3815181 original size:14 final size:14
Alignment explanation
Indices: 3815162--3815197 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3815152 ATTGTTTAAT
3815162 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3815176 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3815190 TGATTTGT
1 TGATTTGT
3815198 TTAATTGATG
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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3815323 original size:14 final size:14
Alignment explanation
Indices: 3815304--3815357 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
3815294 CGAAATGGCT
3815304 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3815318 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
3815337 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3815351 ATCGCAA
1 ATCGCAA
3815358 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:3815406 original size:20 final size:20
Alignment explanation
Indices: 3815381--3815438 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3815371 TCGCATTGCG
*
3815381 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
3815401 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
3815421 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
3815439 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3816522 original size:24 final size:24
Alignment explanation
Indices: 3816490--3816536 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3816480 AGTCAGTATT
* *
3816490 CGAAATTTGATCTTGGTTAATACC
1 CGAAATTTGATATTGGTCAATACC
*
3816514 CGAACTTTGATATTGGTCAATAC
1 CGAAATTTGATATTGGTCAATAC
3816537 ACGGATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACC
Found at i:3816546 original size:24 final size:24
Alignment explanation
Indices: 3816490--3816548 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
3816480 AGTCAGTATT
* * * *
3816490 CGAAATTTGATCTTGGTTAATACC
1 CGAACTTTGATATTGGTCAATACA
3816514 CGAACTTTGATATTGGTCAATACA
1 CGAACTTTGATATTGGTCAATACA
* *
3816538 CGGATTTTGAT
1 CGAACTTTGAT
3816549 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACA
Found at i:3816740 original size:12 final size:12
Alignment explanation
Indices: 3816723--3816747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3816713 ATATAATCCT
3816723 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3816735 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3816747 G
1 G
3816748 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3819061 original size:19 final size:18
Alignment explanation
Indices: 3819039--3819093 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
3819029 GGAAATTACT
3819039 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
3819058 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
3819072 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
3819091 ATC
1 ATC
3819094 ACAACGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 13 0.45
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:3819085 original size:33 final size:33
Alignment explanation
Indices: 3819039--3819164 Score: 164
Period size: 33 Copynumber: 3.8 Consensus size: 33
3819029 GGAAATTACT
3819039 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
3819072 ATCGCAATACGAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
3819104 TTTCGCAATGCAAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3819138 ATCGTAATGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
3819165 ACGGATTTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3819151 original size:66 final size:66
Alignment explanation
Indices: 3819040--3819164 Score: 205
Period size: 66 Copynumber: 1.9 Consensus size: 66
3819030 GAAATTACTA
*
3819040 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCACAACGCTAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCACAACGCTAAT
3819105 T
66 T
* * * *
3819106 TCGCAATGCAAAATGAAAATCGCAACGAGGGAATCGTAATGCGAAATGAAAATCGCAAC
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCACAAC
3819165 ACGGATTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCACAACGCTAAT
T
Found at i:3819198 original size:20 final size:20
Alignment explanation
Indices: 3819170--3819227 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3819160 GCAACACGGA
* *
3819170 TTTAATTTCGCGTTGTGATT
1 TTTATTTTCGCGTTGCGATT
3819190 TTTATTTTCGCGTTGCGATT
1 TTTATTTTCGCGTTGCGATT
* *
3819210 TTCA-TTTCGCATTGCGAT
1 TTTATTTTCGCGTTGCGAT
3819228 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTATTTTCGCGTTGCGATT
Found at i:3819353 original size:14 final size:15
Alignment explanation
Indices: 3819334--3819370 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
3819324 CATCAATTAA
3819334 ACAAATCAAC-TTTT
1 ACAAATCAACTTTTT
3819348 ACAAATC-ACTTTTT
1 ACAAATCAACTTTTT
3819362 ACAAATCAA
1 ACAAATCAA
3819371 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAACTTTTT
Found at i:3820793 original size:21 final size:21
Alignment explanation
Indices: 3820727--3820793 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3820717 GTGAATCGGG
*
3820727 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3820747 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3820769 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3820790 CTCT
1 CTCT
3820794 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3822894 original size:20 final size:19
Alignment explanation
Indices: 3822849--3822907 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
3822839 TCTTTTGGTT
3822849 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
3822868 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
3822889 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
3822908 TAGAATCGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3822917 original size:14 final size:14
Alignment explanation
Indices: 3822898--3822934 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3822888 GGAAATGACT
*
3822898 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
3822912 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
3822926 ATCGCAACG
1 ATCGCAACG
3822935 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3822962 original size:47 final size:48
Alignment explanation
Indices: 3822874--3822967 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 48
3822864 ACGAGATAAT
* *
3822874 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCATACAATCGCAACGA
*
3822922 GAGAATCGCAACGC-GAAATGACTATCGCGACCATACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCATACAATCGCAACG
3822968 CGAAATGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 29 0.67
48 14 0.33
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCATACAATCGCAACGA
Found at i:3823021 original size:19 final size:19
Alignment explanation
Indices: 3822985--3823029 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3822975 AAAATCGCAA
*
3822985 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
3823004 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
3823023 TGCGATT
1 TGCGATT
3823030 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3823606 original size:20 final size:20
Alignment explanation
Indices: 3823581--3823633 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3823571 GTGCTATGTA
3823581 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
3823601 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3823621 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3823634 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3823667 original size:20 final size:20
Alignment explanation
Indices: 3823642--3823695 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3823632 GATTTTGTAT
3823642 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3823662 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3823682 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3823696 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3823680 original size:61 final size:61
Alignment explanation
Indices: 3823582--3823698 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
3823572 TGCTATGTAA
* * * * *
3823582 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
3823643 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
3823699 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:3823714 original size:61 final size:61
Alignment explanation
Indices: 3823582--3823716 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
3823572 TGCTATGTAA
* * * * * ** *
3823582 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
3823643 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
3823705 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3823717 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:3823806 original size:21 final size:21
Alignment explanation
Indices: 3823766--3823806 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3823756 ACTGTATACC
**
3823766 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3823787 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3823807 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:3828015 original size:2 final size:2
Alignment explanation
Indices: 3828008--3828043 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3827998 CAAAAATACA
3828008 AT 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 AT
3828044 CTTTCATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3828484 original size:16 final size:15
Alignment explanation
Indices: 3828464--3828510 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3828454 TAAAAGATAG
*
3828464 TATAAAAACTTAATA
1 TATAAAAACTTAAAA
3828479 TCAT-AAAA-TTAAAA
1 T-ATAAAAACTTAAAA
*
3828493 TATAAAAACTAAAAA
1 TATAAAAACTTAAAA
3828508 TAT
1 TAT
3828511 TATTCGGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 13 0.48
16 2 0.07
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAAAACTTAAAA
Found at i:3830319 original size:31 final size:31
Alignment explanation
Indices: 3830281--3830358 Score: 156
Period size: 31 Copynumber: 2.5 Consensus size: 31
3830271 ATTTAATCTT
3830281 TATTACTTACACATTTTATCAATTTGGTCCC
1 TATTACTTACACATTTTATCAATTTGGTCCC
3830312 TATTACTTACACATTTTATCAATTTGGTCCC
1 TATTACTTACACATTTTATCAATTTGGTCCC
3830343 TATTACTTACACATTT
1 TATTACTTACACATTT
3830359 GGACGAGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (31 bp):
TATTACTTACACATTTTATCAATTTGGTCCC
Found at i:3833091 original size:17 final size:18
Alignment explanation
Indices: 3833059--3833092 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3833049 ATAAATTAAA
*
3833059 AAATTTAGATTTTTTTAG
1 AAATTTAGAGTTTTTTAG
3833077 AAATTTAG-GTTTTTTA
1 AAATTTAGAGTTTTTTA
3833093 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (18 bp):
AAATTTAGAGTTTTTTAG
Found at i:3835289 original size:4 final size:4
Alignment explanation
Indices: 3835282--3835402 Score: 134
Period size: 4 Copynumber: 30.2 Consensus size: 4
3835272 ACATACATAC
* * * * * *
3835282 ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATAT ACAT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * *
3835330 ACAT ATGT ATAT ATGT ATAT ACAT ATGT ATAT ATAT ATAC ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
3835378 ATAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT A
3835403 CAACATATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 99 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (4 bp):
ATAT
Found at i:3836139 original size:3 final size:3
Alignment explanation
Indices: 3836131--3836200 Score: 72
Period size: 3 Copynumber: 22.7 Consensus size: 3
3836121 CGAGACTATA
* *
3836131 TAT TAT TAT TAT TAT TAT TA- TAT TAC AAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3836177 ATAT ATAT ATAT ATAT TAT TAT TA
1 -TAT -TAT -TAT -TAT TAT TAT TA
3836201 CAAATAATAC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 41 0.68
4 15 0.25
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3836165 original size:23 final size:25
Alignment explanation
Indices: 3836134--3836200 Score: 93
Period size: 23 Copynumber: 2.7 Consensus size: 25
3836124 GACTATATAT
3836134 TATTATTATTATTATTATAT-TACA
1 TATTATTATTATTATTATATATACA
*
3836158 -ATTATTATTATTATTATATATATA
1 TATTATTATTATTATTATATATACA
3836182 TATATATATATTATTATTA
1 TAT-TAT-TATTATTATTA
3836201 CAAATAATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 19 0.50
24 3 0.08
25 2 0.05
26 3 0.08
27 11 0.29
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATTATTATTATTATATATACA
Found at i:3836264 original size:17 final size:17
Alignment explanation
Indices: 3836244--3836322 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
3836234 ATCAACCCGA
3836244 TTCAGGCCCAAACCCAG
1 TTCAGGCCCAAACCCAG
*
3836261 TTCAGGCCCAGACCC-G
1 TTCAGGCCCAAACCCAG
*
3836277 ATTCAGGCCCAAACCTAG
1 -TTCAGGCCCAAACCCAG
*
3836295 TTCAGGCCCAGACCCAG
1 TTCAGGCCCAAACCCAG
*
3836312 TTAAGGCCCAA
1 TTCAGGCCCAA
3836323 GAAGCCCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 1 0.02
17 51 0.96
18 1 0.02
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.14
Consensus pattern (17 bp):
TTCAGGCCCAAACCCAG
Found at i:3836281 original size:34 final size:34
Alignment explanation
Indices: 3836238--3836322 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
3836228 TACAAAATCA
3836238 ACCCGATTCAGGCCCAAACCCAGTTCAGGCCCAG
1 ACCCGATTCAGGCCCAAACCCAGTTCAGGCCCAG
*
3836272 ACCCGATTCAGGCCCAAACCTAGTTCAGGCCCAG
1 ACCCGATTCAGGCCCAAACCCAGTTCAGGCCCAG
*
3836306 ACCC-AGTTAAGGCCCAA
1 ACCCGA-TTCAGGCCCAA
3836323 GAAGCCCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 1 0.02
34 47 0.98
ACGTcount: A:0.28, C:0.39, G:0.20, T:0.13
Consensus pattern (34 bp):
ACCCGATTCAGGCCCAAACCCAGTTCAGGCCCAG
Found at i:3837511 original size:19 final size:19
Alignment explanation
Indices: 3837489--3837529 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3837479 ATAAAATAAT
3837489 ATAATGAATAGAAA-AAA-TA
1 ATAAT-AAT-GAAATAAAGTA
3837508 ATAATAATGAAATAAAGTA
1 ATAATAATGAAATAAAGTA
3837527 ATA
1 ATA
3837530 CCATTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (19 bp):
ATAATAATGAAATAAAGTA
Found at i:3838988 original size:46 final size:48
Alignment explanation
Indices: 3838898--3838994 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 48
3838888 CTTAATTTAC
* *
3838898 TTTATTTTCCTAATAAATGCATGCGAACTAGAAATCATGCGGTTA-GA
1 TTTATTTTCCAAATAAATGCATGCGAACTAGAAATCATGAGGTTAGGA
*
3838945 TTTATTTCTCCAAATAAA-GCATG-GAACTAGATTAT-ATGAGGTTAGGA
1 TTTATTT-TCCAAATAAATGCATGCGAACTAGA-AATCATGAGGTTAGGA
3838992 TTT
1 TTT
3838995 TTATGATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
46 16 0.36
47 19 0.43
48 9 0.20
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (48 bp):
TTTATTTTCCAAATAAATGCATGCGAACTAGAAATCATGAGGTTAGGA
Found at i:3841835 original size:49 final size:55
Alignment explanation
Indices: 3841758--3841883 Score: 77
Period size: 56 Copynumber: 2.3 Consensus size: 55
3841748 CTCATCCATC
* * *
3841758 AGAAAAAAAGAGAAAAAAGAGAGCAAAAAATAAAAGAAA-AAGAAGAAA-AAGAAAAAAGA
1 AGAAAAAAA-AG-AAAAA-A-AG-AAAAAAGAAATGAAAGAAGAAAAAAGAAG-AAAAAGA
* *
3841817 AGAAAAAGAAGAAAAAAAAGAAAAAAAGAAA--AAAGAA-AATGAAAGAAG-AAAA-A
1 AGAAAAAAAAG-AAAAAAAG-AAAAAAGAAATGAAAGAAGAA-AAAAGAAGAAAAAGA
3841870 AGAAAAAAAAGAAA
1 AGAAAAAAAAGAAA
3841884 TTGAATTAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
52 3 0.05
53 11 0.18
54 9 0.15
55 6 0.10
56 14 0.23
57 1 0.02
58 8 0.13
59 8 0.13
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (55 bp):
AGAAAAAAAAGAAAAAAAGAAAAAAGAAATGAAAGAAGAAAAAAGAAGAAAAAGA
Found at i:3841836 original size:43 final size:43
Alignment explanation
Indices: 3841784--3841883 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 43
3841774 AAGAGAGCAA
3841784 AAAATAAAAGAAAAAGAAG-AAAAAG-AAA-AAAGAAGAAAAAGAAG
1 AAAA-AAAAGAAAAA-AAGAAAAAAGAAAAGAAAGAAG-AAAA-AAG
3841828 AAAAAAAAGAAAAAAAGAAAAAAGAAAATGAAAGAAGAAAAAAG
1 AAAAAAAAGAAAAAAAGAAAAAAGAAAA-GAAAGAAGAAAAAAG
3841872 AAAAAAAAGAAA
1 AAAAAAAAGAAA
3841884 TTGAATTAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
42 3 0.06
43 16 0.31
44 22 0.42
45 4 0.08
46 7 0.13
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (43 bp):
AAAAAAAAGAAAAAAAGAAAAAAGAAAAGAAAGAAGAAAAAAG
Found at i:3841882 original size:9 final size:9
Alignment explanation
Indices: 3841758--3841883 Score: 116
Period size: 9 Copynumber: 13.6 Consensus size: 9
3841748 CTCATCCATC
3841758 AGAAAAAAA
1 AGAAAAAAA
3841767 GAGAAAAAAGA
1 -AGAAAAAA-A
3841778 GAGCAAAAAATA
1 -AG-AAAAAA-A
*
3841790 A-AAGAAAA
1 AGAAAAAAA
*
3841798 AGAAGAAAA
1 AGAAAAAAA
3841807 AGAAAAAAGA
1 AGAAAAAA-A
*
3841817 AGAAAAAGA
1 AGAAAAAAA
3841826 AGAAAAAAA
1 AGAAAAAAA
3841835 AG-AAAAAA
1 AGAAAAAAA
3841843 AG--AAAAA
1 AGAAAAAAA
*
3841850 AGAAAATGAA
1 AGAAAA-AAA
3841860 AGAAGAAAAA
1 AGAA-AAAAA
3841870 AGAAAAAAA
1 AGAAAAAAA
3841879 AGAAA
1 AGAAA
3841884 TTGAATTAAG
Statistics
Matches: 101, Mismatches: 7, Indels: 17
0.81 0.06 0.14
Matches are distributed among these distances:
7 7 0.07
8 10 0.10
9 42 0.42
10 28 0.28
11 7 0.07
12 7 0.07
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:3843422 original size:52 final size:52
Alignment explanation
Indices: 3843363--3843508 Score: 222
Period size: 51 Copynumber: 2.8 Consensus size: 52
3843353 AATGTCCATA
*
3843363 TTATCCATCTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAG
1 TTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAG
* * *
3843415 TTATCCATGT-GGGTATCTTAAAGGCTCACATCAGCATGAAAAAGACATAAG
1 TTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAG
* * *
3843466 TAATCCATGTGAGGCATCTTGAAGGCTCACACCAGCATAAAAA
1 TTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAA
3843509 GGTTGAAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 47 0.57
52 36 0.43
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (52 bp):
TTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAG
Found at i:3844817 original size:20 final size:20
Alignment explanation
Indices: 3844789--3844843 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3844779 TCTAGAAAAT
*
3844789 TAAAACCTCCGGGTAATTTG
1 TAAAACCTCCGGGTAATCTG
* *
3844809 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCCGGGTAATCTG
*
3844829 TAAAACCTCAGGGTA
1 TAAAACCTCCGGGTA
3844844 GGATGTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCCGGGTAATCTG
Found at i:3844843 original size:119 final size:119
Alignment explanation
Indices: 3844684--3845536 Score: 1391
Period size: 119 Copynumber: 7.2 Consensus size: 119
3844674 ATTTCCCACA
* * *
3844684 AATTTGTAAAACCTCCGGGTCATCTATAAAACCTTAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
3844749 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
3844803 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* *
3844868 AAGCCATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
** * *
3844922 AATTTGTAAATCCTTAGGGTCATCTGTAAAACCTTAGGGTATGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* * *
3844987 AAACGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGAGA
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
*
3845041 AATTTATAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
3845106 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
* * *
3845160 AATTTGTAAATCATCCGGGTCATCTGTAAAACCTTAGGGTAGGATGTTTTTGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* *
3845225 AAGTGATTACTAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
* * * * *
3845279 CATCTGTAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* *
3845344 AAGCGATTACCAAAGTTACTCATTTAATGTTCTAGAAAATTAAAACCTCAGGGT
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
*
3845398 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTCTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* * * * *
3845463 AAGTGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCATCCGGGT
66 AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
* * * *
3845517 CATCTGTAAAACCTCAGGGT
1 AATTTGTAAATCCTCCGGGT
3845537 ATGATGTTTT
Statistics
Matches: 677, Mismatches: 57, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 677 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (119 bp):
AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
AAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
Found at i:3844936 original size:20 final size:20
Alignment explanation
Indices: 3844908--3844962 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3844898 TCTAGAAAAT
* *
3844908 TAAAACCTTCGGGTAATTTG
1 TAAAACCTTAGGGTAATCTG
* *
3844928 TAAATCCTTAGGGTCATCTG
1 TAAAACCTTAGGGTAATCTG
3844948 TAAAACCTTAGGGTA
1 TAAAACCTTAGGGTA
3844963 TGATGTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
TAAAACCTTAGGGTAATCTG
Found at i:3845290 original size:20 final size:20
Alignment explanation
Indices: 3845265--3845318 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3845255 TCTAGAAAAT
3845265 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTG
*
3845285 TAAAACCTTCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTG
*
3845305 TAAAACCTCAGGGT
1 TAAAACCTCCGGGT
3845319 ATGATGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTG
Found at i:3845412 original size:20 final size:20
Alignment explanation
Indices: 3845384--3845438 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3845374 TCTAGAAAAT
*
3845384 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
3845404 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
3845424 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
3845439 GGATGTCTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:3845688 original size:3 final size:3
Alignment explanation
Indices: 3845680--3845743 Score: 76
Period size: 3 Copynumber: 20.7 Consensus size: 3
3845670 CGAGACTATA
* *
3845680 TAT TAT TAT TAT TAT TAT TA- TAT TAC AAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3845727 ATAT ATATT TAT TAT TA
1 -TAT -TA-T TAT TAT TA
3845744 CAAATAATAC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 43 0.80
4 8 0.15
5 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3847905 original size:12 final size:11
Alignment explanation
Indices: 3847887--3847929 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
3847877 CACACACTTT
3847887 CACCAACCGACC
1 CACCAACC-ACC
*
3847899 TACCAACCAACC
1 CACCAACC-ACC
3847911 CACCAACCACC
1 CACCAACCACC
3847922 CACCAACC
1 CACCAACC
3847930 CCATAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.37, C:0.58, G:0.02, T:0.02
Consensus pattern (11 bp):
CACCAACCACC
Found at i:3852816 original size:2 final size:2
Alignment explanation
Indices: 3852809--3852838 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3852799 TTATTATTAT
3852809 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3852839 AATGATCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3855433 original size:21 final size:21
Alignment explanation
Indices: 3855408--3855449 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3855398 AGATATTCTT
3855408 TATTACTAT-TTTATTTTTTTA
1 TATTAC-ATCTTTATTTTTTTA
3855429 TATTACATCTTTATTTTTTTA
1 TATTACATCTTTATTTTTTTA
3855450 ATAAGTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTACATCTTTATTTTTTTA
Found at i:3855471 original size:23 final size:22
Alignment explanation
Indices: 3855445--3855493 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3855435 ATCTTTATTT
*
3855445 TTTTAATAAGTCTGTATGACACG
1 TTTTAATAAGTCT-TATGACACA
* * *
3855468 TTTTCATATGTCTTTTGACACA
1 TTTTAATAAGTCTTATGACACA
3855490 TTTT
1 TTTT
3855494 TCGATCGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.49
Consensus pattern (22 bp):
TTTTAATAAGTCTTATGACACA
Found at i:3858631 original size:12 final size:12
Alignment explanation
Indices: 3858614--3858639 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3858604 AGTTTCAAGC
3858614 TCTTGTTGAGGT
1 TCTTGTTGAGGT
3858626 TCTTGTTGAGGT
1 TCTTGTTGAGGT
3858638 TC
1 TC
3858640 ACCTAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (12 bp):
TCTTGTTGAGGT
Found at i:3866193 original size:19 final size:20
Alignment explanation
Indices: 3866169--3866208 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3866159 TGAACAGTGG
3866169 GGGGAATCGGTACCC-CTGA
1 GGGGAATCGGTACCCTCTGA
*
3866188 GGGGAATCGGTTCCCTCTGA
1 GGGGAATCGGTACCCTCTGA
3866208 G
1 G
3866209 CAATCTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.17, C:0.25, G:0.38, T:0.20
Consensus pattern (20 bp):
GGGGAATCGGTACCCTCTGA
Found at i:3868589 original size:20 final size:21
Alignment explanation
Indices: 3868537--3868597 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
3868527 TTCCCCTGTG
3868537 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
3868560 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
3868580 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
3868598 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:3872447 original size:22 final size:21
Alignment explanation
Indices: 3872405--3872444 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3872395 GAGTTTATTT
*
3872405 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3872426 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3872445 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3881994 original size:129 final size:129
Alignment explanation
Indices: 3881741--3882098 Score: 448
Period size: 129 Copynumber: 2.7 Consensus size: 129
3881731 ATTATCTTCT
* ** * * * * * * *
3881741 ATCGAGAAGAAACAACCTCTCATGACTTAAAGCAGTTATTTCTTACTCCAATCAAAATAAAGA-A
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCATTTATTACTCCAATCGAAATGAAGAGA
* * * ** * * * *
3881805 ATATTGCTATTTCCTTCTAAAATTTGATATTAATTCGAGAGAAAACGATAATATCTAATTACTTC
66 TTA-T--TATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATAACCAATTACTTC
3881870 CA
128 CA
*
3881872 ATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCATTTATTACTCCAATTGAAATGAAGAGA
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCATTTATTACTCCAATCGAAATGAAGAGA
*
3881937 TTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATAACCAATTATTTCCA
66 TTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATAACCAATTACTTCCA
*
3882001 ATCGAGAATAAATGACCTCTCATACCTTAAAACAATCATTTATTACTCCAATCGAAATGAAGAGG
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCATTTATTACTCCAATCGAAATGAAGA-G
* *
3882066 TATTACTATTTCATCCTAAAATTCAATATTAAT
65 -ATTATTATTTCATCCTAAAATTAAATATTAAT
3882099 TCGAATGTTA
Statistics
Matches: 199, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
129 112 0.56
130 1 0.01
131 83 0.42
132 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (129 bp):
ATCGAGAATAAATGACCTCTCATGCCTTAAAACAATCATTTATTACTCCAATCGAAATGAAGAGA
TTATTATTTCATCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATAACCAATTACTTCCA
Found at i:3883136 original size:109 final size:109
Alignment explanation
Indices: 3882942--3883176 Score: 294
Period size: 109 Copynumber: 2.2 Consensus size: 109
3882932 TAACTACACA
* * **
3882942 TGACCAAAATGCAAAAACACGCTTAAATAAGGGAAACAAAACAAAAAATATTCCAAAAAATACAT
1 TGACCAACATGCAAAAACACACTTAAATAAGGGAAACAAAACAAAAAATACCCCAAAAAATACAT
3883007 AAAATGCATGAAAACAGGTAAATAACAACTTTGA-TCCCTACAGG
66 AAAATGCATGAAAACAGGTAAATAACAA-TTTGAGTCCCTACAGG
* ** * * * *
3883051 TGACCAACATGCAAAAACACAC-TAAACTATGGGGGACTAAACAGAAAATACCCCAAAATATATA
1 TGACCAACATGCAAAAACACACTTAAA-TAAGGGAAACAAAACAAAAAATACCCCAAAAAATACA
* * ** *
3883115 TAACATGCATTAAAATGGGTAAATAACAATTTTAGTCCCTACAGG
65 TAAAATGCATGAAAACAGGTAAATAACAATTTGAGTCCCTACAGG
3883160 TGACCAACATGCAAAAA
1 TGACCAACATGCAAAAA
3883177 TGTGACTAAC
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
108 8 0.07
109 100 0.93
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (109 bp):
TGACCAACATGCAAAAACACACTTAAATAAGGGAAACAAAACAAAAAATACCCCAAAAAATACAT
AAAATGCATGAAAACAGGTAAATAACAATTTGAGTCCCTACAGG
Found at i:3884265 original size:44 final size:44
Alignment explanation
Indices: 3884217--3885080 Score: 1204
Period size: 44 Copynumber: 20.1 Consensus size: 44
3884207 GCAAAAACGA
* * * *
3884217 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGTCT-GGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGGAAACTG
**
3884261 TAAGGCTTACCCTTGCACACAGCAAAGAAACCT--GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
* * *
3884303 TAAGGCTTACCCTTGTACACAGCAAAAGGAACCTGGGGAAAAACTG
1 TAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGG-GAAACTG
* * * *
3884349 TAAGGCTTACCCTTGCACATAGTAAAGGGACCTAGGGGAAACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884393 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
*
3884437 TAAGGCTTACCCTTG--CACA-C--A-GGACCTAGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
* *
3884474 TAAGGCTTACCCTTGTACACAGCAAAGGGACCTAGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
* * * * *
3884517 TAAGGCTTACCCTTGCACACAGTAAATGAACCAGGGGCAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884561 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884605 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884649 TAAGGCTTACCCTTG--CACA-C--A-GGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
* * *
3884686 TAAGGCTTACCCTTGCACATAGCAAAGGGACCTAGAGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
* *
3884729 TAAGGCTTACCCTTGCACACAGTAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884773 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
* *
3884817 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAG-AATTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884860 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
*
3884903 TAAGGCTTACCCTTGCACACAGTAAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3884947 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
*
3884991 TAAGGCTTACCCTTGCACACAACAAAGGGACCT-GGGG-AACTGGG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACT--G
*
3885035 TTAAGGCTTACCCTTGCACACAACAAA-GGACCTGGGGG-AACTG
1 -TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
3885078 TAA
1 TAA
3885081 CGGTAATTAA
Statistics
Matches: 748, Mismatches: 48, Indels: 50
0.88 0.06 0.06
Matches are distributed among these distances:
37 40 0.05
38 21 0.03
39 9 0.01
40 2 0.00
41 2 0.00
42 48 0.06
43 211 0.28
44 341 0.46
45 48 0.06
46 26 0.03
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (44 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTG
Found at i:3884567 original size:168 final size:172
Alignment explanation
Indices: 3884217--3885080 Score: 1165
Period size: 168 Copynumber: 5.0 Consensus size: 172
3884207 GCAAAAACGA
* * * *
3884217 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGTCT-GGGGAAACTGTAAGGCTTACCCTTGCACA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGGAAACTGTAAGGCTTACCCTTG-ACA
** * *
3884280 CAGCAAAGAAACCT--GGGAAACTGTAAGGCTTACCCTTGTACACAGCAAAAGGAACCTGGGGAA
63 CAGC-AAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGG--
* * *
3884343 AAACTGTAAGGCTTACCCTTGCACATAGTAAAGGGACCTAGGGGAAACAG
124 -AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAAACTG
3884393 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTG-CACA-
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGACACAG
* *
3884456 C-A-GGACCTAGGGG-AACTGTAAGGCTTACCCTTGTACACAGCAAAGGGACCTAGGGGAACTGT
66 CAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGGGAACTGT
* * *
3884518 AAGGCTTACCCTTGCACACAGTAAATGAACC-AGGGGCAAACTG
130 AAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGG-AAACTG
3884561 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTG-ACACA
3884626 GCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTG--CACA-C--A-GGACCTGGGGGAACT
65 GC-AAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGGGAACT
* *
3884685 GTAAGGCTTACCCTTGCACATAGCAAAGGGACCTAGAGG-AACTG
128 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAAACTG
* *
3884729 TAAGGCTTACCCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTG-ACACA
*
3884794 GCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAGAATT
65 GC-AAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGG-GAACT
*
3884859 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGGGGAACTG
128 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAAACTG
*
3884903 TAAGGCTTACCCTTGCACACAGTAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTG-ACACA
*
3884968 GCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAACTG
65 GC-AAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAACT-
* *
3885033 GGTTAAGGCTTACCCTTGCACACAACAAA-GGACCT-GGGGGAACTG
128 -G-TAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAAACTG
3885078 TAA
1 TAA
3885081 CGGTAATTAA
Statistics
Matches: 636, Mismatches: 27, Indels: 51
0.89 0.04 0.07
Matches are distributed among these distances:
167 5 0.01
168 204 0.32
169 43 0.07
170 26 0.04
171 35 0.06
172 4 0.01
173 17 0.03
174 184 0.29
175 61 0.10
176 57 0.09
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (172 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGACACAG
CAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAACTGTA
AGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAAACTG
Found at i:3884590 original size:212 final size:211
Alignment explanation
Indices: 3884249--3885080 Score: 1276
Period size: 212 Copynumber: 3.9 Consensus size: 211
3884239 GCAAAAGAGT
* ** *
3884249 CTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGAAACCT-GGGAAACTGTAAGGCTTAC
1 CTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAACTGTAAGGCTTAC
* * * * *
3884313 CCTTGTACACAGCAAAAGGAACCTGGGGAAAAACTGTAAGGCTTACCCTTGCACATAGTAAAGGG
66 CCTTGCACACAG-TAAAGGAACCTGGGG-GAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGG
* *
3884378 ACCTAGGGGAAACAGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGC
129 ACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG-AACTGTAAGGC
3884443 TTACCCTTGCACACAGGAC
193 TTACCCTTGCACACAGGAC
* *
3884462 CTAGGGGAACTGTAAGGCTTACCCTTGTACACAGCAAAGGGACCTAGGGGAACTGTAAGGCTTAC
1 CTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAACTGTAAGGCTTAC
* * *
3884527 CCTTGCACACAGTAAATGAACCAGGGGCAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGAC
66 CCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGAC
3884592 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTT
131 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG-AACTGTAAGGCTT
3884657 ACCCTTGCACACAGGAC
195 ACCCTTGCACACAGGAC
* *
3884674 CTGGGGGAACTGTAAGGCTTACCCTTGCACATAGCAAAGGGACCTAGAGGAACTGTAAGGCTTAC
1 CTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAACTGTAAGGCTTAC
3884739 CCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGAC
66 CCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGAC
* *
3884804 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAGAATTGTAAGGCTTA
131 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTA
3884869 CCCTTGCACACAGCAAAGGGAC
196 CCCTTG--CACA-C--A-GGAC
* *
3884891 CTGGGGGAACTGTAAGGCTTACCCTTGCACACAGTAAAGGGACCTGGGGGAAACTGTAAGGCTTA
1 CTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGG-AACTGTAAGGCTTA
* * *
3884956 CCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
65 CCCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
*
3885021 CCT-GGGG-AACTGGGTTAAGGCTTACCCTTGCACACAACAAA-GGACCTGGGGGAACTGTAA
130 CCTGGGGGAAACT--G-TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
3885081 CGGTAATTAA
Statistics
Matches: 574, Mismatches: 34, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
211 19 0.03
212 288 0.50
213 56 0.10
214 30 0.05
216 5 0.01
217 54 0.09
218 97 0.17
219 25 0.04
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (211 bp):
CTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGGGGAACTGTAAGGCTTAC
CCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGAC
CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTA
CCCTTGCACACAGGAC
Found at i:3886596 original size:17 final size:18
Alignment explanation
Indices: 3886563--3886596 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3886553 TCCATTATGT
*
3886563 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
3886581 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
3886597 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:3889525 original size:30 final size:30
Alignment explanation
Indices: 3889491--3889548 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3889481 ATTTTTATAA
3889491 ATTGTTGTTAGTGTGTATAATTCATTCTAG
1 ATTGTTGTTAGTGTGTATAATTCATTCTAG
*
3889521 ATTGTTGTTAGTGTGTATAATTTATTCT
1 ATTGTTGTTAGTGTGTATAATTCATTCT
3889549 TGAAACTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.22, C:0.05, G:0.19, T:0.53
Consensus pattern (30 bp):
ATTGTTGTTAGTGTGTATAATTCATTCTAG
Found at i:3894116 original size:20 final size:20
Alignment explanation
Indices: 3894088--3894139 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3894078 TAGTTAAAAA
**
3894088 TCGCATTGCGATTTTTCATT
1 TCGCATTGCGATTTGCCATT
*
3894108 TCGCGTTGCGATTTGCCATT
1 TCGCATTGCGATTTGCCATT
3894128 TCGCATTGCGAT
1 TCGCATTGCGAT
3894140 AGTTGAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTGCCATT
Found at i:3894159 original size:6 final size:6
Alignment explanation
Indices: 3894148--3894174 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3894138 ATAGTTGAAA
3894148 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
3894175 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3894874 original size:20 final size:20
Alignment explanation
Indices: 3894846--3895061 Score: 113
Period size: 20 Copynumber: 10.6 Consensus size: 20
3894836 ATTTTCAACT
*
3894846 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
*
3894866 ATTGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
** ** *
3894886 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAA-A
*
3894907 ATCGCAAACGCGAAATGGAAAA
1 ATCGC-AACGCGAAATAG-AAA
* **
3894929 ATCGCAACG-AAAACTGTAGACT
1 ATCGCAACGCGAAA---TAGAAA
*
3894951 ATCGCAA--CGAATTTAGAAA
1 ATCGCAACGCGAA-ATAGAAA
* *
3894970 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-ATAGAAA
* **
3894989 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAA--ATAGAAA
*
3895011 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
3895031 ATCGCAACGCGAAAT-GAAAA
1 ATCGCAACGCGAAATAG-AAA
3895051 ATCGCAACGCG
1 ATCGCAACGCG
3895062 GTTTTCAACT
Statistics
Matches: 152, Mismatches: 30, Indels: 28
0.72 0.14 0.13
Matches are distributed among these distances:
19 30 0.20
20 67 0.44
21 14 0.09
22 37 0.24
23 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:3894973 original size:19 final size:19
Alignment explanation
Indices: 3894951--3894998 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3894941 ACTGTAGACT
3894951 ATCGCAACGAATTTAGAAA
1 ATCGCAACGAATTTAGAAA
*
3894970 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTAGAAA
3894989 ATCGCAACGA
1 ATCGCAACGA
3894999 CAACTGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTAGAAA
Found at i:3897965 original size:273 final size:266
Alignment explanation
Indices: 3897440--3897980 Score: 870
Period size: 273 Copynumber: 2.0 Consensus size: 266
3897430 GACGGAAAAG
3897440 ACGATAAAAAGAAAGTCCCTTTATATGTAACACCAAATTGCAAGGCAAGATGAAATAAACAACAA
1 ACGATAAAAAGAAAGTCCCTTTATATGTAACACCAAATTGCAAGGCAAGATGAAATAAACAACAA
3897505 TGTTGACACAGAGCATACCGAGACTGAATCGGCCGTACAAGCCTATCGACAGGAACTCCGAGCGC
66 TGTTGACACAGAGCATACCGAGACTGAATCGGCCGTACAAGCCTATCGACAGGAACTCCGAGCGC
* * * *
3897570 CTGGAAGACGGAATTGTCGCATCGATTTCAATTACACGGACACACAGATCGAAGGCTGGTTATAA
131 CTGGAAGACGGAATTGTCGCATCAATTTCAATTACACGGACACACAGATCAAAGACGGGTTATAA
*
3897635 GAGCGAACAGAGACGAAGATACTCACCACTGATGCATTGAAAATTCGAGCCCCATCAATGTGAAG
196 GAGCGAACAGAGACGAAGATACTCACCACAGATGCATTGAAAATTCGAGCCCCATCAATGTGAAG
3897700 CCTCAA
261 CCTCAA
3897706 ACGATAAAAAGAAAGTCCCTTTATATGTAATACACC-AATTGCAAGGCAAGATGAAATAAACAAC
1 ACGATAAAAAGAAAGTCCCTTTATATGT-A-ACACCAAATTGCAAGGCAAGATGAAATAAACAAC
3897770 AATGTTGACACAGAGCATACCGAGACTGAATCGGCCGGTTGTACAAGCCTATCGACAGGAACTCC
64 AATGTTGACACAGAGCATACCGAGACTGAATCGGCC----GTACAAGCCTATCGACAGGAACTCC
* * * *
3897835 GAGCGCCTGGCATATGGAATTGTTGCATCAATTTCAATTACACGGACACACACAGATCAAAGACG
125 GAGCGCCTGGAAGACGGAATTGTCGCATCAATTTCAATTACACGG--ACACACAGATCAAAGACG
** * *
3897900 GGTTATACA-AGCTTACAGAGACGTAGTTACTCACCACAGATGCATTGAAAATTCGAGCCCCATC
188 GGTTATA-AGAGCGAACAGAGACGAAGATACTCACCACAGATGCATTGAAAATTCGAGCCCCATC
3897964 AATGTGAAGCCTCAA
252 AATGTGAAGCCTCAA
3897979 AC
1 AC
3897981 CATGCTTCTT
Statistics
Matches: 253, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
266 28 0.11
267 65 0.26
268 5 0.02
271 65 0.26
273 89 0.35
274 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (266 bp):
ACGATAAAAAGAAAGTCCCTTTATATGTAACACCAAATTGCAAGGCAAGATGAAATAAACAACAA
TGTTGACACAGAGCATACCGAGACTGAATCGGCCGTACAAGCCTATCGACAGGAACTCCGAGCGC
CTGGAAGACGGAATTGTCGCATCAATTTCAATTACACGGACACACAGATCAAAGACGGGTTATAA
GAGCGAACAGAGACGAAGATACTCACCACAGATGCATTGAAAATTCGAGCCCCATCAATGTGAAG
CCTCAA
Found at i:3907151 original size:24 final size:24
Alignment explanation
Indices: 3907119--3907206 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
3907109 GATATCGGAA
*
3907119 ATCAAAACAGAATTCAGATAAGAT
1 ATCAGAACAGAATTCAGATAAGAT
* * *
3907143 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATAAGAT
* *
3907167 ATCAGAACATAATTCAGGTAATG-T
1 ATCAGAACAGAATTCAGATAA-GAT
3907191 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
3907207 AGTCGGAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 52 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATAAGAT
Found at i:3907183 original size:12 final size:12
Alignment explanation
Indices: 3907124--3907183 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
3907114 CGGAAATCAA
3907124 AACAGAATTCAG
1 AACAGAATTCAG
3907136 ATA-AG-ATATCAG
1 A-ACAGAAT-TCAG
*
3907148 AACAGAATCCAG
1 AACAGAATTCAG
* *
3907160 ATCAGAAATCAG
1 AACAGAATTCAG
*
3907172 AACATAATTCAG
1 AACAGAATTCAG
3907184 GTAATGTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
11 3 0.08
12 31 0.84
13 3 0.08
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:3907194 original size:48 final size:48
Alignment explanation
Indices: 3907116--3907220 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
3907106 GGAGATATCG
*
3907116 GAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCC-AGATCA
1 GAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCAAG-TCA
* * * *
3907164 GAAATCAGAACATAATTCAGGTAATG-TATCAGAACAGAATTCAAGTCG
1 GAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCAAGTCA
3907212 GAAATCAGA
1 GAAATCAGA
3907221 TAAAATATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 47 0.94
49 3 0.06
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (48 bp):
GAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCAAGTCA
Found at i:3907218 original size:24 final size:25
Alignment explanation
Indices: 3907116--3907220 Score: 85
Period size: 24 Copynumber: 4.4 Consensus size: 25
3907106 GGAGATATCG
* *
3907116 GAAATCAAAACAGAATTC-AGATAA
1 GAAATCAGAACAGAATTCAAGATCA
* *
3907140 GATATCAGAACAGAA-TCCAGATCA
1 GAAATCAGAACAGAATTCAAGATCA
* * *
3907164 GAAATCAGAACATAATTC-AGGTAA
1 GAAATCAGAACAGAATTCAAGATCA
* *
3907188 TG-TATCAGAACAGAATTCAAG-TCG
1 -GAAATCAGAACAGAATTCAAGATCA
3907212 GAAATCAGA
1 GAAATCAGA
3907221 TAAAATATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
23 3 0.05
24 56 0.88
25 5 0.08
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (25 bp):
GAAATCAGAACAGAATTCAAGATCA
Found at i:3908632 original size:24 final size:24
Alignment explanation
Indices: 3908605--3908670 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
3908595 GTAAACGGAG
3908605 ATATCAGAAATCAAAACAGAAT-T
1 ATATCAGAAATCAAAACAGAATCT
* * * *
3908628 CATATAAAAAATTAGAACAGAATCT
1 -ATATCAGAAATCAAAACAGAATCT
* *
3908653 AGATCAGAAATCATAACA
1 ATATCAGAAATCAAAACA
3908671 TAGTTAAGGT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATCT
Found at i:3910624 original size:24 final size:24
Alignment explanation
Indices: 3910592--3910645 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3910582 ATCTAAACCA
3910592 TATTCAGTTACCGAATTTTTACCG
1 TATTCAGTTACCGAATTTTTACCG
*
3910616 TATTCAGTTACTGAATTTTTACCG
1 TATTCAGTTACCGAATTTTTACCG
3910640 TATTCA
1 TATTCA
3910646 TATCAAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (24 bp):
TATTCAGTTACCGAATTTTTACCG
Found at i:3911937 original size:31 final size:29
Alignment explanation
Indices: 3911889--3911947 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
3911879 ATTTCAAAAT
3911889 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATAT-TT-ATTTATA
*
3911920 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAA-AAAATATTTATTTAT
3911948 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATGAAAAAAATATTTATTTATA
Found at i:3912042 original size:20 final size:19
Alignment explanation
Indices: 3912003--3912044 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3911993 TTTCTTCGAT
3912003 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
3912022 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
3912042 ATT
1 ATT
3912045 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:3912155 original size:120 final size:120
Alignment explanation
Indices: 3911916--3912148 Score: 294
Period size: 120 Copynumber: 2.0 Consensus size: 120
3911906 TATATTAATT
* * * *
3911916 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAAGTGCCT
* *
3911981 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * *
3912036 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAATTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAAGTGC
* * * *
3912100 TTTAAGACTGC-CCTTTCTT-AATATTGAAAAATAAAT-AATTATTAAAACA
64 CTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
3912149 GGATTAAAAT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 12 0.12
119 21 0.22
120 46 0.47
121 18 0.19
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAAGTGCCT
TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:3912238 original size:3 final size:3
Alignment explanation
Indices: 3912230--3912259 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3912220 TATATGGCTA
*
3912230 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3912260 TTAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3913654 original size:6 final size:6
Alignment explanation
Indices: 3913610--3913644 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3913600 TAAAACAAAA
3913610 ATAATT ATAATT ATAATT ATAATT ATAATT ATAAT
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAAT
3913645 AATATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATAATT
Found at i:3914149 original size:113 final size:113
Alignment explanation
Indices: 3913998--3914491 Score: 652
Period size: 113 Copynumber: 4.3 Consensus size: 113
3913988 ATAGAGTCAT
*
3913998 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * *
3914063 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAA
66 ATTATGAACTCGAC-CTGGAAATGCTGATCCATCAAGTGATGAATTCAA
* ** * * *
3914111 GTAAAAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTTCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
3914176 ATTATGAACTCTAACT-GACACTGCTGATCCACCGAGTGATGAATTCGA
66 ATTATGAACTCGACCTGGA-AATGCTGATCCATCAAGTGATGAATTCAA
3914224 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTTCTTCCTTCTTCAGATGAGT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAA------C-TTCTTCTTCCTTCTTCAGATGAGT
* * *
3914289 TCTTCTCATTATGATCTCGACCTGGAAATGCTGATCCATCGAGTGATGAATTCGA
59 TCTTCTCATTATGAACTCGACCTGGAAATGCTGATCCATCAAGTGATGAATTCAA
*
3914344 GCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
3914409 ATTATGAACTCGACCTGGAAATGCTGATCCATCGAA-TGATGAATTCAA
66 ATTATGAACTCGACCTGGAAATGCTGATCCATC-AAGTGATGAATTCAA
* * *
3914457 TCAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
3914492 CTTATGGAAA
Statistics
Matches: 335, Mismatches: 35, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
112 2 0.01
113 227 0.68
114 3 0.01
120 101 0.30
121 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGACCTGGAAATGCTGATCCATCAAGTGATGAATTCAA
Found at i:3914165 original size:24 final size:23
Alignment explanation
Indices: 3914128--3914174 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3914118 GTTGAACAAA
3914128 TTCTTCTCATTATGAAATTCTTCT
1 TTCTTCTCATTATG-AATTCTTCT
*
3914152 TTCTTCTTCA-TATGAGTTCTTCT
1 TTCTTC-TCATTATGAATTCTTCT
3914175 CATTATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 10 0.48
25 3 0.14
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.55
Consensus pattern (23 bp):
TTCTTCTCATTATGAATTCTTCT
Found at i:3914271 original size:233 final size:228
Alignment explanation
Indices: 3913998--3914494 Score: 678
Period size: 233 Copynumber: 2.2 Consensus size: 228
3913988 ATAGAGTCAT
*
3913998 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAA--CTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTCTTCTTCTTCCTTCTTCAGATGAGTTCTTC
** * * *
3914061 TCATTATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGTAAAAGGTTGAAC
66 TCATTATGAACTCGAC-CTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAAC
* * * *
3914125 AAATTCTTCTCATTATGAAATTCTTCTTTCTTCTTCATATGAGTTCTTCTCATTATGAACTCTAA
130 AAACTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
* * *
3914190 CT-GACACTGCTGATCCACCGAGTGATGAATTCGA
195 CTGGA-AATGCTGATCCACCGAATGATGAATTCAA
3914224 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTTCTTCCTTCTTCAGATGAGT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAA---C-TC-TTCTTCTTCCTTCTTCAGATGAGT
* * * *
3914289 TCTTCTCATTATGATCTCGACCTGGAAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTT
61 TCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTT
* * *
3914354 GAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
126 GAACAAACTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* *
3914419 CGACCTGGAAATGCTGATCCATCGAATGATGAATTCAA
191 CGAACTGGAAATGCTGATCCACCGAATGATGAATTCAA
* * *
3914457 TCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTCTT
3914495 ATGGAAATGT
Statistics
Matches: 237, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
226 32 0.14
228 2 0.01
229 2 0.01
230 1 0.00
232 1 0.00
233 196 0.83
234 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (228 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTCTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTCGACCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
AACTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC
TGGAAATGCTGATCCACCGAATGATGAATTCAA
Found at i:3915697 original size:19 final size:19
Alignment explanation
Indices: 3915673--3915763 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 19
3915663 AAAATAAAAG
3915673 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTTTCAAA
*
3915692 AATAAATTGAA-TCTC--A
1 AATAAATTGAATTTTCAAA
**
3915708 AATAAATTGAATTTAGAGAA
1 AATAAATTGAATTTTCA-AA
*
3915728 AATAAACTTAGAATTTATTAATA
1 AATAAA-TT-GAATTT-TCAA-A
*
3915751 AATAAATAGAATT
1 AATAAATTGAATT
3915764 GTATTCAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
16 12 0.21
17 1 0.02
18 3 0.05
19 11 0.19
20 7 0.12
21 7 0.12
22 8 0.14
23 8 0.14
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (19 bp):
AATAAATTGAATTTTCAAA
Found at i:3916097 original size:16 final size:16
Alignment explanation
Indices: 3916076--3916128 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
3916066 TTAACCCTCC
3916076 TTTTTTATTTTTTATT
1 TTTTTTATTTTTTATT
*
3916092 TTTTTTATTTTTCTCTT
1 TTTTTTATTTTT-TATT
3916109 TTTTTTATTTTTTATT
1 TTTTTTATTTTTTATT
3916125 TTTT
1 TTTT
3916129 CTCTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.09, C:0.04, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTATTTTTTATT
Found at i:3916119 original size:25 final size:25
Alignment explanation
Indices: 3916083--3916162 Score: 103
Period size: 25 Copynumber: 3.2 Consensus size: 25
3916073 TCCTTTTTTA
3916083 TTTTTTATTTTTTTTATTTTTCTCTT
1 TTTTTTA-TTTTTTTATTTTTCTCTT
3916109 TTTTTTA-TTTTTTATTTTTTCTCTT
1 TTTTTTATTTTTTTA-TTTTTCTCTT
* *
3916134 TCTTTT-TTTCTTT-TTTTTCTCTT
1 TTTTTTATTTTTTTATTTTTCTCTT
3916157 TTTTTT
1 TTTTTT
3916163 TCATTTCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
23 15 0.31
24 7 0.14
25 20 0.41
26 7 0.14
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTTATTTTTTTATTTTTCTCTT
Found at i:3916139 original size:12 final size:11
Alignment explanation
Indices: 3916099--3916162 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
3916089 ATTTTTTTTA
3916099 TTTTTCTCTTTT
1 TTTTTCTC-TTT
* *
3916111 TTTTATTTTTTAT
1 TTTT-TCTCTT-T
3916124 TTTTTCTCTTT
1 TTTTTCTCTTT
*
3916135 CTTTTTTTCTTT
1 -TTTTTCTCTTT
3916147 TTTTTCTCTTT
1 TTTTTCTCTTT
3916158 TTTTT
1 TTTTT
3916163 TCATTTCATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
11 16 0.37
12 20 0.47
13 7 0.16
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:3916169 original size:17 final size:15
Alignment explanation
Indices: 3916076--3916176 Score: 69
Period size: 17 Copynumber: 6.1 Consensus size: 15
3916066 TTAACCCTCC
*
3916076 TTTTTTATTTTTTATT
1 TTTTTTATTTCTT-TT
*
3916092 TTTTTTATTTTTCTCTT
1 TTTTTTA--TTTCTTTT
3916109 TTTTTTATTT-TTTAT
1 TTTTTTATTTCTTT-T
*
3916124 TTTTTCTCTTTCTTTTT
1 TTTTT-TATTTC-TTTT
*
3916141 TTCTTTTTTTTCTCTTT
1 TT-TTTTATTTCT-TTT
3916158 TTTTTTCATTTCATTTT
1 TTTTTT-ATTTC-TTTT
3916175 TT
1 TT
3916177 CTTCAAGCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
14 2 0.03
15 9 0.13
16 16 0.23
17 31 0.45
18 11 0.16
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTATTTCTTTT
Found at i:3916174 original size:25 final size:22
Alignment explanation
Indices: 3916076--3916178 Score: 100
Period size: 23 Copynumber: 4.4 Consensus size: 22
3916066 TTAACCCTCC
* *
3916076 TTTTTTATTTTTTATTTTTTTTA
1 TTTTTTCTCTTTT-TTTTTTTTA
*
3916099 TTTTTCTCTTTTTTTTATTTTTTA
1 TTTTT-TCTCTTTTTT-TTTTTTA
3916123 TTTTTTCTCTTTCTTTTTTTCTT-
1 TTTTTTCTCTTT-TTTTTTT-TTA
3916146 TTTTTTCTCTTTTTTTTTCATTTCA
1 TTTTTTCTCTTTTTTTTT--TTT-A
3916171 TTTTTTCT
1 TTTTTTCT
3916179 TCAAGCATAA
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
22 6 0.09
23 31 0.44
24 25 0.36
25 8 0.11
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTTCTCTTTTTTTTTTTTA
Found at i:3916176 original size:1 final size:1
Alignment explanation
Indices: 3916076--3916163 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
3916066 TTAACCCTCC
* * * * * * * * * *
3916076 TTTTTTATTTTTTATTTTTTTTATTTTTCTCTTTTTTTTATTTTTTATTTTTTCTCTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
3916141 TTCTTTTTTTTCTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
3916164 CATTTCATTT
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:3923525 original size:15 final size:15
Alignment explanation
Indices: 3923502--3923533 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3923492 TGCAATGAAT
3923502 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
3923517 AATGCATGTATGCAA
1 AATGAATGTATGCAA
3923532 AA
1 AA
3923534 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:3926839 original size:19 final size:20
Alignment explanation
Indices: 3926795--3926844 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
3926785 AAAAAAAATA
*
3926795 AATAATAAAATAAAATACTT
1 AATAAAAAAATAAAATACTT
**
3926815 -GCAAAAAAATAAAATA-TT
1 AATAAAAAAATAAAATACTT
*
3926833 AATAAAATAATA
1 AATAAAAAAATA
3926845 TATATAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (20 bp):
AATAAAAAAATAAAATACTT
Found at i:3926889 original size:28 final size:27
Alignment explanation
Indices: 3926825--3926891 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
3926815 GCAAAAAAAT
*
3926825 AAAATATTAATAA-AATAATATATATAA
1 AAAATATGAA-AATAATAATATATATAA
* *
3926852 ATACTATGAAAATAATAAGTATATATAA
1 AAAATATGAAAATAATAA-TATATATAA
*
3926880 AAAATTTGAAAA
1 AAAATATGAAAA
3926892 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.06
27 12 0.38
28 18 0.56
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAATATGAAAATAATAATATATATAA
Found at i:3927414 original size:31 final size:29
Alignment explanation
Indices: 3927365--3927423 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
3927355 ATTTCAAAAT
3927365 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATAT-TT-ATTTATA
*
3927396 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAA-AAAATATTTATTTAT
3927424 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATGAAAAAAATATTTATTTATA
Found at i:3927518 original size:20 final size:19
Alignment explanation
Indices: 3927479--3927520 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3927469 TTTCTTCGAT
3927479 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
3927498 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
3927518 ATT
1 ATT
3927521 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:3927631 original size:120 final size:120
Alignment explanation
Indices: 3927392--3927624 Score: 296
Period size: 120 Copynumber: 2.0 Consensus size: 120
3927382 TATATTAATT
* * * *
3927392 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCATAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
* *
3927457 TAAGATAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGATAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * *
3927512 TATATA-ATTTATAAAATAGTATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGC
* *
3927576 TTTAAGACT-GC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGA-TAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
3927625 GGATTAAAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
118 9 0.09
119 25 0.26
120 45 0.46
121 18 0.18
122 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
TAAGATAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:3929092 original size:12 final size:12
Alignment explanation
Indices: 3929076--3929105 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3929066 TAAAACAAAA
3929076 AATAATTATAAT
1 AATAATTATAAT
*
3929088 TATAATTATAAT
1 AATAATTATAAT
3929100 AATAAT
1 AATAAT
3929106 AATATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AATAATTATAAT
Found at i:3930912 original size:36 final size:30
Alignment explanation
Indices: 3930816--3930921 Score: 167
Period size: 30 Copynumber: 3.5 Consensus size: 30
3930806 TGATGGTGAC
*
3930816 GGCGGTGGAGCTGGTATAGCTACCACCGGT
1 GGCGGTGGAGCTGTTATAGCTACCACCGGT
3930846 GGCGGTGGAGCTGTTATAGCTACCACCGGT
1 GGCGGTGGAGCTGTTATAGCTACCACCGGT
* **
3930876 GGCGGTGGAGCTGTTATAGTTACCAGAGGT
1 GGCGGTGGAGCTGTTATAGCTACCACCGGT
*
3930906 GGCGGTGGATCTGTTA
1 GGCGGTGGAGCTGTTA
3930922 CCGTCACCTC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.17, C:0.19, G:0.40, T:0.25
Consensus pattern (30 bp):
GGCGGTGGAGCTGTTATAGCTACCACCGGT
Found at i:3939809 original size:51 final size:51
Alignment explanation
Indices: 3939710--3939810 Score: 114
Period size: 51 Copynumber: 2.0 Consensus size: 51
3939700 CCTTTTCATT
* * *
3939710 TGAAATCCCTAAATTCCCCGTGTTTCCCCTTTCTTCCTCATTAGCTTCCAG
1 TGAAATCCCTAAATTCACCATGTTTCCCCTTTCTTCCTCATTAACTTCCAG
* * * * *
3939761 TGAAATCCTTAGATTCACCATGTTTTCCTTTTC-TCCTTCCTTAACTTCCA
1 TGAAATCCCTAAATTCACCATGTTTCCCCTTTCTTCC-TCATTAACTTCCA
3939811 ATTTTGCTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
50 3 0.07
51 38 0.93
ACGTcount: A:0.19, C:0.33, G:0.08, T:0.41
Consensus pattern (51 bp):
TGAAATCCCTAAATTCACCATGTTTCCCCTTTCTTCCTCATTAACTTCCAG
Found at i:3940471 original size:17 final size:18
Alignment explanation
Indices: 3940432--3940472 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3940422 ACAATAAAGT
*
3940432 TTAAAAT-TATTTTAGAG
1 TTAAAATATATATTAGAG
3940449 TT-AAATATATATTAG-G
1 TTAAAATATATATTAGAG
3940465 TTAAAATA
1 TTAAAATA
3940473 CACAAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTAAAATATATATTAGAG
Found at i:3940611 original size:60 final size:59
Alignment explanation
Indices: 3940476--3940613 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
3940466 TAAAATACAC
* *
3940476 AAATGATCCCTCAATTATAAGATACTACTTTGTTGAGTCCATCGGCCATTAAAAGTTAAA
1 AAATGAT-CCTCAACTATAAGATACTACTTTGTTGAGTCCATCGACCATTAAAAGTTAAA
* * * * * *
3940536 AAATGATCTTCCAACTAT-AGATCATTACTTTGTTTAGTCCCTCGACTATTAAAAGTTATA
1 AAATGATCCT-CAACTATAAGAT-ACTACTTTGTTGAGTCCATCGACCATTAAAAGTTAAA
*
3940596 ATATGATCACTCAACTAT
1 AAATGATC-CTCAACTAT
3940614 TCATTATATT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
59 6 0.09
60 58 0.89
61 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (59 bp):
AAATGATCCTCAACTATAAGATACTACTTTGTTGAGTCCATCGACCATTAAAAGTTAAA
Found at i:3942373 original size:42 final size:42
Alignment explanation
Indices: 3942308--3942440 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
3942298 TATTCAAAGG
* * * *
3942308 GACTCGAGTTCTTAAC-AAGCCGAAACGAGCTACTTAATAATC
1 GACTCGAGTTCTTAACGTA-CCGAAACGAACTACTTGATACTC
*
3942350 GACTCGAGTTCTTAACGTACCGAAGA-GAACTACTTGATACCC
1 GACTCGAGTTCTTAACGTACCGAA-ACGAACTACTTGATACTC
* *
3942392 GACTCGAATTCTTAAAGTACC-AAAGCGAACTACTTGATACTC
1 GACTCGAGTTCTTAACGTACCGAAA-CGAACTACTTGATACTC
3942434 GACTCGA
1 GACTCGA
3942441 AAAGCTCATG
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
40 1 0.01
41 2 0.03
42 74 0.94
43 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (42 bp):
GACTCGAGTTCTTAACGTACCGAAACGAACTACTTGATACTC
Found at i:3944492 original size:24 final size:23
Alignment explanation
Indices: 3944433--3944521 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 23
3944423 AATTAAATAT
3944433 TAAATAAATAAATAACAAAA-C-AA
1 TAAATAAA-AAATAA-AAAATCAAA
*
3944456 TAGAATAATAAAATAAGAAATCAAA
1 TA-AATAA-AAAATAAAAAATCAAA
*
3944481 TCAAATAAAAAATAAAAAATAAAA
1 T-AAATAAAAAATAAAAAATCAAA
* *
3944505 AAAATAGAAAATAAAAA
1 TAAATAAAAAATAAAAA
3944522 GACGAAATTG
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 20 0.36
24 26 0.46
25 9 0.16
26 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.17
Consensus pattern (23 bp):
TAAATAAAAAATAAAAAATCAAA
Found at i:3944502 original size:39 final size:39
Alignment explanation
Indices: 3944420--3944507 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 39
3944410 ATGGTAGAAT
* ** *
3944420 AATAATTAAATATTAAATAAATAAATAACAAAACAATAG
1 AATAATAAAATAAGAAATAAATAAATAACAAAACAATAA
*
3944459 AATAATAAAATAAGAAATCAAATCAAATAA-AAAATAA-AA
1 AATAATAAAATAAGAAAT-AAAT-AAATAACAAAACAATAA
*
3944498 AATAAAAAAA
1 AATAATAAAA
3944508 ATAGAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 25 0.61
40 10 0.24
41 6 0.15
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (39 bp):
AATAATAAAATAAGAAATAAATAAATAACAAAACAATAA
Found at i:3944508 original size:16 final size:16
Alignment explanation
Indices: 3944487--3944521 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3944477 CAAATCAAAT
3944487 AAAAAATAAAAAATAA
1 AAAAAATAAAAAATAA
*
3944503 AAAAAATAGAAAATAA
1 AAAAAATAAAAAATAA
3944519 AAA
1 AAA
3944522 GACGAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAATAAAAAATAA
Found at i:3945834 original size:37 final size:37
Alignment explanation
Indices: 3945739--3946001 Score: 227
Period size: 39 Copynumber: 7.0 Consensus size: 37
3945729 TTTTAAACTA
***
3945739 TATATTATATATAAGTTTTCAAAAACAT-TTTTTTTAAC
1 TATATTATATATAAGTTTTC-AAAA-ATGTTTTCAAAAC
* *
3945777 TATATAATATATAAATGTTTTCAAAAACGTTTTCAAAAC
1 TATATTATATAT-AA-GTTTTCAAAAATGTTTTCAAAAC
* *
3945816 TATATTATATATAAGTTTTCAAAAACATTTTTTTTAAAAAC
1 TATATTATATATAAGTTTTC-AAAA-A--TGTTTTCAAAAC
* *
3945857 TATATAATATACAAATGTTTTCAAAAATGTTTTCAAAAC
1 TATATTATATA-TAA-GTTTTCAAAAATGTTTTCAAAAC
* * *
3945896 TATATAATATATAGGTTTTCAAAAATGCTTTCAAAAAC
1 TATATTATATATAAGTTTTCAAAAATGTTTTC-AAAAC
*
3945934 TATA-TAT-TATATA-TTTT-AAAAATATTTTCAAAAC
1 TATATTATATATA-AGTTTTCAAAAATGTTTTCAAAAC
*
3945968 TATA-TAGTATAT--GTTTTCAAAAATATTTTCAAAA
1 TATATTA-TATATAAGTTTTCAAAAATGTTTTCAAAA
3946002 AAACTATATA
Statistics
Matches: 190, Mismatches: 20, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
34 15 0.08
35 27 0.14
36 11 0.06
37 25 0.13
38 28 0.15
39 46 0.24
40 6 0.03
41 20 0.11
42 6 0.03
43 6 0.03
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATTATATATAAGTTTTCAAAAATGTTTTCAAAAC
Found at i:3945886 original size:12 final size:12
Alignment explanation
Indices: 3945869--3945894 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3945859 TATAATATAC
3945869 AAATGTTTTCAA
1 AAATGTTTTCAA
3945881 AAATGTTTTCAA
1 AAATGTTTTCAA
3945893 AA
1 AA
3945895 CTATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATGTTTTCAA
Found at i:3945889 original size:80 final size:79
Alignment explanation
Indices: 3945739--3945996 Score: 308
Period size: 80 Copynumber: 3.4 Consensus size: 79
3945729 TTTTAAACTA
3945739 TATATTATATATAAGTTTTCAAAAACATTTTTTTT---AACTATATAATATATAAATGTTTTCAA
1 TATATTATATATAAGTTTTCAAAAACATTTTTTTTAAAAACTATATAATATA-AAATGTTTTCAA
*
3945801 AAACGTTTTCAAAAC
65 AAATGTTTTCAAAAC
3945816 TATATTATATATAAGTTTTCAAAAACATTTTTTTTAAAAACTATATAATATACAAATGTTTTCAA
1 TATATTATATATAAGTTTTCAAAAACATTTTTTTTAAAAACTATATAATATA-AAATGTTTTCAA
3945881 AAATGTTTTCAAAAC
65 AAATGTTTTCAAAAC
* * ** * * *
3945896 TATATAATATATAGGTTTTC-AAAA-A-TGCTTTCAAAAACTATAT-AT-T-ATATATTTT-AAA
1 TATATTATATATAAGTTTTCAAAAACATTTTTTTTAAAAACTATATAATATAAAATGTTTTCAAA
*
3945954 AATATTTTCAAAAC
66 AATGTTTTCAAAAC
*
3945968 TATA-TAGTATAT--GTTTTCAAAAATATTTT
1 TATATTA-TATATAAGTTTTCAAAAACATTTT
3945997 CAAAAAAACT
Statistics
Matches: 161, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
70 6 0.04
71 5 0.03
72 26 0.16
73 8 0.05
75 1 0.01
76 2 0.01
77 50 0.31
78 1 0.01
79 4 0.02
80 58 0.36
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (79 bp):
TATATTATATATAAGTTTTCAAAAACATTTTTTTTAAAAACTATATAATATAAAATGTTTTCAAA
AATGTTTTCAAAAC
Found at i:3945962 original size:72 final size:71
Alignment explanation
Indices: 3945709--3946054 Score: 250
Period size: 72 Copynumber: 4.6 Consensus size: 71
3945699 AATAATATGA
* * * ***
3945709 TATATATATTTCAAAATGATTTT-TAAACTATATATTATATATAAGTTTTCAAAAACATTTTTTT
1 TATATAT-TTTAAAAAT-ATTTTCAAAACTATATA--ATATAT-AGTTTTCAAAAATATTTTCAA
*
3945773 TAACTATATAAT
61 AAACTATAT-AT
* ** * *
3945785 ATATAAATGTTTTCAAAAACGTTTTCAAAACTATATTATATATAAGTTTTCAAAAACATTTTTTT
1 -TAT--ATATTTT-AAAAATATTTTCAAAACTATATAATATAT-AGTTTTC-AAAA-A-TATTTT
*
3945850 TAAAAACTATATAAT
58 CAAAAACTATAT-AT
* * * **
3945865 ATACAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATAGGTTTTCAAAAATGCTTTCAA
1 -T--ATATATTTT-AAAAATATTTTCAAAACTATATAATATATA-GTTTTCAAAAATATTTTCAA
3945930 AAACTATATAT
61 AAACTATATAT
*
3945941 TATATATTTTAAAAATATTTTCAAAACTATATAGTATAT-GTTTTCAAAAATATTTTCAAAAAAA
1 TATATATTTTAAAAATATTTTCAAAACTATATAATATATAGTTTTCAAAAATATTTTC--AAAAA
3946005 CTATATAT
64 CTATATAT
*
3946013 TATATACTTTT-AAAACATTTT-AATAACTATATATATTATATA
1 TATATA-TTTTAAAAATATTTTCAA-AACTATATA-A-TATATA
3946055 TATGTTCTAA
Statistics
Matches: 227, Mismatches: 25, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
70 16 0.07
71 2 0.01
72 64 0.28
73 11 0.05
74 5 0.02
75 1 0.00
76 2 0.01
77 32 0.14
78 12 0.05
79 22 0.10
80 59 0.26
82 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (71 bp):
TATATATTTTAAAAATATTTTCAAAACTATATAATATATAGTTTTCAAAAATATTTTCAAAAACT
ATATAT
Found at i:3946170 original size:24 final size:24
Alignment explanation
Indices: 3946125--3946170 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3946115 ATTTGCAAAC
* *
3946125 TATATAACATATAGATATAATATA
1 TATATAACATATAAATAAAATATA
3946149 TATATATACATA-AAATAAAATA
1 TATATA-ACATATAAATAAAATA
3946171 AAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TATATAACATATAAATAAAATATA
Found at i:3947005 original size:165 final size:165
Alignment explanation
Indices: 3946704--3947460 Score: 1086
Period size: 165 Copynumber: 4.6 Consensus size: 165
3946694 ATTTTATTGA
* * * *
3946704 CAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* ** * * *
3946769 CTCGAAGTTCTTTTATTGGCAGATAACCTTTCTAGACTTGAGTTATGCTGCAAATGATGCGCCCT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCT
*
3946834 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* * * *
3946869 CAGATAGCCTTTCTCGACTTAAGCTATACTGCAAATGGTGTACCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * *
3946934 CTCAAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCC
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCT
3946999 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* * ** *
3947034 CAGATAGCCCTTCTCGATTTAAGCTATACTATAAATGATGTGCCTTGGAACTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * *
3947099 CTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCT
3947163 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* * * *
3947198 CAGATAACCCTTCTCGACTTAAGCTAGGCTGTAAATGATGTGCCTCGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
3947263 CTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCT
3947328 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* * *
3947363 CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * *
3947428 CTCAAAGGT-ATTGTGTTGGCAAATAGCCCTTCT
66 CTCGAAGGTCTTTG-GTTGGCAGATAACCCTTCT
3947461 TGTCTTGAGC
Statistics
Matches: 526, Mismatches: 64, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
164 149 0.28
165 377 0.72
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCT
CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:3947184 original size:329 final size:330
Alignment explanation
Indices: 3946704--3947436 Score: 1117
Period size: 329 Copynumber: 2.2 Consensus size: 330
3946694 ATTTTATTGA
* * * *
3946704 CAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * *
3946769 CTCGAAGTTCTTTTATTGGCAGATAACCTTTCTAGACTTGAGTTATGCTGCAAATGATGCGCCCT
66 CTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATACGCCCT
* * *
3946834 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATACT
131 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTAGACT
* * *
3946899 GCAAATGGTGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGTAGATAACCCT
196 GCAAATGATGTACCTCGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
3946964 TCTCGACTTAAGTTATGCTACAAATGATGTGCCCCCGAAGCTGAGTGTAATCGAACTCGGGGGTC
261 TCTCGACTTAAGTTATGCTACAAATGATGTGCCCCCGAAGCTGAGTGTAATCGAACTCGGGGGTC
3947029 TTTGG
326 TTTGG
* * ** *
3947034 CAGATAGCCCTTCTCGATTTAAGCTATACTATAAATGATGTGCCTTGGAACTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * *
3947099 CTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCT
66 CTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATACGCCCT
* *
3947163 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTAGGCT
131 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTAGACT
* * **
3947228 GTAAATGATGTGCCTCGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCT
196 GCAAATGATGTACCTCGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
** *
3947293 TCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
261 TCTCGACTTAAGTTATGCTACAAATGATGTGCCCCCGAAGCTGAGTGTAATCGAACTCGGGGGTC
3947358 TTTGG
326 TTTGG
* * *
3947363 CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
3947428 CTCAAAGGT
66 CTCGAAGGT
3947437 ATTGTGTTGG
Statistics
Matches: 360, Mismatches: 43, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
329 295 0.82
330 65 0.18
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (330 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATACGCCCT
CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTAGACT
GCAAATGATGTACCTCGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
TCTCGACTTAAGTTATGCTACAAATGATGTGCCCCCGAAGCTGAGTGTAATCGAACTCGGGGGTC
TTTGG
Found at i:3952530 original size:17 final size:17
Alignment explanation
Indices: 3952504--3952551 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
3952494 ACAATAGAAT
*
3952504 AATAAAATAAAAAATCA
1 AATAAAATAAAAAATAA
*
3952521 AATCAAATAAAAAATAA
1 AATAAAATAAAAAATAA
3952538 AATAAAATAAAAAA
1 AATAAAATAAAAAA
3952552 ATAGAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (17 bp):
AATAAAATAAAAAATAA
Found at i:3952535 original size:12 final size:12
Alignment explanation
Indices: 3952476--3952564 Score: 65
Period size: 12 Copynumber: 7.2 Consensus size: 12
3952466 ATTAAATATT
3952476 AAATAAATAAATA
1 AAATAAA-AAATA
* *
3952489 ACA-AAACAATA
1 AAATAAAAAATA
*
3952500 GAATAATAAAATA
1 AAATAA-AAAATA
* *
3952513 AAA-AATCAAATC
1 AAATAA-AAAATA
3952525 AAATAAAAAATA
1 AAATAAAAAATA
*
3952537 AAATAAAATAAAA
1 AAATAAAA-AATA
*
3952550 AAATAGAAAATA
1 AAATAAAAAATA
3952562 AAA
1 AAA
3952565 AGACGAAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
11 5 0.08
12 33 0.56
13 21 0.36
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:3952547 original size:42 final size:39
Alignment explanation
Indices: 3952462--3952563 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 39
3952452 ATGGTAGAAT
* ** * * *
3952462 AATAATTAAATATTAAATAAATAAATAACAAAACAATAG
1 AATAATAAAATAAAAAATAAATAAATAAAAAAAAAATAA
3952501 AATAATAAAATAAAAAATCAAATCAAATAAAAAATAAAATAA
1 AATAATAAAATAAAAAAT-AAAT-AAATAAAAAA-AAAATAA
* *
3952543 AATAAAAAAATAGAAAATAAA
1 AATAATAAAATAAAAAATAAA
3952564 AAGACGAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
39 15 0.29
40 4 0.08
41 12 0.23
42 21 0.40
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (39 bp):
AATAATAAAATAAAAAATAAATAAATAAAAAAAAAATAA
Found at i:3953875 original size:42 final size:41
Alignment explanation
Indices: 3953806--3953889 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 41
3953796 TTCAAAATGA
* *
3953806 TTTTTAAACTATATATTATATATATGTTTTCAAAAACGTTT
1 TTTTTAAACTATATAATATATAAATGTTTTCAAAAACGTTT
3953847 TTTTTAAAACTATATAATATATAAATGTTTTCAAAAACGTTT
1 TTTTT-AAACTATATAATATATAAATGTTTTCAAAAACGTTT
3953889 T
1 T
3953890 CAAAACTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 5 0.12
42 35 0.88
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (41 bp):
TTTTTAAACTATATAATATATAAATGTTTTCAAAAACGTTT
Found at i:3956728 original size:48 final size:51
Alignment explanation
Indices: 3956657--3956792 Score: 161
Period size: 48 Copynumber: 2.6 Consensus size: 51
3956647 ATTCTTTCAT
* *
3956657 GGAGTATAAGACTTGAACAATCTTCAGTAAACGTGTCTGCT-CC-C-TCAG
1 GGAGTATAAGACTCGAACAATCTTCAGTAAACATGTCTGCTCCCTCGTCAG
* * *
3956705 GGAGTATAAGACTCGAATAATCTTCAGTAAACATGTTTGGTCCCTATTCGTTCAG
1 GGAGTATAAGACTCGAACAATCTTCAGTAAACATGTCTGCTCCC---TCG-TCAG
*
3956760 GGAGTATAAGACTCGAACAATCTTCAATAAACA
1 GGAGTATAAGACTCGAACAATCTTCAGTAAACA
3956793 GATCCGCTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
48 36 0.49
49 2 0.03
53 1 0.01
55 35 0.47
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (51 bp):
GGAGTATAAGACTCGAACAATCTTCAGTAAACATGTCTGCTCCCTCGTCAG
Found at i:3956785 original size:55 final size:55
Alignment explanation
Indices: 3956748--3957253 Score: 716
Period size: 55 Copynumber: 9.3 Consensus size: 55
3956738 TGTTTGGTCC
* * * *
3956748 CTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCA-ATAAACAGATCCGCTCT
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
*
3956803 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
3956858 CTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
3956913 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
3956968 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
3957023 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
3957078 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ATAAACGGGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
* * *
3957133 CTATTCCTTCAGAGAGTATA-AGACTCG----ATCTTCA-ATAAACGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
* * ** *
3957184 CTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ATGAACTTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
3957235 CTATTCCTTCAGAGAGTAT
1 CTATTCCTTCAGAGAGTAT
3957254 GACTCAATCT
Statistics
Matches: 429, Mismatches: 15, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
51 85 0.20
54 2 0.00
55 340 0.79
56 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
Found at i:3956862 original size:110 final size:110
Alignment explanation
Indices: 3956640--3957253 Score: 711
Period size: 110 Copynumber: 5.7 Consensus size: 110
3956630 ATGACAGTCT
* * * * *
3956640 GCTCCCTATTCTTTCATG-GAGTATAAGACTTGAACAATCTTCAGTAAACGTGTCTGCT--C---
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTAT
* * * **
3956699 -CC-TCAGGGAGTATA-AGACTCGAATAATCTTCAGT-AAACATGTTT
65 TCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCA-TAAAACAGGTCC
* * * * * *
3956743 GGTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACAGATCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATT
3956808 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCC
* * *
3956853 GCTCTCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTC-ATAAAACGGGTCCGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT-AAACGGGTCCGCTCCCTAT
*
3956917 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
65 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCC
*
3956963 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-ATAAAACGGGTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAACGGGTCCGCTCCCTA
*
3957026 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
64 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCC
*
3957073 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTAT
*
3957137 TCCTTCAGAGAGTATA-AGACTCG----ATCTTCA-ATAAAC-GTGTCT
65 TCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACAG-GTCC
* * **
3957179 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAATGAACTTGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATT
3957240 CCTTCAGAGAGTAT
66 CCTTCAGAGAGTAT
3957254 GACTCAATCT
Statistics
Matches: 465, Mismatches: 29, Indels: 35
0.88 0.05 0.07
Matches are distributed among these distances:
102 43 0.09
103 48 0.10
105 3 0.01
106 40 0.09
107 1 0.00
109 7 0.02
110 320 0.69
111 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCC
Found at i:3958647 original size:7 final size:7
Alignment explanation
Indices: 3958635--3958668 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
3958625 TATTTCTCTT
3958635 TTTTTCA
1 TTTTTCA
3958642 TTTTTCA
1 TTTTTCA
3958649 TTTTTTCA
1 -TTTTTCA
3958657 TTTTTCA
1 TTTTTCA
3958664 TTTTT
1 TTTTT
3958669 TATTCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:3958651 original size:22 final size:20
Alignment explanation
Indices: 3958622--3958668 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
3958612 TGAACCCTCC
3958622 TTTTATTTCTCTT-TTTTTCAT
1 TTTTATTT-T-TTATTTTTCAT
3958643 TTTTCATTTTTTCATTTTTCAT
1 TTTT-ATTTTTT-ATTTTTCAT
3958665 TTTT
1 TTTT
3958669 TATTCCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.09
21 5 0.22
22 16 0.70
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTTATTTTTCAT
Found at i:3958652 original size:15 final size:15
Alignment explanation
Indices: 3958634--3958669 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3958624 TTATTTCTCT
3958634 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
3958649 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
3958664 TTTTTT
1 TTTTTT
3958670 ATTCCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:3958653 original size:8 final size:8
Alignment explanation
Indices: 3958634--3958742 Score: 66
Period size: 9 Copynumber: 12.9 Consensus size: 8
3958624 TTATTTCTCT
3958634 TTTTTTCA
1 TTTTTTCA
3958642 -TTTTTCA
1 TTTTTTCA
3958649 TTTTTTCA
1 TTTTTTCA
3958657 -TTTTTCA
1 TTTTTTCA
3958664 TTTTTT-A
1 TTTTTTCA
3958671 TTCCCTTTTCCA
1 TT---TTTT-CA
3958683 TTTTTT--
1 TTTTTTCA
*
3958689 TTCTTTTCG
1 TT-TTTTCA
3958698 TTTTTTCCA
1 TTTTTT-CA
*
3958707 TCATTTTTCTT
1 T--TTTTTC-A
3958718 TTTTTCTCA
1 TTTTT-TCA
3958727 TTTTTCTCA
1 TTTTT-TCA
3958736 TTTTTTC
1 TTTTTTC
3958743 TCTTTTATTT
Statistics
Matches: 83, Mismatches: 3, Indels: 30
0.72 0.03 0.26
Matches are distributed among these distances:
6 2 0.02
7 21 0.25
8 18 0.22
9 26 0.31
10 7 0.08
11 6 0.07
12 3 0.04
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.72
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3958711 original size:27 final size:25
Alignment explanation
Indices: 3958676--3958748 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 25
3958666 TTTTATTCCC
3958676 TTTTC-CATTTTTTTTCTTTTCGT-T
1 TTTTCTCATTTTTTTTCTTTTC-TAT
3958700 TTTTCCATCATTTTTCTTT-TTTTCTCAT
1 TTTT-C-TCATTTTT-TTTCTTTTCT-AT
*
3958728 TTTTCTCATTTTTTCTCTTTT
1 TTTTCTCATTTTTTTTCTTTT
3958749 ATTTCTTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
24 4 0.10
25 3 0.07
26 13 0.32
27 13 0.32
28 8 0.20
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (25 bp):
TTTTCTCATTTTTTTTCTTTTCTAT
Done.