Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 37
Found at i:5751560 original size:83 final size:83
Alignment explanation
Indices: 5751465--5751632 Score: 273
Period size: 83 Copynumber: 2.0 Consensus size: 83
5751455 CATTGCTGCA
* ***
5751465 TTCTATTAATTAATTAATGTTCAATCATTTTGCAAATTTAAGATAATATCGTTCGTCCTTGGTCT
1 TTCTATTAATTAATTAATGTTCAATCATTCTGCAAATTTAAGATAATATCGTTCGTCCTCCATCT
*
5751530 TTGAGCGATAATTGATTT
66 TTGAGCGATAAATGATTT
* *
5751548 TTCTATTAATTAATTAATGTTCAATCATTCTGTAAATTTAAGATAATATTGTTCGTCCTCCATCT
1 TTCTATTAATTAATTAATGTTCAATCATTCTGCAAATTTAAGATAATATCGTTCGTCCTCCATCT
5751613 TTGAGCGATAAATGATTT
66 TTGAGCGATAAATGATTT
5751631 TT
1 TT
5751633 TTTACTAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (83 bp):
TTCTATTAATTAATTAATGTTCAATCATTCTGCAAATTTAAGATAATATCGTTCGTCCTCCATCT
TTGAGCGATAAATGATTT
Found at i:5752082 original size:16 final size:18
Alignment explanation
Indices: 5752037--5752084 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
5752027 TGTTTCTGAC
5752037 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
5752055 GGAATTAAAATCTGT-AA
1 GGAATTAGAATCTGTGAA
*
5752072 -GAATTGGAATCTG
1 GGAATTAGAATCTG
5752085 AATCTGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 14 0.52
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:5752682 original size:31 final size:30
Alignment explanation
Indices: 5752644--5752713 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
5752634 AGTATCACAC
*
5752644 TTAAAAAACCCGACCCAAACCCGAAATCTTT
1 TTAAAAAAACCGACCCAAACCCGAAAT-TTT
* *
5752675 TTAAAAAAACCGACCCGATCCCGAAATTTT
1 TTAAAAAAACCGACCCAAACCCGAAATTTT
*
5752705 TAAAAAAAA
1 TTAAAAAAA
5752714 ATACGACCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.47, C:0.26, G:0.07, T:0.20
Consensus pattern (30 bp):
TTAAAAAAACCGACCCAAACCCGAAATTTT
Found at i:5752721 original size:32 final size:31
Alignment explanation
Indices: 5752654--5752725 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
5752644 TTAAAAAACC
* * *
5752654 CGACCCAAACCCGAAATCTTTTTAAAAAAAC
1 CGACCCGAACCCGAAATCTTTTAAAAAAAAA
*
5752685 CGACCCGATCCCGAAAT-TTTTAAAAAAAAATA
1 CGACCCGAACCCGAAATCTTTT-AAAAAAAA-A
5752717 CGACCCGAA
1 CGACCCGAA
5752726 TACCAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.12
31 22 0.65
32 8 0.24
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (31 bp):
CGACCCGAACCCGAAATCTTTTAAAAAAAAA
Found at i:5755419 original size:34 final size:33
Alignment explanation
Indices: 5755381--5755464 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
5755371 GTAATAAACA
*
5755381 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAA-CAAAATAAATTAA-AATAAA-TCCAACC
5755415 AAATTCAACAAAATAAATTAAAATAAATCCAACC
1 AAATT-AACAAAATAAATTAAAATAAATCCAACC
**
5755449 AAATTAATTAAATAAA
1 AAATTAACAAAATAAA
5755465 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 16 0.36
34 26 0.59
35 2 0.05
ACGTcount: A:0.62, C:0.15, G:0.01, T:0.21
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAAAATAAATCCAACC
Found at i:5755447 original size:24 final size:23
Alignment explanation
Indices: 5755415--5755464 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
5755405 AAAGTCCAAC
*
5755415 AAATTCAACAAAATAAATTAAAAT
1 AAATCCAACAAAATAAATT-AAAT
* *
5755439 AAATCCAACCAAATTAATTAAAT
1 AAATCCAACAAAATAAATTAAAT
5755462 AAA
1 AAA
5755465 GTAAGTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (23 bp):
AAATCCAACAAAATAAATTAAAT
Found at i:5757755 original size:46 final size:47
Alignment explanation
Indices: 5757668--5757780 Score: 156
Period size: 46 Copynumber: 2.4 Consensus size: 47
5757658 TTTACCTTTT
* * *
5757668 AATGTTTCAATTTTTAATTATTTTATATTTTATTTAATTTACCCTCC
1 AATGTTTTAATTTTTGATCATTTTATATTTTATTTAATTTACCCTCC
* * *
5757715 AATGTTTTAA-TTTTGATCATTTTATATTTTATTTATTTTACTCTCT
1 AATGTTTTAATTTTTGATCATTTTATATTTTATTTAATTTACCCTCC
*
5757761 AACGTTTTAATTTTTGATCA
1 AATGTTTTAATTTTTGATCA
5757781 AAATATATCA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 40 0.69
47 18 0.31
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (47 bp):
AATGTTTTAATTTTTGATCATTTTATATTTTATTTAATTTACCCTCC
Found at i:5760224 original size:2 final size:2
Alignment explanation
Indices: 5760217--5760274 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
5760207 ATTTATTGTT
*
5760217 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5760259 -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
5760275 GTGTTTTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5762231 original size:12 final size:13
Alignment explanation
Indices: 5762197--5762238 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
5762187 CATTATCTAA
*
5762197 TTATTATTATTATTT
1 TTATT-TTATT-TAT
5762212 TTATTTTATTTAT
1 TTATTTTATTTAT
5762225 TTA-TTTATTTAT
1 TTATTTTATTTAT
5762237 TT
1 TT
5762239 TTGCATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 11 0.42
13 5 0.19
14 5 0.19
15 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:5763758 original size:45 final size:46
Alignment explanation
Indices: 5763694--5763789 Score: 176
Period size: 45 Copynumber: 2.1 Consensus size: 46
5763684 TTTATTTTCG
5763694 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
5763739 TTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
5763785 TTTTT
1 TTTTT
5763790 GTAAATAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 40 0.82
46 9 0.18
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (46 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:5773531 original size:19 final size:20
Alignment explanation
Indices: 5773496--5773538 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
5773486 ATAAGAAGAA
5773496 AAAAATGAATGAGAAAAAAG
1 AAAAATGAATGAGAAAAAAG
5773516 AAAAATG-ATG-GAAAAAACG
1 AAAAATGAATGAGAAAAAA-G
5773535 AAAA
1 AAAA
5773539 GAAAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAAATGAATGAGAAAAAAG
Found at i:5773554 original size:41 final size:41
Alignment explanation
Indices: 5773509--5773591 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
5773499 AATGAATGAG
* **
5773509 AAAAAAGAAAAATGATGGAAAAAACGAAA-AGAAAAAAAAGA
1 AAAAAAGAAAAAGGAAAG-AAAAACGAAAGAGAAAAAAAAGA
* * *
5773550 AAAAATGTAAAAGGAAAGAAAAATGAAAGAGAAAAAAAAGA
1 AAAAAAGAAAAAGGAAAGAAAAACGAAAGAGAAAAAAAAGA
5773591 A
1 A
5773592 GAGAAAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (41 bp):
AAAAAAGAAAAAGGAAAGAAAAACGAAAGAGAAAAAAAAGA
Found at i:5773561 original size:23 final size:25
Alignment explanation
Indices: 5773526--5773607 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 25
5773516 AAAAATGATG
5773526 GAAAAAACGAAAA-GAAA-AAAAA-
1 GAAAAAACGAAAAGGAAAGAAAAAT
*
5773548 GAAAAAATGTAAAAGGAAAGAAAAAT
1 GAAAAAACG-AAAAGGAAAGAAAAAT
* *
5773574 GAAAGAGAA-AAAAAAGAAGAGAAAAAT
1 GAAA-A-AACGAAAAGGAA-AGAAAAAT
5773601 GAAAAAA
1 GAAAAAA
5773608 AGAGAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 8 0.16
23 4 0.08
24 4 0.08
25 7 0.14
26 12 0.24
27 13 0.26
28 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (25 bp):
GAAAAAACGAAAAGGAAAGAAAAAT
Found at i:5773619 original size:20 final size:20
Alignment explanation
Indices: 5773582--5773619 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5773572 ATGAAAGAGA
*
5773582 AAAAAAAGAAGAGAAAAATG
1 AAAAAAAGAAGAAAAAAATG
5773602 AAAAAAAG-AGAAATAAAA
1 AAAAAAAGAAGAAA-AAAA
5773620 GAAGGGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAAAAAGAAGAAAAAAATG
Found at i:5775128 original size:55 final size:51
Alignment explanation
Indices: 5774934--5775255 Score: 437
Period size: 51 Copynumber: 6.2 Consensus size: 51
5774924 AAACTCGTTT
5774934 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
5774985 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
5775036 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
5775087 GTTGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT
1 GTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * ** *
5775142 ATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** * * *
5775193 GTTGAAGATTATTCGAGTCTTATACTCCCTGAACTAATAGGGAGCAGACACGTTT
1 GTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
5775248 GTTGAAGA
1 GTTGAAGA
5775256 ATGTTTGAGT
Statistics
Matches: 250, Mismatches: 13, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
51 156 0.62
52 1 0.00
54 2 0.01
55 91 0.36
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:5775135 original size:106 final size:105
Alignment explanation
Indices: 5774929--5775255 Score: 489
Period size: 106 Copynumber: 3.1 Consensus size: 105
5774919 GAATCAAACT
5774929 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA-
1 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
5774993 --TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
66 TTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
5775031 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
1 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
5775096 TGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
66 T-TTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * ** *
5775137 CGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGAT
1 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
* * * ** *
5775202 TATTCGAGTCTTATACTCCCTGAACTAATAGGGAGCAGACA
66 T-TTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
5775243 CGTTTGTTGAAGA
1 CGTTTGTTGAAGA
5775256 ATGTTTGAGT
Statistics
Matches: 203, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
102 62 0.31
106 141 0.69
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (105 bp):
CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
TTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:5775266 original size:55 final size:54
Alignment explanation
Indices: 5774929--5775303 Score: 416
Period size: 51 Copynumber: 7.1 Consensus size: 54
5774919 GAATCAAACT
5774929 CGTTTGTTGAAG-A--TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAATTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
5774980 AGTTCGTTGAAG-A--TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAATTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
5775031 AGTTCGTTGAAG-A--TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAATTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
5775082 AGTTCGTTGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAAT-TTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
5775137 CGTTTATTGAAG-A--TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTGTTGAAGAATTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * ** *
5775188 CGTTTGTTGAAG-ATTATTCGAGTCTTATACTCCCTGAACTAATAGGGAGCAGACA
1 CGTTTGTTGAAGAATT-TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * * *
5775243 CGTTTGTTGAAGAATGTTTGAGTCTTAAACTCCCTGAATGAATAAGAAGCAGACA
1 CGTTTGTTGAAGAAT-TTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
5775298 CGTTTG
1 CGTTTG
5775304 CCAAGGATTG
Statistics
Matches: 292, Mismatches: 22, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
51 159 0.54
54 1 0.00
55 127 0.43
56 4 0.01
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (54 bp):
CGTTTGTTGAAGAATTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:5775321 original size:55 final size:55
Alignment explanation
Indices: 5774929--5775367 Score: 349
Period size: 55 Copynumber: 8.3 Consensus size: 55
5774919 GAATCAAACT
* * * *
5774929 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
* * * * * *
5774980 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
* * * * * *
5775031 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
* * * * * * *
5775082 AGTTCGTTGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
* * * * *
5775137 CGTTTATTGAAGA----TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
*
5775188 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACT-AATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAA-TGAATAGGGAGCAGACA
* * * * *
5775243 CGTTTGTTGAAGAATGTTTGAGTCTTAAACTCCCTGAATGAATAAGAAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
** * * * * *
5775298 CGTTTG-CCAAGGATTGTTCGAGTCTTACACTCCTTGAAAGAAAAGGGAGCAGACC
1 CGTTTGTTGAA-GATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
5775353 CGTTAT-TTGAAGATT
1 CGTT-TGTTGAAGATT
5775368 TTTCAAGTAT
Statistics
Matches: 343, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
51 160 0.47
54 5 0.01
55 175 0.51
56 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
Found at i:5775330 original size:110 final size:106
Alignment explanation
Indices: 5774995--5775365 Score: 298
Period size: 106 Copynumber: 3.5 Consensus size: 106
5774985 GTTGAAGATT
* * * * * * * * *
5774995 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAG-ATTGAGTCCTATACTC
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTT-TTTGAAGAATCGAGTCTTAAACTC
* * * * * * ** *
5775059 TCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTT
65 CCTGAAGGAATAAGAAGCAGACACGTTTGTCCAAGATTGTTC
* * * * *
5775101 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAG-ATCGAGTCTTATACTC
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTT-TTGAAGAATCGAGTCTTAAACTC
* * * * * ** *
5775165 TCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTATTC
65 CCTGAAGGAATAAGAAGCAGACACGTTTGTCCAAGATTGTTC
** *
5775207 GAGTCTTATACTCCCTGAACTAATAGGGAGCAGACACGTTTGTTGAAGAATGTTTGAGTCTTAAA
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTT-TTGAAGAA---TCGAGTCTTAAA
*
5775272 CTCCCTGAATGAATAAGAAGCAGACACGTTTG-CCAAGGATTGTTC
62 CTCCCTGAAGGAATAAGAAGCAGACACGTTTGTCCAA-GATTGTTC
* * * *
5775317 GAGTCTTACACTCCTTGAAAGAAAAGGGAGCAGACCCGTTATTTGAAGA
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTT-TTTGAAGA
5775366 TTTTTCAAGT
Statistics
Matches: 226, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
106 138 0.61
107 1 0.00
109 2 0.01
110 84 0.37
111 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (106 bp):
GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTTTGAAGAATCGAGTCTTAAACTCC
CTGAAGGAATAAGAAGCAGACACGTTTGTCCAAGATTGTTC
Found at i:5787008 original size:2 final size:2
Alignment explanation
Indices: 5787001--5787071 Score: 126
Period size: 2 Copynumber: 35.5 Consensus size: 2
5786991 ATCGAATAAA
5787001 AT AT AT AT AT AT AT CAT AT AT AT -T 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 AT AT AT
5787043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5787072 AGAACCCATT
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.01
2 64 0.96
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5789161 original size:32 final size:32
Alignment explanation
Indices: 5789120--5789223 Score: 120
Period size: 32 Copynumber: 3.2 Consensus size: 32
5789110 ATCTAAAAAA
* * *
5789120 TATTTTATAATAGTTTAATAAAAATTAACAAT
1 TATTTTATAATAATTTAATAAAATTTAATAAT
* *
5789152 TATTTTATAATATTTTGATAAAATTTAATAAT
1 TATTTTATAATAATTTAATAAAATTTAATAAT
* * *
5789184 AATTAGT-TAATAATTTAATAAAATTTAATGAT
1 TATT-TTATAATAATTTAATAAAATTTAATAAT
5789216 TATTTTAT
1 TATTTTAT
5789224 GATTTTTGGA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (32 bp):
TATTTTATAATAATTTAATAAAATTTAATAAT
Found at i:5789165 original size:10 final size:10
Alignment explanation
Indices: 5789118--5789212 Score: 55
Period size: 10 Copynumber: 9.0 Consensus size: 10
5789108 ATATCTAAAA
*
5789118 AATATTTTAT
1 AATATTTAAT
5789128 AATAGTTTAAT
1 AATA-TTTAAT
* * *
5789139 AAAAATTAAC
1 AATATTTAAT
*
5789149 AATTATTTTAT
1 AA-TATTTAAT
*
5789160 AATATTTTGAT
1 AATA-TTTAAT
*
5789171 AAAATTTAAT
1 AATATTTAAT
* *
5789181 AATAATTAGTT
1 AATATTTA-AT
5789192 AATAATTTAAT
1 AAT-ATTTAAT
*
5789203 AAAATTTAAT
1 AATATTTAAT
5789213 GATTATTTTA
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
10 30 0.48
11 29 0.46
12 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (10 bp):
AATATTTAAT
Found at i:5796860 original size:60 final size:60
Alignment explanation
Indices: 5796730--5796851 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
5796720 TGAATAGTCT
* * *
5796730 GGTGACTATTTAATAACCTTTAATAGTTAAAGGACTCAATAAAGAAACACCCTATAATCG
1 GGTGACCATTTTATAACCTTTAATAGTTAAAGGACTCAACAAAGAAACACCCTATAATCG
* * *
5796790 GGTGACCATTTTATAA-CTTTCAATGGTTAATA-GACTCAACAAAGAAGCGCCCTATAATCG
1 GGTGACCATTTTATAACCTTT-AATAGTTAA-AGGACTCAACAAAGAAACACCCTATAATCG
5796850 GG
1 GG
5796852 ATATCATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
59 4 0.07
60 49 0.91
61 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (60 bp):
GGTGACCATTTTATAACCTTTAATAGTTAAAGGACTCAACAAAGAAACACCCTATAATCG
Found at i:5797092 original size:20 final size:20
Alignment explanation
Indices: 5797049--5797092 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5797039 AGACCGGCTG
* *
5797049 AAAACCGAAAAAAACCGGGG
1 AAAACCGAAAAAAACCCGGA
5797069 AAAACCGAAAAAAACCCGGA
1 AAAACCGAAAAAAACCCGGA
5797089 AAAA
1 AAAA
5797093 TCGCCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.61, C:0.20, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAACCGAAAAAAACCCGGA
Found at i:5797800 original size:22 final size:21
Alignment explanation
Indices: 5797772--5797812 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5797762 TATAAAAAAT
5797772 TATTTTTATTAAATGTTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
5797794 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
5797813 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:5805432 original size:3 final size:3
Alignment explanation
Indices: 5805424--5805464 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5805414 ACCCCAAAAG
5805424 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5805465 ATAGAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5805587 original size:2 final size:2
Alignment explanation
Indices: 5805580--5805635 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5805570 TTTATTGATA
5805580 AT AT AT 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 AT AT AT
5805622 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5805636 TGTTATTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5805828 original size:13 final size:13
Alignment explanation
Indices: 5805803--5805900 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 13
5805793 AAAAAAATGA
5805803 AAATAACAT-AAAT
1 AAATAA-ATAAAAT
5805816 AAATAAATAAAAT
1 AAATAAATAAAAT
* * *
5805829 GAATGAATGAAAT
1 AAATAAATAAAAT
*
5805842 GAGATAAAATAATAAT
1 -AAAT-AAATAA-AAT
*
5805858 -AATAAATAAGAT
1 AAATAAATAAAAT
5805870 GAAATAAAGTAAAAT
1 -AAATAAA-TAAAAT
*
5805885 AAGAT-GATAAAAT
1 AA-ATAAATAAAAT
5805898 AAA
1 AAA
5805901 CAACATGATG
Statistics
Matches: 66, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
12 5 0.08
13 34 0.52
14 13 0.20
15 11 0.17
16 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.22
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:5813727 original size:17 final size:17
Alignment explanation
Indices: 5813714--5813746 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5813704 CGAATGCATT
5813714 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
5813731 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
5813747 TGAGGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:5813844 original size:64 final size:62
Alignment explanation
Indices: 5813698--5813876 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 62
5813688 GAATTAAATT
*
5813698 GAACATCGAATGCATTCCATGCATCGATGCACACCATGCACCGATGCACTGAGGATTTTATAA
1 GAACATCGAATGCATT-GATGCATCGATGCACACCATGCACCGATGCACTGAGGATTTTATAA
* * *
5813761 GAACATTGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCGA-GCTATTT-T
1 GAACATCGAATGCA-TTGATGCATCGATGCA-CA-CCATGCACCGATGCACT-GAGGAT-TTTAT
5813824 AA
61 AA
* * *
5813826 -AACATCGAATGCACTTGATGCATCGATGTACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCA-TTGATGCATCGATGCACAC-CA-TGCACCGATGCACT
5813877 AAGGTTCCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 28 0.28
64 44 0.44
65 21 0.21
66 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (62 bp):
GAACATCGAATGCATTGATGCATCGATGCACACCATGCACCGATGCACTGAGGATTTTATAA
Found at i:5818786 original size:30 final size:30
Alignment explanation
Indices: 5818750--5818816 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
5818740 CCCGAAGGAC
* *
5818750 CTATCCAGAGGTTACAAAGAACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* * *
5818780 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
5818810 CTATCCA
1 CTATCCA
5818817 TATGTTCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGCAA
Found at i:5823658 original size:21 final size:21
Alignment explanation
Indices: 5823629--5823672 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5823619 ACTCCGGGAG
* *
5823629 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
5823650 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
5823671 CT
1 CT
5823673 TCTCCTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:5824409 original size:19 final size:19
Alignment explanation
Indices: 5824363--5824400 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5824353 AAAAGGGGAG
5824363 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
5824382 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
5824401 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:5824967 original size:64 final size:64
Alignment explanation
Indices: 5824815--5824974 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
5824805 GAATTAAATT
* *
5824815 GAACATTGAATGCATTTTCATGCATCGATGCA-CACCATGCACTGATGCACTGAGTATTTTATAA
1 GAACATCGAATGCA-TTTGATGCATCGATGCACCACCATGCACTGATGCACTGAGTATTTTATAA
* *
5824879 GAACAACGGATGCATTTGATGCATCGATGCACCAGCCATGCA-TCGATGCACTCGAGCTA-TTT-
1 GAACATCGAATGCATTTGATGCATCGATGCACCA-CCATGCACT-GATGCACT-GAG-TATTTTA
5824941 TAA
62 TAA
*
5824944 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCATTTGATGCATCGATGCAC
5824975 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 16 0.19
64 42 0.50
65 18 0.21
66 6 0.07
67 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCACCATGCACTGATGCACTGAGTATTTTATAA
Found at i:5824974 original size:17 final size:19
Alignment explanation
Indices: 5824946--5824994 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5824936 TATTTTAAAA
5824946 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
5824964 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
5824983 CACCGATGCACT
1 CATCGATGCACT
5824995 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:5824990 original size:64 final size:62
Alignment explanation
Indices: 5824815--5824994 Score: 170
Period size: 64 Copynumber: 2.8 Consensus size: 62
5824805 GAATTAAATT
* * *
5824815 GAACATTGAATGCATTTTCATGCATCGATGCACACCA-TGCACTGATGCACTGAGTATTTTATAA
1 GAACATCGAATGCA-TTTGATGCATCGATG--CACCAGTGCACCGATGCACTGAGTATTTTATAA
* * *
5824879 GAACAACGGATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCGAGCTA-TTT-T
1 GAACATCGAATGCATTTGATGCATCGATGCACCAG---TGCACCGATGCACT-GAG-TATTTTAT
5824942 AA
61 AA
*
5824944 -AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCATTTGATGCATCGATGCAC-C--AGTGCACCGATGCACT
5824995 AAGGTTCCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
61 5 0.05
63 14 0.14
64 52 0.54
65 16 0.16
66 6 0.06
67 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (62 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCAGTGCACCGATGCACTGAGTATTTTATAA
Found at i:5828975 original size:18 final size:18
Alignment explanation
Indices: 5828952--5828988 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5828942 TTGCTCACTT
5828952 CTCCTATATGTCCAATGA
1 CTCCTATATGTCCAATGA
*
5828970 CTCCTATATTTCCAATGA
1 CTCCTATATGTCCAATGA
5828988 C
1 C
5828989 CAAGGGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (18 bp):
CTCCTATATGTCCAATGA
Found at i:5831625 original size:33 final size:33
Alignment explanation
Indices: 5831583--5831661 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
5831573 TAAACAAAAA
5831583 TTACCATGCAAGAAAAATTAGTTGATTTAATTT
1 TTACCATGCAAGAAAAATTAGTTGATTTAATTT
5831616 TTACCATGCAAGAAAAATTAGTTGATTTAATTT
1 TTACCATGCAAGAAAAATTAGTTGATTTAATTT
5831649 TTACCATGCAAGA
1 TTACCATGCAAGA
5831662 GAACATGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (33 bp):
TTACCATGCAAGAAAAATTAGTTGATTTAATTT
Found at i:5832180 original size:18 final size:18
Alignment explanation
Indices: 5832157--5832197 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5832147 ATGCTGATAG
5832157 CAATGGTGAAGTGGTGGC
1 CAATGGTGAAGTGGTGGC
5832175 CAATGGTGAAGTGGTGGC
1 CAATGGTGAAGTGGTGGC
5832193 CAATG
1 CAATG
5832198 CTGATGCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.22
Consensus pattern (18 bp):
CAATGGTGAAGTGGTGGC
Found at i:5841753 original size:68 final size:68
Alignment explanation
Indices: 5841676--5841808 Score: 266
Period size: 68 Copynumber: 2.0 Consensus size: 68
5841666 TCGTTAAAAC
5841676 CCCCCTTCTTGATTAATGGAGCTAGTAGGGTAGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGC
1 CCCCCTTCTTGATTAATGGAGCTAGTAGGGTAGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGC
5841741 AAA
66 AAA
5841744 CCCCCTTCTTGATTAATGGAGCTAGTAGGGTAGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGC
1 CCCCCTTCTTGATTAATGGAGCTAGTAGGGTAGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGC
5841809 CTTAGGATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (68 bp):
CCCCCTTCTTGATTAATGGAGCTAGTAGGGTAGCTCCTTAATCAGCGGAAGGAGGAAAAGAGTGC
AAA
Found at i:5852678 original size:15 final size:15
Alignment explanation
Indices: 5852654--5852712 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
5852644 AGGTCGACAG
*
5852654 TTAATAATTATTAAT
1 TTAATTATTATTAAT
5852669 TTAATTATTATT-AT
1 TTAATTATTATTAAT
* *
5852683 TATAATT-TAATAAAT
1 T-TAATTATTATTAAT
*
5852698 TTAA-TATTTTTAAT
1 TTAATTATTATTAAT
5852712 T
1 T
5852713 AAATGATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 15 0.43
15 19 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTATTATTAAT
Found at i:5853290 original size:25 final size:25
Alignment explanation
Indices: 5853262--5853318 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
5853252 TATTTTATGT
5853262 TTTAAAATTAAATCTAAAATTTTAA
1 TTTAAAATTAAATCTAAAATTTTAA
* * *
5853287 TTTAATA-TAAATTTAAAATTTTTA
1 TTTAAAATTAAATCTAAAATTTTAA
*
5853311 TTTTAAAT
1 TTTAAAAT
5853319 AGATAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAAAATTAAATCTAAAATTTTAA
Found at i:5853306 original size:18 final size:19
Alignment explanation
Indices: 5853262--5853307 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5853252 TATTTTATGT
* *
5853262 TTTAAAATTAAATCTAAAA
1 TTTAAAATTTAATATAAAA
*
5853281 TTT-TAATTTAATAT-AAA
1 TTTAAAATTTAATATAAAA
5853298 TTTAAAATTT
1 TTTAAAATTT
5853308 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 6 0.27
18 13 0.59
19 3 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAAATTTAATATAAAA
Found at i:5859589 original size:40 final size:40
Alignment explanation
Indices: 5859534--5859611 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
5859524 AAGAAGAGGC
* *
5859534 CTCTCTCTCTCTGTTTCATCGTTGCAAAGGAGGCCTCTCT
1 CTCTCTCTCTCTGTTTCATCGTCGCAAAGGAGACCTCTCT
*
5859574 CTCTCTCTCTGTGTTTCATCGTCGCAAAGGAGACCTCT
1 CTCTCTCTCTCTGTTTCATCGTCGCAAAGGAGACCTCT
5859612 TGCCTTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (40 bp):
CTCTCTCTCTCTGTTTCATCGTCGCAAAGGAGACCTCTCT
Found at i:5860607 original size:21 final size:20
Alignment explanation
Indices: 5860521--5860678 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
5860511 AAATGACCAA
**
5860521 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5860540 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5860560 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5860580 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5860601 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5860622 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5860642 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5860663 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5860679 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5860707 original size:20 final size:20
Alignment explanation
Indices: 5860645--5860914 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
5860635 CGATTTTCCA
* ** *
5860645 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5860665 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5860685 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5860705 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5860725 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5860745 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5860765 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5860785 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5860805 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5860825 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5860845 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5860865 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5860885 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5860905 AAATCACAAC
1 AAATCGCAAC
5860915 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5861636 original size:24 final size:24
Alignment explanation
Indices: 5861597--5861643 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5861587 AAATTTGGTC
5861597 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5861621 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5861644 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5864124 original size:33 final size:34
Alignment explanation
Indices: 5864073--5864360 Score: 325
Period size: 33 Copynumber: 8.2 Consensus size: 34
5864063 CGGAAATTAC
* *
5864073 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
5864106 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
5864140 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
5864178 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
5864211 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGC-GAAATGAA
5864250 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
5864288 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
5864321 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
5864354 AATCGCA
1 AATCGCA
5864361 TTGCGATTCT
Statistics
Matches: 232, Mismatches: 10, Indels: 26
0.87 0.04 0.10
Matches are distributed among these distances:
32 1 0.00
33 110 0.47
34 17 0.07
35 1 0.00
36 3 0.01
37 1 0.00
38 45 0.19
39 54 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:5864156 original size:19 final size:19
Alignment explanation
Indices: 5864087--5864366 Score: 348
Period size: 19 Copynumber: 15.7 Consensus size: 19
5864077 GCAACGAGAG
5864087 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5864106 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5864120 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5864140 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5864159 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5864178 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5864192 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5864211 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5864230 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5864250 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5864269 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5864288 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5864302 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5864321 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
5864335 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
5864354 AATCGCATTGCGA
1 AATCGCAATGCGA
5864367 TTCTCCCGTT
Statistics
Matches: 229, Mismatches: 10, Indels: 44
0.81 0.04 0.16
Matches are distributed among these distances:
14 42 0.18
15 3 0.01
16 7 0.03
17 7 0.03
18 3 0.01
19 132 0.58
20 35 0.15
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5864214 original size:52 final size:52
Alignment explanation
Indices: 5864073--5864328 Score: 342
Period size: 52 Copynumber: 4.8 Consensus size: 52
5864063 CGGAAATTAC
*
5864073 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
5864120 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
5864178 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
5864230 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
5864288 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
5864329 CGAGAGAATC
Statistics
Matches: 187, Mismatches: 5, Indels: 29
0.85 0.02 0.13
Matches are distributed among these distances:
47 8 0.04
49 1 0.01
50 1 0.01
52 78 0.42
53 30 0.16
54 1 0.01
55 4 0.02
56 2 0.01
57 1 0.01
58 61 0.33
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:5864266 original size:110 final size:106
Alignment explanation
Indices: 5864073--5864366 Score: 495
Period size: 110 Copynumber: 2.8 Consensus size: 106
5864063 CGGAAATTAC
*
5864073 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGGAAAT
5864137 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
5864178 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAAATCGCAATGCGG
5864243 AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
62 AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
5864288 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGGAAAT
* *
5864351 TAAAATCGCATTGCGA
66 GAAAATCGCAATGCGA
5864367 TTCTCCCGTT
Statistics
Matches: 180, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
104 19 0.11
105 53 0.29
106 1 0.01
107 1 0.01
108 2 0.01
110 104 0.58
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (106 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGGAAAT
GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:5864307 original size:14 final size:14
Alignment explanation
Indices: 5864288--5864342 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5864278 GCGAAATGAA
5864288 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5864302 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5864321 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5864335 AATCGCAA
1 AATCGCAA
5864343 TGCGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5864414 original size:53 final size:52
Alignment explanation
Indices: 5864356--5864472 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 52
5864346 GAAATTAAAA
5864356 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
* *
5864409 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTTATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
5864461 TCGCATTGCGAT
1 TCGCATTGCGAT
5864473 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:5864415 original size:19 final size:19
Alignment explanation
Indices: 5864375--5864472 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
5864365 GATTCTCCCG
5864375 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5864395 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5864414 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5864428 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5864447 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
5864466 TTGCGAT
1 TTGCGAT
5864473 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 35 0.50
20 15 0.21
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5864598 original size:14 final size:14
Alignment explanation
Indices: 5864579--5864615 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5864569 CATCAATTAC
5864579 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5864593 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5864607 ACAAATCAA
1 ACAAATCAA
5864616 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5866578 original size:19 final size:19
Alignment explanation
Indices: 5866538--5866691 Score: 166
Period size: 19 Copynumber: 8.6 Consensus size: 19
5866528 TAGTTTACTT
* *
5866538 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5866558 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5866577 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5866596 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5866610 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5866629 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5866643 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5866662 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5866681 TCGCAATGCGA
1 TCGCAACGCGA
5866692 TTTTGGTTTC
Statistics
Matches: 116, Mismatches: 8, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
14 16 0.14
16 11 0.09
17 11 0.09
19 66 0.57
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5866613 original size:14 final size:14
Alignment explanation
Indices: 5866594--5866650 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5866584 GCGAAATGAA
*
5866594 AATCGCAACGACAG
1 AATCGCAACGAAAG
5866608 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5866625 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5866641 AATCGCAACG
1 AATCGCAACG
5866651 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5866621 original size:33 final size:33
Alignment explanation
Indices: 5866575--5866669 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
5866565 GCGAAACCAA
*
5866575 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5866608 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5866641 AATCGCAACGCGAAATGAAAATCGCAACG
1 AATCGCAACGCGAAATGAAAATCGCAACG
5866670 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5866634 original size:52 final size:51
Alignment explanation
Indices: 5866555--5866691 Score: 147
Period size: 52 Copynumber: 2.6 Consensus size: 51
5866545 ACGAAACTTA
** *
5866555 AAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA-CGACA-G
1 AAATCGCAACGCGAAATGAAAATCGCAA-GCGAAA-G--AATCGCAACCGAAATG
*
5866608 -AATCGCAATGCGAAATGAAAATCGCAA-CGAAAGAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATGAAAATCGCAAGCGAAAGAATCGCAAC-CGAAATG
5866658 AAAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 -AAATCGCAACGCGAAATGAAAATCGCAA-GCGA
5866692 TTTTGGTTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
47 8 0.11
49 5 0.07
50 6 0.08
52 50 0.69
54 3 0.04
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAAGCGAAAGAATCGCAACCGAAATG
Found at i:5866722 original size:14 final size:14
Alignment explanation
Indices: 5866703--5866759 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5866693 TTTGGTTTCG
5866703 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5866717 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5866736 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5866750 CGTTGCGATT
1 CGTTGCGATT
5866760 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5866735 original size:33 final size:33
Alignment explanation
Indices: 5866687--5866767 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
5866677 AAAATCGCAA
**
5866687 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5866720 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5866753 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
5866768 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5866770 original size:21 final size:21
Alignment explanation
Indices: 5866744--5866819 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5866734 CGCGTTGCGA
5866744 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
5866765 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
5866785 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
5866806 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
5866820 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:5866800 original size:41 final size:41
Alignment explanation
Indices: 5866743--5866820 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
5866733 TCGCGTTGCG
*
5866743 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
5866784 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
5866821 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:5866941 original size:33 final size:33
Alignment explanation
Indices: 5866899--5866969 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5866889 AATACTAACT
*
5866899 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5866932 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5866965 TGAAA
1 TGAAA
5866970 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5867203 original size:22 final size:22
Alignment explanation
Indices: 5867151--5867205 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5867141 TGGTTGTGAG
**
5867151 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5867173 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5867195 GGATTTCTTCG
1 GGATTTCTTCG
5867206 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5867377 original size:20 final size:20
Alignment explanation
Indices: 5867352--5867505 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
5867342 CTTTAAATAT
5867352 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5867372 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
5867394 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5867413 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
5867433 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5867453 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5867473 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5867493 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5867506 TGAAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5867479 original size:40 final size:40
Alignment explanation
Indices: 5867351--5867505 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
5867341 GCTTTAAATA
*
5867351 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
5867392 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
5867432 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
5867472 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
5867506 TGAAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:5867522 original size:21 final size:21
Alignment explanation
Indices: 5867492--5867570 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
5867482 ATTTTCATAT
*
5867492 TCGCGTTGCGATTTTGAAAAA
1 TCGCATTGCGATTTTGAAAAA
* * * **
5867513 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGAAAAA
* *
5867534 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAAAAA
*
5867555 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
5867571 GAAACTGATT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGAAAAA
Found at i:5867565 original size:42 final size:43
Alignment explanation
Indices: 5867472--5867570 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
5867462 ATTTATGTGT
* *
5867472 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
** *
5867513 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTCAAAAA
*
5867555 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5867571 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 8 0.17
42 36 0.77
43 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
Found at i:5873822 original size:22 final size:23
Alignment explanation
Indices: 5873795--5873842 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
5873785 CCATTTTTAA
5873795 TATTTATGATGGTATATAG-TGG
1 TATTTATGATGGTATATAGATGG
5873817 TATTTATGATGGTATATAGATGG
1 TATTTATGATGGTATATAGATGG
5873840 TAT
1 TAT
5873843 ATTAGTGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
TATTTATGATGGTATATAGATGG
Found at i:5873840 original size:11 final size:11
Alignment explanation
Indices: 5873802--5873844 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
5873792 TAATATTTAT
5873802 GATGGTATATA
1 GATGGTATATA
*
5873813 G-TGGTATTTA
1 GATGGTATATA
5873823 TGATGGTATATA
1 -GATGGTATATA
5873835 GATGGTATAT
1 GATGGTATAT
5873845 TAGTGTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.29
11 12 0.43
12 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (11 bp):
GATGGTATATA
Found at i:5885619 original size:53 final size:53
Alignment explanation
Indices: 5885517--5885726 Score: 296
Period size: 53 Copynumber: 3.9 Consensus size: 53
5885507 TCTTCAAATG
* * * ****
5885517 ACGGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACACTCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCT
* *
5885571 ACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAGCAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* *
5885624 ACGGGTTCTCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTTTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
5885677 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
5885727 GTGTGATTCT
Statistics
Matches: 140, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
53 113 0.81
54 18 0.13
55 9 0.06
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
Found at i:5886274 original size:80 final size:80
Alignment explanation
Indices: 5886136--5886349 Score: 365
Period size: 80 Copynumber: 2.7 Consensus size: 80
5886126 GCTCGAAAGA
* * *
5886136 CTTACAAATGACCCGAAGGATTTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCAC
1 CTTACAAATTACCCGAAGGA-TTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCAC
5886201 TACTCTTCGGTGAAGG
65 TACTCTTCGGTGAAGG
5886217 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
*
5886282 ACTCTTTGGTGAAGG
66 ACTCTTCGGTGAAGG
* *
5886297 CTTACAAATTACCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
5886350 CCCGAAGGAC
Statistics
Matches: 127, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 108 0.85
81 19 0.15
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (80 bp):
CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
ACTCTTCGGTGAAGG
Found at i:5886356 original size:42 final size:42
Alignment explanation
Indices: 5886308--5886390 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
5886298 TTACAAATTA
5886308 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
5886350 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
1 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATG
5886391 ACACTTACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:5886382 original size:22 final size:21
Alignment explanation
Indices: 5886316--5886384 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
5886306 TACCCGAAGA
5886316 ACTTAATCATCATGCTCGAAAG
1 ACTT-ATCATCATGCTCGAAAG
* * *
5886338 ACTTA-C-TGATGGCCCGAAGG
1 ACTTATCATCAT-GCTCGAAAG
5886358 ACTTCATCATCATGCTCGAAAG
1 ACTT-ATCATCATGCTCGAAAG
5886380 ACTTA
1 ACTTA
5886385 CTGATGACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 3 0.08
22 16 0.43
23 3 0.08
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (21 bp):
ACTTATCATCATGCTCGAAAG
Found at i:5907808 original size:60 final size:60
Alignment explanation
Indices: 5907713--5907832 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
5907703 CCATTGGTGT
5907713 AGCGAGTCATGACAGCTTTTAGCCTATCAAATGTGTGTGTACTGATTCGTATAAACAAGG
1 AGCGAGTCATGACAGCTTTTAGCCTATCAAATGTGTGTGTACTGATTCGTATAAACAAGG
*
5907773 AGCGAGTCATGACAGCTTTTAGCCTATCAACTGTGTGTGTACTGATTCGTATAAACAAGG
1 AGCGAGTCATGACAGCTTTTAGCCTATCAAATGTGTGTGTACTGATTCGTATAAACAAGG
5907833 TGCATAATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (60 bp):
AGCGAGTCATGACAGCTTTTAGCCTATCAAATGTGTGTGTACTGATTCGTATAAACAAGG
Found at i:5909306 original size:17 final size:18
Alignment explanation
Indices: 5909266--5909307 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5909256 AAAAAATAAT
*
5909266 TTATGTAAAATCAAATTA
1 TTATTTAAAATCAAATTA
**
5909284 AGATTTAAAAT-AAATTA
1 TTATTTAAAATCAAATTA
5909301 TTATTTA
1 TTATTTA
5909308 TTATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
TTATTTAAAATCAAATTA
Found at i:5911456 original size:113 final size:113
Alignment explanation
Indices: 5911118--5911765 Score: 681
Period size: 113 Copynumber: 5.7 Consensus size: 113
5911108 TAGAGTTATG
5911118 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
* * *
5911182 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAA
* *
5911230 CAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A--AGTTCTTC
* * * * *
5911291 TCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTTAAA
63 TCATTATGAACT-TTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAA
*
5911342 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
*
5911407 TTATGAACTTTCTCTTGAAATGATGATCCATCGAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAA
* * *
5911455 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
**** * *** *
5911520 TTATGAACTCGAACTGGAAATGTTAATGTTGATCTATCTTTTTCTGTGATAGAA-TCAAG
66 TTATGAACTTTCTCTGGAAATG---A---TGATCCATC-----GAATGAT-GAATTCAAA
* *
5911579 CAAAAAGGTTGAACAAGCTCTTCTCATT-TGAACTTCTTCTTCC-TCAT-ATGATAAGTTCTTCT
1 C-AAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATAAGTTCTTCT
* * * * * *
5911641 CATTATGAAC-CT-TCTGGCAACGCTGATCCATCGAATGATGAATTCGAG
64 CATTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAA
* ** * *
5911689 CAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTGTTCTTC
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A--AGTTCTTC
*
5911754 TTATTATGAACT
63 TCATTATGAACT
5911766 CTAACTGAAA
Statistics
Matches: 453, Mismatches: 52, Indels: 59
0.80 0.09 0.10
Matches are distributed among these distances:
109 43 0.09
110 26 0.06
111 5 0.01
112 113 0.25
113 130 0.29
114 18 0.04
115 14 0.03
116 12 0.03
119 8 0.02
121 7 0.02
122 2 0.00
123 25 0.06
124 24 0.05
125 26 0.06
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAA
Found at i:5911711 original size:234 final size:232
Alignment explanation
Indices: 5910999--5911780 Score: 938
Period size: 234 Copynumber: 3.4 Consensus size: 232
5910989 TGTAATCTAG
* *
5910999 CAAAAAGTTGAACAAATTCTCCTCCTTATGAACTTC-T-TT-TTCTTCAGATGAGTTCTTCTCAT
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
5911061 TATGAACTCCT-TCTGGAAATGCTGATGATGATATATCCCTTCTGTGATAGAGTTATGCAAAAGG
66 TATGAACT-CTAACTGGAAATGTTAATGTTGATCTAT--CTTCTGTGATAGAATTAAGCAAAAGG
* *
5911125 TTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAAC
128 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC
* *
5911190 TTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
193 TTTCTCTGGAAAAGATGATCCATCGAATGATGAATTCAAA
5911230 CAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCT
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTCT
* * * *** *
5911292 CATTATGAACTCTACCT-G----G-CAATGTTGATCCATC--AAATGAT-GAATTTAAACAAAAG
63 CATTATGAACTCTAACTGGAAATGTTAATGTTGATCTATCTTCTGTGATAGAA-TTAAGCAAAAG
5911348 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
127 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGA
* *
5911413 ACTTTCTCTTGAAATGATGATCCATCGAATGATGAATTCAAA
191 ACTTTCTCTGGAAAAGATGATCCATCGAATGATGAATTCAAA
5911455 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
* *
5911520 TTATGAACTCGAACTGGAAATGTTAATGTTGATCTATCTTTTTCTGTGATAGAATCAAGCAAAAA
65 TTATGAACTCTAACTGGAAATGTTAATGTTGATCTATC---TTCTGTGATAGAATTAAGC-AAAA
*
5911585 GGTTGAACAAGCTCTTCTCATT-TGAACTTCTTCTTCCTCAT-ATGATAAGTTCTTCTCATTATG
126 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCA-GATAAGTTCTTCTCATTATG
* * * * * *
5911648 AAC-CT-TCTGGCAACGCTGATCCATCGAATGATGAATTCGAG
190 AACTTTCTCTGGAAAAGATGATCCATCGAATGATGAATTCAAA
* * *
5911689 CAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTGTTCTTC
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGA---GTTCTTC
* *
5911754 TTATTATGAACTCTAACTGAAAATGTT
62 TCATTATGAACTCTAACTGGAAATGTT
5911781 GATCTATTAA
Statistics
Matches: 478, Mismatches: 43, Indels: 54
0.83 0.07 0.09
Matches are distributed among these distances:
223 2 0.00
224 48 0.10
225 97 0.20
226 26 0.05
227 2 0.00
228 14 0.03
229 14 0.03
230 2 0.00
231 41 0.09
232 13 0.03
233 3 0.01
234 105 0.22
235 2 0.00
236 26 0.05
237 54 0.11
238 29 0.06
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (232 bp):
CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTAACTGGAAATGTTAATGTTGATCTATCTTCTGTGATAGAATTAAGCAAAAGGTTG
AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTT
CTCTGGAAAAGATGATCCATCGAATGATGAATTCAAA
Found at i:5913293 original size:10 final size:10
Alignment explanation
Indices: 5913278--5913367 Score: 55
Period size: 10 Copynumber: 8.9 Consensus size: 10
5913268 ATCTTGACCC
5913278 CTTTTTTTCT
1 CTTTTTTTCT
5913288 C-TTTTTTCTT
1 CTTTTTTTC-T
*
5913298 CTTCTTTTTTT
1 CTT-TTTTTCT
5913309 C-TTTTTTCT
1 CTTTTTTTCT
5913318 -TCTTTTTTCT
1 CT-TTTTTTCT
5913328 -TTTTTCTTCT
1 CTTTTT-TTCT
*
5913338 -TTTTTCTTTT
1 CTTTTT-TTCT
*
5913348 CTTTTTCTTTT
1 CTTTTT-TTCT
*
5913359 CTTCTTTTC
1 CTTTTTTTC
5913368 ATTTTTTCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
9 17 0.25
10 28 0.41
11 18 0.26
12 5 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:5913297 original size:7 final size:7
Alignment explanation
Indices: 5913281--5913377 Score: 74
Period size: 8 Copynumber: 13.3 Consensus size: 7
5913271 TTGACCCCTT
5913281 TTTTTCTC
1 TTTTT-TC
5913289 TTTTTTC
1 TTTTTTC
*
5913296 -TTCTTC
1 TTTTTTC
5913302 TTTTTTTC
1 -TTTTTTC
5913310 TTTTTTC
1 TTTTTTC
5913317 TTCTTTT-
1 TT-TTTTC
*
5913324 TTCTTT-
1 TTTTTTC
*
5913330 TTTCTTC
1 TTTTTTC
5913337 TTTTTTC
1 TTTTTTC
*
5913344 TTTTCTTT
1 TTTT-TTC
5913352 TTCTTTTC
1 TT-TTTTC
5913360 TTCTTTTC
1 TT-TTTTC
5913368 ATTTTTTC
1 -TTTTTTC
5913376 TT
1 TT
5913378 CAAGCATAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
6 12 0.16
7 25 0.34
8 33 0.45
9 4 0.05
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:5913306 original size:21 final size:20
Alignment explanation
Indices: 5913281--5913378 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 20
5913271 TTGACCCCTT
5913281 TTTTTCTCTTTTTTCTTCTTC
1 TTTTT-TCTTTTTTCTTCTTC
*
5913302 TTTTTT-TCTTTT-TTCTTC
1 TTTTTTCTTTTTTCTTCTTC
5913320 TTTTTTCTTTTTTCTTCTT-
1 TTTTTTCTTTTTTCTTCTTC
*
5913339 TTTTCTTTTCTTTTTCTT-TTC
1 TTTT-TTCT-TTTTTCTTCTTC
5913360 TTCTTTTCATTTTTTCTTC
1 TT-TTTTC-TTTTTTCTTC
5913379 AAGCATAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
18 12 0.18
19 14 0.22
20 11 0.17
21 25 0.38
22 3 0.05
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTTCTTC
Found at i:5920724 original size:15 final size:15
Alignment explanation
Indices: 5920701--5920732 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5920691 TGCGATGGAT
5920701 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
5920716 AATGCATGTATGCAA
1 AATGAATGTATGCAA
5920731 AA
1 AA
5920733 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:5924857 original size:17 final size:18
Alignment explanation
Indices: 5924817--5924858 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5924807 AAAAAATAAT
*
5924817 TTATGTAAAATCAAATTA
1 TTATTTAAAATCAAATTA
**
5924835 AGATTTAAAAT-AAATTA
1 TTATTTAAAATCAAATTA
5924852 TTATTTA
1 TTATTTA
5924859 TTATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
TTATTTAAAATCAAATTA
Found at i:5924929 original size:23 final size:20
Alignment explanation
Indices: 5924892--5924932 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
5924882 ACTATATAAT
5924892 AATAATAAAAATAAAATTTA
1 AATAATAAAAATAAAATTTA
5924912 AATATATAAACAAGTAAAATT
1 AATA-ATAAA-AA-TAAAATT
5924933 AAAACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 2 0.11
23 7 0.39
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAATAAAAATAAAATTTA
Found at i:5926300 original size:3 final size:3
Alignment explanation
Indices: 5926294--5926348 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
5926284 TAATATTTAT
* * * *
5926294 TAA TAA TAA -AA TAA TAA TAA TAA TAA TTA TTA TTA TTA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5926340 TAAA TAA TA
1 T-AA TAA TA
5926349 TTTAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5926317 original size:30 final size:29
Alignment explanation
Indices: 5926281--5926352 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
5926271 TTTGGACCTG
5926281 TAATAATATTTATTAATAATAAAATAATAA
1 TAATAATATTTATTAATAATAAAATAAT-A
* * * *
5926311 TAATAATAATTATTATTATTATAATAATA
1 TAATAATATTTATTAATAATAAAATAATA
5926340 TAAATAATATTTA
1 T-AATAATATTTA
5926353 AATGAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATAATATTTATTAATAATAAAATAATA
Found at i:5935891 original size:19 final size:18
Alignment explanation
Indices: 5935863--5935898 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5935853 TTTTACTAAT
*
5935863 AGAGGAAATATTACAAAG
1 AGAGGAAATAGTACAAAG
5935881 AGAGAGAAATAGTACAAA
1 AGAG-GAAATAGTACAAA
5935899 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.22, T:0.14
Consensus pattern (18 bp):
AGAGGAAATAGTACAAAG
Found at i:5940371 original size:59 final size:59
Alignment explanation
Indices: 5940216--5940387 Score: 168
Period size: 59 Copynumber: 2.9 Consensus size: 59
5940206 TTATCTTTAT
* * * *
5940216 TACGATATACTATCATTCACTTTTATTATATTACCATTCATATTCGTTATAATCTCTGC
1 TACGTTATATTATCATTCACTTTTATTATATTACCATTCATTTTCGTTATAATCTCGGC
* * * * * *
5940275 TACGTTGTATTATCTTTCACCTTTACTATATTACCATTCATTTTTGTT-TCAGTCTCGG-
1 TACGTTATATTATCATTCACTTTTATTATATTACCATTCATTTTCGTTAT-AATCTCGGC
* * * * * *
5940333 TCACGTTATATTATCATTCATTTTTATTATGTTGCCATTTATTTACGTTACAATC
1 T-ACGTTATATTATCATTCACTTTTATTATATTACCATTCATTTTCGTTATAATC
5940388 CATATTAAGT
Statistics
Matches: 88, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
58 2 0.02
59 86 0.98
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (59 bp):
TACGTTATATTATCATTCACTTTTATTATATTACCATTCATTTTCGTTATAATCTCGGC
Found at i:5940469 original size:20 final size:19
Alignment explanation
Indices: 5940433--5940471 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5940423 GTGAGATTTG
* *
5940433 AAAAATAATGTTTATTTAT
1 AAAAATAATATTGATTTAT
5940452 AAAAATAATCATTGATTTAT
1 AAAAATAAT-ATTGATTTAT
5940472 TTGGAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (19 bp):
AAAAATAATATTGATTTAT
Found at i:5943446 original size:13 final size:13
Alignment explanation
Indices: 5943428--5943452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5943418 CAGTTTTGTT
5943428 GTTATTTTTCTTA
1 GTTATTTTTCTTA
5943441 GTTATTTTTCTT
1 GTTATTTTTCTT
5943453 TTCTTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (13 bp):
GTTATTTTTCTTA
Found at i:5952545 original size:24 final size:24
Alignment explanation
Indices: 5952518--5952567 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5952508 CCCGAATTCG
* * *
5952518 AATCTAACCTGATTTTTATTATAA
1 AATCTAACCCGATTTTAATAATAA
*
5952542 AATCTGACCCGATTTTAATAATAA
1 AATCTAACCCGATTTTAATAATAA
5952566 AA
1 AA
5952568 ACTATTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (24 bp):
AATCTAACCCGATTTTAATAATAA
Found at i:5953870 original size:37 final size:37
Alignment explanation
Indices: 5953829--5953899 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
5953819 AGCATAATAT
* * *
5953829 TAGAGTTTTATTAGGATTCAAACTCTTAAAAATATGA
1 TAGAGTCTTACTAGGATTCAAACTCCTAAAAATATGA
* *
5953866 TAGAGTCTTACTATGATTTAAACTCCTAAAAATA
1 TAGAGTCTTACTAGGATTCAAACTCCTAAAAATA
5953900 GGATCCACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (37 bp):
TAGAGTCTTACTAGGATTCAAACTCCTAAAAATATGA
Found at i:5954337 original size:19 final size:19
Alignment explanation
Indices: 5954298--5954336 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5954288 TATTTCATTA
*
5954298 TTATTATGTTTTATGTGTT
1 TTATTATGTTTTATCTGTT
*
5954317 TTATTTTGTTTTATCT-TT
1 TTATTATGTTTTATCTGTT
5954335 TT
1 TT
5954337 TTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.03, G:0.10, T:0.74
Consensus pattern (19 bp):
TTATTATGTTTTATCTGTT
Found at i:5954641 original size:9 final size:9
Alignment explanation
Indices: 5954627--5954651 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5954617 TTGTTTTTAT
5954627 TATTATTAG
1 TATTATTAG
5954636 TATTATTAG
1 TATTATTAG
5954645 TATTATT
1 TATTATT
5954652 CTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (9 bp):
TATTATTAG
Found at i:5954736 original size:19 final size:20
Alignment explanation
Indices: 5954714--5954769 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
5954704 TTTTTATTCC
5954714 TTATCTTTATTT-TATTTTT
1 TTATCTTTATTTATATTTTT
*
5954733 TTATCTTT-TTTACATTTGTT
1 TTATCTTTATTTATATTT-TT
*
5954753 TTA--TTTATTTGTATTTT
1 TTATCTTTATTTATATTTT
5954770 CTTCTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.23
19 19 0.61
20 5 0.16
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (20 bp):
TTATCTTTATTTATATTTTT
Found at i:5960335 original size:21 final size:20
Alignment explanation
Indices: 5960311--5960366 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5960301 CAGTTTCCAA
5960311 ATTCGCAACGCGAATATCT-AG
1 ATTCGCAACGCG-AT-TCTAAG
*
5960332 ATTCGCAACGCGATTGTAAG
1 ATTCGCAACGCGATTCTAAG
*
5960352 ATTCGCAACACGATT
1 ATTCGCAACGCGATT
5960367 TTGAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 18 0.56
21 12 0.38
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTCGCAACGCGATTCTAAG
Found at i:5960399 original size:19 final size:19
Alignment explanation
Indices: 5960371--5960456 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 19
5960361 ACGATTTTGA
*
5960371 AAAATATGTTGCGATAGTT
1 AAAATATGTTGCGATAGTG
* * *
5960390 AAAATGTGTTACGAGAGTTTG
1 AAAATATGTTGCGATAG--TG
*
5960411 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--T-ATGTTGCGATAGTG
*
5960434 AAAAAATGTTGCGATAGTG
1 AAAATATGTTGCGATAGTG
5960453 AAAA
1 AAAA
5960457 ATCCAAAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
19 31 0.60
21 1 0.02
22 8 0.15
23 2 0.04
24 1 0.02
25 9 0.17
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (19 bp):
AAAATATGTTGCGATAGTG
Found at i:5960458 original size:18 final size:19
Alignment explanation
Indices: 5960421--5960457 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5960411 AAAAACGTGT
5960421 TGTTGCGATAGTGAAAAAA
1 TGTTGCGATAGTGAAAAAA
5960440 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
5960458 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAA
Found at i:5962314 original size:29 final size:30
Alignment explanation
Indices: 5962272--5962329 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
5962262 TTTTATAAAA
5962272 ATTTTTAAAAAACT-ATAAAATAAAATAAT
1 ATTTTTAAAAAACTGATAAAATAAAATAAT
*
5962301 ATTTTTAAAAAACTGTTAAAATAAAATAA
1 ATTTTTAAAAAACTGATAAAATAAAATAA
5962330 CAGAGCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (30 bp):
ATTTTTAAAAAACTGATAAAATAAAATAAT
Found at i:5963781 original size:15 final size:16
Alignment explanation
Indices: 5963755--5963784 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5963745 TCATTTAATT
5963755 AAATATAAAAATAAAA
1 AAATATAAAAATAAAA
5963771 AAATA-AAAAATAAA
1 AAATATAAAAATAAA
5963785 TCAAGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAATATAAAAATAAAA
Found at i:5963797 original size:4 final size:4
Alignment explanation
Indices: 5963754--5963805 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
5963744 GTCATTTAAT
*
5963754 TAAA TATAA -AAA TAAA AAAA TAAA -AAA TAAA TCAAGA TAAA TAAA TAAA
1 TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TAAA T-AA-A TAAA TAAA TAAA
5963803 TAA
1 TAA
5963806 TAATTTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 5 0.12
4 28 0.68
5 6 0.15
6 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:5964232 original size:11 final size:11
Alignment explanation
Indices: 5964197--5964238 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5964187 GACTGATTAT
5964197 TTTCTCTTCT-
1 TTTCTCTTCTC
*
5964207 TTTCATCCCTCTC
1 TTTC-T-CTTCTC
5964220 TTTCTCTTCTC
1 TTTCTCTTCTC
5964231 TTTCTCTT
1 TTTCTCTT
5964239 TGTTTTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 14 0.52
12 5 0.19
13 4 0.15
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTCTCTTCTC
Found at i:5966982 original size:27 final size:27
Alignment explanation
Indices: 5966944--5967010 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
5966934 TCTGTAAGAT
5966944 CTTAATATTAGTTTCATTTGTTTTATG
1 CTTAATATTAGTTTCATTTGTTTTATG
* *
5966971 CTTAATTTTAGTTTCATTTGTTTTATT
1 CTTAATATTAGTTTCATTTGTTTTATG
5966998 CTTAATATTAGTT
1 CTTAATATTAGTT
5967011 ACTCCATCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.61
Consensus pattern (27 bp):
CTTAATATTAGTTTCATTTGTTTTATG
Found at i:5968713 original size:9 final size:9
Alignment explanation
Indices: 5968699--5968724 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5968689 AATCTCTTAC
5968699 TATTTTCTA
1 TATTTTCTA
5968708 TATTTTCTA
1 TATTTTCTA
5968717 TATTTTCT
1 TATTTTCT
5968725 TGCATTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (9 bp):
TATTTTCTA
Found at i:5970801 original size:15 final size:15
Alignment explanation
Indices: 5970783--5970816 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5970773 ATTTTATGTG
*
5970783 AATACAAATTATTTT
1 AATACAAATTATTTA
*
5970798 AATATAAATTATTTA
1 AATACAAATTATTTA
5970813 AATA
1 AATA
5970817 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATACAAATTATTTA
Found at i:5975536 original size:2 final size:2
Alignment explanation
Indices: 5975529--5975566 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5975519 CGTTAAACAA
5975529 AT 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 AT
5975567 TGAAATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5978368 original size:23 final size:23
Alignment explanation
Indices: 5978342--5978387 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5978332 CACCACAGCT
* *
5978342 CGTATAAATGTACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* *
5978365 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
5978388 TATAAGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:5983594 original size:23 final size:23
Alignment explanation
Indices: 5983532--5983595 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
5983522 CAGCTAGTAT
*
5983532 AAATGTACCAAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACGTAG
* * * **
5983555 AATTGCACCGAATTGCCGTGTAG
1 AAATGCACCAAAGTGCCACGTAG
5983578 AAATGCACCAAAGTGCCA
1 AAATGCACCAAAGTGCCA
5983596 TATAAGATTG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACGTAG
Found at i:5986303 original size:17 final size:17
Alignment explanation
Indices: 5986281--5986317 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5986271 AACGGTCAAT
*
5986281 GGTCAACGGCCGGGTCG
1 GGTCAACGGACGGGTCG
5986298 GGTCAACGGACGGGTCG
1 GGTCAACGGACGGGTCG
5986315 GGT
1 GGT
5986318 AGGGTCGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.49, T:0.14
Consensus pattern (17 bp):
GGTCAACGGACGGGTCG
Found at i:5993680 original size:30 final size:31
Alignment explanation
Indices: 5993595--5993684 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 31
5993585 AGAGTTGAGG
5993595 GTTACCTATGTCTTTCGGGACATATGGACAT
1 GTTACCTATGTCTTTCGGGACATATGGACAT
*
5993626 GATTACCTATATCTTTCGGGACATATGGACA-
1 G-TTACCTATGTCTTTCGGGACATATGGACAT
* *
5993657 GTTACCTATGT-TCTTAGGAACATATGGA
1 GTTACCTATGTCT-TTCGGGACATATGGA
5993685 TAGGTCATTC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
29 1 0.02
30 22 0.42
31 2 0.04
32 28 0.53
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTACCTATGTCTTTCGGGACATATGGACAT
Found at i:5996032 original size:24 final size:24
Alignment explanation
Indices: 5996005--5996051 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5995995 TAATTAACTG
5996005 AAATATTATTTT-ATTAATATTTTA
1 AAATA-TATTTTGATTAATATTTTA
*
5996029 AAATATATTTTGTTTAATATTTT
1 AAATATATTTTGATTAATATTTT
5996052 TTTAGGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AAATATATTTTGATTAATATTTTA
Found at i:5999585 original size:2 final size:2
Alignment explanation
Indices: 5999580--5999680 Score: 77
Period size: 2 Copynumber: 51.5 Consensus size: 2
5999570 TTTTAGATTT
5999580 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA
* * * * * * *
5999622 TT TA T- TA -A TT TA TA TA TA TA TA TT TA CTA TT TT TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
5999663 T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5999681 TATTTTTACT
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
1 5 0.06
2 73 0.89
3 3 0.04
4 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (2 bp):
TA
Found at i:5999685 original size:32 final size:33
Alignment explanation
Indices: 5999598--5999687 Score: 119
Period size: 32 Copynumber: 2.7 Consensus size: 33
5999588 TATATATATA
**
5999598 TATATATATATATATATTATCAGTTTTATTAATT
1 TATATATATATATATATTAT-TTTTTTATTAATT
* * *
5999632 TATATATATATATTTACTATTTTTTTATTTA-T
1 TATATATATATATATATTATTTTTTTATTAATT
5999664 TATATATATATATATATTATTTTT
1 TATATATATATATATATTATTTTT
5999688 ACTTTTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 23 0.47
33 8 0.16
34 18 0.37
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (33 bp):
TATATATATATATATATTATTTTTTTATTAATT
Found at i:5999694 original size:38 final size:37
Alignment explanation
Indices: 5999622--5999702 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 37
5999612 TATTATCAGT
* *
5999622 TTTATTAATTTATATATATATATTTACTATTTTTTTA
1 TTTATTAATATATATATATATATTTACTACTTTTTTA
* *
5999659 TTTATTATATATATATATATATTATTT-TTACTTTTTTT
1 TTTATTA-ATATATATATATA-TATTTACTACTTTTTTA
5999697 TTTATT
1 TTTATT
5999703 TTTTTATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 7 0.18
38 26 0.68
39 5 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (37 bp):
TTTATTAATATATATATATATATTTACTACTTTTTTA
Found at i:5999704 original size:9 final size:9
Alignment explanation
Indices: 5999692--5999757 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
5999682 ATTTTTACTT
5999692 TTTTTTTTA
1 TTTTTTTTA
5999701 -TTTTTTTA
1 TTTTTTTTA
*
5999709 TTTGTTTTA
1 TTTTTTTTA
* *
5999718 TTTATATT-
1 TTTTTTTTA
* *
5999726 TTTTTCTTC
1 TTTTTTTTA
5999735 TTTTTCTTTA
1 TTTTT-TTTA
5999745 TTTTTTTATA
1 TTTTTTT-TA
5999755 TTT
1 TTT
5999758 ACTTTACTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
8 14 0.30
9 20 0.43
10 12 0.26
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:5999725 original size:23 final size:21
Alignment explanation
Indices: 5999676--5999753 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 21
5999666 TATATATATA
*
5999676 TATATTATTTTTACTTTTTTTT
1 TATATT-TTTTTATTTTTTTTT
5999698 T-TATTTTTTTATTTGTTTTATT
1 TATATTTTTTTATTT-TTTT-TT
* *
5999720 TATATTTTTTTCTTCTTTTTCT
1 TATATTTTTTTATT-TTTTTTT
5999742 T-TATTTTTTTAT
1 TATATTTTTTTAT
5999754 ATTTACTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 8 0.17
21 18 0.38
22 6 0.12
23 15 0.31
24 1 0.02
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.79
Consensus pattern (21 bp):
TATATTTTTTTATTTTTTTTT
Found at i:5999729 original size:35 final size:35
Alignment explanation
Indices: 5999680--5999762 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
5999670 TATATATATA
* *
5999680 TTATTTTTACTTTTTT-TT-TTATTTTTTTATTTGTT
1 TTATTTATACTTTTTTCTTCTT-TTTCTTTATTT-TT
*
5999715 TTATTTATATTTTTTTCTTCTTTTTCTTTATTTTT
1 TTATTTATACTTTTTTCTTCTTTTTCTTTATTTTT
5999750 TTATATT-TACTTT
1 TTAT-TTATACTTT
5999763 ACTAACTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 25 0.61
36 14 0.34
37 2 0.05
ACGTcount: A:0.13, C:0.06, G:0.01, T:0.80
Consensus pattern (35 bp):
TTATTTATACTTTTTTCTTCTTTTTCTTTATTTTT
Found at i:5999753 original size:31 final size:31
Alignment explanation
Indices: 5999693--5999757 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5999683 TTTTTACTTT
*
5999693 TTTTTTTATTTTTTTATTTGTTTTATTTATA
1 TTTTTTTATTTTTTTATTTATTTTATTTATA
* *
5999724 TTTTTTTCTTCTTTTTCTTTATTTT-TTTATA
1 TTTTTTTATT-TTTTTATTTATTTTATTTATA
5999755 TTT
1 TTT
5999758 ACTTTACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.82
Consensus pattern (31 bp):
TTTTTTTATTTTTTTATTTATTTTATTTATA
Found at i:5999831 original size:26 final size:26
Alignment explanation
Indices: 5999798--5999853 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5999788 TTATCTTATC
5999798 TTTTATTTAATTTATTT-TTTCTT-CA
1 TTTTATTTAA-TTATTTATTTCTTACA
5999823 TTTTAATTTAATTATTTATTTCTTACA
1 TTTT-ATTTAATTATTTATTTCTTACA
5999850 TTTT
1 TTTT
5999854 TATCTAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.36
26 12 0.43
27 6 0.21
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTTATTTAATTATTTATTTCTTACA
Done.