Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 18 of 133
Found at i:4399029 original size:24 final size:23
Alignment explanation
Indices: 4398997--4399041 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4398987 TATATTGCTT
* *
4398997 TAAATATTAAGATTAATTATATG
1 TAAATATTAAAATTAAATATATG
4399020 TAAAGTATTAAAATTAAATATA
1 TAAA-TATTAAAATTAAATATA
4399042 ATTTAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (23 bp):
TAAATATTAAAATTAAATATATG
Found at i:4400075 original size:28 final size:29
Alignment explanation
Indices: 4400044--4400108 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
4400034 TTCTAAATTA
4400044 TTTTTTACTA-TTTTGTAACATAAGTAGG
1 TTTTTTACTATTTTTGTAACATAAGTAGG
* *
4400072 TTTTTATA-TATTTTTGTAACTTGAGTAGG
1 TTTTT-TACTATTTTTGTAACATAAGTAGG
*
4400101 TTTCTTAC
1 TTTTTTAC
4400109 ATTAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.54
Consensus pattern (29 bp):
TTTTTTACTATTTTTGTAACATAAGTAGG
Found at i:4403447 original size:18 final size:18
Alignment explanation
Indices: 4403417--4403451 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4403407 ATGAATTATT
4403417 TTTAAATATTATTATTCAA
1 TTTAAATATTATT-TTCAA
4403436 TTTAAA-ATTATTTTCA
1 TTTAAATATTATTTTCA
4403452 TAAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATATTATTTTCAA
Found at i:4403689 original size:41 final size:41
Alignment explanation
Indices: 4403639--4403720 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
4403629 ACTTATACAT
4403639 AATAATTCAAATTCATTAATAATATATGAACGGTCAAATGC
1 AATAATTCAAATTCATTAATAATATATGAACGGTCAAATGC
*
4403680 AATAGTTCAAATTCATTAATAATATATGAACGGTCAAATGC
1 AATAATTCAAATTCATTAATAATATATGAACGGTCAAATGC
4403721 TACATATACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (41 bp):
AATAATTCAAATTCATTAATAATATATGAACGGTCAAATGC
Found at i:4407251 original size:12 final size:12
Alignment explanation
Indices: 4407234--4407260 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4407224 TCAACTCCCA
4407234 ATCCATGACCAC
1 ATCCATGACCAC
4407246 ATCCATGACCAC
1 ATCCATGACCAC
4407258 ATC
1 ATC
4407261 TATTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.41, G:0.07, T:0.19
Consensus pattern (12 bp):
ATCCATGACCAC
Found at i:4410270 original size:58 final size:59
Alignment explanation
Indices: 4410172--4410309 Score: 156
Period size: 58 Copynumber: 2.3 Consensus size: 59
4410162 AAATTAGAAA
* * *
4410172 TATTTTTTCTTTTTGAATCTCTAAATTTTTTACCATTTGGGCCT-ATTTAAAAATTCTCTT
1 TATTTTTTCTTTTT-ATTTTCTAAATTTTTCACCATTTGGG-CTAATTTAAAAATTCTCTT
* * *
4410232 TATTTATTT-TTTTTATTTTCTAAA-TTTTCACCATTTGGGTTAATTTAGAAATTCTTTT
1 TATTT-TTTCTTTTTATTTTCTAAATTTTTCACCATTTGGGCTAATTTAAAAATTCTCTT
* *
4410290 TCTTTTTTCTTTTTTTTTTC
1 TATTTTTTCTTTTTATTTTC
4410310 AGAAAGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
57 4 0.06
58 42 0.63
59 8 0.12
60 10 0.15
61 3 0.04
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.62
Consensus pattern (59 bp):
TATTTTTTCTTTTTATTTTCTAAATTTTTCACCATTTGGGCTAATTTAAAAATTCTCTT
Found at i:4410644 original size:26 final size:25
Alignment explanation
Indices: 4410592--4410646 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
4410582 CTCACCTAGG
*
4410592 AATTTTATATAAATTTATCATTTAA
1 AATTTTATATAAATTTATCATTGAA
4410617 AATTTT-TATAAATTTCATCATTGGAA
1 AATTTTATATAAATTT-ATCATT-GAA
4410643 AATT
1 AATT
4410647 AATATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.33
25 12 0.44
26 6 0.22
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (25 bp):
AATTTTATATAAATTTATCATTGAA
Found at i:4410723 original size:4 final size:4
Alignment explanation
Indices: 4410714--4410752 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
4410704 ATACTCCTAA
* *
4410714 AAAT AAAT AAAC ACAT -AAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4410753 TACCAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 28 0.93
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4410750 original size:19 final size:19
Alignment explanation
Indices: 4410714--4410750 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4410704 ATACTCCTAA
*
4410714 AAATAAATAAACACATAAT
1 AAATAAATAAACAAATAAT
*
4410733 AAATAAATAAATAAATAA
1 AAATAAATAAACAAATAA
4410751 ATTACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATAAATAAACAAATAAT
Found at i:4411979 original size:41 final size:41
Alignment explanation
Indices: 4411927--4412045 Score: 175
Period size: 41 Copynumber: 2.9 Consensus size: 41
4411917 ATAAATGCTC
*
4411927 ACAGAGGCACCATAACTTTGAAAAGTAAAATGCTCATCTAA
1 ACAGAGGCACCACAACTTTGAAAAGTAAAATGCTCATCTAA
* * * * *
4411968 ATAGAGACACCACAACTTTAAAAAGTACAATGCTCCTCTAA
1 ACAGAGGCACCACAACTTTGAAAAGTAAAATGCTCATCTAA
*
4412009 ACAGAGGCACCACAACTTTGAAAAATAAAATGCTCAT
1 ACAGAGGCACCACAACTTTGAAAAGTAAAATGCTCAT
4412046 TGATGATCAT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.45, C:0.22, G:0.13, T:0.21
Consensus pattern (41 bp):
ACAGAGGCACCACAACTTTGAAAAGTAAAATGCTCATCTAA
Found at i:4413657 original size:12 final size:12
Alignment explanation
Indices: 4413640--4413683 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 12
4413630 CCCTTTCGAA
4413640 TTTTTTTTTCTC
1 TTTTTTTTTCTC
4413652 TTTTTTTTTCTTTC
1 TTTTTTTTTC--TC
*
4413666 TTTTTTTTT-TA
1 TTTTTTTTTCTC
4413677 TTTTTTT
1 TTTTTTT
4413684 CATCTATTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 8 0.28
12 10 0.34
14 11 0.38
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:4413683 original size:11 final size:12
Alignment explanation
Indices: 4413642--4413684 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
4413632 CTTTCGAATT
4413642 TTTTTTTCTCTT-
1 TTTTTTTCT-TTA
*
4413654 TTTTTTTCTTTC
1 TTTTTTTCTTTA
4413666 TTTTTTT-TTTA
1 TTTTTTTCTTTA
4413677 TTTTTTTC
1 TTTTTTTC
4413685 ATCTATTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTTA
Found at i:4417730 original size:55 final size:53
Alignment explanation
Indices: 4417640--4417762 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 53
4417630 ATTAAAAATA
* * * * *
4417640 TTTTTTTCTTTTTGAATCTCTAAATTTTTTACCATTTGGGCCTATTTAGAAATTC
1 TTTTTTT-TTTTT-TATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTC
*
4417695 TCTTTATTTTTTTTTATTTCTAAATTTTTCACCATTTGAGTCAATTTAGAAATTC
1 T-TTT-TTTTTTTTTATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTC
4417750 TTTTTTTTTTTTT
1 TTTTTTTTTTTTT
4417763 CAAAAAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
53 9 0.15
54 3 0.05
55 37 0.62
56 8 0.13
57 3 0.05
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (53 bp):
TTTTTTTTTTTTTATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTC
Found at i:4419690 original size:223 final size:218
Alignment explanation
Indices: 4419255--4419697 Score: 753
Period size: 217 Copynumber: 2.0 Consensus size: 218
4419245 TTCACAATAT
*
4419255 ATTTGTATTGGTGTTATTTAAAAAAAAAAAAAAAAAGGTTATGCACCGTGAGTGTTAAGAGAAAA
1 ATTTGTATTGGTGTTATTTAAAAAAAAAAAAAAAAAGGTTATGCACCATGAGTGTTAAGAGAAAA
* *
4419320 GATCATGAATCTTTAATAATCAAGAACTAAATTGTCACTTATAAGAGTTTATTCTTCTTTAAACA
66 GATCATGAATCTTTAATAATCAAGAACTAAACTGTAACTTATAAGAGTTTATTCTTCTTTAAACA
* * *
4419385 AAGCTTTAAAAAAAAAAAACCAAATTCTTAAAATAAATCATAAAACGGACAATGCCTAATTGGAT
131 AAGCTTTAAAAAAAAAAAAACAAATTCTTAAAACAAATCATAAAACGGACAATGCCTAAGTGGAT
4419450 ATAATCCAATAATTTTTGCATCG
196 ATAATCCAATAATTTTTGCATCG
4419473 ATTTGTATTGGTGTTATTT-AAAAAAAAAAAAAAAAGGTTATGCACCATGAGTGTTAAGAGAAAA
1 ATTTGTATTGGTGTTATTTAAAAAAAAAAAAAAAAAGGTTATGCACCATGAGTGTTAAGAGAAAA
4419537 GATCATGAATCTTTAATAATCAAGAACTAAACTGTAACTTATAAGAGTTTATTCTTCTTTAAACA
66 GATCATGAATCTTTAATAATCAAGAACTAAACTGTAACTTATAAGAGTTTATTCTTCTTTAAACA
*
4419602 AAGCTTTAAAAAAGAAAAAAAAAAACAAATTCTTAAAAACAAATCATAAAACGGATAATGCCTAA
131 AAGCTTT----AA-AAAAAAAAAAACAAATTCTT-AAAACAAATCATAAAACGGACAATGCCTAA
*
4419667 GTGGGTATAATCCAATAATTTTTGCATCG
190 GTGGATATAATCCAATAATTTTTGCATCG
4419696 AT
1 AT
4419698 ACAGCATTAT
Statistics
Matches: 211, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
217 114 0.54
218 19 0.09
221 2 0.01
222 19 0.09
223 57 0.27
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (218 bp):
ATTTGTATTGGTGTTATTTAAAAAAAAAAAAAAAAAGGTTATGCACCATGAGTGTTAAGAGAAAA
GATCATGAATCTTTAATAATCAAGAACTAAACTGTAACTTATAAGAGTTTATTCTTCTTTAAACA
AAGCTTTAAAAAAAAAAAAACAAATTCTTAAAACAAATCATAAAACGGACAATGCCTAAGTGGAT
ATAATCCAATAATTTTTGCATCG
Found at i:4419780 original size:2 final size:2
Alignment explanation
Indices: 4419773--4419798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4419763 TAATTTTGTA
4419773 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
4419799 CTCAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4420667 original size:9 final size:9
Alignment explanation
Indices: 4420653--4420717 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 9
4420643 TTTCTTCAAA
4420653 TTTTTATAT
1 TTTTTATAT
4420662 TTTTTATA-
1 TTTTTATAT
4420670 TTTTTA-ACT
1 TTTTTATA-T
4420679 TTTTT-T-T
1 TTTTTATAT
4420686 GTTTTT-TAT
1 -TTTTTATAT
*
4420695 TTTTGAT-T
1 TTTTTATAT
4420703 TTTTTA-AT
1 TTTTTATAT
4420711 TTTTTAT
1 TTTTTAT
4420718 TAGATAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
7 2 0.04
8 29 0.63
9 15 0.33
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTTATAT
Found at i:4420690 original size:24 final size:23
Alignment explanation
Indices: 4420663--4420707 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4420653 TTTTTATATT
4420663 TTTTATATTTTTAACTTTTTTTTG
1 TTTTATATTTTTAA-TTTTTTTTG
* *
4420687 TTTTTTATTTTTGATTTTTTT
1 TTTTATATTTTTAATTTTTTT
4420708 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTATATTTTTAATTTTTTTTG
Found at i:4420707 original size:33 final size:33
Alignment explanation
Indices: 4420653--4420715 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
4420643 TTTCTTCAAA
*
4420653 TTTTTATATTTTTTATATTTTTAACTTTTTTTTG
1 TTTTTATATTTTTGATATTTTTAA-TTTTTTTTG
*
4420687 TTTTT-TATTTTTGATTTTTTTAATTTTTT
1 TTTTTATATTTTTGATATTTTTAATTTTTT
4420716 ATTAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 6 0.22
33 16 0.59
34 5 0.19
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (33 bp):
TTTTTATATTTTTGATATTTTTAATTTTTTTTG
Found at i:4424245 original size:16 final size:15
Alignment explanation
Indices: 4424226--4424275 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 15
4424216 TTTGATTTGT
4424226 AAATATTATATTAATA
1 AAATATTAT-TTAATA
4424242 AAATTATTATTTAAT-
1 AAA-TATTATTTAATA
* *
4424257 ATAT-TTATTTAACA
1 AAATATTATTTAATA
4424271 AAATA
1 AAATA
4424276 CTATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 2 0.07
16 8 0.29
17 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTATTTAATA
Found at i:4425094 original size:19 final size:18
Alignment explanation
Indices: 4425070--4425107 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4425060 TATTTATAGA
4425070 TTTAATTGT-TTAATTATAT
1 TTTAATT-TATTAATT-TAT
4425089 TTTAATTTATTAATTTAT
1 TTTAATTTATTAATTTAT
4425107 T
1 T
4425108 ATTTAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTAATTTATTAATTTAT
Found at i:4425195 original size:33 final size:33
Alignment explanation
Indices: 4425139--4425227 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
4425129 TATAATTTGA
* * * *
4425139 TTATG-ATTTAATAATTAATTATTTGATTCATT
1 TTATGAATATAATATTTAATTATTTAACTCATT
* *
4425171 TTATGAATGTCATATTTAATTATTTAACTCATT
1 TTATGAATATAATATTTAATTATTTAACTCATT
4425204 TTATGAATATAATATTTAATTATT
1 TTATGAATATAATATTTAATTATT
4425228 AATATAACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 5 0.10
33 44 0.90
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (33 bp):
TTATGAATATAATATTTAATTATTTAACTCATT
Found at i:4426096 original size:24 final size:24
Alignment explanation
Indices: 4426064--4426112 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4426054 ACTCTTAAAT
4426064 AAGATTTCACTAAAATTTCTGTGG
1 AAGATTTCACTAAAATTTCTGTGG
4426088 AAGATTTCACTAAAATTTCTGTGG
1 AAGATTTCACTAAAATTTCTGTGG
4426112 A
1 A
4426113 GTGGATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (24 bp):
AAGATTTCACTAAAATTTCTGTGG
Found at i:4435017 original size:70 final size:70
Alignment explanation
Indices: 4434885--4435020 Score: 191
Period size: 70 Copynumber: 1.9 Consensus size: 70
4434875 TACTTGACTA
* ** *
4434885 AGTACTTAGTAAGGAAAGAGTCCTTCAAAACAACAGAAGTAGAATATCATTAGTGAGTATCTTTT
1 AGTACTTAATAAGGAAAGAGTCCTTCAAAACAACAGAAGTAGAATATCATTAGCCAGCATCTTTT
4434950 GATTC
66 GATTC
** * * *
4434955 AGTACTTAATAAGGAAAGAGTTGTTCTAAACCATAGAAGTAGAATATCATTAGCCAGCATCTTTT
1 AGTACTTAATAAGGAAAGAGTCCTTCAAAACAACAGAAGTAGAATATCATTAGCCAGCATCTTTT
4435020 G
66 G
4435021 GATTGTTTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 57 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (70 bp):
AGTACTTAATAAGGAAAGAGTCCTTCAAAACAACAGAAGTAGAATATCATTAGCCAGCATCTTTT
GATTC
Found at i:4439078 original size:19 final size:19
Alignment explanation
Indices: 4439056--4439110 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
4439046 TGCAAATAAT
**
4439056 ATCATGCAATTATAATATA
1 ATCATGCAAAAATAATATA
*
4439075 ATCATGTAAAAATAATATA
1 ATCATGCAAAAATAATATA
*
4439094 ATTATGCAAAAATAATA
1 ATCATGCAAAAATAATA
4439111 ATATATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (19 bp):
ATCATGCAAAAATAATATA
Found at i:4439541 original size:14 final size:14
Alignment explanation
Indices: 4439518--4439559 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
4439508 TTCTAAAATC
*
4439518 TTTCTTTTTGCCTT
1 TTTCTCTTTGCCTT
4439532 TTTCTCTTTGCCTT
1 TTTCTCTTTGCCTT
4439546 TTTCTCTTTGCCTT
1 TTTCTCTTTGCCTT
4439560 CTCTCTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTCTCTTTGCCTT
Found at i:4441047 original size:51 final size:51
Alignment explanation
Indices: 4440988--4441088 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
4440978 ATAGTTCCAT
* * *
4440988 ATTCACAAAGATTTCAAATTTGTAAGATTTTAAGTTTCACAGAGATTTCAA
1 ATTCACAAAGATTCCAAATTCGCAAGATTTTAAGTTTCACAGAGATTTCAA
* *
4441039 ATTCACAAAGATTCCATATTCGCAAGATTTTAAGTTTCGCAGAGATTTCA
1 ATTCACAAAGATTCCAAATTCGCAAGATTTTAAGTTTCACAGAGATTTCA
4441089 GAGTCGTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (51 bp):
ATTCACAAAGATTCCAAATTCGCAAGATTTTAAGTTTCACAGAGATTTCAA
Found at i:4441136 original size:18 final size:17
Alignment explanation
Indices: 4440988--4441160 Score: 66
Period size: 17 Copynumber: 10.2 Consensus size: 17
4440978 ATAGTTCCAT
4440988 ATTCACAAAGATTTCAA
1 ATTCACAAAGATTTCAA
*** *
4441005 ATT-TGTAAGATTTTAA
1 ATTCACAAAGATTTCAA
* *
4441021 GTTTCACAGAGATTTCAA
1 -ATTCACAAAGATTTCAA
* *
4441039 ATTCACAAAGATTCCAT
1 ATTCACAAAGATTTCAA
* *
4441056 ATTCGC-AAGATTTTAA
1 ATTCACAAAGATTTCAA
* * * *
4441072 GTTTCGCAGAGATTTCAG
1 -ATTCACAAAGATTTCAA
* ** **
4441090 AGTC-GTAATTTTTCAA
1 ATTCACAAAGATTTCAA
* *
4441106 ATTCATAAGGATTTCAA
1 ATTCACAAAGATTTCAA
*
4441123 ATTTCACAAAGA-TTCTAG
1 A-TTCACAAAGATTTC-AA
* *
4441141 ATTCACAAGGATTTCGA
1 ATTCACAAAGATTTCAA
4441158 ATT
1 ATT
4441161 TGGCATAGGT
Statistics
Matches: 106, Mismatches: 42, Indels: 16
0.65 0.26 0.10
Matches are distributed among these distances:
16 25 0.24
17 53 0.50
18 28 0.26
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (17 bp):
ATTCACAAAGATTTCAA
Found at i:4441151 original size:35 final size:35
Alignment explanation
Indices: 4441106--4441236 Score: 113
Period size: 35 Copynumber: 3.8 Consensus size: 35
4441096 AATTTTTCAA
* *
4441106 ATTCATAAGGATTTCAAATTTCACAAAGATTCTAG
1 ATTCACAAGGATTTCAAATTTCACAAAGATTCCAG
* ** * *
4441141 ATTCACAAGGATTTCGAATTTGGCATAGGTTCCAG
1 ATTCACAAGGATTTCAAATTTCACAAAGATTCCAG
* **
4441176 ATTCACAA-GATTTCAAGTTTTGCAAATGA-TCCAG
1 ATTCACAAGGATTTCAAATTTCACAAA-GATTCCAG
** * *
4441210 ATTTGCAAAGATTTCAAAATTCACAAA
1 ATTCACAAGGATTTCAAATTTCACAAA
4441237 AAAATCAAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
34 25 0.33
35 51 0.67
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (35 bp):
ATTCACAAGGATTTCAAATTTCACAAAGATTCCAG
Found at i:4441602 original size:46 final size:46
Alignment explanation
Indices: 4441552--4441835 Score: 213
Period size: 46 Copynumber: 6.2 Consensus size: 46
4441542 AGATATTCCT
* * *
4441552 ATCCAAAATTTCAAAGATTTACATTTGAAAAATTTTAGAAATTTAC
1 ATCCAAAATTTCAAAGATTCACATTTGAAAAATATTAGAGATTTAC
* * * * * **
4441598 ATCC-AAATTTTAGAA-TTTCATATTTGAAAAAAAAATAGAGATTCCC
1 ATCCAAAATTTCA-AAGATTCACATTTG-AAAAATATTAGAGATTTAC
* * **
4441644 ATCCAACATTTCAAAGATTCACACTCAAAAAATATTAGAGATTTAC
1 ATCCAAAATTTCAAAGATTCACATTTGAAAAATATTAGAGATTTAC
* * * * *
4441690 AT-CAAAAGTTTCAGAGATTCGCATTCGAAAAAAAATTA-ATATTTCAC
1 ATCCAAAA-TTTCAAAGATTCACATTTG-AAAAATATTAGAGATTT-AC
* * * * *
4441737 AACCAAAATTTCGAAGATTCCCATCTGAAAAATTTTAG-GATTTCAC
1 ATCCAAAATTTCAAAGATTCACATTTGAAAAATATTAGAGATTT-AC
* * * *
4441783 ATCCAAAATTTCAAATATTCATATTTG-AAAA-ATTAGAGATTCAT
1 ATCCAAAATTTCAAAGATTCACATTTGAAAAATATTAGAGATTTAC
4441827 ATCCAAAAT
1 ATCCAAAAT
4441836 CTAAAGGTTT
Statistics
Matches: 182, Mismatches: 46, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
44 14 0.08
45 27 0.15
46 98 0.54
47 38 0.21
48 5 0.03
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (46 bp):
ATCCAAAATTTCAAAGATTCACATTTGAAAAATATTAGAGATTTAC
Found at i:4441606 original size:92 final size:92
Alignment explanation
Indices: 4441488--4441835 Score: 334
Period size: 92 Copynumber: 3.8 Consensus size: 92
4441478 TTTTTATTCA
* * * *
4441488 AAAAATTTAAG-GATTCACATCTAAATTTTAAAATTTCATATTTGAAAAAAAATTAGATATTCCT
1 AAAAATTTTAGAGATTTACATCCAAATTTTAAAATTTCATATTTGAAAAAAAATTAGAGATTCCT
*
4441552 ATCCAAAATTTCAAAGATTTACATTTG
66 ATCCAAAATTTCAAAGATTCACATTTG
* * * *
4441579 AAAAATTTTAGAAATTTACATCCAAATTTTAGAATTTCATATTTGAAAAAAAAATAGAGATTCCC
1 AAAAATTTTAGAGATTTACATCCAAATTTTAAAATTTCATATTTGAAAAAAAATTAGAGATTCCT
* * **
4441644 ATCCAACATTTCAAAGATTCACACTCA
66 ATCCAAAATTTCAAAGATTCACATTTG
* * * * ** * *
4441671 AAAAATATTAGAGATTTACATCAAAAGTTTCAGAGA-TTCGCATTCGAAAAAAAATTA-ATATTT
1 AAAAATTTTAGAGATTTACATCCAAA-TTTTA-AAATTTCATATTTGAAAAAAAATTAGAGA-TT
* * * *
4441734 CAC-AACCAAAATTTCGAAGATTCCCATCTG
63 C-CTATCCAAAATTTCAAAGATTCACATTTG
* *
4441764 AAAAATTTTAG-GATTTCACATCCAAAATTTCAAATATTCATATTTG---AAAAATTAGAGATTC
1 AAAAATTTTAGAGATTT-ACATCCAAATTTTAAAAT-TTCATATTTGAAAAAAAATTAGAGATTC
*
4441825 ATATCCAAAAT
64 CTATCCAAAAT
4441836 CTAAAGGTTT
Statistics
Matches: 203, Mismatches: 44, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
90 19 0.09
91 14 0.07
92 100 0.49
93 68 0.33
94 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (92 bp):
AAAAATTTTAGAGATTTACATCCAAATTTTAAAATTTCATATTTGAAAAAAAATTAGAGATTCCT
ATCCAAAATTTCAAAGATTCACATTTG
Found at i:4441924 original size:81 final size:81
Alignment explanation
Indices: 4441822--4442002 Score: 265
Period size: 81 Copynumber: 2.2 Consensus size: 81
4441812 AAATTAGAGA
* * * *
4441822 TTCATATCCAAAATCTAAAGGTT-TTTTTGAAAAAACTTCCTGGCTTCACAAAAAGATTTTCATT
1 TTCACATCCAAAATTTAAAGGTTCTTTTTCAAAAAA-TTCCTGGCTTCACAAAAAGATTCTCATT
4441886 CAAAAAAATTTTAGGGT
65 CAAAAAAATTTTAGGGT
* * *
4441903 TTCACATCTAAAATTTAAAGGTTCTTTTTCAAAAAATTCTTGGCTTCATAAAAAGATTCTCATTC
1 TTCACATCCAAAATTTAAAGGTTCTTTTTCAAAAAATTCCTGGCTTCACAAAAAGATTCTCATTC
*
4441968 TAAAAAATTTTAGGGT
66 AAAAAAATTTTAGGGT
*
4441984 TTTACATCCAAAATTTAAA
1 TTCACATCCAAAATTTAAA
4442003 AAATTCTCAT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 78 0.88
82 11 0.12
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (81 bp):
TTCACATCCAAAATTTAAAGGTTCTTTTTCAAAAAATTCCTGGCTTCACAAAAAGATTCTCATTC
AAAAAAATTTTAGGGT
Found at i:4442019 original size:81 final size:82
Alignment explanation
Indices: 4441851--4442022 Score: 238
Period size: 81 Copynumber: 2.1 Consensus size: 82
4441841 GGTTTTTTTG
* *
4441851 AAAAAACTTCCTGGCTTCACAAAAAGATTTTCATTCAAAAAAATTTTAGGGTTTCACATCTAAAA
1 AAAAAACTTCCTGGCTTCACAAAAAGATTCTCATTCAAAAAAATTTTAGGGTTTCACATCCAAAA
** **
4441916 TTTAAAGGTTCTTTTTC
66 TTTAAAAATTCTCATTC
* * * *
4441933 AAAAAA-TTCTTGGCTTCATAAAAAGATTCTCATTCTAAAAAATTTTAGGGTTTTACATCCAAAA
1 AAAAAACTTCCTGGCTTCACAAAAAGATTCTCATTCAAAAAAATTTTAGGGTTTCACATCCAAAA
4441997 TTTAAAAAATTCTCATTC
66 TTT-AAAAATTCTCATTC
4442015 AAAAAACT
1 AAAAAACT
4442023 CTTTTAAACA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
81 55 0.71
82 22 0.28
83 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (82 bp):
AAAAAACTTCCTGGCTTCACAAAAAGATTCTCATTCAAAAAAATTTTAGGGTTTCACATCCAAAA
TTTAAAAATTCTCATTC
Found at i:4442169 original size:20 final size:20
Alignment explanation
Indices: 4442144--4442190 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4442134 CTAACAAAGA
*
4442144 CAAATGTCATGCT-AATAATG
1 CAAATGCCAT-CTAAATAATG
*
4442164 CAAATGCCATCTAAATGATG
1 CAAATGCCATCTAAATAATG
4442184 CAAATGC
1 CAAATGC
4442191 AACAATCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (20 bp):
CAAATGCCATCTAAATAATG
Found at i:4443816 original size:17 final size:16
Alignment explanation
Indices: 4443787--4443829 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
4443777 TATTTGAAAT
4443787 AAAAAA-ATGGATAAGG
1 AAAAAATAT-GATAAGG
4443803 AAAAAGATATGATAAGG
1 AAAAA-ATATGATAAGG
*
4443820 TAAAAATATG
1 AAAAAATATG
4443830 TAATGGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 12 0.50
18 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (16 bp):
AAAAAATATGATAAGG
Found at i:4447857 original size:26 final size:25
Alignment explanation
Indices: 4447805--4447864 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
4447795 AGTTATGTGT
* **
4447805 AATAAAAAACACAAACAAAAATGAA
1 AATAAAAAAAACAAACAAAAACAAA
4447830 AATAAAACAAAACAAACAAAAACAAA
1 AATAAAA-AAAACAAACAAAAACAAA
*
4447856 AACAAAAAA
1 AATAAAAAA
4447865 TCATAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.80, C:0.13, G:0.02, T:0.05
Consensus pattern (25 bp):
AATAAAAAAAACAAACAAAAACAAA
Found at i:4447878 original size:20 final size:20
Alignment explanation
Indices: 4447808--4447878 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 20
4447798 TATGTGTAAT
4447808 AAAAAACACAAACAAA-AATGAA
1 AAAAAACA-AAACAAACAA--AA
4447830 AATAAAACAAAACAAACAAAA
1 AA-AAAACAAAACAAACAAAA
*
4447851 ACAAAAACAAAA-AATCATAAA
1 A-AAAAACAAAACAAACA-AAA
4447872 AAAAAAC
1 AAAAAAC
4447879 TTTTCGATCT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
20 10 0.23
21 16 0.36
22 10 0.23
23 8 0.18
ACGTcount: A:0.79, C:0.14, G:0.01, T:0.06
Consensus pattern (20 bp):
AAAAAACAAAACAAACAAAA
Found at i:4458857 original size:49 final size:48
Alignment explanation
Indices: 4458444--4458873 Score: 377
Period size: 50 Copynumber: 8.8 Consensus size: 48
4458434 AACAAATGAA
* *
4458444 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAG-TTTTTCCAAGATACGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTT-CAAGATA-AAT
** * * * *
4458493 TTTTAAAAGTCATTGAGCATCTACTTAGAAGAGCTTTTTCAAGATAATGAA
1 TTTT-AAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAA--AT
* * * * *
4458544 TTTTAAAGTCGTTGAACTTTTGCTTAAAGGAG-TTTTTCCAAGATGATGAA-
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTT-CAAGAT-A--AAT
* * * *
4458594 TTTTAAAGTTGTTGAGCCTCTACTTAGAGGAACTATTCCAAGATAAAGT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAAA-T
4458643 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGATGAA-
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGAT-A--AAT
* * * *
4458693 TTTTAAAGTTATTGAG-CTCTACTTAGAGGAGTTTTTTCAAGATAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAAAT
* * * *
4458740 TTTTAAATTTGTTGAGCCTCTGTTTAGAGAAGCTTTTTCAAGATGAA-
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAAAT
* * * * *
4458787 GTTTAAAGTTGTTGAGCCTTTGCTTAAATGAGCTTTTTTAAGATAAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAAAT
* * * * *
4458835 TTTTAAAAGTTATTGAGTCTTTGCTCATAGGAGCTTTTT
1 TTTT-AAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTT
4458874 AAATTTTCAA
Statistics
Matches: 310, Mismatches: 53, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
46 1 0.00
47 54 0.17
48 28 0.09
49 104 0.34
50 105 0.34
51 15 0.05
52 2 0.01
53 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (48 bp):
TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAAAT
Found at i:4458869 original size:193 final size:200
Alignment explanation
Indices: 4458444--4458873 Score: 477
Period size: 193 Copynumber: 2.2 Consensus size: 200
4458434 AACAAATGAA
* * * *
4458444 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAG-TTTTTCCAAGATACGATTTTTAAAAGTCATTG
1 TTTTAAAGTTATTGAGCCTCTGCTCAGAGGAGCTTTTTCCAAGATACGAATTTTAAAAGTCATTG
* *
4458508 AGCATCTACTTAGAAGAGCTTTTTCAAGATAATGAATTTTAAAGTCGTTGAACTTTTGCTTAAAG
66 AGCATCTACTTAGAAGAGCTTTTTCAAGATAATGAATTTTAAAGTCGTTGAACCTCTGCTTAAAG
* * *
4458573 GAGTTTTTCCAAGATGATGAATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAACTATTCCAAGAT
131 AAGTTTTTCCAAGATGATGAAGTTTAAAGTTGTTGAGCCTCTACTTAAAGGAACTATTCCAAGAT
4458638 AAAGT
196 AAAGT
* * * *
4458643 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTT-CAAGATGATGAATTTT-AAAGTTATT
1 TTTTAAAGTTATTGAGCCTCTGCTCAGAGGAGCTTTTTCCAAGAT-ACGAATTTTAAAAGTCATT
* * * * * * * *
4458706 GAGC-TCTACTTAGAGGAGTTTTTTCAAGAT-A-GATTTTTAAATTTGTTGAGCCTCTGTTTAGA
65 GAGCATCTACTTAGAAGAGCTTTTTCAAGATAATGAATTTTAAAGTCGTTGAACCTCTGCTTAAA
* * * * * **
4458768 GAAGCTTTTT-C-A-A-GATGAAGTTTAAAGTTGTTGAGCCTTTGCTTAAATGAGCTTTTTTAAG
130 GAAG-TTTTTCCAAGATGATGAAGTTTAAAGTTGTTGAGCCTCTACTTAAAGGAACTATTCCAAG
4458829 ATAAA-T
194 ATAAAGT
* * *
4458835 TTTTAAAAGTTATTGAGTCTTTGCTCATAGGAGCTTTTT
1 TTTT-AAAGTTATTGAGCCTCTGCTCAGAGGAGCTTTTT
4458874 AAATTTTCAA
Statistics
Matches: 198, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
192 5 0.03
193 73 0.37
194 1 0.01
195 1 0.01
196 27 0.14
197 6 0.03
198 24 0.12
199 49 0.25
200 12 0.06
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (200 bp):
TTTTAAAGTTATTGAGCCTCTGCTCAGAGGAGCTTTTTCCAAGATACGAATTTTAAAAGTCATTG
AGCATCTACTTAGAAGAGCTTTTTCAAGATAATGAATTTTAAAGTCGTTGAACCTCTGCTTAAAG
AAGTTTTTCCAAGATGATGAAGTTTAAAGTTGTTGAGCCTCTACTTAAAGGAACTATTCCAAGAT
AAAGT
Found at i:4459051 original size:3 final size:3
Alignment explanation
Indices: 4459043--4459082 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
4459033 CATTTTATAT
*
4459043 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4459083 ATTTTTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4459099 original size:10 final size:10
Alignment explanation
Indices: 4459084--4459135 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
4459074 TATTATTATA
4459084 TTTTTTTCTT
1 TTTTTTTCTT
4459094 TTTTTTTCTT
1 TTTTTTTCTT
*
4459104 CTTTGTTTCTT
1 -TTTTTTTCTT
*
4459115 TCTTTTTCTT
1 TTTTTTTCTT
*
4459125 TTTTCTTCTT
1 TTTTTTTCTT
4459135 T
1 T
4459136 CTTTATCCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:4460172 original size:21 final size:23
Alignment explanation
Indices: 4460134--4460175 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4460124 CATTAAAATA
*
4460134 TTTATATTTGTTAGAATAATTTT
1 TTTATATTTGATAGAATAATTTT
4460157 TTTAT-TTTGATA-AATAATT
1 TTTATATTTGATAGAATAATT
4460176 AATTAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTATATTTGATAGAATAATTTT
Found at i:4460423 original size:3 final size:3
Alignment explanation
Indices: 4460415--4460440 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4460405 ACTAATAAAT
4460415 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
4460441 TAAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4463359 original size:18 final size:19
Alignment explanation
Indices: 4463338--4463410 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
4463328 TACAAATAAT
4463338 ATCATGCAATAATAATAT-
1 ATCATGCAATAATAATATA
**
4463356 ATCATGCAATTGTAATATA
1 ATCATGCAATAATAATATA
* *
4463375 ATCATTCAA-AATTTATATA
1 ATCATGCAATAA-TAATATA
* *
4463394 ATTATGCAAAAATAATA
1 ATCATGCAATAATAATA
4463411 ATATATAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 16 0.37
19 25 0.58
20 2 0.05
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (19 bp):
ATCATGCAATAATAATATA
Found at i:4463373 original size:16 final size:16
Alignment explanation
Indices: 4463332--4463365 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
4463322 TTATCATACA
4463332 AATAATATCATGCAAT
1 AATAATATCATGCAAT
4463348 AATAATATATCATGCAAT
1 AAT-A-ATATCATGCAAT
4463366 TGTAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 1 0.06
18 12 0.75
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (16 bp):
AATAATATCATGCAAT
Found at i:4463601 original size:30 final size:29
Alignment explanation
Indices: 4463565--4463621 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4463555 TCATTCAATT
*
4463565 AAAATAACAAGCAAAATAAAACAAAAAAAC
1 AAAATAAAAAGC-AAATAAAACAAAAAAAC
* *
4463595 AAAATAAAAATCAAATAAAATAAAAAA
1 AAAATAAAAAGCAAATAAAACAAAAAA
4463622 TTGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.79, C:0.09, G:0.02, T:0.11
Consensus pattern (29 bp):
AAAATAAAAAGCAAATAAAACAAAAAAAC
Found at i:4466855 original size:15 final size:15
Alignment explanation
Indices: 4466827--4466856 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4466817 AAATATTATT
*
4466827 ATTATTATTATTAAA
1 ATTATTAATATTAAA
4466842 ATTATTAATATTAAA
1 ATTATTAATATTAAA
4466857 TTGAAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTAATATTAAA
Found at i:4467483 original size:177 final size:176
Alignment explanation
Indices: 4467282--4467665 Score: 630
Period size: 177 Copynumber: 2.2 Consensus size: 176
4467272 AGAATTAATG
*
4467282 AAATGATCGAGATTAAACCACGAGTCAAAGGATAACAATAATCGAGATTAAACTGTGACTTTGAA
1 AAATGATCGAGATTAAACCACGAGTCAAAGGATAACAATAATCGAGAATAAACTGTGACTTTGAA
* **
4467347 TTAAAGAGATC-AGGATTGAACAACG-AATC-AGAGAATATTAAGACCGGGATTAAACTGCGAGT
66 TTAAAGAGATCGA-AATTGAAC--CGAAATCGA-AGAATATTAAGACCAAGATTAAACTGCGAGT
*
4467409 GAGAAAAATAAAAACGACTGGGATTAAATCACAAGTCAAAAAAATTATAA
127 GAGAAAAATAAAAACGACTGGGATTAAATCACAAGTCAAAAAAACTATAA
*
4467459 AAATGATCGGGATTAAACCACGAGTCAAAGGATAACAATAATCGAGAATAAACTGTGACTTTGAA
1 AAATGATCGAGATTAAACCACGAGTCAAAGGATAACAATAATCGAGAATAAACTGTGACTTTGAA
*
4467524 TTAAAGAGATCGAAATTGAACCGTAAATCGAAGAATATTAAGATCAAGATTAAACTGCGAGTGAG
66 TTAAAGAGATCGAAATTGAACCG-AAATCGAAGAATATTAAGACCAAGATTAAACTGCGAGTGAG
*
4467589 AAAAATAAAAACGATTGGGATTAAATCACAAGTCAAAAAAACTATAA
130 AAAAATAAAAACGACTGGGATTAAATCACAAGTCAAAAAAACTATAA
4467636 AAATGATCGAGATTAAACCACGAGTCAAAG
1 AAATGATCGAGATTAAACCACGAGTCAAAG
4467666 ATTAAAGATG
Statistics
Matches: 194, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
175 2 0.01
177 190 0.98
178 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (176 bp):
AAATGATCGAGATTAAACCACGAGTCAAAGGATAACAATAATCGAGAATAAACTGTGACTTTGAA
TTAAAGAGATCGAAATTGAACCGAAATCGAAGAATATTAAGACCAAGATTAAACTGCGAGTGAGA
AAAATAAAAACGACTGGGATTAAATCACAAGTCAAAAAAACTATAA
Found at i:4467722 original size:73 final size:73
Alignment explanation
Indices: 4467636--4468348 Score: 333
Period size: 73 Copynumber: 9.8 Consensus size: 73
4467626 AAAACTATAA
*
4467636 AAATGATCGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAA
1 AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAA
4467701 AATTAATG
66 AATTAATG
* * * * * *
4467709 AAATGATTGAGATTAAACCACAAGTCAAAGGA-TAACA-A-CAATCGAGATTAAA-C-TATA-TC
1 AAATGATTGAGATTAAACCACGAGTCAAA-GATTAA-AGATGACT-GGGACTAAACCGCA-AGTC
****
4467768 TTTGAATTAA--
62 AAAAAATTAATG
* * * * ** * * * * * * * * *
4467778 AGA-GATCGAAATTGAACTGCGAATCAGAGAATAAAGA-AATTGAGATTAAATCGCAAGTGAAAA
1 AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAA
**
4467841 AA-TAAAA
66 AATTAATG
* * * * * * * * ** *
4467848 AAATGACTGGGATTAAACCACGAGTCAAATATTAAAAATGATTTGGATTGAATGGCAAGTTAGAA
1 AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCA-AA
*
4467913 AGA-TAA--
65 AAATTAATG
* * * * * * * ** * *
4467919 AAAAGACT-AGGATTAAACCACAAGTTAGAA-AATAAAGAAATGACTAGGATTAAACTACGAGTT
1 AAATGATTGA-GATTAAACCACGAGTCA-AAGATTAAAG--ATGACTGGGACTAAACCGCAAGTC
* *
4467982 AGGAAAACT-ATAG
62 A-AAAAATTAAT-G
* * **
4467995 AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGTGACTAAATCGCAAGTCAGGA
1 AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAA
4468060 AATTAATG
66 AATTAATG
* ** * * * * *
4468068 AAATGA-TCAGGATTAAACCATAAGCCAAAGATTAAAGATGACTGAGACTGAACCGTAAGTTAGA
1 AAATGATTGA-GATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCA-A
*
4468132 AAGA-TAA--
64 AAAATTAATG
* *** * * * * *
4468139 AAGA-GATTGGGATTAAACCGTAAGTTAGAA-AATAAAGAAATGACTGGGATTAAACCACGAGTC
1 AA-ATGATTGAGATTAAACCACGAGTCA-AAGATTAAAG--ATGACTGGGACTAAACCGCAAGTC
*
4468202 AAGAAAACT-ATAG
62 AA-AAAATTAAT-G
* *
4468215 AAATGATCGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGTAAGTCAAAA
1 AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAA
4468280 AATTAATG
66 AATTAATG
* * * *
4468288 AAATGACT-AGGATTAAACCACGAGTCAAATATTAAAGATGACTGAGACTGAACCGCAAGTC
1 AAATGATTGA-GATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTC
4468349 TAGGAACTAT
Statistics
Matches: 477, Mismatches: 122, Indels: 82
0.70 0.18 0.12
Matches are distributed among these distances:
67 12 0.03
68 28 0.06
69 6 0.01
70 2 0.00
71 82 0.17
72 31 0.06
73 208 0.44
74 50 0.10
75 5 0.01
76 52 0.11
77 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.21
Consensus pattern (73 bp):
AAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAA
AATTAATG
Found at i:4467863 original size:37 final size:36
Alignment explanation
Indices: 4467821--4468308 Score: 125
Period size: 37 Copynumber: 13.3 Consensus size: 36
4467811 AAGAAATTGA
* * * *
4467821 GATTAAATCGCAAGTGAAAAAATAAAAAAATGACTGG
1 GATTAAACCACAAGTTAAAAAAT-AAAAAATGACTAG
* * * * * *
4467858 GATTAAACCACGAG-TCAAATATTAAAAATGATTTG
1 GATTAAACCACAAGTTAAAAAATAAAAAATGACTAG
* *** *
4467893 GATTGAATGGCAAGTTAGAAAGATAAAAAA-GACTAG
1 GATTAAACCACAAGTTA-AAAAATAAAAAATGACTAG
*
4467929 GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
1 GATTAAACCACAAGTTAAAAAATAAA-AAATGACTAG
* * * * *
4467966 GATTAAACTACGAGTTAGGAAAACTATAGAAATGA-TTG
1 GATTAAACCACAAGTTA--AAAAATA-AAAAATGACTAG
* * * * *
4468004 AGATTAAACCACGAG-TCAAAGATTAAAGATGACT-G
1 -GATTAAACCACAAGTTAAAAAATAAAAAATGACTAG
* * * * * * *
4468039 TGACTAAATCGCAAGTCAGGAAATTAATGAAATGA-TCAG
1 -GATTAAACCACAAGTTA-AAAAATAA-AAAATGACT-AG
* ** * * *
4468078 GATTAAACCATAAG-CCAAAGATTAAAGATGACT-G
1 GATTAAACCACAAGTTAAAAAATAAAAAATGACTAG
* * ** * * * *
4468112 AGACTGAACCGTAAGTTAGAAAGATAAAAGA-GATTGG
1 -GATTAAACCACAAGTTA-AAAAATAAAAAATGACTAG
** * *
4468149 GATTAAACCGTAAGTTAGAAAATAAAGAAATGACTGG
1 GATTAAACCACAAGTTAAAAAATAAA-AAATGACTAG
* * * *
4468186 GATTAAACCACGAGTCAAGAAAACTATAGAAATGA-TCG
1 GATTAAACCACAAGTTAA-AAAA-TA-AAAAATGACTAG
* * * * * *
4468224 AGATTAAACCACGAG-TCAAAGATTAAAGATGACTGG
1 -GATTAAACCACAAGTTAAAAAATAAAAAATGACTAG
* ** * *
4468260 GACTAAACCGTAAGTCAAAAAATTAATGAAATGACTAG
1 GATTAAACCACAAGTTAAAAAA-TAA-AAAATGACTAG
4468298 GATTAAACCAC
1 GATTAAACCAC
4468309 GAGTCAAATA
Statistics
Matches: 319, Mismatches: 103, Indels: 57
0.67 0.22 0.12
Matches are distributed among these distances:
34 1 0.00
35 82 0.26
36 63 0.20
37 83 0.26
38 41 0.13
39 47 0.15
40 2 0.01
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (36 bp):
GATTAAACCACAAGTTAAAAAATAAAAAATGACTAG
Found at i:4467932 original size:36 final size:37
Alignment explanation
Indices: 4467821--4468308 Score: 179
Period size: 35 Copynumber: 13.3 Consensus size: 37
4467811 AAGAAATTGA
* * * * * *
4467821 GATTAAATCGCAAGTGAAAAAATAAAAAAATGACTGG
1 GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
* * * * * *
4467858 GATTAAACCACGAGTCA-AATATTAA-AAATGATTTG
1 GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
* ***
4467893 GATTGAATGGCAAGTTAGAAAGATAAA-AAA-GACTAG
1 GATTAAACCACAAGTTAGAAA-ATAAAGAAATGACTAG
4467929 GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
1 GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
* * * *
4467966 GATTAAACTACGAGTTAGGAAAACTATAGAAATGA-TTG
1 GATTAAACCACAAGTTA-GAAAA-TAAAGAAATGACTAG
* * *
4468004 AGATTAAACCACGAGTCA-AAGATTAAAG--ATGACT-G
1 -GATTAAACCACAAGTTAGAA-AATAAAGAAATGACTAG
* * * * * *
4468039 TGACTAAATCGCAAGTCAGGAAATTAATGAAATGA-TCAG
1 -GATTAAACCACAAGTTA-GAAAATAAAGAAATGACT-AG
* ** *
4468078 GATTAAACCATAAGCCA-AAGATTAAAG--ATGACT-G
1 GATTAAACCACAAGTTAGAA-AATAAAGAAATGACTAG
* * ** * * *
4468112 AGACTGAACCGTAAGTTAGAAAGATAAA-AGA-GATTGG
1 -GATTAAACCACAAGTTAGAAA-ATAAAGAAATGACTAG
** *
4468149 GATTAAACCGTAAGTTAGAAAATAAAGAAATGACTGG
1 GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
* * * *
4468186 GATTAAACCACGAGTCAAGAAAACTATAGAAATGA-TCG
1 GATTAAACCACAAGT-TAGAAAA-TAAAGAAATGACTAG
* * * *
4468224 AGATTAAACCACGAGTCA-AAGATTAAAG--ATGACTGG
1 -GATTAAACCACAAGTTAGAA-AATAAAGAAATGACTAG
* ** * * *
4468260 GACTAAACCGTAAGTCAAAAAATTAATGAAATGACTAG
1 GATTAAACCACAAGTTAGAAAA-TAAAGAAATGACTAG
4468298 GATTAAACCAC
1 GATTAAACCAC
4468309 GAGTCAAATA
Statistics
Matches: 344, Mismatches: 73, Indels: 67
0.71 0.15 0.14
Matches are distributed among these distances:
34 1 0.00
35 82 0.24
36 80 0.23
37 81 0.24
38 49 0.14
39 51 0.15
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (37 bp):
GATTAAACCACAAGTTAGAAAATAAAGAAATGACTAG
Found at i:4468129 original size:147 final size:144
Alignment explanation
Indices: 4467978--4468359 Score: 364
Period size: 147 Copynumber: 2.6 Consensus size: 144
4467968 TTAAACTACG
*
4467978 AGTTAGGAAAACTATAGAAATGATTGAGATTAAACCACGAGTCAAAGATTAAAGATGACTGTGAC
1 AGTTA-GAAAA-TA-AGAAATGATTGAGATTAAACCACGAGTCAAA-ATTAAAGATGACTGAGAC
* * *
4468043 TAAATCGCAAGTC-AGGAAATTA-ATGAAATGATC-AGGATTAAACCATAAGCCAAAGATTAAAG
62 TAAACCGCAAGTCAAGGAAACTATA-GAAATGATCGA-GATTAAACCACAAGCCAAAGATTAAAG
*
4468105 ATGACTGAGACTGAACCGTA
125 ATGACTGAGACTAAACCGTA
* *** * * *
4468125 AGTTAGAAAGATAA-AAGA-GATTGGGATTAAACCGTAAGTTAGAAAATAAAGAAATGACTGGGA
1 AGTTAGAAA-ATAAGAA-ATGATTGAGATTAAACCACGAGTCA-AAATTAAAG--ATGACTGAGA
* * * * * *
4468188 TTAAACCACGAGTCAAGAAAACTATAGAAATGATCGAGATTAAACCACGAGTCAAAGATTAAAGA
61 CTAAACCGCAAGTCAAGGAAACTATAGAAATGATCGAGATTAAACCACAAGCCAAAGATTAAAGA
*
4468253 TGACTGGGACTAAACCGTA
126 TGACTGAGACTAAACCGTA
* * *
4468272 AGTCAAAAAATTAATGAAATGACT-AGGATTAAACCACGAGTCAAATATTAAAGATGACTGAGAC
1 AGTTAGAAAA-TAA-GAAATGATTGA-GATTAAACCACGAGTCAAA-ATTAAAGATGACTGAGAC
* *
4468336 TGAACCGCAAGTCTAGG-AACTATA
62 TAAACCGCAAGTCAAGGAAACTATA
4468360 TAAGACTAAG
Statistics
Matches: 187, Mismatches: 34, Indels: 29
0.75 0.14 0.12
Matches are distributed among these distances:
144 26 0.14
145 4 0.02
146 33 0.18
147 95 0.51
148 5 0.03
149 24 0.13
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (144 bp):
AGTTAGAAAATAAGAAATGATTGAGATTAAACCACGAGTCAAAATTAAAGATGACTGAGACTAAA
CCGCAAGTCAAGGAAACTATAGAAATGATCGAGATTAAACCACAAGCCAAAGATTAAAGATGACT
GAGACTAAACCGTA
Found at i:4468140 original size:220 final size:220
Alignment explanation
Indices: 4467824--4468347 Score: 712
Period size: 220 Copynumber: 2.4 Consensus size: 220
4467814 AAATTGAGAT
* * ** * * * * *
4467824 TAAATCGCAAGTGAAAAAA-TAAAAAAATGACTGGGATTAAACCACGAGTCAAATATTAAAAATG
1 TAAACCGCAAGTCAAAAAATTAATGAAATGACTAGGATTAAACCACAAGCCAAAGATTAAAGATG
* * **
4467888 ATTTG-GATTGAATGGCAAGTTAGAAAGATAAAAAAGACTAGGATTAAACCACAAGTTAGAAAAT
66 A-CTGAGACTGAACCGCAAGTTAGAAAGATAAAAAAGACTAGGATTAAACCACAAGTTAGAAAAT
* * * *
4467952 AAAGAAATGACTAGGATTAAACTACGAGTTAGGAAAACTATAGAAATGATTGAGATTAAACCACG
130 AAAGAAATGACTAGGATTAAACCACGAGTCAAGAAAACTATAGAAATGATCGAGATTAAACCACG
*
4468017 AGTCAAAGATTAAAGATGACTGTGAC
195 AGTCAAAGATTAAAGATGACTGGGAC
* ** *
4468043 TAAATCGCAAGTCAGGAAATTAATGAAATGA-TCAGGATTAAACCATAAGCCAAAGATTAAAGAT
1 TAAACCGCAAGTCAAAAAATTAATGAAATGACT-AGGATTAAACCACAAGCCAAAGATTAAAGAT
* * * * **
4468107 GACTGAGACTGAACCGTAAGTTAGAAAGATAAAAGAGATTGGGATTAAACCGTAAGTTAGAAAAT
65 GACTGAGACTGAACCGCAAGTTAGAAAGATAAAAAAGACTAGGATTAAACCACAAGTTAGAAAAT
*
4468172 AAAGAAATGACTGGGATTAAACCACGAGTCAAGAAAACTATAGAAATGATCGAGATTAAACCACG
130 AAAGAAATGACTAGGATTAAACCACGAGTCAAGAAAACTATAGAAATGATCGAGATTAAACCACG
4468237 AGTCAAAGATTAAAGATGACTGGGAC
195 AGTCAAAGATTAAAGATGACTGGGAC
* * * *
4468263 TAAACCGTAAGTCAAAAAATTAATGAAATGACTAGGATTAAACCACGAGTCAAATATTAAAGATG
1 TAAACCGCAAGTCAAAAAATTAATGAAATGACTAGGATTAAACCACAAGCCAAAGATTAAAGATG
4468328 ACTGAGACTGAACCGCAAGT
66 ACTGAGACTGAACCGCAAGT
4468348 CTAGGAACTA
Statistics
Matches: 265, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
219 19 0.07
220 245 0.92
221 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (220 bp):
TAAACCGCAAGTCAAAAAATTAATGAAATGACTAGGATTAAACCACAAGCCAAAGATTAAAGATG
ACTGAGACTGAACCGCAAGTTAGAAAGATAAAAAAGACTAGGATTAAACCACAAGTTAGAAAATA
AAGAAATGACTAGGATTAAACCACGAGTCAAGAAAACTATAGAAATGATCGAGATTAAACCACGA
GTCAAAGATTAAAGATGACTGGGAC
Found at i:4469395 original size:10 final size:9
Alignment explanation
Indices: 4469380--4469422 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
4469370 GAATCACTTC
*
4469380 TTTTTTCAT
1 TTTTTTTAT
4469389 TTTTTTTA-
1 TTTTTTTAT
4469397 TTTTTTTAGT
1 TTTTTTTA-T
4469407 TTTTTTGTAT
1 TTTTTT-TAT
4469417 TTTTTT
1 TTTTTT
4469423 CTTCTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.27
9 7 0.23
10 13 0.43
11 2 0.07
ACGTcount: A:0.09, C:0.02, G:0.05, T:0.84
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:4480774 original size:13 final size:14
Alignment explanation
Indices: 4480742--4480782 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
4480732 GTTTTGAAAT
4480742 AGATTTAGGG-TAA
1 AGATTTAGGGTTAA
*
4480755 AGATTTAGGGTTTA
1 AGATTTAGGGTTAA
*
4480769 AG-TTTAAGGTTAA
1 AGATTTAGGGTTAA
4480782 A
1 A
4480783 ACGCAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (14 bp):
AGATTTAGGGTTAA
Found at i:4481249 original size:34 final size:32
Alignment explanation
Indices: 4481195--4481258 Score: 76
Period size: 35 Copynumber: 1.9 Consensus size: 32
4481185 TTTATCATGT
* *
4481195 ATAAATATAAAAACTTAAAA-TAACAAAAATA
1 ATAAATATAAAAAATTAAAATTAAAAAAAATA
4481226 ATAATATATAAAAAAATTAAAAATTAAAAAAAA
1 ATAA-ATAT-AAAAAATT-AAAATTAAAAAAAA
4481259 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.15
32 4 0.15
33 7 0.26
34 4 0.15
35 8 0.30
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (32 bp):
ATAAATATAAAAAATTAAAATTAAAAAAAATA
Found at i:4481533 original size:28 final size:28
Alignment explanation
Indices: 4481470--4481533 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
4481460 ACGTGCGAAT
4481470 CCTCTATGCTCAAAACGACGTCGTTTTA
1 CCTCTATGCTCAAAACGACGTCGTTTTA
*
4481498 -GTCTTATGCTCAAAACGACGTCGTTTTA
1 CCTC-TATGCTCAAAACGACGTCGTTTTA
4481526 CCTCTATG
1 CCTCTATG
4481534 TTTTCTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (28 bp):
CCTCTATGCTCAAAACGACGTCGTTTTA
Found at i:4481773 original size:11 final size:11
Alignment explanation
Indices: 4481744--4481777 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4481734 GATCTTTGAA
*
4481744 TTTTTTTATCTC
1 TTTTTTT-TTTC
4481756 TTTTTTTTTTC
1 TTTTTTTTTTC
4481767 TTTTTTTTTTC
1 TTTTTTTTTTC
4481778 GGACGAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:4482203 original size:14 final size:15
Alignment explanation
Indices: 4482171--4482218 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
4482161 ATTTTTTTCC
*
4482171 ATTTTTTTAA-TATT
1 ATTTTTTAAATTATT
4482185 ATATTTTTAAATTATT
1 AT-TTTTTAAATTATT
4482201 ATTATTATTAAATTATT
1 ATT-TT-TTAAATTATT
4482218 A
1 A
4482219 ATATTAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 8 0.28
17 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTAAATTATT
Found at i:4482206 original size:17 final size:16
Alignment explanation
Indices: 4482181--4482224 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
4482171 ATTTTTTTAA
*
4482181 TATTATATTTTTAAAT
1 TATTATATTATTAAAT
4482197 TATTATTATTATTAAAT
1 TATTA-TATTATTAAAT
4482214 TATTAATATTA
1 TATT-ATATTA
4482225 AACTGAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 19 0.76
18 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATATTATTAAAT
Found at i:4482223 original size:14 final size:14
Alignment explanation
Indices: 4482177--4482226 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
4482167 TTCCATTTTT
* *
4482177 TTAATATTATATTT
1 TTAATATTAAATTA
4482191 TTAA-ATT--ATTA
1 TTAATATTAAATTA
*
4482202 TTATTATTAAATTA
1 TTAATATTAAATTA
4482216 TTAATATTAAA
1 TTAATATTAAA
4482227 CTGAAATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.20
12 3 0.10
13 3 0.10
14 18 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATATTAAATTA
Found at i:4483310 original size:15 final size:14
Alignment explanation
Indices: 4483265--4483320 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 14
4483255 TTGACAAAAA
*
4483265 AATTTAATAATTTA
1 AATTTAATAATTTG
*
4483279 AATTTAAAATGATTTG
1 AATTT--AATAATTTG
4483295 AATTTAAGTAATTTG
1 AATTTAA-TAATTTG
4483310 AATATTAATAA
1 AAT-TTAATAA
4483321 AACTATACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 7 0.20
15 12 0.34
16 16 0.46
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (14 bp):
AATTTAATAATTTG
Found at i:4488832 original size:25 final size:25
Alignment explanation
Indices: 4488791--4488861 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
4488781 GTTTAGAGTT
* * *
4488791 TTATTTATTTATTTATTATTTTTAA
1 TTATTTAATTATATATTATTTTAAA
4488816 TT-TTATAATTATATATT-TATTTAAA
1 TTATT-TAATTATATATTAT-TTTAAA
4488841 TTATTTAATTATA-ATTTATTT
1 TTATTTAATTATATA-TTATTT
4488862 ATTGTTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
24 4 0.11
25 31 0.82
26 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTTAATTATATATTATTTTAAA
Found at i:4488884 original size:4 final size:4
Alignment explanation
Indices: 4488790--4488864 Score: 50
Period size: 4 Copynumber: 19.5 Consensus size: 4
4488780 CGTTTAGAGT
* * * *
4488790 TTTA TTTA TTTA TTTA -TTA TTT- TTAA TTT- TATA ATTA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
4488835 TTTAA ATTA TTTA ATTA -TAA TTTA TTTA TT
1 TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TT
4488865 GTTTATAACA
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
3 9 0.17
4 41 0.77
5 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:4488888 original size:18 final size:18
Alignment explanation
Indices: 4488841--4488888 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
4488831 TTTATTTAAA
**
4488841 TTATTTAATTATAATTTAT
1 TTATTT-ATTATAACATAT
4488860 TTATTGT-TTATAACATAT
1 TTATT-TATTATAACATAT
4488878 TTATTTATTAT
1 TTATTTATTAT
4488889 TCATAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 18 0.72
19 5 0.20
20 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTTATTATAACATAT
Found at i:4488901 original size:23 final size:22
Alignment explanation
Indices: 4488854--4488932 Score: 104
Period size: 24 Copynumber: 3.5 Consensus size: 22
4488844 TTTAATTATA
* *
4488854 ATTTATTTATTGTTTATAACAT
1 ATTTATTTATTATTCATAACAT
4488876 ATTTATTTATTATTCATAAACAT
1 ATTTATTTATTATTCAT-AACAT
4488899 ATTTATTTAATTATTCATGAACAT
1 ATTTATTT-ATTATTCAT-AACAT
*
4488923 ATTCATTTAT
1 ATTTATTTAT
4488933 ATATATTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 15 0.29
23 15 0.29
24 21 0.41
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTTATTTATTATTCATAACAT
Found at i:4488957 original size:50 final size:46
Alignment explanation
Indices: 4488853--4488960 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 46
4488843 ATTTAATTAT
* * *
4488853 AATTTATTT-ATTGTTTATAACATATTTATTTATTATTCATAAACA
1 AATTTATTTAATTATTCATAACATATTCATTTATTATTCATAAACA
* * *
4488898 TATTTATTTAATTATTCATGAACATATTCATTTATATATATTTATAAAGA
1 AATTTATTTAATTATTCAT-AACATATTCA-TT-TAT-TATTCATAAACA
4488948 AATTTATTTAATT
1 AATTTATTTAATT
4488961 TAAATAAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
45 8 0.16
46 7 0.14
47 9 0.18
48 2 0.04
49 3 0.06
50 22 0.43
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (46 bp):
AATTTATTTAATTATTCATAACATATTCATTTATTATTCATAAACA
Found at i:4505175 original size:23 final size:23
Alignment explanation
Indices: 4505149--4505203 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
4505139 TCACTCCAAT
*
4505149 GGCTATTTTATCAAGGATTCAAC
1 GGCTACTTTATCAAGGATTCAAC
4505172 GGCTACTTTATCAAGGATTCAAC
1 GGCTACTTTATCAAGGATTCAAC
4505195 GGCTACTTT
1 GGCTACTTT
4505204 CACTTTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (23 bp):
GGCTACTTTATCAAGGATTCAAC
Found at i:4509459 original size:16 final size:16
Alignment explanation
Indices: 4509434--4509465 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4509424 TCCTGATGAC
*
4509434 ATATCTTTAACAATTG
1 ATATCCTTAACAATTG
4509450 ATATCCTTAACAATTG
1 ATATCCTTAACAATTG
4509466 GTATGAGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATCCTTAACAATTG
Found at i:4510434 original size:17 final size:17
Alignment explanation
Indices: 4510409--4510442 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4510399 TTCTTTGTTT
4510409 TCATATTTCTCAAACCA
1 TCATATTTCTCAAACCA
*
4510426 TCATTTTTCTCAAACCA
1 TCATATTTCTCAAACCA
4510443 AATCTATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (17 bp):
TCATATTTCTCAAACCA
Found at i:4515749 original size:54 final size:53
Alignment explanation
Indices: 4515671--4515775 Score: 174
Period size: 54 Copynumber: 2.0 Consensus size: 53
4515661 AGTCATAGGA
* * *
4515671 AATTATTATAAATAATGAGAATATAACAAAATAGTAAATAATTGTCTACAAGG
1 AATTATCATAAATAATGAAAATATAACAAAATAGTAAATAATTATCTACAAGG
4515724 AATTATCATAAAATAATGAAAATATAACAAAATAGTAAATAATTATCTACAA
1 AATTATCAT-AAATAATGAAAATATAACAAAATAGTAAATAATTATCTACAA
4515776 AGAAAAATTG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 8 0.17
54 40 0.83
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.30
Consensus pattern (53 bp):
AATTATCATAAATAATGAAAATATAACAAAATAGTAAATAATTATCTACAAGG
Found at i:4517365 original size:18 final size:17
Alignment explanation
Indices: 4517315--4517365 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
4517305 AAGATTTTTC
* *
4517315 TTTTTTTTCGAAAAGAT
1 TTTTTTTTCAAAAATAT
*
4517332 TTTTTTTT-AAATATAT
1 TTTTTTTTCAAAAATAT
4517348 ATTTTTTTTCAAAAATAT
1 -TTTTTTTTCAAAAATAT
4517366 CAATAGTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.18
17 16 0.57
18 7 0.25
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTTTTTTCAAAAATAT
Found at i:4518106 original size:51 final size:48
Alignment explanation
Indices: 4518027--4518166 Score: 129
Period size: 51 Copynumber: 2.9 Consensus size: 48
4518017 AATTTTCGTC
* * *
4518027 TTAATGAGAATTGATTTTGAAATCAAATCCCAAAAATCTCTCCTTATCATT
1 TTAATGTGAATTGATTATGAAATTAAATCCCAAAAATCTCTCC-TA-CA-T
* * * *
4518078 TTAATGTGAATTGATTATGGAATTAAATCTCGACAATCTCT-CTACAT
1 TTAATGTGAATTGATTATGAAATTAAATCCCAAAAATCTCTCCTACAT
** * * * *
4518125 CAAATGTCAATTGATTCTGAAATTAAATCGCACAAATCTCTC
1 TTAATGTGAATTGATTATGAAATTAAATCCCAAAAATCTCTC
4518167 AACCACGGTT
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
47 33 0.46
48 2 0.03
49 2 0.03
50 1 0.01
51 34 0.47
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (48 bp):
TTAATGTGAATTGATTATGAAATTAAATCCCAAAAATCTCTCCTACAT
Found at i:4518961 original size:85 final size:86
Alignment explanation
Indices: 4518872--4519048 Score: 191
Period size: 85 Copynumber: 2.1 Consensus size: 86
4518862 AAAAATTTGT
* *
4518872 AAGATTCT-AAACTTCATAGAGATTCTAAATTCACAAAGGTTCCAA-GTTCGCAAGAATTTTTAG
1 AAGATTCTCAAACTTCATAAAGATTCTAAATTCACAAA-GATCCAAGGTTCGCAAGAATTTTTAG
4518935 ATTCATAAAAAAAAAGAATT-AC
65 ATTCATAAAAAAAAA-AATTCAC
** * * * * * *
4518957 AAGATT-TCAAGTTTCGTAAAGGTTTTAGATTCACAAAGATGCAAGGTTCGCAAGGATTTTTAGA
1 AAGATTCTCAAACTTCATAAAGATTCTAAATTCACAAAGATCCAAGGTTCGCAAGAATTTTTAGA
** *
4519021 TTTGTAAGAAAAAAAATTCAC
66 TTCATAAAAAAAAAAATTCAC
4519042 AAGATTC
1 AAGATTC
4519049 CAAGTTTCGT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
84 10 0.13
85 65 0.87
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (86 bp):
AAGATTCTCAAACTTCATAAAGATTCTAAATTCACAAAGATCCAAGGTTCGCAAGAATTTTTAGA
TTCATAAAAAAAAAAATTCAC
Found at i:4519053 original size:85 final size:85
Alignment explanation
Indices: 4518900--4519061 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 85
4518890 GAGATTCTAA
* *
4518900 ATTCACAAAGGTTCCAAGTTCGCAAGAATTTTTAGATTCATAAAAAAAAAGAATTACAAGATTTC
1 ATTCACAAAGGATCCAAGTTCGCAAGAATTTTTAGATTCATAAAAAAAAAGAATTACAAGATTCC
4518965 AAGTTTCGTAAAGGTTTTAG
66 AAGTTTCGTAAAGGTTTTAG
* * ** *
4518985 ATTCACAAA-GATGCAAGGTTCGCAAGGATTTTTAGATTTGTAAGAAAAAA-AATTCACAAGATT
1 ATTCACAAAGGATCCAA-GTTCGCAAGAATTTTTAGATTCATAAAAAAAAAGAATT-ACAAGATT
4519048 CCAAGTTTCGTAAA
64 CCAAGTTTCGTAAA
4519062 AGTGAAAGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 9 0.13
85 59 0.87
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (85 bp):
ATTCACAAAGGATCCAAGTTCGCAAGAATTTTTAGATTCATAAAAAAAAAGAATTACAAGATTCC
AAGTTTCGTAAAGGTTTTAG
Found at i:4520420 original size:18 final size:16
Alignment explanation
Indices: 4520369--4520431 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 16
4520359 AGTTTAAGTC
*
4520369 TTCTTTTTTTCTCTTTT
1 TTCTTTTTTT-TGTTTT
* **
4520386 GTCTCTTTTTTAATTTT
1 TTCT-TTTTTTTGTTTT
4520403 TTCCCTTTTTTTTGTTTT
1 TT--CTTTTTTTTGTTTT
4520421 TTCTTTTTTTT
1 TTCTTTTTTTT
4520432 TTCTCATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 9 0.24
17 8 0.22
18 18 0.49
19 2 0.05
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTTGTTTT
Found at i:4520432 original size:17 final size:17
Alignment explanation
Indices: 4520369--4520432 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
4520359 AGTTTAAGTC
* *
4520369 TTCTTTTTTTCTCTTTT
1 TTCTTTTTTTTTATTTT
* * *
4520386 GTCTCTTTTTTAATTTT
1 TTCTTTTTTTTTATTTT
* *
4520403 TTCCCTTTTTTTTGTTTT
1 TT-CTTTTTTTTTATTTT
4520421 TTCTTTTTTTTT
1 TTCTTTTTTTTT
4520433 TCTCATTTTT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
17 22 0.63
18 13 0.37
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (17 bp):
TTCTTTTTTTTTATTTT
Found at i:4520454 original size:30 final size:29
Alignment explanation
Indices: 4520382--4520459 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 29
4520372 TTTTTTTCTC
* * *
4520382 TTTTGTCTCTTT-TTTAATTTTTTCCCTTT
1 TTTTTTCTCTTTCTTT-TTTTTTTCCATTT
*
4520411 TTTTTGT-TTTTTCTTTTTTTTTTCTCATTT
1 TTTTT-TCTCTTTCTTTTTTTTTTC-CATTT
*
4520441 TTTTTTCTCTTTCTCTTTT
1 TTTTTTCTCTTTCTTTTTT
4520460 GTTGACACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (29 bp):
TTTTTTCTCTTTCTTTTTTTTTTCCATTT
Found at i:4520818 original size:56 final size:57
Alignment explanation
Indices: 4520740--4520848 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 57
4520730 TTGTTTTTTC
* *
4520740 TTTTTTTTGGTGAAGCATATTGGCACTTTGTCCTATC-A-TTTTTACTTTTTTCTTT
1 TTTTTTTTGGTGAAGCACATTGGCACTTTGCCCTATCAATTTTTTACTTTTTTCTTT
* *
4520795 TTTTTTTTGGGTGAAGCACATTGGCATTTTGCCCTATCAATTTTTTATTTTTTT
1 TTTTTTTT-GGTGAAGCACATTGGCACTTTGCCCTATCAATTTTTTACTTTTTT
4520849 ATTTGTCAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
55 8 0.17
56 26 0.55
57 1 0.02
58 12 0.26
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (57 bp):
TTTTTTTTGGTGAAGCACATTGGCACTTTGCCCTATCAATTTTTTACTTTTTTCTTT
Found at i:4524647 original size:27 final size:27
Alignment explanation
Indices: 4524581--4524647 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
4524571 TTCTTACACT
*
4524581 TTTATTTAATTTATTATTATTAAAAGG
1 TTTATTTAAATTATTATTATTAAAAGG
** * *
4524608 TTTATTTTTATTATTATTTTTTAAA-G
1 TTTATTTAAATTATTATTATTAAAAGG
4524634 TTTATCTTAAATTA
1 TTTAT-TTAAATTA
4524648 ACAAAATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTATTTAAATTATTATTATTAAAAGG
Found at i:4526145 original size:119 final size:119
Alignment explanation
Indices: 4525930--4526166 Score: 420
Period size: 119 Copynumber: 2.0 Consensus size: 119
4525920 CCAAATAGAG
4525930 GGCTTATGTTATGCACATACAAATGAATGACAGATATATACAATAAATAGATAATTAGGCAAATA
1 GGCTTATGTTATGCACATACAAATGAATGACAGATATATACAATAAATAGATAATTAGGCAAATA
* *
4525995 TAAAAATGAAAAATAACCAGGTATACATAATGAAAATGAAAATAAATAATAAAT
66 TAAAAATGAAAAATAAACAGGTATACATAATGAAAAGGAAAATAAATAATAAAT
**
4526049 GGCTTATGTTATGCACATGTAAATGAATGACAGATATATACAATAAATAGATAATTAGGCAAATA
1 GGCTTATGTTATGCACATACAAATGAATGACAGATATATACAATAAATAGATAATTAGGCAAATA
* *
4526114 TAAGAATGAAAAATAAACAGGTATACTTAATGAAAAGGAAAATAAATAATAAA
66 TAAAAATGAAAAATAAACAGGTATACATAATGAAAAGGAAAATAAATAATAAA
4526167 GTAGATGTAA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 112 1.00
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (119 bp):
GGCTTATGTTATGCACATACAAATGAATGACAGATATATACAATAAATAGATAATTAGGCAAATA
TAAAAATGAAAAATAAACAGGTATACATAATGAAAAGGAAAATAAATAATAAAT
Found at i:4526648 original size:15 final size:15
Alignment explanation
Indices: 4526628--4526663 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4526618 ATTTTTTCTT
4526628 TTTTTTTTAAAAAGA
1 TTTTTTTTAAAAAGA
* *
4526643 TTTTTTTTAAATATA
1 TTTTTTTTAAAAAGA
4526658 TTTTTT
1 TTTTTT
4526664 AAAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTTTTAAAAAGA
Found at i:4526755 original size:5 final size:5
Alignment explanation
Indices: 4526745--4526791 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
4526735 AATGGGTTAG
* * * *
4526745 AAATA AAATA AAATC AAATC AAATC AAA-A AAATA AAATA AAACA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
4526792 AAGAAAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
4 3 0.08
5 35 0.92
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:4526790 original size:18 final size:19
Alignment explanation
Indices: 4526754--4526793 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4526744 GAAATAAAAT
* *
4526754 AAAATCAAATCAAATCAAA
1 AAAATAAAATCAAAACAAA
4526773 AAAATAAAAT-AAAACAAA
1 AAAATAAAATCAAAACAAA
4526791 AAA
1 AAA
4526794 GAAAAAACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (19 bp):
AAAATAAAATCAAAACAAA
Found at i:4526798 original size:24 final size:24
Alignment explanation
Indices: 4526749--4526800 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4526739 GGTTAGAAAT
* **
4526749 AAAATAAAATCAAATCAAATCAAA
1 AAAATAAAATCAAAACAAAAAAAA
4526773 AAAATAAAAT-AAAACAAAAAAGAA
1 AAAATAAAATCAAAACAAAAAA-AA
4526797 AAAA
1 AAAA
4526801 CCTGCAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.12
Consensus pattern (24 bp):
AAAATAAAATCAAAACAAAAAAAA
Found at i:4533354 original size:14 final size:13
Alignment explanation
Indices: 4533321--4533356 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4533311 ATAATCTTGA
4533321 ATTTTAAAAAGTT
1 ATTTTAAAAAGTT
*
4533334 ATTTTAAAAATTT
1 ATTTTAAAAAGTT
4533347 ATTGTTAAAA
1 ATT-TTAAAA
4533357 GGTTTCAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
ATTTTAAAAAGTT
Found at i:4534339 original size:15 final size:16
Alignment explanation
Indices: 4534321--4534354 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4534311 TTTTAAATTA
*
4534321 AAAAAATAA-ATTTTT
1 AAAAAATAATATATTT
4534336 AAAAAATAATATATTT
1 AAAAAATAATATATTT
4534352 AAA
1 AAA
4534355 TTAGATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAATAATATATTT
Found at i:4534931 original size:14 final size:14
Alignment explanation
Indices: 4534912--4534951 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
4534902 TTCGTTTTAC
4534912 TAAAAATAGTTTTT
1 TAAAAATAGTTTTT
*
4534926 TAAAAATA-ATTTT
1 TAAAAATAGTTTTT
4534939 TAAAAATTAGTTT
1 TAAAAA-TAGTTT
4534952 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 10 0.45
14 10 0.45
15 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
TAAAAATAGTTTTT
Found at i:4538103 original size:2 final size:2
Alignment explanation
Indices: 4538098--4538122 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4538088 TCTCTACCCC
4538098 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 A
4538123 CACATACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4541103 original size:40 final size:42
Alignment explanation
Indices: 4541027--4541112 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 42
4541017 GGTTTAGGAA
* * *
4541027 AAATCAAAACTTTTAGAGATGAATTAAGAAAGATAT-GA-AC
1 AAATCAAAACTTTTAAAGATAAATCAAGAAAGATATGGATAC
* *
4541067 AAATCAAAA-TTTCTAAAGATAAATCAATAAATATATGGATAC
1 AAATCAAAACTTT-TAAAGATAAATCAAGAAAGATATGGATAC
4541109 AAAT
1 AAAT
4541113 AATACGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 3 0.08
40 27 0.71
41 2 0.05
42 6 0.16
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (42 bp):
AAATCAAAACTTTTAAAGATAAATCAAGAAAGATATGGATAC
Found at i:4544053 original size:19 final size:19
Alignment explanation
Indices: 4544037--4544073 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4544027 TTTTAATATT
4544037 AATAATAATAGTAAATAAC
1 AATAATAATAGTAAATAAC
*
4544056 AATAATAATATTAAATAA
1 AATAATAATAGTAAATAA
4544074 AATCTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAATAATAGTAAATAAC
Found at i:4544394 original size:3 final size:3
Alignment explanation
Indices: 4544388--4544443 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
4544378 GGAATTATTA
* *
4544388 AAT AAT AAT AAT ATAT AAT ATAT AAT ATAT AA- ATT AAT AAT ATT AAT
1 AAT AAT AAT AAT A-AT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT
4544435 AAT AAT AAT
1 AAT AAT AAT
4544444 TTTTTATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 1 0.02
3 35 0.78
4 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:4544407 original size:7 final size:7
Alignment explanation
Indices: 4544389--4544441 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
4544379 GAATTATTAA
4544389 ATAATA-
1 ATAATAT
4544395 ATAATAT
1 ATAATAT
4544402 ATAATAT
1 ATAATAT
4544409 ATAATAT
1 ATAATAT
4544416 ATAA-AT
1 ATAATAT
4544422 -TAATAAT
1 ATAAT-AT
4544429 ATTAATA-
1 A-TAATAT
4544436 ATAATA
1 ATAATA
4544442 ATTTTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 3 0.07
6 13 0.31
7 21 0.50
8 1 0.02
9 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:4544741 original size:14 final size:14
Alignment explanation
Indices: 4544616--4544768 Score: 62
Period size: 14 Copynumber: 10.4 Consensus size: 14
4544606 CCTTTTAAAC
4544616 CCTAAAATCAAAAT
1 CCTAAAATCAAAAT
* *
4544630 CATAAAACCCTCTAAAT
1 CCTAAAA---TCAAAAT
*
4544647 CCTAAAATCAAAAC
1 CCTAAAATCAAAAT
*
4544661 CCCAAAATCAAAA-
1 CCTAAAATCAAAAT
* **
4544674 CCTTCAAACACTCCAACC
1 CC-T-AAA-A-TCAAAAT
4544692 CCTAAAA-CTAAAAT
1 CCTAAAATC-AAAAT
* * *
4544706 CCTAAACTCTTTAAAC
1 CCTAAAATC--AAAAT
4544722 CCTAAAATCAAAAT
1 CCTAAAATCAAAAT
* *
4544736 CCTAAACTCCAAA-
1 CCTAAAATCAAAAT
*
4544749 CCTTAAAATCTAAA-
1 CC-TAAAATCAAAAT
4544763 CCTAAA
1 CCTAAA
4544769 CCCTCCGAAC
Statistics
Matches: 105, Mismatches: 22, Indels: 25
0.69 0.14 0.16
Matches are distributed among these distances:
13 9 0.09
14 56 0.53
15 5 0.05
16 16 0.15
17 17 0.16
18 2 0.02
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTAAAATCAAAAT
Found at i:4544779 original size:29 final size:28
Alignment explanation
Indices: 4544643--4544784 Score: 92
Period size: 30 Copynumber: 4.9 Consensus size: 28
4544633 AAAACCCTCT
* * **
4544643 AAATCCTAAAATCAAAACCCCAAAATCA
1 AAATCCTAAACTCCAAACCTTAAAATCA
* *
4544671 AAA-CCTTCAAACACTCCAACCCCTAAAA-CTA
1 AAATCC-T--AA-ACTCCAAACCTTAAAATC-A
* *
4544702 AAATCCTAAACTCTTTAAACCCTAAAATCA
1 AAATCCTAAACTC--CAAACCTTAAAATCA
*
4544732 AAATCCTAAACTCCAAACCTTAAAATCT
1 AAATCCTAAACTCCAAACCTTAAAATCA
*
4544760 AAA-CCTAAACCCTCCGAACCTTAAA
1 AAATCCTAAA--CTCCAAACCTTAAA
4544785 TTTCAAAACC
Statistics
Matches: 93, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
27 8 0.09
28 23 0.25
29 15 0.16
30 27 0.29
31 18 0.19
32 2 0.02
ACGTcount: A:0.48, C:0.32, G:0.01, T:0.20
Consensus pattern (28 bp):
AAATCCTAAACTCCAAACCTTAAAATCA
Found at i:4544967 original size:22 final size:22
Alignment explanation
Indices: 4544937--4544983 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4544927 TAAATCCTTC
*
4544937 AAACATTAAAATTTGAAACCCT
1 AAACATTAAAATTTAAAACCCT
* *
4544959 AAACTTTAAATTTTAAAACCCT
1 AAACATTAAAATTTAAAACCCT
4544981 AAA
1 AAA
4544984 ACATCGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (22 bp):
AAACATTAAAATTTAAAACCCT
Found at i:4544995 original size:16 final size:16
Alignment explanation
Indices: 4544974--4545013 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4544964 TTAAATTTTA
4544974 AAACCCTAAAACATCG
1 AAACCCTAAAACATCG
*
4544990 AAACCCT-AAACCTCG
1 AAACCCTAAAACATCG
4545005 AAACCCTAA
1 AAACCCTAA
4545014 CCTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.47, C:0.35, G:0.05, T:0.12
Consensus pattern (16 bp):
AAACCCTAAAACATCG
Found at i:4561828 original size:20 final size:17
Alignment explanation
Indices: 4561784--4561817 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4561774 TTCTTTGTTT
*
4561784 TTATATTTCTCAAACCA
1 TTATTTTTCTCAAACCA
4561801 TTATTTTTCTCAAACCA
1 TTATTTTTCTCAAACCA
4561818 AATCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATTTTTCTCAAACCA
Found at i:4566821 original size:16 final size:16
Alignment explanation
Indices: 4566796--4566827 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4566786 TCCTGATGAC
*
4566796 ATATCTTTAACAATTG
1 ATATCCTTAACAATTG
4566812 ATATCCTTAACAATTG
1 ATATCCTTAACAATTG
4566828 GTATGAGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATCCTTAACAATTG
Found at i:4567830 original size:17 final size:17
Alignment explanation
Indices: 4567805--4567838 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4567795 TTCTTTGTTT
4567805 TCATATTTCTCAAACCA
1 TCATATTTCTCAAACCA
*
4567822 TCATTTTTCTCAAACCA
1 TCATATTTCTCAAACCA
4567839 AATCTATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (17 bp):
TCATATTTCTCAAACCA
Found at i:4573089 original size:17 final size:16
Alignment explanation
Indices: 4573040--4573089 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
4573030 AAGATTTTTC
* *
4573040 TTTTTTTTTGAAAAGA
1 TTTTTTTTTAAAAATA
*
4573056 TTTTTTTTTAAATATA
1 TTTTTTTTTAAAAATA
4573072 TTTTTTTTTCAAAAATA
1 TTTTTTTTT-AAAAATA
4573089 T
1 T
4573090 CAGTGGTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 22 0.76
17 7 0.24
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTTTTTTTAAAAATA
Found at i:4574651 original size:17 final size:16
Alignment explanation
Indices: 4574609--4574652 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
4574599 CAAGAATGAA
*
4574609 AAATTCGCAAGATTCT
1 AAATTCACAAGATTCT
4574625 AAACTTCACAGAGATTCT
1 AAA-TTCACA-AGATTCT
4574643 AAATTCACAA
1 AAATTCACAA
4574653 AGGTTCCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 11 0.44
18 10 0.40
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (16 bp):
AAATTCACAAGATTCT
Found at i:4574843 original size:67 final size:68
Alignment explanation
Indices: 4574731--4574886 Score: 199
Period size: 67 Copynumber: 2.3 Consensus size: 68
4574721 AGGTTTTAGA
* * * * *
4574731 TTCACAAAGATGCAAGGTTCGTAAGGATTTTTAGATTTACAAGAAA-AAA-ATTCACAAGATTCC
1 TTCACAAAGGTGCAAGGTTCGTAAGGACTTTCAAATTCACAAGAAAGAAAGATTCACAAGATT-C
4574794 AAGT
65 AAGT
* * **
4574798 TTCGCAAAGGTGAAAGGTTCGTAAGGACTTTCAAATTCACAAGAAAGAAAGATTTGCAAGATTCA
1 TTCACAAAGGTGCAAGGTTCGTAAGGACTTTCAAATTCACAAGAAAGAAAGATTCACAAGATTCA
4574863 AGT
66 AGT
*
4574866 TTCACAAAGGTGCAAGATTCG
1 TTCACAAAGGTGCAAGGTTCG
4574887 CAAGAAAGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
67 39 0.52
68 26 0.35
69 10 0.13
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (68 bp):
TTCACAAAGGTGCAAGGTTCGTAAGGACTTTCAAATTCACAAGAAAGAAAGATTCACAAGATTCA
AGT
Found at i:4574935 original size:51 final size:50
Alignment explanation
Indices: 4574832--4574941 Score: 157
Period size: 51 Copynumber: 2.2 Consensus size: 50
4574822 GGACTTTCAA
* *
4574832 ATTCACAAGAAAGAAAGATTTGCAAGATTCAAGTTTCACAAAGGTGCAAG
1 ATTCGCAAGAAAGAAAGATTCGCAAGATTCAAGTTTCACAAAGGTGCAAG
* * **
4574882 ATTCGCAAGAAAGAAAGATTCGTAAGATTTTAAGTTTCGTAAAGGTGCAAG
1 ATTCGCAAGAAAGAAAGATTCGCAAGA-TTCAAGTTTCACAAAGGTGCAAG
4574933 ATTCGCAAG
1 ATTCGCAAG
4574942 GACTTTCAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 24 0.45
51 29 0.55
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (50 bp):
ATTCGCAAGAAAGAAAGATTCGCAAGATTCAAGTTTCACAAAGGTGCAAG
Found at i:4575045 original size:137 final size:137
Alignment explanation
Indices: 4574887--4575159 Score: 336
Period size: 137 Copynumber: 2.0 Consensus size: 137
4574877 GCAAGATTCG
* * ** ** *
4574887 CAAGAAAGAAAGATTCGTAAGATTTTAAGTTTCGTAAAGGTGCAAGATTCGCAAGGACTTTC-AG
1 CAAGAAAGAAAAATTCATAAGATTCCAAGTTTCACAAAAGTGCAAGATTCGCAAGGACTTTCTA-
* * * * *
4574951 ATTCCCAAGAAAGAAAA-TTTTACAAGA-TTCTAAGTTTCATAAAGGTTTTAGATTTATAAAGAT
65 ATTCCCAA-AAAAAAAAGATTCACAAGATTTC-AAGTTTCATAAAGGTTCTAGATTTATAAAAAT
4575014 GCAAGGTTTA
128 GCAAGGTTTA
*
4575024 CAAGAAAGAAAAATTCATAAGATTCCAAGTTTCACAAAAGTGCAAGATTCGTAAGGACTTTCTAA
1 CAAGAAAGAAAAATTCATAAGATTCCAAGTTTCACAAAAGTGCAAGATTCGCAAGGACTTTCTAA
** * *
4575089 TTTGCAAAAAAAAAAGATTCACAAGATTTCAAGTTTCGTAAAGGTTCTAGATTTGTAAAAATGCA
66 TTCCCAAAAAAAAAAGATTCACAAGATTTCAAGTTTCATAAAGGTTCTAGATTTATAAAAATGCA
*
4575154 ATGTTT
131 AGGTTT
4575160 GCAAAGATTT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
136 7 0.06
137 104 0.90
138 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (137 bp):
CAAGAAAGAAAAATTCATAAGATTCCAAGTTTCACAAAAGTGCAAGATTCGCAAGGACTTTCTAA
TTCCCAAAAAAAAAAGATTCACAAGATTTCAAGTTTCATAAAGGTTCTAGATTTATAAAAATGCA
AGGTTTA
Found at i:4576148 original size:34 final size:33
Alignment explanation
Indices: 4576110--4576186 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
4576100 TTAGTTTAAG
* **
4576110 TTTTCCTTTTTTCTTTTT-TGTTTTCTTTTCCTTT
1 TTTTCCTTTTTACTTTTTCTCATTTCTTTT--TTT
4576144 TTTTCCTTTTTACTTTTTCTCATTTCTTTTTTT
1 TTTTCCTTTTTACTTTTTCTCATTTCTTTTTTT
4576177 TTTCTCCTTT
1 TTT-TCCTTT
4576187 GTTGACACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 6 0.16
34 23 0.61
35 9 0.24
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTTCCTTTTTACTTTTTCTCATTTCTTTTTTT
Found at i:4576541 original size:54 final size:54
Alignment explanation
Indices: 4576461--4576575 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
4576451 TCTTTGTTTG
*
4576461 TTTTTTTTTTTTTTTTGGCGAAGCATATTAGCACTTTATCCTATC-ATTTTTCT-
1 TTTTTTTTTTTTTTTTGGCGAAGCATATTAGCACTTTATCCCATCAATTTTT-TA
* * * *
4576514 TTTTTTCTTTTTTTTTGGGTGAAGCATATTAGCATTTTGTCCCATCAATTTTTTA
1 TTTTTT-TTTTTTTTTTGGCGAAGCATATTAGCACTTTATCCCATCAATTTTTTA
4576569 TTTTTTT
1 TTTTTTT
4576576 ATTTGTCAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
53 6 0.11
54 36 0.67
55 12 0.22
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (54 bp):
TTTTTTTTTTTTTTTTGGCGAAGCATATTAGCACTTTATCCCATCAATTTTTTA
Found at i:4578940 original size:16 final size:16
Alignment explanation
Indices: 4578919--4578959 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
4578909 ATGCATGGGA
4578919 ATGAATGCAATGATGC
1 ATGAATGCAATGATGC
4578935 ATGAATGCAATGATGC
1 ATGAATGCAATGATGC
4578951 ATGAATGCA
1 ATGAATGCA
4578960 TGTATACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (16 bp):
ATGAATGCAATGATGC
Found at i:4578942 original size:8 final size:8
Alignment explanation
Indices: 4578919--4578961 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
4578909 ATGCATGGGA
4578919 ATGAATGC
1 ATGAATGC
4578927 AATG-ATGC
1 -ATGAATGC
4578935 ATGAATGC
1 ATGAATGC
4578943 AATG-ATGC
1 -ATGAATGC
4578951 ATGAATGC
1 ATGAATGC
4578959 ATG
1 ATG
4578962 TATACATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 6 0.19
8 19 0.61
9 6 0.19
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (8 bp):
ATGAATGC
Found at i:4581314 original size:21 final size:22
Alignment explanation
Indices: 4581271--4581319 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
4581261 AGCTTTCTAG
*
4581271 GATTCAAATCTCATATTTTTTTA
1 GATTTAAATCTCATA-TTTTTTA
4581294 GATTTAAATCTCATA-TTTTTA
1 GATTTAAATCTCATATTTTTTA
4581315 GATTT
1 GATTT
4581320 TTTTGTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
23 14 0.56
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (22 bp):
GATTTAAATCTCATATTTTTTA
Found at i:4581466 original size:11 final size:11
Alignment explanation
Indices: 4581450--4581483 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
4581440 AACTGAACCG
4581450 AAAAGAAAAAA
1 AAAAGAAAAAA
4581461 AAAAGAGAAAAA
1 AAAAGA-AAAAA
4581473 AAAAGAAAAAA
1 AAAAGAAAAAA
4581484 TATAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:4581491 original size:3 final size:3
Alignment explanation
Indices: 4581485--4581540 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
4581475 AAGAAAAAAT
* *
4581485 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4581533 ATA A-A ATA
1 ATA ATA ATA
4581541 TAAAATGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4582411 original size:5 final size:5
Alignment explanation
Indices: 4582401--4582446 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
4582391 AATGGGTTAG
* *
4582401 AAATA AAATA AAATA AAATC AAA-A AAATA AAATA AAACA AAA-A AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
4582447 ACTTGCGATC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
4 7 0.19
5 30 0.81
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (5 bp):
AAATA
Found at i:4582446 original size:19 final size:19
Alignment explanation
Indices: 4582405--4582445 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4582395 GGTTAGAAAT
4582405 AAAATAAAATAAAATCAAA
1 AAAATAAAATAAAATCAAA
4582424 AAAATAAAATAAAA-CAAA
1 AAAATAAAATAAAATCAAA
4582442 AAAA
1 AAAA
4582446 AACTTGCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (19 bp):
AAAATAAAATAAAATCAAA
Found at i:4589108 original size:14 final size:14
Alignment explanation
Indices: 4589089--4589119 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4589079 TTATTCTTAA
4589089 TTTATTAGTTAATT
1 TTTATTAGTTAATT
*
4589103 TTTATTATTTAATT
1 TTTATTAGTTAATT
4589117 TTT
1 TTT
4589120 TACCAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTATTAGTTAATT
Found at i:4590370 original size:12 final size:12
Alignment explanation
Indices: 4590355--4590393 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4590345 TGAAAAGAGA
4590355 AAAAAAAATAAT
1 AAAAAAAATAAT
*
4590367 AAAATAAATAAT
1 AAAAAAAATAAT
*
4590379 -AAAATAATAAT
1 AAAAAAAATAAT
4590390 AAAA
1 AAAA
4590394 TGGTACCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAAATAAT
Found at i:4590370 original size:20 final size:20
Alignment explanation
Indices: 4590337--4590388 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
4590327 AAAAAAAAGC
4590337 AAAAAA-AATGAAAAGAGAA-A
1 AAAAAATAAT-AAAAGA-AATA
*
4590357 AAAAAATAATAAAATAAATA
1 AAAAAATAATAAAAGAAATA
*
4590377 ATAAAATAATAA
1 AAAAAATAATAA
4590389 TAAAATGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (20 bp):
AAAAAATAATAAAAGAAATA
Found at i:4590704 original size:48 final size:47
Alignment explanation
Indices: 4590515--4590745 Score: 273
Period size: 47 Copynumber: 4.8 Consensus size: 47
4590505 TTTTTAATTT
* * * *
4590515 AAAAAGCTCATCTAATCAAAGGCTCAACAACTTTAAAATTTATCATCTT
1 AAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTTAAAATTTATC-T-TG
* * * * * * * *
4590564 AGGAAAGCTCTTTTAAGTAGAGGCTCAACAACTTTAAAATTCATGTTG
1 A-AAAAGCTCCTCTAAGCAAAGGCTCAATAACTTTAAAATTTATCTTG
* * *
4590612 AAAAAGCTCCTCTAAACAAAGGCTTAATAACTTTAAAATCTATCTTG
1 AAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTTAAAATTTATCTTG
*
4590659 AAAAAACTCCTCTAAGCAAAGGCTCAATAACTTTAAAAATTTATCTTG
1 AAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTT-AAAATTTATCTTG
*
4590707 AAAAAGCTCCTCTAAGCAGAGGCTCAATAACTTTAAAAT
1 AAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTTAAAAT
4590746 CCTCTAAGCA
Statistics
Matches: 154, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
47 71 0.46
48 46 0.30
49 2 0.01
50 35 0.23
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (47 bp):
AAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTTAAAATTTATCTTG
Found at i:4590721 original size:95 final size:97
Alignment explanation
Indices: 4590515--4590746 Score: 281
Period size: 95 Copynumber: 2.4 Consensus size: 97
4590505 TTTTTAATTT
* * * * * * * * *
4590515 AAAAAGCTCATCTAATCAAAGGCTCAACAACTTTAAAATTTATCATCTTAGGAAAGCTCTTTTAA
1 AAAAAGCTCCTCTAAACAAAGGCTCAATAACTTTAAAATCTATCATCTGAGAAAAACTCCTCTAA
* * *
4590580 GTAGAGGCTCAACAACTTTAAAATTCATGTTG
66 GCAAAGGCTCAACAACTTTAAAATTCATCTTG
*
4590612 AAAAAGCTCCTCTAAACAAAGGCTTAATAACTTTAAAATCTATC-T-TGA-AAAAACTCCTCTAA
1 AAAAAGCTCCTCTAAACAAAGGCTCAATAACTTTAAAATCTATCATCTGAGAAAAACTCCTCTAA
* *
4590674 GCAAAGGCTCAATAACTTTAAAAATTTATCTTG
66 GCAAAGGCTCAACAACTTT-AAAATTCATCTTG
* *
4590707 AAAAAGCTCCTCTAAGCAGAGGCTCAATAACTTTAAAATC
1 AAAAAGCTCCTCTAAACAAAGGCTCAATAACTTTAAAATC
4590747 CTCTAAGCAG
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
94 26 0.22
95 50 0.43
96 1 0.01
97 39 0.34
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (97 bp):
AAAAAGCTCCTCTAAACAAAGGCTCAATAACTTTAAAATCTATCATCTGAGAAAAACTCCTCTAA
GCAAAGGCTCAACAACTTTAAAATTCATCTTG
Found at i:4590752 original size:31 final size:31
Alignment explanation
Indices: 4590714--4590776 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4590704 TTGAAAAAGC
4590714 TCCTCTAAGCAGAGGCTCAATAACTTTAAAA
1 TCCTCTAAGCAGAGGCTCAATAACTTTAAAA
4590745 TCCTCTAAGCAGAGGCTCAATAACTTTAAAA
1 TCCTCTAAGCAGAGGCTCAATAACTTTAAAA
4590776 T
1 T
4590777 TTTCATCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (31 bp):
TCCTCTAAGCAGAGGCTCAATAACTTTAAAA
Found at i:4590815 original size:80 final size:79
Alignment explanation
Indices: 4590661--4590825 Score: 258
Period size: 80 Copynumber: 2.1 Consensus size: 79
4590651 CTATCTTGAA
*
4590661 AAAACTCCTCTAAGCAAAGGCTCAATAACTTTAAAAATTTATCTTGAAAAAGCTCCTCTAAGCAG
1 AAAA-TCCTCTAAGCAAAGGCTCAATAACTTTAAAAATTTATCTTGAAAAAGCTCCTCTAAGCAA
4590726 AGGCTCAATAACTTT
65 AGGCTCAATAACTTT
* * * * *
4590741 AAAATCCTCTAAGCAGAGGCTCAATAACTTTAAAATTTTCATCTTGGAAAAGCTTCTCTAAGTAA
1 AAAATCCTCTAAGCAAAGGCTCAATAACTTTAAAAATTT-ATCTTGAAAAAGCTCCTCTAAGCAA
4590806 AGGCTCAATAACTTT
65 AGGCTCAATAACTTT
4590821 AAAAT
1 AAAAT
4590826 TTTCATCTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 33 0.42
80 45 0.58
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (79 bp):
AAAATCCTCTAAGCAAAGGCTCAATAACTTTAAAAATTTATCTTGAAAAAGCTCCTCTAAGCAAA
GGCTCAATAACTTT
Done.