Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 60 of 126
Found at i:17650968 original size:40 final size:40
Alignment explanation
Indices: 17650923--17650999 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
17650913 CAAATTTTAT
* ** *
17650923 AGTTTTGCCACTGGTTTTCTAGCTTTTACAATTTTGCAAC
1 AGTTTTACCACTAATTTTCTAGATTTTACAATTTTGCAAC
* *
17650963 AGTTTTACCACTAATTTTCTAGATTTTATAGTTTTGC
1 AGTTTTACCACTAATTTTCTAGATTTTACAATTTTGC
17651000 CACTGGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (40 bp):
AGTTTTACCACTAATTTTCTAGATTTTACAATTTTGCAAC
Found at i:17650974 original size:69 final size:69
Alignment explanation
Indices: 17650894--17651152 Score: 271
Period size: 69 Copynumber: 3.9 Consensus size: 69
17650884 CAAATTTTAT
* *
17650894 AGTTTTGCCACTAGTTTTTCAAATTTTATAGTTTTGCCACTGGTTTTCTAGCTTTTACAATTTTG
1 AGTTTTGCCACTAGTTTTTCAGATTTTATAGTTTTGCCACTGGTTTTCTAACTTTTACAATTTTG
17650959 CAAC
66 CAAC
* *
17650963 AGTTTTACCACTA-ATTTTCTAGATTTTATAGTTTTGCCACTGGTTTT-TCAACTTTTACAATTT
1 AGTTTTGCCACTAGTTTTTC-AGATTTTATAGTTTTGCCACTGGTTTTCT-AACTTTTACAATTT
* *
17651026 TGCCAT
64 TGCAAC
*
17651032 TGTTTTGCCACT-GTTTTTCAGATTTTATAGTTTTGCCACT-GTTTT-T--C---T--AATTTT-
1 AGTTTTGCCACTAGTTTTTCAGATTTTATAGTTTTGCCACTGGTTTTCTAACTTTTACAATTTTG
*
17651086 --AT
66 CAAC
* * * *
17651088 AGTTTTGCCACT-GATTTTCCAGATTTTATAATTTTACCACTGGTTTTCTAGCTTTTACAATTTT
1 AGTTTTGCCACTAG-TTTTTCAGATTTTATAGTTTTGCCACTGGTTTTCTAACTTTTACAATTTT
17651152 G
65 G
17651153 GCACTATTTT
Statistics
Matches: 163, Mismatches: 13, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
56 14 0.09
57 24 0.15
58 5 0.03
59 7 0.04
61 2 0.01
64 2 0.01
66 6 0.04
67 6 0.04
68 27 0.17
69 70 0.43
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.51
Consensus pattern (69 bp):
AGTTTTGCCACTAGTTTTTCAGATTTTATAGTTTTGCCACTGGTTTTCTAACTTTTACAATTTTG
CAAC
Found at i:17651058 original size:39 final size:40
Alignment explanation
Indices: 17650993--17651076 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
17650983 AGATTTTATA
*
17650993 GTTTTGCCACTGGTTTTTCAACTTTTACAATTTTGCCATT
1 GTTTTGCCACTGGTTTTTCAACTTTTACAATTTTGCCACT
* *
17651033 GTTTTGCCACT-GTTTTTCAGA-TTTTATAGTTTTGCCACT
1 GTTTTGCCACTGGTTTTTCA-ACTTTTACAATTTTGCCACT
17651072 GTTTT
1 GTTTT
17651077 TCTAATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 28 0.70
40 12 0.30
ACGTcount: A:0.15, C:0.18, G:0.14, T:0.52
Consensus pattern (40 bp):
GTTTTGCCACTGGTTTTTCAACTTTTACAATTTTGCCACT
Found at i:17651064 original size:28 final size:29
Alignment explanation
Indices: 17651033--17651163 Score: 158
Period size: 29 Copynumber: 4.6 Consensus size: 29
17651023 TTTTGCCATT
17651033 GTTTTGCCACTGTTTTTC-AGATTTTATA
1 GTTTTGCCACTGTTTTTCTAGATTTTATA
17651061 GTTTTGCCACTGTTTTTCTA-ATTTTATA
1 GTTTTGCCACTGTTTTTCTAGATTTTATA
* *
17651089 GTTTTGCCACTGATTTTCCAGATTTTATA
1 GTTTTGCCACTGTTTTTCTAGATTTTATA
* * * * *
17651118 ATTTTACCACTGGTTTTCTAGCTTTTACA
1 GTTTTGCCACTGTTTTTCTAGATTTTATA
* * *
17651147 ATTTTGGCACTATTTTT
1 GTTTTGCCACTGTTTTT
17651164 TAAAAAAAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (29 bp):
GTTTTGCCACTGTTTTTCTAGATTTTATA
Found at i:17651162 original size:57 final size:56
Alignment explanation
Indices: 17651034--17651162 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 56
17651024 TTTGCCATTG
* * * * * * *
17651034 TTTTGCCACTGTTTTTCAGATTTTATAGTTTTGCCACTGTTTTTCTAATTTTATAG
1 TTTTGCCACTATTTTCCAGATTTTATAATTTTACCACTGGTTTTCTAATTTTACAA
*
17651090 TTTTGCCACTGATTTTCCAGATTTTATAATTTTACCACTGGTTTTCTAGCTTTTACAA
1 TTTTGCCACT-ATTTTCCAGATTTTATAATTTTACCACTGGTTTTCTA-ATTTTACAA
*
17651148 TTTTGGCACTATTTT
1 TTTTGCCACTATTTT
17651163 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 10 0.16
57 37 0.60
58 15 0.24
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (56 bp):
TTTTGCCACTATTTTCCAGATTTTATAATTTTACCACTGGTTTTCTAATTTTACAA
Found at i:17651426 original size:29 final size:29
Alignment explanation
Indices: 17651393--17651448 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
17651383 TACAATATGC
*
17651393 ATGATGTGGTAAATACTATTTGATTAATT
1 ATGATATGGTAAATACTATTTGATTAATT
*
17651422 ATGATATGGTAAATATTATTTGATTAA
1 ATGATATGGTAAATACTATTTGATTAA
17651449 GTATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (29 bp):
ATGATATGGTAAATACTATTTGATTAATT
Found at i:17651468 original size:74 final size:74
Alignment explanation
Indices: 17651347--17651498 Score: 198
Period size: 74 Copynumber: 2.1 Consensus size: 74
17651337 GTAAAATATG
* * **
17651347 TATGACATGGTAAATACTATTTGATTGATAATGCTATACAATATGCATGATGTGGTAAATACTAT
1 TATGACATGGTAAATACTATTTGATTAATAATGCCATACAATATGCATGACATGGTAAATACTAT
17651412 TTGATTAAT
66 TTGATTAAT
* * * * *
17651421 TATGATATGGTAAATATTATTTGATTAAGT-ATTCCATACGATATGCATGACATGGTAAATATTA
1 TATGACATGGTAAATACTATTTGATTAA-TAATGCCATACAATATGCATGACATGGTAAATACTA
*
17651485 TTTGATTGAT
65 TTTGATTAAT
17651495 TATG
1 TATG
17651499 CTATATGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
74 66 0.99
75 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (74 bp):
TATGACATGGTAAATACTATTTGATTAATAATGCCATACAATATGCATGACATGGTAAATACTAT
TTGATTAAT
Found at i:17651478 original size:45 final size:45
Alignment explanation
Indices: 17651422--17651543 Score: 154
Period size: 45 Copynumber: 2.7 Consensus size: 45
17651412 TTGATTAATT
*
17651422 ATGATATGGTAAATATTATTTGATTAAGTATTCCATACGATATGC
1 ATGATATGGTAAATATTATTTGATTAAGTATGCCATACGATATGC
* * * * * *
17651467 ATGACATGGTAAATATTATTTGATTGATTATGCTATATGATATGT
1 ATGATATGGTAAATATTATTTGATTAAGTATGCCATACGATATGC
* * *
17651512 ATGATGTGGTAAATACTATTTGATTAATTATG
1 ATGATATGGTAAATATTATTTGATTAAGTATG
17651544 ATATGGTAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
ATGATATGGTAAATATTATTTGATTAAGTATGCCATACGATATGC
Found at i:17651550 original size:29 final size:29
Alignment explanation
Indices: 17651511--17651567 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
17651501 ATATGATATG
*
17651511 TATGATGTGGTAAATACTATTTGATTAAT
1 TATGATATGGTAAATACTATTTGATTAAT
*
17651540 TATGATATGGTAAATATTATTTGATTAA
1 TATGATATGGTAAATACTATTTGATTAA
17651568 GTATTCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.46
Consensus pattern (29 bp):
TATGATATGGTAAATACTATTTGATTAAT
Found at i:17651550 original size:74 final size:74
Alignment explanation
Indices: 17651467--17651909 Score: 344
Period size: 74 Copynumber: 6.0 Consensus size: 74
17651457 TACGATATGC
* * *
17651467 ATGACATGGTAAATATTATTTGATTGATTATGCTATATGATATGTATGATGTGGTAAATACTATT
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTATT
17651532 TGATTAATT
66 TGATTAATT
* * * * * * * *
17651541 ATGATATGGTAAATATTATTTGATTAAGTATTCTATACGATAAGCATGACACGGTAAATACCATT
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTATT
17651606 TGATTGATTATGT
66 TGATT-A--AT-T
* * *
17651619 ATGCATGACATGGTAAATATTATTTGATTGATTATGCTATACGATATGTATGATATGGTAAATAT
1 ATG-AT---ATGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATATGGTAAATAC
*
17651684 TATTTGA-CAGATT
62 TATTTGATTA-ATT
* *** * ** * * *
17651697 ATGCTATATGATATGCATGACATGA-TAAATAT--TATTTGAT-TG-AT--TAT-GT---TA-TA
1 ATG--ATATGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTA
* * **
17651750 --CGA-CATGT
64 TTTGATTAATT
17651758 ATGATATGGTAAATATTATTTTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTAT
1 ATGATATGGTAAATATTA-TTTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTAT
17651823 TTGATTAATT
65 TTGATTAATT
* * * *
17651833 ATGATATGGTAAATATTATTTGATT-ACGTATTCTATATGATATGCATGACATGGTAAATATTAT
1 ATGATATGGTAAATATTATTTGATTGA-TTATGCTATATGATATGCATGATATGGTAAATACTAT
*
17651897 TTGATTGATT
65 TTGATTAATT
17651907 ATG
1 ATG
17651910 CTATATGATA
Statistics
Matches: 287, Mismatches: 56, Indels: 52
0.73 0.14 0.13
Matches are distributed among these distances:
59 10 0.03
60 3 0.01
61 9 0.03
62 4 0.01
63 7 0.02
64 4 0.01
65 4 0.01
67 3 0.01
68 4 0.01
69 3 0.01
71 4 0.01
72 4 0.01
73 7 0.02
74 113 0.39
75 26 0.09
76 11 0.04
77 2 0.01
78 8 0.03
79 6 0.02
80 1 0.00
82 54 0.19
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (74 bp):
ATGATATGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTATT
TGATTAATT
Found at i:17651553 original size:119 final size:119
Alignment explanation
Indices: 17651342--17651617 Score: 462
Period size: 119 Copynumber: 2.3 Consensus size: 119
17651332 AGATTGTAAA
* *
17651342 ATATGTATGACATGGTAAATACTATTTGATTGATAATGCTATACAATATGCATGATGTGGTAAAT
1 ATATGCATGACATGGTAAATACTATTTGATTGATTATGCTATACAATATGCATGATGTGGTAAAT
17651407 ACTATTTGATTAATTATGATATGGTAAATATTATTTGATTAAGTATTCCATACG
66 ACTATTTGATTAATTATGATATGGTAAATATTATTTGATTAAGTATTCCATACG
* ** *
17651461 ATATGCATGACATGGTAAATATTATTTGATTGATTATGCTATATGATATGTATGATGTGGTAAAT
1 ATATGCATGACATGGTAAATACTATTTGATTGATTATGCTATACAATATGCATGATGTGGTAAAT
*
17651526 ACTATTTGATTAATTATGATATGGTAAATATTATTTGATTAAGTATTCTATACG
66 ACTATTTGATTAATTATGATATGGTAAATATTATTTGATTAAGTATTCCATACG
* * *
17651580 ATAAGCATGACACGGTAAATACCATTTGATTGATTATG
1 ATATGCATGACATGGTAAATACTATTTGATTGATTATG
17651618 TATGCATGAC
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 146 1.00
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (119 bp):
ATATGCATGACATGGTAAATACTATTTGATTGATTATGCTATACAATATGCATGATGTGGTAAAT
ACTATTTGATTAATTATGATATGGTAAATATTATTTGATTAAGTATTCCATACG
Found at i:17651634 original size:37 final size:37
Alignment explanation
Indices: 17651584--17651654 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
17651574 TATACGATAA
17651584 GCATGACACGGTAAATACCATTTGATTGATTATGTAT
1 GCATGACACGGTAAATACCATTTGATTGATTATGTAT
* **
17651621 GCATGACATGGTAAATATTATTTGATTGATTATG
1 GCATGACACGGTAAATACCATTTGATTGATTATG
17651655 CTATACGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (37 bp):
GCATGACACGGTAAATACCATTTGATTGATTATGTAT
Found at i:17651680 original size:45 final size:45
Alignment explanation
Indices: 17651618--17651835 Score: 310
Period size: 45 Copynumber: 4.8 Consensus size: 45
17651608 ATTGATTATG
*
17651618 TATGCATGACATGGTAAATATTATTTGATTGATTATGCTATACGA
1 TATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGA
* ** *
17651663 TATGTATGATATGGTAAATATTATTTGACAGATTATGCTATATGA
1 TATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGA
* * *
17651708 TATGCATGACATGATAAATATTATTTGATTGATTATGTTATACGA
1 TATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGA
* * *
17651753 CATGTATGATATGGTAAATATTATTTTGATTGATTATGCTATATGA
1 TATGCATGATATGGTAAATATTA-TTTGATTGATTATGCTATACGA
* *
17651799 TATGCATGATATGGTAAATACTATTTGATTAATTATG
1 TATGCATGATATGGTAAATATTATTTGATTGATTATG
17651836 ATATGGTAAA
Statistics
Matches: 150, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 110 0.73
46 40 0.27
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
TATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGA
Found at i:17651736 original size:90 final size:91
Alignment explanation
Indices: 17651614--17651835 Score: 358
Period size: 90 Copynumber: 2.5 Consensus size: 91
17651604 TTTGATTGAT
*
17651614 TATG-TATGCATGACATGGTAAATATTATTTGATTGATTATGCTATACGATATGTATGATATGGT
1 TATGATATGCATGACATGGTAAATATTATTTGATTGATTATGCTATACGACATGTATGATATGGT
17651678 AAATATTA-TTTGACAGATTATGCTA
66 AAATATTATTTTGACAGATTATGCTA
* *
17651703 TATGATATGCATGACATGATAAATATTATTTGATTGATTATGTTATACGACATGTATGATATGGT
1 TATGATATGCATGACATGGTAAATATTATTTGATTGATTATGCTATACGACATGTATGATATGGT
**
17651768 AAATATTATTTTGATTGATTATGCTA
66 AAATATTATTTTGACAGATTATGCTA
* * *
17651794 TATGATATGCATGATATGGTAAATACTATTTGATTAATTATG
1 TATGATATGCATGACATGGTAAATATTATTTGATTGATTATG
17651836 ATATGGTAAA
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
89 4 0.03
90 65 0.53
91 53 0.43
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (91 bp):
TATGATATGCATGACATGGTAAATATTATTTGATTGATTATGCTATACGACATGTATGATATGGT
AAATATTATTTTGACAGATTATGCTA
Found at i:17651902 original size:45 final size:45
Alignment explanation
Indices: 17651833--17652082 Score: 281
Period size: 45 Copynumber: 5.6 Consensus size: 45
17651823 TTGATTAATT
* *
17651833 ATGATATGGTAAATATTATTTGATT-ACGTATTCTATATGATATGC
1 ATGATATGATAAATATTATTTGATTGA-TTATTCTATATGATATGC
* * *
17651878 ATGACATGGTAAATATTATTTGATTGATTATGCTATATGATATGC
1 ATGATATGATAAATATTATTTGATTGATTATTCTATATGATATGC
* * *
17651923 ATGATATGATAAATATTATTTGACTAATTATGT-TATATGATATGA
1 ATGATATGATAAATATTATTTGATTGATTAT-TCTATATGATATGC
* * * * *
17651968 ATGACATAACAAATATTATTTGATTGATTATAT-TATACGATATGT
1 ATGATATGATAAATATTATTTGATTGATTAT-TCTATATGATATGC
* **
17652013 ATGATATGATAAATATTATTTGATTGATTATGCTATACAATATGC
1 ATGATATGATAAATATTATTTGATTGATTATTCTATATGATATGC
* * *
17652058 ATGATGTGGTAAATACTATTTGATT
1 ATGATATGATAAATATTATTTGATT
17652083 AACTGTGATA
Statistics
Matches: 176, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 175 0.99
46 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (45 bp):
ATGATATGATAAATATTATTTGATTGATTATTCTATATGATATGC
Found at i:17651927 original size:119 final size:120
Alignment explanation
Indices: 17651713--17652327 Score: 587
Period size: 119 Copynumber: 5.0 Consensus size: 120
17651703 TATGATATGC
* * *
17651713 ATGACATGATAAATATTATTTGATTGATTATGTTATACGACATGTATGATATGGTAAATATTATT
1 ATGACATGATAAATATTATTTGATTGAGTATGTTATACGACATGCATGACATGGTAAATATTATT
* *
17651778 TTGATTGATTATGCTATATGATATGCATGATATGGTAAATACTATTTGATTAATT
66 TTGATTGATTATGCTATATGATATGCATGATATGATAAATACTATTTGACTAATT
* * * *
17651833 ATGATATGGTAAATATTATTTGATT-ACGTAT-TCTATATGATATGCATGACATGGTAAATATTA
1 ATGACATGATAAATATTATTTGATTGA-GTATGT-TATACGACATGCATGACATGGTAAATATTA
*
17651896 -TTTGATTGATTATGCTATATGATATGCATGATATGATAAATATTATTTGACTAATTATGTTAT
64 TTTTGATTGATTATGCTATATGATATGCATGATATGATAAATACTATTTGACT-A--A---T-T
* * * * * * *
17651959 ATGATATGAATGACATAACAAATATTATTTGATTGATTATATTATACGATATGTATGATATGATA
1 ATG--A--CATG--AT---AAATATTATTTGATTGAGTATGTTATACGACATGCATGACATGGTA
** * * * *
17652024 AATATTA-TTTGATTGATTATGCTATACAATATGCATGATGTGGTAAATACTATTTGATTAACT
57 AATATTATTTTGATTGATTATGCTATATGATATGCATGATATGATAAATACTATTTGACTAATT
* * * * * * * * *
17652087 GTGATATGGTAAATATTATTTAATTGATTATGCTATACAATATGCATGATATGGTAAATATTA-T
1 ATGACATGATAAATATTATTTGATTGAGTATGTTATACGACATGCATGACATGGTAAATATTATT
* ** * * *
17652151 TTGATTGATTATGCTATACGATCA-GCACAATGTGGTAAATACTATTTGATTAATT
66 TTGATTGATTATGCTATATGAT-ATGCATGATATGATAAATACTATTTGACTAATT
* * * * *
17652206 ATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGCATGATATGGTAAATATTA-T
1 ATGACATGATAAATATTATTTGATTGAGTATGTTATACGACATGCATGACATGGTAAATATTATT
* * * *
17652270 TTGATTGATTATGCTATATGATATTCATGATATGGTAAATATTATTTGATTAATT
66 TTGATTGATTATGCTATATGATATGCATGATATGATAAATACTATTTGACTAATT
17652325 ATG
1 ATG
17652328 TTATACGATA
Statistics
Matches: 424, Mismatches: 49, Indels: 45
0.82 0.09 0.09
Matches are distributed among these distances:
118 1 0.00
119 256 0.60
120 54 0.13
122 2 0.00
124 3 0.01
125 1 0.00
126 5 0.01
128 4 0.01
130 3 0.01
132 2 0.00
134 1 0.00
135 90 0.21
136 2 0.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (120 bp):
ATGACATGATAAATATTATTTGATTGAGTATGTTATACGACATGCATGACATGGTAAATATTATT
TTGATTGATTATGCTATATGATATGCATGATATGATAAATACTATTTGACTAATT
Found at i:17652072 original size:90 final size:89
Alignment explanation
Indices: 17651832--17652082 Score: 313
Period size: 90 Copynumber: 2.8 Consensus size: 89
17651822 TTTGATTAAT
* * *
17651832 TATGATATGGTAAATATTATTTGATTACGTATTCTATATGATATGCATGACATGGTAAATATTAT
1 TATGATATGATAAATATTATTTGATTA-TTATGCTATATGATATGCATGACATGGTAAATATTAT
* *
17651897 TTGATTGATTATGCTATATGATATG
65 TTGATTGATTATACTATACGATATG
* * * * ***
17651922 CATGATATGATAAATATTATTTGACTAATTATGTTATATGATATGAATGACATAACAAATATTAT
1 TATGATATGATAAATATTATTTGA-TTATTATGCTATATGATATGCATGACATGGTAAATATTAT
*
17651987 TTGATTGATTATATTATACGATATG
65 TTGATTGATTATACTATACGATATG
** ** *
17652012 TATGATATGATAAATATTATTTGATTGATTATGCTATACAATATGCATGATGTGGTAAATACTAT
1 TATGATATGATAAATATTATTTGATT-ATTATGCTATATGATATGCATGACATGGTAAATATTAT
17652077 TTGATT
65 TTGATT
17652083 AACTGTGATA
Statistics
Matches: 134, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 131 0.98
91 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (89 bp):
TATGATATGATAAATATTATTTGATTATTATGCTATATGATATGCATGACATGGTAAATATTATT
TGATTGATTATACTATACGATATG
Found at i:17652104 original size:74 final size:74
Alignment explanation
Indices: 17652014--17652156 Score: 250
Period size: 74 Copynumber: 1.9 Consensus size: 74
17652004 ACGATATGTA
* *
17652014 TGATATGATAAATATTATTTGATTGATTATGCTATACAATATGCATGATGTGGTAAATACTATTT
1 TGATATGATAAATATTATTTAATTGATTATGCTATACAATATGCATGATATGGTAAATACTATTT
17652079 GATTAACTG
66 GATTAACTG
* *
17652088 TGATATGGTAAATATTATTTAATTGATTATGCTATACAATATGCATGATATGGTAAATATTATTT
1 TGATATGATAAATATTATTTAATTGATTATGCTATACAATATGCATGATATGGTAAATACTATTT
17652153 GATT
66 GATT
17652157 GATTATGCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (74 bp):
TGATATGATAAATATTATTTAATTGATTATGCTATACAATATGCATGATATGGTAAATACTATTT
GATTAACTG
Found at i:17652187 original size:45 final size:45
Alignment explanation
Indices: 17652090--17652208 Score: 159
Period size: 45 Copynumber: 2.6 Consensus size: 45
17652080 ATTAACTGTG
* **
17652090 ATATGGTAAATATTATTTAATTGATTATGCTATACAATATGCATG
1 ATATGGTAAATATTATTTGATTGATTATGCTATACAATATGCACA
*
17652135 ATATGGTAAATATTATTTGATTGATTATGCTATACGATCA-GCACA
1 ATATGGTAAATATTATTTGATTGATTATGCTATACAAT-ATGCACA
* * *
17652180 ATGTGGTAAATACTATTTGATTAATTATG
1 ATATGGTAAATATTATTTGATTGATTATG
17652209 ATATGGTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 65 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (45 bp):
ATATGGTAAATATTATTTGATTGATTATGCTATACAATATGCACA
Found at i:17652210 original size:74 final size:74
Alignment explanation
Indices: 17652132--17652282 Score: 214
Period size: 74 Copynumber: 2.0 Consensus size: 74
17652122 TACAATATGC
* * *
17652132 ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATCA-GCACAATGTGGTAAATACTAT
1 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGAT-ATGCACAATATGGTAAATACTAT
17652196 TTGATTAATT
65 TTGATTAATT
* ** *
17652206 ATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGCATGATATGGTAAATATTATT
1 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCACAATATGGTAAATACTATT
*
17652271 TGATTGATT
66 TGATTAATT
17652280 ATG
1 ATG
17652283 CTATATGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 1 0.01
74 67 0.99
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (74 bp):
ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCACAATATGGTAAATACTATT
TGATTAATT
Found at i:17652359 original size:90 final size:90
Alignment explanation
Indices: 17652189--17652377 Score: 317
Period size: 90 Copynumber: 2.1 Consensus size: 90
17652179 AATGTGGTAA
*
17652189 ATACTATTTGATTAATT-ATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGCAT
1 ATACTATATGA-T-ATTCATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGCAT
17652253 GATATGGTAAATATTATTTGATTGATT
64 GATATGGTAAATATTATTTGATTGATT
* * *
17652280 ATGCTATATGATATTCATGATATGGTAAATATTATTTGATTAATTATGTTATACGATATGCGTGA
1 ATACTATATGATATTCATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGCATGA
17652345 TATGGTAAATATTATTTGATTGATT
66 TATGGTAAATATTATTTGATTGATT
17652370 ATACTATA
1 ATACTATA
17652378 CGACACACAT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
89 3 0.03
90 80 0.87
91 9 0.10
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (90 bp):
ATACTATATGATATTCATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGCATGA
TATGGTAAATATTATTTGATTGATT
Found at i:17652392 original size:45 final size:45
Alignment explanation
Indices: 17652206--17652380 Score: 269
Period size: 45 Copynumber: 3.9 Consensus size: 45
17652196 TTGATTAATT
* *
17652206 ATGATATGGTAAATATTATTTGATTAAGTATGTTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTAATTATGCTATACGATATGC
* * *
17652251 ATGATATGGTAAATATTATTTGATTGATTATGCTATATGATATTC
1 ATGATATGGTAAATATTATTTGATTAATTATGCTATACGATATGC
*
17652296 ATGATATGGTAAATATTATTTGATTAATTATGTTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTAATTATGCTATACGATATGC
* * *
17652341 GTGATATGGTAAATATTATTTGATTGATTATACTATACGA
1 ATGATATGGTAAATATTATTTGATTAATTATGCTATACGA
17652381 CACACATGAT
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 117 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (45 bp):
ATGATATGGTAAATATTATTTGATTAATTATGCTATACGATATGC
Found at i:17652608 original size:36 final size:36
Alignment explanation
Indices: 17652567--17652637 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
17652557 CTATATGTGT
* * * *
17652567 GATATGATAAATGTTATTTGATTGATTATGCTATAC
1 GATATGATAAATATTATCTGATTAATTAAGCTATAC
*
17652603 GATATGGTAAATATTATCTGATTAATTAAGCTATA
1 GATATGATAAATATTATCTGATTAATTAAGCTATA
17652638 TGATGTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (36 bp):
GATATGATAAATATTATCTGATTAATTAAGCTATAC
Found at i:17653545 original size:11 final size:13
Alignment explanation
Indices: 17653510--17653546 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
17653500 TTTCTTTCTG
17653510 CCATTTCCA-TTT
1 CCATTTCCATTTT
17653522 CCATTTCCATTTT
1 CCATTTCCATTTT
17653535 CC-TTT-CATTTT
1 CCATTTCCATTTT
17653546 C
1 C
17653547 AAAATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.29
12 12 0.50
13 5 0.21
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (13 bp):
CCATTTCCATTTT
Found at i:17657865 original size:22 final size:21
Alignment explanation
Indices: 17657830--17657876 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17657820 GTGTCTCAAG
*
17657830 AAAATTATAAAAAAAAAAGAAA
1 AAAATAAT-AAAAAAAAAGAAA
* *
17657852 AAAATAATAGAAAAAAAGAAG
1 AAAATAATAAAAAAAAAGAAA
17657873 AAAA
1 AAAA
17657877 GATACATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAATAATAAAAAAAAAGAAA
Found at i:17657873 original size:24 final size:22
Alignment explanation
Indices: 17657830--17657876 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
17657820 GTGTCTCAAG
*
17657830 AAAATTATAAAAAAAAAAGAAA
1 AAAATAATAAAAAAAAAAGAAA
17657852 AAAATAATAGAAAAAAAGAAGAAA
1 AAAATAATA-AAAAAAA-AAGAAA
17657876 A
1 A
17657877 GATACATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 7 0.32
24 7 0.32
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAATAATAAAAAAAAAAGAAA
Found at i:17660859 original size:141 final size:141
Alignment explanation
Indices: 17660703--17660978 Score: 407
Period size: 142 Copynumber: 2.0 Consensus size: 141
17660693 AAAAGTTCTC
* *
17660703 TTTTTAAAACAAAATCACTATTTT-TTTAAAAATTAAAATTTTTATTTCGAAATAGTTAAAAAAA
1 TTTTTAAAACAAAATCACTATTTTACTTAAAAATTAAAATTTTTATTTCGAAATAATTAAAAAAA
* *
17660767 TAAAACTTTGTTTAAAAATTTAAA-ATTTTCTTCTTTCAAATGAC-TAAAAACAGATTTTTAATT
66 TAAAACTTTGTTTAAAAATTTAAACTTTTTC-T-TTTAAAATGACTTAAAAA-AGA-TTTTAATT
17660830 TTAAAAATCTAATTT
127 TTAAAAATCTAATTT
* *
17660845 TTTTTTAAA-AAAATCACTATTTTACTTATAAATTAAAATTTTTATTTCGAAATAATTAAAAAAA
1 TTTTTAAAACAAAATCACTATTTTACTTAAAAATTAAAATTTTTATTTCGAAATAATTAAAAAAA
* * *
17660909 TCAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAAATGCCTTAAAAAAGATTTTATTTTTAA
66 TAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAAATGACTTAAAAAAGATTTTAATTTTAA
17660974 AAATC
131 AAATC
17660979 AAAACTATTA
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
140 16 0.13
141 26 0.21
142 75 0.61
143 5 0.04
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (141 bp):
TTTTTAAAACAAAATCACTATTTTACTTAAAAATTAAAATTTTTATTTCGAAATAATTAAAAAAA
TAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAAATGACTTAAAAAAGATTTTAATTTTAA
AAATCTAATTT
Found at i:17660973 original size:50 final size:48
Alignment explanation
Indices: 17660919--17661093 Score: 142
Period size: 50 Copynumber: 3.5 Consensus size: 48
17660909 TCAAACTTTG
*
17660919 TTTAAAAATTTAAACTTTTTCTTTTAAAATGCCTTAAAAAAGATTTTATT
1 TTTAAAAATCTAAAC-TTTTCTTTT-AAATGCCTTAAAAAAGATTTTATT
* * * * ***
17660969 TTTAAAAATCAAAACTATTATTTCGAAATAG--TTAAAAAA-ATCAAACTTT
1 TTTAAAAATCTAAACTTTTCTTT-TAAAT-GCCTTAAAAAAGATTTTA--TT
*
17661018 GTTTAAAAATTTAAACTTTTTCTTTTAAATGCC-TAAAATATAGATTTTTATT
1 -TTTAAAAATCTAAAC-TTTTCTTTTAAATGCCTTAAAA-A-AGA-TTTTATT
17661070 TTTAAAAATCTAAACTTTTCTTTT
1 TTTAAAAATCTAAACTTTTCTTTT
17661094 TTTAAAGAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
47 3 0.03
48 8 0.08
49 13 0.14
50 45 0.47
51 21 0.22
52 3 0.03
53 1 0.01
54 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (48 bp):
TTTAAAAATCTAAACTTTTCTTTTAAATGCCTTAAAAAAGATTTTATT
Found at i:17661004 original size:100 final size:101
Alignment explanation
Indices: 17660886--17661085 Score: 343
Period size: 100 Copynumber: 2.0 Consensus size: 101
17660876 ATTAAAATTT
17660886 TTATTTCGAAATAATTAAAAAAATCAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAAATGC
1 TTATTTCGAAATAATTAAAAAAATCAAACTTTGTTTAAAAATTTAAACTTTTTCTTTT-AAATGC
17660951 CTTAAAA-A-AGA-TTTTATTTTTAAAAATCAAAACTA
65 C-TAAAATATAGATTTTTATTTTTAAAAATCAAAACTA
*
17660986 TTATTTCGAAATAGTTAAAAAAATCAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAATGCC
1 TTATTTCGAAATAATTAAAAAAATCAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAATGCC
*
17661051 TAAAATATAGATTTTTATTTTTAAAAATCTAAACT
66 TAAAATATAGATTTTTATTTTTAAAAATCAAAACT
17661086 TTTCTTTTTT
Statistics
Matches: 95, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
98 5 0.05
99 8 0.08
100 60 0.63
101 22 0.23
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (101 bp):
TTATTTCGAAATAATTAAAAAAATCAAACTTTGTTTAAAAATTTAAACTTTTTCTTTTAAATGCC
TAAAATATAGATTTTTATTTTTAAAAATCAAAACTA
Found at i:17662275 original size:30 final size:28
Alignment explanation
Indices: 17662237--17662321 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
17662227 AGGGTTTTTC
17662237 TTTAATTTTAAACATTACATACTTTTAA
1 TTTAATTTTAAACATTACATACTTTTAA
* * *
17662265 TTATATATTTTAAA-A--AAATTATGTTTTTA
1 TT-TA-ATTTTAAACATTACA-TA-CTTTTAA
17662294 TTTAATTTTAAACATTACATACTTTTAA
1 TTTAATTTTAAACATTACATACTTTTAA
17662322 AGGGTATGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
27 10 0.23
28 12 0.27
29 12 0.27
30 10 0.23
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (28 bp):
TTTAATTTTAAACATTACATACTTTTAA
Found at i:17662494 original size:17 final size:17
Alignment explanation
Indices: 17662462--17662508 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
17662452 AATTGAACAA
17662462 ATTTTTATAATTTTATAAT
1 ATTTTTAT--TTTTATAAT
17662481 ATTTTTATTTTTATAAT
1 ATTTTTATTTTTATAAT
17662498 -TTATTTATTTT
1 ATT-TTTATTTT
17662509 GAACCAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.07
17 17 0.63
19 8 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTATTTTTATAAT
Found at i:17662784 original size:24 final size:25
Alignment explanation
Indices: 17662723--17662783 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
17662713 TTTTATATTT
17662723 AAAA-TCATTTTTATTATGTAATAA
1 AAAATTCATTTTTATTATGTAATAA
17662747 AAAATTCATTTTTATTATGTAATAA
1 AAAATTCATTTTTATTATGTAATAA
17662772 AAAATTCATTTT
1 AAAATTCATTTT
17662784 ACATGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.11
25 32 0.89
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (25 bp):
AAAATTCATTTTTATTATGTAATAA
Found at i:17668830 original size:26 final size:24
Alignment explanation
Indices: 17668785--17668835 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
17668775 TCAAAATTTA
17668785 TTAT-TTTTTGTAAAAAATATAATT
1 TTATATTTTT-TAAAAAATATAATT
*
17668809 TTATATTTTTTAAAAATTATATATT
1 TTATATTTTTTAAAAAATATA-ATT
17668834 TT
1 TT
17668836 TTTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATATTTTTTAAAAAATATAATT
Found at i:17668836 original size:26 final size:24
Alignment explanation
Indices: 17668780--17668846 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
17668770 TCTTTTCAAA
17668780 ATTTATTAT-TTTTTGTAAAAAATAT
1 ATTT-TTATATTTTT-TAAAAAATAT
*
17668805 AATTTTATATTTTTTAAAAATTATAT
1 ATTTTTATATTTTTTAAAAA--ATAT
* *
17668831 ATTTTTTTAATTTTTA
1 ATTTTTATATTTTTTA
17668847 TGTTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 10 0.29
25 8 0.23
26 17 0.49
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTTTATATTTTTTAAAAAATAT
Found at i:17671290 original size:13 final size:13
Alignment explanation
Indices: 17671272--17671296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17671262 AACTCTATTT
17671272 TTAGGATTAATAA
1 TTAGGATTAATAA
17671285 TTAGGATTAATA
1 TTAGGATTAATA
17671297 TTATTATATT
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTAGGATTAATAA
Found at i:17675655 original size:15 final size:15
Alignment explanation
Indices: 17675635--17675665 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17675625 TTTTAGTCAC
17675635 TTATGTTTGAAATGT
1 TTATGTTTGAAATGT
*
17675650 TTATGTTTGCAATGT
1 TTATGTTTGAAATGT
17675665 T
1 T
17675666 ACGTTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.19, T:0.55
Consensus pattern (15 bp):
TTATGTTTGAAATGT
Found at i:17675830 original size:14 final size:14
Alignment explanation
Indices: 17675811--17675842 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
17675801 GAGAATAAAT
17675811 ATTTAATTAAATAA
1 ATTTAATTAAATAA
*
17675825 ATTTAATTAATTAA
1 ATTTAATTAAATAA
17675839 ATTT
1 ATTT
17675843 TTAAATCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAATTAAATAA
Found at i:17676127 original size:110 final size:108
Alignment explanation
Indices: 17675916--17676145 Score: 347
Period size: 110 Copynumber: 2.1 Consensus size: 108
17675906 CTTCATTTTC
*
17675916 TTTCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAGTTTGAATATTTAAAACCCATTA
1 TTTCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAGCTTGAATATTTAAAACCCATTA
17675981 ACCAAAGATTCAATATTTTGGTTCCAATATCTTCTTCTAGTTAAG
66 ACCAAAGATTCAATATTTTGGTTCCAATA--TTCTTCTAGTTAAG
*
17676026 TTTCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAAACCCA-
1 TTTCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTC-AAGCTTGAATATTT-AAAACCCAT
17676090 TAACCAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTTCTA-TTAAG
64 TAACC-AAAGATTCAATAT-TTTGGTTCCAATA--TTC-TTCTAGTTAAG
17676139 TTTCTTT
1 TTTCTTT
17676146 GAGTTAATGG
Statistics
Matches: 113, Mismatches: 2, Indels: 7
0.93 0.02 0.06
Matches are distributed among these distances:
110 40 0.35
111 17 0.15
112 21 0.19
113 30 0.27
114 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (108 bp):
TTTCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAGCTTGAATATTTAAAACCCATTA
ACCAAAGATTCAATATTTTGGTTCCAATATTCTTCTAGTTAAG
Found at i:17684793 original size:36 final size:36
Alignment explanation
Indices: 17684680--17684783 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
17684670 AATATAATCA
*
17684680 GTCACATGGCACGAAGAACATATCCACATATTTTCT
1 GTCACATGGCATGAAGAACATATCCACATATTTTCT
* * *
17684716 GCCTCATGGCATGAAGAACATATGCACATATTTTCT
1 GTCACATGGCATGAAGAACATATCCACATATTTTCT
* *
17684752 GTCACATGGCATGAAGAACATACCCATATATT
1 GTCACATGGCATGAAGAACATATCCACATATT
17684784 CACTTTCACA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (36 bp):
GTCACATGGCATGAAGAACATATCCACATATTTTCT
Found at i:17684897 original size:23 final size:23
Alignment explanation
Indices: 17684862--17685127 Score: 379
Period size: 23 Copynumber: 11.6 Consensus size: 23
17684852 ATCTTAATTC
17684862 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17684885 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
17684908 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17684931 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17684954 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
17684977 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17685000 TTTGAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
17685023 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17685046 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17685069 CTTAAGCACAAATCAAATTAATA
1 TTTAAGCACAAATCACATTAATA
* ** * *
17685092 TTTAATCTTAAATCATAATAATA
1 TTTAAGCACAAATCACATTAATA
17685115 TTTAAGCACAAAT
1 TTTAAGCACAAAT
17685128 ATAAAAACAC
Statistics
Matches: 212, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 212 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:17686664 original size:53 final size:53
Alignment explanation
Indices: 17686539--17686779 Score: 220
Period size: 53 Copynumber: 4.5 Consensus size: 53
17686529 ATGCAAAAAG
* * *
17686539 GTTCGATGACTT-TGTGTCATCGAGAGTATATGAATCCTATTAAGGATGAAC-A
1 GTTCGATGA-TTATGTATCATCGTGAGTATATGAATCCTATTAAGGATTAACAA
* * * * * * * *
17686591 GGTCTGATTAGTATGAATCATTGCGAGTATATGAATCCTACTACGGATTAACAA
1 GTTC-GATGATTATGTATCATCGTGAGTATATGAATCCTATTAAGGATTAACAA
* * * *
17686645 TTTCGATGATTATGTATCATCGTGAGTCTATGAATCCTATTATGGATTAACAG
1 GTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTAAGGATTAACAA
* * * *
17686698 GTCCGATGATTATGTATCATCGTGAATATATGAATCCTATCACA-GATTTAA-AG
1 GTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTA-AGGA-TTAACAA
* **
17686751 GTTCGATGACTATGGGTCATCGTGAGTAT
1 GTTCGATGATTATGTATCATCGTGAGTAT
17686780 TAAATGAAAT
Statistics
Matches: 152, Mismatches: 32, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
52 4 0.03
53 141 0.93
54 7 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (53 bp):
GTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTAAGGATTAACAA
Found at i:17686756 original size:106 final size:105
Alignment explanation
Indices: 17686535--17686779 Score: 287
Period size: 106 Copynumber: 2.3 Consensus size: 105
17686525 GTAAATGCAA
* *
17686535 AAAGGTTCGATGACTT-TGTGTCATCGAGAGTATATGAATCCTATTAAGGATGAACAGGTCTGAT
1 AAAGGTTCGATGA-TTATGTGTCATCGTGAGTATATGAATCCTATTAAGGATGAACAGGTCCGAT
* * * *
17686599 TAGTATGAATCATTGCGAGTATATGAATCCTACTACGGATT
65 GAGTATGAATCATCGCGAATATATGAATCCTACTACAGATT
** * * * *
17686640 AACAATTTCGATGATTATGTATCATCGTGAGTCTATGAATCCTATTATGGATTAACAGGTCCGAT
1 AA-AGGTTCGATGATTATGTGTCATCGTGAGTATATGAATCCTATTAAGGATGAACAGGTCCGAT
* * *
17686705 GATTATGTATCATCGTGAATATATGAATCCTA-TCACAGATTT
65 GAGTATGAATCATCGCGAATATATGAATCCTACT-ACAGA-TT
* *
17686747 AAAGGTTCGATGACTATGGGTCATCGTGAGTAT
1 AAAGGTTCGATGATTATGTGTCATCGTGAGTAT
17686780 TAAATGAAAT
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
105 5 0.04
106 106 0.92
107 4 0.03
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (105 bp):
AAAGGTTCGATGATTATGTGTCATCGTGAGTATATGAATCCTATTAAGGATGAACAGGTCCGATG
AGTATGAATCATCGCGAATATATGAATCCTACTACAGATT
Found at i:17698669 original size:53 final size:53
Alignment explanation
Indices: 17698589--17698831 Score: 310
Period size: 53 Copynumber: 4.6 Consensus size: 53
17698579 AAATGCAAAA
* * *
17698589 AGGTTCGATGACTT-TGTGTCATCGTGAGTATATCAATCCTATTACAGATGAAC
1 AGGTTCGATGA-TTATGTATCATCGTGAGTATATGAATCCTATTACAGATTAAC
* * *
17698642 AGGTTTGATGATTATGTATCATCGTGAGTATATGAATCCTACTACGGATTAAC
1 AGGTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTACAGATTAAC
* *
17698695 AGGTCCGATGATTATGTATCATCGTGAGTCTATGAATCCTATTACAGATTAAC
1 AGGTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTACAGATTAAC
* * * * *
17698748 ATGTCCAATGATTATGTATCATCGTGAGTATATGAATCCTATCACGGATTTAA-
1 AGGTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTACAGA-TTAAC
* * *
17698801 AGGTTTGATGACTATGTGTCATCGTGAGTAT
1 AGGTTCGATGATTATGTATCATCGTGAGTAT
17698832 TAAATGAAAT
Statistics
Matches: 166, Mismatches: 22, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
52 2 0.01
53 160 0.96
54 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (53 bp):
AGGTTCGATGATTATGTATCATCGTGAGTATATGAATCCTATTACAGATTAAC
Found at i:17698779 original size:106 final size:106
Alignment explanation
Indices: 17698587--17698831 Score: 343
Period size: 106 Copynumber: 2.3 Consensus size: 106
17698577 GTAAATGCAA
***
17698587 AAAGGTTCGATGACTT-TGTGTCATCGTGAGTATATCAATCCTATTACAGATGAACAGGTTTGAT
1 AAAGGTTCGATGA-TTATGTGTCATCGTGAGTATATCAATCCTATTACAGATGAACAGGTCCAAT
17698651 GATTATGTATCATCGTGAGTATATGAATCCTA-CTACGGA-TT
65 GATTATGTATCATCGTGAGTATATGAATCCTATC-ACGGATTT
* * * * * *
17698692 AACAGGTCCGATGATTATGTATCATCGTGAGTCTATGAATCCTATTACAGATTAACATGTCCAAT
1 AA-AGGTTCGATGATTATGTGTCATCGTGAGTATATCAATCCTATTACAGATGAACAGGTCCAAT
17698757 GATTATGTATCATCGTGAGTATATGAATCCTATCACGGATTT
65 GATTATGTATCATCGTGAGTATATGAATCCTATCACGGATTT
* *
17698799 AAAGGTTTGATGACTATGTGTCATCGTGAGTAT
1 AAAGGTTCGATGATTATGTGTCATCGTGAGTAT
17698832 TAAATGAAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
105 4 0.03
106 113 0.93
107 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (106 bp):
AAAGGTTCGATGATTATGTGTCATCGTGAGTATATCAATCCTATTACAGATGAACAGGTCCAATG
ATTATGTATCATCGTGAGTATATGAATCCTATCACGGATTT
Found at i:17701449 original size:29 final size:29
Alignment explanation
Indices: 17701404--17701462 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
17701394 CTACGAAACC
*
17701404 TCTACCCTATTTGGGCAATCCCTAAAAAA
1 TCTACCCTATTTAGGCAATCCCTAAAAAA
17701433 TCTACCCTATTTAGGCAATCCCTAAAAAA
1 TCTACCCTATTTAGGCAATCCCTAAAAAA
17701462 T
1 T
17701463 GTTCTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (29 bp):
TCTACCCTATTTAGGCAATCCCTAAAAAA
Found at i:17705305 original size:16 final size:17
Alignment explanation
Indices: 17705274--17705308 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17705264 TCTTAAATCA
17705274 ATTTATCATCTATAAAAC
1 ATTTATCA-CTATAAAAC
17705292 ATTTATCA-TATAAAAC
1 ATTTATCACTATAAAAC
17705308 A
1 A
17705309 AACCTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTATCACTATAAAAC
Found at i:17706422 original size:380 final size:379
Alignment explanation
Indices: 17705721--17706480 Score: 1101
Period size: 380 Copynumber: 2.0 Consensus size: 379
17705711 ATATATACAT
* * * *
17705721 ATAATCACAATCAAACATATTTTATGTTAATTTGGCTATTTAGACTATGAAACATAAAGTGAGCT
1 ATAATCACAATCAAACACAGTTTATGATAATTTGGCTATTAAGACTATGAAACATAAAGTGAGCT
* * *
17705786 CTATCATCTCACATTGGTTATGCAGATCTCCAACACACGAACACTAGACTCATAGAGTCGAAACA
66 CTATCATCACACATTGGATACGCAGATCTCCAACACACGAACACTAGACTCATAGAGTCGAAACA
* * *
17705851 TATCCTATAAGTGAAGCATATAACTAACACTCTCTAACACACGAAACATATCCTGTTGAATAAAG
131 TATCCTATAAGTGAAGCATATAACTAACACTCTCCAACACACCAAACATATCCCGTTGAATAAAG
* *
17705916 CATAGCTCACATTCCCTTATCTCTCTAACATGTCCTTGGGCCCCACTGCCTCACATATAACACAA
196 CATAACTCACATTCCCTTATCTCTCTAACATGTCCTTGGGCCCCACTGCCCCACATATAACACAA
* *
17705981 ACGTAAGTACTCACAATCCTATAGAATGCTAACTATATCCAAAGGTCTCATAAGATCACAAAGCC
261 ACATAAGTACTCACAATCCTATAGAATGCCAACTATATCCAAAGGTCTCATAAGATCACAAAGCC
*
17706046 AAAACAT-TCACATTATTATTATTACATATTTTTATCATATATTCACTACATATTC
326 AAAACATCT-ACATTATTATTA-CACATATTTTTATCATATATTCACTACATATTC
* * *
17706101 ATAATCATAATCAAACACAGTTTATGATAATTTGGCTGTTAAGACTATGAAACATATAGTGAGCT
1 ATAATCACAATCAAACACAGTTTATGATAATTTGGCTATTAAGACTATGAAACATAAAGTGAGCT
* * * * * *
17706166 TTATCATCACACATTGGATACGCGGATCTCCAACACACTAACACTGGACTTATAGAGTTGAAACA
66 CTATCATCACACATTGGATACGCAGATCTCCAACACACGAACACTAGACTCATAGAGTCGAAACA
* * * **
17706231 TAT-ATCATAAGTGAAGCATATAGCTATCACTCTCCAACACACCAAACATATCCCGTTGAATGGA
131 TATCCT-ATAAGTGAAGCATATAACTAACACTCTCCAACACACCAAACATATCCCGTTGAATAAA
* * * *
17706295 GCATAACTCACATTCCCTTATCTCTCTTATATGTCCTTGGGCCTCAGTGCCCCACATATAACACA
195 GCATAACTCACATTCCCTTATCTCTCTAACATGTCCTTGGGCCCCACTGCCCCACATATAACACA
* * * * *
17706360 AACATGAGTACTCATAATCTTATGGCATGCCAACTATATCCAAAGGTCTCATAAGATCACAAAGC
260 AACATAAGTACTCACAATCCTATAGAATGCCAACTATATCCAAAGGTCTCATAAGATCACAAAGC
* * * *
17706425 CAAAATATCTACATTATTATTACATATTTTTTTATCATATATTCACTGCATATTC
325 CAAAACATCTACATTATTATTACACATATTTTTATCATATATTCACTACATATTC
17706480 A
1 A
17706481 CTTTATTATC
Statistics
Matches: 336, Mismatches: 42, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
379 31 0.09
380 304 0.90
381 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (379 bp):
ATAATCACAATCAAACACAGTTTATGATAATTTGGCTATTAAGACTATGAAACATAAAGTGAGCT
CTATCATCACACATTGGATACGCAGATCTCCAACACACGAACACTAGACTCATAGAGTCGAAACA
TATCCTATAAGTGAAGCATATAACTAACACTCTCCAACACACCAAACATATCCCGTTGAATAAAG
CATAACTCACATTCCCTTATCTCTCTAACATGTCCTTGGGCCCCACTGCCCCACATATAACACAA
ACATAAGTACTCACAATCCTATAGAATGCCAACTATATCCAAAGGTCTCATAAGATCACAAAGCC
AAAACATCTACATTATTATTACACATATTTTTATCATATATTCACTACATATTC
Found at i:17706640 original size:23 final size:23
Alignment explanation
Indices: 17706614--17706708 Score: 109
Period size: 23 Copynumber: 4.1 Consensus size: 23
17706604 ATCTTAATTC
* *
17706614 TTTAATCACAAATTACATTACTA
1 TTTAATCACAAATCACATTAATA
* *
17706637 TTTAATCATAAATCATATTAATA
1 TTTAATCACAAATCACATTAATA
*
17706660 TTTAAGCACAAATCACATTAATA
1 TTTAATCACAAATCACATTAATA
* * * *
17706683 TTTAAGCATAAACCATATTAATA
1 TTTAATCACAAATCACATTAATA
17706706 TTT
1 TTT
17706709 GAGCTATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTAATCACAAATCACATTAATA
Found at i:17706678 original size:46 final size:46
Alignment explanation
Indices: 17706614--17706917 Score: 327
Period size: 46 Copynumber: 6.8 Consensus size: 46
17706604 ATCTTAATTC
* * * * *
17706614 TTTAATCACAAATTACATTACTATTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
* *
17706660 TTTAAGCACAAATCACATTAATATTTAAGCATAAACCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
* *
17706706 TTTGAG--C---T---ATTAATATTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
* * * *
17706744 TTTAAGCACAAATTAAATTAATATTTGAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
* *
17706790 TTTAAACACAAATCACATTAATATTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
* ** * *
17706836 TTTAAGCATAAATCACATTAATACATAACCACAAATCAAATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
* * ** *
17706882 TTTTATCGTAAATCATATTAATATTTAAGCACAAAT
1 TTTAAGCACAAATCACATTAATATTTAAGCACAAAT
17706918 ATAAGAACAC
Statistics
Matches: 220, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
38 32 0.15
40 1 0.00
41 1 0.00
43 1 0.00
44 1 0.00
46 184 0.84
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (46 bp):
TTTAAGCACAAATCACATTAATATTTAAGCACAAATCATATTAATA
Found at i:17706708 original size:69 final size:69
Alignment explanation
Indices: 17706614--17706917 Score: 327
Period size: 69 Copynumber: 4.5 Consensus size: 69
17706604 ATCTTAATTC
* * * * *
17706614 TTTAATCACAAATTACATTACTATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATT
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATT
17706679 AATA
66 AATA
* * * * *
17706683 TTTAAGCATAAACCATATTAATATTT--G-----AGC-TATTAATATTTGAGCACAAATCATATT
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATT
17706740 AATA
66 AATA
* * * *
17706744 TTTAAGCACAAATTAAATTAATATTTGAGCATAAATCATATTAATATTTAAACACAAATCACATT
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATT
17706809 AATA
66 AATA
* * ** * *
17706813 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATACATAACCACAAATCAAATT
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATT
17706878 AATA
66 AATA
* * ** *
17706882 TTTTATCGTAAATCATATTAATATTTAAGCACAAAT
1 TTTAAGCACAAATCATATTAATATTTAAGCATAAAT
17706918 ATAAGAACAC
Statistics
Matches: 195, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
61 51 0.26
62 2 0.01
63 1 0.01
68 2 0.01
69 139 0.71
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (69 bp):
TTTAAGCACAAATCATATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATT
AATA
Found at i:17706718 original size:15 final size:15
Alignment explanation
Indices: 17706698--17706727 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17706688 GCATAAACCA
17706698 TATTAATATTTGAGC
1 TATTAATATTTGAGC
17706713 TATTAATATTTGAGC
1 TATTAATATTTGAGC
17706728 ACAAATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TATTAATATTTGAGC
Found at i:17706740 original size:23 final size:23
Alignment explanation
Indices: 17706713--17706917 Score: 248
Period size: 23 Copynumber: 8.9 Consensus size: 23
17706703 ATATTTGAGC
*
17706713 TATTAATATTTGAGCACAAATCA
1 TATTAATATTTAAGCACAAATCA
*
17706736 TATTAATATTTAAGCACAAATTA
1 TATTAATATTTAAGCACAAATCA
* * *
17706759 AATTAATATTTGAGCATAAATCA
1 TATTAATATTTAAGCACAAATCA
*
17706782 TATTAATATTTAAACACAAATCA
1 TATTAATATTTAAGCACAAATCA
*
17706805 CATTAATATTTAAGCACAAATCA
1 TATTAATATTTAAGCACAAATCA
* *
17706828 CATTAATATTTAAGCATAAATCA
1 TATTAATATTTAAGCACAAATCA
* ** *
17706851 CATTAATACATAACCACAAATCA
1 TATTAATATTTAAGCACAAATCA
* * * **
17706874 AATTAATATTTTATCGTAAATCA
1 TATTAATATTTAAGCACAAATCA
17706897 TATTAATATTTAAGCACAAAT
1 TATTAATATTTAAGCACAAAT
17706918 ATAAGAACAC
Statistics
Matches: 153, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 153 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (23 bp):
TATTAATATTTAAGCACAAATCA
Found at i:17709055 original size:18 final size:18
Alignment explanation
Indices: 17709032--17709130 Score: 128
Period size: 18 Copynumber: 5.5 Consensus size: 18
17709022 CGGAAGGATC
*
17709032 AGCATACTGGCTCGTTTA
1 AGCATACTGGCTCGTTTG
*
17709050 AGCATACTAGCTCGTTTG
1 AGCATACTGGCTCGTTTG
*
17709068 AGCACACTGGCTCGTTTCG
1 AGCATACTGGCTCGTTT-G
* *
17709087 -GCATATTGACTCGTTTG
1 AGCATACTGGCTCGTTTG
*
17709104 AGCATAATGGCTCGTTTG
1 AGCATACTGGCTCGTTTG
17709122 AGCATACTG
1 AGCATACTG
17709131 TCTCATAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
17 1 0.01
18 67 0.97
19 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.32
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTG
Found at i:17711604 original size:19 final size:19
Alignment explanation
Indices: 17711571--17711610 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17711561 CTTACTTCGA
*
17711571 ATGTCCACACGGTTTGAGCC
1 ATGTCCACACAGTTTG-GCC
17711591 ATGT-CACACAGTTTGGCC
1 ATGTCCACACAGTTTGGCC
17711609 AT
1 AT
17711611 ATGATTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 10 0.53
20 4 0.21
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.28
Consensus pattern (19 bp):
ATGTCCACACAGTTTGGCC
Found at i:17713909 original size:18 final size:17
Alignment explanation
Indices: 17713888--17713940 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
17713878 TCTATTTAGT
17713888 TTTCTATTTTTATTTTTA
1 TTTCTA-TTTTATTTTTA
* *
17713906 TTTCTAGTTGTACTTTTAA
1 TTTCTA-TTTTA-TTTTTA
*
17713925 TTTGTATTTTATTTTT
1 TTTCTATTTTATTTTT
17713941 CGCAGTTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 4 0.14
18 14 0.50
19 10 0.36
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTCTATTTTATTTTTA
Found at i:17716510 original size:14 final size:14
Alignment explanation
Indices: 17716453--17716517 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
17716443 GATGTACTTT
17716453 AATATTTAATAATA
1 AATATTTAATAATA
** *
17716467 TTTA-TTAATTAATT
1 AATATTTAA-TAATA
*
17716481 AATATTTACAT-TTA
1 AATATTTA-ATAATA
17716495 AATATTTAATAATA
1 AATATTTAATAATA
17716509 AAT-TTTAAT
1 AATATTTAAT
17716518 CCATATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
13 12 0.31
14 22 0.56
15 4 0.10
16 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTTAATAATA
Found at i:17717674 original size:42 final size:42
Alignment explanation
Indices: 17717627--17717712 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
17717617 AAGTTCTCTT
17717627 TTCTCTTTTTTTCAAACTTTTCTTTAAATCAATGCAAAAAGC
1 TTCTCTTTTTTTCAAACTTTTCTTTAAATCAATGCAAAAAGC
17717669 TTCTCTTTTTTTCAAACTTTTCTTTAAATCAATGCAAAAAGC
1 TTCTCTTTTTTTCAAACTTTTCTTTAAATCAATGCAAAAAGC
17717711 TT
1 TT
17717713 ACCCAAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (42 bp):
TTCTCTTTTTTTCAAACTTTTCTTTAAATCAATGCAAAAAGC
Found at i:17720685 original size:58 final size:58
Alignment explanation
Indices: 17720617--17720729 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
17720607 ACATTAATCG
* *
17720617 CATTAATCACATGAGTACTTAAGCATTTAACACAACACATATTAATCACATTTAAACA
1 CATTAATCACATGAATACTTAAGCATTTAACACAACAAATATTAATCACATTTAAACA
* * * * * *
17720675 CATTAGTCACATGAATATTTTAGTATTTATCACATCAAATATTAATCACATTTAA
1 CATTAATCACATGAATACTTAAGCATTTAACACAACAAATATTAATCACATTTAA
17720730 CCAAATGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (58 bp):
CATTAATCACATGAATACTTAAGCATTTAACACAACAAATATTAATCACATTTAAACA
Found at i:17720776 original size:25 final size:25
Alignment explanation
Indices: 17720699--17720777 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
17720689 ATATTTTAGT
17720699 ATTT-ATCACATCAAATATTAATCAC
1 ATTTAATCACATC-AATATTAATCAC
* * *
17720724 ATTTAACCAAATGAATATT--TCAGC
1 ATTTAATCACATCAATATTAATCA-C
*
17720748 ATTT-GTCACATCACATATTAATCAC
1 ATTTAATCACATCA-ATATTAATCAC
17720773 ATTTA
1 ATTTA
17720778 GTCATATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
23 8 0.20
24 10 0.24
25 15 0.37
26 8 0.20
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTTAATCACATCAATATTAATCAC
Found at i:17722361 original size:10 final size:10
Alignment explanation
Indices: 17722334--17722430 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
17722324 TTCTAATTCT
17722334 ATCACATATTA
1 ATCACAT-TTA
17722345 ATCACATTTA
1 ATCACATTTA
*
17722355 GTCACATTTA
1 ATCACATTTA
*
17722365 ATCACATAAATA
1 ATCACAT--TTA
* *
17722377 TTTCAGAATTTATCA
1 -ATCA-CA-TT-T-A
17722392 CATCACATATTA
1 -ATCACAT-TTA
17722404 ATCACATTTA
1 ATCACATTTA
*
17722414 GTCACATTTA
1 ATCACATTTA
17722424 ATCACAT
1 ATCACAT
17722431 GAATATTTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
10 36 0.54
11 14 0.21
12 3 0.04
13 5 0.07
14 4 0.06
15 5 0.07
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (10 bp):
ATCACATTTA
Found at i:17722405 original size:59 final size:59
Alignment explanation
Indices: 17722334--17722449 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
17722324 TTCTAATTCT
17722334 ATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCAGA-ATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCA-ACATTTATCAC
*
17722393 ATCACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATC
1 ATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCAACATTTATC
17722450 TTATTAACAT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 1 0.02
59 54 0.98
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (59 bp):
ATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCAACATTTATCAC
Found at i:17722478 original size:23 final size:23
Alignment explanation
Indices: 17722452--17722507 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
17722442 CATTTATCTT
* *
17722452 ATTAACATTTAAGCACAAATCAC
1 ATTAATATTTAACCACAAATCAC
* *
17722475 ATTAATATTTGACCATAAATCAC
1 ATTAATATTTAACCACAAATCAC
17722498 ATTAATATTT
1 ATTAATATTT
17722508 TTTTGTGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (23 bp):
ATTAATATTTAACCACAAATCAC
Found at i:17725886 original size:23 final size:23
Alignment explanation
Indices: 17725856--17725906 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
17725846 AAAAAAAATA
*
17725856 TTTAAGCACAAATCACA-TACACT
1 TTTAAGCAAAAATCACATTA-ACT
*
17725879 TTTAAGCAAAAATTACATTAACT
1 TTTAAGCAAAAATCACATTAACT
17725902 TTTAA
1 TTTAA
17725907 CAGATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (23 bp):
TTTAAGCAAAAATCACATTAACT
Found at i:17726361 original size:36 final size:35
Alignment explanation
Indices: 17726314--17726441 Score: 150
Period size: 36 Copynumber: 3.6 Consensus size: 35
17726304 TTCATTATCA
17726314 CATGGCATGAATAACATACCCATAAATTTATTGTCT
1 CATGGCATGAATAACATACCCA-AAATTTATTGTCT
* * * *
17726350 CATGGCATGAATAACATACCTACATATTTACTGTCA
1 CATGGCATGAATAACATACCCA-AAATTTATTGTCT
* * * *
17726386 CATGACATGAATAACATA-ACAACATTTATTATCT
1 CATGGCATGAATAACATACCCAAAATTTATTGTCT
*
17726420 CATGGCATGAATGACATACCCA
1 CATGGCATGAATAACATACCCA
17726442 CATATTTACT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
34 25 0.33
35 3 0.04
36 48 0.63
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (35 bp):
CATGGCATGAATAACATACCCAAAATTTATTGTCT
Found at i:17726437 original size:70 final size:72
Alignment explanation
Indices: 17726311--17726457 Score: 217
Period size: 70 Copynumber: 2.1 Consensus size: 72
17726301 ATATTCATTA
* * * *
17726311 TCACATGGCATGAATAACATACCCATAAATTTATTGTCTCATGGCATGAATAACATACCTACATA
1 TCACATGACATGAATAACATACACATAAATTTATTATCTCATGGCATGAATAACATACCCACATA
17726376 TTTACTG
66 TTTACTG
* *
17726383 TCACATGACATGAATAACATA-ACA-ACATTTATTATCTCATGGCATGAATGACATACCCACATA
1 TCACATGACATGAATAACATACACATAAATTTATTATCTCATGGCATGAATAACATACCCACATA
*
17726446 TTTACTT
66 TTTACTG
17726453 TCACA
1 TCACA
17726458 ACAGTCATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 46 0.68
71 2 0.03
72 20 0.29
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (72 bp):
TCACATGACATGAATAACATACACATAAATTTATTATCTCATGGCATGAATAACATACCCACATA
TTTACTG
Found at i:17733188 original size:28 final size:26
Alignment explanation
Indices: 17733126--17733178 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
17733116 TGATTTTATG
*
17733126 TTCAAATAAAATTATGCACTTAGTTA
1 TTCAAAAAAAATTATGCACTTAGTTA
17733152 TTCAAAAAAAAAATTATGCACTTAGTT
1 TTC--AAAAAAAATTATGCACTTAGTT
17733179 GCTTTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
28 21 0.88
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (26 bp):
TTCAAAAAAAATTATGCACTTAGTTA
Found at i:17735755 original size:18 final size:18
Alignment explanation
Indices: 17735741--17735784 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17735731 CACAGTTCTG
17735741 CAAATTAATACAGTTCAC
1 CAAATTAATACAGTTCAC
* **
17735759 CATATTAATACAAATCAC
1 CAAATTAATACAGTTCAC
*
17735777 TAAATTAA
1 CAAATTAA
17735785 CATAGTTCGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (18 bp):
CAAATTAATACAGTTCAC
Found at i:17736045 original size:24 final size:26
Alignment explanation
Indices: 17736018--17736082 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 26
17736008 AACCTATAAA
17736018 CACATATATTATATAATATA-AA-CC
1 CACATATATTATATAATATACAATCC
* *
17736042 CACACATA--ATATTATATACAATCC
1 CACATATATTATATAATATACAATCC
17736066 CATGCATATATTATATA
1 CA--CATATATTATATA
17736083 TAACACGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 9 0.29
23 2 0.06
24 11 0.35
26 5 0.16
28 4 0.13
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (26 bp):
CACATATATTATATAATATACAATCC
Found at i:17737470 original size:16 final size:17
Alignment explanation
Indices: 17737427--17737471 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
17737417 TTATTAATTC
17737427 TAATTATTTTAATATTT
1 TAATTATTTTAATATTT
* *
17737444 TATTTA-ATTAAT-TTT
1 TAATTATTTTAATATTT
17737459 TAATTATTTTAAT
1 TAATTATTTTAAT
17737472 GATCTAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATTATTTTAATATTT
Found at i:17739898 original size:20 final size:20
Alignment explanation
Indices: 17739873--17739917 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17739863 CATGATTTTT
*
17739873 ATTAAGAGTAAATAG-GCTTA
1 ATTAAGAGTAAA-AGTGATTA
*
17739893 ATTAAGATTAAAAGTGATTA
1 ATTAAGAGTAAAAGTGATTA
17739913 ATTAA
1 ATTAA
17739918 AGCTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (20 bp):
ATTAAGAGTAAAAGTGATTA
Found at i:17741780 original size:21 final size:20
Alignment explanation
Indices: 17741739--17741792 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
17741729 GGAGTTTTTA
17741739 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAAG-AAGACTT
17741760 GTATCGGTAGAAG-AGTTACTT
1 GTATCGGTAGAAGAAG--ACTT
*
17741781 GTCTCGGTAGAA
1 GTATCGGTAGAA
17741793 CTGTCACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.07
21 28 0.93
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (20 bp):
GTATCGGTAGAAGAAGACTT
Found at i:17741801 original size:21 final size:21
Alignment explanation
Indices: 17741756--17741811 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
17741746 TAGAAGTAAG
* *
17741756 ACTTGTATCGGTAGAAGAGTT
1 ACTTGTATCGGTAGAACAGTC
* *
17741777 ACTTGTCTCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
* *
17741798 ACTTATACCGGTAG
1 ACTTGTATCGGTAG
17741812 GAGTCTGCAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:17745466 original size:45 final size:44
Alignment explanation
Indices: 17745410--17745499 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
17745400 AAAATTATTA
* *
17745410 AATTTATTTTTTTAAAAATATATATT-TT-TAATTATTTTAAAATT
1 AATTTA-TTTTTTAAAAATA-AAATTATTAAAATTATTTTAAAATT
*
17745454 AATTTAATTTTTTAAATATAAAATTATTAAAATTATTTTAAAATT
1 AATTT-ATTTTTTAAAAATAAAATTATTAAAATTATTTTAAAATT
17745499 A
1 A
17745500 TAATCATCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
43 4 0.10
44 19 0.47
45 17 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (44 bp):
AATTTATTTTTTAAAAATAAAATTATTAAAATTATTTTAAAATT
Found at i:17746218 original size:6 final size:6
Alignment explanation
Indices: 17746207--17746251 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
17746197 GAGACGTAAT
* * *
17746207 GGAAGG GGAAGG GGAAGT GAAAGG GGAAGA GGAAGG GG-AGG GGAA
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAA
17746252 CAGAAAAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (6 bp):
GGAAGG
Found at i:17746327 original size:11 final size:11
Alignment explanation
Indices: 17746307--17746362 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
17746297 TTTAAAAAAA
*
17746307 TTAAATTAATT
1 TTAAAATAATT
17746318 TTAAAATAATT
1 TTAAAATAATT
17746329 TTAAAAAATAATT
1 TT--AAAATAATT
17746342 TT--AATAATT
1 TTAAAATAATT
* *
17746351 TTTAAATCATT
1 TTAAAATAATT
17746362 T
1 T
17746363 GCTGATGTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 9 0.23
11 19 0.49
13 11 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:17746338 original size:13 final size:13
Alignment explanation
Indices: 17746320--17746345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17746310 AATTAATTTT
17746320 AAAATAATTTTAA
1 AAAATAATTTTAA
17746333 AAAATAATTTTAA
1 AAAATAATTTTAA
17746346 TAATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:17750742 original size:17 final size:17
Alignment explanation
Indices: 17750717--17750759 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
17750707 ATGCATCTTA
17750717 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* **
17750734 TTTAGTTGTTGTTGCAT
1 TTTAATTGTCATTGCAT
*
17750751 TTTACTTGT
1 TTTAATTGT
17750760 TAATTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.58
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:17750760 original size:17 final size:16
Alignment explanation
Indices: 17750728--17750786 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
17750718 TTAATTGTCA
17750728 TTGCATTTTAGTTGTTG
1 TTGCATTTTA-TTGTTG
*
17750745 TTGCATTTTACTTGTTAA
1 TTGCATTTTA-TTGTT-G
*
17750763 TT-CATTTGTATTGTAG
1 TTGCATTT-TATTGTTG
17750779 TTGCATTT
1 TTGCATTT
17750787 CCATTCTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.06
17 29 0.83
18 4 0.11
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (16 bp):
TTGCATTTTATTGTTG
Found at i:17755627 original size:56 final size:55
Alignment explanation
Indices: 17755504--17755642 Score: 161
Period size: 56 Copynumber: 2.5 Consensus size: 55
17755494 ACATGGGCGA
* * * * ** *
17755504 GTGCTAGGCCGTATGTGTATACTATTTTCAGGCACATGGGCGGACACATGGGCAT
1 GTGCTAGGCCATGTGTGTATACTATTTTAAGACACATGGGCAAACACACGGGCAT
** *
17755559 GTGCTAAACCATGTGTGTATACTGTTTTAAGACACATGGGCCAAACACACGGGCAT
1 GTGCTAGGCCATGTGTGTATACTATTTTAAGACACATGGG-CAAACACACGGGCAT
**
17755615 GTGCTAGGCCATGTAAGTATACTATTTT
1 GTGCTAGGCCATGTGTGTATACTATTTT
17755643 TCTATTAAAG
Statistics
Matches: 68, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
55 33 0.49
56 35 0.51
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (55 bp):
GTGCTAGGCCATGTGTGTATACTATTTTAAGACACATGGGCAAACACACGGGCAT
Found at i:17760752 original size:3 final size:3
Alignment explanation
Indices: 17760738--17760787 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
17760728 CGTTGGGCGC
*
17760738 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AGAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT AAT
17760785 AAT
1 AAT
17760788 GCAGGAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:17760771 original size:10 final size:10
Alignment explanation
Indices: 17760738--17760786 Score: 66
Period size: 10 Copynumber: 5.1 Consensus size: 10
17760728 CGTTGGGCGC
*
17760738 AATAACAAT-
1 AATAATAATA
17760747 AATAATAAT-
1 AATAATAATA
17760756 AATAATAATA
1 AATAATAATA
17760766 AATAATAATA
1 AATAATAATA
*
17760776 GATAATAATA
1 AATAATAATA
17760786 A
1 A
17760787 TGCAGGAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
9 17 0.47
10 19 0.53
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:17760771 original size:13 final size:12
Alignment explanation
Indices: 17760738--17760787 Score: 73
Period size: 13 Copynumber: 4.0 Consensus size: 12
17760728 CGTTGGGCGC
*
17760738 AATAACAATAAT
1 AATAATAATAAT
17760750 AATAATAATAAT
1 AATAATAATAAT
17760762 AATAAATAATAAT
1 AAT-AATAATAAT
17760775 AGATAATAATAAT
1 A-ATAATAATAAT
17760788 GCAGGAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 14 0.40
13 19 0.54
14 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:17766638 original size:12 final size:12
Alignment explanation
Indices: 17766623--17766648 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17766613 AATTAAAGAA
17766623 ATAATAGCATTC
1 ATAATAGCATTC
17766635 ATAATAGCATTC
1 ATAATAGCATTC
17766647 AT
1 AT
17766649 CATAATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:17768148 original size:7 final size:6
Alignment explanation
Indices: 17768120--17768149 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
17768110 ATGCTCTATA
17768120 TTTTTC TTTTTC TTTTTC TTTTTC ATTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTT
17768150 TTTCTGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:17769467 original size:3 final size:3
Alignment explanation
Indices: 17769459--17769523 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
17769449 TTCTACAGGA
17769459 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
17769507 CCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TC
17769524 AGCTTGCTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:17771337 original size:17 final size:17
Alignment explanation
Indices: 17771315--17771347 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17771305 GATTCAATAC
*
17771315 TTTAATTCGGTTAATTT
1 TTTAATTCGGGTAATTT
17771332 TTTAATTCGGGTAATT
1 TTTAATTCGGGTAATT
17771348 CGGGTAATTT
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:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (17 bp):
TTTAATTCGGGTAATTT
Found at i:17771811 original size:16 final size:17
Alignment explanation
Indices: 17771764--17771811 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
17771754 TTGAAATTTC
*
17771764 TAAA-ATAAATACTAAT
1 TAAATATAAATAATAAT
*
17771780 TAAATATTAATAATAAT
1 TAAATATAAATAATAAT
*
17771797 T-AATATAAATCATAA
1 TAAATATAAATAATAA
17771812 AAATTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATAAATAATAAT
Found at i:17771948 original size:25 final size:25
Alignment explanation
Indices: 17771895--17771947 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
17771885 TAATTAAATG
17771895 AAAACTTTATTTTTTAGCTATTTTA
1 AAAACTTTATTTTTTAGCTATTTTA
17771920 AAAACTTTA-TTTTTAGCTATTTTA
1 AAAACTTTATTTTTTAGCTATTTTA
17771944 AAAA
1 AAAA
17771948 ATATTTACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (25 bp):
AAAACTTTATTTTTTAGCTATTTTA
Found at i:17782260 original size:122 final size:122
Alignment explanation
Indices: 17781737--17782260 Score: 633
Period size: 122 Copynumber: 4.3 Consensus size: 122
17781727 ATTTATTTTA
* * ** * * ** *
17781737 ACCCACTTCTTTGTACCTCATCAAGAAGATGGAATTT-GAAGTTTCACTCGTATTGAG-TTTCAC
1 ACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTCAAAGTTTTACTCACA-TGAGCTTT-GC
* * * * * * * *
17781800 CTCATTGTTTTGATCTGCTTCTCTGTATCTCATCAAGATGATGACCGCTTCATTGTCTG
64 TTCATTGATTTGGTCTACTTCTCTGTATCTCACCAAGAAGATAACCACTTCATTGTCTG
* ** *
17781859 ACCCAATTCTTTGTATCTCATCAGGAAGATAAGGTTTCGAAGTTTTACTCACATGAG-TTTCGCT
1 ACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTCAAAGTTTTACTCACATGAGCTTT-GCT
* * * * *
17781923 TCATTGATTTGGTCTACTTCTCTGTATCTCATC-AGAAAGATGACCGCTTCGTTCTCTG
65 TCATTGATTTGGTCTACTTCTCTGTATCTCACCAAG-AAGATAACCACTTCATTGTCTG
* * * *
17781981 ACCCACTTCTCTATATCTCATCAGGAAGATGGCGTTTCAAAGTTTTACTCACATGAGCTCTGCTT
1 ACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTCAAAGTTTTACTCACATGAGCTTTGCTT
* *
17782046 CATTGATTTGGTTTACTTCTCTGTATCTCACCAAGAAGATAACCACTTCATTGTCTT
66 CATTGATTTGGTCTACTTCTCTGTATCTCACCAAGAAGATAACCACTTCATTGTCTG
*
17782103 ACCCACTTCTTTGTATCTCATCAGGAAGATTGGGTTTCAAAGTTTTACTCACATGAGCTTTGCTT
1 ACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTCAAAGTTTTACTCACATGAGCTTTGCTT
* * * *
17782168 CATTGATTTGGTCTACTTCTCTGTATCTCACCAAGAAGATAATCACTTTATTTTCTA
66 CATTGATTTGGTCTACTTCTCTGTATCTCACCAAGAAGATAACCACTTCATTGTCTG
* *
17782225 ATCCACTTCTTTGTATCTCATCAGAAAGATGGGGTT
1 ACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTT
17782261 CTCTATATCA
Statistics
Matches: 352, Mismatches: 46, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
121 2 0.01
122 334 0.95
123 16 0.05
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (122 bp):
ACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTCAAAGTTTTACTCACATGAGCTTTGCTT
CATTGATTTGGTCTACTTCTCTGTATCTCACCAAGAAGATAACCACTTCATTGTCTG
Found at i:17783923 original size:15 final size:15
Alignment explanation
Indices: 17783903--17783933 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17783893 TGTGAATGAT
*
17783903 ATTAATCTAATTTAA
1 ATTAATCTAAGTTAA
17783918 ATTAATCTAAGTTAA
1 ATTAATCTAAGTTAA
17783933 A
1 A
17783934 GATAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAATCTAAGTTAA
Found at i:17784195 original size:13 final size:13
Alignment explanation
Indices: 17784177--17784204 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17784167 GTGTTATGGC
17784177 ACATTACTTATGA
1 ACATTACTTATGA
17784190 ACATTACTTATGA
1 ACATTACTTATGA
17784203 AC
1 AC
17784205 GACCGACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (13 bp):
ACATTACTTATGA
Found at i:17787302 original size:17 final size:17
Alignment explanation
Indices: 17787282--17787314 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17787272 GAAGGTATGG
*
17787282 AATCTTAGAGGATTTGT
1 AATCTTAGAAGATTTGT
17787299 AATCTTAGAAGATTTG
1 AATCTTAGAAGATTTG
17787315 ATTATGTAAA
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:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (17 bp):
AATCTTAGAAGATTTGT
Found at i:17787322 original size:23 final size:22
Alignment explanation
Indices: 17787292--17787341 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
17787282 AATCTTAGAG
17787292 GATTTGT-AATCTTAGAAGATTT
1 GATTTGTAAATCTTAG-AGATTT
*
17787314 GATTATGTAAATCTTAGATATTT
1 GATT-TGTAAATCTTAGAGATTT
17787337 GATTT
1 GATTT
17787342 TGTTGATTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 8 0.32
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (22 bp):
GATTTGTAAATCTTAGAGATTT
Found at i:17790847 original size:31 final size:33
Alignment explanation
Indices: 17790784--17790851 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 33
17790774 TTAAAGTTAT
17790784 AATTTCAAATTATTCCAGATTTATGTAATTTTA
1 AATTTCAAATTATTCCAGATTTATGTAATTTTA
17790817 AATTT-AAATTA-T-CAGATTTAAAT-TAATTTTA
1 AATTTCAAATTATTCCAGATTT--ATGTAATTTTA
17790848 AATT
1 AATT
17790852 CATATCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 7 0.21
31 13 0.39
32 8 0.24
33 5 0.15
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (33 bp):
AATTTCAAATTATTCCAGATTTATGTAATTTTA
Found at i:17796810 original size:66 final size:66
Alignment explanation
Indices: 17796686--17796823 Score: 143
Period size: 66 Copynumber: 2.1 Consensus size: 66
17796676 TCATATTTTG
* ** * * *
17796686 AAGTTGTAGTTGTTGTTCGTCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTGCCT-TGGCT
1 AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGAGACTCTACTTCCCTCACTGCTGCCTCT-GCT
17796750 TC
65 TC
* * * * * *
17796752 AAGTTGTAGCTGAAGTTCATCATATTTTTTTTGAGCCTCTATTTCTCTCACTGTTGCCTCTGCTT
1 AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGAGACTCTACTTCCCTCACTGCTGCCTCTGCTT
*
17796817 T
66 C
17796818 AAGTTG
1 AAGTTG
17796824 AGCAATTTGC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (66 bp):
AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGAGACTCTACTTCCCTCACTGCTGCCTCTGCTT
C
Found at i:17803291 original size:19 final size:20
Alignment explanation
Indices: 17803267--17803307 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17803257 GCTGATAATT
17803267 TAAACAA-GAAACACCACTC
1 TAAACAAGGAAACACCACTC
*
17803286 TAAACAAGGAAACACCATTC
1 TAAACAAGGAAACACCACTC
17803306 TA
1 TA
17803308 GAGTACCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.51, C:0.27, G:0.07, T:0.15
Consensus pattern (20 bp):
TAAACAAGGAAACACCACTC
Found at i:17805055 original size:17 final size:19
Alignment explanation
Indices: 17805011--17805065 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
17805001 ATATATCAAT
17805011 AAACTTTAAAACATTAAAC
1 AAACTTTAAAACATTAAAC
*
17805030 AAACATTAAAA-A-TAAAC
1 AAACTTTAAAACATTAAAC
*
17805047 AAATTTTAAATACATTAAA
1 AAACTTTAAA-ACATTAAA
17805066 AATTCTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 11 0.37
20 4 0.13
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (19 bp):
AAACTTTAAAACATTAAAC
Found at i:17805216 original size:20 final size:20
Alignment explanation
Indices: 17805193--17805241 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
17805183 AATAACATCC
*
17805193 AAACAACCAAA-ACAGCAGCA
1 AAACAA-CAAATACAGCAACA
17805213 AAACAACAAATACAGCAACA
1 AAACAACAAATACAGCAACA
*
17805233 AAATAACAA
1 AAACAACAA
17805242 GAAAAATAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.65, C:0.24, G:0.06, T:0.04
Consensus pattern (20 bp):
AAACAACAAATACAGCAACA
Found at i:17805240 original size:23 final size:23
Alignment explanation
Indices: 17805194--17805258 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
17805184 ATAACATCCA
* *
17805194 AACAACCAAAACAGCAGC--AA-
1 AACAACAAAAACAGCAACAAAAT
*
17805214 AACAACAAATACAGCAACAAAAT
1 AACAACAAAAACAGCAACAAAAT
* *
17805237 AACAAGAAAAATAGCAACAAAA
1 AACAACAAAAACAGCAACAAAA
17805259 AAAACAGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
22 2 0.06
23 19 0.53
ACGTcount: A:0.66, C:0.22, G:0.08, T:0.05
Consensus pattern (23 bp):
AACAACAAAAACAGCAACAAAAT
Found at i:17805283 original size:25 final size:26
Alignment explanation
Indices: 17805244--17805310 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 26
17805234 AATAACAAGA
*
17805244 AAAATAGCAACAAAAAAAACAGCATC
1 AAAATAGCAACAAAAAAAACAGCACC
*
17805270 AAAATAGTAA-AAAAAAAACAGCACC
1 AAAATAGCAACAAAAAAAACAGCACC
*
17805295 AAAACAGCAATCAAAA
1 AAAATAGCAA-CAAAA
17805311 TAGTAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.63
26 9 0.26
27 4 0.11
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.07
Consensus pattern (26 bp):
AAAATAGCAACAAAAAAAACAGCACC
Found at i:17805285 original size:38 final size:37
Alignment explanation
Indices: 17805214--17805321 Score: 110
Period size: 37 Copynumber: 2.9 Consensus size: 37
17805204 ACAGCAGCAA
* * ** * *
17805214 AACAACAAATACAGCAACAAAATAACAAGAAAAATAGC
1 AACAACAAAAACAGCATCAAAATAGTAA-AAAAAAAAC
*
17805252 AACAAAAAAAACAGCATCAAAATAGTAAAAAAAAAAC
1 AACAACAAAAACAGCATCAAAATAGTAAAAAAAAAAC
* *
17805289 AGC-ACCAAAACAGCAATCAAAATAGTAAAAAAA
1 AACAACAAAAACAGC-ATCAAAATAGTAAAAAAA
17805322 TAAAACACTA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
36 9 0.15
37 27 0.46
38 23 0.39
ACGTcount: A:0.68, C:0.17, G:0.07, T:0.08
Consensus pattern (37 bp):
AACAACAAAAACAGCATCAAAATAGTAAAAAAAAAAC
Found at i:17805343 original size:18 final size:18
Alignment explanation
Indices: 17805314--17805391 Score: 74
Period size: 18 Copynumber: 4.4 Consensus size: 18
17805304 ATCAAAATAG
17805314 TAAAAAA-A-TAAAACAC
1 TAAAAAACACTAAAACAC
*
17805330 TAAAAAACACTAAAACAG
1 TAAAAAACACTAAAACAC
*
17805348 TAAAAAACACCAAAACAGC
1 TAAAAAACACTAAAACA-C
*
17805367 -AAAAAAGCAACT-AAACAG
1 TAAAAAA-C-ACTAAAACAC
17805385 TAAAAAA
1 TAAAAAA
17805392 ATAGTACCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.14
17 1 0.02
18 29 0.57
19 12 0.24
20 2 0.04
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (18 bp):
TAAAAAACACTAAAACAC
Found at i:17805371 original size:19 final size:18
Alignment explanation
Indices: 17805331--17805392 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
17805321 ATAAAACACT
* *
17805331 AAAAAACACTAAAACAGT
1 AAAAAACACCAAAACAGA
17805349 AAAAAACACCAAAACAGCA
1 AAAAAACACCAAAACAG-A
* * *
17805368 AAAAAGCAACTAAACAGTA
1 AAAAAACACCAAAACAG-A
17805387 AAAAAA
1 AAAAAA
17805393 TAGTACCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
18 16 0.44
19 20 0.56
ACGTcount: A:0.69, C:0.18, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAACACCAAAACAGA
Found at i:17806088 original size:41 final size:40
Alignment explanation
Indices: 17806043--17806262 Score: 233
Period size: 41 Copynumber: 5.3 Consensus size: 40
17806033 ATTTGTAGGA
*
17806043 AAAACGCCGCTAAAGGTCAGAGCATTAGTGGCGTTTATGAG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTAT-AG
* * * * *
17806084 AAAACGCCGCTAAAGATCAAAGCATTAGAGGCTTTTTTAAG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTAT-AG
* * * * *
17806125 AAAACGTCGTTAAATGTCAGGGCATTAGCGGCGTTTATGGG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTAT-AG
* * *
17806166 AAAACGCCACTAAAGGTCAGAGCATTAGTGGAGTTTATAGG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATA-G
** *
17806207 AAAACGCCTTTAAAGGTCAGACCATTAGCGGCGTTTATAGG
1 AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATA-G
17806248 AAAAACGCCGCTAAA
1 -AAAACGCCGCTAAA
17806263 TGGTAAGCAA
Statistics
Matches: 145, Mismatches: 32, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
41 133 0.92
42 12 0.08
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAG
Found at i:17806277 original size:82 final size:80
Alignment explanation
Indices: 17806003--17806282 Score: 276
Period size: 82 Copynumber: 3.4 Consensus size: 80
17805993 TATTTTATAT
* * * *
17806003 AAACACCGCAAAAGGTAAAGCAATAGTGGCATTTGTAGGAAAAACGCCGCTAAAGGTCAGAGCAT
1 AAACGCCGCTAAAGGTAAAGCAATAGTGG-ATTTATAGG-AAAACGCCGTTAAAGGTCAGAGCAT
*
17806068 TAGTGGCGTTTAT-GAGA
64 TAGCGGCGTTTATGGA-A
* * * * * * * * *
17806085 AAACGCCGCTAAAGATCAAAGCATTAGAGGCTTTTTTAAGAAAACGTCGTTAAATGTCAGGGCAT
1 AAACGCCGCTAAAGGT-AAAGCAATAGTGG-ATTTATAGGAAAACGCCGTTAAAGGTCAGAGCAT
*
17806150 TAGCGGCGTTTATGGGA
64 TAGCGGCGTTTATGGAA
* * * * *
17806167 AAACGCCACTAAAGGTCAGAGCATTAGTGGAGTTTATAGGAAAACGCCTTTAAAGGTCAGACCAT
1 AAACGCCGCTAAAGGT-AAAGCAATAGTGGA-TTTATAGGAAAACGCCGTTAAAGGTCAGAGCAT
17806232 TAGCGGCGTTTATAGGAA
64 TAGCGGCGTTTAT-GGAA
*
17806250 AAACGCCGCTAAATGGT-AAGCAATAGTGCATTT
1 AAACGCCGCTAAA-GGTAAAGCAATAGTGGATTT
17806283 TCCCATAAAC
Statistics
Matches: 162, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
81 3 0.02
82 122 0.75
83 34 0.21
84 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (80 bp):
AAACGCCGCTAAAGGTAAAGCAATAGTGGATTTATAGGAAAACGCCGTTAAAGGTCAGAGCATTA
GCGGCGTTTATGGAA
Found at i:17806640 original size:29 final size:30
Alignment explanation
Indices: 17806567--17806650 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
17806557 GATTACATCA
*
17806567 AAATTAAAGTTTCATGTATAT-ATGTGAACC
1 AAATTAAAG-TTCATGTATATAATGCGAACC
* * *
17806597 ACAATTAGAAATTCACGTATATAAT-CGCACC
1 A-AATTA-AAGTTCATGTATATAATGCGAACC
*
17806628 AAATTAAAGTTCATATATATAAT
1 AAATTAAAGTTCATGTATATAAT
17806651 TACTCATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 14 0.32
30 6 0.14
31 20 0.45
32 4 0.09
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTCATGTATATAATGCGAACC
Found at i:17807946 original size:21 final size:21
Alignment explanation
Indices: 17807920--17807962 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17807910 AATATTACAA
17807920 TACATTACAAGTTAAATATAT
1 TACATTACAAGTTAAATATAT
17807941 TACATTACAAGTTAAATATAT
1 TACATTACAAGTTAAATATAT
17807962 T
1 T
17807963 TCAATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (21 bp):
TACATTACAAGTTAAATATAT
Found at i:17808275 original size:47 final size:47
Alignment explanation
Indices: 17808201--17808305 Score: 156
Period size: 47 Copynumber: 2.2 Consensus size: 47
17808191 ATCTGTCCCC
* *
17808201 AAACCCTAAATTTTTCTAATCCCTAATTCTTAATATCTCCTCTCTCA
1 AAACCCCAAATTTCTCTAATCCCTAATTCTTAATATCTCCTCTCTCA
* * *
17808248 AAACCCCAAATTTCTCTAATCCTTAATTCTTAATTTCTCTTCTCTCA
1 AAACCCCAAATTTCTCTAATCCCTAATTCTTAATATCTCCTCTCTCA
*
17808295 AAACCTCAAAT
1 AAACCCCAAAT
17808306 CCCTAATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (47 bp):
AAACCCCAAATTTCTCTAATCCCTAATTCTTAATATCTCCTCTCTCA
Found at i:17808568 original size:14 final size:14
Alignment explanation
Indices: 17808551--17808578 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17808541 CTTTGTATTC
17808551 GTTTACTGGTATGG
1 GTTTACTGGTATGG
17808565 GTTTACTGGTATGG
1 GTTTACTGGTATGG
17808579 TTGGTGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (14 bp):
GTTTACTGGTATGG
Found at i:17812085 original size:28 final size:28
Alignment explanation
Indices: 17812023--17812077 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
17812013 ATGTCGAAAG
17812023 AATAATTTATTATAAATTAATAATATAC
1 AATAATTTATTATAAATTAATAATATAC
17812051 AATAATTTATTATAAATTAATAATATA
1 AATAATTTATTATAAATTAATAATATA
17812078 TACAAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAATTTATTATAAATTAATAATATAC
Found at i:17813078 original size:13 final size:14
Alignment explanation
Indices: 17813060--17813089 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17813050 TATTTTAAAT
17813060 ATTATAAT-GTTTA
1 ATTATAATGGTTTA
17813073 ATTATAATGGTTTA
1 ATTATAATGGTTTA
17813087 ATT
1 ATT
17813090 CGTCGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (14 bp):
ATTATAATGGTTTA
Found at i:17814205 original size:42 final size:40
Alignment explanation
Indices: 17814134--17814293 Score: 119
Period size: 42 Copynumber: 3.9 Consensus size: 40
17814124 ATTAACAGTG
* * **
17814134 TTTTCCATAAACGCCTCTAACGCTCTTTACCTTTTGCGTCGT
1 TTTTCCATAAACGTCGCTATTGCT-TTTACCTTTTGCGT-GT
* *
17814176 TTTTTCATAAACGTCGCTATTGCTTTTTACCTTTTACG-GT
1 TTTTCCATAAACGTCGCTATTGC-TTTTACCTTTTGCGTGT
** *
17814216 ATTTATGGA-AAAGCGTCGCTATTGC-TTTACTTTTTGCGATGT
1 -TTT-TCCATAAA-CGTCGCTATTGCTTTTACCTTTTGCG-TGT
* * *
17814258 TTTACCATAAACGCCGCTATTACTCTTTACCTTTTG
1 TTTTCCATAAACGTCGCTATTGCT-TTTACCTTTTG
17814294 TGTTTATGGT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
40 24 0.26
41 12 0.13
42 56 0.60
43 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (40 bp):
TTTTCCATAAACGTCGCTATTGCTTTTACCTTTTGCGTGT
Found at i:17814429 original size:79 final size:76
Alignment explanation
Indices: 17814158--17814435 Score: 236
Period size: 79 Copynumber: 3.5 Consensus size: 76
17814148 CTCTAACGCT
* * *
17814158 CTTTACCTTTTGCGTCGTTTTTTCATAAACGTCGCTATTGCTTTTTACCTTTTACGGTATTTATG
1 CTTTACCTTTTGCG-CG-TTTTTCATAAACGCCGCTATT--ATTTTACCTTTT-C-GTGTTTATG
17814223 GAAAAGCGTCGCTATTG
60 GAAAAGCGTCGCTATTG
* * * *
17814240 CTTTACTTTTTGCGATGTTTTACCATAAACGCCGCTATTACTCTTTACCTTTT-GTGTTTATGGT
1 CTTTACCTTTTGCG-CGTTTT-TCATAAACGCCGCTATTA-T-TTTACCTTTTCGTGTTTATGGA
*
17814304 AAAGCGTCGCTAATG
62 AAAGCGTCGCTATTG
* * * ** * * *
17814319 TTTTACCTTTTACGGCATTTTTCCCATACGCCGCTATTATTTTACCTTTTGCAGCGTTTATGGGA
1 CTTTACCTTTTGC-GCGTTTTTCATAAACGCCGCTATTATTTTACCTTTT-C-GTGTTTATGGAA
*
17814384 AAGCGTCGCTATTA
63 AAGCGTCGCTATTG
* *
17814398 CTTTACCTTTTG-GCCGTTTATTGAAAAACGCCGCTATT
1 CTTTACCTTTTGCG-CGTTT-TTCATAAACGCCGCTATT
17814436 TGCTTTACTT
Statistics
Matches: 158, Mismatches: 29, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
76 10 0.06
77 2 0.01
78 18 0.11
79 83 0.53
80 1 0.01
81 5 0.03
82 39 0.25
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (76 bp):
CTTTACCTTTTGCGCGTTTTTCATAAACGCCGCTATTATTTTACCTTTTCGTGTTTATGGAAAAG
CGTCGCTATTG
Found at i:17814433 original size:39 final size:40
Alignment explanation
Indices: 17814346--17814457 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
17814336 TTTTTCCCAT
* *
17814346 ACGCCGCTATTATTTTACCTTTT-GCAGCGTTTATGGGAAA
1 ACGCCGCTATTACTTTACCTTTTGGCA-CGTTTATGGAAAA
* * *
17814386 GCGTCGCTATTACTTTACCTTTTGGC-CGTTTATTGAAAA
1 ACGCCGCTATTACTTTACCTTTTGGCACGTTTATGGAAAA
* *
17814425 ACGCCGCTATTTGCTTTA-CTTTTTGCGACGTTT
1 ACGCCGCTA-TTACTTTACCTTTTGGC-ACGTTT
17814458 CGGTCCAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
39 25 0.42
40 27 0.46
41 7 0.12
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (40 bp):
ACGCCGCTATTACTTTACCTTTTGGCACGTTTATGGAAAA
Found at i:17814442 original size:40 final size:40
Alignment explanation
Indices: 17814346--17814457 Score: 106
Period size: 39 Copynumber: 2.8 Consensus size: 40
17814336 TTTTTCCCAT
*
17814346 ACGCCGCTATTAT-TTTACCTTTT-GCAGCGTTTATGGGAAA
1 ACGCCGCTATT-TCTTTACCTTTTGGCA-CGTTTATGGAAAA
* * * *
17814386 GCGTCGCTATTACTTTACCTTTTGGC-CGTTTATTGAAAA
1 ACGCCGCTATTTCTTTACCTTTTGGCACGTTTATGGAAAA
*
17814425 ACGCCGCTATTTGCTTTA-CTTTTTGCGACGTTT
1 ACGCCGCTATTT-CTTTACCTTTTGGC-ACGTTT
17814458 CGGTCCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
39 27 0.47
40 24 0.41
41 7 0.12
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (40 bp):
ACGCCGCTATTTCTTTACCTTTTGGCACGTTTATGGAAAA
Found at i:17818321 original size:19 final size:20
Alignment explanation
Indices: 17818285--17818323 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17818275 ACTTTTTAGA
*
17818285 TTTTAAAAAATTATAAATTT
1 TTTTAAAAAATTACAAATTT
17818305 TTTTAAAAAA-TACAAATTT
1 TTTTAAAAAATTACAAATTT
17818324 AGAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAAAAATTACAAATTT
Found at i:17818357 original size:19 final size:20
Alignment explanation
Indices: 17818326--17818363 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17818316 ACAAATTTAG
17818326 AATTTTTATAAA-TATTTTC
1 AATTTTTATAAATTATTTTC
17818345 AATTTTTGA-AAATTATTTT
1 AATTTTT-ATAAATTATTTT
17818364 GATTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTTTTATAAATTATTTTC
Found at i:17821522 original size:27 final size:27
Alignment explanation
Indices: 17821466--17821546 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
17821456 TGATCTATTA
* *
17821466 AAATA-AAATATTAAAGT-AACAT-AT
1 AAATATAAATATAAAATTAAACATAAT
* *
17821490 AAAAATTAAATATCAAATTTAAACATAAT
1 AAATA-TAAATAT-AAAATTAAACATAAT
* *
17821519 AAATATATATATAAAATTAAACTTAAT
1 AAATATAAATATAAAATTAAACATAAT
17821546 A
1 A
17821547 TAACCCCTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
24 4 0.09
26 6 0.14
27 17 0.39
28 11 0.25
29 6 0.14
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (27 bp):
AAATATAAATATAAAATTAAACATAAT
Found at i:17821907 original size:29 final size:30
Alignment explanation
Indices: 17821845--17821909 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
17821835 AATTTACAAG
**
17821845 AATTGCATAAAATCGAAATTTCATGTATAA
1 AATTGCATAAAATCGAAAAATCATGTATAA
*
17821875 AATTGCATAAAATC-AAAAATCATGTATAC
1 AATTGCATAAAATCGAAAAATCATGTATAA
17821904 AATTGC
1 AATTGC
17821910 CCATTAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (30 bp):
AATTGCATAAAATCGAAAAATCATGTATAA
Found at i:17826738 original size:14 final size:13
Alignment explanation
Indices: 17826703--17826737 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
17826693 TTTTTTATAA
17826703 TTAATTTTAATTT
1 TTAATTTTAATTT
*
17826716 TTACATTTTACTTT
1 TTA-ATTTTAATTT
17826730 TTAATTTT
1 TTAATTTT
17826738 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAATTTTAATTT
Done.