Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 3 of 208
Found at i:905331 original size:14 final size:14
Alignment explanation
Indices: 905312--905351 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
905302 TTGATTAGCA
905312 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
905326 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
905340 GGAAAATGTTTT
1 GTAAAATGTTTT
905352 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:905364 original size:34 final size:35
Alignment explanation
Indices: 905320--905386 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
905310 CAGTAAAATG
* *
905320 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
905354 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
905387 CTTGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:905373 original size:20 final size:20
Alignment explanation
Indices: 905335--905374 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
905325 CGTAAAATGA
**
905335 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
905355 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
905375 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:908112 original size:24 final size:24
Alignment explanation
Indices: 908085--908133 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
908075 TGCAATCGAT
908085 AGGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
908109 AGGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
908133 A
1 A
908134 TGGTTTCAAG
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:0.04, G:0.49, T:0.12
Consensus pattern (24 bp):
AGGGTGAAGAGAGGAGCTGTGGAA
Found at i:909083 original size:18 final size:17
Alignment explanation
Indices: 909050--909088 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
909040 TTGTATAAAT
909050 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
909068 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
909085 TGTG
1 TGTG
909089 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:909341 original size:23 final size:23
Alignment explanation
Indices: 909314--909388 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
909304 AGTGTTATTG
909314 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
909337 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
909360 ATCAGTGGTAGCTTCCGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
909383 ATCAGT
1 ATCAGT
909389 CTGGCACTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:910734 original size:37 final size:39
Alignment explanation
Indices: 910687--910783 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
910677 GGATTAATTT
**
910687 GATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGCC
1 GATGAGGCACTGGGTGCCAATTATTACTTCGAATTAGCC
* ** **
910724 GATGAGGCACTGAGTGTTAAATTATTACTTCGAATTATTC
1 GATGAGGCACTGGGTG-CCAATTATTACTTCGAATTAGCC
910764 GATGAGGCACTGGGTGCCAA
1 GATGAGGCACTGGGTGCCAA
910784 ACTGGTGTGT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
37 15 0.32
38 2 0.04
39 3 0.06
40 27 0.57
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (39 bp):
GATGAGGCACTGGGTGCCAATTATTACTTCGAATTAGCC
Found at i:932990 original size:29 final size:29
Alignment explanation
Indices: 932950--933011 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
932940 TTTATTTTTT
932950 ATTT-TTTAATAATAAAAAGATTAATTTA
1 ATTTATTTAATAATAAAAAGATTAATTTA
*
932978 ATTTATTTAATAATAAAGAGATTAATTTA
1 ATTTATTTAATAATAAAAAGATTAATTTA
933007 ATTTA
1 ATTTA
933012 GTCTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (29 bp):
ATTTATTTAATAATAAAAAGATTAATTTA
Found at i:934083 original size:19 final size:19
Alignment explanation
Indices: 934051--934087 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
934041 ACTAATAACT
* *
934051 TAAAATTTAGAATTAAAAA
1 TAAAAATTAAAATTAAAAA
934070 TAAAAATTAAAATTAAAA
1 TAAAAATTAAAATTAAAA
934088 TACAAATATC
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:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAAAATTAAAATTAAAAA
Found at i:934503 original size:31 final size:30
Alignment explanation
Indices: 934435--934503 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
934425 GATGATGGTC
*
934435 GGACTATAATTTTTAAATTGAAAAAGTATAT
1 GGACTA-AATTTTTAAATTGAAAAAGTATAG
* *
934466 GAACTAAA-TTTTAAATTTTAAATAAGTATAG
1 GGACTAAATTTTTAAA-TTGAAA-AAGTATAG
934497 GGACTAA
1 GGACTAA
934504 CAACATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.22
30 7 0.22
31 18 0.56
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.36
Consensus pattern (30 bp):
GGACTAAATTTTTAAATTGAAAAAGTATAG
Found at i:946832 original size:16 final size:16
Alignment explanation
Indices: 946805--946850 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
946795 AAAAAGTATT
946805 TTAAAAATATTTTAAAA
1 TTAAAAA-ATTTTAAAA
946822 TTAAAAAA-TTTAAAA
1 TTAAAAAATTTTAAAA
*
946837 TTTAAAAATATTTA
1 TTAAAAAAT-TTTA
946851 TTATATCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 14 0.54
16 1 0.04
17 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:946850 original size:17 final size:17
Alignment explanation
Indices: 946804--946850 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
946794 AAAAAAGTAT
946804 TTTAAAAATATTTTAAAA
1 TTTAAAAATA-TTTAAAA
946822 -TTAAAAA-ATTTAAAA
1 TTTAAAAATATTTAAAA
946837 TTTAAAAATATTTA
1 TTTAAAAATATTTA
946851 TTATATCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAAATATTTAAAA
Found at i:949638 original size:44 final size:44
Alignment explanation
Indices: 949555--949638 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
949545 TTAGGGTTTT
* * *
949555 TCTGCTTAACTTTGTAGTGTTGGGCCAGGAACCGTTTTGGGCCG
1 TCTGCTTAACTTTGTAATGTTGGACCAGGAACCGCTTTGGGCCG
* * * *
949599 TCTGTTTAATTTTGTAATGTTGGACTAGGAACTGCTTTGG
1 TCTGCTTAACTTTGTAATGTTGGACCAGGAACCGCTTTGG
949639 ACCGATTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.39
Consensus pattern (44 bp):
TCTGCTTAACTTTGTAATGTTGGACCAGGAACCGCTTTGGGCCG
Found at i:952679 original size:236 final size:236
Alignment explanation
Indices: 952247--952946 Score: 1039
Period size: 236 Copynumber: 3.0 Consensus size: 236
952237 TGGTGACTAA
* * * * * *
952247 TTAAAATACTACACATCGAGTTTACGTTTTATGCATATTTCAAGTTCGAGCAGAACTTGGTCCGG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
* *
952312 AGCCATTAGTTGAAACGGAAGTAACTAATGAGTACGATGAGTGGACTCAAAGTGAACAAACTAAT
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGT---ATGGGTGGACTCAAAGTGAACAAACTAAT
* * * * * *
952377 GAATTTATAACACCCTATCCAGTTTTCGACAATGAGAACTTTATTGCTAACGGGAATGAAGTGAT
128 GAATTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGAT
* * *
952442 CTCCTATCACCAGTCGCAAGTAATAACACTTTTCTCGGAAATTT
193 CTCCAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
952486 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
*
952551 AGCCATTAGTTGAAACCGAAGTTACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
*
952616 TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATTGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGATCTC
952681 CAATCACCAAG-CACAAGTAAGAACACTTTTCTCGGAAATTT
196 CAATCACC-AGTCACAAGTAAGAACACTTTTCTCGGAAATTT
* * *
952722 TTAAAATACTACACATTGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCGGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
* * *
952787 AGCCATTAGTTGAAAACGAAGTAACTAATGAGTACGGGTGGACTCAAAGTGAACAAACTTATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
952852 TTTATAACTCCCTGTCCGGTTTTCGAC-------A--TTA---ATGATGGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGATCTC
*
952905 CAATCACCAGTCACAAGTAAGAACAATTTTCTCGGAAATTT
196 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
952946 T
1 T
952947 GAAGTTTAGT
Statistics
Matches: 431, Mismatches: 28, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
223 2 0.00
224 59 0.14
227 3 0.01
229 1 0.00
236 274 0.64
237 2 0.00
239 90 0.21
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (236 bp):
TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGATCTC
CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
Found at i:957336 original size:18 final size:20
Alignment explanation
Indices: 957299--957337 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
957289 TAAAAAAATT
*
957299 TATTATTTAAATTATTTAAA
1 TATTATTTAAAATATTTAAA
957319 TATT-TTTAAAAT-TTTAAA
1 TATTATTTAAAATATTTAAA
957337 T
1 T
957338 TAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTTAAAATATTTAAA
Found at i:957397 original size:29 final size:32
Alignment explanation
Indices: 957337--957401 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 32
957327 AAATTTTAAA
* **
957337 TTAATATATATATATAATTTTATCTTTTTCTT
1 TTAATATATATATATAATTTAATCTTAATCTT
957369 TTAATAT-TATATAT-ATTTAAT-TTAATCTT
1 TTAATATATATATATAATTTAATCTTAATCTT
957398 TTAA
1 TTAA
957402 AAATTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 6 0.20
31 7 0.23
32 7 0.23
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (32 bp):
TTAATATATATATATAATTTAATCTTAATCTT
Found at i:959874 original size:14 final size:14
Alignment explanation
Indices: 959855--959924 Score: 99
Period size: 14 Copynumber: 5.1 Consensus size: 14
959845 TAAGGTGTAG
959855 TATTTATAACAGTA
1 TATTTATAACAGTA
959869 TATTTATAACAGTA
1 TATTTATAACAGTA
* *
959883 TA-CTAAAACAGTA
1 TATTTATAACAGTA
*
959896 TA-TTAAAACAGTA
1 TATTTATAACAGTA
959909 TATTTATAACAGTA
1 TATTTATAACAGTA
959923 TA
1 TA
959925 ATAAACTAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 23 0.45
14 28 0.55
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (14 bp):
TATTTATAACAGTA
Found at i:959893 original size:27 final size:27
Alignment explanation
Indices: 959862--959929 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
959852 TAGTATTTAT
*
959862 AACAGTATATTTATAACAGTATA-CTAA
1 AACAGTATA-TTAAAACAGTATATCTAA
* *
959889 AACAGTATATTAAAACAGTATATTTAT
1 AACAGTATATTAAAACAGTATATCTAA
*
959916 AACAGTATAATAAA
1 AACAGTATATTAAA
959930 CTAGTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.32
Consensus pattern (27 bp):
AACAGTATATTAAAACAGTATATCTAA
Found at i:959894 original size:13 final size:13
Alignment explanation
Indices: 959853--959929 Score: 84
Period size: 13 Copynumber: 5.8 Consensus size: 13
959843 ATTAAGGTGT
*
959853 AGTAT-TTATAAC
1 AGTATATTAAAAC
*
959865 AGTATATTTATAAC
1 AGTATA-TTAAAAC
*
959879 AGTATACTAAAAC
1 AGTATATTAAAAC
959892 AGTATATTAAAAC
1 AGTATATTAAAAC
*
959905 AGTATATTTATAAC
1 AGTATA-TTAAAAC
*
959919 AGTATAATAAA
1 AGTATATTAAA
959930 CTAGTTATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
12 5 0.09
13 26 0.46
14 25 0.45
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:959911 original size:40 final size:39
Alignment explanation
Indices: 959853--959929 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 39
959843 ATTAAGGTGT
* *
959853 AGTATTTATAACAGTATATTTATAACAGTATACTAAAAC
1 AGTATTTAAAACAGTATATTTATAACAGTATAATAAAAC
959892 AGTATATTAAAACAGTATATTTATAACAGTATAATAAA
1 AGTAT-TTAAAACAGTATATTTATAACAGTATAATAAA
959930 CTAGTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 5 0.14
40 30 0.86
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (39 bp):
AGTATTTAAAACAGTATATTTATAACAGTATAATAAAAC
Found at i:961693 original size:49 final size:51
Alignment explanation
Indices: 961626--961762 Score: 190
Period size: 49 Copynumber: 2.7 Consensus size: 51
961616 AGTGTGGTAA
* * * **
961626 TATGTGAAGGCCACTTTGTAAAGAAAGATAGTTTTGGTCACAA-T-TGTGG
1 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGTCAGTAC
961675 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGTGCAGTAC
1 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGT-CAGTAC
*
961727 TATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG
1 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGG
961763 CTACAAGGGT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
49 41 0.52
50 1 0.01
51 12 0.15
52 25 0.32
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGTCAGTAC
Found at i:963039 original size:29 final size:28
Alignment explanation
Indices: 963006--963075 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
962996 AAGATTAAAA
*
963006 AAATTTAAAAAGTAATTTTAAAA-TATTTT
1 AAATTTAAAAA--AATTTAAAAAGTATTTT
*
963035 CAATTTTAAAAAAATTTAAAAAGTATTTT
1 -AAATTTAAAAAAATTTAAAAAGTATTTT
*
963064 AAAATTAAAAAA
1 AAATTTAAAAAA
963076 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 19 0.54
29 6 0.17
30 10 0.29
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (28 bp):
AAATTTAAAAAAATTTAAAAAGTATTTT
Found at i:963063 original size:39 final size:37
Alignment explanation
Indices: 962976--963068 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 37
962966 AATAAAAATA
962976 AAAAAGTA-TTTAAAATATTTAAGATTAAAAAAATTT
1 AAAAAGTATTTTAAAATATTTAAGATTAAAAAAATTT
**
963012 AAAAAGTAATTTTAAAATATTTTCAATTTTAAAAAAATTT
1 AAAAAGT-ATTTTAAAATA-TTT-AAGATTAAAAAAATTT
963052 AAAAAGTATTTTAAAAT
1 AAAAAGTATTTTAAAAT
963069 TAAAAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
36 7 0.14
37 1 0.02
38 9 0.18
39 13 0.25
40 21 0.41
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (37 bp):
AAAAAGTATTTTAAAATATTTAAGATTAAAAAAATTT
Found at i:965820 original size:236 final size:236
Alignment explanation
Indices: 965397--965868 Score: 653
Period size: 236 Copynumber: 2.0 Consensus size: 236
965387 TGGTGACTAA
* * * * * *
965397 TTAAAATATTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCGAGTAGAACTTGGTCCGG
1 TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTCCAG
*
965462 AGCCATTAGTTGAAACAGAAGTCACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACAGAAGTCACTAAAGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAA
* * * * *
965527 TTTATAACACCATATCTGGTTTTCGACAATGAGAACTCTATTGATGACGGGAATGAAGTGATCTC
131 TTTAGAACACCATATCCGGTTTTCAACAACGAGAACTCTATTGATGACGGGAATGAAGTGAGCTC
*
965592 CAATTACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
196 CAATCACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
**
965633 TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTTTAG
1 TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTCCAG
* *
965698 AGCCATTAGTTGAAATC-GAAGT-AGCTAAAGAGTACG-GATGGACTCGAGGTGAACAAACTAAT
66 AGCCATTAGTTGAAA-CAGAAGTCA-CTAAAGAGTACGAG-TGGACTCAAAGTGAACAAACTAAT
* * * * * *
965760 GAATTTAGAACTCCCTGTCCGGTTTTCAACAACGAGAACTTTATTGATGATGGTAATGAAGTGAG
128 GAATTTAGAACACCATATCCGGTTTTCAACAACGAGAACTCTATTGATGACGGGAATGAAGTGAG
* * * *
965825 CTCTAATCACCAGTCACAAGTAAGAACTCTTTTCTTGTAAATTT
193 CTCCAATCACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
965869 CGAAGTTCAG
Statistics
Matches: 206, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
235 2 0.01
236 203 0.99
237 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (236 bp):
TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTCCAG
AGCCATTAGTTGAAACAGAAGTCACTAAAGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAA
TTTAGAACACCATATCCGGTTTTCAACAACGAGAACTCTATTGATGACGGGAATGAAGTGAGCTC
CAATCACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
Found at i:968654 original size:18 final size:18
Alignment explanation
Indices: 968631--968666 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
968621 TAATTATATT
968631 ATATTTA-ATTATTTTATA
1 ATATTTATATT-TTTTATA
968649 ATATTTATATTTTTTATA
1 ATATTTATATTTTTTATA
968667 TAAGACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTATATTTTTTATA
Found at i:970649 original size:236 final size:233
Alignment explanation
Indices: 970228--970924 Score: 1052
Period size: 236 Copynumber: 3.0 Consensus size: 233
970218 TGGTGACTAA
* ** * *
970228 TTAAAATACTACACATCAAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTTGGTCCGG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
* * * *
970293 AGCCATTAGTTGAAACGGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAATTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
* * *
970358 TTTATAACACCCTATCCAGTTTTCAACAATGAGAACTTTATTGATGACGGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCAGTTTTC-ACAA-GA-AACTTTATTGATGATGGGAATGAAGTGATCTC
*
970423 CCATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
193 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
970464 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
* *
970529 AGTCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTTGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
* *
970594 TTTATAACTCCCTGTCCGGTTTTCGACAACGAAAACTTTATTGATGATTGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCAGTTTTC-ACAA-G-AAACTTTATTGATGATGGGAATGAAGTGATCTC
*
970659 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGAAAATTT
193 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
*
970700 TTAAAATACTACACATTGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
* *
970765 AGCCATTAGTTGAAATCGAAGTAACTAATGAGTATAGGTGGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
*
970830 TTTATAACTCCCTGTCCAGTTTT----AG--AC---ATAGATGATGGGAATGAAGTGATCTCCAA
131 TTTATAACTCCCTGTCCAGTTTTCACAAGAAACTTTATTGATGATGGGAATGAAGTGATCTCCAA
* * *
970886 TAACCAGTCACAAGTAAGATCACTTTTCTCAGAAATTT
196 TCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
970924 T
1 T
970925 GAAGTTTAGT
Statistics
Matches: 428, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
224 62 0.14
227 2 0.00
230 1 0.00
231 1 0.00
236 361 0.84
237 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (233 bp):
TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
TTTATAACTCCCTGTCCAGTTTTCACAAGAAACTTTATTGATGATGGGAATGAAGTGATCTCCAA
TCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
Found at i:973369 original size:51 final size:51
Alignment explanation
Indices: 973314--973417 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 51
973304 TCAATAACGG
* *
973314 AACAGTAACAGTATTCGACACACAAAGTGCTGAATCGGTAAC-GATAACAGT
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAG-TAACAGT
973365 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAACAGT
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAACAGT
973416 AA
1 AA
973418 TCAGCACATA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 49 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (51 bp):
AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAACAGT
Found at i:974823 original size:9 final size:9
Alignment explanation
Indices: 974809--974858 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
974799 CATTTGAATA
974809 AATAATTAT
1 AATAATTAT
974818 AATAATTAT
1 AATAATTAT
*
974827 AATATTTAT
1 AATAATTAT
974836 -ATACA-TAT
1 AATA-ATTAT
*
974844 AATATTTAT
1 AATAATTAT
974853 ATATAA
1 A-ATAA
974859 CTTAAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
8 6 0.18
9 24 0.73
10 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (9 bp):
AATAATTAT
Found at i:978931 original size:18 final size:18
Alignment explanation
Indices: 978903--978947 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
978893 TGCAATATGA
* *
978903 ACACACGCACGCACGCAC
1 ACACACACACGCACACAC
*
978921 GCACACACACGCACACAC
1 ACACACACACGCACACAC
978939 ACACACACA
1 ACACACACA
978948 AAATTTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.49, G:0.11, T:0.00
Consensus pattern (18 bp):
ACACACACACGCACACAC
Found at i:978933 original size:14 final size:14
Alignment explanation
Indices: 978904--978944 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
978894 GCAATATGAA
* *
978904 CACACGCACGCACG
1 CACACACACACACG
*
978918 CACGCACACACACG
1 CACACACACACACG
978932 CACACACACACAC
1 CACACACACACAC
978945 ACAAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.51, G:0.12, T:0.00
Consensus pattern (14 bp):
CACACACACACACG
Found at i:980877 original size:23 final size:25
Alignment explanation
Indices: 980846--980893 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
980836 TTCTGTTATT
980846 AACAGAGA-TTCCCGATCTTTGCCA
1 AACAGAGATTTCCCGATCTTTGCCA
980870 AACA-AGATTTCCCGATCTTTGCCA
1 AACAGAGATTTCCCGATCTTTGCCA
980894 CATCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (25 bp):
AACAGAGATTTCCCGATCTTTGCCA
Found at i:985453 original size:6 final size:6
Alignment explanation
Indices: 985442--985479 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
985432 AGGTGACATG
985442 CATATA CATATA CATATA CATATA CATATA CATATA CA
1 CATATA CATATA CATATA CATATA CATATA CATATA CA
985480 GGTATTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:1004938 original size:19 final size:20
Alignment explanation
Indices: 1004895--1004939 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1004885 GAAAAAAATT
1004895 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
1004915 A-AAAATTATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
1004933 ATAAAAA
1 ATAAAAA
1004940 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 19 0.90
20 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:1004945 original size:19 final size:19
Alignment explanation
Indices: 1004897--1004946 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1004887 AAAAAATTAT
*
1004897 AAAAATAATAAATTTTAGA
1 AAAAATATTAAATTTTAGA
* *
1004916 AAAATTATTAAATTTTAATA
1 AAAAATATTAAATTTT-AGA
1004936 AAAAAT-TTAAA
1 AAAAATATTAAA
1004947 AAATTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATATTAAATTTTAGA
Found at i:1004957 original size:38 final size:38
Alignment explanation
Indices: 1004915--1005027 Score: 104
Period size: 38 Copynumber: 3.0 Consensus size: 38
1004905 TAAATTTTAG
* *
1004915 AAAAATTATTAAATTTTAATAAAAAAT-TTAAAAAATTA
1 AAAAATTATTAAATTTT-ATAAAAAATCGTAAAAAAATA
* ***
1004953 AAAAATAGATTTTTTTTTATAAAAAATCGTAAAAAAATA
1 AAAAAT-TATTAAATTTTATAAAAAATCGTAAAAAAATA
* * * *
1004992 AAAAATTGTAAAATTTTAT-AAATATCATAAAAAAAT
1 AAAAATTATTAAATTTTATAAAAAATCGTAAAAAAAT
1005028 GACCCCTAGT
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
37 15 0.25
38 22 0.37
39 22 0.37
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (38 bp):
AAAAATTATTAAATTTTATAAAAAATCGTAAAAAAATA
Found at i:1010353 original size:23 final size:23
Alignment explanation
Indices: 1010324--1010398 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
1010314 GTGTTATTGA
1010324 TCAGTGGTAGCTTCGGCTACAGT
1 TCAGTGGTAGCTTCGGCTACAGT
* *
1010347 TCGGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACAGT
1010370 TCAGTGGTAGCTTCGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACAGT
1010392 ATCAGTG
1 -TCAGTG
1010399 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 1 0.02
23 47 0.98
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACAGT
Found at i:1011424 original size:2 final size:2
Alignment explanation
Indices: 1011417--1011442 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1011407 TACAGAATTC
1011417 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
1011443 TTGATATTTT
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:1014466 original size:16 final size:16
Alignment explanation
Indices: 1014439--1014482 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1014429 TTTTTAAGTT
*
1014439 TATAATTCTTTATATTA
1 TATAATT-TATATATTA
1014456 TATATATTTTATATATTA
1 TATA-A-TTTATATATTA
1014474 TATAATTTA
1 TATAATTTA
1014483 CAACACATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 5 0.21
18 13 0.54
19 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAATTTATATATTA
Found at i:1014587 original size:16 final size:16
Alignment explanation
Indices: 1014558--1014598 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
1014548 TGTTAAGATG
*
1014558 ATTATATAAAAAAATTC
1 ATTAAATAAAAAAA-TC
1014575 ATTAAATAAAAAAATC
1 ATTAAATAAAAAAATC
1014591 ATTAAATA
1 ATTAAATA
1014599 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAATAAAAAAATC
Found at i:1014618 original size:22 final size:23
Alignment explanation
Indices: 1014575--1014622 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1014565 AAAAAAATTC
1014575 ATTAAATAAAAAAATCATTAAAT
1 ATTAAATAAAAAAATCATTAAAT
*
1014598 ATTAAATTAAAAGAA-CA-TAAAT
1 ATTAAA-TAAAAAAATCATTAAAT
1014620 ATT
1 ATT
1014623 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTAAATAAAAAAATCATTAAAT
Found at i:1023352 original size:10 final size:10
Alignment explanation
Indices: 1023333--1023407 Score: 73
Period size: 10 Copynumber: 7.6 Consensus size: 10
1023323 TTGTCTTATA
1023333 TTTT-TAATT
1 TTTTATAATT
1023342 TTTTATAA-T
1 TTTTATAATT
*
1023351 TTTTATACTT
1 TTTTATAATT
*
1023361 TTTTATAATA
1 TTTTATAATT
*
1023371 TTTTGTAATT
1 TTTTATAATT
1023381 TTTTATTAATT
1 TTTTA-TAATT
* *
1023392 TATTAAAATT
1 TTTTATAATT
*
1023402 TATTAT
1 TTTTAT
1023408 TTTCTATATT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
9 12 0.22
10 33 0.61
11 9 0.17
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1023429 original size:19 final size:21
Alignment explanation
Indices: 1023405--1023451 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1023395 TAAAATTTAT
1023405 TATTTTCT-ATATTTTTA-AA
1 TATTTTCTCATATTTTTACAA
*
1023424 TATTTT-TCATTTTTTTACAA
1 TATTTTCTCATATTTTTACAA
1023444 TATTTTCT
1 TATTTTCT
1023452 TTTTGCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 8 0.33
21 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTCTCATATTTTTACAA
Found at i:1023597 original size:9 final size:9
Alignment explanation
Indices: 1023576--1023635 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
1023566 CAATAAGTTT
*
1023576 TTTTTGTAA
1 TTTTTATAA
1023585 TTTTTAT-A
1 TTTTTATAA
*
1023593 TTTTTGTATA
1 TTTTTATA-A
1023603 TTTTTATAA
1 TTTTTATAA
**
1023612 TGATTATAA
1 TTTTTATAA
*
1023621 TTTTTATTA
1 TTTTTATAA
1023630 TTTTTA
1 TTTTTA
1023636 ATAAAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 7 0.17
9 26 0.63
10 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1023645 original size:28 final size:27
Alignment explanation
Indices: 1023588--1023645 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1023578 TTTGTAATTT
* **
1023588 TTATATTTTTGTATATTTTTATAATGA
1 TTATATTTTTATATATTTTTATAAAAA
1023615 TTATAATTTTTAT-TATTTTTAATAAAAA
1 TTAT-ATTTTTATATATTTTT-ATAAAAA
1023643 TTA
1 TTA
1023646 GTTTTCACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
TTATATTTTTATATATTTTTATAAAAA
Found at i:1033626 original size:3 final size:3
Alignment explanation
Indices: 1033618--1033649 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1033608 CTTTATGGTC
*
1033618 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1033650 TTTAACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1037016 original size:14 final size:14
Alignment explanation
Indices: 1036997--1037036 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1036987 TTGATTGGCA
1036997 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
1037011 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
1037025 GGAAAATGTTTT
1 GTAAAATGTTTT
1037037 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:1037049 original size:34 final size:35
Alignment explanation
Indices: 1037005--1037071 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1036995 CAGTAAAATG
* *
1037005 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
1037039 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
1037072 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:1037058 original size:20 final size:20
Alignment explanation
Indices: 1037020--1037059 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1037010 CGTAAAATGA
**
1037020 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
1037040 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
1037060 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:1038446 original size:27 final size:27
Alignment explanation
Indices: 1038416--1038485 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1038406 AATAATCAAT
*
1038416 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
1038443 TCAATATCTAACCAATTCAAGACATATA
1 TCAATATCCAA-CAATTCAAAACATATA
*
1038471 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
1038486 CTAAAATCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:1042999 original size:6 final size:6
Alignment explanation
Indices: 1042985--1043038 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
1042975 TATGCGAATC
* * ** *
1042985 CAGAAA CAGACA CAGAAA CAAAAA CAGAAA CAGACC CAGAAA CAAAAA
1 CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA
1043033 CAGAAA
1 CAGAAA
1043039 ATAAAATCCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.65, C:0.22, G:0.13, T:0.00
Consensus pattern (6 bp):
CAGAAA
Found at i:1043017 original size:24 final size:24
Alignment explanation
Indices: 1042985--1043038 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1042975 TATGCGAATC
1042985 CAGAAACAGACACAGAAACAAAAA
1 CAGAAACAGACACAGAAACAAAAA
*
1043009 CAGAAACAGACCCAGAAACAAAAA
1 CAGAAACAGACACAGAAACAAAAA
1043033 CAGAAA
1 CAGAAA
1043039 ATAAAATCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.65, C:0.22, G:0.13, T:0.00
Consensus pattern (24 bp):
CAGAAACAGACACAGAAACAAAAA
Found at i:1045447 original size:1 final size:1
Alignment explanation
Indices: 1045443--1045468 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1045433 TTTAAAAGAC
1045443 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1045469 CAAGGCATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1050629 original size:21 final size:22
Alignment explanation
Indices: 1050580--1050629 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1050570 ATATTATTTT
* *
1050580 AAATT-TTTTAATATTTATATT
1 AAATTATTTCAATATTTATATA
*
1050601 ATATTATTTCAATATTTA-ATA
1 AAATTATTTCAATATTTATATA
1050622 AAATTATT
1 AAATTATT
1050630 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTATTTCAATATTTATATA
Found at i:1051007 original size:11 final size:12
Alignment explanation
Indices: 1050993--1051021 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1050983 AAAATTTAAA
1050993 TTAAAT-ATTAT
1 TTAAATAATTAT
1051004 TTAAATAATTAT
1 TTAAATAATTAT
1051016 TTAAAT
1 TTAAAT
1051022 TAAGGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATAATTAT
Found at i:1054799 original size:20 final size:21
Alignment explanation
Indices: 1054749--1054800 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1054739 CGCTTGGAGT
*
1054749 ACTCTTTTCGATATTACTCTA
1 ACTCTTTTCAATATTACTCTA
* *
1054770 ACTTTTTTCAATATTATTCTA
1 ACTCTTTTCAATATTACTCTA
1054791 A-TCTTTTCAA
1 ACTCTTTTCAA
1054801 ATCTGGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (21 bp):
ACTCTTTTCAATATTACTCTA
Found at i:1068545 original size:518 final size:517
Alignment explanation
Indices: 1067569--1068592 Score: 1829
Period size: 518 Copynumber: 2.0 Consensus size: 517
1067559 AGAATCTTTA
*
1067569 ATTCCGCGTGGAGTTTCTCCATCAATCAATGACTCGCGCTTGCTTTTACTTTGGGATAAACTAAC
1 ATTCCGCGTGGAGTTTCTCCATCAAGCAATGACTCGCGCTTGCTTTTACTTTGGGATAAACTAAC
*
1067634 TTTTAATCTTTGATTTTGATATTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTTTT
66 TTTTAATCATTGATTTTGATATTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTTTT
1067699 AGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGTAC
131 AGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGTAC
*
1067764 TATGTTATCACTTAAAAAATATATTTTTCTTTTCGTTTTAGGAATTTTTATTTGTTCTCGTAGTA
196 TATGTTATCACTTAAAAAATATATTTTTCTTTTCGTTTTAGGAATTTTTATCTGTTCTCGTAGTA
*
1067829 TATTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTGGTTTTATGGATAGTTTTGT
261 TATTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTAGTTTTATGGATAGTTTTGT
*
1067894 TGCCGTTCTCTCTAGTTTGATGAATGCTCTAATATTTTTTCGATTTTTACCTACCGCTTTGGATC
326 TGCCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTGGATC
1067959 ATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTTGAAT
391 ATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTTGAAT
1068024 TGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGTTGAAACAGTGT
456 TGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGTTGAAACAGTGT
*
1068086 ATTCCGCGTGGGGTTTCTCCATCAAGCAATGACTCGC-CATTGCTTTTACTTTGGGATAAACTAA
1 ATTCCGCGTGGAGTTTCTCCATCAAGCAATGACTCGCGC-TTGCTTTTACTTTGGGATAAACTAA
1068150 CTTTTAATCATTGATTTTGATATTTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTT
65 CTTTTAATCATTGATTTTGATA-TTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTT
* * *
1068215 TTAGAATTTGATAATTTTTTTTTTTTAGTTTTAGGTCAGGTGGTGACATGATAATATGATATTGT
129 TTAGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGT
* *
1068280 ACTATGTTATCACTTTAAAAATATATTTTTC-TTTCTGTTTTAGGAATTTTTATCTGTTCTTGTA
194 ACTATGTTATCACTTAAAAAATATATTTTTCTTTTC-GTTTTAGGAATTTTTATCTGTTCTCGTA
* *
1068344 GTA-AGTTTTTTTAGTCTTGTTTATACAAATAACTTTAGTTTTACAAGTAGTTTTATGGATAGTT
258 GTATA-TTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTAGTTTTATGGATAGTT
*
1068408 TTGTTGTCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTG
322 TTGTTGCCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTG
1068473 GATCATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTT
387 GATCATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTT
* * * *
1068538 GAATTGTGATAATGCCATTTGTTAACGGGTCGGGTCATGATATTGAAGCTAAAGT
452 GAATTGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGT
1068593 CTTTGTTGTG
Statistics
Matches: 485, Mismatches: 18, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
516 1 0.00
517 86 0.18
518 398 0.82
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.46
Consensus pattern (517 bp):
ATTCCGCGTGGAGTTTCTCCATCAAGCAATGACTCGCGCTTGCTTTTACTTTGGGATAAACTAAC
TTTTAATCATTGATTTTGATATTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTTTT
AGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGTAC
TATGTTATCACTTAAAAAATATATTTTTCTTTTCGTTTTAGGAATTTTTATCTGTTCTCGTAGTA
TATTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTAGTTTTATGGATAGTTTTGT
TGCCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTGGATC
ATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTTGAAT
TGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGTTGAAACAGTGT
Found at i:1071392 original size:14 final size:14
Alignment explanation
Indices: 1071371--1071404 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1071361 TGGTATGGGT
1071371 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
1071384 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
1071398 TTATAGG
1 TTATAGG
1071405 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:1071558 original size:24 final size:25
Alignment explanation
Indices: 1071531--1071580 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1071521 AAGATGAAAG
1071531 TTTAAAGTACATAAAA-GAAAAAAA
1 TTTAAAGTACATAAAACGAAAAAAA
* *
1071555 TTTAAATTACTTAAAACGAAAAAAA
1 TTTAAAGTACATAAAACGAAAAAAA
1071580 T
1 T
1071581 ATGGGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (25 bp):
TTTAAAGTACATAAAACGAAAAAAA
Found at i:1073356 original size:13 final size:13
Alignment explanation
Indices: 1073338--1073362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1073328 ATCAAGAAAG
1073338 CCAGTTGATACTT
1 CCAGTTGATACTT
1073351 CCAGTTGATACT
1 CCAGTTGATACT
1073363 AATGATAGAA
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:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (13 bp):
CCAGTTGATACTT
Found at i:1076526 original size:21 final size:22
Alignment explanation
Indices: 1076477--1076527 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1076467 TATCCTGCCA
* *
1076477 AAAATTATTGGTATTTTTAAAT
1 AAAATTATTAGTATTATTAAAT
* *
1076499 GAAATTATTAGTA-TATTATAT
1 AAAATTATTAGTATTATTAAAT
1076520 AAAATTAT
1 AAAATTAT
1076528 ATAAAGAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
AAAATTATTAGTATTATTAAAT
Found at i:1082822 original size:7 final size:7
Alignment explanation
Indices: 1082798--1082925 Score: 50
Period size: 7 Copynumber: 17.7 Consensus size: 7
1082788 ATTATTTTAA
1082798 ATTATAT
1 ATTATAT
*
1082805 TTTATAGT
1 ATTATA-T
1082813 ATTATAT
1 ATTATAT
1082820 ATTATGAT
1 ATTAT-AT
* *
1082828 TTTAGTAA
1 ATTA-TAT
1082836 ATTCATAT
1 ATT-ATAT
*
1082844 AATA-AT
1 ATTATAT
1082850 ATT-TAAT
1 ATTAT-AT
* *
1082857 ACTACATAG
1 A-T-TATAT
*
1082866 ATTATAA
1 ATTATAT
1082873 ATTATAT
1 ATTATAT
1082880 -TTA-AT
1 ATTATAT
1082885 AATTAT-T
1 -ATTATAT
* *
1082892 ATTTTAA
1 ATTATAT
1082899 ATTATAT
1 ATTATAT
*
1082906 TTTATAGT
1 ATTATA-T
1082914 ATTATAT
1 ATTATAT
1082921 ATTAT
1 ATTAT
1082926 GATTTTAGTA
Statistics
Matches: 88, Mismatches: 19, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
5 2 0.02
6 11 0.12
7 44 0.50
8 26 0.30
9 4 0.05
10 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:1082872 original size:101 final size:101
Alignment explanation
Indices: 1082746--1082961 Score: 391
Period size: 101 Copynumber: 2.2 Consensus size: 101
1082736 TATTCTATTG
*
1082746 AGAA-ATTTAA-ACAACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 AGAATATTTAATACTACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1082809 TAGTATTATATATTATGATTTTAGTAAATTCATATA
66 TAGTATTATATATTATGATTTTAGTAAATTCATATA
* *
1082845 ATAATATTTAATACTACATAGATTATAAATTATATTTAATAATTATTATTTTAAATTATATTTTA
1 AGAATATTTAATACTACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1082910 TAGTATTATATATTATGATTTTAGTAAATTCATATA
66 TAGTATTATATATTATGATTTTAGTAAATTCATATA
1082946 AGAATATTTAATACTA
1 AGAATATTTAATACTA
1082962 AGAATTTTAT
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
99 3 0.03
100 6 0.05
101 102 0.92
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (101 bp):
AGAATATTTAATACTACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
TAGTATTATATATTATGATTTTAGTAAATTCATATA
Found at i:1082905 original size:26 final size:26
Alignment explanation
Indices: 1082765--1082925 Score: 95
Period size: 26 Copynumber: 6.2 Consensus size: 26
1082755 AACAACATAG
*
1082765 ATTATAAATTATATTTAATAATAATT
1 ATTATAAATTATATTTAATAATTATT
* *
1082791 ATTTTAAATTATATTT--T-A-TAGT
1 ATTATAAATTATATTTAATAATTATT
* *
1082813 ATTATATATTATGATTTTAGTAA--ATT
1 ATTATAAATTAT-A-TTTAATAATTATT
* * * *
1082839 CA-TAT-AATAATATTTAATACTACATAG
1 -ATTATAAATTATATTTAATAAT-TAT-T
1082866 ATTATAAATTATATTTAATAATTATT
1 ATTATAAATTATATTTAATAATTATT
* *
1082892 ATTTTAAATTATATTTTATAGTATTATAT
1 ATTATAAATTATATTTAATA--ATTAT-T
1082921 ATTAT
1 ATTAT
1082926 GATTTTAGTA
Statistics
Matches: 102, Mismatches: 18, Indels: 27
0.69 0.12 0.18
Matches are distributed among these distances:
22 12 0.12
23 8 0.08
24 5 0.05
25 4 0.04
26 42 0.41
27 7 0.07
28 19 0.19
29 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATAAATTATATTTAATAATTATT
Found at i:1083294 original size:44 final size:46
Alignment explanation
Indices: 1083239--1083327 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
1083229 CATCTTATTA
*
1083239 CATTCAACCAAACACAAGA-ATACC-ATTACGCCTCTATTCCATTC
1 CATTCAACCAAACAAAAGATATACCTATTACGCCTCTATTCCATTC
* * * *
1083283 CATTTAACCAAACAAAATATTTACCTATTACGTCTCTATTCCATT
1 CATTCAACCAAACAAAAGATATACCTATTACGCCTCTATTCCATT
1083328 ACGCATCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 16 0.42
45 4 0.11
46 18 0.47
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.31
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGATATACCTATTACGCCTCTATTCCATTC
Found at i:1083330 original size:16 final size:15
Alignment explanation
Indices: 1083309--1083361 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
1083299 ATATTTACCT
1083309 ATTACGTCTCTATTCC
1 ATTACG-CTCTATTCC
*
1083325 ATTACGCATCTATTTC
1 ATTACGC-TCTATTCC
*
1083341 ATTACACCTCTATTCC
1 ATTAC-GCTCTATTCC
1083357 ATTAC
1 ATTAC
1083362 AACGAACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.25, C:0.30, G:0.04, T:0.42
Consensus pattern (15 bp):
ATTACGCTCTATTCC
Found at i:1083362 original size:16 final size:16
Alignment explanation
Indices: 1083316--1083362 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1083306 CCTATTACGT
*
1083316 CTCTATTCCATTACGC
1 CTCTATTCCATTACAC
* *
1083332 ATCTATTTCATTACAC
1 CTCTATTCCATTACAC
1083348 CTCTATTCCATTACA
1 CTCTATTCCATTACA
1083363 ACGAACCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.32, G:0.02, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAC
Found at i:1085448 original size:18 final size:18
Alignment explanation
Indices: 1085425--1085466 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1085415 CCACAGGAAA
*
1085425 GATAATCTTAGCTTTGAG
1 GATAATCCTAGCTTTGAG
*
1085443 GATAATCCTAGCTTTGCG
1 GATAATCCTAGCTTTGAG
1085461 GATAAT
1 GATAAT
1085467 AGTTTGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (18 bp):
GATAATCCTAGCTTTGAG
Found at i:1085743 original size:31 final size:31
Alignment explanation
Indices: 1085708--1085773 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1085698 TAATTCCATC
1085708 TATCTGCTTTTGATTCTATCCAATTAAAATA
1 TATCTGCTTTTGATTCTATCCAATTAAAATA
1085739 TATCTGCTTTTGATTCTATCCAATTAAAATA
1 TATCTGCTTTTGATTCTATCCAATTAAAATA
1085770 -ATCT
1 TATCT
1085774 TAAATTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (31 bp):
TATCTGCTTTTGATTCTATCCAATTAAAATA
Found at i:1085898 original size:24 final size:24
Alignment explanation
Indices: 1085854--1085901 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1085844 GATACATCCA
* *
1085854 TACTAAAATAAATTATTTTAAAAT
1 TACTAAAATAAATGATGTTAAAAT
1085878 TACTAAAAATAAATGA-GTTAAAAT
1 TACT-AAAATAAATGATGTTAAAAT
1085902 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
TACTAAAATAAATGATGTTAAAAT
Found at i:1094363 original size:32 final size:32
Alignment explanation
Indices: 1094319--1094383 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1094309 TAATAAGGTA
1094319 AGATTTCGATCCTTAATTATAAGGATTCCAAC
1 AGATTTCGATCCTTAATTATAAGGATTCCAAC
* *
1094351 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCGATCCTTAATTATAAGGATTCCAAC
1094383 A
1 A
1094384 ATAGAAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
AGATTTCGATCCTTAATTATAAGGATTCCAAC
Found at i:1104882 original size:35 final size:35
Alignment explanation
Indices: 1104814--1104882 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1104804 AGCTGAAAAC
*
1104814 TATAAAAAATACATTTATAATAAATTTTGCTATTT
1 TATAAAAAATAAATTTATAATAAATTTTGCTATTT
*
1104849 TATAGAAAAATGAAATTT-TAAT-AATTTTTCTATT
1 TATA-AAAAAT-AAATTTATAATAAATTTTGCTATT
1104883 AATTCAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.50
36 10 0.33
37 5 0.17
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (35 bp):
TATAAAAAATAAATTTATAATAAATTTTGCTATTT
Found at i:1111128 original size:17 final size:18
Alignment explanation
Indices: 1111106--1111140 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1111096 TCGAACGGCG
1111106 GAAAAGAAG-AAGGGAAA
1 GAAAAGAAGAAAGGGAAA
1111123 GAAAAGAAGAAAGGGAAA
1 GAAAAGAAGAAAGGGAAA
1111141 ATTGGGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAAAGAAGAAAGGGAAA
Found at i:1115866 original size:30 final size:32
Alignment explanation
Indices: 1115823--1115899 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
1115813 TTTATAATTG
*
1115823 TTAAAATATAA-TTTTACTAATTTTTAAAGGA
1 TTAAAATATAATTTTTACTAATTTTTAAAAGA
* * *
1115854 TTAAATTA-AATTTTTATTATTTTTTAAAAGA
1 TTAAAATATAATTTTTACTAATTTTTAAAAGA
* *
1115885 TTAAAGTGTAATTTT
1 TTAAAATATAATTTT
1115900 ATCATTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 2 0.05
31 30 0.79
32 6 0.16
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (32 bp):
TTAAAATATAATTTTTACTAATTTTTAAAAGA
Found at i:1116381 original size:23 final size:23
Alignment explanation
Indices: 1116355--1116401 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1116345 TATAAGATAG
1116355 TCACTAAACTAATCGAATTTGTC
1 TCACTAAACTAATCGAATTTGTC
1116378 TCACTAAACTAATCGAATTTGTC
1 TCACTAAACTAATCGAATTTGTC
1116401 T
1 T
1116402 TTGTTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (23 bp):
TCACTAAACTAATCGAATTTGTC
Found at i:1116870 original size:162 final size:163
Alignment explanation
Indices: 1116575--1116878 Score: 459
Period size: 162 Copynumber: 1.9 Consensus size: 163
1116565 TTCTTTTTTC
* * *
1116575 TTTTCTTTGCGACATTTCACCTAAAACGCTAAAAAAATAAATTTATTAGTTAAGTTTGATAAAAA
1 TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATAAGTTTGATAAAAA
* *
1116640 AAATAGAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTCTTTT
66 AAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTTT
1116705 AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
131 AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
* * *
1116738 TTTTCTTTGTGACATTTTACCTAAAAAGCTACAAAAATAAATTTATCAGATATA-TTTGATAAAA
1 TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATA-AGTTTGATAAAA
* * * * * *
1116802 AAAA-CCAAGAAATAGGAACACCAGAAAGATCCAAAATAATATTTTTCATCTTTTTTCATTATTT
65 AAAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTT
1116866 TAAAATTAACCCT
130 TAAAATTAACCCT
1116879 CAATACACAA
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 65 0.52
163 60 0.48
164 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (163 bp):
TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATAAGTTTGATAAAAA
AAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTTT
AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
Found at i:1123994 original size:2 final size:2
Alignment explanation
Indices: 1123983--1124016 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1123973 AAAATTTAAT
1123983 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1124017 GTTTCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1127315 original size:31 final size:31
Alignment explanation
Indices: 1127255--1127316 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1127245 AATAACAATC
*
1127255 TAGTAACTTAAATGAAAATTTTCATATAGTT
1 TAGTAACTTAAATGAAAATTTTCAAATAGTT
1127286 TAGTAACTTAAATGAAAATTTAT-AAATAGTT
1 TAGTAACTTAAATGAAAATTT-TCAAATAGTT
1127317 CAGTGATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (31 bp):
TAGTAACTTAAATGAAAATTTTCAAATAGTT
Found at i:1131472 original size:39 final size:39
Alignment explanation
Indices: 1131428--1131502 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
1131418 TCCAAACAAA
1131428 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
1 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
1131467 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACC
1 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACC
1131503 AGTAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (39 bp):
GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
Found at i:1135360 original size:15 final size:15
Alignment explanation
Indices: 1135340--1135370 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1135330 CGCCAAACAG
1135340 CTTTTTTATTCACAA
1 CTTTTTTATTCACAA
1135355 CTTTTTTATTCACAA
1 CTTTTTTATTCACAA
1135370 C
1 C
1135371 GACCATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTTTTTATTCACAA
Found at i:1143199 original size:207 final size:207
Alignment explanation
Indices: 1142844--1143258 Score: 830
Period size: 207 Copynumber: 2.0 Consensus size: 207
1142834 AAAGGCTAGA
1142844 TGTTGTAGTTCGAATTCTAGATTTATTAGATGTTCACTCTTTTATGTAGCTACATAAATAAAGGT
1 TGTTGTAGTTCGAATTCTAGATTTATTAGATGTTCACTCTTTTATGTAGCTACATAAATAAAGGT
1142909 AAATTAGTGAAAATTGGGCAAATTAGGTCTTACACGTTAGATTCAAGAACAAATTGGTTCTTCTG
66 AAATTAGTGAAAATTGGGCAAATTAGGTCTTACACGTTAGATTCAAGAACAAATTGGTTCTTCTG
1142974 TTAAAAGTTTTATCCATTTTTACTATTAAAATTAGTCCATGTATGTCAGCACAAGGTGTACATGT
131 TTAAAAGTTTTATCCATTTTTACTATTAAAATTAGTCCATGTATGTCAGCACAAGGTGTACATGT
1143039 CACGTATAATTG
196 CACGTATAATTG
1143051 TGTTGTAGTTCGAATTCTAGATTTATTAGATGTTCACTCTTTTATGTAGCTACATAAATAAAGGT
1 TGTTGTAGTTCGAATTCTAGATTTATTAGATGTTCACTCTTTTATGTAGCTACATAAATAAAGGT
1143116 AAATTAGTGAAAATTGGGCAAATTAGGTCTTACACGTTAGATTCAAGAACAAATTGGTTCTTCTG
66 AAATTAGTGAAAATTGGGCAAATTAGGTCTTACACGTTAGATTCAAGAACAAATTGGTTCTTCTG
1143181 TTAAAAGTTTTATCCATTTTTACTATTAAAATTAGTCCATGTATGTCAGCACAAGGTGTACATGT
131 TTAAAAGTTTTATCCATTTTTACTATTAAAATTAGTCCATGTATGTCAGCACAAGGTGTACATGT
1143246 CACGTATAATTG
196 CACGTATAATTG
1143258 T
1 T
1143259 CTGGTTATTT
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 208 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (207 bp):
TGTTGTAGTTCGAATTCTAGATTTATTAGATGTTCACTCTTTTATGTAGCTACATAAATAAAGGT
AAATTAGTGAAAATTGGGCAAATTAGGTCTTACACGTTAGATTCAAGAACAAATTGGTTCTTCTG
TTAAAAGTTTTATCCATTTTTACTATTAAAATTAGTCCATGTATGTCAGCACAAGGTGTACATGT
CACGTATAATTG
Found at i:1146360 original size:22 final size:22
Alignment explanation
Indices: 1146332--1146373 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1146322 AGAATTTAAA
1146332 TTTTATAAAGGGATATAAAATT
1 TTTTATAAAGGGATATAAAATT
1146354 TTTTATAAAGGGATATAAAA
1 TTTTATAAAGGGATATAAAA
1146374 ATTAAGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
TTTTATAAAGGGATATAAAATT
Found at i:1147380 original size:13 final size:13
Alignment explanation
Indices: 1147362--1147386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1147352 CTAAAGCCCT
1147362 TATAAACTAGAAG
1 TATAAACTAGAAG
1147375 TATAAACTAGAA
1 TATAAACTAGAA
1147387 ACCTTCCATA
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:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TATAAACTAGAAG
Found at i:1156438 original size:55 final size:57
Alignment explanation
Indices: 1156342--1156523 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 57
1156332 CTAGTAATAT
* * * * * * *
1156342 CTAACTATTAGTAAATTATTTTTTGGTCACTCAATTGTGAAAAGTTACAAGATGGTTA
1 CTAATTATTAGT-AATTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
* * *
1156400 CCTAATTATTAGT-A-T-TTTTTTGGTCACCCAACCATGAAAAGCTACAAAATGATCA
1 -CTAATTATTAGTAATTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
*
1156455 CTAATTATTAGTAAATTTCTTTTTTGGTCACCTAACTATGAAAAGTTACAAAATGGTCA
1 CTAATTATTAGT-AA-TTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
1156514 CTCAATTATT
1 CT-AATTATT
1156524 CAATTTTTTT
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
54 12 0.12
55 32 0.31
56 2 0.02
57 1 0.01
58 1 0.01
59 49 0.47
60 7 0.07
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (57 bp):
CTAATTATTAGTAATTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
Found at i:1157771 original size:25 final size:27
Alignment explanation
Indices: 1157743--1157792 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1157733 GGACTCAAAT
1157743 TTTGGAAATTT-T-AGAA-GAAAATAAG
1 TTTGG-AATTTATAAGAAGGAAAATAAG
1157768 TTTGGAATTTATAAGAAGGAAAATA
1 TTTGGAATTTATAAGAAGGAAAATA
1157793 TTTGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 4 0.18
27 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (27 bp):
TTTGGAATTTATAAGAAGGAAAATAAG
Found at i:1157796 original size:25 final size:23
Alignment explanation
Indices: 1157739--1157796 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
1157729 CCAGGGACTC
1157739 AAAT-TTTGGAAATTTTAGAAGA
1 AAATATTTGGAAATTTTAGAAGA
1157761 AAATAAGTTTGG-AATTTATAAGAAGGA
1 AAAT-A-TTTGGAAATTT-T-AGAA-GA
1157788 AAATATTTG
1 AAATATTTG
1157797 AATAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
22 4 0.13
24 5 0.17
25 10 0.33
26 5 0.17
27 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (23 bp):
AAATATTTGGAAATTTTAGAAGA
Found at i:1166197 original size:14 final size:14
Alignment explanation
Indices: 1166178--1166207 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1166168 TTTTTGAGAA
1166178 TTTAGTCATTTTAC
1 TTTAGTCATTTTAC
1166192 TTTAGTCATTTTAC
1 TTTAGTCATTTTAC
1166206 TT
1 TT
1166208 GCCTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAGTCATTTTAC
Found at i:1168282 original size:60 final size:60
Alignment explanation
Indices: 1168189--1168758 Score: 575
Period size: 60 Copynumber: 9.6 Consensus size: 60
1168179 CTCAAGGTAA
* ** * *
1168189 TAATTTGTCGTTAGCTTAAA-TCCCAGCATTAAGCCTTTTGTATTGAGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * *
1168249 TAATTTGTTGTTAGCTTAAA-TACCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * * * * *
1168309 TAATTTGTTGTTAGCTTAAA-TCCCTGCATTAA--ATGTTCGCAATGTGCTCCACGTGTTGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCT-TTTGTAACGTGTTCCACGTGATGT
* ** * * *
1168368 TAATTTCTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTCATGACATGTTCCACGTGATAT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * *
1168428 TAATTTGTTGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGCTCCACGTGAGGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
** * *
1168488 TAATTTGCCGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * *
1168548 TAATTTGCTGTTAGCTTAAAGTCCAGCCTTAGGCCTTTTGTAACGAGTTCCACGTGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * * * * *
1168608 TAATTTGTTGTTTGCTTAAA-TCCCAGCATTAAACCTTCTG--ATGTGCTCCGCGTG-TCAT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGAT-GT
* * ** ** * *
1168666 TAGTTTGTTGTTAACTTAAAGTCTTGCATTAAGCCTTTCATAACGTGCTCCACATGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
1168726 TAATTTGTTGTTAGCTTAAA-TCCTAGCATTAAG
1 TAATTTGTTGTTAGCTTAAAGTCC-AGCATTAAG
1168759 TCTTCTCCAA
Statistics
Matches: 428, Mismatches: 71, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
57 1 0.00
58 41 0.10
59 51 0.12
60 333 0.78
61 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (60 bp):
TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
Found at i:1176784 original size:16 final size:15
Alignment explanation
Indices: 1176761--1176803 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1176751 ATTTTTAAAA
1176761 AATATATTTATATTAT
1 AATATATTTATATT-T
* *
1176777 ATTATATTAATATTT
1 AATATATTTATATTT
*
1176792 AATATTTTTATA
1 AATATATTTATA
1176804 CATTTTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATATATTTATATTT
Found at i:1186181 original size:17 final size:18
Alignment explanation
Indices: 1186154--1186187 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1186144 ACTTGTTTTA
1186154 AAAATATTTTAAAATATT
1 AAAATATTTTAAAATATT
1186172 AAAA-ATTTTAAAATAT
1 AAAATATTTTAAAATAT
1186188 AATTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATTTTAAAATATT
Found at i:1191870 original size:29 final size:31
Alignment explanation
Indices: 1191817--1191880 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
1191807 TGAGAAGCCT
*
1191817 TTATTTGAACACTTTTGAAAATGTTTGACCC
1 TTATTTGAACACTTTTGAAAATGTTTAACCC
* *
1191848 TTATTTGACCA-TTTT-AAAATGTTTAACTC
1 TTATTTGAACACTTTTGAAAATGTTTAACCC
1191877 TTAT
1 TTAT
1191881 GTAAGCAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATTTGAACACTTTTGAAAATGTTTAACCC
Found at i:1192451 original size:41 final size:41
Alignment explanation
Indices: 1192394--1192474 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
1192384 AAACCTGGGT
1192394 CCTTTAGTTCAATGTAA-GCTAAAAACTAGTGTAACTAGGGC
1 CCTTTAGTTCAATGTAATG-TAAAAACTAGTGTAACTAGGGC
1192435 CCTTTAGTTCAATGTAATGTAAAAACTAGTGTAACTAGGG
1 CCTTTAGTTCAATGTAATGTAAAAACTAGTGTAACTAGGG
1192475 ATGGCAATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (41 bp):
CCTTTAGTTCAATGTAATGTAAAAACTAGTGTAACTAGGGC
Found at i:1200588 original size:90 final size:90
Alignment explanation
Indices: 1200407--1200845 Score: 400
Period size: 89 Copynumber: 4.8 Consensus size: 90
1200397 CAAAATACTA
* * * * ** *
1200407 GAACTAAATCAGTTACAAAACTCATCTCCAAAATTACAGAGCCAACAAAAAAAAAAAACTCTAGA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAG-C--C---AAATTAAAACTCTATA
* **
1200472 ATTCAAACTTTTTAAAAAAAAAATTCAAATATTT
60 ATTCAAAC-ATTT--AAAAAAAATTCAAATATGC
* * *
1200506 GAACTGAATCACTTACAAAATTCATCTGCATAATTACAAAGCCAAATTAAAACTCTATAATTTAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
1200571 ACATTTAAAAAAAATTCAAATATGC
66 ACATTTAAAAAAAATTCAAATATGC
* * * *
1200596 GAAGTGGATCACTTACAAGACTCATCTGCAAAATTACAAAGCTAAATTAAAACTC---AATTCAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
* * * * *
1200658 ACTTTTTTTTTTACAAAAATTCAAATACGT
66 AC-----ATTTAAAAAAAATTCAAATATGC
* * * * * *
1200688 GAACGGAACCACTTACGAAACTCATCTGCAAAATTACAAAGCCAAATAAAAACTCTAGAATACAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
*****
1200753 ACATTT-TTTTTAATTCAAATATGC
66 ACATTTAAAAAAAATTCAAATATGC
* * *
1200777 GAACTGAATCACTTACAAAACTTATCTGCAAAATTACAAAGCTAAATTAAACCTCTATAATTCAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
1200842 ACAT
66 ACAT
1200846 GAAAGAGAAA
Statistics
Matches: 281, Mismatches: 51, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
87 8 0.03
89 71 0.25
90 69 0.25
92 68 0.24
93 20 0.07
95 8 0.03
96 1 0.00
98 1 0.00
99 35 0.12
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (90 bp):
GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
ACATTTAAAAAAAATTCAAATATGC
Found at i:1200703 original size:182 final size:181
Alignment explanation
Indices: 1200490--1200827 Score: 487
Period size: 182 Copynumber: 1.9 Consensus size: 181
1200480 TTTTTAAAAA
** * * * * *
1200490 AAAAATTCAAATATTTGAACTGAATCACTTACAAAATTCATCTGCATAATTACAAAGCCAAATTA
1 AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
* ** * * *
1200555 AAACTCTATAATTTAAACATTTAAAAAAAATTCAAATATGCGAAGTGGATCACTTACAAGACTCA
66 AAACTCTAGAATACAAACATTT-AAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCA
1200620 TCTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
130 TCTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
*
1200672 AAAAATTCAAATACGTGAACGGAACCACTTACGAAACTCATCTGCAAAATTACAAAGCCAAATAA
1 AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
***** *
1200737 AAACTCTAGAATACAAACATTTTTTTTAATTCAAATATGCGAACTGAATCACTTACAAAACTTAT
66 AAACTCTAGAATACAAACATTTAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCAT
1200802 CTGCAAAATTACAAAGCTAAATTAAA
131 CTGCAAAATTACAAAGCTAAATTAAA
1200828 CCTCTATAAT
Statistics
Matches: 136, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
181 60 0.44
182 76 0.56
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (181 bp):
AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
AAACTCTAGAATACAAACATTTAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCAT
CTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
Found at i:1202326 original size:25 final size:24
Alignment explanation
Indices: 1202298--1202345 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1202288 TTTACATGAT
*
1202298 GATAGTGTAAATTTGTCACTATATG
1 GATAGTG-AAATTTCTCACTATATG
*
1202323 GATATTGAAATTTCTCACTATAT
1 GATAGTGAAATTTCTCACTATAT
1202346 TTATTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (24 bp):
GATAGTGAAATTTCTCACTATATG
Found at i:1202709 original size:27 final size:27
Alignment explanation
Indices: 1202657--1202710 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1202647 AAACTTCTAA
*
1202657 TATAAAACACATTACTTTATTTTATTT
1 TATAAAACACATTACTTTATTATATTT
* *
1202684 TATAAATCACATT-TTTTATTAATATTT
1 TATAAAACACATTACTTTATT-ATATTT
1202711 AATATTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (27 bp):
TATAAAACACATTACTTTATTATATTT
Found at i:1207975 original size:44 final size:44
Alignment explanation
Indices: 1207927--1208021 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 44
1207917 TTATACAGTC
*
1207927 AAATTATGTTCATGTCATATTTGCACTTTCATTTTGGTCATTCA
1 AAATTATGTTCATATCATATTTGCACTTTCATTTTGGTCATTCA
*
1207971 AAATTATGTTCATATCATATTTGCATTTTCATTTTGGTCATTCA
1 AAATTATGTTCATATCATATTTGCACTTTCATTTTGGTCATTCA
1208015 ATAATTA
1 A-AATTA
1208022 GGTCGGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 43 0.90
45 5 0.10
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (44 bp):
AAATTATGTTCATATCATATTTGCACTTTCATTTTGGTCATTCA
Found at i:1211384 original size:22 final size:22
Alignment explanation
Indices: 1211359--1211406 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1211349 AATATTTTTT
* *
1211359 TATAAAATTTAATTATAAAA-TA
1 TATAAAATTCAA-TACAAAATTA
1211381 TATAAAATTCAATACAAAATTA
1 TATAAAATTCAATACAAAATTA
1211403 TATA
1 TATA
1211407 TTTTTAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAAATTCAATACAAAATTA
Found at i:1219059 original size:31 final size:31
Alignment explanation
Indices: 1219024--1219089 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1219014 AGATATGATC
1219024 TTTTAAATACACGAAAATATTAGAACTCGAA
1 TTTTAAATACACGAAAATATTAGAACTCGAA
* *
1219055 TTTTAAATACACGAAATTATTAGAACTTGAA
1 TTTTAAATACACGAAAATATTAGAACTCGAA
1219086 TTTT
1 TTTT
1219090 TTGTATTACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (31 bp):
TTTTAAATACACGAAAATATTAGAACTCGAA
Found at i:1220438 original size:2 final size:2
Alignment explanation
Indices: 1220431--1220457 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1220421 TTTATTGGGT
1220431 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1220458 TTCTTTACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1233818 original size:13 final size:14
Alignment explanation
Indices: 1233802--1233835 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1233792 AATAAATATA
1233802 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
1233815 TATTTTTTAATTTT
1 TATTTTTTAATTTT
1233829 TAATTTT
1 T-ATTTT
1233836 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:1240077 original size:17 final size:17
Alignment explanation
Indices: 1240055--1240088 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1240045 CATTTACGAG
1240055 CCAAATGTCGTTTTTAA
1 CCAAATGTCGTTTTTAA
*
1240072 CCAAATGTGGTTTTTAA
1 CCAAATGTCGTTTTTAA
1240089 AAGATTTTTG
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:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
CCAAATGTCGTTTTTAA
Found at i:1241030 original size:21 final size:21
Alignment explanation
Indices: 1240982--1241023 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240972 TTTTCCTAGG
* *
1240982 ATGTGAATTAGATTGAATTGA
1 ATGTAAATTAGATTAAATTGA
*
1241003 ATGTAAATTATATTAAATTGA
1 ATGTAAATTAGATTAAATTGA
1241024 TGCTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGTAAATTAGATTAAATTGA
Found at i:1241513 original size:26 final size:25
Alignment explanation
Indices: 1241483--1241548 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
1241473 GCAACTCTTA
* *
1241483 TGAGCGTCCCGTTATATGGCTC-TTCG
1 TGAGCTTCCCGTTA-AAGGCTCATT-G
*
1241509 TGAGCTTCTCGATTAAAGGCTCATTG
1 TGAGCTTCCCG-TTAAAGGCTCATTG
1241535 TGAGCTTCCCGTTA
1 TGAGCTTCCCGTTA
1241549 GTGTGCGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.09
26 26 0.76
27 5 0.15
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGTTAAAGGCTCATTG
Found at i:1241613 original size:24 final size:24
Alignment explanation
Indices: 1241586--1241644 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1241576 GCTATCTGAT
*
1241586 GCTACCTGTTAATTGCTCTTCGAA
1 GCTACCCGTTAATTGCTCTTCGAA
* * *
1241610 GCTACCCATTGATTGCTCTTCGGA
1 GCTACCCGTTAATTGCTCTTCGAA
1241634 GCTACCCGTTA
1 GCTACCCGTTA
1241645 TAGGCTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (24 bp):
GCTACCCGTTAATTGCTCTTCGAA
Found at i:1243873 original size:36 final size:36
Alignment explanation
Indices: 1243825--1243896 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1243815 GGTTGGTGTC
*
1243825 GGTGTTTGAGGGTCAAGCTAAATCTGAGCTTAGATT
1 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1243861 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1243897 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (36 bp):
GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
Found at i:1246113 original size:10 final size:11
Alignment explanation
Indices: 1246087--1246112 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1246077 TTAAAAATAA
1246087 AAAAATATTTT
1 AAAAATATTTT
1246098 AAAAATATTTT
1 AAAAATATTTT
1246109 AAAA
1 AAAA
1246113 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1246810 original size:17 final size:18
Alignment explanation
Indices: 1246789--1246823 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1246779 TGAAAAATAA
1246789 ATTTTT-AATT-TTTTTT
1 ATTTTTAAATTATTTTTT
1246805 ATTTTTAAATTATTTTTT
1 ATTTTTAAATTATTTTTT
1246823 A
1 A
1246824 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTAAATTATTTTTT
Found at i:1251019 original size:18 final size:18
Alignment explanation
Indices: 1250992--1251027 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1250982 GTATAAAGAG
*
1250992 AATTAAATAAAATGTTTT
1 AATTAAATAAAATATTTT
*
1251010 AATTAGATAAAATATTTT
1 AATTAAATAAAATATTTT
1251028 TTATAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AATTAAATAAAATATTTT
Found at i:1251327 original size:38 final size:38
Alignment explanation
Indices: 1251284--1251390 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 38
1251274 TAATAAATAT
**
1251284 ATTTTTATT-ATTTTATTTAATTTTAAAATAC-TTTTAA
1 ATTTTT-TTAATTTTAAATAATTTTAAAATACTTTTTAA
* *
1251321 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTA
1 ATTTTTTTAATTTT-AAATAATTTTAAAATACTTTTTAA
*
1251360 ATTTTTTTAATTTTAAAATATTTTTAAAATA
1 ATTTTTTTAATTTT-AAATAATTTTAAAATA
1251391 AATTTTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
36 2 0.03
37 11 0.18
38 14 0.23
39 35 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (38 bp):
ATTTTTTTAATTTTAAATAATTTTAAAATACTTTTTAA
Found at i:1251329 original size:27 final size:28
Alignment explanation
Indices: 1251293--1251364 Score: 110
Period size: 27 Copynumber: 2.5 Consensus size: 28
1251283 TATTTTTATT
1251293 ATTTTATTTAATTTTAAAATACTTTT-AA
1 ATTTT-TTTAATTTTAAAATACTTTTAAA
1251321 ATTTTTTTAATTTTAAAATACTTTTAAA
1 ATTTTTTTAATTTTAAAATACTTTTAAA
1251349 ATACTTTTTTAATTTT
1 AT--TTTTTTAATTTT
1251365 TTTAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 20 0.49
28 9 0.22
30 12 0.29
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTTTTAATTTTAAAATACTTTTAAA
Found at i:1251363 original size:39 final size:39
Alignment explanation
Indices: 1251304--1251406 Score: 154
Period size: 39 Copynumber: 2.6 Consensus size: 39
1251294 TTTTATTTAA
*
1251304 TTTTAAAATAC-TTTTAAATTTTTTTAATTTTAAAATAC
1 TTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATAC
*
1251342 TTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATAC
*
1251381 TTTTAAAATAAATTTTTTTAATTTTT
1 TTTTAAAAT--ACTTTTTTAATTTTT
1251407 AAAATAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
38 11 0.19
39 34 0.58
41 14 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (39 bp):
TTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATAC
Found at i:1251426 original size:22 final size:21
Alignment explanation
Indices: 1251378--1251426 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
1251368 AATTTTAAAA
*
1251378 TATTTTTAAAATAAATTTTTT
1 TATTTTTAAAATAAATTTTTG
1251399 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
1251422 TATTT
1 TATTT
1251427 ATTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:1268465 original size:17 final size:17
Alignment explanation
Indices: 1268443--1268476 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1268433 CTTTGAAATT
1268443 TTTTTCAAATATATATG
1 TTTTTCAAATATATATG
* *
1268460 TTTTTCAGATTTATATG
1 TTTTTCAAATATATATG
1268477 CTCTAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTTCAAATATATATG
Found at i:1291774 original size:129 final size:127
Alignment explanation
Indices: 1291532--1291803 Score: 314
Period size: 129 Copynumber: 2.1 Consensus size: 127
1291522 CGGTAAGAAC
* * * * *
1291532 ACCCGACTCGGTAGGAAAATAGTGACGATATTTATAACCTAGGCCGAATATCATATGGGTTGTCC
1 ACCCGACCCGGTAAGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATACGGGTTATCC
* *
1291597 ACTCGTCCCGAAACATAACTAGTGACCATATCACAATAGAGTCCGAGTCACATATGAGCTATCA
66 ACTCGTCCAGAAACATAACTAGTGACCATAT--CAATAGAATCCGAGTCACATATGAGCTATCA
* * *
1291661 ACCCGACCCGGTAAGAAACTAGTGACGATGTTTATAACCGAGTCCGAATATCATACGGGTTATCC
1 ACCCGACCCGGTAAGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATACGGGTTATCC
* * ** * * * *
1291726 ACTTGATCCAGTAGGA-AACTAGTGAAACGATAGT-AGTAGAATCTGAGTCACATATGGGCTATC
66 ACTCG-TCCAGAAACATAACTAGTG--ACCATA-TCAATAGAATCCGAGTCACATATGAGCTATC
1291789 A
127 A
1291790 ACCCGACCCGGTAA
1 ACCCGACCCGGTAA
1291804 AATCCGAGTA
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
129 109 0.90
130 6 0.05
131 5 0.04
132 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (127 bp):
ACCCGACCCGGTAAGAAAATAGTGACGATATTTATAACCGAGGCCGAATATCATACGGGTTATCC
ACTCGTCCAGAAACATAACTAGTGACCATATCAATAGAATCCGAGTCACATATGAGCTATCA
Found at i:1295993 original size:17 final size:17
Alignment explanation
Indices: 1295973--1296008 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1295963 TTTTTCTGAA
1295973 TTAGTAAATTTTGTGAT
1 TTAGTAAATTTTGTGAT
*
1295990 TTAGTGAATTTTGTGAT
1 TTAGTAAATTTTGTGAT
1296007 TT
1 TT
1296009 TAAAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (17 bp):
TTAGTAAATTTTGTGAT
Found at i:1296747 original size:21 final size:21
Alignment explanation
Indices: 1296721--1296764 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1296711 TTGTACTGAA
1296721 ATTCTGAATATAAAATTTTGT
1 ATTCTGAATATAAAATTTTGT
1296742 ATTCTGAATATAAAATTTTGT
1 ATTCTGAATATAAAATTTTGT
1296763 AT
1 AT
1296765 AGTAGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (21 bp):
ATTCTGAATATAAAATTTTGT
Found at i:1301209 original size:19 final size:20
Alignment explanation
Indices: 1301174--1301216 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1301164 CTTTTGTAAA
1301174 TTTTTATACTTTCATATATT
1 TTTTTATACTTTCATATATT
1301194 TTTTTATA-TTAT-ATATATT
1 TTTTTATACTT-TCATATATT
1301213 TTTT
1 TTTT
1301217 AAAATTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTATACTTTCATATATT
Found at i:1303213 original size:30 final size:30
Alignment explanation
Indices: 1303179--1303249 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1303169 GTATTACAAA
*
1303179 TATATTTTTACATAATTTATTTCATCCCAT
1 TATATTTTTACATAATTTATTTCAACCCAT
1303209 TATATTTTTACATAATTTATTTCAACCCAT
1 TATATTTTTACATAATTTATTTCAACCCAT
*
1303239 CATATTTTTAC
1 TATATTTTTAC
1303250 TTCTCCTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (30 bp):
TATATTTTTACATAATTTATTTCAACCCAT
Found at i:1305392 original size:19 final size:20
Alignment explanation
Indices: 1305349--1305391 Score: 65
Period size: 17 Copynumber: 2.3 Consensus size: 20
1305339 TCTTTTGTAA
1305349 ATTTTTATACTTTCATATAT
1 ATTTTTATACTTTCATATAT
1305369 ATTTTTATA--TT-ATATAT
1 ATTTTTATACTTTCATATAT
1305386 ATTTTT
1 ATTTTT
1305392 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.52
18 2 0.09
20 9 0.39
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTATACTTTCATATAT
Found at i:1312941 original size:6 final size:6
Alignment explanation
Indices: 1312930--1312964 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
1312920 TCCAAATATA
1312930 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
1312965 TCATTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Done.