Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 30 of 33
Found at i:5077882 original size:23 final size:24
Alignment explanation
Indices: 5077832--5077883 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
5077822 ATATAAATGA
*
5077832 TAAAAAGATTATACATTCTATTTATT
1 TAAAAAAATTATACA-T-TATTTATT
*
5077858 TAAAAAAATTATACA-TATTTTTT
1 TAAAAAAATTATACATTATTTATT
5077881 TAA
1 TAA
5077884 TTGAAGTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
26 14 0.58
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAAAAAATTATACATTATTTATT
Found at i:5078312 original size:21 final size:21
Alignment explanation
Indices: 5078288--5078426 Score: 58
Period size: 21 Copynumber: 6.5 Consensus size: 21
5078278 TTTATTAAAT
5078288 TATAATTATATATAATATTTA
1 TATAATTATATATAATATTTA
*
5078309 TATATTTATATA-AAT-TTTA
1 TATAATTATATATAATATTTA
*
5078328 -ATAAATTA-ATAATTTATATTATA
1 TAT-AATTATAT-A-TAATATT-TA
* * *
5078351 TAAAATT-TAAAAATATATTTA
1 TATAATTATATATA-ATATTTA
* *
5078372 TATCGTATTATAT-T-ATATTTT
1 TAT--AATTATATATAATATTTA
* *
5078393 TATTATTTTATATATCATATTTA
1 TA-TA-ATTATATATAATATTTA
*
5078416 AATAATTATAT
1 TATAATTATAT
5078427 CTAAAATTAT
Statistics
Matches: 85, Mismatches: 17, Indels: 32
0.63 0.13 0.24
Matches are distributed among these distances:
18 4 0.05
19 9 0.11
20 3 0.04
21 37 0.44
22 12 0.14
23 17 0.20
24 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
TATAATTATATATAATATTTA
Found at i:5078318 original size:19 final size:18
Alignment explanation
Indices: 5078283--5078359 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 18
5078273 TATATTTTAT
5078283 TAAA-TTATAATTATATA
1 TAAATTTATAATTATATA
5078300 TAATATTTATATATT-TATA
1 TAA-ATTTATA-ATTATATA
*
5078319 TAAATTT-TAA-TAAAT-
1 TAAATTTATAATTATATA
5078334 TAATAATTTAT-ATTATATA
1 T-A-AATTTATAATTATATA
5078353 -AAATTTA
1 TAAATTTA
5078360 AAAATATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
15 2 0.04
16 10 0.20
17 12 0.24
18 10 0.20
19 12 0.24
20 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATTTATAATTATATA
Found at i:5078625 original size:13 final size:14
Alignment explanation
Indices: 5078594--5078630 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5078584 ATTTATTTAT
5078594 ATATTTTTATATGA
1 ATATTTTTATATGA
5078608 ATATTTTTA-AT-A
1 ATATTTTTATATGA
5078620 ATTATTTTTAT
1 A-TATTTTTAT
5078631 TGTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.10
13 10 0.48
14 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
ATATTTTTATATGA
Found at i:5078649 original size:25 final size:27
Alignment explanation
Indices: 5078575--5078664 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
5078565 TTAATTAAAA
* *
5078575 TATAT-AATAATTTATTTATATATTTT
1 TATATGAATATTTTATTTATTTATTTT
* *
5078601 TATATGAATATTTT-TAATAATTATTTT
1 TATATGAATATTTTAT-TTATTTATTTT
*
5078628 TAT-TG-TTATTTTATTTATTTATATTTT
1 TATATGAATATTTTATTTA-TT-TATTTT
*
5078655 TATATAAATA
1 TATATGAATA
5078665 CATACTTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
25 8 0.17
26 10 0.21
27 27 0.56
28 1 0.02
29 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TATATGAATATTTTATTTATTTATTTT
Found at i:5078715 original size:17 final size:16
Alignment explanation
Indices: 5078694--5078731 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
5078684 TTAATTTAAA
5078694 TTAAATAAA-TATTTAT
1 TTAAATAAACT-TTTAT
5078710 TATAAATAAACTTTTAT
1 T-TAAATAAACTTTTAT
5078727 TTAAA
1 TTAAA
5078732 AAAGTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATAAACTTTTAT
Found at i:5079294 original size:16 final size:17
Alignment explanation
Indices: 5079259--5079295 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5079249 TCAGCTGTAA
5079259 TTATAAATTAAATATAT
1 TTATAAATTAAATATAT
*
5079276 TTATAAGTTAAAT-TAT
1 TTATAAATTAAATATAT
5079292 TTAT
1 TTAT
5079296 TTGTGAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATAAATTAAATATAT
Found at i:5079417 original size:24 final size:24
Alignment explanation
Indices: 5079373--5079419 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5079363 AATATTATGT
* *
5079373 AATTTTATATAATATGTAATATTG
1 AATTTTATAAAATATGAAATATTG
5079397 AATTTTATAAAATTAT-AAATATT
1 AATTTTATAAAA-TATGAAATATT
5079420 TTATTGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AATTTTATAAAATATGAAATATTG
Found at i:5080654 original size:74 final size:74
Alignment explanation
Indices: 5080560--5080699 Score: 208
Period size: 74 Copynumber: 1.9 Consensus size: 74
5080550 GTCTACCAAA
* * * *
5080560 ATTCTGTCATTTTGGCGACCAAAATTTATGTGGCGAGCACAGGTCTGACAGTCAAAGTGAGTATT
1 ATTCTGTCATTCTGGCGACCAAAATTTATATGACGAGCACAGGTCTGACAGCCAAAGTGAGTATT
5080625 GATATCAGG
66 GATATCAGG
* * * *
5080634 ATTCTGTCCTTCTGGCGACCAAGATTTATATGACGAGCACAGGTCTGGCAGCCAGAGTGAGTATT
1 ATTCTGTCATTCTGGCGACCAAAATTTATATGACGAGCACAGGTCTGACAGCCAAAGTGAGTATT
5080699 G
66 G
5080700 GCGATCAGGG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 58 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (74 bp):
ATTCTGTCATTCTGGCGACCAAAATTTATATGACGAGCACAGGTCTGACAGCCAAAGTGAGTATT
GATATCAGG
Found at i:5081233 original size:78 final size:77
Alignment explanation
Indices: 5081095--5081601 Score: 447
Period size: 78 Copynumber: 6.5 Consensus size: 77
5081085 AATTGAAGTT
* * * * * * * *
5081095 ACTTAGTGTCACTAATAATATTAATGCCATGGTGGCGATTAAGATCATGGTACAATGGTGGCGAG
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGTAC-ATGGTGGCTAG
* *
5081160 CATGATTGGAGTG
65 CAAGATCGGAGTG
* * * * *
5081173 ACTTGGTGCCACTAACAGTATTGATGCCATGGTGGGGATCAGGATCGTAGTATCATGGTGGCTAG
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGTA-CATGGTGGCTAG
*
5081238 CAAGATTGGAGTG
65 CAAGATCGGAGTG
* * * * * * *
5081251 TCATGGTGTCACTGATAGTATTGATGCCATGGTAGTGATCAGGATCATAGTGACATGGTGGCTCG
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGT-ACATGGTGGCTAG
* * *
5081316 TAGGATCGAAGTG
65 CAAGATCGGAGTG
* * * * * * * * * *
5081329 CCATGGTGTCACTGACAGTATTGGTGCCTTGGTGACGATCAGGATCGTGGTGCCATGGTGGCAAG
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGT-ACATGGTGGCTAG
*
5081394 CAAGATCGGATTG
65 CAAGATCGGAGTG
* * ** * * *
5081407 ACTTGATGTCACTGACAGTACTGATATCGTGGTGGCGATCAAGATCATAGTGACATGGTAGCTAA
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGT-ACATGGTGGCTAG
*
5081472 CAAGATCGAAGTG
65 CAAGATCGGAGTG
* * * * * * * *
5081485 ACTTAGTGCCACTGACAGTATTGATGCCGTGGTAGTGATCAAGATCGTAGTACCATGATAGCTAG
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGTA-CATGGTGGCTAG
*
5081550 CAAGATCAGAGTG
65 CAAGATCGGAGTG
* * *
5081563 CCATGGTGTCACTGACAGTAGTGATGCCATGGTGGCGAT
1 ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGAT
5081602 TAGAGTGATT
Statistics
Matches: 346, Mismatches: 80, Indels: 6
0.80 0.19 0.01
Matches are distributed among these distances:
77 1 0.00
78 343 0.99
79 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (77 bp):
ACTTGGTGTCACTGACAGTATTGATGCCATGGTGGCGATCAAGATCATAGTACATGGTGGCTAGC
AAGATCGGAGTG
Found at i:5083093 original size:75 final size:75
Alignment explanation
Indices: 5082919--5083094 Score: 174
Period size: 75 Copynumber: 2.3 Consensus size: 75
5082909 ATTTTTCTAG
* * * * ** * *
5082919 CGATCAGGATTTAAGTGACAAGCACAGGTTTGACAGCCAGAGTGAGTGTTGTTTATTAGGATTCT
1 CGATCAAGATTTATGTGACAAGCACAGGTCTGACAGCCAGAGTGAGTATTGGCTATCAGGATTCC
* * *
5082984 GTTTTTCTGG
66 ATCTTTCTGA
* * * ** *
5082994 CGA-CTAAAATTTATATGGCAAGCACAGGTCTGGTAGCCCGAGTGAGTATTGGCTATCAGGATTC
1 CGATC-AAGATTTATGTGACAAGCACAGGTCTGACAGCCAGAGTGAGTATTGGCTATCAGGATTC
5083058 CATCTTTCTGA
65 CATCTTTCTGA
*
5083069 CGATCAAGATTTATGTGACGAGCACA
1 CGATCAAGATTTATGTGACAAGCACA
5083095 AACCTGACAG
Statistics
Matches: 78, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
74 1 0.01
75 76 0.97
76 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (75 bp):
CGATCAAGATTTATGTGACAAGCACAGGTCTGACAGCCAGAGTGAGTATTGGCTATCAGGATTCC
ATCTTTCTGA
Found at i:5083276 original size:24 final size:23
Alignment explanation
Indices: 5083249--5083310 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
5083239 TTGTTTAAAA
* *
5083249 TTAATTAATATATTATAGATTTT
1 TTAATTAATATATTATAGAATGT
* *
5083272 GTTAATAAATATTTTA-AGAATGT
1 -TTAATTAATATATTATAGAATGT
*
5083295 TTAATTAAAATATTAT
1 TTAATTAATATATTAT
5083311 TTATAATAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 12 0.40
23 5 0.17
24 13 0.43
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TTAATTAATATATTATAGAATGT
Found at i:5083655 original size:30 final size:28
Alignment explanation
Indices: 5083621--5083676 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
5083611 ATTAAGTTAT
5083621 TTTTAAGA-TGTAATATTTAATAAATTTAAA
1 TTTTAA-ATTGTAATATTT-AT-AATTTAAA
*
5083651 TTTTAAATTTTAATATTTATAATTTA
1 TTTTAAATTGTAATATTTATAATTTA
5083677 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 3 0.12
30 15 0.62
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTTAAATTGTAATATTTATAATTTAAA
Found at i:5085418 original size:2 final size:2
Alignment explanation
Indices: 5085411--5085439 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5085401 TTTGGTGTTT
5085411 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 T
5085440 GCTTTAGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5086114 original size:17 final size:17
Alignment explanation
Indices: 5086065--5086118 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
5086055 ATGGATCTAG
5086065 TAAAA-TTAAATTCTGATT
1 TAAAATTTAAATT-T-ATT
* *
5086083 CAAAATTT-TATTTATT
1 TAAAATTTAAATTTATT
5086099 TAAAATTTAAATTTATT
1 TAAAATTTAAATTTATT
5086116 TAA
1 TAA
5086119 TTATTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 10 0.33
17 11 0.37
18 7 0.23
19 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
TAAAATTTAAATTTATT
Found at i:5087676 original size:20 final size:20
Alignment explanation
Indices: 5087639--5087699 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
5087629 TTTAAAATAT
5087639 AAATAATTAATTTTTTTAAAAG
1 AAATAATTAA--TTTTTAAAAG
* ** *
5087661 ATATAATTAATTTTTATTAT
1 AAATAATTAATTTTTAAAAG
*
5087681 AAATAATTATTTTTTAAAA
1 AAATAATTAATTTTTAAAA
5087700 TTAAAAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 22 0.71
22 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATAATTAATTTTTAAAAG
Found at i:5094543 original size:13 final size:13
Alignment explanation
Indices: 5094525--5094551 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5094515 TGACCATCGA
5094525 TCGGTTTGAATGT
1 TCGGTTTGAATGT
5094538 TCGGTTTGAATGT
1 TCGGTTTGAATGT
5094551 T
1 T
5094552 TTTTCGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.30, T:0.48
Consensus pattern (13 bp):
TCGGTTTGAATGT
Found at i:5095665 original size:2 final size:2
Alignment explanation
Indices: 5095658--5095686 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5095648 AAGACATGTT
5095658 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 T
5095687 GTATTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5097067 original size:23 final size:23
Alignment explanation
Indices: 5097041--5097084 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5097031 TACAATTATT
* *
5097041 TTTAAGATGTAATATTTTATAAA
1 TTTAAAATGTAAAATTTTATAAA
*
5097064 TTTAAAATTTAAAATTTTATA
1 TTTAAAATGTAAAATTTTATA
5097085 TTTATGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TTTAAAATGTAAAATTTTATAAA
Found at i:5097664 original size:18 final size:19
Alignment explanation
Indices: 5097617--5097666 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
5097607 AGTATTATAT
5097617 TTTTATATATTT-TTTACA
1 TTTTATATATTTATTTACA
* *
5097635 TATTA-ATAATTTATTT-TA
1 TTTTATAT-ATTTATTTACA
5097653 TTTTATATATTTAT
1 TTTTATATATTTAT
5097667 ATATGTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.08
18 19 0.73
19 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATATATTTATTTACA
Found at i:5097839 original size:11 final size:11
Alignment explanation
Indices: 5097822--5097861 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
5097812 AACATATTCG
5097822 TATATTTATAT
1 TATATTTATAT
*
5097833 CATATTTATAT
1 TATATTTATAT
*
5097844 TATTTTTATAT
1 TATATTTATAT
5097855 TATATTT
1 TATATTT
5097862 TAATTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:5097871 original size:20 final size:22
Alignment explanation
Indices: 5097826--5097875 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
5097816 TATTCGTATA
* *
5097826 TTTATATCATATTTATATTATT
1 TTTATATTATATTTATAATATT
5097848 TTTATATTATATTT-TAAT-TT
1 TTTATATTATATTTATAATATT
5097868 TTTATATT
1 TTTATATT
5097876 TATCTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 3 0.12
22 13 0.50
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATATTATATTTATAATATT
Found at i:5098036 original size:23 final size:22
Alignment explanation
Indices: 5097998--5098044 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
5097988 AATTACATAT
*
5097998 TTATATTTATATTTTTTATTAT
1 TTATATTTATAGTTTTTATTAT
* *
5098020 TTATTATTTGTAGTTTTTATCAT
1 TTA-TATTTATAGTTTTTATTAT
5098043 TT
1 TT
5098045 CAAATATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TTATATTTATAGTTTTTATTAT
Found at i:5099049 original size:17 final size:18
Alignment explanation
Indices: 5099023--5099058 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5099013 TCGAATTCAG
*
5099023 TTATATAAAAT-TTTAAA
1 TTATAAAAAATATTTAAA
5099040 TTATAAAAAATATTTAAA
1 TTATAAAAAATATTTAAA
5099058 T
1 T
5099059 AAATACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATAAAAAATATTTAAA
Found at i:5099077 original size:18 final size:19
Alignment explanation
Indices: 5099050--5099087 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5099040 TTATAAAAAA
5099050 TATTTAAATA-AATACTAAT
1 TATTTAAATATAATA-TAAT
5099069 TATTT-AATATAATATAAT
1 TATTTAAATATAATATAAT
5099087 T
1 T
5099088 TAAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAAATATAATATAAT
Found at i:5099111 original size:22 final size:21
Alignment explanation
Indices: 5099070--5099120 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
5099060 AATACTAATT
5099070 ATTTAATATAATATAATTTAA
1 ATTTAATATAATATAATTTAA
5099091 ATTT-ATATAATTATTAATTT-A
1 ATTTAATATAA-TA-TAATTTAA
*
5099112 ATTAAATAT
1 ATTTAATAT
5099121 TTATAAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAATATAATATAATTTAA
Found at i:5099133 original size:26 final size:27
Alignment explanation
Indices: 5099074--5099133 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
5099064 CTAATTATTT
5099074 AATA-TAATATAATTTAAATTTATATA
1 AATATTAATATAATTTAAATTTATATA
* *
5099100 ATTATTAATTTAA-TTAAATATT-TATA
1 AATATTAATATAATTTAAAT-TTATATA
*
5099126 AATGTTAA
1 AATATTAA
5099134 AAATCTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AATATTAATATAATTTAAATTTATATA
Found at i:5099410 original size:6 final size:6
Alignment explanation
Indices: 5099389--5099428 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
5099379 TTTTTAGACT
*
5099389 TTTATA TTTTAAA TTTATA TTTATA TTTATA TTTATA TTT
1 TTTATA -TTTATA TTTATA TTTATA TTTATA TTTATA TTT
5099429 TAATTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:5099434 original size:6 final size:7
Alignment explanation
Indices: 5099388--5099435 Score: 52
Period size: 6 Copynumber: 7.6 Consensus size: 7
5099378 TTTTTTAGAC
5099388 TTTTATA
1 TTTTATA
5099395 TTTTA-A
1 TTTTATA
*
5099401 ATTTATA
1 TTTTATA
5099408 -TTTATA
1 TTTTATA
5099414 -TTTATA
1 TTTTATA
5099420 -TTTATA
1 TTTTATA
5099426 TTTTA-A
1 TTTTATA
5099432 TTTT
1 TTTT
5099436 TGAAAGCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTATA
Found at i:5100101 original size:20 final size:21
Alignment explanation
Indices: 5100076--5100114 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5100066 TTCCCGTGTG
5100076 AATGTATCGATACA-ATTTTT
1 AATGTATCGATACATATTTTT
5100096 AATGTATCGATACATATTT
1 AATGTATCGATACATATTT
5100115 GAAAATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
AATGTATCGATACATATTTTT
Found at i:5100717 original size:18 final size:20
Alignment explanation
Indices: 5100678--5100717 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5100668 AAAAGTTATT
5100678 ATTTTATAATTAATTTTAAA
1 ATTTTATAATTAATTTTAAA
*
5100698 ATTTTAT-ATT-ATTTTCAA
1 ATTTTATAATTAATTTTAAA
5100716 AT
1 AT
5100718 AATATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTATAATTAATTTTAAA
Found at i:5104212 original size:2 final size:2
Alignment explanation
Indices: 5104205--5104239 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5104195 AAGACAATTT
* *
5104205 TA TA TA TA TA TT TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5104240 TCAATACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:5104220 original size:12 final size:12
Alignment explanation
Indices: 5104203--5104240 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5104193 CAAAGACAAT
5104203 TTTATATATATA
1 TTTATATATATA
5104215 TTTATATATATA
1 TTTATATATATA
* *
5104227 TATATATTTATA
1 TTTATATATATA
5104239 TT
1 TT
5104241 CAATACCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTATATATATA
Found at i:5105287 original size:2 final size:2
Alignment explanation
Indices: 5105280--5105311 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5105270 CATCCCAATG
*
5105280 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5105312 AACACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5111508 original size:2 final size:2
Alignment explanation
Indices: 5111501--5111539 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5111491 TTATTCTAAC
*
5111501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5111540 AATAATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5112270 original size:2 final size:2
Alignment explanation
Indices: 5112263--5112299 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5112253 ATTAAAATGA
5112263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5112300 CACTTGTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5112657 original size:2 final size:2
Alignment explanation
Indices: 5112650--5112676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5112640 TATTTTTATC
5112650 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
5112677 TTAATTAGTT
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:5114106 original size:2 final size:2
Alignment explanation
Indices: 5114099--5114123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5114089 ATAAATTATG
5114099 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 T
5114124 TAAGTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5115654 original size:23 final size:23
Alignment explanation
Indices: 5115601--5115648 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5115591 AATTTAAACA
*
5115601 TATCTAAATTTAAATTAAAAATT
1 TATCTAAACTTAAATTAAAAATT
5115624 TATCTAAACTTAAATTAAAAATT
1 TATCTAAACTTAAATTAAAAATT
5115647 TA
1 TA
5115649 ATTAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
TATCTAAACTTAAATTAAAAATT
Found at i:5115722 original size:19 final size:20
Alignment explanation
Indices: 5115679--5115728 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5115669 AAATCTAATT
*
5115679 AAAATAAAAAATAGACTGAAC
1 AAAAT-AAAAATAGACTGAAA
*
5115700 AAAATAAAAATA-ACTTAAA
1 AAAATAAAAATAGACTGAAA
5115719 AAAATAAAAA
1 AAAATAAAAA
5115729 AAGTGATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 15 0.56
20 7 0.26
21 5 0.19
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.16
Consensus pattern (20 bp):
AAAATAAAAATAGACTGAAA
Found at i:5115797 original size:22 final size:22
Alignment explanation
Indices: 5115770--5115842 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
5115760 TTTAATTATT
5115770 TTAATTTTAAATTTAAAATTAA
1 TTAATTTTAAATTTAAAATTAA
5115792 TTAATTTTAATATTTAAATTGATTAAA
1 TTAATTTTAA-ATTTAAA---ATT-AA
*
5115819 TTAATTTT-AATTT-AAATAAA
1 TTAATTTTAAATTTAAAATTAA
5115839 TTAA
1 TTAA
5115843 ATTGATTGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
20 6 0.13
21 2 0.04
22 10 0.22
23 7 0.16
24 2 0.04
25 4 0.09
26 4 0.09
27 10 0.22
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAATTTTAAATTTAAAATTAA
Found at i:5116271 original size:2 final size:2
Alignment explanation
Indices: 5116264--5116298 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5116254 CAAAATTGGT
5116264 TA TA TA 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
5116299 CTGTTTTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5116982 original size:21 final size:22
Alignment explanation
Indices: 5116958--5117014 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 22
5116948 ATTGATTTAA
5116958 ATTTTTAT-TTAATTAAAATTT
1 ATTTTTATATTAATTAAAATTT
*
5116979 ATTTTTACTTAATTATTTAAAATTT
1 ATTTTTA--T-ATTAATTAAAATTT
5117004 ATTTTTATATT
1 ATTTTTATATT
5117015 TTATAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 7 0.23
22 3 0.10
23 2 0.06
25 19 0.61
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTATATTAATTAAAATTT
Found at i:5117018 original size:24 final size:25
Alignment explanation
Indices: 5116962--5117010 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5116952 ATTTAAATTT
*
5116962 TTATTTAATTAAAATTTATTTTTAC
1 TTATTTATTTAAAATTTATTTTTAC
*
5116987 TTAATTATTTAAAATTTATTTTTA
1 TTATTTATTTAAAATTTATTTTTA
5117011 TATTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTTATTTAAAATTTATTTTTAC
Found at i:5118430 original size:30 final size:30
Alignment explanation
Indices: 5118394--5118450 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
5118384 ATATAATAAA
*
5118394 ATTTTTTAAGATTTATAATAGAAGTGAATT
1 ATTTTTTAAGATTTATAACAGAAGTGAATT
5118424 ATTTTTTAAGATTTATAACAGAAGTGA
1 ATTTTTTAAGATTTATAACAGAAGTGA
5118451 GTGAACGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (30 bp):
ATTTTTTAAGATTTATAACAGAAGTGAATT
Found at i:5125310 original size:2 final size:2
Alignment explanation
Indices: 5125303--5125342 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5125293 ATTATAACAA
*
5125303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5125343 GTATGTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5125427 original size:2 final size:2
Alignment explanation
Indices: 5125420--5125449 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5125410 AACTAAATTT
*
5125420 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5125450 AAAGGGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5126028 original size:18 final size:18
Alignment explanation
Indices: 5125946--5126028 Score: 52
Period size: 18 Copynumber: 4.8 Consensus size: 18
5125936 GTCATTTGGA
* * *
5125946 AGAGGTATAGAGGGATAT
1 AGAGGGATAGAGGAAGAT
*
5125964 AGAGGAATAGA-G-AGAT
1 AGAGGGATAGAGGAAGAT
5125980 AGAGGGA-A-AGGTAAGA-
1 AGAGGGATAGAGG-AAGAT
* *
5125996 A-AGGTGATGGAGGAATAT
1 AGAGG-GATAGAGGAAGAT
5126014 AGAGGGATAGAGGAA
1 AGAGGGATAGAGGAA
5126029 AAAAAGAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
14 1 0.02
15 5 0.10
16 12 0.24
17 7 0.14
18 23 0.45
19 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.41, T:0.14
Consensus pattern (18 bp):
AGAGGGATAGAGGAAGAT
Found at i:5131434 original size:10 final size:10
Alignment explanation
Indices: 5131414--5131458 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
5131404 GTCATTTGGA
*
5131414 AGAGGTATAG
1 AGAGATATAG
*
5131424 AGGGATATAG
1 AGAGATATAG
5131434 AG-GA-ATAG
1 AGAGATATAG
5131442 AGAGATATAG
1 AGAGATATAG
5131452 AGAGATA
1 AGAGATA
5131459 GAGGGAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 6 0.19
9 4 0.13
10 21 0.68
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.18
Consensus pattern (10 bp):
AGAGATATAG
Found at i:5131441 original size:8 final size:9
Alignment explanation
Indices: 5131414--5131462 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
5131404 GTCATTTGGA
5131414 AGAGG-TAT
1 AGAGGATAT
5131422 AGAGGGATAT
1 AGA-GGATAT
5131432 AGAGGA-AT
1 AGAGGATAT
5131440 AGAGAGATAT
1 AGAG-GATAT
*
5131450 AGA-GAGAT
1 AGAGGATAT
5131458 AGAGG
1 AGAGG
5131463 GAAAGGTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
8 16 0.46
9 8 0.23
10 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.16
Consensus pattern (9 bp):
AGAGGATAT
Found at i:5131441 original size:18 final size:18
Alignment explanation
Indices: 5131414--5131464 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
5131404 GTCATTTGGA
*
5131414 AGAGGTATAGAGGGATAT
1 AGAGGAATAGAGGGATAT
*
5131432 AGAGGAATAGAGAGATAT
1 AGAGGAATAGAGGGATAT
5131450 AGA-GAGATAGAGGGA
1 AGAGGA-ATAGAGGGA
5131465 AAGGTAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.16
Consensus pattern (18 bp):
AGAGGAATAGAGGGATAT
Found at i:5131517 original size:17 final size:18
Alignment explanation
Indices: 5131479--5131517 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5131469 TAAGAAAGGT
* *
5131479 GATAGAGGAATATAAAGG
1 GATAGAGGAATAAAAAGA
5131497 GATAGAGGAA-AAAAAGA
1 GATAGAGGAATAAAAAGA
5131514 GATA
1 GATA
5131518 TAGAGAGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.13
Consensus pattern (18 bp):
GATAGAGGAATAAAAAGA
Found at i:5132475 original size:29 final size:30
Alignment explanation
Indices: 5132410--5132479 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
5132400 CTTTTAAATG
* *
5132410 AATTTTATTTTTTAATTTATATTATAATAA
1 AATTTTAATATTTAATTTATATTATAATAA
*
5132440 AATTTTAATATTTATTTTATATT-TAA-AA
1 AATTTTAATATTTAATTTATATTATAATAA
5132468 AATTTTTAATAT
1 AA-TTTTAATAT
5132480 AAAAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 12 0.33
30 20 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
AATTTTAATATTTAATTTATATTATAATAA
Found at i:5132582 original size:19 final size:18
Alignment explanation
Indices: 5132538--5132594 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
5132528 ATAAAAAATT
5132538 ATTTATTATAAATATAAA
1 ATTTATTATAAATATAAA
** * *
5132556 ATGAATTATTTAATATTAA
1 ATTTATTA-TAAATATAAA
5132575 ATTTATTA-AAA-ATAAA
1 ATTTATTATAAATATAAA
5132591 ATTT
1 ATTT
5132595 TTAATTTGTA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 8 0.27
17 2 0.07
18 6 0.20
19 14 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTTATTATAAATATAAA
Found at i:5132629 original size:23 final size:25
Alignment explanation
Indices: 5132578--5132629 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
5132568 ATATTAAATT
*
5132578 TATTAAAAATAAAATTTTTAATTTG
1 TATTAAAAATAAAATTTTTAATTTA
*
5132603 TATT-AAAAT-AAATTTTTATTTTA
1 TATTAAAAATAAAATTTTTAATTTA
5132626 TATT
1 TATT
5132630 TTACATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.64
24 5 0.20
25 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTAAAAATAAAATTTTTAATTTA
Found at i:5132678 original size:17 final size:17
Alignment explanation
Indices: 5132605--5132678 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 17
5132595 TTAATTTGTA
*
5132605 TTAAAATAAATTTTTAT
1 TTAAAATAATTTTTTAT
* **
5132622 TT--TAT-ATTTTACAT
1 TTAAAATAATTTTTTAT
*
5132636 TT-AAATAAATTTTTA-
1 TTAAAATAATTTTTTAT
*
5132651 ATAAAATTAATTTTTTAT
1 TTAAAA-TAATTTTTTAT
5132669 TTAAAATAAT
1 TTAAAATAAT
5132679 GACTTAATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
14 8 0.20
15 5 0.12
16 8 0.20
17 15 0.37
18 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAATAATTTTTTAT
Found at i:5138634 original size:14 final size:15
Alignment explanation
Indices: 5138615--5138643 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5138605 CCCCCCCCCC
5138615 CAAAAAAAAA-AAAA
1 CAAAAAAAAAGAAAA
5138629 CAAAAAAAAAGAAAA
1 CAAAAAAAAAGAAAA
5138644 ACAACCAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAGAAAA
Found at i:5138637 original size:16 final size:16
Alignment explanation
Indices: 5138616--5138647 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5138606 CCCCCCCCCC
5138616 AAAAAAAAAAAAACAA
1 AAAAAAAAAAAAACAA
*
5138632 AAAAAAAGAAAAACAA
1 AAAAAAAAAAAAACAA
5138648 CCAGCAGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAACAA
Found at i:5139341 original size:107 final size:107
Alignment explanation
Indices: 5139155--5139407 Score: 488
Period size: 107 Copynumber: 2.4 Consensus size: 107
5139145 TAAGAAATGA
**
5139155 TTTTTTTTTTTTTTTAATTTGGTCCTATACAATTTTTTTGAAGGATTTCTTCCCATCTATCATGA
1 TTTTTTTTTTCCTTTAATTTGGTCCTATACAATTTTTTTGAAGGATTTCTTCCCATCTATCATGA
5139220 TGAATCTTTTTGTCTACATCTTAATTTCAAACTTATTTATTG
66 TGAATCTTTTTGTCTACATCTTAATTTCAAACTTATTTATTG
5139262 TTTTTTTTTTCCTTTAATTTGGTCCTATACAATTTTTTTGAAGGATTTCTTCCCATCTATCATGA
1 TTTTTTTTTTCCTTTAATTTGGTCCTATACAATTTTTTTGAAGGATTTCTTCCCATCTATCATGA
5139327 TGAATCTTTTTGTCTACATCTTAATTTCAAACTTATTTATTG
66 TGAATCTTTTTGTCTACATCTTAATTTCAAACTTATTTATTG
5139369 TTTTTTTTTTCCTTTAATTTGGTCCTATACAATTTTTTT
1 TTTTTTTTTTCCTTTAATTTGGTCCTATACAATTTTTTT
5139408 ATTGCTAGAT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 144 1.00
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (107 bp):
TTTTTTTTTTCCTTTAATTTGGTCCTATACAATTTTTTTGAAGGATTTCTTCCCATCTATCATGA
TGAATCTTTTTGTCTACATCTTAATTTCAAACTTATTTATTG
Found at i:5141368 original size:2 final size:2
Alignment explanation
Indices: 5141361--5141391 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5141351 GCGTTTATGG
5141361 CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5141392 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:5141396 original size:2 final size:2
Alignment explanation
Indices: 5141391--5141416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5141381 TCTCTCTCTC
5141391 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5141417 ATTGGTCGAA
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):
TA
Found at i:5142359 original size:3 final size:3
Alignment explanation
Indices: 5142351--5142380 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5142341 GTACAAAATG
*
5142351 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5142381 GCCAGCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5150265 original size:12 final size:11
Alignment explanation
Indices: 5150238--5150276 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
5150228 TATATAATCA
5150238 AATAAAATATT
1 AATAAAATATT
*
5150249 AATAAATTATAT
1 AATAAAATAT-T
5150261 AATAAAAATATT
1 AAT-AAAATATT
5150273 AATA
1 AATA
5150277 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATAAAATATT
Found at i:5151124 original size:16 final size:16
Alignment explanation
Indices: 5151100--5151171 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 16
5151090 TATATCAATT
5151100 ATTTAAATTAATTTAA
1 ATTTAAATTAATTTAA
* *
5151116 ATTTTAATTATTTTAA
1 ATTTAAATTAATTTAA
* * *
5151132 ATTGAAATTATTTTAT
1 ATTTAAATTAATTTAA
** *
5151148 GCTTAAATTATTTTAA
1 ATTTAAATTAATTTAA
5151164 ATTTAAAT
1 ATTTAAAT
5151172 AGTTAGAGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTAAATTAATTTAA
Found at i:5151141 original size:32 final size:32
Alignment explanation
Indices: 5151104--5151171 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
5151094 TCAATTATTT
* *
5151104 AAATTAATTTAAATTTTAATTATTTTAAATTG
1 AAATTAATTTAAACTTAAATTATTTTAAATTG
* ** *
5151136 AAATTATTTTATGCTTAAATTATTTTAAATTT
1 AAATTAATTTAAACTTAAATTATTTTAAATTG
5151168 AAAT
1 AAAT
5151172 AGTTAGAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (32 bp):
AAATTAATTTAAACTTAAATTATTTTAAATTG
Found at i:5154815 original size:23 final size:24
Alignment explanation
Indices: 5154769--5154815 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5154759 GTAAAGCATA
*
5154769 ATATGAAACTTTGTACTTTATTTT
1 ATATAAAACTTTGTACTTTATTTT
* *
5154793 ATATAAAATTTTG-ACTTTTTTTT
1 ATATAAAACTTTGTACTTTATTTT
5154816 TTGTTGTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
ATATAAAACTTTGTACTTTATTTT
Found at i:5160845 original size:24 final size:24
Alignment explanation
Indices: 5160818--5160890 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
5160808 GCAAGGGACG
*
5160818 ACGATGACTGGGTGCAGTCGGAAA
1 ACGATGACTGGGTGCAGTCAGAAA
** * * *
5160842 ACGATGACTGCTTGCGGTCCGAAG
1 ACGATGACTGGGTGCAGTCAGAAA
*
5160866 ATGATGACTGGGTGCAGTCAGAAA
1 ACGATGACTGGGTGCAGTCAGAAA
5160890 A
1 A
5160891 AAAGCCAGCT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (24 bp):
ACGATGACTGGGTGCAGTCAGAAA
Found at i:5162331 original size:2 final size:2
Alignment explanation
Indices: 5162324--5162354 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5162314 TCAAACTGAA
*
5162324 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5162355 AATTGTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5165464 original size:12 final size:12
Alignment explanation
Indices: 5165449--5165478 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5165439 CGAAAAGCTC
*
5165449 CTAGAGCTAGAG
1 CTAGAACTAGAG
5165461 CTAGAACTAGAG
1 CTAGAACTAGAG
5165473 CTAGAA
1 CTAGAA
5165479 ATTTAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.17
Consensus pattern (12 bp):
CTAGAACTAGAG
Found at i:5166868 original size:2 final size:2
Alignment explanation
Indices: 5166861--5166886 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5166851 AAACTGAAAC
5166861 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
5166887 TGTTATTTCA
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:5171544 original size:18 final size:17
Alignment explanation
Indices: 5171510--5171564 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5171500 TGTTTAAAGT
5171510 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
5171527 ATTTTGATATGTTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
5171544 A-TTCATA-TTATATAA
1 ATTTTATATTTATATAA
5171559 ATTTTA
1 ATTTTA
5171565 AGCTATTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 5 0.16
16 5 0.16
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:5173059 original size:6 final size:6
Alignment explanation
Indices: 5173050--5173074 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5173040 ATATGCATAT
5173050 ATATAG ATATAG ATATAG ATATAG A
1 ATATAG ATATAG ATATAG ATATAG A
5173075 CATATATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
ATATAG
Found at i:5177688 original size:2 final size:2
Alignment explanation
Indices: 5177681--5177709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5177671 TTTCATGTAT
5177681 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 T
5177710 GAATGTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5178939 original size:2 final size:2
Alignment explanation
Indices: 5178932--5178960 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5178922 TCTTCCTTTT
5178932 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 T
5178961 TTGTATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5183580 original size:2 final size:2
Alignment explanation
Indices: 5183573--5183604 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5183563 CACGTCAGAC
5183573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5183605 AATAATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5188177 original size:3 final size:3
Alignment explanation
Indices: 5188171--5188203 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5188161 CTCCTACTAC
*
5188171 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5188204 CGATAACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5188204 original size:9 final size:9
Alignment explanation
Indices: 5188171--5188209 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5188161 CTCCTACTAC
*
5188171 TAATAATAA
1 TAATAACAA
*
5188180 TAATAATAA
1 TAATAACAA
5188189 TAATAACAA
1 TAATAACAA
*
5188198 TAATAACGA
1 TAATAACAA
5188207 TAA
1 TAA
5188210 CATAATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (9 bp):
TAATAACAA
Found at i:5188307 original size:18 final size:20
Alignment explanation
Indices: 5188280--5188318 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
5188270 ATTCAAGTAA
5188280 TTAATATT-AATAT-AATAT
1 TTAATATTAAATATAAATAT
*
5188298 TTAATCTTAAATATAAATAT
1 TTAATATTAAATATAAATAT
5188318 T
1 T
5188319 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATATTAAATATAAATAT
Found at i:5189703 original size:42 final size:41
Alignment explanation
Indices: 5189587--5189746 Score: 135
Period size: 42 Copynumber: 3.8 Consensus size: 41
5189577 CTTTTGACAG
* * * **
5189587 GGACAGAAGTGATTGGACCTTTTTGAGGCTGACTATGGGAGG
1 GGACAGAAGTGATTGGACCTTGTTGAGACTGATTATGGG-CT
* * * *
5189629 GGACAGAAAT-AGTTGGATCTTTTTGAGGCTGATTATGGGCT
1 GGACAGAAGTGA-TTGGACCTTGTTGAGACTGATTATGGGCT
* *
5189670 GAGACAGAAGTGATAGGACCTTGTTGAGACTGATTTTGGGCTT
1 G-GACAGAAGTGATTGGACCTTGTTGAGACTGATTATGGGC-T
** *
5189713 GGACAGAAGCAATGGGACCTTGTTG-GAACTGATT
1 GGACAGAAGTGATTGGACCTTGTTGAG-ACTGATT
5189747 TTGCGCTTGA
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
41 3 0.03
42 93 0.94
43 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.29
Consensus pattern (41 bp):
GGACAGAAGTGATTGGACCTTGTTGAGACTGATTATGGGCT
Found at i:5189764 original size:42 final size:42
Alignment explanation
Indices: 5189685--5189764 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
5189675 AGAAGTGATA
* *
5189685 GGACCTTGTTGAGACTGATTTTGGGCTTGGACAGAAGCAATG
1 GGACCTTGTTGAGACTGATTTTGCGCTTGGAAAGAAGCAATG
5189727 GGACCTTGTTG-GAACTGATTTTGCGCTT-GAAATGAAGC
1 GGACCTTGTTGAG-ACTGATTTTGCGCTTGGAAA-GAAGC
5189765 TTCACCACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (42 bp):
GGACCTTGTTGAGACTGATTTTGCGCTTGGAAAGAAGCAATG
Found at i:5190746 original size:2 final size:2
Alignment explanation
Indices: 5190741--5190782 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5190731 ATGCACACAC
*
5190741 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5190783 CTGTATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5192489 original size:3 final size:3
Alignment explanation
Indices: 5192436--5192470 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5192426 TGCGCAAACC
*
5192436 ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5192471 TCCCCACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5192988 original size:131 final size:132
Alignment explanation
Indices: 5192632--5193002 Score: 390
Period size: 137 Copynumber: 2.8 Consensus size: 132
5192622 TTTATTGATT
* * * *
5192632 GCTGGGAAATTGCATGTTACGGCTGGTGAAATTAGTGGAAAAGAACTTTGGAATCGGTCAAAACC
1 GCTGGGAAATTGCATGTT-TGGGTGGTGAAATTAGGGGAAAAGAACTTTGGAATCAGTCAAAACC
* * * *
5192697 ATAGGTAGCGTTTAAGATAAGAGATAAAGGGTAAGATAAAAGCCTAACACCCTTTCAATGGTAAG
65 CTAGGTAGCGTTTAAGATAAGAGAAAAAGGGAAAGAT---A-CCGAACACCCTTTCAATGGTAAG
*
5192762 AGAGATT
126 AGAGATC
* * ** ** * *
5192769 GCTGGGAAATAGCATGTTTGAGTAATGAAATTAGTGAAAAAAGAAATTTGGGATCAGTCAAAACC
1 GCTGGGAAATTGCATGTTTGGGTGGTGAAATTAG-GGGAAAAGAACTTTGGAATCAGTCAAAACC
* *
5192834 CTAGGTAGTGTTTAAGATAAGAGACAAAGGGAAAG-T-CCGAA-ACCCTTTCAATGGTGAGAGAG
65 CTAGGTAGCGTTTAAGATAAGAGAAAAAGGGAAAGATACCGAACACCCTTTCAATGGT-A-AGAG
5192896 AGATC
128 AGATC
* * * * *
5192901 GCTGGGAGATTTCATGTTTGGGTGGTGAAATTAGGGGAAAGGAACTTCGAAATCAGTCAAAACCC
1 GCTGGGAAATTGCATGTTTGGGTGGTGAAATTAGGGGAAAAGAACTTTGGAATCAGTCAAAACCC
** *
5192966 TAGCAAGGGTTTAAGATAAGAGATAAAAGGG-AAGATA
66 TAGGTAGCGTTTAAGATAAGAGA-AAAAGGGAAAGATA
5193003 AAAGCTTAAA
Statistics
Matches: 193, Mismatches: 35, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
130 14 0.07
131 52 0.27
132 43 0.22
136 12 0.06
137 72 0.37
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.23
Consensus pattern (132 bp):
GCTGGGAAATTGCATGTTTGGGTGGTGAAATTAGGGGAAAAGAACTTTGGAATCAGTCAAAACCC
TAGGTAGCGTTTAAGATAAGAGAAAAAGGGAAAGATACCGAACACCCTTTCAATGGTAAGAGAGA
TC
Found at i:5193568 original size:19 final size:22
Alignment explanation
Indices: 5193527--5193574 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
5193517 AATATTTTCA
5193527 TAAAAAATTAATTAAATAAAAAT
1 TAAAAAATTAATTAAAT-AAAAT
5193550 TAAAAAATT-A-TAAAT-AAAT
1 TAAAAAATTAATTAAATAAAAT
5193569 TAAAAA
1 TAAAAA
5193575 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.40
21 5 0.20
22 1 0.04
23 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATTAATTAAATAAAAT
Found at i:5193581 original size:26 final size:24
Alignment explanation
Indices: 5193526--5193583 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 24
5193516 TAATATTTTC
*
5193526 ATAAAAAATTAATTAAATAAAAAT
1 ATAAAAAATTAAATAAATAAAAAT
5193550 -TAAAAAATTATAAATAAATTAAAAAT
1 ATAAAAAA-T-TAAATAAA-TAAAAAT
5193576 ATAAAAAA
1 ATAAAAAA
5193584 AAAATCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.24
24 1 0.03
25 7 0.24
26 7 0.24
27 7 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAAAAAATTAAATAAATAAAAAT
Found at i:5201959 original size:21 final size:22
Alignment explanation
Indices: 5201889--5201960 Score: 85
Period size: 21 Copynumber: 3.2 Consensus size: 22
5201879 AAATAAATTT
5201889 TTTACATATTAATTATTTATGTTATA
1 TTTA-ATATT-ATT-TTTAT-TTATA
*
5201915 -TTAATATTCTTTTTATTTATA
1 TTTAATATTATTTTTATTTATA
5201936 TTTAAT-TTATTTTTATTTATA
1 TTTAATATTATTTTTATTTATA
5201957 TTTA
1 TTTA
5201961 TCTAACAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 23 0.53
22 10 0.23
23 2 0.05
24 5 0.12
25 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (22 bp):
TTTAATATTATTTTTATTTATA
Found at i:5202571 original size:27 final size:26
Alignment explanation
Indices: 5202523--5202577 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
5202513 CAAGTTTTTA
*
5202523 TTTTTTAAAGTAATTATCTTTTAAAT
1 TTTTTTAAAGTAATTATATTTTAAAT
*
5202549 TTTTTTAAA-TAATATCATATTTTATAT
1 TTTTTTAAAGTAAT-T-ATATTTTAAAT
5202576 TT
1 TT
5202578 ATATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTTAAAGTAATTATATTTTAAAT
Found at i:5202583 original size:13 final size:14
Alignment explanation
Indices: 5202560--5202634 Score: 53
Period size: 15 Copynumber: 5.3 Consensus size: 14
5202550 TTTTTAAATA
*
5202560 ATATCATATTTTAT
1 ATATTATATTTTAT
*
5202574 AT-TTATATTTTTT
1 ATATTATATTTTAT
5202587 ATATTATAATTTTAT
1 ATATTAT-ATTTTAT
* ** *
5202602 TTAAAATATTATAT
1 ATATTATATTTTAT
* *
5202616 ATATATAAATATTAT
1 ATAT-TATATTTTAT
5202631 ATAT
1 ATAT
5202635 AAATCATGAT
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
13 11 0.24
14 14 0.31
15 20 0.44
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTATATTTTAT
Found at i:5206588 original size:22 final size:22
Alignment explanation
Indices: 5206563--5206608 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5206553 TATTATTTAC
5206563 ATAAATAAATAATA-AAATATTA
1 ATAAATAAATAATATAAA-ATTA
* *
5206585 ATAATTAAATTATATAAAATTA
1 ATAAATAAATAATATAAAATTA
5206607 AT
1 AT
5206609 TTACTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAATAAATAATATAAAATTA
Found at i:5209206 original size:2 final size:2
Alignment explanation
Indices: 5209194--5209227 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5209184 ATGTCTCTTT
5209194 TA TA TA T- 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
5209228 TCTTCCTTTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5212810 original size:2 final size:2
Alignment explanation
Indices: 5212803--5212841 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5212793 ATACTTATGT
5212803 TA TA TA TA TA 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 TA TA T
5212842 TGGTAAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5213006 original size:14 final size:14
Alignment explanation
Indices: 5212983--5213025 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
5212973 AAATTTAATT
*
5212983 TAATTA-ATTTTTA
1 TAATTATATTTTAA
5212996 TAATTATATTTTAA
1 TAATTATATTTTAA
*
5213010 AAATTATA-TTTAA
1 TAATTATATTTTAA
5213023 TAA
1 TAA
5213026 ATTTATATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTATATTTTAA
Found at i:5213814 original size:2 final size:2
Alignment explanation
Indices: 5213807--5213837 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5213797 CAACCATATG
5213807 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5213838 TACTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5216617 original size:2 final size:2
Alignment explanation
Indices: 5216612--5216668 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
5216602 TTTTGAGGTA
* * * * * *
5216612 TG TG TG TG TG TG TG TG TG TG TG TA TA TA TA TA TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5216654 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
5216669 ATGTATAGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.51
Consensus pattern (2 bp):
TG
Found at i:5226096 original size:6 final size:6
Alignment explanation
Indices: 5226085--5226118 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5226075 TTCCCAATAA
5226085 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
5226119 GTTGGGAGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:5226468 original size:3 final size:3
Alignment explanation
Indices: 5226462--5226494 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5226452 CAACAACAAC
5226462 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5226495 CACAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5228380 original size:16 final size:16
Alignment explanation
Indices: 5228359--5228390 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5228349 AATTTAAAAA
5228359 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
*
5228375 TTTAAATTTAGATTAT
1 TTTAAATTTAAATTAT
5228391 ATATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:5231493 original size:16 final size:16
Alignment explanation
Indices: 5231461--5231507 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5231451 TATCATTATA
*
5231461 ATATAAATTATTAAAT
1 ATATAAAATATTAAAT
5231477 ATATAAAATA-TATAAT
1 ATATAAAATATTA-AAT
5231493 AT-TAATAATATTAAA
1 ATATAA-AATATTAAA
5231508 ATAATATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.19
16 20 0.74
17 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAAATATTAAAT
Found at i:5231495 original size:23 final size:24
Alignment explanation
Indices: 5231455--5231510 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
5231445 AGTAAATATC
*
5231455 ATTATAATATAAATTATT-A-AAT
1 ATTAAAATATAAATTATTAATAAT
5231477 ATATAAAATATATAA-TATTAATAAT
1 AT-TAAAATATA-AATTATTAATAAT
5231502 ATTAAAATA
1 ATTAAAATA
5231511 ATATTGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 2 0.07
23 12 0.41
24 10 0.34
25 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTAAAATATAAATTATTAATAAT
Found at i:5231521 original size:25 final size:25
Alignment explanation
Indices: 5231461--5231510 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5231451 TATCATTATA
*
5231461 ATATAA-ATTATTAAATATATAAAAT
1 ATATAATATTAAT-AATATATAAAAT
5231486 ATATAATATTAATAATAT-TAAAAT
1 ATATAATATTAATAATATATAAAAT
5231510 A
1 A
5231511 ATATTGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAATATTAATAATATATAAAAT
Found at i:5237079 original size:33 final size:31
Alignment explanation
Indices: 5237040--5237110 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
5237030 TAAAAGTGAA
* *
5237040 TTTAAAAGGTTT-AAATTATTTTTTAAAATTTT
1 TTTAAAA-GTTTAAAAATATATTTT-AAATTTT
*
5237072 TTATAAAATTTTAAAAATATATTTTAAATTTT
1 TT-TAAAAGTTTAAAAATATATTTTAAATTTT
5237104 TTTAAAA
1 TTTAAAA
5237111 TTCTGTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 5 0.15
32 14 0.41
33 15 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAAAAGTTTAAAAATATATTTTAAATTTT
Found at i:5237083 original size:11 final size:10
Alignment explanation
Indices: 5237057--5237112 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
5237047 GGTTTAAATT
5237057 ATTTTTTAAA
1 ATTTTTTAAA
5237067 ATTTTTTATAA
1 ATTTTTTA-AA
* *
5237078 AATTTTAAAA
1 ATTTTTTAAA
5237088 ATATATTTTAAA
1 AT-T-TTTTAAA
*
5237100 TTTTTTTAAA
1 ATTTTTTAAA
5237110 ATT
1 ATT
5237113 CTGTTTGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 20 0.54
11 10 0.27
12 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:5237244 original size:29 final size:29
Alignment explanation
Indices: 5237203--5237293 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 29
5237193 ACATTAATAA
* *
5237203 TTTTAATTCATATTATATAAATTTTTAAT
1 TTTTAATTTATATTAAATAAATTTTTAAT
5237232 TTTTAATTTATATTAAAATAAATTTGTT-AT
1 TTTTAATTTATATT-AAATAAATTT-TTAAT
* * *
5237262 TTTTTATTTATATATAAATAAAATTTAAAT
1 TTTTAATTTATAT-TAAATAAATTTTTAAT
5237292 TT
1 TT
5237294 AAATGTAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.26
30 36 0.68
31 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TTTTAATTTATATTAAATAAATTTTTAAT
Found at i:5237286 original size:31 final size:30
Alignment explanation
Indices: 5237174--5237293 Score: 99
Period size: 30 Copynumber: 4.1 Consensus size: 30
5237164 TTTTTATATT
* **
5237174 TTTTTAATTT-T-TTAAAGATACATTAATAA
1 TTTTTAATTTATATTAAA-ATAAATTTTTAA
* *
5237203 -TTTTAATTCATATT-ATATAAATTTTTAA
1 TTTTTAATTTATATTAAAATAAATTTTTAA
5237231 TTTTTAATTTATATTAAAATAAATTTGTT-A
1 TTTTTAATTTATATTAAAATAAATTT-TTAA
* * *
5237261 TTTTTTATTTATA-TATAAATAAAATTTAAA
1 TTTTTAATTTATATTA-AAATAAATTTTTAA
5237291 TTT
1 TTT
5237294 AAATGTAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 13
0.76 0.10 0.13
Matches are distributed among these distances:
28 17 0.23
29 18 0.24
30 37 0.50
31 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTAATTTATATTAAAATAAATTTTTAA
Found at i:5237997 original size:165 final size:167
Alignment explanation
Indices: 5237710--5238039 Score: 495
Period size: 165 Copynumber: 2.0 Consensus size: 167
5237700 TCCAGCTTCG
* *
5237710 GTCGGCTCCCCTACAAAACTAATCTTCTTCCTTACTTTTTGGGTTCTTCTTCCCTCTTTTTTTTT
1 GTCGGCTCCCCCACAAAACTAATCTTCTTCCTTACTTTTTGGGTTCTTCTT-CCTC--TTTCTTT
*
5237775 TTTTTTTCCGTTGTTCTGCTCAAGTTTATTTGATCGCAATACCCAATGCCCACTGTGTTGTTCTG
63 TTTTTTTCCGTTGTTCTGCTCAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTG
* * *
5237840 GAAGATGAAGAGGGAACTCTGTTATCTCCTCCTTTAGCTT
128 GAAGAAGAAGAAGAAACTCTGTTATCTCCTCCTTTAGCTT
* *
5237880 GTCGGCTCCCCCCACAAAACTAATCTTTTTCTTTACTTTTTGGGTTCTTCTT-C-C-TTCTTTTT
1 GTCGGCT-CCCCCACAAAACTAATCTTCTTCCTTACTTTTTGGGTTCTTCTTCCTCTTTCTTTTT
* * * *
5237942 TTTTTCCTTTGTTTTGTTGAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGA
65 TTTTTCCGTTGTTCTGCTCAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGA
5238007 AGAAGAAGAAGAAACTCTGTTATCTCCTCCTTT
130 AGAAGAAGAAGAAACTCTGTTATCTCCTCCTTT
5238040 TCAACCCAAA
Statistics
Matches: 147, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
165 97 0.66
168 1 0.01
169 1 0.01
170 7 0.05
171 41 0.28
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (167 bp):
GTCGGCTCCCCCACAAAACTAATCTTCTTCCTTACTTTTTGGGTTCTTCTTCCTCTTTCTTTTTT
TTTTCCGTTGTTCTGCTCAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGAA
GAAGAAGAAGAAACTCTGTTATCTCCTCCTTTAGCTT
Found at i:5238921 original size:2 final size:2
Alignment explanation
Indices: 5238914--5238942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5238904 AATGGATTTC
5238914 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5238943 GCTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5239636 original size:2 final size:2
Alignment explanation
Indices: 5239629--5239669 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5239619 ATGTTTTATG
*
5239629 TA TA TA TA TA TA TA TA TG 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 TA TA TA T
5239670 TAGGCTTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5242979 original size:2 final size:2
Alignment explanation
Indices: 5242972--5243025 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
5242962 GCTTTTTCTT
* *
5242972 TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5243014 TA TA TA TA TA TA
1 TA TA TA TA TA TA
5243026 CACATACATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5243779 original size:2 final size:2
Alignment explanation
Indices: 5243774--5243805 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5243764 AGAGATAGGG
5243774 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5243806 ATGTATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:5245070 original size:89 final size:90
Alignment explanation
Indices: 5244919--5245108 Score: 346
Period size: 89 Copynumber: 2.1 Consensus size: 90
5244909 TGCCTTATTC
*
5244919 TGCTTGCTTAACTTGTGCTGTATTGCGGGTAAAAATTAGGGATTTTAGGGTTTAGAGAACCTTTG
1 TGCTTGCTTAACTTGTGCTGTATTGCAGGTAAAAATTAGGGATTTTAGGGTTTAGAGAACCTTTG
5244984 TGGCGAAGTACTT-GAACTTCTGGG
66 TGGCGAAGTACTTGGAACTTCTGGG
*
5245008 TGCTTGCTTAAGTTGTGCTGTATTGCAGGTAAAAATTAGGGATTTTAGGGTTTAGAGAACCTTTG
1 TGCTTGCTTAACTTGTGCTGTATTGCAGGTAAAAATTAGGGATTTTAGGGTTTAGAGAACCTTTG
5245073 TGGCGAAGTACTTGGAACTTCTGGG
66 TGGCGAAGTACTTGGAACTTCTGGG
*
5245098 TGCTTTCTTAA
1 TGCTTGCTTAA
5245109 TTATAATTGT
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 76 0.78
90 21 0.22
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (90 bp):
TGCTTGCTTAACTTGTGCTGTATTGCAGGTAAAAATTAGGGATTTTAGGGTTTAGAGAACCTTTG
TGGCGAAGTACTTGGAACTTCTGGG
Found at i:5246415 original size:399 final size:400
Alignment explanation
Indices: 5245642--5246444 Score: 1509
Period size: 399 Copynumber: 2.0 Consensus size: 400
5245632 GTATGCATAC
5245642 TTCTAGGATGTTGAGGATCTATGTTTTCTCGCTTCCATTTCTGACAAATAGTTTATAGAGTTCTT
1 TTCTAGGATGTTGAGGATCTATGTTTTCTCGCTTCCATTTCTGACAAATAGTTTATAGAGTTCTT
*
5245707 TGTACTGTTTCAGTTAATTATTTGAAGTGCCGTGTCATTCTTAAACATATTTATCTTTGGATTTT
66 TATACTGTTTCAGTTAATTATTTGAAGTGCCGTGTCATTCTTAAACATATTTATCTTTGGATTTT
5245772 CTTTTGTGTAGCTTTGTACACGTGAATTTGAGACAAGGCGTGCCTCATACCACTGGCTGTTACAT
131 CTTTTGTGTAGCTTTGTACACGTGAATTTGAGACAAGGCGTGCCTCATACCACTGGCTGTTACAT
5245837 GTACTGGACCTGTTCTAGAAGTTTGTTACTCCATTTCTTTTGATGTCCTCAAGGATTTTAGAAGT
196 GTACTGGACCTGTTCTAGAAGTTTGTTACTCCATTTCTTTTGATGTCCTCAAGGATTTTAGAAGT
* *
5245902 AAATATGGATTGGATTGATGGTATTTTTTGTTTAGCATTTTAAAAGGTTCTAGAGTCTATTACAC
261 AAAGATGGATTGGATTGATGATATTTTTTGTTTAGCATTTTAAAAGGTTCTAGAGTCTATTACAC
5245967 TTTATGCTATCCTTTTTTATACTCCAGGAATTGCTTGGAGAGGACCCGTTCCAGAGAGTATTGGG
326 TTTATGCTATCCTTTTTTATACTCCAGGAATTGCTTGGAGAGGACCCGTTCCAGAGAGTATTGGG
5246032 AAGTAAGTAT
391 AAGTAAGTAT
*
5246042 TTCTAGGATGTTGAGGATCTATGTTTTCTCGC-TGCATTTCTGACAAATAGTTTATAGAGTTCTT
1 TTCTAGGATGTTGAGGATCTATGTTTTCTCGCTTCCATTTCTGACAAATAGTTTATAGAGTTCTT
*
5246106 TATACTGTTTCAGTTAATTATTTGAAGTGCTGTGTCATTCTTAAACATATTTATCTTTGGATTTT
66 TATACTGTTTCAGTTAATTATTTGAAGTGCCGTGTCATTCTTAAACATATTTATCTTTGGATTTT
* *
5246171 CTTTTGTGTAGCTTTGTACACGTGAATTTGAGACGAGGCGTGCTTCATACCACTGGCTGTTACAT
131 CTTTTGTGTAGCTTTGTACACGTGAATTTGAGACAAGGCGTGCCTCATACCACTGGCTGTTACAT
5246236 GTACTGGACCTGTTCTAGAAGTTTGTTACTCCATTTCTTTTGATGTCCTCAAGGATTTTAGAAGT
196 GTACTGGACCTGTTCTAGAAGTTTGTTACTCCATTTCTTTTGATGTCCTCAAGGATTTTAGAAGT
*
5246301 TAAGATGGATTGGATTGATGATATTTTTTGTTTAGCATTTTAAAAGGTTCTAGAGTCTATTACAC
261 AAAGATGGATTGGATTGATGATATTTTTTGTTTAGCATTTTAAAAGGTTCTAGAGTCTATTACAC
* *
5246366 TTTATGCTATCCTTTTTTATTCTCCATGAATTGCTTGGAGAGGACCCGTTCCAGAGAGTATTGGG
326 TTTATGCTATCCTTTTTTATACTCCAGGAATTGCTTGGAGAGGACCCGTTCCAGAGAGTATTGGG
5246431 AAGTAAGTAT
391 AAGTAAGTAT
5246441 TTCT
1 TTCT
5246445 CGACCTGTTT
Statistics
Matches: 393, Mismatches: 10, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
399 361 0.92
400 32 0.08
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (400 bp):
TTCTAGGATGTTGAGGATCTATGTTTTCTCGCTTCCATTTCTGACAAATAGTTTATAGAGTTCTT
TATACTGTTTCAGTTAATTATTTGAAGTGCCGTGTCATTCTTAAACATATTTATCTTTGGATTTT
CTTTTGTGTAGCTTTGTACACGTGAATTTGAGACAAGGCGTGCCTCATACCACTGGCTGTTACAT
GTACTGGACCTGTTCTAGAAGTTTGTTACTCCATTTCTTTTGATGTCCTCAAGGATTTTAGAAGT
AAAGATGGATTGGATTGATGATATTTTTTGTTTAGCATTTTAAAAGGTTCTAGAGTCTATTACAC
TTTATGCTATCCTTTTTTATACTCCAGGAATTGCTTGGAGAGGACCCGTTCCAGAGAGTATTGGG
AAGTAAGTAT
Found at i:5256701 original size:18 final size:19
Alignment explanation
Indices: 5256666--5256702 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
5256656 AGTGTAGAAT
5256666 TATTACAAATATTATAAAA
1 TATTACAAATATTATAAAA
5256685 TATT-CAAAT-TTATTAAAA
1 TATTACAAATATTA-TAAAA
5256703 AAATATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTACAAATATTATAAAA
Found at i:5256720 original size:23 final size:21
Alignment explanation
Indices: 5256681--5256725 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
5256671 CAAATATTAT
* *
5256681 AAAATATTCAAATTTATTAAA
1 AAAATATTCAAAATTATCAAA
5256702 AAAATATATCAATAATTATCAAA
1 AAAATAT-TCAA-AATTATCAAA
5256725 A
1 A
5256726 TTACTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATTCAAAATTATCAAA
Found at i:5256786 original size:21 final size:20
Alignment explanation
Indices: 5256762--5256836 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 20
5256752 ATTGATGATC
5256762 ATTAAAATTATATCAAATGTT
1 ATTAAAATTATAT-AAATGTT
*
5256783 ATTAAAA--ATATAATAGGTGT
1 ATTAAAATTATATAA-ATGT-T
* * *
5256803 AATCAAATTATGTAAAATGTT
1 ATTAAAATTATAT-AAATGTT
*
5256824 ATTACAATTATAT
1 ATTAAAATTATAT
5256837 TAAAATTATA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 6 0.15
21 17 0.43
22 6 0.15
23 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (20 bp):
ATTAAAATTATATAAATGTT
Found at i:5256843 original size:11 final size:11
Alignment explanation
Indices: 5256823--5256896 Score: 71
Period size: 11 Copynumber: 6.9 Consensus size: 11
5256813 TGTAAAATGT
*
5256823 TATTACAATTA
1 TATTAAAATTA
5256834 TATTAAAATTA
1 TATTAAAATTA
*
5256845 TATTAAAGTT-
1 TATTAAAATTA
* *
5256855 TGTTAAAATCA
1 TATTAAAATTA
* *
5256866 TA-TCAAATAA
1 TATTAAAATTA
*
5256876 TAATAAAATTA
1 TATTAAAATTA
5256887 TATTAAAATT
1 TATTAAAATT
5256897 GCTAGCAATT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
10 15 0.30
11 35 0.70
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:5257471 original size:89 final size:90
Alignment explanation
Indices: 5257296--5257471 Score: 264
Period size: 90 Copynumber: 2.0 Consensus size: 90
5257286 TCTCAGTCTG
* * *
5257296 CTTCATGACTGTTATCTACTTGATATTATTGTTCTAACATTTGCACCAAATCTTGATGGATTTGT
1 CTTCATGACTGTTATCTACTTGACATAATTATTCTAACATTTGCACCAAATCTTGATGGATTTGT
*
5257361 CATGGGGGAAGGTGCTCGAGTTCTA
66 CATGGAGGAAGGTGCTCGAGTTCTA
* * * *
5257386 CTTCATGAGTGTTATCTACTTGACATAATTATTTTAACTTTTGCACC-AATTTTGATGGATTTGT
1 CTTCATGACTGTTATCTACTTGACATAATTATTCTAACATTTGCACCAAATCTTGATGGATTTGT
*
5257450 CATGGAGGAAGGTGCTGGAGTT
66 CATGGAGGAAGGTGCTCGAGTT
5257472 TTGCTCTTAG
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 36 0.47
90 41 0.53
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (90 bp):
CTTCATGACTGTTATCTACTTGACATAATTATTCTAACATTTGCACCAAATCTTGATGGATTTGT
CATGGAGGAAGGTGCTCGAGTTCTA
Found at i:5258492 original size:11 final size:11
Alignment explanation
Indices: 5258473--5258502 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5258463 GAGTGGAATA
*
5258473 TTTTCTTTTTT
1 TTTTGTTTTTT
5258484 TTTTGTTTTTT
1 TTTTGTTTTTT
5258495 TTTTGTTT
1 TTTTGTTT
5258503 GTTTACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:5258498 original size:15 final size:16
Alignment explanation
Indices: 5258473--5258506 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5258463 GAGTGGAATA
*
5258473 TTTTCTTTTTTTTTTG
1 TTTTCTTTTTTGTTTG
5258489 TTTT-TTTTTTGTTTG
1 TTTTCTTTTTTGTTTG
5258504 TTT
1 TTT
5258507 ACATGTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (16 bp):
TTTTCTTTTTTGTTTG
Found at i:5258714 original size:2 final size:2
Alignment explanation
Indices: 5258707--5258746 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5258697 AATGGATTTC
5258707 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5258747 TTATAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5263486 original size:22 final size:24
Alignment explanation
Indices: 5263452--5263500 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
5263442 CCTTGTCGTA
5263452 TCATTGTCATTTT-TT-TTGTCTC
1 TCATTGTCATTTTATTGTTGTCTC
*
5263474 TCATTGCTC-TTTTATTGTTGTTTC
1 TCATTG-TCATTTTATTGTTGTCTC
5263498 TCA
1 TCA
5263501 AGGACTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 10 0.43
23 4 0.17
24 9 0.39
ACGTcount: A:0.10, C:0.18, G:0.10, T:0.61
Consensus pattern (24 bp):
TCATTGTCATTTTATTGTTGTCTC
Done.