Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 36 of 52
Found at i:5989878 original size:21 final size:20
Alignment explanation
Indices: 5989838--5989879 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5989828 TTTAATTTAA
*
5989838 TATTTAATTTTAAATTAAAT
1 TATTTAATTTTAAATCAAAT
*
5989858 TATTTATATTTTAACTCAAAT
1 TATTTA-ATTTTAAATCAAAT
5989879 T
1 T
5989880 TAAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTAATTTTAAATCAAAT
Found at i:5989911 original size:15 final size:16
Alignment explanation
Indices: 5989888--5989926 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5989878 TTTAAATTTT
5989888 AACTAAAAAA-TATTA
1 AACTAAAAAACTATTA
*
5989903 AACTCAAAAACTATTA
1 AACTAAAAAACTATTA
*
5989919 AAATAAAA
1 AACTAAAA
5989927 TATTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
AACTAAAAAACTATTA
Found at i:5990338 original size:5 final size:5
Alignment explanation
Indices: 5990328--5990370 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
5990318 TTTCCTAATA
*
5990328 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA- AAAAA AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
5990371 GCTTCCTCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5990348 original size:15 final size:14
Alignment explanation
Indices: 5990327--5990370 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
5990317 TTTTCCTAAT
5990327 AAAAACAAAACAAA
1 AAAAACAAAACAAA
5990341 ACAAAACAAAACAAA
1 A-AAAACAAAACAAA
*
5990356 AAAAAAAAAACAAA
1 AAAAACAAAACAAA
5990370 A
1 A
5990371 GCTTCCTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAACAAA
Found at i:5992683 original size:2 final size:2
Alignment explanation
Indices: 5992678--5992703 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5992668 AGAGAGAAAG
5992678 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
5992704 TTACTTTTTT
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:6003841 original size:24 final size:25
Alignment explanation
Indices: 6003785--6003845 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
6003775 ATAAGCGATT
* *
6003785 AATAAAAGTAAAATTATCAATATAA
1 AATAAAAATCAAATTATCAATATAA
6003810 AATAAAAATCAAATTATCAAGT-T-A
1 AATAAAAATCAAATTATCAA-TATAA
*
6003834 AATGAAAATCAA
1 AATAAAAATCAA
6003846 TCTTACCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.38
25 19 0.59
26 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (25 bp):
AATAAAAATCAAATTATCAATATAA
Found at i:6006335 original size:33 final size:33
Alignment explanation
Indices: 6006293--6006358 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
6006283 TTGCATTTTA
*
6006293 TTAATTTTTTTTTGTCGATATGATAGAGAGATC
1 TTAATTTTTTTTGGTCGATATGATAGAGAGATC
*
6006326 TTAATTTTTTTTGGTCGATATGATAGAGGGATC
1 TTAATTTTTTTTGGTCGATATGATAGAGAGATC
6006359 AAATGGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (33 bp):
TTAATTTTTTTTGGTCGATATGATAGAGAGATC
Found at i:6008761 original size:13 final size:13
Alignment explanation
Indices: 6008725--6008768 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6008715 ATAATTTATT
6008725 TATTT-AAATTT-
1 TATTTAAAATTTA
*
6008736 TTTTTAAATATTTA
1 TATTTAAA-ATTTA
6008750 TATTTAAAATTTA
1 TATTTAAAATTTA
6008763 TATTTA
1 TATTTA
6008769 TTATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.14
12 2 0.07
13 15 0.54
14 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTAAAATTTA
Found at i:6008778 original size:17 final size:14
Alignment explanation
Indices: 6008725--6008784 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 14
6008715 ATAATTTATT
6008725 TATTTAAAT-TTT-
1 TATTTAAATATTTA
6008737 T-TTTAAATATTTA
1 TATTTAAATATTTA
6008750 TATTTAAA-ATTTA
1 TATTTAAATATTTA
*
6008763 TATTT--AT-TATA
1 TATTTAAATATTTA
6008774 TATTTAAATAT
1 TATTTAAATAT
6008785 AAATATAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
11 16 0.40
12 4 0.10
13 13 0.32
14 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAAATATTTA
Found at i:6010906 original size:20 final size:22
Alignment explanation
Indices: 6010883--6010922 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6010873 ATTTTTATTA
6010883 AAAT-TTAAT-TAAAAATATAT
1 AAATATTAATATAAAAATATAT
*
6010903 AAATATTATTATAAAAATAT
1 AAATATTAATATAAAAATAT
6010923 TTTTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATTAATATAAAAATATAT
Found at i:6010989 original size:6 final size:6
Alignment explanation
Indices: 6010978--6011007 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6010968 AAATTAAATC
*
6010978 AAATTT AAATTT AAAATT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
6011008 TTTTAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:6010999 original size:12 final size:12
Alignment explanation
Indices: 6010967--6011004 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6010957 AATTATCAAA
*
6010967 AAAATTAAA-TC
1 AAAATTAAATTT
*
6010978 AAATTTAAATTT
1 AAAATTAAATTT
6010990 AAAATTAAATTT
1 AAAATTAAATTT
6011002 AAA
1 AAA
6011005 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:6010999 original size:18 final size:18
Alignment explanation
Indices: 6010973--6011007 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6010963 CAAAAAAATT
6010973 AAATCAAATTTAAATTTA
1 AAATCAAATTTAAATTTA
*
6010991 AAATTAAATTTAAATTT
1 AAATCAAATTTAAATTT
6011008 TTTTAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATCAAATTTAAATTTA
Found at i:6014249 original size:10 final size:11
Alignment explanation
Indices: 6014228--6014257 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
6014218 AAACTTATAA
6014228 AAAATTTGAAT
1 AAAATTTGAAT
6014239 AAAATTT-AAT
1 AAAATTTGAAT
6014249 AAAATTTGA
1 AAAATTTGA
6014258 TTTGATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (11 bp):
AAAATTTGAAT
Found at i:6014726 original size:30 final size:31
Alignment explanation
Indices: 6014690--6014763 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 31
6014680 ATATTTTTAA
*
6014690 TTTATTATAAATCATAATAA-TAATAATAA-T
1 TTTATTATAAAT-ATAATAATTAAAAATAATT
* *
6014720 TTTATTA-ATTATATTATAATTAAAAATAATT
1 TTTATTATA-AATATAATAATTAAAAATAATT
6014751 TTTATTATAAATA
1 TTTATTATAAATA
6014764 AATTAAACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
29 7 0.19
30 17 0.47
31 11 0.31
32 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TTTATTATAAATATAATAATTAAAAATAATT
Found at i:6014776 original size:42 final size:43
Alignment explanation
Indices: 6014730--6014821 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 43
6014720 TTTATTAATT
*
6014730 ATATTATAATTAAAAATAATTTT-TATT-ATAAAT-AAATTAAA
1 ATATTAT-ATTAAAAATAATTTTATATTAATAAATAAAAATAAA
* * *
6014771 CATATTATATTCAAAATTATTTTATTTTAATAAATAAAAATAAA
1 -ATATTATATTAAAAATAATTTTATATTAATAAATAAAAATAAA
6014815 ATATTAT
1 ATATTAT
6014822 TTAGGATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
41 13 0.30
42 10 0.23
43 13 0.30
44 7 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (43 bp):
ATATTATATTAAAAATAATTTTATATTAATAAATAAAAATAAA
Found at i:6015439 original size:2 final size:2
Alignment explanation
Indices: 6015432--6015461 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6015422 TTTCTTTCTG
6015432 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
6015462 TTAATAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6015661 original size:23 final size:24
Alignment explanation
Indices: 6015630--6015684 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
6015620 TTCTTTACAA
*
6015630 TTATATTATTATAAA-ATTAATATT
1 TTAT-TTATTAAAAATATTAATATT
*
6015654 TTATTTA-TAAAAATATTTATATT
1 TTATTTATTAAAAATATTAATATT
6015677 TT-TTTATT
1 TTATTTATT
6015685 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.33
23 14 0.52
24 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATTTATTAAAAATATTAATATT
Found at i:6016987 original size:7 final size:7
Alignment explanation
Indices: 6016975--6016999 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6016965 TGATTTATAA
6016975 AAAATTT
1 AAAATTT
6016982 AAAATTT
1 AAAATTT
6016989 AAAATTT
1 AAAATTT
6016996 AAAA
1 AAAA
6017000 ATGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:6017216 original size:2 final size:2
Alignment explanation
Indices: 6017209--6017259 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
6017199 TATTTTTAGA
6017209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6017251 AT AT AT AT A
1 AT AT AT AT A
6017260 AAATTTCTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6021663 original size:22 final size:22
Alignment explanation
Indices: 6021638--6021687 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
6021628 TCTATGCCAA
6021638 TTATTTGTGTTTGAA-AAAATAT
1 TTATTT-TGTTTGAATAAAATAT
6021660 TTATTTTGTTTGAATAAAAT-T
1 TTATTTTGTTTGAATAAAATAT
*
6021681 TTTTTTT
1 TTATTTT
6021688 ACGTGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (22 bp):
TTATTTTGTTTGAATAAAATAT
Found at i:6021927 original size:39 final size:39
Alignment explanation
Indices: 6021873--6021949 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
6021863 ATGTGTTTTT
6021873 CTTTTGAAAGAATTGATAATTAAGTTTTAATCAAAATTG
1 CTTTTGAAAGAATTGATAATTAAGTTTTAATCAAAATTG
6021912 CTTTTGAAAGAATTGATAATTAAGTTTTAATCAAAATT
1 CTTTTGAAAGAATTGATAATTAAGTTTTAATCAAAATT
6021950 TTCGAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (39 bp):
CTTTTGAAAGAATTGATAATTAAGTTTTAATCAAAATTG
Found at i:6022171 original size:29 final size:29
Alignment explanation
Indices: 6022138--6022216 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 29
6022128 TTATTGAAAG
* *
6022138 GTTATGGATGATAAATATAATTTTTAAAA
1 GTTATGGATGATAAATAAAACTTTTAAAA
* *
6022167 GTTATGTATTAATAAAATAAAACTTTTAAAA
1 GTTATGGA-TGAT-AAATAAAACTTTTAAAA
*
6022198 GTCATGGATGA-AAATAAAA
1 GTTATGGATGATAAATAAAA
6022217 GGTTAGTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
28 8 0.20
29 7 0.17
30 5 0.12
31 21 0.51
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (29 bp):
GTTATGGATGATAAATAAAACTTTTAAAA
Found at i:6022284 original size:29 final size:29
Alignment explanation
Indices: 6022174--6022284 Score: 77
Period size: 29 Copynumber: 3.9 Consensus size: 29
6022164 AAAGTTATGT
*
6022174 ATTAAT-AAAATAAAA-CTTTTAAA-AGTC
1 ATTAATGAAAATAAAATCTTATAAAGA-TC
** ** *
6022201 ATGGATGAAAATAAAAGGTTAGTAAAGATT
1 ATTAATGAAAATAAAATCTTA-TAAAGATC
* * * *
6022231 ATAAATAATAAATATAAT-TTTTAAAGATC
1 ATTAATGA-AAATAAAATCTTATAAAGATC
6022260 ATTAATGAAAATAAAATCTTATAAA
1 ATTAATGAAAATAAAATCTTATAAA
6022285 AACTTAGAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
27 4 0.06
28 17 0.27
29 21 0.34
30 12 0.19
31 8 0.13
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (29 bp):
ATTAATGAAAATAAAATCTTATAAAGATC
Found at i:6022382 original size:11 final size:11
Alignment explanation
Indices: 6022366--6022423 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
6022356 CATTTACATT
6022366 TTTATATTATA
1 TTTATATTATA
6022377 TTTATA-TA-A
1 TTTATATTATA
* *
6022386 TTTTTATTATT
1 TTTATATTATA
6022397 TTTATATTATA
1 TTTATATTATA
* *
6022408 TTTTTATTATT
1 TTTATATTATA
6022419 TTTAT
1 TTTAT
6022424 TTAAAATGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 6 0.16
10 4 0.11
11 28 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTATA
Found at i:6022389 original size:22 final size:21
Alignment explanation
Indices: 6022363--6022423 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
6022353 ATACATTTAC
*
6022363 ATTTTTATATTATATTTATATA
1 ATTTTT-TATTATTTTTATATA
*
6022385 A-TTTTTATTATTTTTATATT
1 ATTTTTTATTATTTTTATATA
6022405 ATATTTTTATTATTTTTAT
1 AT-TTTTTATTATTTTTAT
6022424 TTAAAATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.40
21 4 0.11
22 17 0.49
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTTATTATTTTTATATA
Found at i:6022401 original size:31 final size:31
Alignment explanation
Indices: 6022363--6022424 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6022353 ATACATTTAC
6022363 ATTTTTATATTATATTTATATAATTTTTATT
1 ATTTTTATATTATATTTATATAATTTTTATT
* *
6022394 ATTTTTATATTATATTTTTATTATTTTTATT
1 ATTTTTATATTATATTTATATAATTTTTATT
6022425 TAAAATGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (31 bp):
ATTTTTATATTATATTTATATAATTTTTATT
Found at i:6022943 original size:23 final size:23
Alignment explanation
Indices: 6022916--6022963 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6022906 TAAAATATAA
*
6022916 ATATTATGTATTTA-TTTAAATTT
1 ATATTAT-TAATTATTTTAAATTT
*
6022939 ATATTATTAATTATTTTATATTT
1 ATATTATTAATTATTTTAAATTT
6022962 AT
1 AT
6022964 TATAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATTATTAATTATTTTAAATTT
Found at i:6023267 original size:3 final size:3
Alignment explanation
Indices: 6023259--6023286 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6023249 CAATCCCTCT
6023259 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6023287 CCTCTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:6024947 original size:16 final size:16
Alignment explanation
Indices: 6024926--6024957 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6024916 GTTGTACAAC
6024926 TTTTAATTGGATTGTA
1 TTTTAATTGGATTGTA
*
6024942 TTTTAATTGGTTTGTA
1 TTTTAATTGGATTGTA
6024958 ACTTTTATGT
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:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTTAATTGGATTGTA
Found at i:6030827 original size:17 final size:18
Alignment explanation
Indices: 6030805--6030838 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6030795 ATAATTGTTA
6030805 TTTTATAATTT-TAATTT
1 TTTTATAATTTATAATTT
*
6030822 TTTTATTATTTATAATT
1 TTTTATAATTTATAATT
6030839 ATTATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATAATTTATAATTT
Found at i:6032544 original size:2 final size:2
Alignment explanation
Indices: 6032537--6032581 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
6032527 AAGGGTGTCG
*
6032537 AT AT AT AT AT AT AT AG 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
6032579 AT A
1 AT A
6032582 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6032586 original size:2 final size:2
Alignment explanation
Indices: 6032581--6032619 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6032571 ATATATATAT
6032581 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6032620 AAAAGTGCTA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6033955 original size:21 final size:21
Alignment explanation
Indices: 6033929--6033980 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
6033919 TTTTTAATTT
*
6033929 TTTTATA-TATAAAAGATCATG
1 TTTTATATTA-AAAAGATCATA
6033950 TTTTATATTCAAAAAGATCATA
1 TTTTATATT-AAAAAGATCATA
*
6033972 TCTTATATT
1 TTTTATATT
6033981 CATATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 19 0.70
23 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (21 bp):
TTTTATATTAAAAAGATCATA
Found at i:6033964 original size:22 final size:22
Alignment explanation
Indices: 6033939--6033982 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6033929 TTTTATATAT
* *
6033939 AAAAGATCATGTTTTATATTCA
1 AAAAGATCATATCTTATATTCA
6033961 AAAAGATCATATCTTATATTCA
1 AAAAGATCATATCTTATATTCA
6033983 TATTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (22 bp):
AAAAGATCATATCTTATATTCA
Found at i:6034010 original size:17 final size:17
Alignment explanation
Indices: 6033988--6034026 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6033978 ATTCATATTT
*
6033988 AAATATGTA-TTAATAAA
1 AAATATCTACTTAA-AAA
6034005 AAATATCTACTTAAAAA
1 AAATATCTACTTAAAAA
6034022 AAATA
1 AAATA
6034027 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATATCTACTTAAAAA
Found at i:6034846 original size:31 final size:31
Alignment explanation
Indices: 6034738--6034857 Score: 125
Period size: 31 Copynumber: 3.7 Consensus size: 31
6034728 ATTAGTATTT
*
6034738 ATATATTTTT-ATAATTAAATTTAAACAAAAA
1 ATAT-TTTTTAATTATTAAATTTAAACAAAAA
* ** *
6034769 ATATTTTTTAATTATTAAATAATAATTATTAAA
1 ATATTTTTTAATTATTAAAT-TTAAACA-AAAA
* *
6034802 TTAGGCTTTTTAATTATTAAATTTAAACAAAAA
1 ATA--TTTTTTAATTATTAAATTTAAACAAAAA
6034835 ATATTTTTTAATTATTAAATTTA
1 ATATTTTTTAATTATTAAATTTA
6034858 TCATACCATG
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
30 5 0.07
31 32 0.45
32 4 0.06
33 10 0.14
34 4 0.06
35 16 0.23
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (31 bp):
ATATTTTTTAATTATTAAATTTAAACAAAAA
Found at i:6036275 original size:2 final size:2
Alignment explanation
Indices: 6036264--6036298 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6036254 TTATATACAA
* *
6036264 AT AT AA AT AT AT AT GT 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 A
6036299 CACACAAAGA
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6036889 original size:33 final size:33
Alignment explanation
Indices: 6036847--6036915 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
6036837 ACATTTTTTC
* * *
6036847 TATTTTTAATTTAATAATATT-AAGAATAAATGT
1 TATTATTAATTTAACAATATTAAAGAA-AAATAT
*
6036880 TATTATTAATTTAACAGTATTAAAGAAAAATAT
1 TATTATTAATTTAACAATATTAAAGAAAAATAT
6036913 TAT
1 TAT
6036916 CTTAAAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (33 bp):
TATTATTAATTTAACAATATTAAAGAAAAATAT
Found at i:6037599 original size:2 final size:2
Alignment explanation
Indices: 6037594--6037636 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6037584 TCTCTCTCTC
*
6037594 TA TA TA TA TA TA TA TA CA 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 TA TA TA TA TA
6037636 T
1 T
6037637 TTCTATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6040393 original size:2 final size:2
Alignment explanation
Indices: 6040386--6040410 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6040376 TAGATTTGTT
6040386 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
6040411 CATGTTTCGC
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:6042085 original size:2 final size:2
Alignment explanation
Indices: 6042078--6042111 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6042068 TCTTCCCAGT
*
6042078 TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6042112 AATGAGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:6042959 original size:2 final size:2
Alignment explanation
Indices: 6042952--6042991 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
6042942 ATTCTATCAC
* *
6042952 AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6042992 GCGATTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:6044566 original size:10 final size:10
Alignment explanation
Indices: 6044553--6044585 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6044543 ATATAAATCG
6044553 TATAAAAAAT
1 TATAAAAAAT
6044563 TATAAAAAA-
1 TATAAAAAAT
*
6044572 TATATAAAAT
1 TATAAAAAAT
6044582 TATA
1 TATA
6044586 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:6045006 original size:2 final size:2
Alignment explanation
Indices: 6044999--6045045 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
6044989 TAGAAACTTA
*
6044999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
6045041 AT AT A
1 AT AT A
6045046 GAGGATCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6046377 original size:26 final size:26
Alignment explanation
Indices: 6046348--6046400 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6046338 GATTAAGTTA
*
6046348 TTTAAAAAAT-TAATAAATAAAATTAT
1 TTTAAAAAATATAA-AAATAAAAATAT
* *
6046374 TTTAATAAATATAAAATTAAAAATAT
1 TTTAAAAAATATAAAAATAAAAATAT
6046400 T
1 T
6046401 AATATTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTAAAAAATATAAAAATAAAAATAT
Found at i:6046689 original size:18 final size:18
Alignment explanation
Indices: 6046636--6046706 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
6046626 TAAATATTTA
*
6046636 ATTAAATCAAT-AATTAT
1 ATTAAATAAATAAATTAT
*
6046653 A-TAAATTTAAATTATATTAT
1 ATTAAA--TAAA-TAAATTAT
6046673 ATTAAATAAATAAATTAT
1 ATTAAATAAATAAATTAT
* * *
6046691 TTTAAGTTAATAAATT
1 ATTAAATAAATAAATT
6046707 TAAAATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.09
17 1 0.02
18 23 0.53
19 5 0.12
20 6 0.14
21 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (18 bp):
ATTAAATAAATAAATTAT
Found at i:6046700 original size:23 final size:22
Alignment explanation
Indices: 6046660--6046705 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
6046650 TATATAAATT
6046660 TAAATTATATTATATTAAATAAA
1 TAAATTATATTATATT-AATAAA
*
6046683 TAAATTATTTTA-AGTTAATAAA
1 TAAATTATATTATA-TTAATAAA
6046705 T
1 T
6046706 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATTATATTATATTAATAAA
Found at i:6047376 original size:23 final size:23
Alignment explanation
Indices: 6047350--6047423 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
6047340 AGCACGACAT
6047350 AAATATAATATAAAAAATAAT-TA
1 AAATATAAT-TAAAAAATAATATA
*
6047373 AAATATAATTTAACAAAA-AATACA
1 AAATATAA-TTAA-AAAATAATATA
6047397 TAAATAT-ATTAAAAAATACATATA
1 -AAATATAATTAAAAAATA-ATATA
6047421 AAA
1 AAA
6047424 ATTTATATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
22 4 0.09
23 22 0.51
24 11 0.26
25 6 0.14
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATATAATTAAAAAATAATATA
Found at i:6047531 original size:14 final size:14
Alignment explanation
Indices: 6047514--6047549 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6047504 TTTTTTTTCC
6047514 CTTTCCTACCCTTT
1 CTTTCCTACCCTTT
* *
6047528 CTTTCCTTCTCTTT
1 CTTTCCTACCCTTT
6047542 CTTTCCTA
1 CTTTCCTA
6047550 TTTCTTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (14 bp):
CTTTCCTACCCTTT
Found at i:6047572 original size:16 final size:14
Alignment explanation
Indices: 6047553--6047586 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
6047543 TTTCCTATTT
6047553 CTTTTCTTCCTTTCTC
1 CTTTTCTT-CTTTC-C
6047569 CTTTTCTTCTTTCC
1 CTTTTCTTCTTTCC
6047583 CTTT
1 CTTT
6047587 CTCGCATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 5 0.28
16 8 0.44
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
CTTTTCTTCTTTCC
Found at i:6047576 original size:21 final size:22
Alignment explanation
Indices: 6047525--6047589 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
6047515 TTTCCTACCC
*
6047525 TTTCTTTCCTTCTCTTTCTTTCCTA
1 TTTCTTTTCTTC-CTTTC--TCCTA
6047550 TTTCTTTTCTTCCTTTCTCCT-
1 TTTCTTTTCTTCCTTTCTCCTA
*
6047571 TTTCTTCTT-TCCCTTTCTC
1 TTTCTT-TTCTTCCTTTCTC
6047590 GCATGCTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 15 0.41
22 6 0.16
24 5 0.14
25 11 0.30
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTCTTTTCTTCCTTTCTCCTA
Found at i:6047881 original size:57 final size:58
Alignment explanation
Indices: 6047802--6047916 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
6047792 AAGATACAAA
* * * *
6047802 TTTAATTAAATCACTATAATAAATTATG-AAAAAATATCATAAATTGAGATATGATAC
1 TTTAAATAAATCACTATAATAAATTATGTAAAAAATAACATAAATAGAGATACGATAC
* * * *
6047859 TTTAAATAAATTATTATGATAAATTATGTAAAATATAACATAAATAGAGATACGATAC
1 TTTAAATAAATCACTATAATAAATTATGTAAAAAATAACATAAATAGAGATACGATAC
6047917 AAACATGACA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
57 24 0.49
58 25 0.51
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (58 bp):
TTTAAATAAATCACTATAATAAATTATGTAAAAAATAACATAAATAGAGATACGATAC
Found at i:6048029 original size:23 final size:24
Alignment explanation
Indices: 6048003--6048050 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
6047993 ACACGACATG
* * *
6048003 AACATAATATAGAGAATAAT-TAA
1 AACACAATATAAAAAATAATATAA
6048026 AACACAATATAAAAAATAATATAA
1 AACACAATATAAAAAATAATATAA
6048050 A
1 A
6048051 TATGATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (24 bp):
AACACAATATAAAAAATAATATAA
Found at i:6049283 original size:21 final size:21
Alignment explanation
Indices: 6049257--6049314 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
6049247 AAGTATTAAT
6049257 ATATAAAATATTTATATAA-AA
1 ATAT-AAATATTTATATAAGAA
*
6049278 ATAT-AATATTATAAATAAGAA
1 ATATAAATATT-TATATAAGAA
*
6049299 ATATAAATATATATAT
1 ATATAAATATTTATAT
6049315 TTTTTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.19
20 6 0.19
21 14 0.45
22 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAAATATTTATATAAGAA
Found at i:6049286 original size:13 final size:15
Alignment explanation
Indices: 6049244--6049292 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
6049234 CATAAATAAA
*
6049244 ATAAAGTATTAATAT
1 ATAAAATATTAATAT
*
6049259 ATAAAATATTTATAT
1 ATAAAATATTAATAT
6049274 A-AAAATA-TAATATT
1 ATAAAATATTAATA-T
6049288 ATAAA
1 ATAAA
6049293 TAAGAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAAAATATTAATAT
Found at i:6049292 original size:16 final size:15
Alignment explanation
Indices: 6049175--6049292 Score: 53
Period size: 16 Copynumber: 7.1 Consensus size: 15
6049165 AAAAATATTT
*
6049175 AAAATATAATATAAA
1 AAAATATAATATATA
*
6049190 AATAATATGCAGATAACATA
1 AA-AATAT--A-AT-ATATA
6049210 AAAATA-AATACGTATA
1 AAAATATAATA--TATA
*
6049226 AAAATATACATAAATAAA
1 AAAATATA-AT--ATATA
6049244 ATAAAGTATTAATATAT-
1 A-AAA-TA-TAATATATA
*
6049261 AAAATAT-TTATATA
1 AAAATATAATATATA
6049275 AAAATATAATATTATA
1 AAAATATAATA-TATA
6049291 AA
1 AA
6049293 TAAGAAATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 33
0.66 0.06 0.28
Matches are distributed among these distances:
13 5 0.06
14 9 0.11
15 8 0.10
16 24 0.30
17 2 0.03
18 10 0.13
19 9 0.11
20 10 0.13
21 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAATATAATATATA
Found at i:6049343 original size:17 final size:19
Alignment explanation
Indices: 6049319--6049368 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
6049309 ATATATTTTT
6049319 TCTTTTTTTTCTCTCTTA-
1 TCTTTTTTTTCTCTCTTAG
*
6049337 T-TTTTTTTTCTTTCTTAG
1 TCTTTTTTTTCTCTCTTAG
6049355 TCTTTTTTTATCTC
1 TCTTTTTTT-TCTC
6049369 ATTTATCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.56
18 2 0.07
19 7 0.26
20 3 0.11
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (19 bp):
TCTTTTTTTTCTCTCTTAG
Found at i:6050089 original size:31 final size:32
Alignment explanation
Indices: 6050051--6050110 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
6050041 AGCTATCAAC
* *
6050051 ATTTTTCTTAATATAGAT-TAAAATTTTTAAT
1 ATTTTTCTCAATATAAATATAAAATTTTTAAT
*
6050082 ATTTTTCTCAATATAAATATATAATTTTT
1 ATTTTTCTCAATATAAATATAAAATTTTT
6050111 TTATTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (32 bp):
ATTTTTCTCAATATAAATATAAAATTTTTAAT
Found at i:6050655 original size:17 final size:17
Alignment explanation
Indices: 6050610--6050656 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
6050600 ATGAACTTGG
*
6050610 ATAATTTTTAAATCCGA
1 ATAATTTTTAAATTCGA
* *
6050627 AT-A-TTATAAATTTGA
1 ATAATTTTTAAATTCGA
6050642 ATAATTTTTAAATTC
1 ATAATTTTTAAATTC
6050657 AGATATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (17 bp):
ATAATTTTTAAATTCGA
Found at i:6050670 original size:30 final size:32
Alignment explanation
Indices: 6050610--6050670 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
6050600 ATGAACTTGG
*
6050610 ATAATTTTTAAATCCGAATATTATAAATTTGA
1 ATAATTTTTAAATCAGAATATTATAAATTTGA
6050642 ATAATTTTTAAATTCAG-ATA-TA-AAATTTG
1 ATAATTTTTAAA-TCAGAATATTATAAATTTG
6050671 CTATCCGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 7 0.26
31 2 0.07
32 15 0.56
33 3 0.11
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (32 bp):
ATAATTTTTAAATCAGAATATTATAAATTTGA
Found at i:6050890 original size:17 final size:17
Alignment explanation
Indices: 6050868--6050903 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6050858 TTTTAAAATA
*
6050868 ATTTAATAAATATGAAT
1 ATTTAATAAATATCAAT
*
6050885 ATTTAATAGATATCAAT
1 ATTTAATAAATATCAAT
6050902 AT
1 AT
6050904 CTTATGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTTAATAAATATCAAT
Found at i:6050992 original size:22 final size:21
Alignment explanation
Indices: 6050954--6050997 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
6050944 ATAAACAAAT
* *
6050954 AATAAATAAATTTAAATATAA
1 AATAAAAAAATTCAAATATAA
*
6050975 AATAAAAAGAATTCAAATTTAA
1 AATAAAAA-AATTCAAATATAA
6050997 A
1 A
6050998 TATTTCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAAAAAAATTCAAATATAA
Found at i:6051520 original size:35 final size:34
Alignment explanation
Indices: 6051481--6051553 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 34
6051471 ATTCTATTTT
**
6051481 ATATAGTATTCAGTTTAGTTTTTGGCAAACTAGTA
1 ATATAGTATTCAGTTTAGTTTTTCACAAACTAG-A
6051516 ATATAGTATTCAGTTTAGTTTTTCACAAACTAGA
1 ATATAGTATTCAGTTTAGTTTTTCACAAACTAGA
6051550 ATAT
1 ATAT
6051554 TACAATTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (34 bp):
ATATAGTATTCAGTTTAGTTTTTCACAAACTAGA
Found at i:6051770 original size:21 final size:22
Alignment explanation
Indices: 6051715--6051770 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 22
6051705 TAAATTCAAA
*
6051715 TAAAATAATATTATTATGCTAAT
1 TAAAA-AATATTATTATACTAAT
* * *
6051738 TCAAAAA-CTTATT-TACTATT
1 TAAAAAATATTATTATACTAAT
6051758 TAAAAAATATTAT
1 TAAAAAATATTAT
6051771 AATATTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 11 0.42
21 9 0.35
22 2 0.08
23 4 0.15
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAAATATTATTATACTAAT
Found at i:6051787 original size:19 final size:18
Alignment explanation
Indices: 6051741--6051794 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
6051731 TGCTAATTCA
*
6051741 AAAACTTATTTACTATTT
1 AAAACTTATTTAATATTT
**
6051759 AAAAAATATTATAATATTT
1 AAAACTTATT-TAATATTT
*
6051778 AAAACTTATTTTATATT
1 AAAACTTATTTAATATT
6051795 AATATTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAACTTATTTAATATTT
Found at i:6052027 original size:4 final size:4
Alignment explanation
Indices: 6052018--6052051 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
6052008 AAAATTGCTC
6052018 CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
6052052 ATAAAGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:6053298 original size:26 final size:27
Alignment explanation
Indices: 6053261--6053313 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
6053251 AAGAAAAAAA
6053261 AAATCCATTTAACGTTTCACCATTTTC
1 AAATCCATTTAACGTTTCACCATTTTC
6053288 AAAT-CATTTAACGTTTCACCATTTTC
1 AAATCCATTTAACGTTTCACCATTTTC
6053314 TTTCTTACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATCCATTTAACGTTTCACCATTTTC
Found at i:6061020 original size:2 final size:2
Alignment explanation
Indices: 6061013--6061052 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6061003 TGGTGAGCCC
6061013 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
6061053 ATGTGTCTGC
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:6061202 original size:10 final size:10
Alignment explanation
Indices: 6061189--6061213 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6061179 CCTAAAAGTA
6061189 AAAAAAAAAG
1 AAAAAAAAAG
6061199 AAAAAAAAAG
1 AAAAAAAAAG
6061209 AAAAA
1 AAAAA
6061214 GGGAATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:6061592 original size:11 final size:11
Alignment explanation
Indices: 6061576--6061652 Score: 70
Period size: 11 Copynumber: 6.8 Consensus size: 11
6061566 TTTTTATAAA
6061576 TTATATTATA-
1 TTATATTATAT
6061586 TT-TA-TATAT
1 TTATATTATAT
*
6061595 TTAAATTATAT
1 TTATATTATAT
*
6061606 TTATTTATTATTTT
1 TTA--TATTA-TAT
6061620 TTATATTATAT
1 TTATATTATAT
6061631 TTATATTATAT
1 TTATATTATAT
6061642 AATTATATTAT
1 --TTATATTAT
6061653 GTTGCGTAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 3 0.05
11 21 0.38
12 5 0.09
13 13 0.24
14 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTATAT
Found at i:6061646 original size:19 final size:19
Alignment explanation
Indices: 6061515--6061650 Score: 62
Period size: 19 Copynumber: 7.4 Consensus size: 19
6061505 TCTCCACGTT
6061515 TTATCATTTATA-TATTATAA
1 TTAT-ATTTATATTA-TATAA
*
6061535 TTATTTTTAAGTTATTATATAA
1 TTATATTT-A--TATTATATAA
** *
6061557 TTATATAAAT-TTTTATAAA
1 TTATATTTATATTATAT-AA
*
6061576 TTATA-TTATATTTATATAT
1 TTATATTTATA-TTATATAA
*
6061595 TTA-AATTATATT-TAT--
1 TTATATTTATATTATATAA
6061610 TTAT-TATT-T-TT-TAT-A
1 TTATAT-TTATATTATATAA
6061625 TTATATTTATATTATATAA
1 TTATATTTATATTATATAA
6061644 TTATATT
1 TTATATT
6061651 ATGTTGCGTA
Statistics
Matches: 90, Mismatches: 10, Indels: 33
0.68 0.08 0.25
Matches are distributed among these distances:
14 5 0.06
15 10 0.11
16 4 0.04
17 5 0.06
18 13 0.14
19 28 0.31
20 10 0.11
21 1 0.01
22 12 0.13
23 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
TTATATTTATATTATATAA
Found at i:6061650 original size:13 final size:13
Alignment explanation
Indices: 6061580--6061652 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
6061570 TATAAATTAT
6061580 ATTATATTTATATA
1 ATTATA-TTATATA
* * *
6061594 TTTAAATTATATTT
1 ATTATATTATA-TA
*
6061608 ATT-TATTAT-TT
1 ATTATATTATATA
*
6061619 TTTATATTATAT-
1 ATTATATTATATA
6061631 -TTATATTATATA
1 ATTATATTATATA
6061643 ATTATATTAT
1 ATTATATTAT
6061653 GTTGCGTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
11 15 0.31
12 6 0.12
13 20 0.42
14 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATATTATATA
Found at i:6061878 original size:11 final size:11
Alignment explanation
Indices: 6061862--6061945 Score: 59
Period size: 11 Copynumber: 7.9 Consensus size: 11
6061852 ATAAAGAAAT
6061862 TTTAATATATA
1 TTTAATATATA
6061873 TTTAATATATA
1 TTTAATATATA
*
6061884 -TTAA-AAATA
1 TTTAATATATA
* *
6061893 TATAAAATAT-
1 TTTAATATATA
*
6061903 TTTAAAATATAA
1 TTTAATATAT-A
** *
6061915 CATAATA-ATT
1 TTTAATATATA
6061925 TTTAATATATA
1 TTTAATATATA
*
6061936 TTAAATATAT
1 TTTAATATAT
6061946 TATAAACGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
9 4 0.07
10 21 0.38
11 27 0.48
12 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTAATATATA
Found at i:6061882 original size:9 final size:10
Alignment explanation
Indices: 6061863--6061947 Score: 50
Period size: 10 Copynumber: 8.3 Consensus size: 10
6061853 TAAAGAAATT
6061863 TTAATATATA
1 TTAATATATA
6061873 TTTAATATATA
1 -TTAATATATA
*
6061884 TTAA-AAATA
1 TTAATATATA
* *
6061893 TATAAAATATT
1 T-TAATATATA
*
6061904 TTAAAATATAA
1 TTAATATAT-A
* *
6061915 CATAATA-ATTT
1 -TTAATATA-TA
6061926 TTAATATATA
1 TTAATATATA
6061936 TTAA-ATATA
1 TTAATATATA
6061945 TTA
1 TTA
6061948 TAAACGGAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
9 13 0.22
10 25 0.42
11 16 0.27
12 5 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (10 bp):
TTAATATATA
Found at i:6062318 original size:26 final size:24
Alignment explanation
Indices: 6062262--6062318 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 24
6062252 TTAAATTTAA
*
6062262 TAATTTATATATTTTTATTATAAT
1 TAATTTAAATATTTTTATTATAAT
6062286 TATATTTAAAATATTTTATATT-TAAAT
1 TA-ATTT-AAATATTTT-TATTAT-AAT
6062313 TAATTT
1 TAATTT
6062319 TTATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.07
25 4 0.14
26 13 0.46
27 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTTAAATATTTTTATTATAAT
Found at i:6062340 original size:22 final size:22
Alignment explanation
Indices: 6062306--6062347 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
6062296 ATATTTTATA
*
6062306 TTTAAATTAA-TTTTTATTAAT
1 TTTAAAATAATTTTTTATTAAT
6062327 TTTAAAATATATTTTTTATTA
1 TTTAAAATA-ATTTTTTATTA
6062348 TATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 1 0.06
23 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAAAATAATTTTTTATTAAT
Found at i:6062364 original size:19 final size:18
Alignment explanation
Indices: 6062333--6062375 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
6062323 TAATTTTAAA
6062333 ATATATTTTTTATTATAT
1 ATATATTTTTTATTATAT
6062351 -TATATTTTAATTATTATAT
1 ATATATTTT--TTATTATAT
6062370 ATATAT
1 ATATAT
6062376 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATATTTTTTATTATAT
Found at i:6063553 original size:19 final size:19
Alignment explanation
Indices: 6063507--6063576 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
6063497 TAATATTATT
6063507 ATATAATATAAAAATTAAAA
1 ATATAATATAAAAA-TAAAA
6063527 TTTGATATAATATAAAAATAAAA
1 ----ATATAATATAAAAATAAAA
** *
6063550 ATATAATACGAATATAAAA
1 ATATAATATAAAAATAAAA
*
6063569 TTATAATA
1 ATATAATA
6063577 AAATTTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 23 0.55
23 5 0.12
24 14 0.33
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
ATATAATATAAAAATAAAA
Found at i:6063590 original size:20 final size:20
Alignment explanation
Indices: 6063562--6063630 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
6063552 ATAATACGAA
*
6063562 TATAAAATTATAATAAAATT
1 TATATAATTATAATAAAATT
6063582 TATATAATT-T--T--AA-T
1 TATATAATTATAATAAAATT
6063596 TAT-TAA-TATAATAAAATT
1 TATATAATTATAATAAAATT
6063614 TATATAAATATATAATA
1 TATAT-AAT-TATAATA
6063631 TAAAATTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 18
0.67 0.02 0.32
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 4 0.11
15 3 0.08
17 3 0.08
18 4 0.11
19 2 0.05
20 10 0.26
22 7 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATAATTATAATAAAATT
Found at i:6065090 original size:11 final size:11
Alignment explanation
Indices: 6065076--6065137 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
6065066 ACGATATAAA
6065076 TATATAAATAT
1 TATATAAATAT
*
6065087 TATAAAAATA-
1 TATATAAATAT
*
6065097 TATAATAAAAAT
1 TAT-ATAAATAT
6065109 TAT-TAAA-A-
1 TATATAAATAT
*
6065117 TAT-TAAATTT
1 TATATAAATAT
6065127 TATATAAATAT
1 TATATAAATAT
6065138 AAAATAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 10 0.24
11 20 0.49
12 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATATAAATAT
Found at i:6065092 original size:9 final size:8
Alignment explanation
Indices: 6065069--6065201 Score: 64
Period size: 8 Copynumber: 15.9 Consensus size: 8
6065059 ATATAATACG
6065069 ATATAAAT
1 ATATAAAT
6065077 ATATAAAT
1 ATATAAAT
*
6065085 ATTATAAAA
1 A-TATAAAT
6065094 ATATATAAT
1 ATATA-AAT
6065103 A-A-AAAT
1 ATATAAAT
6065109 -TATTAAA-
1 ATA-TAAAT
6065116 ATATTAAATTTT
1 ATA-TAAA---T
6065128 ATATAAAT
1 ATATAAAT
6065136 ATA-AAAT
1 ATATAAAT
*
6065143 AATTTAAAT
1 -ATATAAAT
6065152 ATAATTATAAT
1 AT-A-TA-AAT
6065163 ATAATAAA-
1 AT-ATAAAT
6065171 ATATAAAT
1 ATATAAAT
*
6065179 ATACAAAT
1 ATATAAAT
6065187 -TATTAAAT
1 ATA-TAAAT
*
6065195 TTATAAA
1 ATATAAA
6065202 AGAGGATCCA
Statistics
Matches: 101, Mismatches: 6, Indels: 36
0.71 0.04 0.25
Matches are distributed among these distances:
6 4 0.04
7 12 0.12
8 49 0.49
9 18 0.18
10 4 0.04
11 11 0.11
12 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:6065110 original size:22 final size:21
Alignment explanation
Indices: 6065075--6065119 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
6065065 TACGATATAA
*
6065075 ATATATAAATATTATAAAAAT
1 ATATATAAAAATTATAAAAAT
*
6065096 ATATAATAAAAATTATTAAAAT
1 ATAT-ATAAAAATTATAAAAAT
6065118 AT
1 AT
6065120 TAAATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATAAAAATTATAAAAAT
Found at i:6065121 original size:75 final size:78
Alignment explanation
Indices: 6065042--6065193 Score: 170
Period size: 75 Copynumber: 2.0 Consensus size: 78
6065032 ATAATATATT
* * * *
6065042 TATTAAAAATAATTTAAATATAATACGATATAAATAT-A-TA-AATATTATAAAAATATATAATA
1 TATTAAAAATAATATAAATATAAAACAATATAAATATAATTATAATATAAT-AAAATATA-AATA
6065104 -A-AAATTATTAAAA
64 TACAAATTATTAAAA
** * * *
6065117 TATTAAATTTTATATAAATATAAAATAATTTAAATATAATTATAATATAATAAAATATAAATATA
1 TATTAAAAATAATATAAATATAAAACAATATAAATATAATTATAATATAATAAAATATAAATATA
6065182 CAAATTATTAAA
66 CAAATTATTAAA
6065194 TTTATAAAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
75 29 0.46
76 5 0.08
77 11 0.17
78 18 0.29
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (78 bp):
TATTAAAAATAATATAAATATAAAACAATATAAATATAATTATAATATAATAAAATATAAATATA
CAAATTATTAAAA
Found at i:6065139 original size:6 final size:6
Alignment explanation
Indices: 6065128--6065181 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
6065118 ATTAAATTTT
* *
6065128 ATATAA ATATAA A-AT-A ATTTAA ATATAA TTAT-A ATAT-A ATA-AA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
6065171 ATATAA ATATA
1 ATATAA ATATA
6065182 CAAATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 2 0.05
5 15 0.38
6 23 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:6065168 original size:16 final size:16
Alignment explanation
Indices: 6065056--6065176 Score: 63
Period size: 16 Copynumber: 7.6 Consensus size: 16
6065046 AAAAATAATT
**
6065056 TAAATATAATACGATA
1 TAAATATAATAAAATA
6065072 TAAATAT-ATAAATATTA
1 TAAATATAATAAA-A-TA
* *
6065089 TAAAAAT-ATATAATA
1 TAAATATAATAAAATA
* *
6065104 AAAAT-TATTAAAATA
1 TAAATATAATAAAATA
* *
6065119 TTAAATTTTATATAAATA
1 -TAAATATAATA-AAATA
*
6065137 TAAA-ATAATTTAAATA
1 TAAATATAA-TAAAATA
* *
6065153 TAATTATAATATAATA
1 TAAATATAATAAAATA
6065169 -AAATATAA
1 TAAATATAA
6065177 ATATACAAAT
Statistics
Matches: 79, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
14 1 0.01
15 21 0.27
16 28 0.35
17 24 0.30
18 5 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
TAAATATAATAAAATA
Found at i:6069860 original size:23 final size:23
Alignment explanation
Indices: 6069812--6069862 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6069802 CTTCTCATGA
* * **
6069812 ATATAAAGCAATTAGAGCAATGT
1 ATATAAAACAATTAGACCAAACT
6069835 ATATAAAACAATTAGACCAAACT
1 ATATAAAACAATTAGACCAAACT
6069858 ATATA
1 ATATA
6069863 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (23 bp):
ATATAAAACAATTAGACCAAACT
Found at i:6075688 original size:24 final size:24
Alignment explanation
Indices: 6075661--6075750 Score: 108
Period size: 24 Copynumber: 3.6 Consensus size: 24
6075651 ATATTTTTTG
6075661 TTTCTTTATATTTTATAACAATTA
1 TTTCTTTATATTTTATAACAATTA
*
6075685 TTTCTTTATATTTTATAATAATTGTTA
1 TTTCTTTATATTTTATAACAA---TTA
* * *
6075712 TTTCTTGATATTTTTATAACTATTG
1 TTTCTTTATA-TTTTATAACAATTA
6075737 TTTCTTTATATTTT
1 TTTCTTTATATTTT
6075751 GTAGCTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
24 24 0.43
25 11 0.20
27 12 0.21
28 9 0.16
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (24 bp):
TTTCTTTATATTTTATAACAATTA
Found at i:6078156 original size:33 final size:33
Alignment explanation
Indices: 6078119--6078181 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
6078109 ATTAATTCTT
* *
6078119 TAAGATTGTTCAAGGGGATTCTAATTTATTAGA
1 TAAGATTATTCAAGGGAATTCTAATTTATTAGA
*
6078152 TAAGATTATTCAAGGGAATTTTAATTTATT
1 TAAGATTATTCAAGGGAATTCTAATTTATT
6078182 GGACTTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (33 bp):
TAAGATTATTCAAGGGAATTCTAATTTATTAGA
Found at i:6078463 original size:19 final size:21
Alignment explanation
Indices: 6078441--6078480 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
6078431 ATAATATATT
6078441 TAATAATA-TAA-ATAAAAAA
1 TAATAATAGTAATATAAAAAA
6078460 TAATAATAGTAATATAAAAAA
1 TAATAATAGTAATATAAAAAA
6078481 ATATCATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (21 bp):
TAATAATAGTAATATAAAAAA
Found at i:6082929 original size:2 final size:2
Alignment explanation
Indices: 6082922--6082961 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
6082912 TAAAGAAAAC
* *
6082922 TA TA TA TA TA TA TA CA 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 TA TA TA TA TA
6082962 CTGACGACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6085068 original size:21 final size:21
Alignment explanation
Indices: 6085042--6085085 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6085032 ATTAAAATAT
*
6085042 TATTTTTTG-TTAATATTTATA
1 TATTTTATGATTAA-ATTTATA
6085063 TATTTTATGATTAAATTTATA
1 TATTTTATGATTAAATTTATA
6085084 TA
1 TA
6085086 AAAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TATTTTATGATTAAATTTATA
Found at i:6085263 original size:2 final size:2
Alignment explanation
Indices: 6085256--6085287 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6085246 TCAAATTTAC
6085256 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
6085288 GATTCTATGA
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):
AT
Found at i:6088101 original size:3 final size:3
Alignment explanation
Indices: 6088087--6088128 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
6088077 TACTTAAAGG
*
6088087 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6088129 TTACTTTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:6088265 original size:31 final size:31
Alignment explanation
Indices: 6088230--6088302 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 31
6088220 TTCAAAACGT
6088230 AAAATAATTTTTTTAAATAACAAAATATACA
1 AAAATAATTTTTTTAAATAACAAAATATACA
**
6088261 AAAATAA---TTTTAAATAACAAAATATATG
1 AAAATAATTTTTTTAAATAACAAAATATACA
*
6088289 TAAATAATTTTTTT
1 AAAATAATTTTTTT
6088303 CCGTGAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 25 0.69
31 11 0.31
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAATAATTTTTTTAAATAACAAAATATACA
Found at i:6089468 original size:30 final size:30
Alignment explanation
Indices: 6089416--6089473 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
6089406 TAAAGTAATA
* * *
6089416 TTTAAAAATATATATAATTAATACATTATT
1 TTTAAAAATAAATAAAAATAATACATTATT
* *
6089446 TTTAAAATTAAATAAAAATAATATATTA
1 TTTAAAAATAAATAAAAATAATACATTA
6089474 AATATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAAAATAAATAAAAATAATACATTATT
Found at i:6090280 original size:33 final size:32
Alignment explanation
Indices: 6090234--6090306 Score: 74
Period size: 33 Copynumber: 2.2 Consensus size: 32
6090224 CGTTTCATTT
* * *
6090234 ATTTTAATTTTAATTATATTGAAAATAAATATC
1 ATTTTAA-CTTAATAATATTGAAAACAAATATC
* * *
6090267 ATTCTTAACTTAATAATTTTGAGAACAAATATT
1 ATT-TTAACTTAATAATATTGAAAACAAATATC
6090300 ATTTTAA
1 ATTTTAA
6090307 AAATTTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 4 0.12
33 25 0.76
34 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (32 bp):
ATTTTAACTTAATAATATTGAAAACAAATATC
Found at i:6091405 original size:16 final size:16
Alignment explanation
Indices: 6091386--6091416 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6091376 TCCTTTTTCT
*
6091386 TTTTTAATTTTTTTAA
1 TTTTTAATATTTTTAA
6091402 TTTTTAATATTTTTA
1 TTTTTAATATTTTTA
6091417 TGGTAATCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAATATTTTTAA
Found at i:6092188 original size:20 final size:20
Alignment explanation
Indices: 6092154--6092203 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6092144 ATCAATCATT
*
6092154 TTTAGAAAATAATTGAT-TTT
1 TTTA-AAAATAATTGATCTTG
*
6092174 TATTAAAAATGATTGATCTTG
1 T-TTAAAAATAATTGATCTTG
6092195 TTTAAAAAT
1 TTTAAAAAT
6092204 CTATAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTAAAAATAATTGATCTTG
Found at i:6093568 original size:21 final size:19
Alignment explanation
Indices: 6093550--6093609 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
6093540 TATTAAAAGT
6093550 TGCATTTTTTCATCCAAAAAA
1 TGCATTTTTTCATCC--AAAA
*
6093571 TACATTTTTTCATCCAACCAA
1 TGCATTTTTTCATCCAA--AA
*
6093592 TGCATTATTTCATCCAAA
1 TGCATTTTTTCATCCAAA
6093610 GATACCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
21 31 0.91
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (19 bp):
TGCATTTTTTCATCCAAAA
Found at i:6096798 original size:20 final size:20
Alignment explanation
Indices: 6096773--6096819 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
6096763 ATATTTTGGA
6096773 AATGATTTGGAATGAAATAG
1 AATGATTTGGAATGAAATAG
6096793 AATGATTTGGAATGAAATAG
1 AATGATTTGGAATGAAATAG
6096813 AATGATT
1 AATGATT
6096820 ATTTTGGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (20 bp):
AATGATTTGGAATGAAATAG
Found at i:6097765 original size:40 final size:37
Alignment explanation
Indices: 6097679--6097782 Score: 97
Period size: 40 Copynumber: 2.7 Consensus size: 37
6097669 ATCGATTTAA
*
6097679 TTTAATTTAAA-TTAATATTTAATAA-TTTAAAAATAT
1 TTTAATTTAAATTTAATA-TAAATAATTTTAAAAATAT
* *
6097715 TTT-ATTTAAATTTAATTATAAAATAATTTTATAAATTT
1 TTTAATTTAAATTTAA-TAT-AAATAATTTTAAAAATAT
*
6097753 TTTAATTATAAATAATAAATATAAATAATT
1 TTTAATT-TAAAT--TTAATATAAATAATT
6097783 AAATTAAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
35 7 0.12
36 8 0.14
37 7 0.12
38 12 0.21
39 3 0.05
40 13 0.23
41 3 0.05
42 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
TTTAATTTAAATTTAATATAAATAATTTTAAAAATAT
Found at i:6097775 original size:28 final size:28
Alignment explanation
Indices: 6097725--6097778 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6097715 TTTATTTAAA
**
6097725 TTTAATTATAAAATAATTTTATAAATTT
1 TTTAATTATAAAATAATAATATAAATTT
6097753 TTTAATTAT-AAATAATAAATATAAAT
1 TTTAATTATAAAATAAT-AATATAAAT
6097779 AATTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAATTATAAAATAATAATATAAATTT
Found at i:6098467 original size:39 final size:39
Alignment explanation
Indices: 6098394--6098470 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
6098384 AAAAGTTTAA
* * *
6098394 TAAATATATTTTTATGGTGATAAATATATGTAATAAATAG
1 TAAATATATTTTTA-GGTAATAAATAAATATAATAAATAG
6098434 TAAATATATTTTGTA-GTAATAAATAAATATAATAAAT
1 TAAATATATTTT-TAGGTAATAAATAAATATAATAAAT
6098471 TAAAAACGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 19 0.58
40 12 0.36
41 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (39 bp):
TAAATATATTTTTAGGTAATAAATAAATATAATAAATAG
Found at i:6098938 original size:11 final size:11
Alignment explanation
Indices: 6098922--6098975 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
6098912 TCTAAGTTTA
*
6098922 TTTTTTATCAT
1 TTTTTTATTAT
6098933 TTTTTTATTAT
1 TTTTTTATTAT
6098944 TTTATTT-TTAT
1 TTT-TTTATTAT
*
6098955 TTTTTTA-AAT
1 TTTTTTATTAT
6098965 TCTTTTTATTA
1 T-TTTTTATTA
6098976 ATTTGAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 6 0.17
11 26 0.72
12 4 0.11
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:6102641 original size:46 final size:45
Alignment explanation
Indices: 6102582--6102677 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 45
6102572 ACTTAACTAA
*
6102582 TAAAAATATTAAAATATTATTTTTAATT-TTAAATAA-ATTTTAAAAT
1 TAAAAATAATAAAA-A-TATTTTTAATTATTAAATAATATTTT-AAAT
* *
6102628 TAAAATTAATAAAAATATTTTTAATTAATTAATTAATATTTTAAAT
1 TAAAAATAATAAAAATATTTTTAATT-ATTAAATAATATTTTAAAT
6102674 TAAA
1 TAAA
6102678 TTGAATCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 11 0.25
45 1 0.02
46 27 0.61
47 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (45 bp):
TAAAAATAATAAAAATATTTTTAATTATTAAATAATATTTTAAAT
Found at i:6103222 original size:16 final size:16
Alignment explanation
Indices: 6103183--6103273 Score: 62
Period size: 16 Copynumber: 5.6 Consensus size: 16
6103173 AAATTAATTA
6103183 ATTTAAATTTGAAAATG
1 ATTTAAATTT-AAAATG
** *
6103200 AACTAAATTTTAAATG
1 ATTTAAATTTAAAATG
6103216 ATTTAAA-TTAAGAATG
1 ATTTAAATTTAA-AATG
* *
6103232 ATTTTGAATTCT-AAATA
1 A-TTTAAATT-TAAAATG
**
6103249 ATCCAAATTTAAAATG
1 ATTTAAATTTAAAATG
6103265 A-TTAAATTT
1 ATTTAAATTT
6103274 GATAAATATG
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
15 10 0.18
16 25 0.45
17 17 0.31
18 2 0.04
19 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (16 bp):
ATTTAAATTTAAAATG
Found at i:6104038 original size:19 final size:17
Alignment explanation
Indices: 6104016--6104050 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
6104006 TGTTTAAAAT
6104016 ATTATTTTATATTAAATTA
1 ATTATTTT-TA-TAAATTA
6104035 ATTATTTTTATAAATT
1 ATTATTTTTATAAATT
6104051 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTTTTATAAATTA
Found at i:6104148 original size:37 final size:38
Alignment explanation
Indices: 6104036--6104152 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 38
6104026 ATTAAATTAA
*
6104036 TTATTTTTATAAATTTTAAAAAATAATATAATAATATAATAATTT
1 TTATTTTT-TAAA-TATAAAAAAT-AT-T-AT-ATA-AATAATTT
* * *
6104081 TTATTTTTTAAATTTTAAATAATATT-TATAAATATTTT
1 TTATTTTTTAAA-TATAAAAAATATTATATAAATAATTT
6104119 TTATTTTTTTAAA-ATAAAAAAT-TTATATAAATAA
1 TTA-TTTTTTAAATATAAAAAATATTATATAAATAA
6104153 ATAATATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
36 2 0.03
37 15 0.23
38 10 0.15
39 12 0.18
40 1 0.02
42 1 0.02
43 2 0.03
44 14 0.22
45 8 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TTATTTTTTAAATATAAAAAATATTATATAAATAATTT
Found at i:6105743 original size:27 final size:29
Alignment explanation
Indices: 6105697--6105767 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 29
6105687 GTCACTCATT
6105697 TGTTTGTCAAAAAT-AGTGG-TTATTTTG
1 TGTTTGTCAAAAATGAGTGGTTTATTTTG
* *
6105724 TGTTTGTAAAAAATGA-TGGTTTCTTTTG
1 TGTTTGTCAAAAATGAGTGGTTTATTTTG
* *
6105752 TATTTGTCAAATATGA
1 TGTTTGTCAAAAATGA
6105768 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (29 bp):
TGTTTGTCAAAAATGAGTGGTTTATTTTG
Found at i:6110325 original size:28 final size:27
Alignment explanation
Indices: 6110270--6110340 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
6110260 GCCACCCATT
*
6110270 TGTTTGTCAAAAATTGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
6110297 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
6110325 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
6110341 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:6111665 original size:18 final size:18
Alignment explanation
Indices: 6111642--6111678 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6111632 ATAATTCCTT
6111642 ATATAAA-AAACTAAGTAA
1 ATATAAATAAA-TAAGTAA
6111660 ATATAAATAAATAAGTAA
1 ATATAAATAAATAAGTAA
6111678 A
1 A
6111679 AACACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (18 bp):
ATATAAATAAATAAGTAA
Found at i:6114695 original size:20 final size:19
Alignment explanation
Indices: 6114650--6114700 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
6114640 AAATAATAAT
*
6114650 TTAAATTAAATTAAATCAA
1 TTAAATTAAATAAAATCAA
6114669 TTCAAATT-AATAAAATTCATA
1 TT-AAATTAAATAAAA-TCA-A
6114690 TTAAATATAAA
1 TTAAAT-TAAA
6114701 AATTTTTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 8 0.31
20 12 0.46
21 4 0.15
22 2 0.08
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAATTAAATAAAATCAA
Found at i:6116417 original size:23 final size:24
Alignment explanation
Indices: 6116374--6116431 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
6116364 AAAAATTGAT
*
6116374 TTAAAAAATCAAGTGATTTTTTTA
1 TTAAAAAATCAAGTGAATTTTTTA
6116398 TTAAAAAATCAAGT-AATTTTTTA
1 TTAAAAAATCAAGTGAATTTTTTA
6116421 TTAAAAAATCA
1 TTAAAAAATCA
6116432 TAATCTTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (24 bp):
TTAAAAAATCAAGTGAATTTTTTA
Found at i:6116979 original size:18 final size:17
Alignment explanation
Indices: 6116952--6116986 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6116942 ATTTAGTAAG
6116952 AAAATATATTAAATATAA
1 AAAATATATTAAA-ATAA
*
6116970 AAAATTTATTAAAATAA
1 AAAATATATTAAAATAA
6116987 TAATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATATATTAAAATAA
Found at i:6117478 original size:11 final size:10
Alignment explanation
Indices: 6117443--6117521 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 10
6117433 TAATATAGTT
6117443 ATATAATAAA
1 ATATAATAAA
*
6117453 ATATGATAAA
1 ATATAATAAA
6117463 A-ATAATTAAA
1 ATATAA-TAAA
**
6117473 ATATAATATT
1 ATATAATAAA
*
6117483 ATATAAAAATA
1 ATATAATAA-A
6117494 ATATAA-AAA
1 ATATAATAAA
* *
6117503 ATATATTAAT
1 ATATAATAAA
6117513 ATATGAATA
1 ATAT-AATA
6117522 TATTAAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
9 9 0.17
10 32 0.59
11 13 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
ATATAATAAA
Found at i:6117488 original size:27 final size:28
Alignment explanation
Indices: 6117458--6117515 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
6117448 ATAAAATATG
*
6117458 ATAAAAATAAT-TAAAATATAATATT-AT
1 ATAAAAATAATATAAAAAAT-ATATTAAT
6117485 ATAAAAATAATATAAAAAATATATTAAT
1 ATAAAAATAATATAAAAAATATATTAAT
6117513 ATA
1 ATA
6117516 TGAATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAAAAATAATATAAAAAATATATTAAT
Found at i:6117504 original size:30 final size:27
Alignment explanation
Indices: 6117448--6117516 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 27
6117438 TAGTTATATA
6117448 ATAA-AATATGATAAAAATAATTAAAAT
1 ATAATAATAT-ATAAAAATAATTAAAAT
*
6117475 ATAATATTATATAAAAATAATATAAAAAAT
1 ATAATAATATATAAAAATAAT-T--AAAAT
*
6117505 ATATTAATATAT
1 ATAATAATATAT
6117517 GAATATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 15 0.43
28 5 0.14
30 15 0.43
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (27 bp):
ATAATAATATATAAAAATAATTAAAAT
Found at i:6117524 original size:38 final size:40
Alignment explanation
Indices: 6117441--6117522 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
6117431 TATAATATAG
*
6117441 TTATATAATAA-AATATGATAAAAATA-ATTAAAATATAATA
1 TTATATAAAAATAATAT-A-AAAAATATATTAAAATATAATA
*
6117481 TTATATAAAAATAATATAAAAAATATATTAATATATGAATA
1 TTATATAAAAATAATATAAAAAATATATTAAAATAT-AATA
6117522 T
1 T
6117523 ATTAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 7 0.19
40 20 0.54
41 10 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
TTATATAAAAATAATATAAAAAATATATTAAAATATAATA
Found at i:6117536 original size:38 final size:39
Alignment explanation
Indices: 6117441--6117547 Score: 98
Period size: 40 Copynumber: 2.7 Consensus size: 39
6117431 TATAATATAG
6117441 TTATATAATAAA-ATATGATAAAAATA-ATTAAAATATAATA
1 TTATATAA-AAATA-AT-ATAAAAATATATTAAAATATAATA
*
6117481 TTATATAAAAATAATATAAAAAATATATTAATATATGAATA
1 TTATATAAAAATAATAT-AAAAATATATTAAAATAT-AATA
* * *
6117522 -TAT-T-AAATTTATATAAATATATATTA
1 TTATATAAAAATAATATAAAAATATATTA
6117548 TTTTAAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
37 11 0.19
38 10 0.17
39 13 0.22
40 21 0.36
41 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (39 bp):
TTATATAAAAATAATATAAAAATATATTAAAATATAATA
Done.